Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_pilon, 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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 24
Found at i:2725850 original size:8 final size:8
Alignment explanation
Indices: 2725839--2725904 Score: 53
Period size: 8 Copynumber: 7.8 Consensus size: 8
2725829 CAAAAAGGGC
2725839 AAAAAGAA
1 AAAAAGAA
2725847 AAAAAGAA
1 AAAAAGAA
2725855 TAAGCAAA-AA
1 -AA--AAAGAA
*
2725865 ACAAAAGCA
1 A-AAAAGAA
2725874 AAAAAGAA
1 AAAAAGAA
2725882 CAAAAAGAA
1 -AAAAAGAA
* *
2725891 AAAAGGAC
1 AAAAAGAA
2725899 AAAAAG
1 AAAAAG
2725905 CACATGCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 28 0.60
9 13 0.28
10 3 0.06
11 3 0.06
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2725863 original size:14 final size:13
Alignment explanation
Indices: 2725840--2725881 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2725830 AAAAAGGGCA
*
2725840 AAAAGAAAAAAAG
1 AAAAGCAAAAAAG
*
2725853 AATAAGCAAAAAAC
1 AA-AAGCAAAAAAG
2725867 AAAAGCAAAAAAG
1 AAAAGCAAAAAAG
2725880 AA
1 AA
2725882 CAAAAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAAGCAAAAAAG
Found at i:2725892 original size:27 final size:27
Alignment explanation
Indices: 2725840--2725893 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2725830 AAAAAGGGCA
* *
2725840 AAAAGAAAAAAAGAATAAGCAAAAAAC
1 AAAAGAAAAAAAGAACAAGAAAAAAAC
* *
2725867 AAAAGCAAAAAAGAACAAAAAGAAAAA
1 AAAAGAAAAAAAGAACAAGAA-AAAAA
2725894 AGGACAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAAAAGAACAAGAAAAAAAC
Found at i:2725903 original size:16 final size:15
Alignment explanation
Indices: 2725838--2725904 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
2725828 ACAAAAAGGG
2725838 CAAAAAGAAAAAA-A
1 CAAAAAGAAAAAAGA
* * *
2725852 GAATAAGCAAAAA-A
1 CAAAAAGAAAAAAGA
2725866 C-AAAAGCAAAAAAGAA
1 CAAAAAG-AAAAAAG-A
2725882 CAAAAAGAAAAAAGGA
1 CAAAAAGAAAAAA-GA
2725898 CAAAAAG
1 CAAAAAG
2725905 CACATGCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 4 0.10
14 16 0.38
16 16 0.38
17 6 0.14
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.01
Consensus pattern (15 bp):
CAAAAAGAAAAAAGA
Found at i:2727611 original size:106 final size:105
Alignment explanation
Indices: 2727480--2728193 Score: 966
Period size: 106 Copynumber: 7.0 Consensus size: 105
2727470 ATATCGTGCC
* * *
2727480 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTCCC
2727545 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2727586 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTCCC
*
2727651 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2727692 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTCCC
*
2727757 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2727798 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTCCCA
2727856 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2727896 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAAT---CAA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTCCCA
2727954 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2727990 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC----AACAA---ACA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTCCCA
*
2728048 ATTTC----CCAATCTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
2728084 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGATTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAA-TTCC
** * * *
2728148 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2728190 ACTC
1 ACTC
2728194 GGAACAATAC
Statistics
Matches: 559, Mismatches: 32, Indels: 34
0.89 0.05 0.05
Matches are distributed among these distances:
93 5 0.01
94 159 0.28
98 106 0.19
102 4 0.01
103 2 0.00
104 1 0.00
106 282 0.50
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2727925 original size:98 final size:98
Alignment explanation
Indices: 2727650--2728193 Score: 730
Period size: 94 Copynumber: 5.5 Consensus size: 98
2727640 AACAATTTCC
*
2727650 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
2727715 TTCACGACGAAGGGACCACTGGTTGTCAACAAACAA
66 TTCACGACGAAGGGACCGCTGATTGTCAAC--A-AA
*
2727751 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGT
1 -----CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* *
2727816 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
61 TCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAA
*
2727854 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
2727919 TTCACGACGAAGGGACCGCTGATTGTCAATC-AA
66 TTCACGACGAAGGGACCGCTGATTGTCAA-CAAA
2727952 CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
2728013 TTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 TTCACGACGAAGGGACCGCTGATTGTCAACAAA
* * *
2728046 CAATTTC----CCAATCTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
2728107 TTCACAACGAAGGGA-CGACTGATTGTCAACAAA
66 TTCACGACGAAGGGACCG-CTGATTGTCAACAAA
* *
2728140 CAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 CAA--T-----TT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
2728194 GGAACAATAC
Statistics
Matches: 405, Mismatches: 18, Indels: 30
0.89 0.04 0.07
Matches are distributed among these distances:
93 3 0.01
94 172 0.42
96 1 0.00
98 100 0.25
101 2 0.00
102 1 0.00
103 2 0.00
104 1 0.00
106 123 0.30
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (98 bp):
CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
TTCACGACGAAGGGACCGCTGATTGTCAACAAA
Found at i:2727931 original size:43 final size:43
Alignment explanation
Indices: 2727870--2728119 Score: 155
Period size: 43 Copynumber: 5.4 Consensus size: 43
2727860 CAGAGCCAAT
2727870 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* * * * *
2727913 TTCAACTTCACGACGAAGGGACCGCTGATTGTCAAT-CA-ACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA----T-ATTG-GACTCCAGACAA--T-GCAAG
*
2727964 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* *** ** * *
2728007 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAA-
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA--T-GCAAG
* **
2728057 TCTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAG
1 T-TCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
2728101 TTCAACTTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
2728120 GACGACTGAT
Statistics
Matches: 155, Mismatches: 30, Indels: 44
0.68 0.13 0.19
Matches are distributed among these distances:
43 56 0.36
44 9 0.06
45 9 0.06
46 12 0.08
48 13 0.08
49 9 0.06
50 10 0.06
51 37 0.24
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
Found at i:2732429 original size:17 final size:18
Alignment explanation
Indices: 2732407--2732491 Score: 93
Period size: 18 Copynumber: 4.8 Consensus size: 18
2732397 ATTCTAAATG
*
2732407 TTTACAATTATTAGAT-A
1 TTTACAGTTATTAGATGA
* *
2732424 TTTACAGTTATCACATGA
1 TTTACAGTTATTAGATGA
* * *
2732442 TTTTCAGTTATCATATG-
1 TTTACAGTTATTAGATGA
*
2732459 TTTACAGTTATTAGATGT
1 TTTACAGTTATTAGATGA
2732477 TTTACAGTTATTAGA
1 TTTACAGTTATTAGA
2732492 CGTAGATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
17 27 0.47
18 31 0.53
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (18 bp):
TTTACAGTTATTAGATGA
Found at i:2732449 original size:18 final size:17
Alignment explanation
Indices: 2732404--2732487 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
2732394 TGAATTCTAA
* * *
2732404 ATGTTTACAATTATTAG
1 ATGTTTACAGTTATCAC
*
2732421 ATATTTACAGTTATCAC
1 ATGTTTACAGTTATCAC
* *
2732438 ATGATTTTCAGTTATCAT
1 ATG-TTTACAGTTATCAC
* *
2732456 ATGTTTACAGTTATTAG
1 ATGTTTACAGTTATCAC
2732473 ATGTTTTACAGTTAT
1 ATG-TTTACAGTTAT
2732488 TAGACGTAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
17 29 0.53
18 26 0.47
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (17 bp):
ATGTTTACAGTTATCAC
Found at i:2732921 original size:170 final size:170
Alignment explanation
Indices: 2732639--2732980 Score: 596
Period size: 170 Copynumber: 2.0 Consensus size: 170
2732629 ACATTCGTGT
* * * *
2732639 ACCAATGTTCAGCTCCTTTAGTGCTCAGGTTATGGTTGGATTAAAGTGCATCATATCACAGTTTC
1 ACCAATGTTAAGATCCTTTAGTGCTCAAGTTATGATTGGATTAAAGTGCATCATATCACAGTTTC
2732704 AGTTATGATTCAGCACCGTGTTGTGCCTAGTGCGCGCCTTATACTCACGCACCTTATATTATCTT
66 AGTTATGATTCAGCACCGTGTTGTGCCTAGTGCGCGCCTTATACTCACGCACCTTATATTATCTT
* *
2732769 ACATATACATTGGGTTATAGAAGTAAGTGTGAACGTTGTG
131 ACATATACATTGGGTTATAGAAGTAAGTGTAAAAGTTGTG
2732809 ACCAATGTTAAGATCCTTTAGTGCTCAAGTTATGATTGGATTAAAGTGCATCATATCACAGTTTC
1 ACCAATGTTAAGATCCTTTAGTGCTCAAGTTATGATTGGATTAAAGTGCATCATATCACAGTTTC
* *
2732874 AGTTATGATTC-GACACCGTGTTGTGCCTAGTGTGCGCCTTATACTCACGCACCTTATATTCTCT
66 AGTTATGATTCAG-CACCGTGTTGTGCCTAGTGCGCGCCTTATACTCACGCACCTTATATTATCT
2732938 TACATATACATTGGGTTATAGAAGTAAGTGTAAAAGTTGTG
130 TACATATACATTGGGTTATAGAAGTAAGTGTAAAAGTTGTG
2732979 AC
1 AC
2732981 AATTATAAAA
Statistics
Matches: 163, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
169 1 0.01
170 162 0.99
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (170 bp):
ACCAATGTTAAGATCCTTTAGTGCTCAAGTTATGATTGGATTAAAGTGCATCATATCACAGTTTC
AGTTATGATTCAGCACCGTGTTGTGCCTAGTGCGCGCCTTATACTCACGCACCTTATATTATCTT
ACATATACATTGGGTTATAGAAGTAAGTGTAAAAGTTGTG
Found at i:2739477 original size:18 final size:18
Alignment explanation
Indices: 2739450--2739554 Score: 60
Period size: 18 Copynumber: 6.0 Consensus size: 18
2739440 AATTCTAAAT
2739450 ATTT-ACAGTTATCAGAC
1 ATTTCACAGTTATCAGAC
* * *
2739467 ATTTCACAGTTATTATAT
1 ATTTCACAGTTATCAGAC
* *
2739485 ATTT-ACAATTATCAGATG
1 ATTTCACAGTTATCAGA-C
2739503 ATTTTCA-A-TTATCAG--
1 A-TTTCACAGTTATCAGAC
* *
2739518 ATGTTCACAGTTATCATAT
1 AT-TTCACAGTTATCAGAC
* *
2739537 GTTTTACAGTTATCAGAC
1 ATTTCACAGTTATCAGAC
2739555 GTAGATTAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
14 1 0.01
15 5 0.07
16 1 0.01
17 19 0.28
18 35 0.52
19 5 0.07
20 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (18 bp):
ATTTCACAGTTATCAGAC
Found at i:2739888 original size:15 final size:16
Alignment explanation
Indices: 2739868--2739900 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2739858 TTATGACAAT
2739868 ACATAAAA-GAAAAGA
1 ACATAAAATGAAAAGA
2739883 ACATAAAATTGAAAAGA
1 ACATAAAA-TGAAAAGA
2739900 A
1 A
2739901 AGTTATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
ACATAAAATGAAAAGA
Found at i:2751443 original size:21 final size:21
Alignment explanation
Indices: 2751420--2751499 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
2751410 CAAAACCTGT
*
2751420 TGAAAATCCTACAGCCACTAT
1 TGAAAATCCTACAGCCACTAC
2751441 TGAAAATCCTACAGCCACTAC
1 TGAAAATCCTACAGCCACTAC
* *
2751462 TGAAATTCCTACAGCCACTGC
1 TGAAAATCCTACAGCCACTAC
*
2751483 TGAAATTCCTACAGCCA
1 TGAAAATCCTACAGCCA
2751500 TTGTAATTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.23
Consensus pattern (21 bp):
TGAAAATCCTACAGCCACTAC
Found at i:2753980 original size:2 final size:2
Alignment explanation
Indices: 2753975--2754001 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2753965 GGGGGGGGGG
2753975 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 G
2754002 GTTATTTAGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2757751 original size:23 final size:23
Alignment explanation
Indices: 2757717--2757772 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2757707 TTGTTGATTG
