Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 35 of 45
Found at i:6183647 original size:20 final size:22
Alignment explanation
Indices: 6183624--6183685 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 22
6183614 ATATTAAAAT
6183624 TTAAATA-AATATAAAATATA-
1 TTAAATATAATATAAAATATAC
* *
6183644 TTAATTATAAT-TATAATATAC
1 TTAAATATAATATAAAATATAC
* *
6183665 TAAAATATATTATAAAATATA
1 TTAAATATAATATAAAATATA
6183686 AAGCGTAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 14 0.42
21 11 0.33
22 8 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATATAATATAAAATATAC
Found at i:6183683 original size:49 final size:49
Alignment explanation
Indices: 6183571--6183687 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
6183561 ATATAAAAAT
* * *
6183571 AATATAAATATATTATAAAATTTATATAATATAAATTATTAATATATTAA
1 AATATAAATA-AATATAAAATATATATAATATAAATTATTAATATACTAA
*
6183621 AATTTAAATAAATATAAAATATAT-TAAT-TATAATTA-TAATATACTAA
1 AATATAAATAAATATAAAATATATATAATATA-AATTATTAATATACTAA
*
6183668 AATATATTATAAAATATAAA
1 AATATA-AAT-AAATATAAA
6183688 GCGTAATCCC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
47 17 0.29
48 11 0.19
49 21 0.36
50 9 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (49 bp):
AATATAAATAAATATAAAATATATATAATATAAATTATTAATATACTAA
Found at i:6189471 original size:2 final size:2
Alignment explanation
Indices: 6189466--6189513 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6189456 AGGAGGTGGC
6189466 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
6189508 TA TA TA
1 TA TA TA
6189514 GAACTTCTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6192186 original size:2 final size:2
Alignment explanation
Indices: 6192181--6192224 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
6192171 AAAATGAAGG
*
6192181 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6192223 GA
1 GA
6192225 ACTGACGGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6192898 original size:15 final size:15
Alignment explanation
Indices: 6192878--6192961 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 15
6192868 AGTAAAAAAA
* *
6192878 TTAAAAAGTTCAAAC
1 TTAAAAAATTCAAAT
*
6192893 TTAAAAAATTTAAAT
1 TTAAAAAATTCAAAT
* * *
6192908 TTGAAATAGTTTAAAT
1 TT-AAAAAATTCAAAT
6192924 TTAAAATAATTCAAAAT
1 TTAAAA-AATTC-AAAT
* *
6192941 TAAAAAAATTTAAAT
1 TTAAAAAATTCAAAT
6192956 TTAAAA
1 TTAAAA
6192962 GAATCTGAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
15 26 0.47
16 20 0.36
17 9 0.16
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (15 bp):
TTAAAAAATTCAAAT
Found at i:6192922 original size:16 final size:16
Alignment explanation
Indices: 6192878--6192961 Score: 73
Period size: 16 Copynumber: 5.4 Consensus size: 16
6192868 AGTAAAAAAA
* *
6192878 TTAAAA-AGTTCAAAC
1 TTAAAATAGTTTAAAT
*
6192893 TTAAAA-AATTTAAAT
1 TTAAAATAGTTTAAAT
*
6192908 TTGAAATAGTTTAAAT
1 TTAAAATAGTTTAAAT
* * *
6192924 TTAAAATAATTCAAAA
1 TTAAAATAGTTTAAAT
* *
6192940 TTAAAAAAATTTAAAT
1 TTAAAATAGTTTAAAT
6192956 TTAAAA
1 TTAAAA
6192962 GAATCTGAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
15 17 0.30
16 39 0.70
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (16 bp):
TTAAAATAGTTTAAAT
Found at i:6192954 original size:32 final size:30
Alignment explanation
Indices: 6192874--6192961 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 30
6192864 TTTGAGTAAA
* * *
6192874 AAAATTAAAAAGTTCAAACTTAAAAAATTT
1 AAAATTAAAAAGTTTAAATTTAAAAAATTC
* *
6192904 AAATTTGAAATAGTTTAAATTTAAAATAATTC
1 AAAATT-AAAAAGTTTAAATTTAAAA-AATTC
*
6192936 AAAATTAAAAAAATTTAAATTTAAAA
1 AAAATT-AAAAAGTTTAAATTTAAAA
6192962 GAATCTGAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 5 0.11
31 16 0.34
32 26 0.55
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATTAAAAAGTTTAAATTTAAAAAATTC
Found at i:6195948 original size:2 final size:2
Alignment explanation
Indices: 6195941--6195987 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
6195931 ATGACTTTAC
6195941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6195983 AT AT A
1 AT AT A
6195988 CACACATACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6197364 original size:19 final size:17
Alignment explanation
Indices: 6197329--6197367 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
6197319 TATAGATTTT
*
6197329 AATAAATATATATTAAA
1 AATAAATATATAATAAA
6197346 AATAACATATTATAATAAA
1 AATAA-ATA-TATAATAAA
6197365 AAT
1 AAT
6197368 TTACTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATATATAATAAA
Found at i:6200803 original size:21 final size:21
Alignment explanation
Indices: 6200779--6200825 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6200769 TTTGAAGCTG
6200779 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
6200799 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
6200820 ATTTTG
1 ATTTTG
6200826 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:6200965 original size:13 final size:13
Alignment explanation
Indices: 6200947--6200985 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
6200937 ATAATCCCCC
* *
6200947 TGTATCGATATAG
1 TGTATCGATACAA
6200960 TGTATCGATACAA
1 TGTATCGATACAA
6200973 TGTATCGATACAA
1 TGTATCGATACAA
6200986 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6207191 original size:13 final size:13
Alignment explanation
Indices: 6207173--6207198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6207163 AATTTTTTGG
6207173 TGTATCGATACAT
1 TGTATCGATACAT
6207186 TGTATCGATACAT
1 TGTATCGATACAT
6207199 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6207938 original size:22 final size:20
Alignment explanation
Indices: 6207898--6207938 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
6207888 ACATAACTTA
*
6207898 ATTTAGTAAAAAAAAATAAT
1 ATTTAATAAAAAAAAATAAT
6207918 ATTTAATAATAAAAAAGATAA
1 ATTTAATAA-AAAAAA-ATAA
6207939 AATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
ATTTAATAAAAAAAAATAAT
Found at i:6208426 original size:22 final size:22
Alignment explanation
Indices: 6208401--6208443 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6208391 TTCGATACCA
6208401 TTTACATATTTAATTTTTTAAT
1 TTTACATATTTAATTTTTTAAT
* * *
6208423 TTTATATTTTTATTTTTTTAA
1 TTTACATATTTAATTTTTTAA
6208444 AAAAATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTACATATTTAATTTTTTAAT
Found at i:6208769 original size:26 final size:25
Alignment explanation
Indices: 6208721--6208769 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
6208711 ATATTTCTTA
* *
6208721 AAAAGAAAATAAAAAGTTCTTAACG
1 AAAAGAAAATAAAAAGATATTAACG
6208746 AAAAGAAAATAAAAAAGATATTAA
1 AAAAGAAAAT-AAAAAGATATTAA
6208770 TGAGTGCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.18
Consensus pattern (25 bp):
AAAAGAAAATAAAAAGATATTAACG
Found at i:6208996 original size:22 final size:23
Alignment explanation
Indices: 6208971--6209024 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
6208961 TATATTTTAC
* *
6208971 TTTTAATAAATAAAAATA-TATT
1 TTTTAAAAAATAAAAACATTATT
6208993 TTTTAAAAAATAAAAACATTATT
1 TTTTAAAAAATAAAAACATTATT
*
6209016 TTTCAAAAA
1 TTTTAAAAA
6209025 GAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTAAAAAATAAAAACATTATT
Found at i:6209047 original size:14 final size:14
Alignment explanation
Indices: 6209013--6209047 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6209003 TAAAAACATT
*
6209013 ATTTTTCAAAAAGA
1 ATTTTTTAAAAAGA
*
6209027 ATTTTTTAATAAGA
1 ATTTTTTAAAAAGA
6209041 ATTTTTT
1 ATTTTTT
6209048 TACTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (14 bp):
ATTTTTTAAAAAGA
Found at i:6209239 original size:17 final size:17
Alignment explanation
Indices: 6209197--6209241 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
6209187 AAAGAGTAAT
6209197 ATTTGTTAAATATCTAA
1 ATTTGTTAAATATCTAA
* *
6209214 ATCTGTTAAATATTTAA
1 ATTTGTTAAATATCTAA
*
6209231 ATTTATTAAAT
1 ATTTGTTAAAT
6209242 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (17 bp):
ATTTGTTAAATATCTAA
Found at i:6210576 original size:16 final size:16
