Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 7 of 121
Found at i:883768 original size:18 final size:20
Alignment explanation
Indices: 883726--883768 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
883716 TATTAAAAAG
*
883726 ATAAATTTTAAATTTATTTA
1 ATAAATTTTAAATTTATATA
*
883746 TTAAA-TTT-AATTTATATA
1 ATAAATTTTAAATTTATATA
883764 ATAAA
1 ATAAA
883769 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.65
19 3 0.15
20 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAATTTTAAATTTATATA
Found at i:887250 original size:34 final size:34
Alignment explanation
Indices: 887200--887267 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
887190 TTATCAAATT
*
887200 ATCTTTACTATCAGGACTAATTTTGAACAATTTA
1 ATCTTTACTATCAGGACTAATTTCGAACAATTTA
* *
887234 ATCTTTATTATTAGGACTAATTTCGAACAATTTA
1 ATCTTTACTATCAGGACTAATTTCGAACAATTTA
887268 GATTGTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (34 bp):
ATCTTTACTATCAGGACTAATTTCGAACAATTTA
Found at i:892298 original size:24 final size:23
Alignment explanation
Indices: 892270--892315 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
892260 CCCCCAATTT
*
892270 TTTGTTCCTTAATGTTGTTTTTTC
1 TTTGTGCCTTAAT-TTGTTTTTTC
*
892294 TTTGTGCCTTAATTTTTTTTTT
1 TTTGTGCCTTAATTTGTTTTTT
892316 ACCCGTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.70
Consensus pattern (23 bp):
TTTGTGCCTTAATTTGTTTTTTC
Found at i:893828 original size:22 final size:22
Alignment explanation
Indices: 893803--893858 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
893793 TTTATTTTTT
*
893803 ATTTATATAT-TATTTTAATAAA
1 ATTTATATATATATTTAAAT-AA
*
893825 ATTTTTA-ATATATTTAAATAA
1 ATTTATATATATATTTAAATAA
893846 ATTTATATATATA
1 ATTTATATATATA
893859 ATAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTATATATATATTTAAATAA
Found at i:893871 original size:21 final size:21
Alignment explanation
Indices: 893818--893872 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
893808 TATATTATTT
893818 TAATAAA-ATTTTTA-ATATA
1 TAATAAATATTTTTATATATA
* **
893837 T-TTAAATAAATTTATATATA
1 TAATAAATATTTTTATATATA
893857 TAATAAATATTTTTAT
1 TAATAAATATTTTTAT
893873 TTTATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 6 0.22
21 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATAAATATTTTTATATATA
Found at i:893906 original size:18 final size:18
Alignment explanation
Indices: 893875--893916 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
893865 ATTTTTATTT
* *
893875 TATA-AAAATTTAAAATA
1 TATATAAAATATAAAAAA
893892 TATATAAAATATAAAAAA
1 TATATAAAATATAAAAAA
893910 TATATAA
1 TATATAA
893917 TTCGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TATATAAAATATAAAAAA
Found at i:893997 original size:13 final size:12
Alignment explanation
Indices: 893946--894006 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 12
893936 TTTTTTTAAT
*
893946 TTTAATTCAAAA
1 TTTAATTCTAAA
893958 TTTAATT-TAAA
1 TTTAATTCTAAA
* **
893969 TTTAATATATGTA
1 TTTAAT-TCTAAA
893982 TTTAATATCTAAA
1 TTTAAT-TCTAAA
893995 TTTAA-TCTAAA
1 TTTAATTCTAAA
894006 T
1 T
894007 CCAATACAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
11 16 0.39
12 8 0.20
13 17 0.41
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (12 bp):
TTTAATTCTAAA
Found at i:903482 original size:28 final size:27
Alignment explanation
Indices: 903429--903482 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
903419 ATTAATTTTT
* * * *
903429 AAAATTAATAAATTTAATTTGGTTAAC
1 AAAAATAATAAATATAATTCGATTAAC
903456 AAAAATAATATAATATAATTCGATTAA
1 AAAAATAATA-AATATAATTCGATTAA
903483 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
AAAAATAATAAATATAATTCGATTAAC
Found at i:907728 original size:22 final size:23
Alignment explanation
Indices: 907703--907745 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
907693 AAAGAATAGT
907703 TAACTAGCGATCATGC-AGAAGA
1 TAACTAGCGATCATGCGAGAAGA
*
907725 TAACTAGTGATCATGCGAGAA
1 TAACTAGCGATCATGCGAGAA
907746 CAAATGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (23 bp):
TAACTAGCGATCATGCGAGAAGA
Found at i:908163 original size:18 final size:19
Alignment explanation
Indices: 908127--908165 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
908117 AATTGCACTT
908127 ATAAAATCATAAAATTAAA
1 ATAAAATCATAAAATTAAA
*
908146 ATAAAATCA-AACATTAAA
1 ATAAAATCATAAAATTAAA
908164 AT
1 AT
908166 TTTAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAATCATAAAATTAAA
Found at i:922509 original size:295 final size:295
Alignment explanation
Indices: 921979--922565 Score: 1066
Period size: 295 Copynumber: 2.0 Consensus size: 295
921969 TTTGGAGCTT
921979 CATTAAGTTTATGAATTTGACTTAAGTATGCCTTAGCCACATCTAAAGCAATGTAAAGAACAAAA
1 CATTAAGTTTATGAATTTGACTTAAGTATGCCTTAGCCACATCTAAAGCAATGTAAAGAACAAAA
922044 CAAGGCAAGAAATGTGCATATTTGATAAATTTGTCAATAATGACCATAATACAATTGAATTTCTA
66 CAAGGCAAGAAATGTGCATATTTGATAAATTTGTCAATAATGACCATAATACAATTGAATTTCTA
* **
922109 AGAGTGAAGCAGTCTTTCCACAAAGTCAATGGTGATCACCAAGATAAGCAACATGCCCACCTTTA
131 AGAGTGAAGCAGTCCTTCCACAAAGTCAACAGTGATCACCAAGATAAGCAACATGCCCACCTTTA
922174 TTCCTTTAACACGCATCACACTATTACACATAATCTTACACTTCATCTTAAGCCAATAAAAATAA
196 TTCCTTTAACACGCATCACACTATTACACATAATCTTACACTTCATCTTAAGCCAATAAAAATAA
922239 AGTTTGAGTCTATAATAGGTTGTTTGGATTCCCTC
261 AGTTTGAGTCTATAATAGGTTGTTTGGATTCCCTC
*
922274 CATTAAGTTTATGAATTTGACTTAAGTATGCCTTAGCCATATCTAAAGCAATGTAAAGAACAAAA
1 CATTAAGTTTATGAATTTGACTTAAGTATGCCTTAGCCACATCTAAAGCAATGTAAAGAACAAAA
* *
922339 CAAGGCAAGAAATGTGCATATTTGGTAAATTTGTCAATAATGACCATAATACAATTGAATTTTTA
66 CAAGGCAAGAAATGTGCATATTTGATAAATTTGTCAATAATGACCATAATACAATTGAATTTCTA
* * * *
922404 AGATTGAAGTAGTCCTTCCACAAAGTCCACAGTGATCACCAAGATAAGCAACATGCTCACCTTTA
131 AGAGTGAAGCAGTCCTTCCACAAAGTCAACAGTGATCACCAAGATAAGCAACATGCCCACCTTTA
*
922469 TTCCTTTAACACGCATCACACTATTACACATAATCTTACACTTCATCTTAGGCCAATAAAAATAA
196 TTCCTTTAACACGCATCACACTATTACACATAATCTTACACTTCATCTTAAGCCAATAAAAATAA
*
922534 ATTTTGAGTCTATAATAGGTTGTTTGGATTCC
261 AGTTTGAGTCTATAATAGGTTGTTTGGATTCC
922566 TAAATGACCT
Statistics
Matches: 280, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
295 280 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (295 bp):
CATTAAGTTTATGAATTTGACTTAAGTATGCCTTAGCCACATCTAAAGCAATGTAAAGAACAAAA
CAAGGCAAGAAATGTGCATATTTGATAAATTTGTCAATAATGACCATAATACAATTGAATTTCTA
AGAGTGAAGCAGTCCTTCCACAAAGTCAACAGTGATCACCAAGATAAGCAACATGCCCACCTTTA
TTCCTTTAACACGCATCACACTATTACACATAATCTTACACTTCATCTTAAGCCAATAAAAATAA
AGTTTGAGTCTATAATAGGTTGTTTGGATTCCCTC
Found at i:925342 original size:27 final size:27
Alignment explanation
Indices: 925310--925363 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
925300 TATCAAATAC
*
925310 ATTTTTTAAAAAATAGAAAATAAAAACT
1 ATTTTCTAAAAAATA-AAAATAAAAACT
925338 ATTTTCTAAAAAATAAAAATAAAAAC
1 ATTTTCTAAAAAATAAAAATAAAAAC
925364 AAAAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTTTCTAAAAAATAAAAATAAAAACT
Found at i:937069 original size:22 final size:22
Alignment explanation
Indices: 937028--937077 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
937018 AATAAATCAT
*
937028 AAAAAATAATTTTAAAATATAAC
1 AAAAAAGAATTTTAAAATAT-AC
* *
937051 AAAAAAGAATTTT-ACATATCC
1 AAAAAAGAATTTTAAAATATAC
937072 AAAAAA
1 AAAAAA
937078 AAAAAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 12 0.50
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAAGAATTTTAAAATATAC
Found at i:943895 original size:2 final size:2
Alignment explanation
Indices: 943890--943914 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
943880 AAAAAAAAAA
943890 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
943915 AGCTTGCGAC
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:944731 original size:5 final size:5
Alignment explanation
Indices: 944703--944748 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
944693 TATTTCATAA
*
944703 ATATT ATATTT AAATT -TATAT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATA-TT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT
944749 TTCATAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 2 0.06
5 27 0.75
6 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:945019 original size:20 final size:20
Alignment explanation
Indices: 944983--945021 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
944973 TATTTCACAT
*
944983 TTGATAAAAAATTTTAATTA
1 TTGATAAAAAATATTAATTA
945003 TTGATAAATAAA-ATTAATT