* *
2757717 TAAA-GAATATGTTCA-TGAATAT
1 TAAATGAACATGTTCATTG-ATAC
2757739 TAAATGAACATGTTCATTGATAC
1 TAAATGAACATGTTCATTGATAC
2757762 TAAATGAACAT
1 TAAATGAACAT
2757773 ATAGGGGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 4 0.13
23 24 0.80
24 2 0.07
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (23 bp):
TAAATGAACATGTTCATTGATAC
Found at i:2758348 original size:18 final size:18
Alignment explanation
Indices: 2758325--2758374 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2758315 TGTCCTCATC
2758325 CCCATTTGAACTTCGAGA
1 CCCATTTGAACTTCGAGA
*
2758343 CCCATTTGAACTTCGGGA
1 CCCATTTGAACTTCGAGA
2758361 CCCATTTGAACTTC
1 CCCATTTGAACTTC
2758375 AGGAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (18 bp):
CCCATTTGAACTTCGAGA
Found at i:2767704 original size:30 final size:31
Alignment explanation
Indices: 2767670--2767736 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
2767660 AATTGATTTT
* *
2767670 TTAAAATA-TAAATCACTCAAATTTGAATTA
1 TTAAAATATTAAATCACTAAAATTTAAATTA
* *
2767700 TTAAAA-ATTAAATTATTAAAATTTAAATTA
1 TTAAAATATTAAATCACTAAAATTTAAATTA
2767730 TTAAAAT
1 TTAAAAT
2767737 TTGAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAATATTAAATCACTAAAATTTAAATTA
Found at i:2767715 original size:15 final size:15
Alignment explanation
Indices: 2767695--2767787 Score: 102
Period size: 15 Copynumber: 6.4 Consensus size: 15
2767685 CTCAAATTTG
2767695 AATTATTAAAAATTA
1 AATTATTAAAAATTA
*
2767710 AATTATTAAAATTTA
1 AATTATTAAAAATTA
* *
2767725 AATTATTAAAATTTG
1 AATTATTAAAAATTA
2767740 AATTATTAAAAA--A
1 AATTATTAAAAATTA
* * *
2767753 AATTACTGAAATTTA
1 AATTATTAAAAATTA
*
2767768 AATT-TTAAAAAATA
1 AATTATTAAAAATTA
2767782 AATTAT
1 AATTAT
2767788 ATTTTTTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
13 9 0.14
14 10 0.16
15 45 0.70
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTATTAAAAATTA
Found at i:2767737 original size:45 final size:43
Alignment explanation
Indices: 2767670--2767777 Score: 137
Period size: 45 Copynumber: 2.5 Consensus size: 43
2767660 AATTGATTTT
* * * *
2767670 TTAAAATATAAATCACTCAAATTTGAATTATTAAAAATTAAATTA
1 TTAAAATTTAAATTATTAAAATTTGAATTATTAAAAA--AAATTA
2767715 TTAAAATTTAAATTATTAAAATTTGAATTATTAAAAAAAATTA
1 TTAAAATTTAAATTATTAAAATTTGAATTATTAAAAAAAATTA
* *
2767758 CTGAAATTTAAATT-TTAAAA
1 TTAAAATTTAAATTATTAAAA
2767778 AATAAATTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 6 0.11
43 18 0.32
45 33 0.58
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (43 bp):
TTAAAATTTAAATTATTAAAATTTGAATTATTAAAAAAAATTA
Found at i:2767744 original size:30 final size:30
Alignment explanation
Indices: 2767688--2767750 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2767678 TAAATCACTC
*
2767688 AAATTTGAATTATTAAAAATTAAATTATTA
1 AAATTTAAATTATTAAAAATTAAATTATTA
* *
2767718 AAATTTAAATTATTAAAATTTGAATTATTA
1 AAATTTAAATTATTAAAAATTAAATTATTA
2767748 AAA
1 AAA
2767751 AAAATTACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTAAATTATTAAAAATTAAATTATTA
Found at i:2767894 original size:16 final size:16
Alignment explanation
Indices: 2767870--2767912 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2767860 AAGAGTTTTT
* *
2767870 TAAAAATTATTTATTA
1 TAAATATTATTTATAA
**
2767886 TAAATATTAAATATAA
1 TAAATATTATTTATAA
2767902 TAAATATTATT
1 TAAATATTATT
2767913 ATTTATCATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATATTATTTATAA
Found at i:2767983 original size:19 final size:19
Alignment explanation
Indices: 2767933--2767984 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
2767923 ATTTAAAATT
* *
2767933 ATATTATTTTAAAATATTAA
1 ATATTATTTT-TATTATTAA
*
2767953 ATAATT-TATTTATTATTAA
1 AT-ATTATTTTTATTATTAA
2767972 ATATTATTTTTAT
1 ATATTATTTTTAT
2767985 AAATTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 3 0.12
19 15 0.58
20 5 0.19
21 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTATTTTTATTATTAA
Found at i:2767993 original size:15 final size:17
Alignment explanation
Indices: 2767947--2767994 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
2767937 TATTTTAAAA
2767947 TATTAAATAATTTATTTAT
1 TATTAAAT--TTTATTTAT
*
2767966 TATTAAATATTATTT-T
1 TATTAAATTTTATTTAT
2767982 TA-TAAATTTTATT
1 TATTAAATTTTATT
2767995 AATAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 6 0.22
19 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTAAATTTTATTTAT
Found at i:2768119 original size:22 final size:20
Alignment explanation
Indices: 2768071--2768173 Score: 57
Period size: 22 Copynumber: 5.0 Consensus size: 20
2768061 AGTAATAGTA
*
2768071 TTTATTATAT-TTTAAAAAT
1 TTTATTATATATTTAAATAT
*
2768090 ATTAATTAGTATATTTAAATAT
1 -TTTATTA-TATATTTAAATAT
* *
2768112 CTTTATTAAAATATATAAATAT
1 -TTTATT-ATATATTTAAATAT
* * * *
2768134 TATTATTAAATATATAAAAAA
1 T-TTATTATATATTTAAATAT
*
2768155 TTTA-TATATTATTAAAATA
1 TTTATTATA-TATTTAAATA
2768174 AAAATATAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.05
20 16 0.24
21 17 0.26
22 29 0.44
23 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
TTTATTATATATTTAAATAT
Found at i:2768152 original size:30 final size:28
Alignment explanation
Indices: 2768118--2768181 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
2768108 ATATCTTTAT
2768118 TAAAATATATAAATATTATTATTAAATATA
1 TAAAATATATAAATA-TATTATTAAA-ATA
**
2768148 TAAAA-A-ATTTATATATTATTAAAATA
1 TAAAATATATAAATATATTATTAAAATA
2768174 -AAAATATA
1 TAAAATATA
2768182 ATATCTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 11 0.37
28 5 0.17
29 1 0.03
30 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAATATATAAATATATTATTAAAATA
Found at i:2768185 original size:22 final size:22
Alignment explanation
Indices: 2768114--2768185 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 22
2768104 TTAAATATCT
2768114 TTATTAAAATATATAAATAT--TA
1 TTATTAAAATA-A-AAATATAATA
*
2768136 TTATTAAATATATAAAAAATTTATATA
1 TTATT-AA-A-AT-AAAAATATA-ATA
2768163 TTATTAAAATAAAAATATAATA
1 TTATTAAAATAAAAATATAATA
2768185 T
1 T
2768186 CTTATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
22 9 0.22
23 10 0.24
24 8 0.20
25 4 0.10
26 3 0.07
27 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTAAAATAAAAATATAATA
Found at i:2768185 original size:24 final size:25
Alignment explanation
Indices: 2768118--2768275 Score: 69
Period size: 27 Copynumber: 6.0 Consensus size: 25
2768108 ATATCTTTAT
2768118 TAAAATATATAAATATTATTATTAAATA
1 TAAAA-ATAT-AATA-TATTATTAAATA
* *
2768146 TATAAAAAATTTATATATTATTAAA-A
1 TA-AAAATA-TAATATATTATTAAATA
* * *
2768172 TAAAAATATAATATCTTATATTATTA
1 TAAAAATATAATATATTAT-TAAATA
*
2768198 TAAATAA-ATTGAT-TATTA-TATAATA
1 TAAA-AATA-TAATATATTATTA-AATA
*
2768223 TTAAAAATATAATAT-TATATT-ATTA
1 -TAAAAATATAATATAT-TATTAAATA
*
2768248 TAAATATTAATAAATATATT-TTAAATA
1 TAAA-AAT-AT-AATATATTATTAAATA
2768275 T
1 T
2768276 TTTAATAATT
Statistics
Matches: 98, Mismatches: 15, Indels: 35
0.66 0.10 0.24
Matches are distributed among these distances:
24 14 0.14
25 21 0.21
26 25 0.26
27 26 0.27
28 8 0.08
29 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
TAAAAATATAATATATTATTAAATA
Found at i:2768241 original size:50 final size:50
Alignment explanation
Indices: 2768115--2768253 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 50
2768105 TAAATATCTT
*
2768115 TATTAAAATATATAAATATTATTATTAAATATATAAA-AAATTTATATATTATTAA
1 TATTAAAA-ATAT-AATATTA-TATT--AT-TATAAATAAATTGATATATTATTAA
*
2768170 -AATAAAAATATAATATCTTATATTATTATAAATAAATTGAT-TATTATATAA
1 TATTAAAAATATAATA--TTATATTATTATAAATAAATTGATATATTAT-TAA
2768221 TATTAAAAATATAATATTATATTATTATAAATA
1 TATTAAAAATATAATATTATATTATTATAAATA
2768254 TTAATAAATA
Statistics
Matches: 76, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
50 29 0.38
51 12 0.16
52 18 0.24
53 8 0.11
54 9 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (50 bp):
TATTAAAAATATAATATTATATTATTATAAATAAATTGATATATTATTAA
Found at i:2768275 original size:52 final size:51
Alignment explanation
Indices: 2768115--2768276 Score: 138
Period size: 50 Copynumber: 3.1 Consensus size: 51
2768105 TAAATATCTT
**
2768115 TATTAAAATATATAAATA-TTATTATTAAATATATAAA-AAATTTATATATTATTAAA
1 TATTAAAA-ATAT-AATACTTA-TATT--AT-TATAAATAAATAAATATATT-TTAAA
** *
2768171 -A-TAAAAATATAATATCTTATATTATTATAAATAAATTGAT-TATTATATAA
1 TATTAAAAATATAATA-CTTATATTATTATAAATAAATAAATATATTTTA-AA
2768221 TATTAAAAATATAATA-TTATATTATTATAAATATTAATAAATATATTTTAAA
1 TATTAAAAATATAATACTTATATTATTATAAATA--AATAAATATATTTTAAA
2768273 TATT
1 TATT
2768277 TTAATAATTA
Statistics
Matches: 92, Mismatches: 5, Indels: 22
0.77 0.04 0.18
Matches are distributed among these distances:
49 2 0.02
50 29 0.32
51 10 0.11
52 28 0.30
53 14 0.15
54 8 0.09
55 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (51 bp):
TATTAAAAATATAATACTTATATTATTATAAATAAATAAATATATTTTAAA
Found at i:2768519 original size:42 final size:42
Alignment explanation
Indices: 2768465--2768576 Score: 188
Period size: 42 Copynumber: 2.7 Consensus size: 42
2768455 ATGAATTACA
*
2768465 TTCCAGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
2768507 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
2768549 TTCCGGAAAATGAATTACATGAAACAAA
1 TTCCGGAAAACGAATTACGTGAAACAAA
2768577 TACGAGATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:2780394 original size:13 final size:14
Alignment explanation
Indices: 2780376--2780404 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2780366 AATGTACTAT
2780376 TTATTTT-TCTCAA
1 TTATTTTATCTCAA
2780389 TTATTTTATCTCAA
1 TTATTTTATCTCAA
2780403 TT
1 TT
2780405 CTAATTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTTATCTCAA
Found at i:2780863 original size:18 final size:18
Alignment explanation
Indices: 2780840--2780891 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
2780830 ACTTAGAATT
2780840 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
* *
2780858 TGTCCCGAAGGACCATTA
1 TGTCCCAAAGGACCACTA
2780876 TGTCCCAAAGGACCAC
1 TGTCCCAAAGGACCAC
2780892 ATATTACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:2781345 original size:2 final size:2
Alignment explanation
Indices: 2781340--2781380 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2781330 ATTCACACAC
2781340 AT AT AT AT AT AT AT AT AT A- 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
2781381 GTTCTCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2783371 original size:5 final size:6
Alignment explanation
Indices: 2783336--2783370 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2783326 CTTTTCAAGT
*
2783336 TTTTCTA TTTCTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
2783371 AAGCTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.88
7 3 0.12
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:2790128 original size:368 final size:370
Alignment explanation
Indices: 2789451--2790190 Score: 1441
Period size: 368 Copynumber: 2.0 Consensus size: 370
2789441 TAGTTAATTA
2789451 TTTTCCCCCTTGATCTTTTCCTCAACTTTGTGTATGACTGTACTGCAAAATCATCAATCATACAT
1 TTTTCCCCCTTGATCTTTTCCTCAACTTTGTGTATGACTGTACTGCAAAATCATCAATCATACAT
2789516 TTCCTAAATAGGATTTAGCTAGCTTCAAGGCTGTTAAAGCTGCACTTATGCTTCTTGGATAAAAT
66 TTCCTAAATAGGATTTAGCTAGCTTCAAGGCTGTTAAAGCTGCACTTATGCTTCTTGGATAAAAT