Alignment explanation
Indices: 6210555--6210585 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6210545 TAAATTTAAA
6210555 AATAAATAATTAAATG
1 AATAAATAATTAAATG
6210571 AATAAATAATTAAAT
1 AATAAATAATTAAAT
6210586 TAGAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAAATAATTAAATG
Found at i:6214092 original size:50 final size:51
Alignment explanation
Indices: 6213964--6214098 Score: 200
Period size: 51 Copynumber: 2.7 Consensus size: 51
6213954 TTTTAACCAG
* * *
6213964 ATGTATCGATACATTGCAAAATGTATCGATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGAAAGA
*
6214015 ATGTATCGATACATTGAAAGATGTATCGATACATCTAGGTAAAAA-AAAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGAAAGA
* * *
6214065 ATGTATCAATATATTGAAAAATATATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
6214099 TCATACATGT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
50 34 0.45
51 42 0.55
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGAAAGA
Found at i:6214152 original size:24 final size:20
Alignment explanation
Indices: 6214064--6214138 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
6214054 TAAAAAAAAG
*
6214064 AATGTATCAATATATTGAAA
1 AATGTATCAATACATTGAAA
* * * *
6214084 AATATATCGATACATTCATA
1 AATGTATCAATACATTGAAA
*
6214104 CATGTATCAATACATTGAAA
1 AATGTATCAATACATTGAAA
6214124 AATGTATCAATACAT
1 AATGTATCAATACAT
6214139 ATAGGAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (20 bp):
AATGTATCAATACATTGAAA
Found at i:6216766 original size:57 final size:59
Alignment explanation
Indices: 6216699--6216840 Score: 175
Period size: 57 Copynumber: 2.5 Consensus size: 59
6216689 TAGAATGGTG
*
6216699 CTAAAATGTATAAAATTACATAATAGTTC-TTAAAT-CAT-GAAAATAACTAAAATGAC
1 CTAAAATGTATGAAATTACATAATAGTTCTTTAAATGCATGGAAAATAACTAAAATGAC
* * * * *
6216755 TTCAAAATGTATGAAATTACATAATA-ATCTTTTAATGCATGGAAAATGACTTAAATGAC
1 CT-AAAATGTATGAAATTACATAATAGTTCTTTAAATGCATGGAAAATAACTAAAATGAC
* *
6216814 CTAAGATGCATGAAATTACATAATAGT
1 CTAAAATGTATGAAATTACATAATAGT
6216841 ATTTGTAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
56 3 0.04
57 27 0.38
58 24 0.34
59 17 0.24
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (59 bp):
CTAAAATGTATGAAATTACATAATAGTTCTTTAAATGCATGGAAAATAACTAAAATGAC
Found at i:6217990 original size:166 final size:163
Alignment explanation
Indices: 6217632--6218213 Score: 555
Period size: 166 Copynumber: 3.5 Consensus size: 163
6217622 TAAAAAAGTT
** * * *
6217632 TCAAATATTATCAATTAATTCCCATCAAATCAGTTTTGAAAAATTCTTTCATTTTCATGAATTTT
1 TCAAATATTATCAATTAATTCATATTAAATCAATTTTCAAAAATTCTTTCATTTTCATGAA-TTT
* * * * * *
6217697 TGAATTATTTTCTTGAAGTTTCCCTTTTTTTC-GGAATACGAAGTTTCTTCTCCATAAATTTTTT
65 TGAATT-TTTCCTTGAAATTT--ATTTTTTTCTGAAATACGGAGTTTTTTCT-CATAAATTTTTT
* *
6217761 CG-GAGGGATTTTTTTTTTGTTTTTAATTTTCAAAATTCA
126 CGAG-GGGA-TTTTTCTTGGTTTTTAATTTTCAAAATTCA
* * * * * * *
6217800 TCAAATATTATTATTTAATTCATATAAAATCAATTTTTAAAAATTCTTTTATTTTCATTAGTCTT
1 TCAAATATTATCAATTAATTCATATTAAATCAATTTTCAAAAATTCTTTCATTTTCATGAAT-TT
* * * *
6217865 GGAATTTTTCCATAAAATTTATTTTTTTCTGAAATACGGAGTTTTTTGCTCTATAAATTTTTTAG
65 TGAATTTTTCCTTGAAATTTATTTTTTTCTGAAATACGGAGTTTTTT-CTC-ATAAATTTTTTCG
*
6217930 AGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
128 AGGGGATTTTTCTTGGTTTTTAATTTTCAAAATTCA
* * * *
6217966 TCAAATATTATCAATTATTTCATATTAATTCAGTTTTCAAAAATT-TATTCATTTCCATGAATTT
1 TCAAATATTATCAATTAATTCATATTAAATCAATTTTCAAAAATTCT-TTCATTTTCATGAATTT
** * * * *
6218030 TGAATTTTTTCCTTGAAATGCCA-TTTTTTCTAAAATAC-GATGTTTTCTTTTTCGTGAATTTTT
65 TGAA-TTTTTCCTTGAAAT-TTATTTTTTTCTGAAATACGGA-G-TTT-TTTCTCATAAATTTTT
** *
6218093 TCGAGATGATTTTTCTTGGTTTTTAATTTTGAAAAGTT-A
125 TCGAGGGGATTTTTCTTGGTTTTTAATTTTCAAAA-TTCA
* * * * * * * *
6218132 TAAAATATTATTATTTATTTTATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTT
1 TCAAATATTATCAATTAATTCATATTAAATCAATTTTCAAAAATTCTTTCATTTTCATGAATTTT
6218197 GAATTTTTCCTTGAAAT
66 GAATTTTTCCTTGAAAT
6218214 CCCCTTTATC
Statistics
Matches: 348, Mismatches: 53, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
165 30 0.09
166 219 0.63
167 37 0.11
168 62 0.18
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (163 bp):
TCAAATATTATCAATTAATTCATATTAAATCAATTTTCAAAAATTCTTTCATTTTCATGAATTTT
GAATTTTTCCTTGAAATTTATTTTTTTCTGAAATACGGAGTTTTTTCTCATAAATTTTTTCGAGG
GGATTTTTCTTGGTTTTTAATTTTCAAAATTCA
Found at i:6218451 original size:2 final size:2
Alignment explanation
Indices: 6218444--6218475 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6218434 CAATCAGATT
6218444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6218476 ACAGCAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6218906 original size:12 final size:12
Alignment explanation
Indices: 6218891--6218926 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
6218881 GAAATAAAAA
6218891 AAGAAAATATAG
1 AAGAAAATATAG
6218903 AAGAAAATATAG
1 AAGAAAATATAG
6218915 AA-AAAA-ATAG
1 AAGAAAATATAG
6218925 AA
1 AA
6218927 AAGATAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 14 0.58
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAGAAAATATAG
Found at i:6221943 original size:58 final size:58
Alignment explanation
Indices: 6221774--6221972 Score: 186
Period size: 58 Copynumber: 3.4 Consensus size: 58
6221764 TAGAATGACC
* * * * * *
6221774 TTAAAATGCATAAAATTACATAAATGATCTTTAAATCATGATAAATTTAGTAAAATGACA
1 TTAAAATGCATAAAATGACATAAA-AATCTTTAAATCATGAAAAATAT-CTAAAATGCCA
* * * * * * *
6221834 TTAAAGTGCATGAAATGTCATAAAAGTCCTTAAATCATGAAAATTAACTAAAATGCCA
1 TTAAAATGCATAAAATGACATAAAAATCTTTAAATCATGAAAAATATCTAAAATGCCA
* * * *
6221892 TTAAAATGCATGAAATGACATAAAAAACTTTAAGTCATGAAAAATGTCTAAAATAGCACA
1 TTAAAATGCATAAAATGACATAAAAATCTTTAAATCATGAAAAATATCTAAAAT-GC-CA
*
6221952 --AATATGCATAAAATGACATAA
1 TTAAAATGCATAAAATGACATAA
6221973 TAGTCCTCAA
Statistics
Matches: 113, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
58 73 0.65
59 18 0.16
60 22 0.19
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (58 bp):
TTAAAATGCATAAAATGACATAAAAATCTTTAAATCATGAAAAATATCTAAAATGCCA
Found at i:6225563 original size:23 final size:26
Alignment explanation
Indices: 6225528--6225583 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
6225518 GTTGTTTTTG
6225528 TTATTCTCATCATTTTAGTGAGCTTA
1 TTATTCTCATCATTTTAGTGAGCTTA
6225554 TTATTCTCATCATTTTAGTGAGCTTA
1 TTATTCTCATCATTTTAGTGAGCTTA
6225580 TTAT
1 TTAT
6225584 GCTTCCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (26 bp):
TTATTCTCATCATTTTAGTGAGCTTA
Found at i:6229334 original size:12 final size:12
Alignment explanation
Indices: 6229310--6229342 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
6229300 TAATGTATAT
6229310 CTAAATACATTCA
1 CTAAAT-CATTCA
6229323 CTAAATCATTCA
1 CTAAATCATTCA
6229335 CTAAATCA
1 CTAAATCA
6229343 ATTAGCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (12 bp):
CTAAATCATTCA
Found at i:6230896 original size:18 final size:17
Alignment explanation
Indices: 6230875--6230915 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
6230865 TTTAATAATT
6230875 ATTTTGTGCTTATTTTAG
1 ATTTTGT-CTTATTTTAG
*
6230893 ATTTTGTTTTATTTTAG
1 ATTTTGTCTTATTTTAG
6230910 ACTTTT
1 A-TTTT
6230916 TATTTGTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (17 bp):
ATTTTGTCTTATTTTAG
Found at i:6240362 original size:10 final size:10
Alignment explanation
Indices: 6240360--6240394 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6240350 TTATTTAAAT
6240360 TTAAATTTAA
1 TTAAATTTAA
6240370 TTAAATTTAA
1 TTAAATTTAA
* *
6240380 TTATATTTAT
1 TTAAATTTAA
6240390 TTAAA
1 TTAAA
6240395 AATATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:6240363 original size:6 final size:6
Alignment explanation
Indices: 6240352--6240442 Score: 59
Period size: 6 Copynumber: 14.8 Consensus size: 6
6240342 TAATTAATTT
*
6240352 ATTTAA ATTTAA ATTT-A A-TTAA ATTT-A A-TTAT ATTT-- ATTTAAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT--AA
6240396 ATATTAATA ATTTAA ATTTATA CATTTAA ATTTAAA ATTTAA ATTTA
1 AT-TT-A-A ATTTAA ATTTA-A -ATTTAA ATTT-AA ATTTAA ATTTA