1 TTGATAAA-AAATATTAATT
945022 TTTATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TTGATAAAAAATATTAATTA
Found at i:945086 original size:20 final size:20
Alignment explanation
Indices: 945047--945087 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
945037 TTTATATTTT
*
945047 AAATAATTATATTTGAATAA
1 AAATAATTATATATGAATAA
945067 AAATAATTATCATATG-ATAA
1 AAATAATTAT-ATATGAATAA
945087 A
1 A
945088 TGATCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (20 bp):
AAATAATTATATATGAATAA
Found at i:949658 original size:16 final size:18
Alignment explanation
Indices: 949623--949671 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
949613 AACTATTTAA
*
949623 ATATAAACAGATTATTATT
1 ATATAAA-AGATTATGATT
949642 A-ATAAAAG-TTATGATT
1 ATATAAAAGATTATGATT
949658 ATATAAAAGATTAT
1 ATATAAAAGATTAT
949672 AATCATCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.30
17 9 0.33
18 9 0.33
19 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (18 bp):
ATATAAAAGATTATGATT
Found at i:950361 original size:23 final size:23
Alignment explanation
Indices: 950309--950357 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
950299 ACAAAAAATA
* * *
950309 TAAATATAAATATTTATTTATAT
1 TAAATTTATATATTAATTTATAT
950332 TAAATTTATATATTAATTT-TAT
1 TAAATTTATATATTAATTTATAT
950354 TAAA
1 TAAA
950358 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTATATATTAATTTATAT
Found at i:950368 original size:22 final size:23
Alignment explanation
Indices: 950324--950368 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
950314 ATAAATATTT
*
950324 ATTTATATTAAATTTATATATTA
1 ATTTATATTAAATTTATAAATTA
950347 ATTT-TATTAAAATTT-TAAATTA
1 ATTTATATT-AAATTTATAAATTA
950369 TATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTATATTAAATTTATAAATTA
Found at i:950389 original size:12 final size:11
Alignment explanation
Indices: 950366--950395 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
950356 AAATTTTAAA
950366 TTATATTATTT
1 TTATATTATTT
950377 TTATATCTATTT
1 TTATAT-TATTT
950389 TTATATT
1 TTATATT
950396 GTATCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATTATTT
Found at i:950942 original size:16 final size:16
Alignment explanation
Indices: 950921--950973 Score: 60
Period size: 14 Copynumber: 3.6 Consensus size: 16
950911 TTTTTATTTA
950921 TATATATTTATAAAAT
1 TATATATTTATAAAAT
*
950937 TATATATTTA-AATAT
1 TATATATTTATAAAAT
*
950952 T-TATATTT-TAAAAA
1 TATATATTTATAAAAT
950966 TA-ATATTT
1 TATATATTT
950974 TATTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 17 0.53
15 5 0.16
16 10 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTATAAAAT
Found at i:953220 original size:2 final size:2
Alignment explanation
Indices: 953213--953241 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
953203 CAAGGTAATG
953213 AT 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 AT A
953242 AATAGATAGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:956567 original size:11 final size:11
Alignment explanation
Indices: 956547--956580 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
956537 AATAATCAAG
956547 TTAAATTTAAA
1 TTAAATTTAAA
**
956558 TTTTATTTAAA
1 TTAAATTTAAA
956569 TTAAATTTAAA
1 TTAAATTTAAA
956580 T
1 T
956581 AACTTATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:966366 original size:37 final size:38
Alignment explanation
Indices: 966288--966375 Score: 119
Period size: 37 Copynumber: 2.3 Consensus size: 38
966278 TCAATATATA
966288 TATATATATATATATTATAATTTTATTATTTATTTAATTT
1 TATAT-TATATATATTATAA-TTTATTATTTATTTAATTT
*
966328 TATGATTATATATATTATAA-TT-TTATTTATTTATTTT
1 TAT-ATTATATATATTATAATTTATTATTTATTTAATTT
966365 TATATT-TATAT
1 TATATTATATAT
966376 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
35 5 0.11
36 3 0.07
37 17 0.37
38 2 0.04
40 17 0.37
41 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (38 bp):
TATATTATATATATTATAATTTATTATTTATTTAATTT
Found at i:977160 original size:15 final size:16
Alignment explanation
Indices: 977140--977169 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
977130 TAATTTGAAA
977140 ATATAAAA-AATTATC
1 ATATAAAATAATTATC
977155 ATATAAAATAATTAT
1 ATATAAAATAATTAT
977170 AATTTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAAAATAATTATC
Found at i:977532 original size:3 final size:3
Alignment explanation
Indices: 977526--977564 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
977516 ACTACTTCAT
977526 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
977565 AAACATAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:978014 original size:22 final size:21
Alignment explanation
Indices: 977989--978031 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
977979 CGATATATAT
977989 AAATT-TGATTACATGATAATCA
1 AAATTATGATTA-ATG-TAATCA
*
978011 AAATTATTATTAATGTAATCA
1 AAATTATGATTAATGTAATCA
978032 CTAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTATGATTAATGTAATCA
Found at i:978206 original size:22 final size:22
Alignment explanation
Indices: 978174--978247 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
978164 CAGTTTTTTT
*
978174 TTTTTTATAATGTCTTAAAATTA
1 TTTTTT-TAATATCTTAAAATTA
*
978197 TTTTTTTAATATC-TAAAATTT
1 TTTTTTTAATATCTTAAAATTA
* * *
978218 TTATTTTTTATATTTTAAATTTA
1 TT-TTTTTAATATCTTAAAATTA
978241 TTTTTTT
1 TTTTTTT
978248 GATAATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.21
22 20 0.47
23 14 0.33
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTTTTTAATATCTTAAAATTA
Found at i:979732 original size:21 final size:21
Alignment explanation
Indices: 979708--979752 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
979698 TTTATATATA
*
979708 ATTATAATAATTTTAAATTAT
1 ATTATAATAATATTAAATTAT
* * *
979729 ATTATATTTATATTATATTAT
1 ATTATAATAATATTAAATTAT
979750 ATT
1 ATT
979753 TTAACTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATAATAATATTAAATTAT
Found at i:981979 original size:21 final size:21
Alignment explanation
Indices: 981955--982004 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
981945 AATTAATTTG
* *
981955 TAATTTTTTTAATTTAATAAT
1 TAATTTTATTAATTTAATAAA
*
981976 TAA-TTTATTAATTTTATAAA
1 TAATTTTATTAATTTAATAAA
981996 TATATTTTA
1 TA-ATTTTA
982005 GTGAACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.67
21 4 0.17
22 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTTTATTAATTTAATAAA
Found at i:993424 original size:7 final size:7
Alignment explanation
Indices: 993412--993442 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
993402 TTAAATTATA
993412 TAATAAT
1 TAATAAT
993419 TAATAAT
1 TAATAAT
993426 TAATAAT
1 TAATAAT
*
993433 TAATATT
1 TAATAAT
993440 TAA
1 TAA
993443 ATTATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAATAAT
Found at i:993755 original size:23 final size:24
Alignment explanation
Indices: 993729--993776 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
993719 ATAATATATG
993729 ACATTCAT-ATAAT-CATTTATTTA
1 ACATT-ATCATAATACATTTATTTA
*
993752 ACATTATCATAATATATTTATTTA
1 ACATTATCATAATACATTTATTTA
993776 A
1 A
993777 TGTATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 10 0.45
24 10 0.45
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (24 bp):
ACATTATCATAATACATTTATTTA
Found at i:995188 original size:15 final size:15
Alignment explanation
Indices: 995168--995214 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
995158 CTTATTTATA
*
995168 TTTGTTTAAGGTTTG
1 TTTGTTTAAGATTTG
995183 TTTGTTTAA-ATTTG
1 TTTGTTTAAGATTTG
* *
995197 TTTGGTTATGATTTG
1 TTTGTTTAAGATTTG
995212 TTT
1 TTT
995215 ATTGTTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (15 bp):
TTTGTTTAAGATTTG
Found at i:995190 original size:25 final size:25
Alignment explanation
Indices: 995162--995216 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
995152 TTAAAGCTTA
995162 TTTATATTTGTTTAAGGTT-TG-TTTG
1 TTTATATTTGTTT--GGTTATGATTTG
*
995187 TTTAAATTTGTTTGGTTATGATTTG
1 TTTATATTTGTTTGGTTATGATTTG
995212 TTTAT
1 TTTAT
995217 TGTTGATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 20 0.77
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (25 bp):
TTTATATTTGTTTGGTTATGATTTG
Found at i:999882 original size:25 final size:25
Alignment explanation
Indices: 999848--999895 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
999838 TAAACAAATT
999848 TAGAATATCTTCAAGATGATTAGAA
1 TAGAATATCTTCAAGATGATTAGAA