2789581 TCAATTAGCGTGCTTAATTGCGTATGTCTTTGTTTGCAGCAACAATTATACATTTACTACTTGTC
131 TCAATTAGCGTGCTTAATTGCGTATGTCTTTGTTTGCAGCAACAATTATACATTTACTACTTGTC
2789646 ACAATCTGCCCATGTAGGTTTATAAGCTTTCTTCTGTGTTAGTGATAGAGCCTTTTGAAAGTATC
196 ACAATCTGCCCATGTAGGTTTATAAGCTTTCTTCTGTGTTAGTGATAGAGCCTTTTGAAAGTATC
2789711 TTTTATGTTCACTCACTAATATAACCAATGTTTTGTGTTTTAGGTGC-TTTGAGCCGGTTGAGAT
261 TTTTATGTTCACTCACTAATATAACCAATGTTTTGTGTTTTAGGTGCTTTTGAGCCGGTTGAGAT
2789775 TGTTTTTAAGTCCTGGATATCC-CATGAGGAAATATTGAGAACGT
326 TGTTTTTAAGTCCTGGATATCCACATGAGGAAATATTGAGAACGT
2789819 TTTTCCCCCTTGATCTTTTCCTCAACTTTGTGTATGACTGTACTGCAAAATCATCAATCATACAT
1 TTTTCCCCCTTGATCTTTTCCTCAACTTTGTGTATGACTGTACTGCAAAATCATCAATCATACAT
2789884 TTCCTAAATAGGATTTAGCTAGCTTCAAGGCTGTTAAAGCTGCACTTATGCTTCTTGGATAAAAT
66 TTCCTAAATAGGATTTAGCTAGCTTCAAGGCTGTTAAAGCTGCACTTATGCTTCTTGGATAAAAT
2789949 TCAATTAGCGTGCTTAATTGCGTATGTCTTTGTTTGCAGCAACAAGTTATACATTTACTACTTGT
131 TCAATTAGCGTGCTTAATTGCGTATGTCTTTGTTTGCAGCAACAA-TTATACATTTACTACTTGT
2790014 CACAATCTGCCCATGTAGGTTTATAAGCTTTCTTCTGTGTTAGTGATAGAGCCTTTTGAAAGTAT
195 CACAATCTGCCCATGTAGGTTTATAAGCTTTCTTCTGTGTTAGTGATAGAGCCTTTTGAAAGTAT
2790079 CTTTTATGTTCA-TCACTAATATAACCAATGTTTTGTGTTTTAGGTGCTTTTGAGCCGGTTGAGA
260 CTTTTATGTTCACTCACTAATATAACCAATGTTTTGTGTTTTAGGTGCTTTTGAGCCGGTTGAGA
*
2790143 TTGTTTTTAAGTCCTGGATATCCATATGAGGAAATATTGAGAACGT
325 TTGTTTTTAAGTCCTGGATATCCACATGAGGAAATATTGAGAACGT
2790189 TT
1 TT
2790191 CACAATCAAA
Statistics
Matches: 368, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
368 210 0.57
369 135 0.37
370 23 0.06
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (370 bp):
TTTTCCCCCTTGATCTTTTCCTCAACTTTGTGTATGACTGTACTGCAAAATCATCAATCATACAT
TTCCTAAATAGGATTTAGCTAGCTTCAAGGCTGTTAAAGCTGCACTTATGCTTCTTGGATAAAAT
TCAATTAGCGTGCTTAATTGCGTATGTCTTTGTTTGCAGCAACAATTATACATTTACTACTTGTC
ACAATCTGCCCATGTAGGTTTATAAGCTTTCTTCTGTGTTAGTGATAGAGCCTTTTGAAAGTATC
TTTTATGTTCACTCACTAATATAACCAATGTTTTGTGTTTTAGGTGCTTTTGAGCCGGTTGAGAT
TGTTTTTAAGTCCTGGATATCCACATGAGGAAATATTGAGAACGT
Found at i:2794541 original size:31 final size:31
Alignment explanation
Indices: 2794486--2794545 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2794476 TAAACTTTAT
* *
2794486 GCATGAGGGGATAGTTTCAGTTATGCATCCA
1 GCATGAGGGGATAGTATCAATTATGCATCCA
* *
2794517 GCATTAGGGGATGGTATCAATTATGCATC
1 GCATGAGGGGATAGTATCAATTATGCATC
2794546 TATAACAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (31 bp):
GCATGAGGGGATAGTATCAATTATGCATCCA
Found at i:2798059 original size:2 final size:2
Alignment explanation
Indices: 2798052--2798095 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2798042 TATAAAGCTT
2798052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2798094 TA
1 TA
2798096 ATCTTTCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2799681 original size:36 final size:36
Alignment explanation
Indices: 2799640--2799770 Score: 262
Period size: 36 Copynumber: 3.6 Consensus size: 36
2799630 TTTACTTAAT
2799640 TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
2799676 TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
2799712 TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
2799748 TAGTTTATTAGTTTAAGTTATAT
1 TAGTTTATTAGTTTAAGTTATAT
2799771 AAAAATTATG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (36 bp):
TAGTTTATTAGTTTAAGTTATATTATAATAAAAGAA
Found at i:2801330 original size:139 final size:139
Alignment explanation
Indices: 2801126--2801408 Score: 530
Period size: 139 Copynumber: 2.0 Consensus size: 139
2801116 ATATAATCCA
2801126 GGTATGTGAAATAATGAAAAAGATTATGGGTTTATATGAAAAGTGATGAAAGAGATATGAAATGA
1 GGTATGTGAAATAATGAAAAAGATTATGGGTTTATATGAAAAGTGATGAAAGAGATATGAAATGA
2801191 GAAATGTATTCATATTAAAGCCCATGTTATATGATACGAGAGCTATAGGTATAGTTGGCATGCCA
66 GAAATGTATTCATATTAAAGCCCATGTTATATGATACGAGAGCTATAGGTATAGTTGGCATGCCA
2801256 AGAGTCGAG
131 AGAGTCGAG
2801265 GGTATGTGAAATAATGAAAAAGATTATGGGTTTATATGAAAAGTGATGAAAGAGATATGAAATGA
1 GGTATGTGAAATAATGAAAAAGATTATGGGTTTATATGAAAAGTGATGAAAGAGATATGAAATGA
* * *
2801330 GAAATGTATTCATATTAAAGCTCATGTTATATGATACGAGAGTTATAGGTATAGTTGGCATGCTA
66 GAAATGTATTCATATTAAAGCCCATGTTATATGATACGAGAGCTATAGGTATAGTTGGCATGCCA
*
2801395 AGAGTCGAT
131 AGAGTCGAG
2801404 GGTAT
1 GGTAT
2801409 ATTAGTCATT
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (139 bp):
GGTATGTGAAATAATGAAAAAGATTATGGGTTTATATGAAAAGTGATGAAAGAGATATGAAATGA
GAAATGTATTCATATTAAAGCCCATGTTATATGATACGAGAGCTATAGGTATAGTTGGCATGCCA
AGAGTCGAG
Found at i:2801436 original size:22 final size:22
Alignment explanation
Indices: 2801417--2801601 Score: 262
Period size: 22 Copynumber: 8.4 Consensus size: 22
2801407 ATATTAGTCA
*
2801417 TTCGGGACGTATCCAGTAGTCC
1 TTCGGGACGTATCCAGTGGTCC
* *
2801439 TTCAGGACGTATTCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
2801461 TTCGGGACATATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
* *
2801483 TTCGGAACGTATCCAATGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
2801505 TTTCGGGACGTATCCAATGGTCC
1 -TTCGGGACGTATCCAGTGGTCC
* *
2801528 TTCAGGACGTATCCAGTGGTCT
1 TTCGGGACGTATCCAGTGGTCC
*
2801550 TTCGGGACGTATCCAGTGGTCT
1 TTCGGGACGTATCCAGTGGTCC
*
2801572 TTCGGGACGTATCTAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
2801594 TTCGGGAC
1 TTCGGGAC
2801602 ATAGTGATCA
Statistics
Matches: 146, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
22 125 0.86
23 21 0.14
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCC
Found at i:2801568 original size:89 final size:88
Alignment explanation
Indices: 2801417--2801601 Score: 280
Period size: 89 Copynumber: 2.1 Consensus size: 88
2801407 ATATTAGTCA
* *
2801417 TTCGGGACGTATCCAGTAGTCCTTCAGGACGTATTCAGTGGTCCTTCGGGACATATCCAGTGGTC
1 TTCGGGACGTATCCAATAGTCCTTCAGGACGTATCCAGTGGTCCTTCGGGACATATCCAGTGGTC
2801482 CTTCGGAACGTATCCAATGGTCC
66 CTTCGGAACGTATCCAATGGTCC
* * *
2801505 TTTCGGGACGTATCCAATGGTCCTTCAGGACGTATCCAGTGGTCTTTCGGGACGTATCCAGTGGT
1 -TTCGGGACGTATCCAATAGTCCTTCAGGACGTATCCAGTGGTCCTTCGGGACATATCCAGTGGT
* * * *
2801570 CTTTCGGGACGTATCTAGTGGTCC
65 CCTTCGGAACGTATCCAATGGTCC
2801594 TTCGGGAC
1 TTCGGGAC
2801602 ATAGTGATCA
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 8 0.09
89 79 0.91
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (88 bp):
TTCGGGACGTATCCAATAGTCCTTCAGGACGTATCCAGTGGTCCTTCGGGACATATCCAGTGGTC
CTTCGGAACGTATCCAATGGTCC
Found at i:2808445 original size:22 final size:22
Alignment explanation
Indices: 2808420--2808577 Score: 198
Period size: 22 Copynumber: 7.4 Consensus size: 22
2808410 ATATTAGTCC
*
2808420 TTCGGGACGTATCCAGTGGTCA
1 TTCGGGACGTATCCAGTGGTCT
* *
2808442 TTCGGGATGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCT
* *
2808464 TTCAGGACATATCCAGTGGTCT
1 TTCGGGACGTATCCAGTGGTCT
*
2808486 TTCGGGACGTATCCAGTGGTCA
1 TTCGGGACGTATCCAGTGGTCT
* *
2808508 TTCTGGACCTATCCAGTGGTCT
1 TTCGGGACGTATCCAGTGGTCT
*
2808530 TTCGGGACGTATCTAGTGGTCT
1 TTCGGGACGTATCCAGTGGTCT
*
2808552 TTCGGGA--TAT--AGTGGTCC
1 TTCGGGACGTATCCAGTGGTCT
2808570 TTCGGGAC
1 TTCGGGAC
2808578 AAATACTGAA
Statistics
Matches: 119, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.12
20 3 0.03
22 102 0.86
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.32
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCT
Found at i:2810141 original size:14 final size:15
Alignment explanation
Indices: 2810122--2810162 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2810112 TTGTTATTTG
2810122 TTTAAAATTA-AATA
1 TTTAAAATTAGAATA
*
2810136 TTT-AAATTAGACTA
1 TTTAAAATTAGAATA
2810150 TTTATAAATTAGA
1 TTTA-AAATTAGA
2810163 TTTAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
16 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTAAAATTAGAATA
Found at i:2810220 original size:24 final size:24
Alignment explanation
Indices: 2810193--2810349 Score: 126
Period size: 24 Copynumber: 6.4 Consensus size: 24
2810183 TTTAAATATT
*
2810193 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATCATTATTAG
2810217 TAATCATTATTAAATCATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
2810241 TAATTATTA-TAATTTCATTATTTAG
1 TAATCATTATTAA-ATCATTA-TTAG
* * *
2810266 TAATCATTATT--ATCA-AATCAC
1 TAATCATTATTAAATCATTATTAG
2810287 TAAAT-ATTACTAATAAATCATTATTAG
1 T-AATCATTA-T--TAAATCATTATTAG
* *
2810314 TAATCATTACTAAATCATATCATTAC
1 TAATCATTATTAAATCAT-T-ATTAG
2810340 TAAATCATTA
1 T-AATCATTA
2810350 ATTATCAAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
21 7 0.07
22 5 0.05
23 6 0.06
24 46 0.43
25 13 0.12
26 13 0.12
27 16 0.15
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (24 bp):
TAATCATTATTAAATCATTATTAG
Found at i:2810234 original size:35 final size:35
Alignment explanation
Indices: 2810189--2810277 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 35
2810179 TCTATTTAAA
*
2810189 TATTTAATCATTATTAAATAATTATTAGTAA-TCAT
1 TATTAAATCATTATTAAATAATTATTA-TAATTCAT
*
2810224 TATTAAATCATTATT-AGTAATTATTATAATTTCAT
1 TATTAAATCATTATTAAATAATTATTATAA-TTCAT
2810259 TATTTAGTAATCATTATTA
1 TA-TTA--AATCATTATTA
2810278 TCAAATCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
33 3 0.07
34 10 0.22
35 20 0.43
36 3 0.07
38 10 0.22
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (35 bp):
TATTAAATCATTATTAAATAATTATTATAATTCAT
Found at i:2810272 original size:14 final size:13
Alignment explanation
Indices: 2810193--2810277 Score: 83
Period size: 11 Copynumber: 6.9 Consensus size: 13
2810183 TTTAAATATT
2810193 TAATCATTATTA-
1 TAATCATTATTAG
*
2810205 -AATAATTATTAG
1 TAATCATTATTAG
2810217 TAATCATTATTA-
1 TAATCATTATTAG
2810229 -AATCATTATTAG
1 TAATCATTATTAG
* *
2810241 TAATTATTA-TAA
1 TAATCATTATTAG
*
2810253 T-TTCATTATTTAG
1 TAATCATTA-TTAG
2810266 TAATCATTATTA
1 TAATCATTATTA
2810278 TCAAATCACT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
11 26 0.45
12 3 0.05
13 23 0.40
14 6 0.10
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (13 bp):
TAATCATTATTAG
Found at i:2810304 original size:73 final size:75
Alignment explanation
Indices: 2810227--2810391 Score: 203
Period size: 76 Copynumber: 2.2 Consensus size: 75
2810217 TAATCATTAT
* * *
2810227 TAAATCATTATTAGTAATTATTA-TAATTTCAT-TATTTAGT-AATCATT-ATTATCAAATCACT
1 TAAATCATTATTAGTAATCATTACTAA-ATCATATA-TTACTAAATCATTAATTATCAAATCACT
*
2810288 AAATATTACTAA
64 AAATATTAATAA
*
2810300 TAAATCATTATTAGTAATCATTACTAAATCATATCATTACTAAATCATTAATTATCAAATCATTA
1 TAAATCATTATTAGTAATCATTACTAAATCATAT-ATTACTAAATCATTAATTATCAAATCACTA
* *
2810365 ATTTTTAATAA
65 AATATTAATAA
*
2810376 TAAATCATTAGTAGTA
1 TAAATCATTATTAGTA
2810392 TCGGTACTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
73 26 0.33
74 8 0.10
75 8 0.10
76 37 0.47
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (75 bp):
TAAATCATTATTAGTAATCATTACTAAATCATATATTACTAAATCATTAATTATCAAATCACTAA
ATATTAATAA
Found at i:2810337 original size:16 final size:16
Alignment explanation
Indices: 2810316--2810347 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2810306 ATTATTAGTA
2810316 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
2810332 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
2810348 TAATTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:2810345 original size:27 final size:25
Alignment explanation