6240443 CTTAAGTTTA
Statistics
Matches: 71, Mismatches: 1, Indels: 26
0.72 0.01 0.27
Matches are distributed among these distances:
4 8 0.11
5 7 0.10
6 31 0.44
7 9 0.13
8 11 0.15
9 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:6240437 original size:13 final size:13
Alignment explanation
Indices: 6240394--6240442 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
6240384 ATTTATTTAA
6240394 AAATATTAATAATTT
1 AAAT-TTAA-AATTT
*
6240409 AAATTTATACATTT
1 AAATTTA-AAATTT
6240423 AAATTTAAAATTT
1 AAATTTAAAATTT
6240436 AAATTTA
1 AAATTTA
6240443 CTTAAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.39
14 14 0.45
15 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:6241238 original size:196 final size:196
Alignment explanation
Indices: 6240879--6241239 Score: 491
Period size: 196 Copynumber: 1.8 Consensus size: 196
6240869 TTTAATTAAA
* * *
6240879 TTTAAAAAATTTAAGATATGATTTGTAAAATTAATTGTTAAAATATTTTTTGATATAAGTATACA
1 TTTAAAAAATTTAAGATATAATTTATAAAATTAATTATTAAAATATTTTTTGATATAAGTATACA
* *** *
6240944 AATTTAATTTAACTTTTTTTAGATAATTTAAACTTTTTTAAAATATGATTTTTTTATTTATAAAA
66 AATTTAATTTAACTTTTTTAAGATAATTTAAAAAATTTTAAAATATAATTTTTTTATTTATAAAA
* *
6241009 TTAATTTAATTTATTTTTACATGTATTATTTTTTAGTAATGACTTAAATATAAATTTTCTTTAAA
131 TTAATTTAATTTATTTGTA-ATGAATTATTTTTTAGTAATGACTTAAATATAAATTTTCTTTAAA
6241074 AT
195 AT
* * *
6241076 TTTAAAAAA-TTAAGGTATAATTTATAAAATTAATTATTAAAATATTTTTTGATATAATTATATA
1 TTTAAAAAATTTAAGATATAATTTATAAAATTAATTATTAAAATATTTTTTGATATAAGTATACA
*
6241140 AATTTAATTT-A-TTTTTTAAG-TAATTTAAAAAAATTTTAAAATCTAATTTATTTTTATTT-TC
66 AATTTAATTTAACTTTTTTAAGATAATTT-AAAAAATTTTAAAATATAA-TT-TTTTTATTTAT-
6241201 AAAATTAATTTAATTTATTTGT-ATGAAATTTATTTTTTA
127 AAAATTAATTTAATTTATTTGTAATG-AA-TTATTTTTTA
6241240 TTTTATTATA
Statistics
Matches: 144, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
193 6 0.04
194 25 0.17
195 5 0.03
196 99 0.69
197 9 0.06
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (196 bp):
TTTAAAAAATTTAAGATATAATTTATAAAATTAATTATTAAAATATTTTTTGATATAAGTATACA
AATTTAATTTAACTTTTTTAAGATAATTTAAAAAATTTTAAAATATAATTTTTTTATTTATAAAA
TTAATTTAATTTATTTGTAATGAATTATTTTTTAGTAATGACTTAAATATAAATTTTCTTTAAAA
T
Found at i:6241284 original size:22 final size:21
Alignment explanation
Indices: 6241259--6241303 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6241249 ATATAAATTT
6241259 AAAATATT-AATTATAAAAATAA
1 AAAAT-TTAAATTATAAAAA-AA
*
6241281 AAAATTTAAATTTTAAAAAAA
1 AAAATTTAAATTATAAAAAAA
6241302 AA
1 AA
6241304 GAGGTCACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATTTAAATTATAAAAAAA
Found at i:6242230 original size:51 final size:50
Alignment explanation
Indices: 6242175--6242319 Score: 152
Period size: 50 Copynumber: 2.9 Consensus size: 50
6242165 TCCTATTATG
*
6242175 AAAAATCGATGTTCTGAAAATAAAACCGAGGTTAGAGTATCCCCGATTGTA
1 AAAAATCGATGTTCTGAAAATAAAACCG-GGTTAGAGTATCCCCGATGGTA
** *
6242226 AAAAATCGATGTTCT-AGAAATAAAATTGGGGTTAGAGT-TCCCCGATGGTG
1 AAAAATCGATGTTCTGA-AAATAAAA-CCGGGTTAGAGTATCCCCGATGGTA
* * * *
6242276 AAAAAT-TAGTGTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
1 AAAAATCGA-TGTTCTGAAAATAAAACCGG-GTTAGAGTATCCCC
6242320 TAAAAAATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
49 3 0.04
50 37 0.47
51 37 0.47
52 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (50 bp):
AAAAATCGATGTTCTGAAAATAAAACCGGGTTAGAGTATCCCCGATGGTA
Found at i:6242296 original size:50 final size:51
Alignment explanation
Indices: 6242175--6242319 Score: 134
Period size: 51 Copynumber: 2.9 Consensus size: 51
6242165 TCCTATTATG
* ** * *
6242175 AAAAATCGATGTTCT-GAAAATAAAACCGAGGTTAGAGTATCCCCGATTGTA
1 AAAAATAGATGTTCTAG-AAATAAAATTGGGGTTAGAGTATCCCCGATGGTA
*
6242226 AAAAATCGATGTTCTAGAAATAAAATTGGGGTTAGAGT-TCCCCGATGGTGA
1 AAAAATAGATGTTCTAGAAATAAAATTGGGGTTAGAGTATCCCCGATGGT-A
* * * ** * *
6242277 AAAATTAG-TGTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
1 AAAAATAGATGTTCTAGAAATAAAATTGGGGTTAGAGTATCCCC
6242320 TAAAAAATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
50 33 0.42
51 45 0.57
52 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAAATAGATGTTCTAGAAATAAAATTGGGGTTAGAGTATCCCCGATGGTA
Found at i:6242394 original size:51 final size:51
Alignment explanation
Indices: 6242330--6242431 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
6242320 TAAAAAATAA
* *
6242330 CGAGGTTGGAGTATCCTCGATTGTGAAAAATCAGTGTTTTAAAAATAAAAC
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTAAAAATAAAAC
** **
6242381 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAAC
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTAAAAATAAAAC
6242432 TAGGGTTAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTAAAAATAAAAC
Found at i:6242428 original size:180 final size:180
Alignment explanation
Indices: 6242093--6242442 Score: 429
Period size: 180 Copynumber: 1.9 Consensus size: 180
6242083 CATTCCTCGA
* * *
6242093 TGAAAAATTTAATATTTTGGAGATAAAGACAGGGTTGGAGTATCACCTCAGAAATAACGAGGCTA
1 TGAAAAATTTAATATTTTGGAAATAAAGACAGGGTTGGAGTATCACCTAAAAAATAACGAGGCTA
* *
6242158 GCGTATTTCCTATTATGAAAAATCGATGTTCTGAAAATAAAACCGAGGTTAGAGTATCCCCGATT
66 GAGTA-TTCCTATTATGAAAAATCGATGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCGATT
* * *
6242223 GTAAAAAATCGATGTTCTAGAAATAAAATTGGGGTTAGAGTTCCCCGATGG
130 ATAAAAAATCGATGTTCTAGAAATAAAACTAGGGTTAGAGTTCCCCGATGG
* * * * *
6242274 TGAAAAA-TTAGTGTTTTGGAAATAAA-ACCGGAGTTGGAGTATCCCCTAAAAAATAACGAGGTT
1 TGAAAAATTTAATATTTTGGAAATAAAGACAGG-GTTGGAGTATCACCTAAAAAATAACGAGGCT
* * * *
6242337 GGAGTA-TCCTCGATTGTGAAAAATC-AGTGTTTTAAAAATAAAACCGAGGTTGGAGTATCCCCG
65 AGAGTATTCCT--ATTATGAAAAATCGA-TGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCG
* * * * *
6242400 ATTATGAAAAATTGGTGTTTTGGAAATAAAACTAGGGTTAGAG
127 ATTATAAAAAATCGATGTTCTAGAAATAAAACTAGGGTTAGAG
6242443 CATTCTCTCG
Statistics
Matches: 143, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
178 4 0.03
179 5 0.03
180 127 0.89
181 7 0.05
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (180 bp):
TGAAAAATTTAATATTTTGGAAATAAAGACAGGGTTGGAGTATCACCTAAAAAATAACGAGGCTA
GAGTATTCCTATTATGAAAAATCGATGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCGATTA
TAAAAAATCGATGTTCTAGAAATAAAACTAGGGTTAGAGTTCCCCGATGG
Found at i:6242457 original size:130 final size:129
Alignment explanation
Indices: 6242201--6242526 Score: 377
Period size: 130 Copynumber: 2.5 Consensus size: 129
6242191 AAAATAAAAC
* * * * * *
6242201 CGAGGTTAGAGTATCCCCGATTGTAAAAAATCGATGTTCTAGAAATAAAATTGGGGTTAGAGT-T
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATCG-TGTTTTAAAAATAAAATCGGGGTTGGAGTAT
* * * *
6242265 CCCCGATGGTGAAAAATTAGTGTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTAAAAAATAA
65 CCCCGATGATGAAAAATTAGTGTTTTGGAAATAAAACAGGAGTTAGAGCATCCCCTAAAAAATAA
* * *
6242330 CGAGGTTGGAGTATCCTCGATTGTGAAAAATCAGTGTTTTAAAAATAAAACCGAGGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATC-GTGTTTTAAAAATAAAATCGGGGTTGGAGTAT
* * * * **
6242395 CCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACTAGG-GTTAGAGCATTCTCTCGAAAATA
65 CCCCGATGATGAAAAATTAGTGTTTTGGAAATAAAAC-AGGAGTTAGAGCATCCCCTAAAAAATA
6242459 A
129 A
* * * * * *
6242460 CAAGTTTGGAGTATCCCCGATTATGAAAATTTTGTGTTTTGAAAATAAAATCGGGGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATTGTGAAAA-ATCGTGTTTTAAAAATAAAATCGGGGTTGGAGTAT
6242525 CC
65 CC
6242527 TTTTGAAAAT
Statistics
Matches: 165, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
129 52 0.32
130 110 0.67
131 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (129 bp):
CGAGGTTGGAGTATCCCCGATTGTGAAAAATCGTGTTTTAAAAATAAAATCGGGGTTGGAGTATC
CCCGATGATGAAAAATTAGTGTTTTGGAAATAAAACAGGAGTTAGAGCATCCCCTAAAAAATAA
Found at i:6242550 original size:28 final size:30
Alignment explanation
Indices: 6242496--6242553 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 30
6242486 AAATTTTGTG
6242496 TTTTGAAAATAAAATCGGGGTTGGAGTATCC
1 TTTTGAAAAT-AAATCGGGGTTGGAGTATCC
6242527 TTTTGAAAAT-AA-CGGGGTTGGAGTATC
1 TTTTGAAAATAAATCGGGGTTGGAGTATC