999873 TAGAATATCTTCAAGATGATTAG
1 TAGAATATCTTCAAGATGATTAG
999896 GCATATCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (25 bp):
TAGAATATCTTCAAGATGATTAGAA
Found at i:1001393 original size:20 final size:20
Alignment explanation
Indices: 1001357--1001394 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1001347 ATTTTATTTT
*
1001357 TTTTATTATTTTAATAAAAA
1 TTTTAATATTTTAATAAAAA
1001377 TTTTAATATATTT-ATAAA
1 TTTTAATAT-TTTAATAAA
1001395 TTTTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATATTTTAATAAAAA
Found at i:1003499 original size:20 final size:22
Alignment explanation
Indices: 1003474--1003532 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
1003464 GTTCGAGATG
1003474 AATTTATATTTAATATTAA-T-
1 AATTTATATTTAATATTAACTC
*
1003494 AATTTATATATTTAT-TTAAGCTC
1 AATTTATAT-TTAATATTAA-CTC
1003517 AATTTA-ATTTAATATT
1 AATTTATATTTAATATT
1003533 TTAAATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 13 0.41
21 8 0.25
22 5 0.16
23 6 0.19
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (22 bp):
AATTTATATTTAATATTAACTC
Found at i:1003685 original size:14 final size:15
Alignment explanation
Indices: 1003668--1003698 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1003658 TATATTTATA
1003668 TAATTATA-ATATTT
1 TAATTATATATATTT
1003682 TAATTATATATATTT
1 TAATTATATATATTT
1003697 TA
1 TA
1003699 TTTGAGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTATATATATTT
Found at i:1011891 original size:16 final size:18
Alignment explanation
Indices: 1011859--1011896 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
1011849 GACAAATTAA
1011859 AATATGATATGATAATAT
1 AATATGATATGATAATAT
1011877 AATATGA-AT-ATAATAT
1 AATATGATATGATAATAT
1011893 AATA
1 AATA
1011897 AAAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 2 0.10
18 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
AATATGATATGATAATAT
Found at i:1012037 original size:18 final size:18
Alignment explanation
Indices: 1011986--1012037 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1011976 ATTTTTATAT
*
1011986 TAATATAAATAGTAATATA
1 TAATATAAATA-TAAAATA
* ** *
1012005 TAATTTTTATGTAAAATA
1 TAATATAAATATAAAATA
1012023 TAATATAAATATAAA
1 TAATATAAATATAAA
1012038 TTTTATTATT
Statistics
Matches: 24, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TAATATAAATATAAAATA
Found at i:1014763 original size:18 final size:18
Alignment explanation
Indices: 1014711--1014764 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1014701 TTATATTTTC
*
1014711 ATATCAATATAAATTATAAT
1 ATAT-AATATAAA-TATAAA
* **
1014731 ATATAATTTTTATATAAA
1 ATATAATATAAATATAAA
1014749 ATATAATATAAATATA
1 ATATAATATAAATATA
1014765 TCAATTATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 18 0.67
19 5 0.19
20 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATATAAATATAAA
Found at i:1015009 original size:2 final size:2
Alignment explanation
Indices: 1015004--1015049 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1014994 GAAAAAGGTG
*
1015004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1015045 TA TA T
1 TA TA T
1015050 TATTTCAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1015075 original size:16 final size:18
Alignment explanation
Indices: 1015041--1015077 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1015031 ATATATATAG
*
1015041 ATTATATATTATTTCAAA
1 ATTATATATTATATCAAA
1015059 ATTATA-ATTATAT-AAA
1 ATTATATATTATATCAAA
1015075 ATT
1 ATT
1015078 TTCATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 6 0.33
18 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATATATTATATCAAA
Found at i:1020043 original size:9 final size:9
Alignment explanation
Indices: 1020026--1020058 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1020016 AATTTTAAAA
1020026 ATTAA-TCG
1 ATTAATTCG
1020034 ATTAATTCG
1 ATTAATTCG
*
1020043 ATCAATTCG
1 ATTAATTCG
1020052 ATTAATT
1 ATTAATT
1020059 TTTTCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (9 bp):
ATTAATTCG
Found at i:1021386 original size:15 final size:14
Alignment explanation
Indices: 1021363--1021397 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1021353 ATTGTTATTA
1021363 TATTGAATTTAAGTT
1 TATTGAATTTAA-TT
*
1021378 TATTTAATTTAATT
1 TATTGAATTTAATT
1021392 TATTGA
1 TATTGA
1021398 GTTCAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (14 bp):
TATTGAATTTAATT
Found at i:1021527 original size:17 final size:17
Alignment explanation
Indices: 1021476--1021528 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
1021466 TGAAATTTAA
1021476 ATTTTAATATATTATTATT
1 ATTTTAATATA-TA-TATT
* *
1021495 ATTTTAATAAAAATATT
1 ATTTTAATATATATATT
*
1021512 ATTTTATTATATATATT
1 ATTTTAATATATATATT
1021529 TATATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 18 0.62
18 1 0.03
19 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAATATATATATT
Found at i:1021564 original size:102 final size:96
Alignment explanation
Indices: 1021453--1021633 Score: 238
Period size: 102 Copynumber: 1.8 Consensus size: 96
1021443 CTCCAACAAC
*
1021453 TAACAAATTTAAT-TGAAATTTAAATTTTAATATATTATTATTATTTTAATAAAAATATTATTTT
1 TAACAAATTTAATCAG-AATTTAAATTTTAATATATT-TTATTATTTTAAT-AAAATATTA---T
1021517 ATTATATATATTTATATATATAAAAGGACTTCAATAAT
60 ATTATATAT-TTTATATATATAAAAGGACTTCAATAAT
* ** *
1021555 TAACGAATTTAATCAGTTTTTTAATTTTAATATATTTTATTATTTTAATAAAATATTATATTATA
1 TAACAAATTTAATCAGAATTTAAATTTTAATATATTTTATTATTTTAATAAAATATTATATTATA
*
1021620 TCTTTTATATATAT
66 TATTTTATATATAT
1021634 TTCAAAGTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
96 11 0.15
97 9 0.12
100 9 0.12
101 13 0.18
102 29 0.40
103 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (96 bp):
TAACAAATTTAATCAGAATTTAAATTTTAATATATTTTATTATTTTAATAAAATATTATATTATA
TATTTTATATATATAAAAGGACTTCAATAAT
Found at i:1021824 original size:14 final size:15
Alignment explanation
Indices: 1021800--1021829 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1021790 AATTGAGATT
1021800 TAATCAAATTTTAAA
1 TAATCAAATTTTAAA
1021815 TAAT-AAATTTTAAA
1 TAATCAAATTTTAAA
1021829 T
1 T
1021830 CAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATCAAATTTTAAA
Found at i:1025500 original size:5 final size:5
Alignment explanation
Indices: 1025490--1025537 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
1025480 AAAATTTTAA
1025490 ATTAT ATTAT ATTTAT ATTAT ATTTAT ATTAT A-T-T ATTAT ATTAT ATT
1 ATTAT ATTAT A-TTAT ATTAT A-TTAT ATTAT ATTAT ATTAT ATTAT ATT
1025538 TTAAATTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 25 0.64
6 10 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTAT
Found at i:1025504 original size:16 final size:16
Alignment explanation
Indices: 1025485--1025546 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
1025475 TTATTAAAAT
1025485 TTTAAATTATATTATA
1 TTTAAATTATATTATA
*
1025501 TTTATATTATATTTATA
1 TTTAAATTATA-TTATA
*
1025518 TTATATTATTATATTATA
1 TT-TA-AATTATATTATA
1025536 TTTTAAATTAT
1 -TTTAAATTAT
1025547 GAAATTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 10 0.25
17 12 0.30
18 9 0.22
19 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAATTATATTATA
Found at i:1025505 original size:27 final size:26
Alignment explanation
Indices: 1025418--1025546 Score: 87
Period size: 27 Copynumber: 5.2 Consensus size: 26
1025408 GTATCATAAT
*
1025418 TTATATTATTATA-TAA-A-TTTAAA
1 TTATATTATTTTATTAATATTTTAAA
* *
1025441 ATATATT-TTTTATT--T-TATTAAA
1 TTATATTATTTTATTAATATTTTAAA
* *
1025463 TTTATATAATTATTATTAAAATTTTAAA
1 -TTATATTATT-TTATTAATATTTTAAA
* *
1025491 TTATATTATATTTA-TATTATATTTATA
1 TTATATTAT-TTTATTAATAT-TTTAAA
*
1025518 TTATATTATTATATT-ATATTTTAAA
1 TTATATTATTTTATTAATATTTTAAA
1025543 TTAT
1 TTAT
1025547 GAAATTTAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
22 9 0.11
23 12 0.15
24 2 0.03
25 14 0.17
26 10 0.12
27 26 0.32
28 7 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATATTATTTTATTAATATTTTAAA
Found at i:1025507 original size:11 final size:11
Alignment explanation
Indices: 1025491--1025538 Score: 78
Period size: 11 Copynumber: 4.2 Consensus size: 11
1025481 AAATTTTAAA
1025491 TTATATTATAT
1 TTATATTATAT
1025502 TTATATTATAT
1 TTATATTATAT
1025513 TTATATTATATT
1 TTATATTATA-T
1025525 ATTATATTATAT
1 -TTATATTATAT
1025537 TT
1 TT
1025539 TAAATTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 23 0.66
12 2 0.06