Indices: 2810285--2810364 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 25
2810275 TTATCAAATC
2810285 ACTAAAT-ATTACTAATAAATCATT
1 ACTAAATCATTACTAATAAATCATT
* *
2810309 ATTAGTAATCATTACTAAATCATATCATT
1 ACTA--AATCATTACT-AAT-AAATCATT
* *
2810338 ACTAAATCATTAATTATCAAATCATT
1 ACTAAATCATTACTAAT-AAATCATT
2810364 A
1 A
2810365 ATTTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
24 3 0.07
26 14 0.31
27 15 0.33
28 3 0.07
29 10 0.22
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (25 bp):
ACTAAATCATTACTAATAAATCATT
Found at i:2810959 original size:371 final size:373
Alignment explanation
Indices: 2810279--2811019 Score: 1098
Period size: 371 Copynumber: 2.0 Consensus size: 373
2810269 TCATTATTAT
* *
2810279 CAAATCACTAAATATTACTAATAAATCATTATTAGTAATCATTACTAAATCATATCATTACTAAA
1 CAAATCACTAAATATTACTAATAAATAATTATTAGTAATCATTACTAAATCATATAATTACTAAA
* * * *
2810344 TCATTAATTATCAAATCATTAATTTTTAATAATAAATCATTAGTAGTATCGGTACTATTTTGAGG
66 TCATTAAATATCAAATCATTAAATATTAATAATAAATCATTAGTAG-A---GTACCATTTTGAGG
* * * * * *
2810409 TTCTGTTTCCATGGTATCGGTATTGCCTTAGCAGTATCAGTATTACTTAGTTTAAATTGAGTTTT
127 TTATGTTTCCATGGTATCGGTACTGCCTTAGCAATAACAATACTACTTAGTTTAAATTGAGTTTT
*
2810474 TACTCGATTAAATTTCAAAACCTTTAGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAAT
192 TACTCAATTAAATTTCAAAACCTTTAGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAAT
** * * * *
2810539 CGAATATAATCTTAAAATTTATAAAAATTAATTAATAAATTTGTTTGGTATTTTAAAAAATCAAA
257 AAAATATAATCTTAAAATTTATAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAA
*
2810604 AATCATTATCAAATCTTTTAAATTTATTATTAGTAATCATTAGTATCAAATA
322 AATCATTATCAAATCATTTAAATTTATTATTAGTAATCATTAGTATCAAATA
* **
2810656 CAAATCATTAAATATTTA-TAATAAATAATTATTAGTAATCATTACTAAATCATATAATTTTTAA
1 CAAATCACTAAATA-TTACTAATAAATAATTATTAGTAATCATTACTAAATCATATAATTACTAA
*
2810720 ATCATTAAATATCAAATCGA-TAAATATTAGTAATAAATCA-TA-TCA-A-TACCATTTTGAGGT
65 ATCATTAAATATCAAATC-ATTAAATATTAATAATAAATCATTAGT-AGAGTACCATTTTGAGGT
* * *
2810780 TATGTTTCCATGGTATTGGTACTGCCTTAGCAATAACAATACTATTTAGTTTAAATTGAATTTTT
128 TATGTTTCCATGGTATCGGTACTGCCTTAGCAATAACAATACTACTTAGTTTAAATTG-AGTTTT
* *
2810845 TACTCAATTAAATTTCAAAACTTTTAGTAAAATATTTTCATTTGAGTAAGGAGTAAAAATTGAAT
192 TACTCAATTAAATTTCAAAACCTTTAGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAAT
*
2810910 AAAATTTAATCTTAAAATTTATAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAA
257 AAAATATAATCTTAAAATTTATAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAA
2810975 AATCATTATCAAATCATTTAAATTTATTATTAGTAATCATTAGTA
322 AATCATTATCAAATCATTTAAATTTATTATTAGTAATCATTAGTA
2811020 AACCATTAGT
Statistics
Matches: 330, Mismatches: 30, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
370 63 0.19
371 169 0.51
374 1 0.00
375 1 0.00
376 3 0.01
377 89 0.27
378 4 0.01
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (373 bp):
CAAATCACTAAATATTACTAATAAATAATTATTAGTAATCATTACTAAATCATATAATTACTAAA
TCATTAAATATCAAATCATTAAATATTAATAATAAATCATTAGTAGAGTACCATTTTGAGGTTAT
GTTTCCATGGTATCGGTACTGCCTTAGCAATAACAATACTACTTAGTTTAAATTGAGTTTTTACT
CAATTAAATTTCAAAACCTTTAGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAATAAAA
TATAATCTTAAAATTTATAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAAAATC
ATTATCAAATCATTTAAATTTATTATTAGTAATCATTAGTATCAAATA
Found at i:2811028 original size:11 final size:11
Alignment explanation
Indices: 2811003--2811038 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2810993 TAAATTTATT
2811003 ATTAGT-AATC
1 ATTAGTAAATC
*
2811013 ATTAGTAAACC
1 ATTAGTAAATC
2811024 ATTAGTAAATC
1 ATTAGTAAATC
2811035 ATTA
1 ATTA
2811039 AATATCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (11 bp):
ATTAGTAAATC
Found at i:2811661 original size:693 final size:697
Alignment explanation
Indices: 2810306--2811990 Score: 2507
Period size: 693 Copynumber: 2.4 Consensus size: 697
2810296 CTAATAAATC
* * * *
2810306 ATTATTAGTAATCATTACTAAATCATATCATTACTAAATCATTAATTATCAAATCATTAATTTTT
1 ATTATTAGTAATCATTAGTAAA-C----CATTAGTAAATCATTAAATATCAAATCATTAAATTTT
* *
2810371 AATAATAAATCATTAGTAGTATCGGTACTATTTTGAGGTTCTGTTTCCATGGTATCGGTATTGCC
61 AATAATAAATCATTAGTAGTATCGGTACCATTTTGAGGTT-TGTTTCCATGGTATCAGTATTGCC
2810436 TTAGCAGTATC-AGTATTACTTAGTTTAAATTGAG-TTTTTACTCGATTAAATTTCAAAACCTTT
125 TTAGCAGTATCGA-TATTACTTAGTTTAAATTGAGTTTTTTACTCGATTAAATTTCAAAACCTTT
2810499 AGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTATAAA
189 AGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTATAAA
*
2810564 AATTAATTAATAAATTTGTTTGGTATTTTAAAAAATC------A--A-AAATCATTATCAAATCT
254 AATTAATTAACAAATTTGTTTGGTA-TTTAAAAAATCAAAAATATTATAAATCATTATCAAATCT
*
2810620 TTTAAATTTATTATTAGTAATCATTAGTATCAAATACAAATCATTAAATATTTATAATAAATAAT
318 TTTAAATTTATTATTAGTAATCATTAGTATCAAACACAAATCATTAAATATTTATAATAAATAAT
* * * * *
2810685 TATTAGTAATCATTACTAAATCATATAATTTTTAAATCATTAAATATCAAATCGATAAATATTAG
383 TATTAGTAATCATTACTAAATCATATAAATATCAAATCATTAAACATCAAATCAATAAATATTAG
* *
2810750 TAATAAATCATATCAATACCATTTTGAGGTTATGTTTCCATGGTATTGGTACTGCCTTAGCAATA
448 TAAT-AATCAGAT-AATA-CATTTTGAGGTTATGTTTCCATGGTATCGGTACTGCCTTAGCAATA
* * *
2810815 ACAATACTATTTAGTTTAAATTGAATTTTTTACTCAATTAAATTTCAAAACTTTTAGTAAAATAT
510 ACAATACTACTTAGTTTAAATTGAATTTTTTACTCAATTAAATTTCAAAACCTTTAGTAAAAAAT
* * * *
2810880 TTTCATTTGAGTAAGGAGTAAAAATTGAATAAAATTTAATCTTAAAATTTATAAAAATTAATTAA
575 TTTCATTTGAGAAAGGAATAAAAATTAAATAAAATATAATCTTAAAATTTATAAAAATTAATTAA
2810945 CAAATTTATTTGGTATTTAAAAAAATAAAAAATCATTATCAAATCATT-T-AAAT-TT
640 CAAATTTATTTGGTATTTAAAAAAATAAAAAATCATTATCAAATCATTATCAAATCTT
2811000 ATTATTAGTAATCATTAGTAAACCATTAGTAAATCATTAAATATCAAATCATTAAATTTTAATAA
1 ATTATTAGTAATCATTAGTAAACCATTAGTAAATCATTAAATATCAAATCATTAAATTTTAATAA
2811065 TAAATCATTAGTAGTATCGGTACCATTTTGAGGTTATGTTTCCATGGTATCAGTATTGCCTTAGC
66 TAAATCATTAGTAGTATCGGTACCATTTTGAGGTT-TGTTTCCATGGTATCAGTATTGCCTTAGC
* *
2811130 ATTATCGATATTACTTAGTTTAAATTGAGTTTTTTTATTCGATTAAATTTCAAAACCTTTAGTAA
130 AGTATCGATATTACTTAGTTTAAATTGAG-TTTTTTACTCGATTAAATTTCAAAACCTTTAGTAA
2811195 AAAATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTATAAAAAATT
194 AAAATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTAT-AAAAATT
*
2811260 AATTAACAAATTTATTTGGTATTTAAAAAAATCAAAAATTATTATCAAATCATTATCAAATCTTT
258 AATTAACAAATTTGTTTGGTATTT-AAAAAATCAAAAA-TATTAT-AAATCATTATCAAATCTTT
*
2811325 TAAATTTATTATTAGTAATCATTAGTATCAAACCCAAATCATTAAATATTTATAATAAATAATTA
320 TAAATTTATTATTAGTAATCATTAGTATCAAACACAAATCATTAAATATTTATAATAAATAATTA
* *
2811390 TTAGTAATTATTACTAAATCAT-TAAATATCAAATCATTAAACAT-TAAT-AATAAATCATTAGT
385 TTAGTAATCATTACTAAATCATATAAATATCAAATCATTAAACATCAAATCAATAAAT-ATTAGT
* * * * * * *
2811452 AGT-ATC-GGT-AT-CATTTTGAGGTTCTGTTTCTATGG-ATCGGTACTGCCTTAGCAGTATCGA
449 AATAATCAGATAATACATTTTGAGGTTATGTTTCCATGGTATCGGTACTGCCTTAGCAATAACAA
* *
2811512 TACTACTTAGTTTAAATT-AAGTTTTTTACTCGATTAAATTTCAAATCCTTTAGTAAAAAATTTT
514 TACTACTTAGTTTAAATTGAA-TTTTTTACTCAATTAAATTTCAAAACCTTTAGTAAAAAATTTT
*
2811576 CATTTGAGAAATGAATAAAAATTAAATAAAATATAATCTTAAAATTTATAAAAATTAATTAACAA
578 CATTTGAGAAAGGAATAAAAATTAAATAAAATATAATCTTAAAATTTATAAAAATTAATTAACAA
* *
2811641 ATTTGTTTGGTATTTAAAAAAATAAAAAATTATTATCAAATCATTATCAAATCTT
643 ATTTATTTGGTATTTAAAAAAATAAAAAATCATTATCAAATCATTATCAAATCTT
* * * * ** *
2811696 -TTA-AATTTATTATTAGT-AATTATTAGT--ATC---AAAT-CCAAATCATTAAATTTTAATAA
1 ATTATTAGTAATCATTAGTAAACCATTAGTAAATCATTAAATATCAAATCATTAAATTTTAATAA
* *
2811752 TAAATCATTAGTAGTATCAGTACCATTTTGAGGTTTCGTTTCAATGGTATCAGTATTGCCTTAGC
66 TAAATCATTAGTAGTATCGGTACCATTTTGAGGTTT-GTTTCCATGGTATCAGTATTGCCTTAGC
2811817 AGTATCGATATTACTTAGTTTAAATTGAGTTTTTTACTCGATTAAATTTCAAAACCTTTAGTAAA
130 AGTATCGATATTACTTAGTTTAAATTGAGTTTTTTACTCGATTAAATTTCAAAACCTTTAGTAAA
*
2811882 AAATTTTCATTTGAGTTAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTATAAAAATTAA
195 AAATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTATAAAAATTAA
*
2811947 TTAACAAATTTGTTTGGTATTTAAAAAATAAAAAATATTATAAA
260 TTAACAAATTTGTTTGGTATTTAAAAAATCAAAAATATTATAAA
2811991 ATTAGTAGTA
Statistics
Matches: 914, Mismatches: 55, Indels: 56
0.89 0.05 0.05
Matches are distributed among these distances:
682 3 0.00
683 6 0.01
684 12 0.01
685 30 0.03
686 91 0.10
687 110 0.12
688 4 0.00
689 127 0.14
690 1 0.00
691 96 0.11
692 36 0.04
693 189 0.21
694 54 0.06
695 7 0.01
696 4 0.00
698 1 0.00
699 4 0.00
700 6 0.01
701 12 0.01
702 18 0.02
703 103 0.11
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (697 bp):
ATTATTAGTAATCATTAGTAAACCATTAGTAAATCATTAAATATCAAATCATTAAATTTTAATAA
TAAATCATTAGTAGTATCGGTACCATTTTGAGGTTTGTTTCCATGGTATCAGTATTGCCTTAGCA
GTATCGATATTACTTAGTTTAAATTGAGTTTTTTACTCGATTAAATTTCAAAACCTTTAGTAAAA
AATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTTAAAATTTATAAAAATTAAT
TAACAAATTTGTTTGGTATTTAAAAAATCAAAAATATTATAAATCATTATCAAATCTTTTAAATT
TATTATTAGTAATCATTAGTATCAAACACAAATCATTAAATATTTATAATAAATAATTATTAGTA
ATCATTACTAAATCATATAAATATCAAATCATTAAACATCAAATCAATAAATATTAGTAATAATC
AGATAATACATTTTGAGGTTATGTTTCCATGGTATCGGTACTGCCTTAGCAATAACAATACTACT
TAGTTTAAATTGAATTTTTTACTCAATTAAATTTCAAAACCTTTAGTAAAAAATTTTCATTTGAG
AAAGGAATAAAAATTAAATAAAATATAATCTTAAAATTTATAAAAATTAATTAACAAATTTATTT
GGTATTTAAAAAAATAAAAAATCATTATCAAATCATTATCAAATCTT
Found at i:2811708 original size:372 final size:375
Alignment explanation
Indices: 2810984--2811767 Score: 1227
Period size: 372 Copynumber: 2.1 Consensus size: 375
2810974 AAATCATTAT
* * * * * *
2810984 CAAATCATTTAA-ATTTATTATTAGTAATCATTAGTAAACCATTAGTAAATCATTAAATATCAAA
1 CAAATCATTAAATATTTATAATAAATAATTATTAGT-AACCATTACTAAATCATTAAATATCAAA
**
2811048 TCATTAAATTTTAATAATAAATCATTAGTAGTATCGGTACCATTTTGAGGTTATGTTTCCATGGT
65 TCATTAAACATTAATAATAAATCATTAGTAGTATCGGTACCATTTTGAGGTTATGTTTCCATGGT
* * * * *
2811113 ATCAGTATTGCCTTAGCATTATCGATATTACTTAGTTTAAATTGAGTTTTTTTATTCGATTAAAT
130 ATCAGTACTGCCTTAGCAGTATCGATACTACTTAGTTTAAATTAAGTTTTTTTACTCGATTAAAT
* * * **
2811178 TTCAAAACCTTTAGTAAAAAATTTTCATTTGAGTAAGGAGTAAAAATTGAATCGAATATAATCTT
195 TTCAAAACCTTTAGTAAAAAATTTTCATTTGAGAAAGGAATAAAAATTAAATAAAATATAATCTT
*
2811243 AAAATTTATAAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATCAAAAATTATTATCAA
260 AAAATTTATAAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAAAATTATTATCAA
2811308 ATCATTATCAAATCTTTTAAATTTATTATTAGTAATCATTAGTATCAAACC
325 ATCATTATCAAATCTTTTAAATTTATTATTAGTAATCATTAGTATCAAACC
**
2811359 CAAATCATTAAATATTTATAATAAATAATTATTAGTAATTATTACTAAATCATTAAATATCAAAT
1 CAAATCATTAAATATTTATAATAAATAATTATTAGTAACCATTACTAAATCATTAAATATCAAAT
* * *
2811424 CATTAAACATTAATAATAAATCATTAGTAGTATCGGTATCATTTTGAGGTTCTGTTTCTATGG-A
66 CATTAAACATTAATAATAAATCATTAGTAGTATCGGTACCATTTTGAGGTTATGTTTCCATGGTA
*
2811488 TCGGTACTGCCTTAGCAGTATCGATACTACTTAGTTTAAATTAAG-TTTTTTACTCGATTAAATT
131 TCAGTACTGCCTTAGCAGTATCGATACTACTTAGTTTAAATTAAGTTTTTTTACTCGATTAAATT
* *
2811552 TCAAATCCTTTAGTAAAAAATTTTCATTTGAGAAATGAATAAAAATTAAATAAAATATAATCTTA
196 TCAAAACCTTTAGTAAAAAATTTTCATTTGAGAAAGGAATAAAAATTAAATAAAATATAATCTTA
*
2811617 AAATTTAT-AAAAATTAATTAACAAATTTGTTTGGTATTTAAAAAAATAAAAAATTATTATCAAA
261 AAATTTATAAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAAAATTATTATCAAA
* *
2811681 TCATTATCAAATCTTTTAAATTTATTATTAGTAATTATTAGTATCAAATC
326 TCATTATCAAATCTTTTAAATTTATTATTAGTAATCATTAGTATCAAACC
* *
2811731 CAAATCATTAAAT-TTTAATAATAAATCATTAGTAGTA
