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 135 of 160
Found at i:25266042 original size:10 final size:10
Alignment explanation
Indices: 25266024--25266063 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
25266014 ATGGCTGTTT
*
25266024 CATACATATA
1 CATATATATA
25266034 CATATATATA
1 CATATATATA
*
25266044 TATATATATA
1 CATATATATA
*
25266054 TATATATATA
1 CATATATATA
25266064 TGGTGTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (10 bp):
CATATATATA
Found at i:25279961 original size:10 final size:10
Alignment explanation
Indices: 25279933--25279966 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
25279923 TAGTATGAGC
*
25279933 CAATACAGAT
1 CAATACAAAT
25279943 CAATA-AAAT
1 CAATACAAAT
25279952 CAATACAAAT
1 CAATACAAAT
25279962 CAATA
1 CAATA
25279967 TAAAGCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (10 bp):
CAATACAAAT
Found at i:25288464 original size:66 final size:66
Alignment explanation
Indices: 25288358--25288488 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
25288348 GGGTTTCTCG
*
25288358 ATTATAATTTACACTTTAAGACTTAACCATTAATACTCCAAAAATTGAAAAAGATTATTTACTCA
1 ATTATAATTTACACTTTAAGACTTAACCATCAATACTCCAAAAATTGAAAAAGATTATTTACTCA
25288423 T
66 T
25288424 ATTATAATTTACACTTTAAGACTTAACCATCAATACTCCAAAAATTGAAAAAGATTATTTACTCA
1 ATTATAATTTACACTTTAAGACTTAACCATCAATACTCCAAAAATTGAAAAAGATTATTTACTCA
25288489 CCTCTAATAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (66 bp):
ATTATAATTTACACTTTAAGACTTAACCATCAATACTCCAAAAATTGAAAAAGATTATTTACTCA
T
Found at i:25291545 original size:2 final size:2
Alignment explanation
Indices: 25291538--25291564 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25291528 AAATACCTCA
25291538 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
25291565 AAGAAAGTAA
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:25297535 original size:2 final size:2
Alignment explanation
Indices: 25297528--25297552 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25297518 CGCTCCTCAA
25297528 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 A
25297553 AAATATGATG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25298568 original size:193 final size:186
Alignment explanation
Indices: 25298483--25298852 Score: 432
Period size: 193 Copynumber: 2.0 Consensus size: 186
25298473 GTTTTTATAC
* * * *
25298483 AAAAAAATTTTAAATAACCTTTTTATA-TTTT-T-ATAAA-ATTTT-T-TTTGTACAAACAGCTT
1 AAAAAAATATTAAATAACCTTTTTATATTTTTATAATAAATATTTTATGTTTCTAAAAAAAGCTT
* *
25298542 AAATAATTATTTTATATTTTTATAAATAAATTATTTAAAATATTGTTGTACAAAAAATGTCATAA
66 AAATAATTATTTTATATTTTTATAAATAAATTATTTAAAATATT-TTATACAAAAAATGTCTTAA
* * *
25298607 ATAATTTTTTTATATTTTAAGATTTAAAATTAATATTTTTACAAAAAATATTATGTAT
130 ATAATTTTTTTATATTTTAAAATTT-AGATTAATATTTTTATAAAAAATATTATGTAT
** **
25298665 AAAAACGTATTAAATAATTTTTTTATATTTTTATAAATAAATTATTTTAAAATGTTTCTAAAAAA
1 AAAAAAATATTAAATAACCTTTTTATATTTTTAT-AATAAA-TATTTT---ATGTTTCTAAAAAA
* * *
25298730 ATCTTAAATAGTTATTTTATATTTTTATAAATAAATTATTTAAAACGT-TTTTATACAAAAAATA
61 AGCTTAAATAATTATTTTATATTTTTATAAATAAATTATTTAAAA--TATTTTATACAAAAAATG
* *
25298794 TTTTAAATAATTATTTTATATTTTAAAATTTATGATTAATATTTTTATAAAAAA-ATTAT
124 TCTTAAATAATTTTTTTATATTTTAAAATTTA-GATTAATATTTTTATAAAAAATATTAT
25298853 TTAAGGTTTC
Statistics
Matches: 156, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
182 22 0.14
183 4 0.03
184 1 0.01
186 5 0.03
188 5 0.03
192 7 0.04
193 109 0.70
194 2 0.01
195 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (186 bp):
AAAAAAATATTAAATAACCTTTTTATATTTTTATAATAAATATTTTATGTTTCTAAAAAAAGCTT
AAATAATTATTTTATATTTTTATAAATAAATTATTTAAAATATTTTATACAAAAAATGTCTTAAA
TAATTTTTTTATATTTTAAAATTTAGATTAATATTTTTATAAAAAATATTATGTAT
Found at i:25298727 original size:59 final size:58
Alignment explanation
Indices: 25298672--25298817 Score: 193
Period size: 59 Copynumber: 2.4 Consensus size: 58
25298662 TATAAAAACG
* *
25298672 TATTAAATAATTTTTTTATATTTTTATAAATAAATTATTTTAAAATGTTTCTAAAAAAA
1 TATTAAATAATTATTTTATATTTTTATAAATAAATTA-TTTAAAACGTTTCTAAAAAAA
* * *
25298731 TCTTAAATAGTTATTTTATATTTTTATAAATAAATTATTTAAAACGTTTTTATACAAAAAA
1 TATTAAATAATTATTTTATATTTTTATAAATAAATTATTTAAAACG--TTTCTA-AAAAAA
25298792 TATTTTAAATAATTATTTTATATTTT
1 TA--TTAAATAATTATTTTATATTTT
25298818 AAAATTTATG
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 8 0.11
59 34 0.45
60 5 0.07
61 7 0.09
63 21 0.28
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (58 bp):
TATTAAATAATTATTTTATATTTTTATAAATAAATTATTTAAAACGTTTCTAAAAAAA
Found at i:25298835 original size:21 final size:20
Alignment explanation
Indices: 25298790--25298838 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
25298780 TTATACAAAA
25298790 AATATTTTAAATAATTATTT
1 AATATTTTAAATAATTATTT
* *
25298810 TATATTTTAAA-ATTTATGATT
1 AATATTTTAAATAATTAT--TT
25298831 AATATTTT
1 AATATTTT
25298839 TATAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
AATATTTTAAATAATTATTT
Found at i:25299747 original size:20 final size:21
Alignment explanation
Indices: 25299711--25299751 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
25299701 ATCGAAATTA
25299711 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
25299733 ATAAAATATTATTTTTAAA
1 ATAAAATATTATTTTTAAA
25299752 TACAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:25299758 original size:19 final size:20
Alignment explanation
Indices: 25299710--25299761 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
25299700 AATCGAAATT
25299710 AATAAAATATTATTTTTTAAA
1 AATAAAATATTATTTTTT-AA
25299731 ATATAAAATATTA-TTTTT-A
1 A-ATAAAATATTATTTTTTAA
25299750 AATACAAATATT
1 AATA-AAATATT
25299762 TAAAAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
21 6 0.21
22 11 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAAAATATTATTTTTTAA
Found at i:25304123 original size:21 final size:21
Alignment explanation
Indices: 25304099--25304140 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25304089 CCAGTGATAC
* *
25304099 AGAGGATGATGACGAAGATGA
1 AGAGGAGGATAACGAAGATGA
*
25304120 AGAGGAGGATAACGCAGATGA
1 AGAGGAGGATAACGAAGATGA
25304141 TCAAGATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.38, T:0.12
Consensus pattern (21 bp):
AGAGGAGGATAACGAAGATGA
Found at i:25304257 original size:15 final size:15
Alignment explanation
Indices: 25304237--25304337 Score: 58
Period size: 15 Copynumber: 6.7 Consensus size: 15
25304227 ATGGAGGGAG
25304237 TGATGAAGAGGATGA
1 TGATGAAGAGGATGA
* *
25304252 TGATGAGGATGATGA
1 TGATGAAGAGGATGA
** * *
25304267 TGATGGGGACGAAGA
1 TGATGAAGAGGATGA
* *
25304282 TGATGAGGAGGAGGA
1 TGATGAAGAGGATGA
* * *
25304297 GGATGAAGAAGAGGA
1 TGATGAAGAGGATGA
* * *
25304312 GGACGAAGAAGATGA
1 TGATGAAGAGGATGA
* *
25304327 GGATGATGAGG
1 TGATGAAGAGG
25304338 TTCCTCAGCC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 70 1.00
ACGTcount: A:0.38, C:0.02, G:0.46, T:0.15
Consensus pattern (15 bp):
TGATGAAGAGGATGA
Found at i:25304267 original size:12 final size:12
Alignment explanation
Indices: 25304237--25304269 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25304227 ATGGAGGGAG
*
25304237 TGATGAAGAGGA
1 TGATGATGAGGA
25304249 TGATGATGAGGA
1 TGATGATGAGGA
25304261 TGATGATGA
1 TGATGATGA
25304270 TGGGGACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.24
Consensus pattern (12 bp):
TGATGATGAGGA
Found at i:25304270 original size:18 final size:18
Alignment explanation
Indices: 25304247--25304335 Score: 70
Period size: 18 Copynumber: 4.9 Consensus size: 18
25304237 TGATGAAGAG
*
25304247 GATGATGATGAGGATGAT
1 GATGATGAGGAGGATGAT
* * *
25304265 GATGATGGGGACGAAGAT
1 GATGATGAGGAGGATGAT
* *
25304283 GATGAGGAGGAGGAGGAT
1 GATGATGAGGAGGATGAT
* * * *
25304301 GAAGAAGAGGAGGACGAA
1 GATGATGAGGAGGATGAT
* *
25304319 GAAGATGAGGATGATGA
1 GATGATGAGGAGGATGA
25304336 GGTTCCTCAG
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.38, C:0.02, G:0.45, T:0.15
Consensus pattern (18 bp):
GATGATGAGGAGGATGAT
Found at i:25307579 original size:19 final size:18
Alignment explanation
Indices: 25307542--25307580 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
25307532 AGGTGGTCGT
* *
25307542 GGTGGTGGTGGATGAGGA
1 GGTGGAGGTGGAGGAGGA
25307560 GGTGGAGGTGGGAGGAGGA
1 GGTGGAGGT-GGAGGAGGA
25307579 GG
1 GG
25307581 CGAGGGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.18, C:0.00, G:0.67, T:0.15
Consensus pattern (18 bp):
GGTGGAGGTGGAGGAGGA