13 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1025770 original size:31 final size:31
Alignment explanation
Indices: 1025735--1025794 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1025725 TAAAAAAATT
* *
1025735 ATTTATTAATCAAATAATATCATTTAATTTA
1 ATTTATTAATAAAATAAAATCATTTAATTTA
*
1025766 ATTTATTAATAAAATAAAATTATTTAATT
1 ATTTATTAATAAAATAAAATCATTTAATT
1025795 CATTGATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTTATTAATAAAATAAAATCATTTAATTTA
Found at i:1027869 original size:2 final size:2
Alignment explanation
Indices: 1027862--1027886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1027852 CCAAAATTTC
1027862 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 T
1027887 TGTGTATGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1034552 original size:15 final size:15
Alignment explanation
Indices: 1034528--1034559 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1034518 CTTTTACATC
1034528 TAAAAAAAATAATAA
1 TAAAAAAAATAATAA
*
1034543 TAAAAGAAATAATAA
1 TAAAAAAAATAATAA
1034558 TA
1 TA
1034560 CAATACGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
TAAAAAAAATAATAA
Found at i:1034898 original size:20 final size:19
Alignment explanation
Indices: 1034870--1034967 Score: 58
Period size: 20 Copynumber: 5.0 Consensus size: 19
1034860 CGGTTAATTT
1034870 TTTTG-ATTAATTTGATTAA
1 TTTTGAATTAATTT-ATTAA
*
1034889 TTTTGAATTAAATTATTTAA
1 TTTTGAATTAATTTA-TTAA
* * *
1034909 TATTAAATTATTTTTATTAA
1 TTTTGAATTA-ATTTATTAA
* *
1034929 --TTAAATTAAATTATTTAA
1 TTTTGAATTAATTTA-TTAA
*
1034947 TTTTAAAATTTAATTTATTAA
1 TTTT-GAA-TTAATTTATTAA
1034968 AATTAATTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
17 3 0.05
18 12 0.19
19 6 0.10
20 25 0.40
21 10 0.16
22 7 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTGAATTAATTTATTAA
Found at i:1034940 original size:23 final size:24
Alignment explanation
Indices: 1034900--1034944 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1034890 TTTGAATTAA
*
1034900 ATTATTTAATATTAAATTATTTTT
1 ATTAATTAATATTAAATTATTTTT
1034924 ATTAATTAA-ATTAAATTATTT
1 ATTAATTAATATTAAATTATTT
1034945 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTAATTAATATTAAATTATTTTT
Found at i:1034946 original size:18 final size:18
Alignment explanation
Indices: 1034894--1034948 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
1034884 ATTAATTTTG
1034894 AATTAAATTATTTAATATTA
1 AATTAAATTATTT-A-ATTA
* *
1034914 AATT-ATTTTTATTAATTA
1 AATTAAATTAT-TTAATTA
1034932 AATTAAATTATTTAATT
1 AATTAAATTATTTAATT
1034949 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 14 0.48
19 9 0.31
20 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTAAATTATTTAATTA
Found at i:1035416 original size:27 final size:27
Alignment explanation
Indices: 1035385--1035437 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1035375 ACTTAATAGG
1035385 AAAATGTCTAATATTATTTTACTAAGA
1 AAAATGTCTAATATTATTTTACTAAGA
*
1035412 AAAATGTTTAATATTATTTTACTAAG
1 AAAATGTCTAATATTATTTTACTAAG
1035438 TTGAGTTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (27 bp):
AAAATGTCTAATATTATTTTACTAAGA
Found at i:1036575 original size:8 final size:8
Alignment explanation
Indices: 1036562--1036588 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1036552 ATTGCCATTT
1036562 TTTATAAA
1 TTTATAAA
1036570 TTTATAAA
1 TTTATAAA
1036578 TTTATAAA
1 TTTATAAA
1036586 TTT
1 TTT
1036589 TTTAATGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTATAAA
Found at i:1038830 original size:54 final size:54
Alignment explanation
Indices: 1038772--1038888 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 54
1038762 AAAATAATAA
*
1038772 TAAAAATAAAAATAATTTC-AAATTTTCA-A-AAAAAGTTAAAGAATTAATTTTTCT
1 TAAAAATAAAAAT--TTTCAAAATTTT-AGAGAAAAAGTTAAAGAATCAATTTTTCT
*
1038826 TAAAAATAAAAATTTTCAAAAAATTTTATGAGAAAAAGTTAAAGTATCAATTTTTCT
1 TAAAAATAAAAATTTTC--AAAATTTTA-GAGAAAAAGTTAAAGAATCAATTTTTCT
1038883 TAAAAA
1 TAAAAA
1038889 ACTTCAATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
52 4 0.07
54 14 0.25
55 7 0.13
56 1 0.02
57 29 0.53
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (54 bp):
TAAAAATAAAAATTTTCAAAATTTTAGAGAAAAAGTTAAAGAATCAATTTTTCT
Found at i:1042066 original size:22 final size:23
Alignment explanation
Indices: 1042041--1042086 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1042031 CTTGTTACAT
1042041 AAATT-ATATAAATTTTAA-ATAA
1 AAATTGAT-TAAATTTTAATATAA
*
1042063 AAATTGATTAATTTTTAATATAA
1 AAATTGATTAAATTTTAATATAA
1042086 A
1 A
1042087 TACTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATTGATTAAATTTTAATATAA
Found at i:1051550 original size:18 final size:19
Alignment explanation
Indices: 1051513--1051554 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1051503 AACAAATCTA
* *
1051513 AAATAAAAGTTATATTATT
1 AAATAAAAATAATATTATT
1051532 AAATAAAAATAAT-TTATT
1 AAATAAAAATAATATTATT
1051550 AAATA
1 AAATA
1051555 TATAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATAAAAATAATATTATT
Found at i:1054889 original size:4 final size:4
Alignment explanation
Indices: 1054880--1054907 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1054870 TTTGCGATAA
1054880 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1054908 CATAATAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1058668 original size:16 final size:17
Alignment explanation
Indices: 1058647--1058679 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1058637 GAATCTTGAA
1058647 TGTTGACT-ATTTTATT
1 TGTTGACTCATTTTATT
1058663 TGTTGACTCATTTTATT
1 TGTTGACTCATTTTATT
1058680 ATTGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (17 bp):
TGTTGACTCATTTTATT
Found at i:1063494 original size:19 final size:18
Alignment explanation
Indices: 1063470--1063515 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
1063460 TTTTTATTAT
*
1063470 ATAAAAATAATAAAAATTC
1 ATAAAAATAA-AAAAATAC
1063489 AT-AAAATAAAAAAATAC
1 ATAAAAATAAAAAAATAC
1063506 ATATAAAATA
1 ATA-AAAATA
1063516 TGTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.38
18 7 0.29
19 8 0.33
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATAAAAAAATAC
Found at i:1065026 original size:12 final size:13
Alignment explanation
Indices: 1065003--1065035 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1064993 TATAAAATAA
1065003 TTATCATATTATT
1 TTATCATATTATT
1065016 TTATC-TATTATT
1 TTATCATATTATT
1065028 TTAT-ATAT
1 TTATCATAT
1065036 AAAATATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATCATATTATT
Found at i:1072031 original size:15 final size:15
Alignment explanation
Indices: 1072011--1072048 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1072001 ATTCATTAAC
1072011 AACAAATAAATCATA
1 AACAAATAAATCATA
*
1072026 AACAAATAAATCTTA
1 AACAAATAAATCATA
1072041 AACAAATA
1 AACAAATA
1072049 TAAATGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (15 bp):
AACAAATAAATCATA
Found at i:1077128 original size:111 final size:111
Alignment explanation
Indices: 1076984--1077209 Score: 434
Period size: 111 Copynumber: 2.0 Consensus size: 111
1076974 ACAAACAAAA
1076984 CAATCTATCTCCTTTCCATAAGCAGAAGTGACTAAACTTTGTAAAACATTCAAAGAACATGAAAA
1 CAATCTATCTCCTTTCCATAAGCAGAAGTGACTAAACTTTGTAAAACATTCAAAGAACATGAAAA
1077049 CTATTAAAATAAAGAACACACAGAAAAAACCCCCCAAAAGTACAAC
66 CTATTAAAATAAAGAACACACAGAAAAAACCCCCCAAAAGTACAAC
*
1077095 CAATCTATCTTCTTTCCATAAGCAGAAGTGACTAAACTTTGTAAAACATTCAAAGAACATGAAAA
1 CAATCTATCTCCTTTCCATAAGCAGAAGTGACTAAACTTTGTAAAACATTCAAAGAACATGAAAA
*
1077160 CTATTAAAATAAAGAACACATAGAAAAAACCCCCCAAAAGTACAAC
66 CTATTAAAATAAAGAACACACAGAAAAAACCCCCCAAAAGTACAAC
1077206 CAAT
1 CAAT
1077210 TGATTCACAT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.21
Consensus pattern (111 bp):
CAATCTATCTCCTTTCCATAAGCAGAAGTGACTAAACTTTGTAAAACATTCAAAGAACATGAAAA
CTATTAAAATAAAGAACACACAGAAAAAACCCCCCAAAAGTACAAC
Found at i:1078782 original size:27 final size:27
Alignment explanation
Indices: 1078752--1078804 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1078742 TTTAAATTTG
*
1078752 ATTTAATTTAATAT-TATATAAAATTAT
1 ATTTAATTTAAT-TCGATATAAAATTAT
* *
1078779 ATTTTATTTGATTCGATATAAAATTA
1 ATTTAATTTAATTCGATATAAAATTA
1078805 ATGAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
ATTTAATTTAATTCGATATAAAATTAT
Found at i:1078847 original size:16 final size:16
Alignment explanation