6242554 TCCGATTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 15 0.56
29 2 0.07
31 10 0.37
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.33
Consensus pattern (30 bp):
TTTTGAAAATAAATCGGGGTTGGAGTATCC
Found at i:6242597 original size:158 final size:158
Alignment explanation
Indices: 6242384--6242684 Score: 444
Period size: 158 Copynumber: 1.9 Consensus size: 158
6242374 ATAAAACCGA
* * * * * *
6242384 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACTAGGGTTAGAGCATTCT
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAACCAAGGTTAGAGCATCCC
* * * *
6242449 CTC-GAAAATAACAAGTTTGGAGTATCCCCGATTATGAAAATTTTGTGTTTT-GAAAATAAAATC
66 CTCAG-AAATAACAAGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAG-AAATAAAACC
6242512 GGGGTTGGAGTATCCTTTTGAAAATAACGG
129 GGGGTTGGAGTATCCTTTTGAAAATAACGG
* *
6242542 GGTTGGAGTATCTCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCAAGGTTAGAGCATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAACCAAGGTTAGAGCATCCC
**
6242607 CTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGG
66 CTCAGAAATAACAAGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGG
6242672 GGTTGGAGTATCC
131 GGTTGGAGTATCC
6242685 CCTCAGAAGT
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
158 125 0.98
159 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (158 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAACCAAGGTTAGAGCATCCC
CTCAGAAATAACAAGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGG
GGTTGGAGTATCCTTTTGAAAATAACGG
Found at i:6242669 original size:79 final size:80
Alignment explanation
Indices: 6242384--6242692 Score: 374
Period size: 79 Copynumber: 3.9 Consensus size: 80
6242374 ATAAAACCGA
* * * *
6242384 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACTAGGGTTAGAGCATTCT
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTAGAGCATCCC
**
6242449 CTC-GAAAATAACAA
66 CTCAGAAAATAACGG
* * * * * * *
6242463 GTTTGGAGTATCCCCGATTATGAAAATTTTGTGTTTTGAAAATAAAATCGGGGTTGGAGTAT-CC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTAGAGCATCCC
* **
6242527 TTTTGAAAATAACGG
66 CTCAGAAAATAACGG
* * * *
6242542 GGTTGGAGTATCTCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCAAGGTTAGAGCATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTAGAGCATCCC
6242607 CTCAG-AAATAACGG
66 CTCAGAAAATAACGG
* * *
6242621 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTT-AGAAATAAAACCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGA-AAATAAAACCAGGGTTAGAGCATCC
6242685 CCTCAGAA
65 CCTCAGAA
6242693 GTAAAAACAT
Statistics
Matches: 191, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
78 3 0.02
79 183 0.96
80 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (80 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTAGAGCATCCC
CTCAGAAAATAACGG
Found at i:6245078 original size:20 final size:20
Alignment explanation
Indices: 6245053--6245104 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
6245043 TAAAACCCAG
6245053 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
6245073 AATGTATCGATATAATGAAC
1 AATGTATCGATACAATGAAC
*
6245093 AGTGTATCGATA
1 AATGTATCGATA
6245105 AAAATTGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:6245769 original size:34 final size:34
Alignment explanation
Indices: 6245705--6245783 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
6245695 CTCTTTGAGA
* *
6245705 ACAAAGGAAAAGGAGTACGTCCTGCTCTTCGAGG
1 ACAAAGGAAAAAGAGTACGTCCTGCCCTTCGAGG
* *
6245739 ACAAAGGAAAAAGAGTATG-CTTTGCCCTTCGAGG
1 ACAAAGGAAAAAGAGTACGTC-CTGCCCTTCGAGG
6245773 ACAAAGGAAAA
1 ACAAAGGAAAA
6245784 GAGAATGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 1 0.03
34 39 0.98
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (34 bp):
ACAAAGGAAAAAGAGTACGTCCTGCCCTTCGAGG
Found at i:6245844 original size:42 final size:42
Alignment explanation
Indices: 6245764--6245874 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 42
6245754 TATGCTTTGC
* * **
6245764 CCTTCGAGGACAAAGGAAAAGA-G-AATGAAATGGGTCCTGCT
1 CCTT-GAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGCT
6245805 CCTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGCT
1 CCTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGCT
*
6245847 CTTTGAGGACAAAGGAAAAGAAGGAAAT
1 CCTTGAGGACAAAGGAAAA-AAGGAAAT
6245875 TAAAGCACGT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 16 0.26
41 5 0.08
42 33 0.53
43 8 0.13
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.16
Consensus pattern (42 bp):
CCTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGCT
Found at i:6245972 original size:61 final size:60
Alignment explanation
Indices: 6245882--6246337 Score: 579
Period size: 61 Copynumber: 7.5 Consensus size: 60
6245872 AATTAAAGCA
* * * * * **
6245882 CGTCTTGCTTTTTGGGGACTAGAATGTGCCACCAACTTGTGTGGGCTTTGCAAGGAGAAAG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAG
*
6245943 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCATCTTGTGTGGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-G
* * *
6246004 CGTCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-G
* * * * *
6246065 CATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTGAAAAGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-G
* * * **
6246126 TGTCCGGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATAAAAAG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * * *
6246186 ACGTCTTGCCCTTTGAGGACTAAAAGGTGCCATCAACTTGTGTGGGCTTTAAAATGAAAAG
1 -CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
6246247 ACGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 -C--GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
6246310 ACGTCATGCTCTTTGAGGACTGAAAGGT
1 -CGTCCTGCTCTTTGAGGACTAAAAGGT
6246338 TAAAAGATTT
Statistics
Matches: 351, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
60 4 0.01
61 289 0.82
63 58 0.17
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (60 bp):
CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
Found at i:6247327 original size:14 final size:13
Alignment explanation
Indices: 6247308--6247359 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
6247298 AAGTAGGTTA
6247308 TTTTCTTTTTTCTT
1 TTTTCTTTTTT-TT
6247322 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
6247335 TTTGTCTTTTGTTTT
1 TTT-TCTTTT-TTTT
6247350 GTTTT-TTTTT
1 -TTTTCTTTTT
6247360 AAAAGGAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.17
14 21 0.60
15 5 0.14
16 3 0.09
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:6247346 original size:7 final size:7
Alignment explanation
Indices: 6247308--6247344 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
6247298 AAGTAGGTTA
6247308 TTTTCTT
1 TTTTCTT
6247315 TTTTCTT
1 TTTTCTT
6247322 TTTTCTT
1 TTTTCTT
6247329 TTTT-TT
1 TTTTCTT
6247335 TTTGTCTT
1 TTT-TCTT
6247343 TT
1 TT
6247345 GTTTTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.18
7 19 0.68
8 4 0.14
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:6247354 original size:21 final size:20
Alignment explanation
Indices: 6247313--6247359 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
6247303 GGTTATTTTC
*
6247313 TTTTTTCTTTTTTCTTTTTT
1 TTTTTTCTTTTTTCTTGTTT
6247333 TTTTTGTCTTTTGTT-TTGTTT
1 TTTTT-TCTTTT-TTCTTGTTT
6247354 TTTTTT
1 TTTTTT
6247360 AAAAGGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 16 0.67
22 2 0.08
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTTGTTT
Found at i:6257652 original size:4 final size:4
Alignment explanation
Indices: 6257643--6257671 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6257633 AAAACAAAAC
6257643 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
6257672 GAGATGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:6261051 original size:19 final size:19
Alignment explanation
Indices: 6261027--6261093 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
6261017 CAGTAGCTAA
6261027 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
6261046 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