Found at i:25318852 original size:6 final size:6
Alignment explanation
Indices: 25318846--25318880 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
25318836 AATCAGCATA
*
25318846 TATATA TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT
25318881 GCATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:25318890 original size:18 final size:18
Alignment explanation
Indices: 25318852--25318890 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25318842 CATATATATA
** *
25318852 TATATTTATATTTATATT
1 TATATTTATATGCATAAT
25318870 TATATTTATATGCATAAT
1 TATATTTATATGCATAAT
25318888 TAT
1 TAT
25318891 GATAGGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TATATTTATATGCATAAT
Found at i:25319001 original size:2 final size:2
Alignment explanation
Indices: 25318988--25319034 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
25318978 ATAATTATGC
*
25318988 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25319030 AT AT A
1 AT AT A
25319035 AGCTAGGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25324086 original size:20 final size:20
Alignment explanation
Indices: 25324063--25324117 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
25324053 AATTAATAAA
*
25324063 AATTATATATATTTAAAGAT
1 AATTATATATATTTAAAAAT
*
25324083 AATTTTAT-TAATTTAAAAAT
1 AATTATATAT-ATTTAAAAAT
* *
25324103 TATAATA-ATATTTAA
1 AATTATATATATTTAA
25324118 GTCAATCGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTATATATATTTAAAAAT
Found at i:25324566 original size:3 final size:3
Alignment explanation
Indices: 25324558--25324587 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25324548 ATAAATAAAT
*
25324558 TAA TAA TAA GAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25324588 AGTACACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:25325010 original size:15 final size:15
Alignment explanation
Indices: 25324992--25325026 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
25324982 TTAATAAATG
25324992 AAAATTTAAAAATAA
1 AAAATTTAAAAATAA
*
25325007 AAAAGTTAAAAATAA
1 AAAATTTAAAAATAA
25325022 AAAAT
1 AAAAT
25325027 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATTTAAAAATAA
Found at i:25325050 original size:16 final size:16
Alignment explanation
Indices: 25324992--25325051 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
25324982 TTAATAAATG
25324992 AAAAT-TTAAAAA-TA
1 AAAATATTAAAAATTA
*
25325006 AAAA-AGTTAAAAATAA
1 AAAATA-TTAAAAATTA
*
25325022 AAAATATT-TAAATTA
1 AAAATATTAAAAATTA
*
25325037 AAATTATTAAAAATT
1 AAAATATTAAAAATT
25325052 TTATGCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 4 0.11
15 19 0.53
16 12 0.33
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAATATTAAAAATTA
Found at i:25326587 original size:32 final size:32
Alignment explanation
Indices: 25326546--25326610 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
25326536 CCCATCATGT
*
25326546 TTGATAATAATAATAAAAACAATTGTAATCGA
1 TTGATAATAATAACAAAAACAATTGTAATCGA
25326578 TTGATAATAATAACAAAAACAATTGTAATCGA
1 TTGATAATAATAACAAAAACAATTGTAATCGA
25326610 T
1 T
25326611 GCTTGGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (32 bp):
TTGATAATAATAACAAAAACAATTGTAATCGA
Found at i:25328037 original size:21 final size:21
Alignment explanation
Indices: 25327975--25328037 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
25327965 TATTTTTAAC
25327975 CAATAGATTAATAATTGACAT
1 CAATAGATTAATAATTGACAT
* * *
25327996 -AAT-TATTAATATTCTTA-AT
1 CAATAGATTAATAAT-TGACAT
25328015 CAATAGATTAATAATTGACAT
1 CAATAGATTAATAATTGACAT
25328036 CA
1 CA
25328038 CTATTTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 10 0.31
20 10 0.31
21 12 0.38
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (21 bp):
CAATAGATTAATAATTGACAT
Found at i:25330653 original size:29 final size:29
Alignment explanation
Indices: 25330620--25330678 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
25330610 GACTAACGAA
*
25330620 AGAATAGAAAAGAATTGAAAGGAGAAAAT
1 AGAATAGAAAAGAATTGAAAAGAGAAAAT
* *
25330649 AGAATAGAGAATAATTGAAAAGAGAAAAT
1 AGAATAGAAAAGAATTGAAAAGAGAAAAT
25330678 A
1 A
25330679 TTTTTTCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (29 bp):
AGAATAGAAAAGAATTGAAAAGAGAAAAT
Found at i:25330674 original size:15 final size:14
Alignment explanation
Indices: 25330632--25330677 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
25330622 AATAGAAAAG
*
25330632 AATTGAAAGGAGAA
1 AATTGAAAAGAGAA
* *
25330646 AATAGAATAGAGAA
1 AATTGAAAAGAGAA
25330660 TAATTGAAAAGAGAA
1 -AATTGAAAAGAGAA
25330675 AAT
1 AAT
25330678 ATTTTTTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (14 bp):
AATTGAAAAGAGAA
Found at i:25332469 original size:22 final size:22
Alignment explanation
Indices: 25332444--25332488 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
25332434 GCTAATTAGT
25332444 AAGGGTGAATCCAAATAATGTA
1 AAGGGTGAATCCAAATAATGTA
25332466 AAGGGTGAATCCAAATAATGTA
1 AAGGGTGAATCCAAATAATGTA
25332488 A
1 A
25332489 TGGGACGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (22 bp):
AAGGGTGAATCCAAATAATGTA
Found at i:25332845 original size:17 final size:16
Alignment explanation
Indices: 25332825--25332858 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25332815 ACATGGCTGT
*
25332825 ATATATATAAAAATTAA
1 ATATAT-TAAAAAGTAA
25332842 ATATATTAAAAAGTAA
1 ATATATTAAAAAGTAA
25332858 A
1 A
25332859 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATATTAAAAAGTAA
Found at i:25343142 original size:14 final size:14
Alignment explanation
Indices: 25343123--25343152 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25343113 CCACTTAGAT
25343123 AATCCATCAATTAG
1 AATCCATCAATTAG
25343137 AATCCATCAATTAG
1 AATCCATCAATTAG
25343151 AA
1 AA
25343153 GTTCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (14 bp):
AATCCATCAATTAG
Found at i:25345679 original size:2 final size:2
Alignment explanation
Indices: 25345672--25345701 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25345662 TTAATTCTCA
25345672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25345702 TGCAGCAAAG
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):
AT
Found at i:25352043 original size:15 final size:15
Alignment explanation
Indices: 25352016--25352048 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
25352006 TAAATATAAT
25352016 TTTTATGTGATTTGAG
1 TTTTATGTGATTTG-G
25352032 TTTTAT-TGATTTGG
1 TTTTATGTGATTTGG
25352046 TTT
1 TTT
25352049 CATTTTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (15 bp):
TTTTATGTGATTTGG
Found at i:25352167 original size:19 final size:19
Alignment explanation
Indices: 25352143--25352185 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
25352133 ATTTTTATTT
25352143 TATAAAAATT-T-AAAATA
1 TATAAAAATTATAAAAATA
25352160 TATATAAAATTAATAAAAATA
1 TATA-AAAATT-ATAAAAATA
25352181 TATAA
1 TATAA
25352186 TTTAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
20 2 0.09
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TATAAAAATTATAAAAATA
Found at i:25352262 original size:13 final size:13
Alignment explanation
Indices: 25352230--25352271 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
25352220 AAAGTTGATG
*
25352230 TAAATTTTATATA
1 TAAATTTTATATT
*
25352243 TATATTTTATATT
1 TAAATTTTATATT
25352256 TAAA-TTTAT-TT
1 TAAATTTTATATT
25352267 TAAAT
1 TAAAT
25352272 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 6 0.24
12 5 0.20
13 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATTTTATATT
Found at i:25353792 original size:20 final size:20
Alignment explanation
Indices: 25353767--25353804 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25353757 TATGGCATTT
*
25353767 ATAAATTTAATTAATTGTAA
1 ATAAATGTAATTAATTGTAA
*
25353787 ATAAATGTATTTAATTGT
1 ATAAATGTAATTAATTGT
25353805 TTGTGTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
ATAAATGTAATTAATTGTAA
Found at i:25359846 original size:16 final size:16
Alignment explanation
Indices: 25359825--25359858 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25359815 TGAGAAAGAT
*
25359825 TTTAATTAATCTTAAC
1 TTTAATCAATCTTAAC
*
25359841 TTTAATCGATCTTAAC
1 TTTAATCAATCTTAAC
25359857 TT
1 TT
25359859 AGAGCAGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTAATCAATCTTAAC
Found at i:25361423 original size:12 final size:12
Alignment explanation
Indices: 25361406--25361445 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