Indices: 1078826--1078878 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
1078816 TTTTTAAATT
1078826 TAAATATAAAATTAAA
1 TAAATATAAAATTAAA
*
1078842 TAAATATAAAA-TATA
1 TAAATATAAAATTAAA
*
1078857 TAAATATTAAATTAAA
1 TAAATATAAAATTAAA
1078873 TAAATA
1 TAAATA
1078879 ATTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAATATAAAATTAAA
Found at i:1079128 original size:30 final size:31
Alignment explanation
Indices: 1079094--1079169 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1079084 TAAAAAACTT
* * *
1079094 AAATTGCAATATTTATAA-TTTTTTATTTTC
1 AAATTACAATATTTAAAATTTTTTTATTGTC
* *
1079124 AAATTACGATTTTTAAAATTTTTTTATTGTC
1 AAATTACAATATTTAAAATTTTTTTATTGTC
*
1079155 AAAATACAATTATTT
1 AAATTACAA-TATTT
1079170 TTAATCCGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
30 14 0.39
31 18 0.50
32 4 0.11
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.53
Consensus pattern (31 bp):
AAATTACAATATTTAAAATTTTTTTATTGTC
Found at i:1083873 original size:58 final size:58
Alignment explanation
Indices: 1083744--1084075 Score: 399
Period size: 58 Copynumber: 5.8 Consensus size: 58
1083734 TTTATGCAAA
* ** * *
1083744 GAAAATTGATACTTTTAACTTTTTTTC-AAAA-GTTTTTTTGAAA-CTTTAATTTCGAA-
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAGC-TTATTTTC-AAG
* * *
1083800 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTATTTTTGAAAACTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTTTGAAAGCTTATTTTCAAG
* *
1083858 GAAAATTGATGCTTTCAACTTTT-CTCCAAAAATATTTTTTGGAAAGCTTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTGAAAGCTTATTTTCAAG
* * * *
1083916 GAAAATTGATGCTTTCAACTTTTCTTC-AAAATATTTTTTAGAAAGCCTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAGCTTATTTTCAAG
* *
1083973 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT-GAAAGCTTATTTTCAAG
* * *
1084032 GAAAATTGATACTTTCAATTTTTCCTCAAAATTTTTTTTTTGAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAA
1084076 TTTTATCTAA
Statistics
Matches: 241, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
56 23 0.10
57 61 0.25
58 101 0.42
59 56 0.23
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (58 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAGCTTATTTTCAAG
Found at i:1084112 original size:6 final size:6
Alignment explanation
Indices: 1084088--1084170 Score: 100
Period size: 6 Copynumber: 13.7 Consensus size: 6
1084078 TTATCTAAAG
*
1084088 AAAAT- AAAATAA TAAAATA AAAATA AAAATA AAAATA AAAATG AAAATAA
1 AAAATA AAAAT-A -AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A
1084138 AAAATA AAGAA-A AAAATA AAAAT- AAAATA AAAA
1 AAAATA AA-AATA AAAATA AAAATA AAAATA AAAA
1084171 ATATTAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
5 12 0.17
6 44 0.64
7 8 0.12
8 5 0.07
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1084173 original size:18 final size:18
Alignment explanation
Indices: 1084088--1084169 Score: 98
Period size: 19 Copynumber: 4.5 Consensus size: 18
1084078 TTATCTAAAG
1084088 AAAATAAAATAATAAAATA
1 AAAATAAAATAA-AAAATA
1084107 AAAATAAAA-ATAAAAATA
1 AAAATAAAATA-AAAAATA
1084125 AAAATGAAAATAAAAAATA
1 AAAAT-AAAATAAAAAATA
*
1084144 AAGAAAAAAAT-AAAAAT-
1 AA-AATAAAATAAAAAATA
1084161 AAAATAAAA
1 AAAATAAAA
1084170 AATATTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.11
17 2 0.04
18 18 0.32
19 28 0.49
20 3 0.05
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAAAAATA
Found at i:1084611 original size:12 final size:13
Alignment explanation
Indices: 1084584--1084616 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1084574 CCAATCGGGT
*
1084584 AAAGGAAAGAAGA
1 AAAGAAAAGAAGA
1084597 AAAGAAAAGAA-A
1 AAAGAAAAGAAGA
1084609 AAAGAAAA
1 AAAGAAAA
1084617 ATAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAGA
Found at i:1084641 original size:17 final size:17
Alignment explanation
Indices: 1084614--1084858 Score: 61
Period size: 17 Copynumber: 13.3 Consensus size: 17
1084604 AGAAAAAAGA
1084614 AAAATAAAATAATAAAAT
1 AAAA-AAAATAATAAAAT
*
1084632 AAAAAAAATAATAAGGAT
1 AAAAAAAATAATAA-AAT
* * * * *
1084650 -AATATATTGAT-TAAT
1 AAAAAAAATAATAAAAT
*
1084665 AGATAAATAATAATAATAAT
1 A-A-AAAAAATAATAA-AAT
*
1084685 AGATAAATAATATATATAAAT
1 A-A-AAAAAATA-ATA-AAAT
* *
1084706 AGATAAATAATAATAATAT
1 A-A-AAAAAATAATAAAAT
* *
1084725 ATAAATAAATAA-ATAAT
1 A-AAAAAAATAATAAAAT
1084742 AAAAATAAA-AATAAAAT
1 AAAAA-AAATAATAAAAT
* * *
1084759 ACAATAAATATATATTAAT
1 AAAAAAAATA-ATA-AAAT
**
1084778 AAATAGTAATAAT-AAAT
1 AAA-AAAAATAATAAAAT
1084795 AAATAATAAATACATAAAAT
1 AAA-AA-AAATA-ATAAAAT
1084815 ACAAAATAAAGTAAAATAAAAT
1 A-AAAA-AAA-T--AATAAAAT
*
1084837 AAAAAATATAA-AAATAT
1 AAAAAAAATAATAAA-AT
1084854 AAAAA
1 AAAAA
1084859 TACAAAAATA
Statistics
Matches: 176, Mismatches: 29, Indels: 45
0.70 0.12 0.18
Matches are distributed among these distances:
15 2 0.01
16 11 0.06
17 50 0.28
18 27 0.15
19 15 0.09
20 36 0.20
21 25 0.14
22 9 0.05
23 1 0.01
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAAAAATAATAAAAT
Found at i:1084685 original size:41 final size:42
Alignment explanation
Indices: 1084648--1084811 Score: 133
Period size: 41 Copynumber: 4.1 Consensus size: 42
1084638 AATAATAAGG
*
1084648 ATAATATATTGATTAATAGATAAATAATAATAATAAT-AGATAA
1 ATAATATA-T-ATAAATAGATAAATAATAATAATAATAAGATAA
1084691 ATAATATATATAAATAGATAAATAATAATAATATATAA-ATAA
1 ATAATATATATAAATAGATAAATAATAATAATA-ATAAGATAA
*
1084733 ATAA-ATA-ATAAA-A-ATAAA-AATAA-AAT-A-CA-ATAA
1 ATAATATATATAAATAGATAAATAATAATAATAATAAGATAA
*
1084766 AT-ATATATTAATAAATAG-T-AATAATAAATAAATAATAA-ATAC
1 ATAATATA-T-ATAAATAGATAAATAAT-AAT-AATAATAAGATAA
1084808 ATAA
1 ATAA
1084812 AATACAAAAT
Statistics
Matches: 102, Mismatches: 4, Indels: 30
0.75 0.03 0.22
Matches are distributed among these distances:
32 1 0.01
33 10 0.10
34 1 0.01
36 10 0.10
37 10 0.10
38 7 0.07
39 1 0.01
40 8 0.08
41 27 0.26
42 17 0.17
43 10 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (42 bp):
ATAATATATATAAATAGATAAATAATAATAATAATAAGATAA
Found at i:1084701 original size:4 final size:3
Alignment explanation
Indices: 1084616--1084803 Score: 73
Period size: 3 Copynumber: 58.7 Consensus size: 3
1084606 AAAAAAGAAA
* * * * * *
1084616 AAT AA- AAT AAT AA- AAT AAA AAA AAT AAT AAG GAT AAT -AT ATT GATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
1084662 AAT AGAT AAAT AAT AAT AAT AAT AGAT AAAT AAT -AT ATAT AAAT AGAT
1 AAT A-AT -AAT AAT AAT AAT AAT A-AT -AAT AAT AAT A-AT -AAT A-AT
* *
1084710 AAAT AAT AAT AAT ATAT AAAT AAAT AAAT AAT AAA AAT AAA AAT AA-
1 -AAT AAT AAT AAT A-AT -AAT -AAT -AAT AAT AAT AAT AAT AAT AAT
* * *
1084756 AAT -AC AAT AAAT ATAT ATT AAT AAAT AGT AAT AAT AAAT AAAT AAT
1 AAT AAT AAT -AAT A-AT AAT AAT -AAT AAT AAT AAT -AAT -AAT AAT
1084802 AA
1 AA
1084804 ATACATAAAA
Statistics
Matches: 146, Mismatches: 18, Indels: 42
0.71 0.09 0.20
Matches are distributed among these distances:
2 11 0.08
3 83 0.57
4 47 0.32
5 5 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1084797 original size:68 final size:69
Alignment explanation
Indices: 1084662--1084834 Score: 192
Period size: 68 Copynumber: 2.4 Consensus size: 69
1084652 TATATTGATT
* * *
1084662 AATAGATAAATAATAATAATAATAGATAAATAATATATATAAATAGATAAATAATAATAATATAT
1 AATACATAAA-AATAAAAATAA-A-ATAAATAA-ATATATAAATAGATAAATAATAATAATAAAT
1084727 AAATAAATA
62 AAAT-AATA
* *
1084736 AATA-ATAAAAATAAAAATAAAATACAATAAATATAT-ATTA-ATAAATAGTAATAATAAATAAA
1 AATACATAAAAATAAAAATAAAATA-AATAAATATATAAATAGATAAATAATAATAATAAATAAA
1084798 TAATA
65 TAATA
*
1084803 AATACAT-AAAATACAAAATAAAGTAAAATAAA
1 AATACATAAAAATA-AAAATAAAAT-AAATAAA
1084835 ATAAAAAATA
Statistics
Matches: 90, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
67 14 0.16
68 38 0.42
69 4 0.04
70 9 0.10
71 6 0.07
72 10 0.11
73 5 0.06
74 4 0.04
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (69 bp):
AATACATAAAAATAAAAATAAAATAAATAAATATATAAATAGATAAATAATAATAATAAATAAAT
AATA
Found at i:1084848 original size:68 final size:68
Alignment explanation
Indices: 1084607--1084877 Score: 190
Period size: 68 Copynumber: 4.0 Consensus size: 68
1084597 AAAGAAAAGA
* * ** * ** * *
1084607 AAAAAGAAAAATAAAATAATA-AAATAAAAAA-AAT-AATAAGGATAATATATTGATTAATAGAT
1 AAAAATAAAAATAAAATAAAATAAATAAAAAATAATAAATAATAATAATAAATAAATAAATAAAT
1084669 AAAT
66 -AAT
* * * * *
1084673 AATAATAATAAT-AGAT-AAATAATATATATAAATAGATAAATAATAATAATATATAAATAAATA
1 AAAAATAAAAATAAAATAAAATAA-ATA-AAAAATA-ATAAATAATAATAATAAATAAATAAATA