6261061 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
6261078 TTATGTATCGATACAA
1 TTATGTATCGATACAA
6261094 ATCGTTGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
14 1 0.02
16 6 0.14
18 1 0.02
19 25 0.60
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Found at i:6261067 original size:13 final size:13
Alignment explanation
Indices: 6261049--6261073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6261039 ACAACACTTA
6261049 TGTATCGATACAT
1 TGTATCGATACAT
6261062 TGTATCGATACA
1 TGTATCGATACA
6261074 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6261069 original size:32 final size:32
Alignment explanation
Indices: 6261030--6261092 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
6261020 TAGCTAATTA
6261030 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
6261062 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
6261093 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:6261891 original size:49 final size:48
Alignment explanation
Indices: 6261732--6262714 Score: 1050
Period size: 43 Copynumber: 20.8 Consensus size: 48
6261722 GATGTTAATG
* *
6261732 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAA-GTGCCAATA
* * *
6261784 TGCTGATTCAAGGCCAGCTATATTAGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
6261827 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG-TGCCAATA
* *
6261876 TGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
*
6261919 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGAAAAAGGATGTCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--AG---AA-G-TGCCAATA
*
6261974 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG-TGCCAATA
* * *
6262023 TGCTGATTCAAGGCTAGCTATATTGGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
*
6262066 TGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG-TGCCAATA
* *
6262115 TGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
*
6262158 TGCTGATTCAAGGCCAGCTACATTGGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
* *
6262201 TGCTGATTCAAGGCCAGCGACATTGGACTT--A-AAG-A-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
6262244 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG--AA-GTGCCAATA
* * *
6262295 TGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
* *
6262338 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAA-GTGCCAATA
* * *
6262387 TGCTGATTCAAGGCTAGCTATATTGGACTT--A-AAG--GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
*
6262430 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG-TGCCAATA
* * *
6262479 TGCTGATTCAAGGCCAACTATATTGGACTTAAAGGTGAAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA---GAAGAA-GTGCCAATA
*
6262531 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAA-AAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA----GAAGAA-GTGCCAATA
* * *
6262583 TACTGATTCAAGGCCAACTATATTGGACTT--A-AAG--GTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
*
6262626 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG-TGCCAATA
* *
6262675 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG
6262715 GTGAGAAAAG
Statistics
Matches: 813, Mismatches: 61, Indels: 117
0.82 0.06 0.12
Matches are distributed among these distances:
43 334 0.41
44 3 0.00
45 9 0.01
46 28 0.03
47 4 0.00
48 9 0.01
49 228 0.28
50 4 0.00
51 35 0.04
52 111 0.14
53 7 0.01
54 1 0.00
55 40 0.05
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (48 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGCCAATA
Found at i:6261906 original size:92 final size:90
Alignment explanation
Indices: 6261775--6262709 Score: 1006
Period size: 92 Copynumber: 10.0 Consensus size: 90
6261765 GATGGAAAAG
* * *
6261775 GTGCCAATATGCTGATTCAAGGCCAGCTATATTAGACTT-AAAG-GTGCCAATGTGCTGATTCAA
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGAGTGCCAATATGCTGATTCAA
*
6261838 GGCCAGCTACATTGGACTTAAAGAAGAA
66 GGCCAGCTATATTGGACTT--A-AAGAA
* *
6261866 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAAG-GTGCCAATGTGCTGATTCA
1 G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGAGTGCCAATATGCTGATTCA
*
6261929 AGGCCAGCTACATTGGACTTAAAGATGAGAAAAA
65 AGGCCAGCTATATTGGACTT--A-A--AG---AA
* *
6261963 GGATGTCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAAGATGCCAATATGCTG
1 -G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-AAG-AG-TGCCAATATGCTG
*
6262028 ATTCAAGGCTAGCTATATTGGACTTAAAG--
60 ATTCAAGGCCAGCTATATTGGACTTAAAGAA
* *
6262057 GTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGATGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-AAG-AG-TGCCAATATGCTGAT
6262122 TCAAGGCCAGCTATATTGGACTTAAAG--
62 TCAAGGCCAGCTATATTGGACTTAAAGAA
* *
6262149 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAG-GTGCCAATGTGCTGATTCAA
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGAGTGCCAATATGCTGATTCAA
* *
6262212 GGCCAGCGACATTGGACTTAAAG-A
66 GGCCAGCTATATTGGACTTAAAGAA
*
6262236 -TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAATGTGCCAATATGCTG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-AAG---A-GTGCCAATATGCTG
*
6262300 ATTCAAGGCCAGCGATATTGGACTTAAAG--
60 ATTCAAGGCCAGCTATATTGGACTTAAAGAA
* *
6262329 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAA-A-G-A-GTGCCAATATGCTGAT
*
6262394 TCAAGGCTAGCTATATTGGACTTAAAG--
62 TCAAGGCCAGCTATATTGGACTTAAAGAA
*
6262421 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAA-A-G-AG-TGCCAATATGCTGAT
*
6262486 TCAAGGCCAACTATATTGGACTTAAAGGTGAAAAA
62 TCAAGGCCAGCTATATTGGACTTAAA---G---AA
* * *
6262521 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAGGTGCCAATATAC
1 -GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-----AAGA-GTGCCAATATGC
*
6262586 TGATTCAAGGCCAACTATATTGGACTTAAAG--
58 TGATTCAAGGCCAGCTATATTGGACTTAAAGAA
*
6262617 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT--A-AAAGAG-TGCCAATATGCTGAT
6262682 TCAAGGCCAGCTATATTGGACTTAAAGA
62 TCAAGGCCAGCTATATTGGACTTAAAGA
6262710 TGAAGGTGAG
Statistics
Matches: 766, Mismatches: 32, Indels: 90
0.86 0.04 0.10
Matches are distributed among these distances:
86 77 0.10
87 1 0.00
88 1 0.00
89 6 0.01
90 1 0.00
91 3 0.00
92 383 0.50
93 4 0.01
94 81 0.11
95 39 0.05
96 2 0.00
97 3 0.00
98 37 0.05
99 2 0.00
100 1 0.00
101 42 0.05
102 3 0.00
103 1 0.00
104 76 0.10
105 1 0.00
106 1 0.00
107 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (90 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGAGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGAA
Found at i:6262057 original size:22 final size:21
Alignment explanation
Indices: 6262032--6262099 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
6262022 ATGCTGATTC
6262032 AAGGCTAGCTATATTGGACTTA
1 AAGGCTAGCTA-ATTGGACTTA
* *
6262054 AAGG-T-GCCAATGTGCTGA-TTC
1 AAGGCTAGCTAAT-TG--GACTTA
6262075 AAGGCTAGCTACATTGGACTTA
1 AAGGCTAGCTA-ATTGGACTTA
6262097 AAG
1 AAG
6262100 AAGAAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 9 0.26
22 12 0.34
23 5 0.14
24 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (21 bp):
AAGGCTAGCTAATTGGACTTA
Found at i:6262170 original size:21 final size:21
Alignment explanation
Indices: 6262146--6262213 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
6262136 ATTGGACTTA
6262146 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* * *
6262167 AAGGCCAGCTACAT-TG--GACTTA
1 AAGG--TGCCA-ATGTGCTGA-TTC
6262189 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
6262210 AAGG
1 AAGG
6262214 CCAGCGACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:6262442 original size:21 final size:20
Alignment explanation
Indices: 6262375--6262442 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
6262365 CTTAAAGATG
6262375 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
6262396 AAGGCTAGCTATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
6262418 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
6262439 AAGG
1 AAGG
6262443 CCAGCTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:6262617 original size:22 final size:22