25361396 TACTTTCAAG
25361406 ATAATAACAATA
1 ATAATAACAATA
* *
25361418 ATAATAGCAACA
1 ATAATAACAATA
*
25361430 ATAATAATAATA
1 ATAATAACAATA
25361442 ATAA
1 ATAA
25361446 CTTACACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (12 bp):
ATAATAACAATA
Found at i:25363721 original size:15 final size:15
Alignment explanation
Indices: 25363701--25363734 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25363691 CCCATTCAGG
25363701 CATCCCATGTTTTTA
1 CATCCCATGTTTTTA
*
25363716 CATCCCATGTTTTTG
1 CATCCCATGTTTTTA
25363731 CATC
1 CATC
25363735 ATGTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (15 bp):
CATCCCATGTTTTTA
Found at i:25374935 original size:39 final size:39
Alignment explanation
Indices: 25374880--25374955 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
25374870 ATGAATTTTG
** * * *
25374880 AAATATTATTTGTGATTGTTTGTTATATTTAATAAATGA
1 AAATATTATTCATGATTGATTATTAAATTTAATAAATGA
25374919 AAATATTATTCATGATTGATTATTAAATTTAATAAAT
1 AAATATTATTCATGATTGATTATTAAATTTAATAAAT
25374956 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (39 bp):
AAATATTATTCATGATTGATTATTAAATTTAATAAATGA
Found at i:25381728 original size:24 final size:22
Alignment explanation
Indices: 25381687--25381749 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
25381677 TCTCATACAT
* *
25381687 ATAAAAATTAAAAATAAAAATTA
1 ATAAAAA-TATAAATTAAAATTA
*
25381710 CATAAAAATATAAATTAAATTTA
1 -ATAAAAATATAAATTAAAATTA
25381733 ATAAAATATATATAATT
1 ATAAAA-ATATA-AATT
25381750 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.18
23 17 0.50
24 11 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAAAATATAAATTAAAATTA
Found at i:25385708 original size:32 final size:32
Alignment explanation
Indices: 25385672--25385743 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 32
25385662 TCGTGAAGTG
* * * *
25385672 TTATAATTTTTCGATAATTTATTTTTGAAAAA
1 TTATAATTTTTCAAAAATATATTTTTAAAAAA
*
25385704 TTATAATATTTTTTAAAAATATATTTTTAAAAAA
1 TTAT-A-ATTTTTCAAAAATATATTTTTAAAAAA
25385738 TTATAA
1 TTATAA
25385744 AATTTATCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
32 5 0.15
33 2 0.06
34 26 0.79
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
TTATAATTTTTCAAAAATATATTTTTAAAAAA
Found at i:25385709 original size:21 final size:19
Alignment explanation
Indices: 25385691--25385748 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
25385681 TTCGATAATT
25385691 TATTTTTGAAAAATTATAA
1 TATTTTTGAAAAATTATAA
*
25385710 TATTTTT-TAAAA--AT-A
1 TATTTTTGAAAAATTATAA
*
25385725 TATTTTTAAAAAATTATAA
1 TATTTTTGAAAAATTATAA
*
25385744 AATTT
1 TATTT
25385749 ATCGAATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 8 0.25
16 6 0.19
18 6 0.19
19 12 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTTTTGAAAAATTATAA
Found at i:25386444 original size:23 final size:23
Alignment explanation
Indices: 25386409--25386452 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
25386399 TTTGATTTGA
*
25386409 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
25386432 TTTAATATAAATATAAAATTA
1 TTTAAAATAAATATAAAATTA
25386453 AATAAACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:25386463 original size:16 final size:17
Alignment explanation
Indices: 25386433--25386474 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
25386423 AATATTATTT
*
25386433 TTAATATAAATATAAAA
1 TTAATATAAACATAAAA
25386450 TTAA-ATAAACATAAAA
1 TTAATATAAACATAAAA
*
25386466 -AAATATAAA
1 TTAATATAAA
25386475 ATTAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 16 0.73
17 4 0.18
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAATATAAACATAAAA
Found at i:25386859 original size:32 final size:34
Alignment explanation
Indices: 25386790--25386859 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
25386780 ACAATGAATG
*
25386790 TAATATTTAAATTTTAAAATTTATTAATTAAATA
1 TAATATTTAAATTTTAAAATTTATTAATCAAATA
* *
25386824 TAATA-TTAACTTTTAATA-TTATTAACTCAAA-A
1 TAATATTTAAATTTTAAAATTTATTAA-TCAAATA
25386856 TAAT
1 TAAT
25386860 GATATATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.38
33 15 0.47
34 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (34 bp):
TAATATTTAAATTTTAAAATTTATTAATCAAATA
Found at i:25387058 original size:15 final size:15
Alignment explanation
Indices: 25387017--25387051 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25387007 TCAATTAATT
*
25387017 ATTTAATATTTTAAA
1 ATTTAAAATTTTAAA
*
25387032 ATTTAAAATTTTATA
1 ATTTAAAATTTTAAA
25387047 ATTTA
1 ATTTA
25387052 CATTTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTAAAATTTTAAA
Found at i:25388819 original size:30 final size:30
Alignment explanation
Indices: 25388778--25388834 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
25388768 TTAATTATTT
* * *
25388778 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
25388808 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
25388835 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:25388832 original size:20 final size:20
Alignment explanation
Indices: 25388805--25388858 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
25388795 ATGATATTTT
25388805 TAAATATTTATATTTAAAAAA
1 TAAATATTT-TATTTAAAAAA
25388826 T-AATATTTTATATTAAAAAA
1 TAAATATTTTAT-TTAAAAAA
25388846 TAAATATTTTATT
1 TAAATATTTTATT
25388859 AATTTCGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.10
20 17 0.55
21 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATATTTTATTTAAAAAA
Found at i:25388837 original size:21 final size:21
Alignment explanation
Indices: 25388805--25388857 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
25388795 ATGATATTTT
25388805 TAAATA-TTTATATTTAAAAAA
1 TAAATATTTTATA-TTAAAAAA
25388826 T-AATATTTTATATTAAAAAA
1 TAAATATTTTATATTAAAAAA
25388846 TAAATATTTTAT
1 TAAATATTTTAT
25388858 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATATTTTATATTAAAAAA
Found at i:25391033 original size:2 final size:2
Alignment explanation
Indices: 25391020--25391054 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
25391010 ATTCCTCAGC
*
25391020 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25391055 TCCTGATTTT
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25395270 original size:19 final size:19
Alignment explanation
Indices: 25395248--25395285 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25395238 TTTGATGTCC
25395248 TTTTCTTATTCATTGATTT
1 TTTTCTTATTCATTGATTT
25395267 TTTTCTTATTCATTGATTT
1 TTTTCTTATTCATTGATTT
25395286 GATAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTCTTATTCATTGATTT
Found at i:25402772 original size:11 final size:11
Alignment explanation
Indices: 25402756--25402790 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
25402746 AATATAATTT
25402756 AAAATTTAATA
1 AAAATTTAATA
25402767 AAAA-TTAATA
1 AAAATTTAATA
*
25402777 TAAATTTAATA
1 AAAATTTAATA
25402788 AAA
1 AAA
25402791 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTTAATA
Found at i:25402774 original size:10 final size:10
Alignment explanation
Indices: 25402755--25402791 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
25402745 TAATATAATT
25402755 TAAAATTTAA
1 TAAAATTTAA
*
25402765 TAAAAATTAA
1 TAAAATTTAA
25402775 TATAAATTTAA
1 TA-AAATTTAA
25402786 TAAAAT
1 TAAAAT
25402792 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATTTAA
Found at i:25402781 original size:21 final size:21
Alignment explanation
Indices: 25402709--25402804 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 21
25402699 ATGTGATATA
25402709 ATAATATTTATATAAAAA-TAAT
1 ATAA-ATTTA-ATAAAAATTAAT
* *
25402731 ATAAAAAATTAA-AATAATATAAT
1 AT--AAATTTAATAAAAAT-TAAT
*
25402754 TTAAAATTTAATAAAAATTAAT
1 AT-AAATTTAATAAAAATTAAT
* *
25402776 ATAAATTTAAT-AAAATAAAA
1 ATAAATTTAATAAAAATTAAT
25402796 ATAAATTTA
1 ATAAATTTA
25402805 TAATTTTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
20 16 0.26
21 13 0.21
22 16 0.26
23 14 0.23
24 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAATTTAATAAAAATTAAT
Found at i:25405002 original size:33 final size:33
Alignment explanation
Indices: 25404965--25405030 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
25404955 TATATTCGGA
*
25404965 GTTCCCATAGGTGGAGTGTTTTATTTGTAAGGT
1 GTTCCCATAGGCGGAGTGTTTTATTTGTAAGGT
*
25404998 GTTCCCATAGGCGGGGTGTTTTATTTGTAAGGT
1 GTTCCCATAGGCGGAGTGTTTTATTTGTAAGGT