1084736 AATAAT
63 AATAAT
* * * * *
1084742 AAAAATAAAAATAAAATACAATAAATATATATTAATAAATAGTAATAATAAATAAAT-AATAAAT
1 AAAAATAAAAATAAAATAAAATAAATAAAAAATAATAAATAATAATAATAAATAAATAAATAAAT
1084806 ACAT
66 A-AT
*
1084810 -AAAATACAAAATAAAGTAAAATAAAATAAAAAAT-ATAAA-AAT-ATAA-AAATACAA-AAATA
1 AAAAATA-AAAATAAAATAAAAT-AAATAAAAAATAATAAATAATAATAATAAATA-AATAAATA
1084869 CAA-AAT
63 -AATAAT
1084875 AAA
1 AAA
1084878 GTGGGCCTAC
Statistics
Matches: 162, Mismatches: 28, Indels: 30
0.74 0.13 0.14
Matches are distributed among these distances:
64 2 0.01
65 12 0.07
66 25 0.15
67 22 0.14
68 42 0.26
69 26 0.16
70 28 0.17
71 5 0.03
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (68 bp):
AAAAATAAAAATAAAATAAAATAAATAAAAAATAATAAATAATAATAATAAATAAATAAATAAAT
AAT
Found at i:1084851 original size:8 final size:8
Alignment explanation
Indices: 1084832--1084873 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1084822 AAAGTAAAAT
1084832 AAAATA-A
1 AAAATACA
*
1084839 AAAATATA
1 AAAATACA
*
1084847 AAAATATA
1 AAAATACA
1084855 AAAATACA
1 AAAATACA
1084863 AAAATACA
1 AAAATACA
1084871 AAA
1 AAA
1084874 TAAAGTGGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATACA
Found at i:1085215 original size:41 final size:41
Alignment explanation
Indices: 1085070--1085350 Score: 268
Period size: 41 Copynumber: 6.7 Consensus size: 41
1085060 TCCTTTAAGT
*
1085070 AGAGGCTCAACGACTTTGAAAAACATAATCAAAGCTCCTCTAATC
1 AGAGGCTCAACGACTTTG-AAAA-ATAA--ATAGCTCCTCTAATC
* *
1085115 AGAGGCTCAACGACTTTG-AAAATGAATAAAGCTCTTCTAAAT-
1 AGAGGCTCAACGACTTTGAAAAAT-AA-ATAGCTCCTCT-AATC
* * **
1085157 AGAGG-TCAATGAATTTGAAAAATAAACGGCTCCTCTAATC
1 AGAGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATC
* * *
1085197 AGAGACTTAACGACTTTGAAAAATAAATAGCTCATCTAATC
1 AGAGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATC
*
1085238 TA-AGGCTCAACGACTTTTGAAAAA-AAATGGCTCCTCTAATC
1 -AGAGGCTCAACGAC-TTTGAAAAATAAATAGCTCCTCTAATC
* * * *
1085279 AGAGGCATC-ACAACTTTGAAAATTAAATAAAGCTCTTCTAAAC
1 AGAGGC-TCAACGACTTTGAAAAATAAAT--AGCTCCTCTAATC
1085322 AGAGGCTCAACGACTTTGGAAAAATAAAT
1 AGAGGCTCAACGACTTT-GAAAAATAAAT
1085351 TGCTTCTTGA
Statistics
Matches: 197, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
39 3 0.02
40 21 0.11
41 78 0.40
42 36 0.18
43 31 0.16
44 10 0.05
45 18 0.09
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (41 bp):
AGAGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATC
Found at i:1085344 original size:84 final size:82
Alignment explanation
Indices: 1085070--1085350 Score: 311
Period size: 82 Copynumber: 3.3 Consensus size: 82
1085060 TCCTTTAAGT
**
1085070 AGAGGCTCAACGACTTTGAAAAACATAATCAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAA
1 AGAGGCTCAACGACTTTG-AAAA-ATAA--ATGGCTCCTCTAATCAGAGGCTC-ACGACTTTGAA
* *
1085135 AATGAATAAAGCTCTTCTAAAT
61 AATAAATAAAGCTCTTCTAAAC
* * * * *
1085157 AGAGG-TCAATGAATTTGAAAAATAAACGGCTCCTCTAATCAGAGACTTAACGACTTTGAAAAAT
1 AGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGC-TCACGACTTTG-AAAAT
* *
1085221 AAAT--AGCTCATCTAATC
64 AAATAAAGCTCTTCTAAAC
*
1085238 TA-AGGCTCAACGACTTTTGAAAAA-AAATGGCTCCTCTAATCAGAGGCATCACAACTTTGAAAA
1 -AGAGGCTCAACGAC-TTTGAAAAATAAATGGCTCCTCTAATCAGAGGC-TCACGACTTTGAAAA
1085301 TTAAATAAAGCTCTTCTAAAC
63 -TAAATAAAGCTCTTCTAAAC
1085322 AGAGGCTCAACGACTTTGGAAAAATAAAT
1 AGAGGCTCAACGACTTT-GAAAAATAAAT
1085351 TGCTTCTTGA
Statistics
Matches: 164, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
81 17 0.10
82 69 0.42
83 22 0.13
84 33 0.20
85 8 0.05
86 10 0.06
87 5 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (82 bp):
AGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTCACGACTTTGAAAATAA
ATAAAGCTCTTCTAAAC
Found at i:1086364 original size:19 final size:20
Alignment explanation
Indices: 1086342--1086379 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1086332 TTTTTTTCCA
1086342 TTTTTCTTTC-TTTTTTTTT
1 TTTTTCTTTCATTTTTTTTT
*
1086361 TTTTTTTTTCATTTTTTTT
1 TTTTTCTTTCATTTTTTTT
1086380 ATTTCAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (20 bp):
TTTTTCTTTCATTTTTTTTT
Found at i:1096867 original size:57 final size:58
Alignment explanation
Indices: 1096798--1097068 Score: 350
Period size: 58 Copynumber: 4.7 Consensus size: 58
1096788 TTGTGTAGAA
** * *
1096798 AAAATTGATACTTTCAACTTTTTCTCAAAAAT-TTTTTTTGAAATTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAGCTTATTTTCAAGG
* * * * * *
1096855 AAAATTGATACTTTCAACTTTTCCACAAAAAT-TCATTTTTGAAAACTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTTGAAAGCTTATTTTCAAGG
* * *
1096913 AAAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAGCTTATTTTCAAGG
* * *
1096971 AAAATTGATACTTTCAACTTTTTCTC-AAAATATTTCTTAGAAAGCTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAGCTTATTTTCAAGG
*
1097028 AAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTT
1097069 TTAATTTTAT
Statistics
Matches: 185, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
57 84 0.45
58 96 0.52
59 5 0.03
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAGCTTATTTTCAAGG
Found at i:1096922 original size:58 final size:58
Alignment explanation
Indices: 1096797--1097067 Score: 313
Period size: 57 Copynumber: 4.7 Consensus size: 58
1096787 TTTGTGTAGA
* * ** * *
1096797 AAAAATTGATACTTTCAACTTTTTCTCAAAAATT-TTTTTTGAAATTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTAGAAAGCTTATTTTCAAG
* * * *
1096854 GAAAATTGATACTTTCAACTTTTCCACAAAAATTCATTTTT-GAAAACTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATT-ATTTTTAGAAAGCTTATTTTCAAG
* *
1096912 AAAAATTGATATTTTCAACTTTTTCC-CAAAAA-TATTTTTTGGAAAGCTTATTTTCAAG
1 AAAAATTGATACTTTCAAC-TTTTCCTCAAAAATTA-TTTTTAGAAAGCTTATTTTCAAG
* *
1096970 GAAAATTGATACTTTCAACTTTTTCTC-AAAA-TATTTCTTAGAAAGCTTATTTTCAA-
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTT-TTAGAAAGCTTATTTTCAAG
1097026 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTT
1 A-AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TATTTTT
1097068 TTTAATTTTA
Statistics
Matches: 185, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
56 4 0.02
57 91 0.49
58 72 0.39
59 13 0.07
60 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTAGAAAGCTTATTTTCAAG
Found at i:1096935 original size:115 final size:114
Alignment explanation
Indices: 1096796--1097077 Score: 363
Period size: 115 Copynumber: 2.4 Consensus size: 114
1096786 TTTTGTGTAG
*
1096796 AAAAAATTGATACTTTCAACTTTTTCTCAAAAAT-TTTTTTTGAAATTTTAATTTCGAGGAAAAT
1 AAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTAATTTCAAGGAAAAT
*
1096860 TGATACTTTCAACTTTTCCACAAAAATTCATTT-TT-GAAAACTTATTTTTA
66 TGATACTTTCAACTTTTCCAC-AAAA-T-ATTTCTTAGAAAACTTATTTTCA
* * * ** *
1096910 AGAAAAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAGCTTATTTTCAAGGAAAA
1 A-AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTAATTTCAAGGAAAA
* * *
1096975 TTGATACTTTCAACTTTTTCTCAAAATATTTCTTAGAAAGCTTATTTTCA
65 TTGATACTTTCAACTTTTCCACAAAATATTTCTTAGAAAACTTATTTTCA
* **
1097025 AAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTTAATTTTA
1 AA-AAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTTGAAATTTTA
1097078 TCTAAAGAAA
Statistics
Matches: 143, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
113 4 0.03
114 5 0.03
115 80 0.56
116 54 0.38
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (114 bp):
AAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTAATTTCAAGGAAAAT
TGATACTTTCAACTTTTCCACAAAATATTTCTTAGAAAACTTATTTTCA
Found at i:1097095 original size:5 final size:5
Alignment explanation
Indices: 1097085--1097116 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1097075 TTATCTAAAG
1097085 AAAAT AAAAT -AAA- AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1097117 AATTAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1097103 original size:13 final size:13
Alignment explanation
Indices: 1097080--1097111 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
1097070 TAATTTTATC
1097080 TAAAGAAAATAAAA
1 TAAA-AAAATAAAA
1097094 TAAAAAAATAAAA
1 TAAAAAAATAAAA
1097107 TAAAA
1 TAAAA
1097112 TAAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:1097108 original size:18 final size:18
Alignment explanation
Indices: 1097085--1097123 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1097075 TTATCTAAAG
1097085 AAAATAAAATAAAAAAAT
1 AAAATAAAATAAAAAAAT
*
1097103 AAAATAAAATAAAAAATT