1 CAAATCATTAAATATTT-ATAATAAATAATTATTAGTA
2811768 TCAGTACCAT
Statistics
Matches: 375, Mismatches: 32, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
371 3 0.01
372 133 0.35
373 84 0.22
374 41 0.11
375 95 0.25
376 19 0.05
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (375 bp):
CAAATCATTAAATATTTATAATAAATAATTATTAGTAACCATTACTAAATCATTAAATATCAAAT
CATTAAACATTAATAATAAATCATTAGTAGTATCGGTACCATTTTGAGGTTATGTTTCCATGGTA
TCAGTACTGCCTTAGCAGTATCGATACTACTTAGTTTAAATTAAGTTTTTTTACTCGATTAAATT
TCAAAACCTTTAGTAAAAAATTTTCATTTGAGAAAGGAATAAAAATTAAATAAAATATAATCTTA
AAATTTATAAAAAATTAATTAACAAATTTATTTGGTATTTAAAAAAATAAAAAATTATTATCAAA
TCATTATCAAATCTTTTAAATTTATTATTAGTAATCATTAGTATCAAACC
Found at i:2812108 original size:21 final size:21
Alignment explanation
Indices: 2812078--2812174 Score: 72
Period size: 21 Copynumber: 4.5 Consensus size: 21
2812068 GTATCAAATC
*
2812078 TAAATCATTAAATATTTATAA
1 TAAATCATTAAATATTCATAA
* * *
2812099 TAAATAATTATTAATAATCATTAC
1 TAAATCATTA--AATATTCA-TAA
*
2812123 TAAACCATTAAATA-TCA-AA
1 TAAATCATTAAATATTCATAA
*
2812142 TCCAAATCATTAAATATTTATAA
1 T--AAATCATTAAATATTCATAA
*
2812165 TAAATAATTA
1 TAAATCATTA
2812175 TTAGTATCAT
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.03
21 32 0.54
22 6 0.10
23 9 0.15
24 10 0.17
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATCATTAAATATTCATAA
Found at i:2812110 original size:66 final size:66
Alignment explanation
Indices: 2812052--2812177 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
2812042 ATTATTAGTA
* * * *
2812052 CATTAGTAAATCATT-AGTATCAAATCTAAATCATTAAATATTTATAATAAATAATTATTAATAA
1 CATTACTAAACCATTAAATATCAAATCCAAATCATTAAATATTTATAATAAATAATTATTAATAA
2812116 T
66 T
2812117 CATTACTAAACCATTAAATATCAAATCCAAATCATTAAATATTTATAATAAATAATTATTA
1 CATTACTAAACCATTAAATATCAAATCCAAATCATTAAATATTTATAATAAATAATTATTA
2812178 GTATCATCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
65 13 0.23
66 43 0.77
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (66 bp):
CATTACTAAACCATTAAATATCAAATCCAAATCATTAAATATTTATAATAAATAATTATTAATAA
T
Found at i:2815136 original size:34 final size:36
Alignment explanation
Indices: 2815056--2815142 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
2815046 CAAAATGATC
* * *
2815056 ATTTCCAATACTAGTGGAATAACCTAATTTGAGTAT
1 ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
*
2815092 ATTTCAAATACTAGTGGGATAACCTAA-CT-AGCAT
1 ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
*
2815126 ATTTCTAATACTAGTGG
1 ATTTCAAATACTAGTGG
2815143 TATGGCCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 20 0.43
35 1 0.02
36 25 0.54
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (36 bp):
ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
Found at i:2819090 original size:22 final size:23
Alignment explanation
Indices: 2819065--2819109 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2819055 AAACACTAAC
2819065 ATTTATATAGCTAT-TAACAAAT
1 ATTTATATAGCTATATAACAAAT
*
2819087 ATTTATATAGCTATATAATAAAT
1 ATTTATATAGCTATATAACAAAT
2819110 CGTTTAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (23 bp):
ATTTATATAGCTATATAACAAAT
Found at i:2820283 original size:36 final size:33
Alignment explanation
Indices: 2820225--2820312 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 33
2820215 GGCAAAATGG
* *
2820225 TCAT-TTTCAATAC-AGTAGAATAACCTAATTTGA
1 TCATATTTCAATACTAGTGGAATAACCTAA-CT-A
2820258 GT-ATATTTCAAATACTAGTGGAATAACCTAACTA
1 -TCATATTTC-AATACTAGTGGAATAACCTAACTA
2820292 TCATATTTCTAATACTAGTGG
1 TCATATTTC-AATACTAGTGG
2820313 TATGGCCTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
33 3 0.06
34 24 0.51
35 6 0.13
36 14 0.30
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (33 bp):
TCATATTTCAATACTAGTGGAATAACCTAACTA
Found at i:2825114 original size:128 final size:128
Alignment explanation
Indices: 2824886--2825141 Score: 494
Period size: 128 Copynumber: 2.0 Consensus size: 128
2824876 CGGGTGGAGG
*
2824886 GTATATATTTTTTGGGTTAGGTCCGGTGAAGGATATAAAATTTTCAGATCGAATCAGGTTGGCCA
1 GTATATATTTTTTGGGTTAGGTCCGATGAAGGATATAAAATTTTCAGATCGAATCAGGTTGGCCA
2824951 AAACCCGACACAAACCTGACTCATGCCCATCCCTATTCTAAATCCCACCAATTTCTACACCTA
66 AAACCCGACACAAACCTGACTCATGCCCATCCCTATTCTAAATCCCACCAATTTCTACACCTA
*
2825014 GTATATATTTTTTGGGTTAGGTCCGATGAAGGATATAAAATTTTCAGGTCGAATCAGGTTGGCCA
1 GTATATATTTTTTGGGTTAGGTCCGATGAAGGATATAAAATTTTCAGATCGAATCAGGTTGGCCA
2825079 AAACCCGACACAAACCTGACTCATGCCCATCCCTATTCTAAATCCCACCAATTTCTACACCTA
66 AAACCCGACACAAACCTGACTCATGCCCATCCCTATTCTAAATCCCACCAATTTCTACACCTA
2825142 CCTTCATTTG
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 126 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (128 bp):
GTATATATTTTTTGGGTTAGGTCCGATGAAGGATATAAAATTTTCAGATCGAATCAGGTTGGCCA
AAACCCGACACAAACCTGACTCATGCCCATCCCTATTCTAAATCCCACCAATTTCTACACCTA
Found at i:2828417 original size:82 final size:82
Alignment explanation
Indices: 2828265--2828418 Score: 186
Period size: 82 Copynumber: 1.9 Consensus size: 82
2828255 CGAGTTTGAA
* * * * * * * *
2828265 TTCGAGCTTCAATTAAACTATGTTTGAGAAATGTTTTGAGTACAAGTTTTTTCGAGCTCGAGTTT
1 TTCGAGCTTCAATCAAACTATGTTTGAGAAATATTTCGAATACAAATTTTTTCAAACTCGAGTCT
2828330 CAATTTTTTATTACGAG
66 CAATTTTTTATTACGAG
* *
2828347 TTCGAGCTTCAATCAAAGCTATGTTTGA-TAATATTTCGAATTCAAATTTTTTCAAACTCGAG-C
1 TTCGAGCTTCAATCAAA-CTATGTTTGAGAAATATTTCGAATACAAATTTTTTCAAACTCGAGTC
*
2828410 TCAAATTTT
65 TCAATTTTT
2828419 AAATGTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
81 8 0.13
82 42 0.70
83 10 0.17
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (82 bp):
TTCGAGCTTCAATCAAACTATGTTTGAGAAATATTTCGAATACAAATTTTTTCAAACTCGAGTCT
CAATTTTTTATTACGAG
Found at i:2830108 original size:2 final size:2
Alignment explanation
Indices: 2830101--2830126 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2830091 TTAACATGCA
2830101 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
2830127 GCTTTTGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2830521 original size:29 final size:29
Alignment explanation
Indices: 2830489--2830577 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
2830479 ATAATCAAGT
2830489 GACTATTTTATAACTTTTAATAGTCGGAG
1 GACTATTTTATAACTTTTAATAGTCGGAG
**** * *
2830518 GACTAAAAAAAGTAACGTCTT-ATAGTTAGGA-
1 GACT-ATTTTA-TAAC-TTTTAATAG-TCGGAG
2830549 GACTATTTTATAACTTTTAATAGTCGGAG
1 GACTATTTTATAACTTTTAATAGTCGGAG
2830578 ACTTAATAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
28 7 0.17
29 12 0.29
30 4 0.10
31 12 0.29
32 7 0.17
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (29 bp):
GACTATTTTATAACTTTTAATAGTCGGAG
Found at i:2830785 original size:42 final size:42
Alignment explanation
Indices: 2830726--2830811 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
2830716 ATTTGCTCCC
*
2830726 TTAAGGGATTAATGCATCCATCCCTGCTCTTTATAAGGTGTA
1 TTAAGGGATTAATGCATCCATCCCTGCTCTTTATAAGGTATA
*
2830768 TTAAGGGTTTAATGCATCCATCCCTGCTCTTTATAAGGTATA
1 TTAAGGGATTAATGCATCCATCCCTGCTCTTTATAAGGTATA
2830810 TT
1 TT
2830812 TATGGATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (42 bp):
TTAAGGGATTAATGCATCCATCCCTGCTCTTTATAAGGTATA
Found at i:2831347 original size:13 final size:13
Alignment explanation
Indices: 2831331--2831361 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2831321 TTACAACAAC
2831331 AGAGAAGATAGGA
1 AGAGAAGATAGGA
2831344 AGAGAAGATAGGA
1 AGAGAAGATAGGA
2831357 A-AGAA
1 AGAGAA
2831362 TAATAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.06
Consensus pattern (13 bp):
AGAGAAGATAGGA
Found at i:2832254 original size:24 final size:23
Alignment explanation
Indices: 2832223--2832275 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
2832213 AGTTTTCACC
2832223 TTCCTTT-ATCTACTTTTATTTTAT
1 TTCCTTTAATCTACTTTT-TTTT-T
*
2832247 TTCCTTTAAATCTTCTTTTTTTTT
1 TTCCTTT-AATCTACTTTTTTTTT
2832271 TTCCT
1 TTCCT
2832276 GGTTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 13 0.50
25 4 0.15
26 9 0.35
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (23 bp):
TTCCTTTAATCTACTTTTTTTTT
Found at i:2834111 original size:19 final size:19
Alignment explanation
Indices: 2834087--2834127 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2834077 AAAAATTATT
*
2834087 TATATTTGGA-TTCTAAAGG
1 TATATTT-GACTTATAAAGG
2834106 TATATTTGACTTATAAAGG
1 TATATTTGACTTATAAAGG
2834125 TAT
1 TAT
2834128 TGAATAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (19 bp):
TATATTTGACTTATAAAGG
Found at i:2834169 original size:21 final size:19
Alignment explanation
Indices: 2834141--2834181 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2834131 ATAAGATGTT
2834141 AGAAGTGTTAGAAAGGATTG
1 AGAAGTGTTAG-AAGGATTG
*
2834161 AGAACGTGTTTGAAGGATTG
1 AGAA-GTGTTAGAAGGATTG
2834181 A
1 A
2834182 AATGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.02, G:0.34, T:0.27
Consensus pattern (19 bp):
AGAAGTGTTAGAAGGATTG
Found at i:2835854 original size:453 final size:453
Alignment explanation
Indices: 2835008--2835857 Score: 1396
Period size: 453 Copynumber: 1.9 Consensus size: 453
2834998 TGATTTCATT
*
2835008 TTGATAGGATCGAGTCATTCATTTTTCAAACAACTTCTCAGTGGGTTACCCATCCTTGGATTACT
1 TTGATAGGATCGAGTCATTCATTTTTCAAACAACTTCTCAGTGGGTCACCCATCCTTGGATTACT
*
2835073 CTGGTTCAAGCACGCTTAACTACAGAGTTCTGAAGCGAATGGTCACCATTTCATCTTAAAACCAA
66 CTGGTTCAAGCACGCTTAACTACAGAGTTCTGAAGCGAATGATCACCATTTCATCTTAAAACCAA
* *
2835138 TTGGTGATAAGTAGGTGAGCCATTTTAACCTCATATCTTTATAGCGGGTGATCACTGGTTTCCCC
131 TTAGTGATAAGTAGGTGAGCCATTTTAACCTCATATCTTTATAGCAGGTGATCACTGGTTTCCCC
** *
2835203 CAAGCCAAGGTGGATTATTGTGGGGGCACCCCCCACAGTTCACCACGGCATTGTAGAGCCTCGCA
196 CAAGCCAAGGTGGATTATTGTGGGGGCACCCCCCACAGTTCACCACGGCATTACAGAGCCCCGCA
* *
2835268 TCTATAGCGTGCTGCAGGCTGGCCTAGGGGCTTCGCAAGGCACTCGTGAGCCTCGGCAGGTTGCG
261 TCTATAGCGTGCTACAGGCTGGCCTAGGGGCTTCGCAAGGCACACGTGAGCCTCGGCAGGTTGCG
* * * * *
2835333 CTATCACGCACCTGATATCACACTCATACATGATAGAATCCCTAAGGGTGATCGTTGGACCCCAT
326 CTATCACACACCTGATATCACACCCATACACGATAAAATCCCTAAGGGTGATCGCTGGACCCCAT
2835398 AACCCAATAATCACCCCCAACGACACCTGGGGGATTCGAACATGCAACATGTTCTGATACCAC
391 AACCCAATAATCACCCCCAACGACACCTGGGGGATTCGAACATGCAACATGTTCTGATACCAC
* ** *
2835461 TTGATAGGGTCGAGTCATTCATTTTTTGAACAACTTCTCAGTGGGTCACTCATCCTTGGATTACT
1 TTGATAGGATCGAGTCATTCATTTTTCAAACAACTTCTCAGTGGGTCACCCATCCTTGGATTACT
*
2835526 CTGGTTCAAGCACGCTTAACTACAGAGTTCTGAAGCGAATGATCACCA-TTCTTTCTTAAAACCA
66 CTGGTTCAAGCACGCTTAACTACAGAGTTCTGAAGCGAATGATCACCATTTC-ATCTTAAAACCA
* * *
2835590 ATTAGTGATAAGTAGGTGGGCCATTTTAATCTCATATCTTTGTAGCAGGTGATCACTGGTTTCCC
130 ATTAGTGATAAGTAGGTGAGCCATTTTAACCTCATATCTTTATAGCAGGTGATCACTGGTTTCCC
* **
2835655 CCAAGCCAAGGTGGATTCTTGTGGGGGCACCCCCCACAGTTCACCATTGCATTACAGAGCCCCGC
195 CCAAGCCAAGGTGGATTATTGTGGGGGCACCCCCCACAGTTCACCACGGCATTACAGAGCCCCGC
* * *
2835720 ATCTATAGCGTGCTACAGGCTGGCCTAGGGGCTTCGCAAGGCACACTTGGGCCTCGGCAGGTTGG
260 ATCTATAGCGTGCTACAGGCTGGCCTAGGGGCTTCGCAAGGCACACGTGAGCCTCGGCAGGTTGC
* * **
2835785 GCTGTTACACACCTGATATCGTACCCATACACGATAAAATCCCTAAGGGTGATCGCTGGACCCCA
325 GCTATCACACACCTGATATCACACCCATACACGATAAAATCCCTAAGGGTGATCGCTGGACCCCA
2835850 TAACCCAA
390 TAACCCAA
2835858 CACATCTGAG
Statistics
Matches: 364, Mismatches: 32, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
452 3 0.01