25405031 AATCCAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.17, C:0.11, G:0.32, T:0.41
Consensus pattern (33 bp):
GTTCCCATAGGCGGAGTGTTTTATTTGTAAGGT
Found at i:25405235 original size:27 final size:27
Alignment explanation
Indices: 25405197--25405257 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
25405187 ACGATATTGT
25405197 ATGTTTTACATTGATCAAATAATGTGA
1 ATGTTTTACATTGATCAAATAATGTGA
25405224 ATGTTTTACATTGATCAAATAATGTGA
1 ATGTTTTACATTGATCAAATAATGTGA
25405251 ATGTTTT
1 ATGTTTT
25405258 GATCAAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (27 bp):
ATGTTTTACATTGATCAAATAATGTGA
Found at i:25405260 original size:22 final size:24
Alignment explanation
Indices: 25405206--25405264 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 24
25405196 TATGTTTTAC
25405206 ATTGATCAAATAATGTGAATGTTTT
1 ATTGATCAAATAATGTGAATG-TTT
25405231 ACATTGATCAAATAATGTGAATG-TT
1 --ATTGATCAAATAATGTGAATGTTT
25405256 -TTGATCAAA
1 ATTGATCAAA
25405265 GTTTCTAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.28
25 2 0.06
27 21 0.66
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (24 bp):
ATTGATCAAATAATGTGAATGTTT
Found at i:25409318 original size:44 final size:44
Alignment explanation
Indices: 25409248--25409331 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
25409238 CGATGTGAGA
**
25409248 TTCAAGATTTTTTTTTAGGTCCGTGACATT-TTTTCTCACCTAAT
1 TTCAAGATTTTTCCTTAGGTCCGTGACATTCTTTTC-CACCTAAT
* *
25409292 TTCAGGATTTTTCCTTAGGTCTGTGACATTCTTTTCCACC
1 TTCAAGATTTTTCCTTAGGTCCGTGACATTCTTTTCCACC
25409332 CAATCTCGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 30 0.86
45 5 0.14
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (44 bp):
TTCAAGATTTTTCCTTAGGTCCGTGACATTCTTTTCCACCTAAT
Found at i:25416085 original size:2 final size:2
Alignment explanation
Indices: 25416078--25416103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25416068 AATGATAATT
25416078 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
25416104 AGATTAAGCT
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:25419193 original size:15 final size:16
Alignment explanation
Indices: 25419169--25419206 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25419159 ATCTCTTAAA
25419169 ATTTTAATTG-ATTTT
1 ATTTTAATTGCATTTT
* *
25419184 ATTTTTATTGCCTTTT
1 ATTTTAATTGCATTTT
25419200 ATTTTAA
1 ATTTTAA
25419207 GATGTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (16 bp):
ATTTTAATTGCATTTT
Found at i:25424303 original size:17 final size:17
Alignment explanation
Indices: 25424270--25424303 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25424260 ATAATAGGAT
*
25424270 TGAATAAAATAATATTA
1 TGAATAAAATAAGATTA
*
25424287 TGAATAAAATTAGATTA
1 TGAATAAAATAAGATTA
25424304 AATAATATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
TGAATAAAATAAGATTA
Found at i:25426244 original size:6 final size:6
Alignment explanation
Indices: 25426233--25426270 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
25426223 ATTATTCATG
*
25426233 CTCGAA CTCGAA CTCGGA CTCGAA CTCG-A CTCGAA CTC
1 CTCGAA CTCGAA CTCGAA CTCGAA CTCGAA CTCGAA CTC
25426271 AGACTCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.18
Consensus pattern (6 bp):
CTCGAA
Found at i:25426253 original size:12 final size:12
Alignment explanation
Indices: 25426233--25426276 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
25426223 ATTATTCATG
*
25426233 CTCGAACTCGAA
1 CTCGGACTCGAA
25426245 CTCGGACTCGAA
1 CTCGGACTCGAA
25426257 CTC-GACTCGAA
1 CTCGGACTCGAA
*
25426268 CTCAGACTC
1 CTCGGACTC
25426277 TAAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.18
Consensus pattern (12 bp):
CTCGGACTCGAA
Found at i:25436949 original size:5 final size:5
Alignment explanation
Indices: 25436911--25436948 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
25436901 AGGTACTTTA
* *
25436911 TTTTC TTTTG TTTTC TTTTC TTTTT TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
25436949 TAATCAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (5 bp):
TTTTC
Found at i:25436949 original size:15 final size:15
Alignment explanation
Indices: 25436911--25436948 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
25436901 AGGTACTTTA
25436911 TTTTCTTTTGTTTTC
1 TTTTCTTTTGTTTTC
*
25436926 TTTTCTTTTTTTTTC
1 TTTTCTTTTGTTTTC
25436941 TTTT-TTTT
1 TTTTCTTTT
25436949 TAATCAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTGTTTTC
Found at i:25439066 original size:81 final size:81
Alignment explanation
Indices: 25438931--25439092 Score: 274
Period size: 81 Copynumber: 2.0 Consensus size: 81
25438921 CATATAATTG
25438931 GTGTTGTCAACTGAACTCTGATAGGAAGAAATTGGTTGCTTAATCATTGATTTATCGA-TCTCAG
1 GTGTTGTCAACTGAACTCTGATAGGAAGAAATTGGTTGCTTAATCATTGATTTATC-ATTCTCAG
25438995 TATGATACCAAGTACTA
65 TATGATACCAAGTACTA
**
25439012 GTGTTGTTTACTGAACTCTGATAGGAAGAAATTGGTTGCTTAATCACTT-ATTTATCATTCTCAG
1 GTGTTGTCAACTGAACTCTGATAGGAAGAAATTGGTTGCTTAATCA-TTGATTTATCATTCTCAG
25439076 TATGATACCAAGTACTA
65 TATGATACCAAGTACTA
25439093 TTACAAGATT
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
80 1 0.01
81 74 0.96
82 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (81 bp):
GTGTTGTCAACTGAACTCTGATAGGAAGAAATTGGTTGCTTAATCATTGATTTATCATTCTCAGT
ATGATACCAAGTACTA
Found at i:25452234 original size:2 final size:2
Alignment explanation
Indices: 25452229--25452261 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
25452219 GATTAGTGTG
25452229 TA TA TA TA TA TA TA TA TA TGA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA T
25452262 TTATTGCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25456370 original size:6 final size:6
Alignment explanation
Indices: 25456348--25456418 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
25456338 TGGGCCACGG
* * *
25456348 GACCAA -ACTCAA AACCAA GACCAA GACCAA GACCAA GACCAT GACCAT
1 GACCAA GAC-CAA GACCAA GACCAA GACCAA GACCAA GACCAA GACCAA
* * *
25456396 GACCAT GACCAT GACCAT GACCA
1 GACCAA GACCAA GACCAA GACCA
25456419 TGAGTCTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
5 2 0.03
6 57 0.93
7 2 0.03
ACGTcount: A:0.44, C:0.34, G:0.14, T:0.08
Consensus pattern (6 bp):
GACCAA
Found at i:25456419 original size:6 final size:6
Alignment explanation
Indices: 25456361--25456421 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
25456351 CAAACTCAAA
* * * *
25456361 ACCAAG ACCAAG ACCAAG ACCAAG ACCATG ACCATG ACCATG ACCATG
1 ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG
25456409 ACCATG ACCATG A
1 ACCATG ACCATG A
25456422 GTCTTTCACC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.41, C:0.33, G:0.16, T:0.10
Consensus pattern (6 bp):
ACCATG
Found at i:25463609 original size:3 final size:3
Alignment explanation
Indices: 25463601--25463632 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
25463591 GAATCTTTTA
25463601 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25463633 GAACAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25466410 original size:2 final size:2
Alignment explanation
Indices: 25466398--25466434 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
25466388 GCTGACAAAG
*
25466398 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25466435 GAAAAAAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25467155 original size:16 final size:17
Alignment explanation
Indices: 25467131--25467162 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25467121 TCGATTTTAA
25467131 TATATTTTACAAAATTT
1 TATATTTTACAAAATTT
25467148 TATA-TTTACAAAATT
1 TATATTTTACAAAATT
25467163 GAATTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATTTTACAAAATTT
Found at i:25467871 original size:16 final size:16
Alignment explanation
Indices: 25467843--25467887 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
25467833 CATAATTAAA
25467843 AATAAT-TAT-AAATT
1 AATAATATATAAAATT
25467857 AATAATATATAAAATT
1 AATAATATATAAAATT
* *
25467873 AATAAAAAATAAAAT
1 AATAATATATAAAAT
25467888 ATTAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 6 0.22
15 3 0.11
16 18 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATATATAAAATT
Found at i:25467897 original size:16 final size:16
Alignment explanation
Indices: 25467852--25467897 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
25467842 AAATAATTAT
*
25467852 AAATTAATAATATATA
1 AAATTAATAAAATATA
*
25467868 AAATTAATAAAAAATAA
1 AAATTAATAAAATAT-A