1 AAAATAAAATAAAAAAAT
1097121 AAA
1 AAA
1097124 CAATTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAATAAAATAAAAAAAT
Found at i:1098066 original size:23 final size:23
Alignment explanation
Indices: 1098040--1098164 Score: 110
Period size: 23 Copynumber: 5.3 Consensus size: 23
1098030 AATAATAAGG
1098040 ATAAT-ATATTGATTAATAGATAA
1 ATAATAATATT-ATTAATAGATAA
* *
1098063 ATAATAATAATAATAATAGATAA
1 ATAATAATATTATTAATAGATAA
*
1098086 ATAATAATATATATAAATAGATAA
1 ATAATAATAT-TATTAATAGATAA
* * * *
1098110 ATAATAATAATAATAAAAAATAAA
1 ATAATAATATTATTAATAGAT-AA
* *
1098134 ATAAAAATA-TATTAATAAATAGTA
1 ATAATAATATTATTAATAGATA--A
1098158 ATAATAA
1 ATAATAA
1098165 ATAAATAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
22 1 0.01
23 41 0.49
24 41 0.49
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
ATAATAATATTATTAATAGATAA
Found at i:1098070 original size:3 final size:3
Alignment explanation
Indices: 1098062--1098179 Score: 84
Period size: 3 Copynumber: 37.7 Consensus size: 3
1098052 TTAATAGATA
1098062 AAT AAT AAT AAT AAT AAT AGAT AAAT AAT AAT -AT ATAT AAAT AGAT
1 AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT A-AT -AAT A-AT
* *
1098108 AAAT AAT AAT AAT AAT AA- AA- AAT AA- AAT AAA AAT -AT ATT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1098150 AAAT AGT AAT AAT AAAT AAAT AAAT AAT AA
1 -AAT AAT AAT AAT -AAT -AAT -AAT AAT AA
1098180 ATACATAAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
2 10 0.10
3 58 0.60
4 26 0.27
5 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1098107 original size:47 final size:49
Alignment explanation
Indices: 1098040--1098191 Score: 179
Period size: 47 Copynumber: 3.1 Consensus size: 49
1098030 AATAATAAGG
* * *
1098040 ATAATATATTGATTAATAGATAAATAATAATAATAATAATAGATAAATA
1 ATAATATATTAATAAATAGATAAATAATAATAATAATAATAAATAAATA
*
1098089 ATAATATA-T-ATAAATAGATAAATAATAATAATAATAAAAAATAAAATA
1 ATAATATATTAATAAATAGATAAATAATAATAATAATAATAAAT-AAATA
* *
1098137 AAAATATATTAATAAATAG-T-AATAATAAATAAATAAATAATAAATACATA
1 ATAATATATTAATAAATAGATAAATAAT-AAT-AAT-AATAATAAATAAATA
1098187 A-AATA
1 ATAATA
1098192 CAAAATAAAG
Statistics
Matches: 91, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
47 30 0.33
48 19 0.21
49 17 0.19
50 16 0.18
51 9 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (49 bp):
ATAATATATTAATAAATAGATAAATAATAATAATAATAATAAATAAATA
Found at i:1098131 original size:7 final size:7
Alignment explanation
Indices: 1098106--1098253 Score: 52
Period size: 7 Copynumber: 19.7 Consensus size: 7
1098096 ATATAAATAG
*
1098106 ATAAATA
1 ATAAAAA
1098113 ATAATAATA
1 ATAA-AA-A
1098122 ATAAAAA
1 ATAAAAA
1098129 AT--AAA
1 ATAAAAA
1098134 ATAAAAA
1 ATAAAAA
1098141 TATATTAATAA
1 -ATA--AA-AA
**
1098152 ATAGTA-
1 ATAAAAA
*
1098158 ATAATAA
1 ATAAAAA
1098165 ATAAATAA
1 ATAAA-AA
*
1098173 ATAATAA
1 ATAAAAA
1098180 ATACATAAA
1 ATA-A-AAA
*
1098189 ATACAAA
1 ATAAAAA
1098196 ATAAAGTAA
1 ATAAA--AA
* *
1098205 A-ATATA
1 ATAAAAA
1098211 ATAAAAAA
1 AT-AAAAA
1098219 ATAAAAA
1 ATAAAAA
*
1098226 TATAAGAA
1 -ATAAAAA
1098234 ATATAAAA
1 ATA-AAAA
*
1098242 ATACAAA
1 ATAAAAA
1098249 ATAAA
1 ATAAA
1098254 GTGAGCCTAC
Statistics
Matches: 106, Mismatches: 17, Indels: 36
0.67 0.11 0.23
Matches are distributed among these distances:
5 5 0.05
6 7 0.07
7 42 0.40
8 32 0.30
9 13 0.12
10 5 0.05
11 2 0.02
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (7 bp):
ATAAAAA
Found at i:1098190 original size:24 final size:22
Alignment explanation
Indices: 1098054--1098240 Score: 131
Period size: 23 Copynumber: 8.3 Consensus size: 22
1098044 TATATTGATT
*
1098054 AATAGATAAATAATAATAATAA
1 AATAAATAAATAATAATAATAA
*
1098076 TAATAGATAAATAATAATATATATA
1 -AATAAATAAATAATAATA-ATA-A
*
1098101 AATAGATAAATAATAATAAT--
1 AATAAATAAATAATAATAATAA
1098121 AATAAA-AAATAA-AATAA-AA
1 AATAAATAAATAATAATAATAA
*
1098140 ATATATTAATAAATAGTAATAAT-A
1 A-ATA--AATAAATAATAATAATAA
1098164 AATAAATAAATAATAAATACATAA
1 AATAAATAAATAAT-AATA-ATAA
*
1098188 AATACAAAATAAAGTAAAATATAATAA
1 AAT---AAATAAA-TAATA-ATAATAA
*
1098215 AA-AAATAAA-AAT-ATAAGAA
1 AATAAATAAATAATAATAATAA
1098234 ATATAAA
1 A-ATAAA
1098241 AATACAAAAT
Statistics
Matches: 138, Mismatches: 6, Indels: 42
0.74 0.03 0.23
Matches are distributed among these distances:
18 5 0.04
19 14 0.10
20 9 0.07
21 14 0.10
22 6 0.04
23 37 0.27
24 32 0.23
25 1 0.01
27 14 0.10
28 6 0.04
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (22 bp):
AATAAATAAATAATAATAATAA
Found at i:1098206 original size:67 final size:65
Alignment explanation
Indices: 1098061--1098230 Score: 168
Period size: 67 Copynumber: 2.6 Consensus size: 65
1098051 ATTAATAGAT
* *
1098061 AAATAATAATAATAATA-A-TAGATAAATAATAATATATATAAATAGATAAATAATAATAATAAT
1 AAATAA-AATAA-AATATATTA-ATAAATAATAATATAAATAAATAAATAAATAATAATAATAAT
1098124 AAA
63 AAA
*
1098127 AAATAAAATAAAAATATATTAATAAATAGTAATAATAAATAAATAAAT-AATAAATACATAA-AA
1 AAATAAAAT-AAAATATATTAATAAATAATAAT-ATAAATAAATAAATAAAT-AATA-ATAATAA
*
1098190 TACA
62 TAAA
* * * *
1098194 AAATAAAGTAAAATATAATAAAAAAATAAAAATATAA
1 AAATAAAATAAAATAT-ATTAATAAATAATAATATAA
1098231 GAAATATAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
65 7 0.08
66 34 0.39
67 43 0.49
68 4 0.05
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (65 bp):
AAATAAAATAAAATATATTAATAAATAATAATATAAATAAATAAATAAATAATAATAATAATAAA
Found at i:1098208 original size:10 final size:9
Alignment explanation
Indices: 1098059--1098224 Score: 59
Period size: 10 Copynumber: 18.1 Consensus size: 9
1098049 TGATTAATAG
1098059 ATAAATAATA
1 ATAAATAA-A
1098069 ATAATAATAATA
1 AT-A-AATAA-A
1098081 GATAAATAATA
1 -ATAAATAA-A
*
1098092 ATATATATAA
1 ATAAATA-AA
*
1098102 ATAGAT-AA
1 ATAAATAAA
1098110 AT-AATAATA
1 ATAAATAA-A
1098119 AT-AAT-AA
1 ATAAATAAA
1098126 A-AAATAAA
1 ATAAATAAA
1098134 ATAAA-AATA
1 ATAAATAA-A
*
1098143 TATTAAT-AA
1 -ATAAATAAA
*
1098152 AT-AGTAATA
1 ATAAATAA-A
1098161 ATAAAT-AA
1 ATAAATAAA
1098169 ATAAATAATAA
1 ATAAAT-A-AA
*
1098180 ATACATAAA
1 ATAAATAAA
*
1098189 AT--ACAAA
1 ATAAATAAA
1098196 ATAAAGTAAA
1 ATAAA-TAAA
1098206 ATATAATAAA
1 ATA-AATAAA
1098216 A-AAATAAA
1 ATAAATAAA
1098224 A
1 A
1098225 ATATAAGAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 46
0.69 0.05 0.26
Matches are distributed among these distances:
7 15 0.12
8 28 0.22
9 21 0.17
10 33 0.26
11 18 0.14
12 8 0.06
13 2 0.02
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (9 bp):
ATAAATAAA
Found at i:1098221 original size:54 final size:55
Alignment explanation
Indices: 1098108--1098255 Score: 155
Period size: 54 Copynumber: 2.7 Consensus size: 55
1098098 ATAAATAGAT
* * *
1098108 AAATAATAATAATAATAAA-AAATAAAATA-AAAATATATTAATAAATAGTAATAAT
1 AAATAA-AA-AATAATAAATAAATAAAATACAAAATAAAGTAATAAATAGTAATAAA
*
1098163 AAATAAATAAATAATAAATACATAAAATACAAAATAAAGT-A-AAATA-TAATAAAA
1 AAATAAA-AAATAATAAATAAATAAAATACAAAATAAAGTAATAAATAGTAAT-AAA
* *
1098217 AAATAAAAATATAAGAAATATA-AAAATACAAAATAAAGT
1 AAATAAAAA-ATAATAAATAAATAAAATACAAAATAAAGT
1098256 GAGCCTACCT
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
53 23 0.28
54 34 0.41
55 17 0.21
56 8 0.10
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (55 bp):
AAATAAAAAATAATAAATAAATAAAATACAAAATAAAGTAATAAATAGTAATAAA
Found at i:1098243 original size:8 final size:8
Alignment explanation
Indices: 1098211--1098249 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1098201 GTAAAATATA
*
1098211 ATAAAAAA
1 ATAAAAAT
1098219 ATAAAAAT
1 ATAAAAAT
1098227 ATAAGAAAT
1 ATAA-AAAT
1098236 ATAAAAAT
1 ATAAAAAT
*
1098244 ACAAAA
1 ATAAAA
1098250 TAAAGTGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (8 bp):
ATAAAAAT
Found at i:1098250 original size:30 final size:28
Alignment explanation
Indices: 1098186--1098253 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
1098176 ATAAATACAT
*
1098186 AAAATACAAAATAAAGTAAAATATAATAAA
1 AAAATA-AAAATAAAG-AAAATATAAAAAA
1098216 AAAATAAAAATATAAG-AAATATAAAAATA
1 AAAATAAAAATA-AAGAAAATATAAAAA-A
1098245 CAAAATAAA
1 -AAAATAAA
1098254 GTGAGCCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 10 0.29
29 7 0.21
30 17 0.50
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAATAAAAATAAAGAAAATATAAAAAA
Found at i:1104347 original size:27 final size:28
Alignment explanation
Indices: 1104294--1104349 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1104284 TGGCCTTTGA