Alignment explanation
Indices: 6262592--6262659 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
6262582 ATACTGATTC
6262592 AAGGCCAACTATATTGGACTTA
1 AAGGCCAACTATATTGGACTTA
** *
6262614 AAGGTGCCAA-TATGCT-GA-TTC
1 AA-G-GCCAACTATATTGGACTTA
* *
6262635 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAACTATATTGGACTTA
6262657 AAG
1 AAG
6262660 AAAAAGATGC
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.18
22 9 0.27
23 5 0.15
24 5 0.15
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (22 bp):
AAGGCCAACTATATTGGACTTA
Found at i:6262638 original size:21 final size:21
Alignment explanation
Indices: 6262571--6262638 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
6262561 AAAGGTGGAA
6262571 AAGGTGCCAATATACTGATTC
1 AAGGTGCCAATATACTGATTC
* *
6262592 AA-G-GCCAACTATATTGGACTTA
1 AAGGTGCCAA-TATACT-GA-TTC
*
6262614 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATACTGATTC
6262635 AAGG
1 AAGG
6262639 CCAGCTACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
19 5 0.14
20 6 0.16
21 10 0.27
22 6 0.16
23 5 0.14
24 5 0.14
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATACTGATTC
Found at i:6262810 original size:43 final size:43
Alignment explanation
Indices: 6262745--6262861 Score: 198
Period size: 43 Copynumber: 2.7 Consensus size: 43
6262735 GCTAATATGT
* * * *
6262745 TGATTCACGGCCAACGATATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
6262788 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
6262831 TGATTCAAGGCCAGCTACATTGGACTTAAAG
1 TGATTCAAGGCCAGCTACATTGGACTTAAAG
6262862 ATGAAGATAC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
Found at i:6262819 original size:22 final size:22
Alignment explanation
Indices: 6262794--6262861 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
6262784 GTGCTGATTC
6262794 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
* * *
6262816 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTACAT-TG--GACTTA
6262837 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
6262859 AAG
1 AAG
6262862 ATGAAGATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (22 bp):
AAGGCCAGCTACATTGGACTTA
Found at i:6262840 original size:21 final size:21
Alignment explanation
Indices: 6262773--6262840 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
6262763 ATTGGACTTA
6262773 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* * *
6262794 AAGGCCAGCTACAT-TG--GACTTA
1 AAGG--TGCCA-ATGTGCTGA-TTC
6262816 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
6262837 AAGG
1 AAGG
6262841 CCAGCTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:6262932 original size:34 final size:34
Alignment explanation
Indices: 6262883--6263711 Score: 1294
Period size: 34 Copynumber: 24.5 Consensus size: 34
6262873 ACCAACTTGT
* *
6262883 GTGGGCTTTTGAAAAGGAAAAAGATGCCACGGAGTT
1 GTGGGC-TTTGAAAA-GAAAAAGGTGCCACGGAGTG
* * * *
6262919 ATGGAC-TTAAAAAGGAAAAAAGGTGCCACGGAGTT
1 GTGGGCTTTGAAAA-G-AAAAAGGTGCCACGGAGTG
* *
6262954 GTGGGCTGTCAAAAG-AAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
6262987 GTGGGCTTTGAAAAG-AAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263020 GT-GGCTTTCAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263053 GTGGGCTTTCAAAAG-AAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
* * *
6263086 GTGGGCTTTAAAAAGAAAAAAGTGCCACGGAATG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
6263120 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
6263154 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
* *
6263188 GTGGGCTTTGAAATGAAAAAGGTGCCATGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263222 GTGGGCTTTCAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263256 GTGGGCTTTCAAAAG-AAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263289 GTGGGCTTTGAAAAGAAAATGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263323 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGTGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
* *
6263357 GTGGGCTTTGAAATGAAAAAGGTGCCACGGAGTT
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
6263391 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263425 GTGGGCTTTGAAATGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
* *
6263459 GTGGGCTTTGAAATGAAAAAGGTGCCGCGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
* *
6263493 GTGGGCTTTGAAAAGAAAAGGGTGCCATGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
* *
6263527 GTGGGCTTTGAAATGAAAAATGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263561 GTGGGCTTTGAAATGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
6263595 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
6263629 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263663 GTGGGCTTTCAAAAG-AAAAGGTGCCACGGAGTG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
*
6263696 GTGGGCTTTGAGAAGA
1 GTGGGCTTTGAAAAGA
6263712 GATTGCCACT
Statistics
Matches: 739, Mismatches: 47, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
32 11 0.01
33 165 0.22
34 531 0.72
35 23 0.03
36 9 0.01
ACGTcount: A:0.31, C:0.12, G:0.37, T:0.19
Consensus pattern (34 bp):
GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTG
Found at i:6274372 original size:78 final size:79
Alignment explanation
Indices: 6274268--6274442 Score: 217
Period size: 78 Copynumber: 2.2 Consensus size: 79
6274258 GAGATAAAGA
* * * * *
6274268 CGGGGTTGGAGTATCCCTTCAGAAATAACGAGGCTGTAGTATCCCCGGTTATGAAAAATCGGTGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACGAGGCTGGAGTATCCCCGATTATGAAAAATCGATGT
*
6274333 TCTAAAAATAAACT
66 TCTAAAAATAAAAT
* * * * *
6274347 -GGGGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACGAGGCTGGAGTATCCCCGATTATGAAAAATCGATGT
* *
6274411 TTTGAAAATAAAAT
66 TCTAAAAATAAAAT
*
6274425 CGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
6274443 GATGGTGGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 65 0.80
79 16 0.20
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAACGAGGCTGGAGTATCCCCGATTATGAAAAATCGATGT
TCTAAAAATAAAAT
Found at i:6274381 original size:28 final size:30
Alignment explanation
Indices: 6274336--6274391 Score: 98
Period size: 28 Copynumber: 1.9 Consensus size: 30
6274326 TCGGTGTTCT
6274336 AAAAATAAACTGGGGTTGGAGTATCCCCTC
1 AAAAATAAACTGGGGTTGGAGTATCCCCTC
6274366 AAAAAT-AA-TGGGGTTGGAGTATCCCC
1 AAAAATAAACTGGGGTTGGAGTATCCCC
6274392 GATTGTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 18 0.69
29 2 0.08
30 6 0.23
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (30 bp):
AAAAATAAACTGGGGTTGGAGTATCCCCTC
Found at i:6274440 original size:51 final size:50
Alignment explanation
Indices: 6274376--6274492 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 50
6274366 AAAAATAATG
*
6274376 GGGTTGGAGTATCCCCGATTGTGGAAAATCGA-TGTTTTGAAAATAAAA-T
1 GGGTTGGAGTATCCCCGATGGTGGAAAAT-GAGTGTTTTGAAAATAAAACT
* *
6274425 CGAGGTTGGAGTATCCCCGATGGTGGAAAATTAGTGTTTTGGAAATAAAACT
1 -G-GGTTGGAGTATCCCCGATGGTGGAAAATGAGTGTTTTGAAAATAAAACT
6274477 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
6274493 TCGAAAATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
50 17 0.28
51 43 0.70
52 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATGGTGGAAAATGAGTGTTTTGAAAATAAAACT
Found at i:6274455 original size:129 final size:129
Alignment explanation
Indices: 6274322--6274569 Score: 338
Period size: 129 Copynumber: 1.9 Consensus size: 129
6274312 CCGGTTATGA
* * * * *
6274322 AAAATCGGTGTTCTAAAAAT-AAACTGGGGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGT
1 AAAATCAGTGTTCTAAAAATAAAACT-GGGTTGGAGTATCCCCTCAAAAATAACGGAGCTAGAGT
* * *
6274386 ATCCCCGATTGTGGAAAATC-GATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCGATGGTG
65 ATCCCCGATTGTGAAAAATCAG-TGTTTTGAAAATAAAACCGAGGTTGAAGTATCCCCGATGGTG
6274450 G
129 G
* * ** *
6274451 AAAATTAGTGTTTTGGAAATAAAACTGGGTTGGAGTATCCCCTCGAAAATAACGGAGCTAGAGTA
1 AAAATCAGTGTTCTAAAAATAAAACTGGGTTGGAGTATCCCCTCAAAAATAACGGAGCTAGAGTA
*
6274516 TCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCC
66 TCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGAGGTTGAAGTATCC
6274570 TCTCAAAAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 97 0.94
130 6 0.06
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (129 bp):
AAAATCAGTGTTCTAAAAATAAAACTGGGTTGGAGTATCCCCTCAAAAATAACGGAGCTAGAGTA
TCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGAGGTTGAAGTATCCCCGATGGTGG
Found at i:6274601 original size:79 final size:78
Alignment explanation
Indices: 6274428--6274650 Score: 286
Period size: 79 Copynumber: 2.8 Consensus size: 78
6274418 ATAAAATCGA
* * * * *
6274428 GGTTGGAGTATCCCCGATGGTGGAAAATTAGTGTTTTGGAAATAAAA-CTGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGGGGTTGAAGTATCCC
*
6274492 CTCGAAAATAACG
66 CTCAAAAATAACG
* * *
6274505 GAGCTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCC
1 G-GTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGGGGTTGAAGTATCC
*
6274570 TCTCAAAAATAACAG
65 CCTCAAAAATAAC-G
* * * * *
6274585 GGTTGGAGCATCCCCGATTGTGAAAAATCAATGTTTTGGATATAAAACTGGGGTTGAAGCATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGGGGTTGAAGTATCCC
6274650 C
66 C
6274651 CCGAGAGTAT
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
77 1 0.01
78 40 0.32
79 81 0.65
80 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGGGGTTGAAGTATCCC
CTCAAAAATAACG
Found at i:6274740 original size:79 final size:79
Alignment explanation
Indices: 6274655--6274950 Score: 323
Period size: 79 Copynumber: 3.8 Consensus size: 79
6274645 ATCCCCCCGA
* ** * *
6274655 GAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGTATCTCCTTGA
1 GAGTATCCCCGATTATGAAAAATCAGTGTTTTAAAAATAAAATCAGGGTTGGAGTATC-CCTTCA
**
6274720 -AAATAACAGGGTTG
65 GAAATAATGGGGTTG
* * * * * *
6274734 GAGTATCCCTGATTGTGAAAAATC-GATGTTTTAAAAATAAAACCAGAGTTGGAGCATCCCCTCA
1 GAGTATCCCCGATTATGAAAAATCAG-TGTTTTAAAAATAAAATCAGGGTTGGAGTATCCCTTCA
6274798 GAAATAATGGGGTTG
65 GAAATAATGGGGTTG
* * * *
6274813 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTAAAAATAAAA-CTGGGGTTGGAGTATCCTTTT
1 GAGTATCCCCGATTATGA-AAAATCAGTGTTTTAAAAATAAAATC-AGGGTTGGAGTATCCCTTC
*
6274876 AGATATAATGGGGTTG
64 AGAAATAATGGGGTTG
* * **
6274892 GAGTATCCCTGATTATGAAAAATCAGTGTTTTGAAAAT-AAATTGGGGTTGGAGTATCCC
1 GAGTATCCCCGATTATGAAAAATCAGTGTTTTAAAAATAAAATCAGGGTTGGAGTATCCC
6274951 CTCGGAAGTA
Statistics
Matches: 185, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
78 25 0.14
79 158 0.85
80 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (79 bp):
GAGTATCCCCGATTATGAAAAATCAGTGTTTTAAAAATAAAATCAGGGTTGGAGTATCCCTTCAG
AAATAATGGGGTTG
Found at i:6274774 original size:144 final size:144
Alignment explanation
Indices: 6274510--6274794 Score: 401
Period size: 144 Copynumber: 2.0 Consensus size: 144
6274500 TAACGGAGCT
*
6274510 AGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCCTCTCA
1 AGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCAGGGTTGAAGTATCCTCTCA
** * ** *
6274575 AAAATAACAGGGTTGGAGCATCCCCGATTGTGAAAAATCAATGTTTTGGATATAAAACTGGGGTT
66 AAAATAACAGGGTTGGAGCATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACCAGAGTT
6274640 GAAGCATCCCCCCG
131 GAAGCATCCCCCCG
** * * *
6274654 AGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGTAT-CTCCTT
1 AGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCAGGGTTGAAGTATCCT-CTC
* * * *
6274718 GAAAATAACAGGGTTGGAGTATCCCTGATTGTGAAAAATCGATGTTTTAAAAATAAAACCAGAGT
65 AAAAATAACAGGGTTGGAGCATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACCAGAGT
*
6274783 TGGAGCATCCCC
130 TGAAGCATCCCC
6274795 TCAGAAATAA
Statistics
Matches: 123, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
143 2 0.02
144 121 0.98
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (144 bp):
AGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCAGGGTTGAAGTATCCTCTCA
AAAATAACAGGGTTGGAGCATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACCAGAGTT
GAAGCATCCCCCCG
Found at i:6274823 original size:223 final size:222
Alignment explanation
Indices: 6274433--6274863 Score: 571
Period size: 223 Copynumber: 1.9 Consensus size: 222
6274423 ATCGAGGTTG
* * *
6274433 GAGTATCCCCGATGGTGGAAAATTAGTGTTTTGGAAATAAAACTGGGTTGGAGTATCCCCTCGAA
1 GAGTATCCCCGATGGTGAAAAATTAGTGTTTTGAAAATAAAACAGGGTTGGAGTATCCCCTCGAA
* * *
6274498 AATAACGGAGCTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGGGGTTGA
66 AATAACGGAGCTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTAAAAATAAAACCAGAGTTGA
* * * ** *
6274563 AGTATCCTCTCAAAAATAACAGGGTTGGAGCATCCCCGATTGT-GAAAAATCAATGTTTTGGATA
131 AGCATCCCCTCAAAAATAACAGGGTTGGAGCATCCCCGATTATAG-AAAATCAATGTTTTAAAAA
6274627 TAAAACTGGGGTTGAAGCATCCCCCCGA
195 TAAAACTGGGGTTGAAGCATCCCCCCGA
* * * *
6274655 GAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGTATCTCCTTGA
1 GAGTATCCCCGATGGTGAAAAATTAGTGTTTTGAAAATAAAA-CAGGGTTGGAGTATCCCCTCGA
* * *
6274720 AAATAACAGG-GTTGGAGTATCCCTGATTGTGAAAAATC-GATGTTTTAAAAATAAAACCAGAGT
65 AAATAAC-GGAGCTAGAGTATCCCCGATTGTGAAAAATCAG-TGTTTTAAAAATAAAACCAGAGT
* * ** * * *
6274783 TGGAGCATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTAAA
128 TGAAGCATCCCCTCAAAAATAACAGGGTTGGAGCATCCCCGATTATAGAAAATCAATGTTTTAAA
6274848 AATAAAACTGGGGTTG
193 AATAAAACTGGGGTTG
6274864 GAGTATCCTT
Statistics
Matches: 179, Mismatches: 26, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
222 39 0.22
223 137 0.77
224 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (222 bp):
GAGTATCCCCGATGGTGAAAAATTAGTGTTTTGAAAATAAAACAGGGTTGGAGTATCCCCTCGAA
AATAACGGAGCTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTAAAAATAAAACCAGAGTTGA
AGCATCCCCTCAAAAATAACAGGGTTGGAGCATCCCCGATTATAGAAAATCAATGTTTTAAAAAT
AAAACTGGGGTTGAAGCATCCCCCCGA
Found at i:6275726 original size:34 final size:34
Alignment explanation
Indices: 6275683--6275799 Score: 182
Period size: 34 Copynumber: 3.4 Consensus size: 34
6275673 TTTGCTCTTT
*
6275683 GAGGACAAAGGAAAAATAGTATGTCCTACTATTC
1 GAGGACAAAGGAAAAATAGTATGTCCTGCTATTC
*
6275717 GAGGACAAAGGAAAAATAGTACGTCCTGCTATTC
1 GAGGACAAAGGAAAAATAGTATGTCCTGCTATTC
*
6275751 GAGGACAAAGG-AAAATGAGTATGTCCTGCTTTTC
1 GAGGACAAAGGAAAAAT-AGTATGTCCTGCTATTC
*
6275785 AAGGACAAAGGAAAA
1 GAGGACAAAGGAAAA
6275800 GAGAATTAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
33 5 0.07
34 68 0.89
35 3 0.04
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (34 bp):
GAGGACAAAGGAAAAATAGTATGTCCTGCTATTC
Found at i:6275863 original size:42 final size:42
Alignment explanation
Indices: 6275773--6275916 Score: 159
Period size: 42 Copynumber: 3.4 Consensus size: 42
6275763 AAATGAGTAT
* * * *
6275773 GTCCTGCT-TTTCAAGGACAAAGGAAAAGA-G-AATTAAATGG
1 GTCCTGCTCTTT-GAGGACAAAGGAAAAAAGGAAATAAAATGC
*
6275813 GTCCTGCTCCTTGAGGACAAAGGAAAAAAGGAAATAAAATGC
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGC
* * *
6275855 GTCATGCTCTTTGAGGATAAAGGAAAAGAAGGAAATTAAAACGC
1 GTCCTGCTCTTTGAGGACAAAGGAAAA-AAGGAAA-TAAAATGC
*
6275899 GTCCTGCTCTTTGGGGAC
1 GTCCTGCTCTTTGAGGAC
6275917 TAGAAGGTGC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 23 0.26
41 3 0.03
42 32 0.37
43 7 0.08
44 22 0.25
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.22
Consensus pattern (42 bp):
GTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGC
Found at i:6276070 original size:61 final size:61
Alignment explanation
Indices: 6275892--6276407 Score: 454
Period size: 61 Copynumber: 8.5 Consensus size: 61
6275882 GAAGGAAATT
* * * * **
6275892 AAAACGCGTCCTGCTCTTTGGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTT--AAAAGG
* * * * ** *
6275955 AAAA-TCGTCCTGCTCTTTGAGGACT---A-CTACCACCAGCTCATGTGGGCTTCAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
* * *
6276011 AAAAGGTGTCCTACTCTTTGAGGAGTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
* ** * * * *
6276072 AAAAGGCATATTGCTCTTTGAGGACTGAAAGATGCCACCAACTTATATAGGCTTTAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
* * * * * *
6276133 AAAATGCGTCTTGCACTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