25467885 AATATTAATAAAA
1 AA-ATTAATAAAA
25467898 ATGATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 13 0.50
17 3 0.12
18 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAATAAAATATA
Found at i:25468115 original size:21 final size:22
Alignment explanation
Indices: 25468091--25468136 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
25468081 ACATAAATAT
25468091 TAATTA-TTATATATTAATAAA
1 TAATTATTTATATATTAATAAA
*
25468112 TAA-TATTTATATTTTAATAAA
1 TAATTATTTATATATTAATAAA
25468133 TAAT
1 TAAT
25468137 AATAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTATTTATATATTAATAAA
Found at i:25468137 original size:21 final size:21
Alignment explanation
Indices: 25468097--25468137 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
25468087 ATATTAATTA
25468097 TTATATATTAATAAATAATAT
1 TTATATATTAATAAATAATAT
*
25468118 TTATATTTTAATAAATAATA
1 TTATATATTAATAAATAATA
25468138 ATAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATATATTAATAAATAATAT
Found at i:25468148 original size:21 final size:21
Alignment explanation
Indices: 25468104--25468148 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25468094 TTATTATATA
* * *
25468104 TTAATAAATAATATTTATATT
1 TTAATAAATAATAATAATAAT
25468125 TTAATAAATAATAATAATAAT
1 TTAATAAATAATAATAATAAT
25468146 TTA
1 TTA
25468149 TTAGTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATAAATAATAATAATAAT
Found at i:25468804 original size:17 final size:18
Alignment explanation
Indices: 25468756--25468804 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
25468746 ATTTAATTTT
25468756 ATATTTATATT-AAAATA
1 ATATTTATATTAAAAATA
25468773 ATAATTTATATTTAAAAATA
1 AT-ATTTATA-TTAAAAATA
25468793 ATATTT-TATTAA
1 ATATTTATATTAA
25468805 TTTCAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 6 0.21
20 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTATATTAAAAATA
Found at i:25471924 original size:41 final size:41
Alignment explanation
Indices: 25471873--25471956 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
25471863 TAGTTTGATT
* * *
25471873 ATTTAATTATATTTTAATTAATTGATTA-TTAAGTAATTATA
1 ATTTAATTATAATATAA-TAATTAATTATTTAAGTAATTATA
* * *
25471914 ATTTGATTATAATATAATAATTAATTATTTAATTGATTATA
1 ATTTAATTATAATATAATAATTAATTATTTAAGTAATTATA
25471955 AT
1 AT
25471957 GCTTTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
40 9 0.25
41 27 0.75
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (41 bp):
ATTTAATTATAATATAATAATTAATTATTTAAGTAATTATA
Found at i:25473010 original size:56 final size:56
Alignment explanation
Indices: 25472924--25473038 Score: 185
Period size: 56 Copynumber: 2.1 Consensus size: 56
25472914 GCGTTTATAG
* *
25472924 TTTCTACCTTTATCCTCGTCTGTTTAGCTATTTTTTACGGTATTTTAATTTTAGTT
1 TTTCTACCTTTATCCTCATCTGTTTAGCTATATTTTACGGTATTTTAATTTTAGTT
* * *
25472980 TTTCTACCTTTATCCTCATCTGTTTTGCTATATTTTAGGGTATTTTAATTTTGGTT
1 TTTCTACCTTTATCCTCATCTGTTTAGCTATATTTTACGGTATTTTAATTTTAGTT
25473036 TTT
1 TTT
25473039 TAGTATATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.16, C:0.15, G:0.11, T:0.58
Consensus pattern (56 bp):
TTTCTACCTTTATCCTCATCTGTTTAGCTATATTTTACGGTATTTTAATTTTAGTT
Found at i:25476027 original size:3 final size:3
Alignment explanation
Indices: 25476019--25476046 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25476009 TATTTTTTGT
25476019 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25476047 ATCATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25477467 original size:4 final size:4
Alignment explanation
Indices: 25477460--25477485 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25477450 TACATACATA
25477460 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
25477486 AACTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:25480791 original size:13 final size:13
Alignment explanation
Indices: 25480757--25480793 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
25480747 TTTGTCCTTT
25480757 GTCCTTTGTTAAA
1 GTCCTTTGTTAAA
*
25480770 GT-GTTTGTTAAA
1 GTCCTTTGTTAAA
25480782 GTCCTTTGTTAA
1 GTCCTTTGTTAA
25480794 TGCCAACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.49
Consensus pattern (13 bp):
GTCCTTTGTTAAA
Found at i:25484544 original size:28 final size:26
Alignment explanation
Indices: 25484497--25484559 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
25484487 TAAAAAATTC
25484497 ATTTATTAATAAAAAGATAT-ATGATTT
1 ATTTATTAATAAAAAGATATCAT--TTT
*
25484524 ATTTCATTAATAAGATA-ATATCATTTT
1 ATTT-ATTAATAA-AAAGATATCATTTT
25484551 ATTTATTAA
1 ATTTATTAA
25484560 CAATATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 5 0.16
27 11 0.34
28 12 0.38
29 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
ATTTATTAATAAAAAGATATCATTTT
Found at i:25492955 original size:39 final size:39
Alignment explanation
Indices: 25492880--25492956 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
25492870 GGTACCAGCA
* ** *
25492880 ATGTGCCACTAAGGACAGTGGACCCTTGTTGGAGTGGGT
1 ATGTGCCACCAAGGACAGTGGACCCTCATTGAAGTGGGT
*
25492919 ATGTGCCACCGAGGACAGTGGACCCTCATTGAAGTGGG
1 ATGTGCCACCAAGGACAGTGGACCCTCATTGAAGTGGG
25492957 GAGGATGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (39 bp):
ATGTGCCACCAAGGACAGTGGACCCTCATTGAAGTGGGT
Found at i:25493231 original size:80 final size:80
Alignment explanation
Indices: 25493098--25493251 Score: 272
Period size: 80 Copynumber: 1.9 Consensus size: 80
25493088 ATCAAAACGG
* *
25493098 ACAATACCTCACAAGTTGATTTGAACACGGACATCTAGCCAGTGATTATATATTTACATATGTTG
1 ACAATACCTCACAAGTTGATGTGAACACGGACATCTAGCCAGTGATTATATATTCACATATGTTG
25493163 ATGATGTTTGAGCAA
66 ATGATGTTTGAGCAA
* *
25493178 ACAATACCTCACAAGTTGATGTGGACACTGACATCTAGCCAGTGATTATATATTCACATATGTTG
1 ACAATACCTCACAAGTTGATGTGAACACGGACATCTAGCCAGTGATTATATATTCACATATGTTG
25493243 ATGATGTTT
66 ATGATGTTT
25493252 CTTTTTCAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (80 bp):
ACAATACCTCACAAGTTGATGTGAACACGGACATCTAGCCAGTGATTATATATTCACATATGTTG
ATGATGTTTGAGCAA
Found at i:25493567 original size:69 final size:68
Alignment explanation
Indices: 25493456--25493594 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 68
25493446 TCATTTAAAT
* *
25493456 AATGCTATAATGATTCTTTTCTTAAATGTTGCCTTCATTTCCATGGTTTGCCCATTTTATTCATC
1 AATGCTATAATGATTCTTCTCTTAAATATTGCCTTCATTTCCATGG-TTGCCCATTTTATTCATC
25493521 ATAA
65 ATAA
* * *
25493525 AATGCTATAATGATTCTTCTCTTAAATATTGCTTTGATTTCCATGGTTGTCCATTTTATTCATCA
1 AATGCTATAATGATTCTTCTCTTAAATATTGCCTTCATTTCCATGGTTGCCCATTTTATTCATCA
25493590 TAA
66 TAA
25493593 AA
1 AA
25493595 CATTGGTGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 23 0.35
69 42 0.65
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (68 bp):
AATGCTATAATGATTCTTCTCTTAAATATTGCCTTCATTTCCATGGTTGCCCATTTTATTCATCA
TAA
Found at i:25493841 original size:29 final size:29
Alignment explanation
Indices: 25493773--25493841 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
25493763 GAACTAAAAT
* *
25493773 TTTTAAAAAATAATATTATAAAGATTAAA
1 TTTTAAAAAATAATACTAGAAAGATTAAA
*** *
25493802 TTTTTTTAAATAATACTAG-AGGAATTAAA
1 TTTTAAAAAATAATACTAGAAAG-ATTAAA
25493831 TTTTAAAAAAT
1 TTTTAAAAAAT
25493842 CGAAGAGTGC
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (29 bp):
TTTTAAAAAATAATACTAGAAAGATTAAA
Found at i:25515307 original size:20 final size:19
Alignment explanation
Indices: 25515263--25515308 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
25515253 TTATACTTAT
25515263 TCTGTGTATGTATTTGTTG
1 TCTGTGTATGTATTTGTTG
*
25515282 TGTGTGTAATGTATTT-TGTG
1 TCTGTGT-ATGTATTTGT-TG
25515302 TCTGTGT
1 TCTGTGT
25515309 CTATACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.11, C:0.04, G:0.28, T:0.57
Consensus pattern (19 bp):
TCTGTGTATGTATTTGTTG
Found at i:25526732 original size:14 final size:14
Alignment explanation
Indices: 25526699--25526737 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
25526689 TTTAAAATCA
*
25526699 AAATTAAAAAATTT
1 AAATTAAAATATTT
**
25526713 TGATTAAAATATTT
1 AAATTAAAATATTT
25526727 AAATTAAAATA
1 AAATTAAAATA
25526738 ATATAAGTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
AAATTAAAATATTT
Found at i:25527082 original size:18 final size:18
Alignment explanation
Indices: 25527055--25527100 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
25527045 TGCAATTTAC
*
25527055 AAAAATAAATATAAAATA-
1 AAAAAAAAATATAAAA-AG
25527073 AAAAAAAAAT-TAAAAAG