453 361 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (453 bp):
TTGATAGGATCGAGTCATTCATTTTTCAAACAACTTCTCAGTGGGTCACCCATCCTTGGATTACT
CTGGTTCAAGCACGCTTAACTACAGAGTTCTGAAGCGAATGATCACCATTTCATCTTAAAACCAA
TTAGTGATAAGTAGGTGAGCCATTTTAACCTCATATCTTTATAGCAGGTGATCACTGGTTTCCCC
CAAGCCAAGGTGGATTATTGTGGGGGCACCCCCCACAGTTCACCACGGCATTACAGAGCCCCGCA
TCTATAGCGTGCTACAGGCTGGCCTAGGGGCTTCGCAAGGCACACGTGAGCCTCGGCAGGTTGCG
CTATCACACACCTGATATCACACCCATACACGATAAAATCCCTAAGGGTGATCGCTGGACCCCAT
AACCCAATAATCACCCCCAACGACACCTGGGGGATTCGAACATGCAACATGTTCTGATACCAC
Found at i:2835895 original size:15 final size:15
Alignment explanation
Indices: 2835869--2835925 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
2835859 ACATCTGAGT
*
2835869 ATATGTTATATGTG-
1 ATATGTTCTATGTGA
2835883 ATAATGTTCTATGTGA
1 AT-ATGTTCTATGTGA
* *
2835899 ATATGTGCTAAGTGA
1 ATATGTTCTATGTGA
2835914 ATATGTTCTATG
1 ATATGTTCTATG
2835926 GGATATATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
14 2 0.06
15 32 0.89
16 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (15 bp):
ATATGTTCTATGTGA
Found at i:2836137 original size:24 final size:24
Alignment explanation
Indices: 2836088--2836152 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
2836078 CTACGTGGTC
* *
2836088 CTTCGG-GACAAA-TCTATGTGGCA
1 CTTCGGTG-CAAATTCTATATGGAA
*
2836111 CTTCGGTGCATATTCTATATGGAA
1 CTTCGGTGCAAATTCTATATGGAA
*
2836135 CTTTGGTGCAAATTCTAT
1 CTTCGGTGCAAATTCTAT
2836153 GTGGCAGTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 9 0.26
24 26 0.74
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTATATGGAA
Found at i:2837732 original size:12 final size:12
Alignment explanation
Indices: 2837717--2837746 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2837707 TTATATAACC
2837717 GACATGGAAACT
1 GACATGGAAACT
2837729 GACATGGAAACT
1 GACATGGAAACT
2837741 GACATG
1 GACATG
2837747 ATGAATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.17
Consensus pattern (12 bp):
GACATGGAAACT
Found at i:2841963 original size:12 final size:12
Alignment explanation
Indices: 2841946--2841970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2841936 AGGCTGGAAT
2841946 AGTAGGCATGAA
1 AGTAGGCATGAA
2841958 AGTAGGCATGAA
1 AGTAGGCATGAA
2841970 A
1 A
2841971 TGCTGATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
AGTAGGCATGAA
Found at i:2842249 original size:9 final size:9
Alignment explanation
Indices: 2842235--2842264 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2842225 TAATAAAACA
2842235 TTTCTTTCT
1 TTTCTTTCT
2842244 TTTCTTTCTT
1 TTTCTTTC-T
2842254 TTTCTTTCT
1 TTTCTTTCT
2842263 TT
1 TT
2842265 GTTATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:2843038 original size:21 final size:20
Alignment explanation
Indices: 2842998--2843039 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2842988 TTTGATCGAC
*
2842998 ATTTACTTTTCTTATATTAT
1 ATTTAATTTTCTTATATTAT
*
2843018 ATTTAATTTTCTT-TATTTT
1 ATTTAATTTTCTTATATTAT
2843037 ATT
1 ATT
2843040 CTAGAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTAATTTTCTTATATTAT
Found at i:2843272 original size:23 final size:23
Alignment explanation
Indices: 2843227--2843272 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2843217 AGATTACTTA
* * * *
2843227 TTTATACAACTTTTTAGAGTTAT
1 TTTATAAAACTTTTAACAATTAT
2843250 TTTATAAAACTTTTAACAATTAT
1 TTTATAAAACTTTTAACAATTAT
2843273 ATTTTTGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTATAAAACTTTTAACAATTAT
Found at i:2845449 original size:35 final size:35
Alignment explanation
Indices: 2845403--2845473 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2845393 TTTTTTTCAC
2845403 ATAGTCAAATTAAATTAGTAGATGTAGGGGAATAG
1 ATAGTCAAATTAAATTAGTAGATGTAGGGGAATAG
2845438 ATAGTCAAATTAAATTAGTAGATGTAGGGGAATAG
1 ATAGTCAAATTAAATTAGTAGATGTAGGGGAATAG
2845473 A
1 A
2845474 AGAGTAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (35 bp):
ATAGTCAAATTAAATTAGTAGATGTAGGGGAATAG
Found at i:2867111 original size:2 final size:2
Alignment explanation
Indices: 2867104--2867140 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2867094 AACAAAAATA
2867104 AT AT AT AT 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 AT AT AT AT A
2867141 CATACATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2868444 original size:43 final size:43
Alignment explanation
Indices: 2868396--2868515 Score: 213
Period size: 43 Copynumber: 2.8 Consensus size: 43
2868386 TTTCAAGCCA
*
2868396 GATTTCAACTCCACGATGAAGGATATCGTGCCCACAAATCCAC
1 GATTTCAACTCCACGACGAAGGATATCGTGCCCACAAATCCAC
*
2868439 GATTTCAACTCCACGACGGAGGATATCGTGCCCACAAATCCAC
1 GATTTCAACTCCACGACGAAGGATATCGTGCCCACAAATCCAC
*
2868482 GATTTCAACTTCACGACGAAGGATATCGTGCCCA
1 GATTTCAACTCCACGACGAAGGATATCGTGCCCA
2868516 TGTACACAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
GATTTCAACTCCACGACGAAGGATATCGTGCCCACAAATCCAC
Found at i:2869035 original size:80 final size:79
Alignment explanation
Indices: 2868805--2869048 Score: 308
Period size: 80 Copynumber: 3.0 Consensus size: 79
2868795 GATGTCATTG
* * * * * * *
2868805 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAACATAACTCAAGGCTAG
1 AAGACCTTCGAGTTCGATTACACTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGGCAAG
* *
2868870 AAGGGTTATTTGCCAATAA
65 AAAGGTTATATGCC----A
*
2868889 AAGACCTTCGAGTTCGATTACTCTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAGA
2868954 AAGGTTATATGCCA
66 AAGGTTATATGCCA
* *
2868968 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGATTACACTCAGCTC-AAGGCACATCATTTGCAGCATAGCTTAAGGCAAG
* *
2869033 AAAGGTTGTCTGCCA
65 AAAGGTTATATGCCA
2869048 A
1 A
2869049 CCAAAGACCT
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 30 0.21
80 46 0.32
83 42 0.29
84 27 0.19
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (79 bp):
AAGACCTTCGAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAGA
AAGGTTATATGCCA
Found at i:2869229 original size:83 final size:83
Alignment explanation
Indices: 2869063--2869297 Score: 341
Period size: 83 Copynumber: 2.8 Consensus size: 83
2869053 AGACCTTTCG
* * *
2869063 AGGCACATCATTTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAGT--AA-ACCTTCGAG
1 AGGCACATCA-TTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTC-GTCAAAGACCTTCGAG
*
2869125 TTCGATTACACTCAGCTCAA
64 TTCGATTACACTAAGCTCAA
* *
2869145 AGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
1 AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCGTCAAAGACCTTCGAGTT
2869210 CGATTACACTAAGCTCAA
66 CGATTACACTAAGCTCAA
* * * *
2869228 AGGCACATCATTTACAGCGTAACTCAAGGCGAGAAGGAATATTTGTCATCAAAGACCTTCGAGTT
1 AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCGTCAAAGACCTTCGAGTT
2869293 CGATT
66 CGATT
2869298 GCATTCAACT
Statistics
Matches: 139, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.01
81 33 0.24
82 12 0.09
83 92 0.66
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (83 bp):
AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCGTCAAAGACCTTCGAGTT
CGATTACACTAAGCTCAA
Found at i:2869310 original size:83 final size:83
Alignment explanation
Indices: 2869063--2869345 Score: 340
Period size: 83 Copynumber: 3.4 Consensus size: 83
2869053 AGACCTTTCG
* * *
2869063 AGGCACATCATTTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAGT--AA-ACCTTCGAG
1 AGGCACATCA-TTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCA-TCAAAGACCTTCGAG
*
2869125 TTCGATTACACTCAGCTCAA
64 TTCGATTACACTCAACTCAA
* * *
2869145 AGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
1 AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCATCAAAGACCTTCGAGTT
2869210 CGATTACACT-AAGCTCAA
66 CGATTACACTCAA-CTCAA
* * *
2869228 AGGCACATCATTTACAGCGTAACTCAAGGCGAGAAGGAATATTTGTCATCAAAGACCTTCGAGTT
1 AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCATCAAAGACCTTCGAGTT
* *
2869293 CGATTGCATTCAACTCAA
66 CGATTACACTCAACTCAA
* * * * *
2869311 AGGAAAATCAAATTTAAAACATAACTCAAGCCGAG
1 AGGCACATC--ATTTACAGCATAACTCAAGGCGAG
2869346 GTTTTTAACT
Statistics
Matches: 174, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
80 1 0.01
81 33 0.19
82 13 0.07
83 105 0.60
84 2 0.01
85 20 0.11
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (83 bp):
AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGATATCTGTCATCAAAGACCTTCGAGTT
CGATTACACTCAACTCAA
Found at i:2869523 original size:26 final size:26
Alignment explanation
Indices: 2869494--2869554 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
2869484 AAATTTTTAA
2869494 ACCAAGG-TCTTTAAATCAAGAAGAAG
1 ACCAAGGCT-TTTAAATCAAGAAGAAG
2869520 ACCAAGGCTTTTAAATCAAGAAGAAG
1 ACCAAGGCTTTTAAATCAAGAAGAAG
2869546 ACCAAGGCT
1 ACCAAGGCT
2869555 CAATTCCAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 33 0.97
27 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (26 bp):
ACCAAGGCTTTTAAATCAAGAAGAAG
Found at i:2871056 original size:6 final size:6
Alignment explanation
Indices: 2871045--2871072 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2871035 ATGATTGAAC
2871045 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
2871073 TTGCAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:2876202 original size:24 final size:24
Alignment explanation
Indices: 2876165--2876223 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2876155 ATTTTTGTCT
*
2876165 TTGTGACACATTTTT-CTCTGCTC
1 TTGTGACACTTTTTTCCTCTGCTC
* *
2876188 TTGTGACACTTTTTTCCTTTGCTT
1 TTGTGACACTTTTTTCCTCTGCTC
*
2876212 TTGTGGCACTTT
1 TTGTGACACTTT
2876224 CTTATGGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.10, C:0.22, G:0.15, T:0.53
Consensus pattern (24 bp):
TTGTGACACTTTTTTCCTCTGCTC
Found at i:2877095 original size:19 final size:19
Alignment explanation
Indices: 2877052--2877104 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2877042 AAATAACCAA
* *
2877052 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACACGAACT
*
2877071 CAAATTCGCAATACGAACT
1 CAAATTCGCAACACGAACT
*
2877090 CCAATTTCGCAACAC
1 -CAAATTCGCAACAC
2877105 AGTTTCCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:2877143 original size:20 final size:20
Alignment explanation
Indices: 2877089--2877143 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2877079 CAATACGAAC
* *
2877089 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACTCAGTT
2877109 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACTCAGTT
**
2877129 TTGAAATTCGCAACT
1 TCCAAATTCGCAACT
2877144 TGAATTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (20 bp):
TCCAAATTCGCAACTCAGTT
Found at i:2877253 original size:26 final size:26
Alignment explanation
Indices: 2877215--2877264 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2877205 CACGTTTATT
* * * *
2877215 TTCGCAACGCGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
2877241 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
2877265 CAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:2877383 original size:21 final size:22
Alignment explanation
Indices: 2877359--2877408 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2877349 TCACTCTCTA
* *
2877359 CGGCGACAT-TGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
2877380 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
2877402 CGGCGAC