*
1104294 TTTGAAAAAATAAACTTTTTTATTTTTT
1 TTTGAAAAAATAAACTCTTTTATTTTTT
1104322 TTTGAAAAAATAAACTCTTTTATTTTTT
1 TTTGAAAAAATAAACTCTTTTATTTTTT
1104350 AAAGTTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTGAAAAAATAAACTCTTTTATTTTTT
Found at i:1104533 original size:27 final size:29
Alignment explanation
Indices: 1104485--1104574 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 29
1104475 TTTTTTAAAT
* **
1104485 AAATAAATTATTTAATTTTTAA-AA-TCA
1 AAATAAAATATTTAATAATTAATAATTCA
*
1104512 AAATAAAATATTTAATAATTAATAATTTA
1 AAATAAAATATTTAATAATTAATAATTCA
* * *
1104541 AAAT-AAATAATT-ATAAATAATATATTTA
1 AAATAAAATATTTAATAATTAATA-ATTCA
1104569 AAATAA
1 AAATAA
1104575 TTTTAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 28 0.53
28 18 0.34
29 7 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
AAATAAAATATTTAATAATTAATAATTCA
Found at i:1104551 original size:24 final size:24
Alignment explanation
Indices: 1104515--1104561 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1104505 AAAATCAAAA
** *
1104515 TAAAATATTTAATAATTAATAATT
1 TAAAATAAATAATAATAAATAATT
*
1104539 TAAAATAAATAATTATAAATAAT
1 TAAAATAAATAATAATAAATAAT
1104562 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAATAAATAATAATAAATAATT
Found at i:1104567 original size:28 final size:28
Alignment explanation
Indices: 1104511--1104588 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 28
1104501 TTTTAAAATC
* *
1104511 AAAATAAAATATTTAATAATTAATAATTT
1 AAAAT-AAATAATTAATAAATAATAATTT
1104540 AAAATAAATAATT-ATAAATAATATATTT
1 AAAATAAATAATTAATAAATAATA-ATTT
*
1104568 AAAAT-AAT-TTTAATAAATAAT
1 AAAATAAATAATTAATAAATAAT
1104589 TATCGACAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.05
27 21 0.48
28 16 0.36
29 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATAAATAATTAATAAATAATAATTT
Found at i:1104575 original size:14 final size:14
Alignment explanation
Indices: 1104511--1104575 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
1104501 TTTTAAAATC
*
1104511 AAAATAAAATATTT
1 AAAATAATATATTT
1104525 AATAATTAATA-ATTT
1 AA-AA-TAATATATTT
*
1104540 AAAATAA-ATAATT
1 AAAATAATATATTT
1104553 ATAAATAATATATTT
1 A-AAATAATATATTT
1104568 AAAATAAT
1 AAAATAAT
1104576 TTTAATAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 1 0.02
13 7 0.16
14 17 0.40
15 14 0.33
16 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATAATATATTT
Found at i:1105198 original size:13 final size:13
Alignment explanation
Indices: 1105182--1105244 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
1105172 TTTTATATTA
1105182 ATATTTTAAAAAT
1 ATATTTTAAAAAT
1105195 ATA-TTTAAAAAT
1 ATATTTTAAAAAT
*
1105207 -TTTATTTAAAAAT
1 ATAT-TTTAAAAAT
*
1105220 -TTTTATTAATAAAAT
1 ATATT-TT-A-AAAAT
1105235 ATATTTTAAA
1 ATATTTTAAA
1105245 TCCATTTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
11 1 0.02
12 10 0.24
13 19 0.45
14 2 0.05
15 7 0.17
16 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATTTTAAAAAT
Found at i:1105203 original size:12 final size:12
Alignment explanation
Indices: 1105181--1105219 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1105171 ATTTTATATT
1105181 AATAT-TTTAAA
1 AATATATTTAAA
1105192 AATATATTTAAA
1 AATATATTTAAA
*
1105204 AATTTTATTTAAA
1 AA-TATATTTAAA
1105217 AAT
1 AAT
1105220 TTTTATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATATTTAAA
Found at i:1105226 original size:14 final size:13
Alignment explanation
Indices: 1105186--1105222 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1105176 ATATTAATAT
*
1105186 TTTAAAAA-TATA
1 TTTAAAAATTTTA
1105198 TTTAAAAATTTTA
1 TTTAAAAATTTTA
1105211 TTTAAAAATTTT
1 TTTAAAAATTTT
1105223 TATTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTAAAAATTTTA
Found at i:1106273 original size:28 final size:27
Alignment explanation
Indices: 1106242--1106304 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1106232 AATGAATAAG
* *
1106242 TTTATTAAAAAATTTAATTTTTTATATA
1 TTTATTAAAAAAGTTAA-TATTTATATA
** *
1106270 TTTATTTTAAAAGTTAATATTTATTTA
1 TTTATTAAAAAAGTTAATATTTATATA
1106297 TTTATTAA
1 TTTATTAA
1106305 TGAGGTGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTATTAAAAAAGTTAATATTTATATA
Found at i:1107193 original size:11 final size:11
Alignment explanation
Indices: 1107177--1107201 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1107167 TTAACTTCTT
1107177 CATTGTATGTG
1 CATTGTATGTG
1107188 CATTGTATGTG
1 CATTGTATGTG
1107199 CAT
1 CAT
1107202 GTGCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (11 bp):
CATTGTATGTG
Found at i:1116437 original size:18 final size:18
Alignment explanation
Indices: 1116414--1116449 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1116404 GAAGAAAAGT
1116414 TTCCTGATCACCTAAATC
1 TTCCTGATCACCTAAATC
1116432 TTCCTGATCACCTAAATC
1 TTCCTGATCACCTAAATC
1116450 AAACGTTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.06, T:0.33
Consensus pattern (18 bp):
TTCCTGATCACCTAAATC
Found at i:1117581 original size:11 final size:11
Alignment explanation
Indices: 1117567--1117605 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1117557 TAAAATTAAA
1117567 AAATATATATT
1 AAATATATATT
*
1117578 AAATATACATT
1 AAATATATATT
1117589 AAATGA-ATATT
1 AAAT-ATATATT
1117600 AAATAT
1 AAATAT
1117606 TTTATTTTTT
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:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
AAATATATATT
Found at i:1117752 original size:33 final size:33
Alignment explanation
Indices: 1117711--1117793 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
1117701 ATCATGTTGT
** * *
1117711 TATATATATTTGTATTAATTATTTTTATTCATA
1 TATATATATTCATATTAATCATATTTATTCATA
* *
1117744 TATATATATTCATGTTAATCATATTTATTTATA
1 TATATATATTCATATTAATCATATTTATTCATA
1117777 TATATATTATTCATATT
1 TATATA-TATTCATATT
1117794 TATTTATATC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 33 0.79
34 9 0.21
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (33 bp):
TATATATATTCATATTAATCATATTTATTCATA
Found at i:1117805 original size:15 final size:15
Alignment explanation
Indices: 1117744--1117810 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
1117734 TTTATTCATA
*
1117744 TATAT-ATATTCATGT
1 TATATCATATTTAT-T
1117759 TA-ATCATATTTATT
1 TATATCATATTTATT
1117773 TATAT-ATA--TA-T
1 TATATCATATTTATT
1117784 TAT-TCATATTTATT
1 TATATCATATTTATT
1117798 TATATCATATTTA
1 TATATCATATTTA
1117811 AATAAATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
10 1 0.02
11 7 0.16
12 2 0.05
13 2 0.05
14 12 0.27
15 20 0.45
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (15 bp):
TATATCATATTTATT
Found at i:1117808 original size:21 final size:19
Alignment explanation
Indices: 1117761--1117810 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
1117751 ATTCATGTTA
1117761 ATCATATTTATTTATATAT
1 ATCATATTTATTTATATAT
*
1117780 AT-ATTATTCATATTTATTTAT
1 ATCA-TATT--TATTTATATAT
1117801 ATCATATTTA
1 ATCATATTTA
1117811 AATAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 1 0.04
19 8 0.31
21 16 0.62
22 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
ATCATATTTATTTATATAT
Found at i:1119290 original size:20 final size:20
Alignment explanation
Indices: 1119261--1119306 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1119251 ATATTAGATT
*
1119261 AAAA-TTTAAATATAATAAA
1 AAAATTTTAAAAATAATAAA
* *
1119280 AAAATTTTAAAAATACTATA
1 AAAATTTTAAAAATAATAAA
1119300 AAAATTT
1 AAAATTT
1119307 ATTTATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTTTAAAAATAATAAA
Found at i:1130057 original size:15 final size:15
Alignment explanation
Indices: 1130035--1130067 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1130025 AATTAAACAA
1130035 AAATAAATT-AAATT
1 AAATAAATTAAAATT
1130049 AAATCAAATTAAAATT
1 AAAT-AAATTAAAATT
1130065 AAA
1 AAA
1130068 ATTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 5 0.29
16 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAATTAAAATT
Found at i:1133966 original size:22 final size:22
Alignment explanation
Indices: 1133920--1133968 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1133910 TTTTTACATA
* * *
1133920 TTATTAATTTTTTCATTGAACT
1 TTATTAATTTATTAATTGAAAT
*
1133942 TTATTAATTTATTAATTTAAAT
1 TTATTAATTTATTAATTGAAAT
1133964 TTATT
1 TTATT
1133969 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTAATTTATTAATTGAAAT
Done.