1 AAAAAAAAATATAAAAAG
*
25527090 GAAAAAAAATA
1 AAAAAAAAATA
25527101 GCGTCGCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 14 0.58
18 9 0.38
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (18 bp):
AAAAAAAAATATAAAAAG
Found at i:25533161 original size:2 final size:2
Alignment explanation
Indices: 25533154--25533192 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25533144 AATAATTAGT
25533154 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
25533193 CATTTTGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25534904 original size:34 final size:33
Alignment explanation
Indices: 25534866--25534975 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 33
25534856 CTTTAAAGGT
*
25534866 TTTTAGATATTTATTTTTGAAAAATTTTTAAAAA
1 TTTTAGAAATTTATTTTTG-AAAATTTTTAAAAA
* * * *
25534900 TTTTAAAAAGTGTA-TTTTCAAAATTTCTTAATAA
1 TTTTAGAAA-TTTATTTTTGAAAATTT-TTAAAAA
*
25534934 TTTTCAGACATTTATTTTTG-AAATTTTTAAAAA
1 TTTT-AGAAATTTATTTTTGAAAATTTTTAAAAA
* *
25534967 CTTTCGAAA
1 TTTTAGAAA
25534976 ATAAATTTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
32 3 0.05
33 16 0.27
34 30 0.51
35 10 0.17
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (33 bp):
TTTTAGAAATTTATTTTTGAAAATTTTTAAAAA
Found at i:25535595 original size:34 final size:33
Alignment explanation
Indices: 25535526--25535613 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 33
25535516 TTATAATGTT
* *
25535526 TTTTTGAAATACAATTTTTGATATAAGAAAGAAG
1 TTTTTGAAATA-AATTTTTAATATAAGAAAAAAG
**
25535560 TTTTTGAAAATAAATTTTTAATATATTAAAAAAG
1 TTTTTG-AAATAAATTTTTAATATAAGAAAAAAG
*
25535594 TTTTCT-AAATGAATTTTTAA
1 TTTT-TGAAATAAATTTTTAA
25535614 AAATTTATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 13 0.28
34 28 0.60
35 6 0.13
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (33 bp):
TTTTTGAAATAAATTTTTAATATAAGAAAAAAG
Found at i:25536193 original size:6 final size:6
Alignment explanation
Indices: 25536184--25536212 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
25536174 CAAAAACAAA
25536184 TAATAC TAATAC TAATAC TAATAC TAATA
1 TAATAC TAATAC TAATAC TAATAC TAATA
25536213 TTCCATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
TAATAC
Found at i:25536433 original size:3 final size:3
Alignment explanation
Indices: 25536425--25536458 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
25536415 ACCCAGCAAC
* *
25536425 AAG AAG AAG AAG AAG AAG CAG AAG AAG AGG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
25536459 GCAGCCGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25539699 original size:18 final size:18
Alignment explanation
Indices: 25539656--25539697 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
25539646 GGTATAAATT
25539656 TGTAAAATACCTGGAAAC
1 TGTAAAATACCTGGAAAC
25539674 TGTAAAATACCTGGAAAC
1 TGTAAAATACCTGGAAAC
25539692 T-TAAAA
1 TGTAAAA
25539698 ATCAGTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (18 bp):
TGTAAAATACCTGGAAAC
Found at i:25544715 original size:16 final size:15
Alignment explanation
Indices: 25544696--25544739 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
25544686 ATCCAAAACC
25544696 AAAAAACATAAAAGTGA
1 AAAAAACA-AAAA-TGA
25544713 AAAAGAACAAAAATGA
1 AAAA-AACAAAAATGA
25544729 AAAAAA-AAAAA
1 AAAAAACAAAAA
25544740 AAAAAACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 2 0.08
16 7 0.27
17 8 0.31
18 4 0.15
ACGTcount: A:0.80, C:0.05, G:0.09, T:0.07
Consensus pattern (15 bp):
AAAAAACAAAAATGA
Found at i:25545365 original size:15 final size:15
Alignment explanation
Indices: 25545342--25545390 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
25545332 TCATTAAATA
*
25545342 AAAAATAAACAAAAT
1 AAAAATAAACAAAAG
* *
25545357 AACAATAAAAAAAAG
1 AAAAATAAACAAAAG
*
25545372 AAAAATAAGCAAAA-
1 AAAAATAAACAAAAG
25545386 AAAAA
1 AAAAA
25545391 AGGAAAAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.82, C:0.06, G:0.04, T:0.08
Consensus pattern (15 bp):
AAAAATAAACAAAAG
Found at i:25545376 original size:21 final size:22
Alignment explanation
Indices: 25545338--25545402 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
25545328 AACTTCATTA
25545338 AATAAAAAATAA-ACAAAATAA-C
1 AATAAAAAA-AAGA-AAAATAAGC
25545360 AATAAAAAAAAGAAAAATAAGC
1 AATAAAAAAAAGAAAAATAAGC
*
25545382 AA-AAAAAAAAGGAAAAGTAAG
1 AATAAAAAAAA-GAAAAATAAG
25545403 ATCATTGAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
21 17 0.44
22 22 0.56
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (22 bp):
AATAAAAAAAAGAAAAATAAGC
Found at i:25551960 original size:12 final size:13
Alignment explanation
Indices: 25551945--25551987 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
25551935 ATATTTTATC
*
25551945 ATTAATTTTAAT-
1 ATTAATTATAATA
25551957 ATT-ATTATAATA
1 ATTAATTATAATA
25551969 ATTAA-TATAATA
1 ATTAATTATAATA
25551981 ATTAATT
1 ATTAATT
25551988 TTATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 7 0.26
12 18 0.67
13 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTAATTATAATA
Found at i:25552007 original size:18 final size:18
Alignment explanation
Indices: 25551940--25552006 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
25551930 AACACATATT
25551940 TTATCATTAATTTTAATA
1 TTATCATTAATTTTAATA
* *
25551958 TTATTA-TAATAATTAATA
1 TTATCATTAAT-TTTAATA
* * *
25551976 TAATAATTAATTTTATTA
1 TTATCATTAATTTTAATA
25551994 TTATCATT-ATTTT
1 TTATCATTAATTTT
25552007 TTAATTTACT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
17 9 0.23
18 26 0.67
19 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATCATTAATTTTAATA
Found at i:25562962 original size:118 final size:116
Alignment explanation
Indices: 25562743--25562979 Score: 291
Period size: 118 Copynumber: 2.0 Consensus size: 116
25562733 AAAAACCTCC
* * * * *
25562743 TTTAAAAAAAATTTTATTTTTAAGAAAAATTGATGCATTCAACTTTTTTCCAAAATATATTTAGA
1 TTTAAAAAAAATCTTATTTTCAAGAAAAATTGATACATTCAACTTTTCTCAAAAATATATTTAGA
* *
25562808 AACTTTAATTTCGAAAAAAATTGATACTTTCAACTTTTTCTCGAAAATATT
66 AACTTTAATTTCGAAAAAAATTGACACTTTCAACTTTTTCTCAAAAATATT
* * *
25562859 TTTAGAAAAAAA-CTTATTTTCAAGGAAAATTGATACTTTCAACTTCTTCTCAAAAATATTTTTT
1 TTTA-AAAAAAATCTTATTTTCAAGAAAAATTGATACATTCAACTT-TTCTCAAAAATA-TATTT
** *
25562923 AGAAAGC-TT-ATTTTTAAGGAAAATTGACACTTTCAACTTTTTCTCAAAAATATT
63 AGAAA-CTTTAATTTCGAA-AAAAATTGACACTTTCAACTTTTTCTCAAAAATATT
25562977 TTT
1 TTT
25562980 TTATCTTTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
116 32 0.31
117 23 0.22
118 47 0.46
119 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (116 bp):
TTTAAAAAAAATCTTATTTTCAAGAAAAATTGATACATTCAACTTTTCTCAAAAATATATTTAGA
AACTTTAATTTCGAAAAAAATTGACACTTTCAACTTTTTCTCAAAAATATT
Found at i:25562980 original size:58 final size:56
Alignment explanation
Indices: 25562756--25562979 Score: 254
Period size: 58 Copynumber: 3.9 Consensus size: 56
25562746 AAAAAAAATT
* * * *
25562756 TTATTTTTAAGAAAAATTGATGCATTCAACTTTTT-TCCAAAATATATTTAGAAAC
1 TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTAGAAAC
** *
25562811 TTTAATTTCGAA-AAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTAGAAAAAAAC
1 -TT-ATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTAG----AAAC
* * *
25562872 TTATTTTCAAGGAAAATTGATACTTTCAACTTCTTCTCAAAAATATTTTTTAGAAAGC
1 TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTAGAAA-C
* *
25562930 TTATTTTTAAGGAAAATTGACACTTTCAACTTTTTCTCAAAAATATTTTT
1 TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT
25562980 TTATCTTTTT
Statistics
Matches: 145, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
56 24 0.17
57 28 0.19
58 43 0.30
59 6 0.04
60 33 0.23
61 11 0.08
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (56 bp):
TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTAGAAAC
Found at i:25563140 original size:229 final size:229
Alignment explanation
Indices: 25562865--25563320 Score: 772
Period size: 229 Copynumber: 2.0 Consensus size: 229
25562855 TATTTTTAGA
*
25562865 AAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTTCTTCTCAAAAATATTTTTTAGAAAGC
1 AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTCTTCTCAAAAATATTTTTTAGAAAGC
*
25562930 TTATTTTTAAGGAAAATTGACACTTTCAACTTTTTCTCAAAAATATTTTTTT-ATCTTTTTATCT
66 TTA-TTTTAAAGAAAATTGACACTTTCAAC-TTTTCTCAAAAATATTTTTTTAATCTTTTTATCT
* * * *
25562994 TCAAGGGTCATTTAAAATATGC-CCGACAAATCAAAATTTCTTGTGAAACAGTTTAAACTTACTT
129 TCAAGGGTCATTTAAAAGATGCTCCGACAAATCAAAATTCCCTATGAAACAGTTTAAACTTACTT