1 CGGCGAC
2877409 CCCCCTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:2877774 original size:20 final size:20
Alignment explanation
Indices: 2877751--2877789 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2877741 TTTGAAACTT
2877751 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
2877771 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
2877790 CGCAACGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:2879434 original size:18 final size:18
Alignment explanation
Indices: 2879407--2879446 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2879397 ACTTCGACAC
*
2879407 CGAGATCTATCACCTGAT
1 CGAGAGCTATCACCTGAT
2879425 CGAGAGCTATCACCTGAT
1 CGAGAGCTATCACCTGAT
2879443 CGAG
1 CGAG
2879447 CCAATTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.23
Consensus pattern (18 bp):
CGAGAGCTATCACCTGAT
Found at i:2879620 original size:21 final size:21
Alignment explanation
Indices: 2879596--2879645 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2879586 GTTAGGGGAG
2879596 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTGCT
*
2879617 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCAGTGCT
2879638 TTACGTGA
1 TTACGTGA
2879646 CGACAATGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTGCT
Found at i:2879762 original size:21 final size:21
Alignment explanation
Indices: 2879596--2879771 Score: 83
Period size: 21 Copynumber: 8.4 Consensus size: 21
2879586 GTTAGGGGAG
2879596 TTACGTGATGAGGTCAG-TGCT
1 TTACGTGATGAGGT-AGCTGCT
* *
2879617 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTAGCTGCT
* ** ** *
2879638 TTACGTGACGA-CAATGGGGCA
1 TTACGTGATGAGGTA-GCTGCT
** * *
2879659 TGGCGTAATGAGGTAG-GGTCT
1 TTACGTGATGAGGTAGCTG-CT
* **
2879680 TTACGTGGTGAGGTAGCTATT
1 TTACGTGATGAGGTAGCTGCT
* * *
2879701 TTAAGTGATGA--TAATGGTTCT
1 TTACGTGATGAGGT-A-GCTGCT
* *
2879722 TTACGTGGTGAGGTATCTGCT
1 TTACGTGATGAGGTAGCTGCT
2879743 TTACGTGATGAGGTAGCTGCT
1 TTACGTGATGAGGTAGCTGCT
*
2879764 CTACGTGA
1 TTACGTGA
2879772 GATTGTTTCA
Statistics
Matches: 112, Mismatches: 34, Indels: 18
0.68 0.21 0.11
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 104 0.93
22 2 0.02
23 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.33
Consensus pattern (21 bp):
TTACGTGATGAGGTAGCTGCT
Found at i:2880077 original size:21 final size:21
Alignment explanation
Indices: 2880051--2880159 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 21
2880041 GAAGAAGCTC
* *
2880051 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* *
2880072 GATCCACCTCCCATTGTTCAT
1 GATCCACCTCCCATCGTTCAG
* ** *
2880093 GATTCACCTGTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
2880114 GAGGCC-CCTCTCATCGTTCAG
1 GA-TCCACCTCCCATCGTTCAG
*
2880135 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATCGTTCAG
2880156 GATC
1 GATC
2880160 AACATGCCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 2 0.03
21 69 0.96
22 1 0.01
ACGTcount: A:0.20, C:0.37, G:0.16, T:0.28
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:2889815 original size:20 final size:20
Alignment explanation
Indices: 2889786--2889824 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2889776 AAAGCTCATA
*
2889786 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
2889806 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
2889825 GTGGTGGAAT
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:2892372 original size:18 final size:18
Alignment explanation
Indices: 2892349--2892384 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2892339 AAGGCGGTTG
*
2892349 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2892367 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2892385 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2894380 original size:9 final size:9
Alignment explanation
Indices: 2894368--2894396 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2894358 CGGGGACTTC
2894368 TTCTTCTTT
1 TTCTTCTTT
2894377 TTCTTCTTT
1 TTCTTCTTT
2894386 TTCTTCTTT
1 TTCTTCTTT
2894395 TT
1 TT
2894397 TAGGGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:2895593 original size:20 final size:20
Alignment explanation
Indices: 2895547--2895714 Score: 89
Period size: 20 Copynumber: 8.5 Consensus size: 20
2895537 AAAACATTTA
* *
2895547 TGTTGCGAAAATAAAAGT--
1 TGTTGCGAAATTAAAATTCG
*
2895565 TGTTACGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
**
2895585 TGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* *
2895605 TGTTGCG-AATTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
** *
2895625 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
* *
2895645 TGTTGCGAATTTAAAAATCG
1 TGTTGCGAAATTAAAATTCG
* * *
2895665 CGTTGCTAAA-CAGAAATTCG
1 TGTTGCGAAATTA-AAATTCG
*
2895685 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
*
2895705 AGTTGCGAAA
1 TGTTGCGAAA
2895715 AAGAAATTTG
Statistics
Matches: 112, Mismatches: 28, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
18 15 0.13
19 12 0.11
20 72 0.64
21 10 0.09
22 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:2895633 original size:40 final size:39
Alignment explanation
Indices: 2895547--2895741 Score: 150
Period size: 40 Copynumber: 4.9 Consensus size: 39
2895537 AAAACATTTA
* * * *
2895547 TGTTGCGAAAATAAAAGT-TGTTACGAAATTA-AAATTCG
1 TGTTGCGAAAACAAAATTGTGTTGCG-AATTAGAAAATCG
*
2895585 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCT
1 TGTTGCGAAAACAAAATT-GTGTTGCGAATTAGAAAATCG
* *
2895625 TGTTGCGAAAAGGAAACTTGTGTTGCGAATTTA-AAAATCG
1 TGTTGCGAAAA-CAAAATTGTGTTGCGAA-TTAGAAAATCG
* * *
2895665 CGTTGC-TAAACAGAAATTCGCGTTGCGAATTCAG-AAATCG
1 TGTTGCGAAAACA-AAATT-GTGTTGCGAATT-AGAAAATCG
* *
2895705 AGTTGCGAAAA-AGAAATTTGCGTTGCGAATTCAGAAA
1 TGTTGCGAAAACA-AAA-TTGTGTTGCGAATT-AGAAA
2895742 TTGAGTTACG
Statistics
Matches: 130, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
38 17 0.13
39 14 0.11
40 84 0.65
41 15 0.12
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (39 bp):
TGTTGCGAAAACAAAATTGTGTTGCGAATTAGAAAATCG
Found at i:2895682 original size:80 final size:80
Alignment explanation
Indices: 2895565--2895735 Score: 211
Period size: 80 Copynumber: 2.1 Consensus size: 80
2895555 AAATAAAAGT
* * * * * **
2895565 TGTTACGAAATTAAAATTCGTGTTGCGAAAACAAAATTCGTGTTGCGAATT-AGAAAATCTTGTT
1 TGTTGCGAATTTAAAAATCGCGTTGCGAAAACAAAATTCGCGTTGCGAATTCAG-AAATCGAGTT
*
2895629 GCGAAAAGGAAACTTG
65 GCGAAAAAGAAACTTG
*
2895645 TGTTGCGAATTTAAAAATCGCGTTGC-TAAACAGAAATTCGCGTTGCGAATTCAGAAATCGAGTT
1 TGTTGCGAATTTAAAAATCGCGTTGCGAAAACA-AAATTCGCGTTGCGAATTCAGAAATCGAGTT
*
2895709 GCGAAAAAGAAATTTG
65 GCGAAAAAGAAACTTG
*
2895725 CGTTGCGAATT
1 TGTTGCGAATT
2895736 CAGAAATTGA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 5 0.06
80 71 0.91
81 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (80 bp):
TGTTGCGAATTTAAAAATCGCGTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGAGTTG
CGAAAAAGAAACTTG
Found at i:2895729 original size:20 final size:20
Alignment explanation
Indices: 2895578--2895743 Score: 90
Period size: 20 Copynumber: 8.2 Consensus size: 20
2895568 TACGAAATTA
*
2895578 AAATTCGTGTTGCGAAAACA-
1 AAATTCGCGTTGCG-AAACAG
* **
2895598 AAATTCGTGTTGCGAATTAG
1 AAATTCGCGTTGCGAAACAG
* **
2895618 AAAATCTTGTTGCGAAA-AGG
1 AAATTCGCGTTGCGAAACA-G
* **
2895638 AAACTT-GTGTTGCGAATTTA-
1 AAA-TTCGCGTTGCGAA-ACAG
* *
2895658 AAAATCGCGTTGCTAAACAG
1 AAATTCGCGTTGCGAAACAG
*
2895678 AAATTCGCGTTGCGAATTCAG
1 AAATTCGCGTTGCGAA-ACAG
* *
2895699 AAA-TCGAGTTGCGAAAAAG
1 AAATTCGCGTTGCGAAACAG
* *
2895718 AAATTTGCGTTGCGAATTCAG
1 AAATTCGCGTTGCGAA-ACAG
2895739 AAATT
1 AAATT
2895744 GAGTTACGAA
Statistics
Matches: 113, Mismatches: 23, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
19 11 0.10
20 87 0.77
21 14 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (20 bp):
AAATTCGCGTTGCGAAACAG
Found at i:2895742 original size:40 final size:40
Alignment explanation
Indices: 2895586--2895753 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
2895576 TAAAATTCGT
* **
2895586 GTTGCGAAAACA-AAATTCGTGTTGCGAATT-AGAAAATCTT
1 GTTGCGAAAA-AGAAATTCGCGTTGCGAATTCAG-AAATCGA
* * * * *
2895626 GTTGCGAAAAGGAAACTT-GTGTTGCGAATTTAAAAATCGC
1 GTTGCGAAAAAGAAA-TTCGCGTTGCGAATTCAGAAATCGA
* *
2895666 GTTGCTAAACAGAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCGA
* *
2895706 GTTGCGAAAAAGAAATTTGCGTTGCGAATTCAGAAATTGA
1 GTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCGA
*
2895746 GTTACGAA
1 GTTGCGAA
2895754 TTTGAAATTC
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 103 0.95
41 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (40 bp):
GTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCGA
Found at i:2895755 original size:20 final size:20
Alignment explanation
Indices: 2895675--2895755 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
2895665 CGTTGCTAAA
*
2895675 CAGAAATTCGCGTTGCGAATT
1 CAGAAATT-GAGTTGCGAATT
* *
2895696 CAGAAATCGAGTTGCGAA-A
1 CAGAAATTGAGTTGCGAATT
* *
2895715 AAGAAATTTGCGTTGCGAATT
1 CAGAAA-TTGAGTTGCGAATT
*
2895736 CAGAAATTGAGTTACGAATT
1 CAGAAATTGAGTTGCGAATT
2895756 TGAAATTCCG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.10
20 31 0.65
21 12 0.25
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (20 bp):
CAGAAATTGAGTTGCGAATT
Found at i:2895763 original size:80 final size:80
Alignment explanation
Indices: 2895593--2895753 Score: 191
Period size: 80 Copynumber: 2.0 Consensus size: 80
2895583 CGTGTTGCGA
* ** * * *
2895593 AAACA-AAATTCGTGTTGCGAATTAGAAAATCTTGTTGCGAAAAGGAAACTTGTGTTGCGAATTT
1 AAACAGAAATTCGCGTTGCGAATTAGAAAATCGAGTTGCGAAAAAGAAACTTGCGTTGCGAATTC
* * *
2895657 AAAAATCGCGTTGCT
66 AAAAATCGAGTTACG
*
2895672 AAACAGAAATTCGCGTTGCGAATTCAG-AAATCGAGTTGCGAAAAAGAAATTTGCGTTGCGAATT
1 AAACAGAAATTCGCGTTGCGAATT-AGAAAATCGAGTTGCGAAAAAGAAACTTGCGTTGCGAATT
* *
2895736 CAGAAATTGAGTTACG
65 CAAAAATCGAGTTACG
2895752 AA
1 AA
2895754 TTTGAAATTC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
79 5 0.07
80 61 0.90
81 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (80 bp):
AAACAGAAATTCGCGTTGCGAATTAGAAAATCGAGTTGCGAAAAAGAAACTTGCGTTGCGAATTC
AAAAATCGAGTTACG
Found at i:2895825 original size:20 final size:20
Alignment explanation
Indices: 2895802--2895910 Score: 78
Period size: 20 Copynumber: 5.4 Consensus size: 20
2895792 TGGAAACTAC
* *
2895802 GTTGCGAAATTAGAGTTCGT
1 GTTGCGAAATTAGAATTCGA
* * *
2895822 GTTGCGAATTTAGAAAATCGC
1 GTTGCGAAATTAG-AATTCGA
*
2895843 GTTGCGAAA-AAGAAATTCGA
1 GTTGCGAAATTAG-AATTCGA
* *
2895863 GTTGCGAATTTCAAAATT-GA
1 GTTGCGAAATT-AGAATTCGA
* * *
2895883 GTTGCGAAATTGGAGTTCGT
1 GTTGCGAAATTAGAATTCGA
2895903 GTTGCGAA
1 GTTGCGAA
2895911 TTTGTTGGTT
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.04
20 49 0.71
21 16 0.23
22 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (20 bp):
GTTGCGAAATTAGAATTCGA
Found at i:2895907 original size:40 final size:41
Alignment explanation
Indices: 2895802--2895913 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 41
2895792 TGGAAACTAC
* * *
2895802 GTTGCGAAATTAGAGTTCGTGTTGCGAATTTAGAAAATCGC
1 GTTGCGAAATTGGAGTTCGTGTTGCGAATTTACAAAATCGA
** * * * *
2895843 GTTGCGAAAAAGAAATTCGAGTTGCGAATTT-CAAAATTGA
1 GTTGCGAAATTGGAGTTCGTGTTGCGAATTTACAAAATCGA