*
25563058 GGTGTCCAACACAAAAACAAATGAATAGCTTCCTAG
194 GGTGTCCAACACAAAAACAAATGAACAGCTTCCTAG
*
25563094 AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGC
1 AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTCTTCTCAAAAATATTTTTTAGAAAGC
25563159 TTATTTTAAAGAAAATTGACACTTTCAACTTTTCTCAAAAATATTTTTTTAATCTTTTTATCTTC
66 TTATTTTAAAGAAAATTGACACTTTCAACTTTTCTCAAAAATATTTTTTTAATCTTTTTATCTTC
* *
25563224 AAGGGTCATTTAAAAGATGCTTCGACAAATCAAAATTCCCTATGAAACAGTTTAAACTTATTTGG
131 AAGGGTCATTTAAAAGATGCTCCGACAAATCAAAATTCCCTATGAAACAGTTTAAACTTACTTGG
**
25563289 TGTCCAACATGAAAACAAATGAACAGCTTCCT
196 TGTCCAACACAAAAACAAATGAACAGCTTCCT
25563321 GCATCACATT
Statistics
Matches: 213, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
227 21 0.10
228 58 0.27
229 134 0.63
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (229 bp):
AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTCTTCTCAAAAATATTTTTTAGAAAGC
TTATTTTAAAGAAAATTGACACTTTCAACTTTTCTCAAAAATATTTTTTTAATCTTTTTATCTTC
AAGGGTCATTTAAAAGATGCTCCGACAAATCAAAATTCCCTATGAAACAGTTTAAACTTACTTGG
TGTCCAACACAAAAACAAATGAACAGCTTCCTAG
Found at i:25563209 original size:57 final size:58
Alignment explanation
Indices: 25563100--25563207 Score: 184
Period size: 56 Copynumber: 1.9 Consensus size: 58
25563090 CTAGAAAAAA
* *
25563100 CTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAG
1 CTTATTTTAAAGAAAAATTGACACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAG
25563158 CTTATTTTAAAG-AAAATTGACACTTTCAAC-TTTTCTCAAAAATATTTTTT
1 CTTATTTTAAAGAAAAATTGACACTTTCAACTTTTTCTCAAAAATATTTTTT
25563208 TAATCTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 20 0.42
57 17 0.35
58 11 0.23
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (58 bp):
CTTATTTTAAAGAAAAATTGACACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAG
Found at i:25565834 original size:42 final size:42
Alignment explanation
Indices: 25565773--25566066 Score: 282
Period size: 42 Copynumber: 7.1 Consensus size: 42
25565763 AAACAAAGGT
*
25565773 TCCTCTAAGCAGAGGCTCAATGACTTTGAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCTCAATGACTTTGAAAAAATAAATTGC
* * *
25565815 TCCTCTAAACAAAGACTCAATGACTTTTAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCTCAATGACTTTGAAAAAATAAATTGC
* *
25565857 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAATGGC
1 TCCTCTAAACAGAGGCTCAATGACTTTGAAAAAATAAATTGC
* **
25565899 TCCTCTAATCAGAGGCTCAATGACTTTGAAAAAATAAATTAA
1 TCCTCTAAACAGAGGCTCAATGACTTTGAAAAAATAAATTGC
* * * *
25565941 TTCTCTAGGAA-A-AAGC-AACATGAC-TT-CAAAAATAAA-TGC
1 TCCTCTA--AACAGAGGCTCA-ATGACTTTGAAAAAATAAATTGC
* * * ** * *
25565980 TCTTCTAAACAGAGGCACCACAACATT-AAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCTCAATGACTTTGAAAAAATAAATTGC
* *
25566021 TCCTCTAAACAGAAG-T-AACGAAACTTTGAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCTCAATG--ACTTTGAAAAAATAAATTGC
25566063 TCCT
1 TCCT
25566067 TAATAATCAT
Statistics
Matches: 204, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
37 2 0.01
38 1 0.00
39 14 0.07
40 19 0.09
41 23 0.11
42 143 0.70
43 1 0.00
44 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (42 bp):
TCCTCTAAACAGAGGCTCAATGACTTTGAAAAAATAAATTGC
Found at i:25565947 original size:84 final size:84
Alignment explanation
Indices: 25565740--25565947 Score: 263
Period size: 84 Copynumber: 2.4 Consensus size: 84
25565730 TTAACGACAG
** ** * *
25565740 AGACTCAACAACTTTGAAAAAATAAACAAAGGTTCCTCTAAGCAGAGGCTCAATGACTTTGAAAA
1 AGACTCAATGACTTTGAAAAAATAAATTAA--TT-CTCTAAACAGAGGCTCAACGACTTTGAAAA
*
25565805 AATAAATTGCTCCTCTAAACAA
63 AATAAATGGCTCCTCTAAACAA
* ** *
25565827 AGACTCAATGACTTTTAAAAAATAAATTGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAAT
1 AGACTCAATGACTTTGAAAAAATAAATTAATTCTCTAAACAGAGGCTCAACGACTTTGAAAAAAT
* *
25565892 AAATGGCTCCTCTAATCAG
66 AAATGGCTCCTCTAAACAA
*
25565911 AGGCTCAATGACTTTGAAAAAATAAATTAATTCTCTA
1 AGACTCAATGACTTTGAAAAAATAAATTAATTCTCTA
25565948 GGAAAAAGCA
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
84 79 0.77
85 1 0.01
87 23 0.22
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (84 bp):
AGACTCAATGACTTTGAAAAAATAAATTAATTCTCTAAACAGAGGCTCAACGACTTTGAAAAAAT
AAATGGCTCCTCTAAACAA
Found at i:25565964 original size:126 final size:123
Alignment explanation
Indices: 25565736--25566060 Score: 338
Period size: 126 Copynumber: 2.6 Consensus size: 123
25565726 AGACTTAACG
* * * *
25565736 ACAGAGACTCAACAACTTTGAAAAAATAAACAAAGGTTCCTCTAAGCAGAGGCTCAATGACTTTG
1 ACAGAGGCTCAACAACTTTGAAAAAAT--A-AATGGCTCCTCTAAACAGAGGCTCAATGACTTTG
** *
25565801 AAAAAATAAATTGCTCCTCTAAACAAAGACTCAATGACTTTTAAAAAATAAATTGCTCCTCTAA
63 AAAAAATAAATTAATCCTCTAAACAAAGACACAATGAC--TTAAAAAATAAA-TGCTCCTCTAA
* *
25565865 ACAGAGGCTCAACGACTTTGAAAAAATAAATGGCTCCTCTAATCAGAGGCTCAATGACTTTGAAA
1 ACAGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAA
* * *
25565930 AAATAAATTAATTCTCTAGGAA-AAAG-CA-ACATGACTTCAAAAATAAATGCTCTTCTAA
66 AAATAAATTAATCCTCTA--AACAAAGACACA-ATGACTTAAAAAATAAATGCTCCTCTAA
* * * * * * *
25565988 ACAGAGGCACCACAACATT-AAAAAGTAAATTGCTCCTCTAAACAGAAG-T-AACGAAACTTTGA
1 ACAGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAAACAGAGGCTCAATG--ACTTTGA
25566050 AAAAATAAATT
64 AAAAATAAATT
25566061 GCTCCTTAAT
Statistics
Matches: 171, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
120 3 0.02
121 1 0.01
122 43 0.25
123 25 0.15
124 11 0.06
125 1 0.01
126 55 0.32
127 5 0.03
128 2 0.01
129 25 0.15
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (123 bp):
ACAGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAA
AAATAAATTAATCCTCTAAACAAAGACACAATGACTTAAAAAATAAATGCTCCTCTAA
Found at i:25567904 original size:8 final size:8
Alignment explanation
Indices: 25567893--25567956 Score: 59
Period size: 8 Copynumber: 8.6 Consensus size: 8
25567883 ATTTGAAAAT
25567893 TTTTTTCA
1 TTTTTTCA
*
25567901 TTTTCTCA
1 TTTTTTCA
25567909 -TTTTT--
1 TTTTTTCA
25567914 TTTTTTCA
1 TTTTTTCA
25567922 -TTTTT--
1 TTTTTTCA
*
25567927 TTTTCTCTA
1 TTTTTTC-A
25567936 TTTTTTCA
1 TTTTTTCA
25567944 TTTTTTCA
1 TTTTTTCA
25567952 TTTTT
1 TTTTT
25567957 CATCATCTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
6 9 0.20
7 9 0.20
8 21 0.47
9 6 0.13
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:25567925 original size:11 final size:11
Alignment explanation
Indices: 25567911--25567949 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
25567901 TTTTCTCATT
25567911 TTTTTTTTTCA
1 TTTTTTTTTCA
25567922 TTTTTTTTTC-
1 TTTTTTTTTCA
*
25567932 TCTATTTTTTCA
1 T-TTTTTTTTCA
25567944 TTTTTT
1 TTTTTT
25567950 CATTTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:25567925 original size:30 final size:29
Alignment explanation
Indices: 25567891--25567987 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 29
25567881 CAATTTGAAA
25567891 ATTTTTTTCATTTTCTCATTTTTTTTTTTC
1 ATTTTTTTCATTTTCT-ATTTTTTTTTTTC
*
25567921 ATTTTTTT--TTCTCTATTTTTTCATTTTTTC
1 ATTTTTTTCATTTTCTA-TTTTT--TTTTTTC
* * *
25567951 ATTTTTCATCATCTTCT-TTTCTTTTTTCTC
1 ATTTTT-TTCATTTTCTATTT-TTTTTTTTC
25567981 ATTTTTT
1 ATTTTTT
25567988 ATCCATTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
27 1 0.02
28 10 0.19
30 33 0.61
31 4 0.07
32 2 0.04
33 4 0.07
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (29 bp):
ATTTTTTTCATTTTCTATTTTTTTTTTTC
Found at i:25572082 original size:20 final size:20
Alignment explanation
Indices: 25572035--25572073 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25572025 CTTTTTTCTC
*
25572035 AAAAAAAAAAACCTCTTTTA
1 AAAAAAAAAAACCTATTTTA
*
25572055 AAAAAAAAAAACTTATTTT
1 AAAAAAAAAAACCTATTTT
25572074 TAAGAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAAAAAACCTATTTTA
Found at i:25572141 original size:127 final size:124
Alignment explanation
Indices: 25571950--25572288 Score: 337
Period size: 127 Copynumber: 2.7 Consensus size: 124
25571940 TTTGTGCAGA
* * *** *** * *
25571950 AAAAATTGATGCTTTCAACCTTTCCCCAAAAATATTTTTTTTAATTTTAATTTCGAGACAAATTG
1 AAAAATTGATACTTTCAACTTTTTTTC-AAAATATTTTTAGAAACTTTAATTTCGAGAAAAATTG
25572015 ATACTTTCAACTTTTTTCTCAAAAAAAAAAACCTCTTTTAAAAAAAAAAAACTTATTTTTAAG
65 ATACTTTCAACTTTTTTCTCAAAAAAAAAAACC-CTTTT--AAAAAAAAAACTTATTTTTAAG
*
25572078 AAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTTAGAAACTTTAATCTCGAGAAAAATTGA
1 AAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTTAGAAACTTTAATTTCGAGAAAAATTGA
* *** ****
25572143 TACTTTCAAC-TTTTCCT-AAAAAAAACCTCCCTTTTTTTTAAAAAACTTATTTTTAAG
66 TACTTTCAACTTTTTTCTCAAAAAAAAAAACCCTTTTAAAAAAAAAACTTATTTTTAAG
* * * **
25572200 GAAAATTGATACTTTCAA-TTTTTTTAAAAAAATATTTTTTAGAAAGC-TTATTTTTAAGAAAAA
1 AAAAATTGATACTTTCAACTTTTTTT--CAAAATA-TTTTTAGAAA-CTTTAATTTCGAGAAAAA
* *
25572263 TTGACACTTTTAACTTTTTT-TCAAAA
62 TTGATACTTTCAACTTTTTTCTCAAAA
25572289 TATTTTTTTA
Statistics
Matches: 177, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
121 7 0.04
122 35 0.20
123 6 0.03
124 40 0.23
125 19 0.11
126 6 0.03
127 42 0.24
128 22 0.12
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (124 bp):
AAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTTAGAAACTTTAATTTCGAGAAAAATTGA
TACTTTCAACTTTTTTCTCAAAAAAAAAAACCCTTTTAAAAAAAAAACTTATTTTTAAG
Found at i:25572250 original size:58 final size:58
Alignment explanation
Indices: 25572063--25572298 Score: 221
Period size: 58 Copynumber: 4.0 Consensus size: 58
25572053 TAAAAAAAAA
*
25572063 AAACTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTTT--CAAAATA-TTTTTAG
1 AAACTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTTTAAAAAAATATTTTTTAG
* * ** * * *
25572118 AAACTTTAATCTCGAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTCCCTTTTTTTTA
1 AAAC-TTATTTTTAAGAAAAATTGATACTTTCAACTTTT-TTTAAAAAAA------TATTTTTT-
*
25572183 AA
57 AG
*
25572185 AAACTTATTTTTAAGGAAAATTGATACTTTCAA-TTTTTTTAAAAAAATATTTTTTAG
1 AAACTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTTTAAAAAAATATTTTTTAG
* * * *
25572242 AAAGCTTATTTTTAAGAAAAATTGACACTTTTAACTTTTTTTCAAAATAT-TTTTTTA
1 AAA-CTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTTTAAAAAAATATTTTTTA
25572299 ATTTTTTTAT
Statistics
Matches: 144, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
55 4 0.03
56 30 0.21
57 5 0.03
58 41 0.28
59 17 0.12
64 8 0.06
65 5 0.03
66 29 0.20
67 5 0.03
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.45
Consensus pattern (58 bp):
AAACTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTTTAAAAAAATATTTTTTAG
Found at i:25572619 original size:230 final size:229
Alignment explanation
Indices: 25572182--25572635 Score: 707
Period size: 230 Copynumber: 2.0 Consensus size: 229
25572172 CCTTTTTTTT
* * * *
25572182 AAAAAACTTATTTTTAAGGAAAATTGATACTTTCAATTTTTTTAAAAAAATATTTTTTAGAAAGC
1 AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAAATTTCTTAAAAAAATATTTTTTAGAAAGC
* *
25572247 TTATTTTTAAGAAAAATTGACACTTTTAACTTTTTTTCAAAATATTTTTTTAATTTTTTTATCTT
66 TTATTTTTAAGAAAAATTGACACTTTCAACTTTTTTTCAAAATATTTTTTTAATCTTTTTATCTT
* * * *
25572312 CAAGGGTCATTTAAAAGATGCCTGACAAATCAAAATTTCTTATGAAATAGTTTAAACTTACTTGG
131 CAAAGATCATTTAAAAAATGCCTGACAAATCAAAATTTCTTATGAAATAGTTTAAACTTACTTGA
25572377 TGTCCAACACGAAAACAAATGAACAGCTTTCTAG
196 TGTCCAACACGAAAACAAATGAACAGCTTTCTAG
* *
25572411 AAAAAATTTATTTTCAAGAAAAATTGATACTTTCAACATTTCTTCAAAAAA-ATTTTTTAGAAAG
1 AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAA-ATTTCTTAAAAAAATATTTTTTAGAAAG
25572475 CTTATTTTTAAGAAAAATTGACACTTTCAACTTTTTTTCAAAAATATTTTTTTAATCTTTTTATC
65 CTTATTTTTAAGAAAAATTGACACTTTCAACTTTTTTTC-AAAATATTTTTTTAATCTTTTTATC
* *
25572540 TTCAAAGATCATTTAAAAAATGTCC-GACAAATCAAAA-TTCTATGTGAAATAGTTTAAACTTAT
129 TTCAAAGATCATTTAAAAAATG-CCTGACAAATCAAAATTTCT-TATGAAATAGTTTAAACTTAC
* *
25572603 TTGATGTCTAACACGAAAACAAATGAATAGCTT
192 TTGATGTCCAACACGAAAACAAATGAACAGCTT
25572636 CCTGCATCGC
Statistics
Matches: 205, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
229 88 0.43
230 115 0.56
231 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (229 bp):
AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAAATTTCTTAAAAAAATATTTTTTAGAAAGC
TTATTTTTAAGAAAAATTGACACTTTCAACTTTTTTTCAAAATATTTTTTTAATCTTTTTATCTT
CAAAGATCATTTAAAAAATGCCTGACAAATCAAAATTTCTTATGAAATAGTTTAAACTTACTTGA
TGTCCAACACGAAAACAAATGAACAGCTTTCTAG
Found at i:25577023 original size:40 final size:40
Alignment explanation
Indices: 25576977--25577298 Score: 237
Period size: 40 Copynumber: 8.2 Consensus size: 40
25576967 AAAAATTATT
* * **
25576977 TATCAAATAAGACATTTGTAAGAAGAAACGTTTTAATTGA
1 TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
* * *
25577017 TATCAAATAAGGCATTTATAAGAACAAA-GCCTTAATTGA
1 TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
** * *
25577056 TATCAAATAAGGTGTTTGTAGGAACAAA-GCCTTAAATGA
1 TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
* * * * ** * *
25577095 TATCAAATAAGATGTTTGTAGGAAGAAATGTATTAAATAA
1 TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
* * * ** * * **
25577135 TACCAATTAAGTCACTTGTAAGAATAAACACAGTAATTGA
1 TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
* * * *
25577175 TACCAAATAA-A-GTGCTTGTAAGAGCAAATGTCTTAATTGA
1 TATCAAATAAGACGT--TTGTAAGAACAAACGCCTTAATTGA
* *
25577215 TATCAAATAAAACGTTTGTAGGAACAAA--CCTTAATTGA
1 TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
*
25577253 TATCAAATAAGAC-TCTTGTAGGAACAAATC-CCTTAATTGA
1 TATCAAATAAGACGT-TTGTAAGAACAAA-CGCCTTAATTGA
25577293 TATCAA
1 TATCAA
25577299 TCAATTAAGT
Statistics
Matches: 229, Mismatches: 45, Indels: 16
0.79 0.16 0.06
Matches are distributed among these distances:
37 1 0.00
38 34 0.15
39 69 0.30
40 122 0.53
41 1 0.00
42 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (40 bp):
TATCAAATAAGACGTTTGTAAGAACAAACGCCTTAATTGA
Found at i:25577880 original size:197 final size:199
Alignment explanation
Indices: 25577522--25577888 Score: 512
Period size: 197 Copynumber: 1.8 Consensus size: 199
25577512 TATGATTGTA
* * * *
25577522 AGATTTTAGTTACTGTTAAAAATTTAATATTTTTTTACGTAATCGAATTATTTTAAATCAAACGT
1 AGATTTTAGATACTATTAAAAATATAATATTTTTTTAC-TAATCAAATTATTTTAAATCAAACGT
*
25577587 AAAAAATAAATACTCATTATCAAAATTTTTAAAAAAAAATTATAATTTTTTTTTGAATCAAACAC
65 AAAAAATAAATACTCATTATCAAAA-TTTTAAAAAAAAATTATAA-TTTTTTTTCAATCAAACAC
25577652 ACTGTTAAAAATTTTTACAACTAACAATAAAAAGAGATTATTTTTTTAAGAAGATGTGAGTTTTT
128 ACTGTTAAAAATTTTTACAACTAACAATAAAAAGAGATTATTTTTTTAAGAAGATGTGAGTTTTT
25577717 AATAGTG
193 AATAGTG
*
25577724 AGATTTTAGATACTATT-AAAATCATAATATTTTTTATA-TAATTAAATTATTTTAAATCAAACG
1 AGATTTTAGATACTATTAAAAAT-ATAATATTTTTT-TACTAATCAAATTATTTTAAATCAAACG
* * *
25577787 TACAAAATAAATACTTATTAGT-AAAA-TTT-AAAAAAAATTATGAA-TTTTTTTCAATCAAATA
64 TAAAAAATAAATACTCATTA-TCAAAATTTTAAAAAAAAATTAT-AATTTTTTTTCAATCAAACA
* ***
25577848 CACTGTTAAAAGTTTTTACAACTGGTAATAAAAAGAGATTA
127 CACTGTTAAAAATTTTTACAACTAACAATAAAAAGAGATTA
25577889 AAAGATTCTA
Statistics
Matches: 148, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
197 52 0.35
198 12 0.08
199 5 0.03
201 50 0.34
202 27 0.18
203 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (199 bp):
AGATTTTAGATACTATTAAAAATATAATATTTTTTTACTAATCAAATTATTTTAAATCAAACGTA
AAAAATAAATACTCATTATCAAAATTTTAAAAAAAAATTATAATTTTTTTTCAATCAAACACACT
GTTAAAAATTTTTACAACTAACAATAAAAAGAGATTATTTTTTTAAGAAGATGTGAGTTTTTAAT
AGTG
Found at i:25582179 original size:25 final size:27
Alignment explanation
Indices: 25582133--25582182 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
25582123 TAAATTTATC
**
25582133 TTTAAATGTATAATTTTTATTAATTTA
1 TTTAAATGTATAATTTAAATTAATTTA
25582160 TTTAAAT-T-TAATTTAAATTAATT
1 TTTAAATGTATAATTTAAATTAATT
25582183 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 1 0.05
27 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTAAATGTATAATTTAAATTAATTTA
Found at i:25582758 original size:29 final size:30
Alignment explanation
Indices: 25582687--25582780 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
25582677 AAATTCCTTA
* *
25582687 AAAAATAATACTATAAGGGCTAAATTTATT
1 AAAAATAATATTATAAGGACTAAATTTATT
*
25582717 AAAAATAATATTACAAGGACTAAATTTATT
1 AAAAATAATATTATAAGGACTAAATTTATT
* *
25582747 -TAAATAATATTATAAGGACTAAA-TTACT
1 AAAAATAATATTATAAGGACTAAATTTATT
25582775 AAAAAT
1 AAAAAT
25582781 CGAAGAGTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
28 4 0.07
29 25 0.45
30 27 0.48
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAAATAATATTATAAGGACTAAATTTATT
Found at i:25587692 original size:22 final size:22
Alignment explanation
Indices: 25587667--25587712 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
25587657 AATAACAACA
*
25587667 TAGTAGTAAATAATT-AATAACT
1 TAGTAATAAATAATTGAA-AACT
*
25587689 TAGTAATTAATAATTGAAAACT
1 TAGTAATAAATAATTGAAAACT
25587711 TA
1 TA
25587713 AATGTAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (22 bp):
TAGTAATAAATAATTGAAAACT
Done.