2895883 GTTGCGAAATTGGAGTTCGTGTTGCGAATTT
1 GTTGCGAAATTGGAGTTCGTGTTGCGAATTT
2895914 GTTGGTTATT
Statistics
Matches: 57, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
40 32 0.56
41 25 0.44
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (41 bp):
GTTGCGAAATTGGAGTTCGTGTTGCGAATTTACAAAATCGA
Found at i:2901677 original size:21 final size:20
Alignment explanation
Indices: 2901653--2901711 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
2901643 ATTTACCGTG
2901653 ATTGCGGCCTTCGCGGGCGCT
1 ATTGCGG-CTTCGCGGGCGCT
* *
2901674 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGG-CTTCGCGGGCGCT
2901695 ATTGCGGCTGTCGCGGG
1 ATTGCGGCT-TCGCGGG
2901712 TAACTCGGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.07, C:0.29, G:0.41, T:0.24
Consensus pattern (20 bp):
ATTGCGGCTTCGCGGGCGCT
Found at i:2902532 original size:40 final size:40
Alignment explanation
Indices: 2902477--2902559 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
2902467 AATTACACAA
2902477 TATTAGAATCATTTTATGCATTTTCAGAAGAATGGAGGTG
1 TATTAGAATCATTTTATGCATTTTCAGAAGAATGGAGGTG
* *
2902517 TATTAGAATCATTTTATGCATTTTCAGCAGAATGGAGTTG
1 TATTAGAATCATTTTATGCATTTTCAGAAGAATGGAGGTG
2902557 TAT
1 TAT
2902560 GAGGTACAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (40 bp):
TATTAGAATCATTTTATGCATTTTCAGAAGAATGGAGGTG
Found at i:2902745 original size:11 final size:11
Alignment explanation
Indices: 2902729--2902762 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
2902719 TTTATTTTTA
2902729 TTCTTACACTT
1 TTCTTACACTT
2902740 TTCTTACACTT
1 TTCTTACACTT
2902751 TTCTTACACTT
1 TTCTTACACTT
2902762 T
1 T
2902763 GCAGTGACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (11 bp):
TTCTTACACTT
Found at i:2916445 original size:35 final size:35
Alignment explanation
Indices: 2916391--2916461 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
2916381 GTAGCAAGGT
*
2916391 TATTTGTAAGTGGACAAACTAGATAGATCTAGTAA
1 TATTTGTAAGTGGACAAACTAGATAGATATAGTAA
* ** *
2916426 TATTTGTAGGTGGGTAAACTAGGTAGATATAGTAA
1 TATTTGTAAGTGGACAAACTAGATAGATATAGTAA
2916461 T
1 T
2916462 GATACTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (35 bp):
TATTTGTAAGTGGACAAACTAGATAGATATAGTAA
Found at i:2916508 original size:11 final size:11
Alignment explanation
Indices: 2916492--2916516 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2916482 GGTATAAGAG
2916492 GGTTAATATAC
1 GGTTAATATAC
2916503 GGTTAATATAC
1 GGTTAATATAC
2916514 GGT
1 GGT
2916517 GTTACAGGAT
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:2917017 original size:180 final size:182
Alignment explanation
Indices: 2916670--2917141 Score: 723
Period size: 181 Copynumber: 2.6 Consensus size: 182
2916660 GATCCAAATT
* * * **
2916670 AAAAATGTATCTATCCACAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * * *
2916735 AAATCGGTAAAGCGGTATCAGATATATTTAAAGTGTCGGTACTTTAATATAAGGATTGGCACTTC
66 AAACCGGTAAAACGCTATCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * *
2916800 GTTAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTCGATACTTT-A
131 GTGAATTTAAAAGAGAAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
2916851 AAAAATGTATCGATCCACTACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
2916916 AAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTATCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
2916980 GTGAATTTAAAAGAGAAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
2917032 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
2917097 AAACCGGTAAAACGCTATCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGCTATCGGATATATTAAAAGTGTCGATACTTT
2917142 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
180 63 0.24
181 200 0.76
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTATCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:2918947 original size:19 final size:22
Alignment explanation
Indices: 2918899--2918953 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
2918889 TTTTTTGTGT
2918899 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAA-GATAGTATAA
2918922 TTATTATATAAAA-ATA-TA-AA
1 TT-TTATATAAAAGATAGTATAA
2918942 TTTTATTATAAA
1 TTTTA-TATAAA
2918954 TGCAGGTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 2 0.07
22 3 0.10
23 2 0.07
24 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
TTTTATATAAAAGATAGTATAA
Found at i:2919259 original size:15 final size:15
Alignment explanation
Indices: 2919239--2919271 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2919229 TGGTTGTATT
*
2919239 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
2919254 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
2919269 GGG
1 GGG
2919272 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:2919380 original size:21 final size:21
Alignment explanation
Indices: 2919354--2919418 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2919344 AAGACAATCA
*
2919354 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
2919375 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2919396 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2919417 AG
1 AG
2919419 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2919494 original size:33 final size:33
Alignment explanation
Indices: 2919452--2919517 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2919442 AAATAGATGG
*
2919452 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2919485 AGTGGTGAAAGATGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2919518 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2921336 original size:19 final size:19
Alignment explanation
Indices: 2921312--2921360 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2921302 AATGTAGGGT
2921312 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2921331 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2921350 TAATTTTGTAT
1 TAATTTTGTAT
2921361 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2921933 original size:200 final size:200
Alignment explanation
Indices: 2921590--2922574 Score: 1769
Period size: 200 Copynumber: 4.9 Consensus size: 200
2921580 AATTTACAAT
2921590 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
2921655 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
2921720 ATGAGAGATTAGGTAT-ATAATATGTATCGACACTTTTTTATTTTGTGTCGATACTATTGGTCCA
131 ATGAGAGAATAGGTGTAAT-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
2921784 GAATGA
195 GAATGA
*
2921790 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* *
2921855 CGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2921920 ATGAGAGATTAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2921985 AATGA
196 AATGA
* * * *
2921990 ATGGCAAACAGGGTACAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
2922055 CGAAACCCATAAGTATAATGTAATAGGTAA-TTTTCAATCTAACAGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2922119 ATGAGAGAATAGGTGTAATATATGTATCGACAGTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2922184 AATGA
196 AATGA
* *
2922189 ATGGCAAACAGGGTGCAACCATAAAATATCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
2922254 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
2922319 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2922384 AATGA
196 AATGA
* *
2922389 ATGGCAAACAGAGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAATAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
2922454 CGAAACCCATAAG-ATAAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTT
66 CGAAACCCATAAGTAT-AATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTT
*
2922518 TATGAGATAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
130 TATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
2922575 ATTTAAATAT
Statistics
Matches: 757, Mismatches: 25, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
199 193 0.25
200 562 0.74
201 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:2922334 original size:399 final size:400
Alignment explanation
Indices: 2921590--2922574 Score: 1769
Period size: 399 Copynumber: 2.5 Consensus size: 400
2921580 AATTTACAAT
2921590 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
2921655 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
2921720 ATGAGAGATTAGGTAT-ATAATATGTATCGACACTTTTTTATTTTGTGTCGATACTATTGGTCCA
131 ATGAGAGAATAGGTGTAAT-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
* *
2921784 GAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
195 GAATGAATGGCAAACAGGGTGCAACCATAAAATATCGATCCATATATAAAAAGTGTCGATCCCAA
*
2921849 AAACATCGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACC
260 AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACC
*
2921914 GGTTTTATGAGAGATTAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTG
325 GGTTTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTG
2921979 GTCCAGAATGA
390 GTCCAGAATGA
* * * *
2921990 ATGGCAAACAGGGTACAACCATAAAATGTCGATCCATATATAAAAGGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
2922055 CGAAACCCATAAGTATAATGTAATAGGTAA-TTTTCAATCTAACAGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2922119 ATGAGAGAATAGGTGTAATATATGTATCGACAGTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
*
2922184 AATGAATGGCAAACAGGGTGCAACCATAAAATATCGATCCATATATAAAAAGTGTCGATCCCAGA
196 AATGAATGGCAAACAGGGTGCAACCATAAAATATCGATCCATATATAAAAAGTGTCGATCCCAAA
*
2922249 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCG
2922314 GTTTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
326 GTTTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
2922379 TCCAGAATGA
391 TCCAGAATGA
* *
2922389 ATGGCAAACAGAGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAATAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
2922454 CGAAACCCATAAG-ATAAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTT
66 CGAAACCCATAAGTAT-AATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTT
*
2922518 TATGAGATAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
130 TATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
2922575 ATTTAAATAT
Statistics
Matches: 558, Mismatches: 24, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
398 2 0.00
399 376 0.67
400 180 0.32
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGAATGGCAAACAGGGTGCAACCATAAAATATCGATCCATATATAAAAAGTGTCGATCCCAAA
AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCG
GTTTTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGG
TCCAGAATGA
Found at i:2924076 original size:18 final size:18
Alignment explanation
Indices: 2924053--2924089 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2924043 GTGGACAACC
*
2924053 AAGCTGTCAATGAAGATG
1 AAGCTGACAATGAAGATG
*
2924071 AAGCTGACGATGAAGATG
1 AAGCTGACAATGAAGATG
2924089 A
1 A
2924090 CGATGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.19
Consensus pattern (18 bp):
AAGCTGACAATGAAGATG
Found at i:2924084 original size:12 final size:12
Alignment explanation
Indices: 2924062--2924107 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2924052 CAAGCTGTCA
*
2924062 ATGAAGATGAAG
1 ATGACGATGAAG
*
2924074 CTGACGATGAAG
1 ATGACGATGAAG
*
2924086 ATGACGATGATG
1 ATGACGATGAAG
*
2924098 ATGATGATGA
1 ATGACGATGA
2924108 TGATCCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Done.