** * * * * * * *
6276194 AAAAGGTATCCTACTTTTTGACGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
* * * * *
6276255 AAAAGACGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAATGAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAA-G-G
* * * * * *
6276318 AAAATGTGTCATGCTCTTTGAGGACTAAAA-AGTGCCACCAACTTATATGGGC--TACAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGA-TGCCACCAACTTGTGTGGGCTTTAAAAGG
* * * *
6276377 AAAAGACGTCTTACTCTTTGAGGACTGAAAG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAG
6276408 GTTAAAAGGT
Statistics
Matches: 369, Mismatches: 75, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
56 8 0.02
57 17 0.05
58 18 0.05
59 25 0.07
60 2 0.01
61 232 0.63
62 19 0.05
63 48 0.13
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGG
Found at i:6276408 original size:183 final size:181
Alignment explanation
Indices: 6275898--6276409 Score: 577
Period size: 183 Copynumber: 2.8 Consensus size: 181
6275888 AATTAAAACG
* * **
6275898 CGTCCTGCTCTTTGGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGGGAAAAT-CG
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTT--AAAAGGAAAATGCG
* * * * *
6275962 TCCTGCTCTTTGAGGACT---ACTACCACCAGCTCATGTGGGCTTCAAAAGGAAAAGGTGTCCTA
64 TCATGCTCTTTGAGGACTAAAAGTGCCACCAACTTATGTGGGCTT-AAAAGGAAAAGGTGTCCTA
* * * *
6276024 CTCTTTGAGGAGTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
128 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGA
* ** * * *
6276078 CATATTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTATATAGGCTTTAAAAGGAAAATGCGT
1 CGTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAATGCGT
* * * * * *
6276142 CTTGCACTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGTATCCTA
65 CATGCTCTTTGAGGACT-AAAAGTGCCACCAACTTATGTGGGC-TTAAAAGGAAAAGGTGTCCTA
* * * *
6276207 CTTTTTGACGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAGA
128 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGA
* *
6276261 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAATGAAAAAATGTG
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAA-G-GAAAATGCG
* * ** *
6276326 TCATGCTCTTTGAGGACTAAAAAGTGCCACCAACTTATATGGGC-TACAAGGAAAAGACGTCTTA
64 TCATGCTCTTTGAGGACT-AAAAGTGCCACCAACTTATGTGGGCTTAAAAGGAAAAGGTGTCCTA
6276390 CTCTTTGAGGACTGAAAGGT
128 CTCTTTGAGGACTGAAAGGT
6276410 TAAAAGGTTT
Statistics
Matches: 272, Mismatches: 50, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
178 9 0.03
179 19 0.07
180 39 0.14
183 157 0.58
184 4 0.01
185 44 0.16
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (181 bp):
CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAATGCGTC
ATGCTCTTTGAGGACTAAAAGTGCCACCAACTTATGTGGGCTTAAAAGGAAAAGGTGTCCTACTC
TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGA
Found at i:6281827 original size:25 final size:25
Alignment explanation
Indices: 6281799--6281847 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6281789 TTCATATGAG
*
6281799 TTTTCATTATGTG-TTTTTTTTTATA
1 TTTTCATTAT-TGCTTTATTTTTATA
*
6281824 TTTTGATTATTGCTTTATTTTTAT
1 TTTTCATTATTGCTTTATTTTTAT
6281848 GTTGTCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.71
Consensus pattern (25 bp):
TTTTCATTATTGCTTTATTTTTATA
Found at i:6282121 original size:20 final size:20
Alignment explanation
Indices: 6282094--6282151 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
6282084 ATTTAGACTT
6282094 ATTTAAAAAAATACAGAAAAA
1 ATTTAAAAAAATA-AGAAAAA
6282115 A-TTAAAAAAATAA-AAAAA
1 ATTTAAAAAAATAAGAAAAA
6282133 ATTTTAAAAAAATAGAGAA
1 A-TTTAAAAAAATA-AGAA
6282152 TGAGTGGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 6 0.18
19 1 0.03
20 22 0.67
21 2 0.06
22 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
ATTTAAAAAAATAAGAAAAA
Found at i:6282332 original size:111 final size:111
Alignment explanation
Indices: 6282153--6282353 Score: 366
Period size: 111 Copynumber: 1.8 Consensus size: 111
6282143 AATAGAGAAT
**
6282153 GAGTGGCCTGGGTTTAAAATCCAGGCCACCTTTGTGGAAAATGGTCATTGTGACCCATGCACCAA
1 GAGTGGCCTAAGTTTAAAATCCAGGCCACCTTTGTGGAAAATGGTCATTGTGACCCATGCACCAA
6282218 AGTTAAGCTTTAGTCATAAATTAACCACCAAAAAAAAGAGAAAAAC
66 AGTTAAGCTTTAGTCATAAATTAACCACCAAAAAAAAGAGAAAAAC
* *
6282264 GAGTGGCCTAAGTTTCAAATCTAGGCCACCTTTGTGGAAAATGGTCATTGTGACCCATGCACCAA
1 GAGTGGCCTAAGTTTAAAATCCAGGCCACCTTTGTGGAAAATGGTCATTGTGACCCATGCACCAA
6282329 AGTTAAGCTTTAGTCATAAATTAAC
66 AGTTAAGCTTTAGTCATAAATTAAC
6282354 AAAAGAATAG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (111 bp):
GAGTGGCCTAAGTTTAAAATCCAGGCCACCTTTGTGGAAAATGGTCATTGTGACCCATGCACCAA
AGTTAAGCTTTAGTCATAAATTAACCACCAAAAAAAAGAGAAAAAC
Found at i:6283097 original size:6 final size:6
Alignment explanation
Indices: 6283076--6283119 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
6283066 ATGGGTGAAA
* * *
6283076 AAAAAGG AAGAAG AAAAAG AAAAAG AAAAAG AAGAAG AAGAAG A
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
6283120 TGGAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6283101 original size:12 final size:12
Alignment explanation
Indices: 6283076--6283119 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
6283066 ATGGGTGAAA
6283076 AAAAAGGAAGAAG
1 AAAAA-GAAGAAG
*
6283089 AAAAAGAAAAAG
1 AAAAAGAAGAAG
6283101 AAAAAGAAGAAG
1 AAAAAGAAGAAG
*
6283113 AAGAAGA
1 AAAAAGA
6283120 TGGAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:6284623 original size:20 final size:20
Alignment explanation
Indices: 6284598--6284648 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
6284588 ACCCTGAAAA
6284598 GTATCGATACACATTTG-AAT
1 GTATCGATACACA-TTGCAAT
* *
6284618 GTATCGATACAGATTGCATT
1 GTATCGATACACATTGCAAT
6284638 GTATCGATACA
1 GTATCGATACA
6284649 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATACACATTGCAAT
Found at i:6284652 original size:13 final size:13
Alignment explanation
Indices: 6284634--6284658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6284624 ATACAGATTG
6284634 CATTGTATCGATA
1 CATTGTATCGATA
6284647 CATTGTATCGAT
1 CATTGTATCGAT
6284659 CTATGACCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:6284772 original size:13 final size:13
Alignment explanation
Indices: 6284754--6284779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6284744 ACACACAGTA
6284754 TGTATCGATACAT
1 TGTATCGATACAT
6284767 TGTATCGATACAT
1 TGTATCGATACAT
6284780 CATAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6291097 original size:20 final size:20
Alignment explanation
Indices: 6291062--6291102 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
6291052 CAAATTTCTT
6291062 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
6291084 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
6291103 AAGAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:6293374 original size:20 final size:20
Alignment explanation
Indices: 6293349--6293399 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
6293339 ACCCTGAAAA
6293349 GTATCGATACACATTTG-AAT
1 GTATCGATACACA-TTGCAAT
* *
6293369 GTATCGATACAGATTGCATT
1 GTATCGATACACATTGCAAT
6293389 GTATCGATACA
1 GTATCGATACA
6293400 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATACACATTGCAAT
Found at i:6293403 original size:13 final size:13
Alignment explanation
Indices: 6293385--6293413 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6293375 ATACAGATTG
6293385 CATTGTATCGATA
1 CATTGTATCGATA
6293398 CATTGTATCGATA
1 CATTGTATCGATA
6293411 CAT
1 CAT
6293414 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:6293445 original size:21 final size:20
Alignment explanation
Indices: 6293401--6293453 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6293391 ATCGATACAT
**
6293401 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
6293421 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
6293442 TGTATCAATACA
1 TGTATCGATACA
6293454 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:6293523 original size:13 final size:13
Alignment explanation
Indices: 6293505--6293532 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6293495 ACACACAGTA
6293505 TGTATCGATACAT
1 TGTATCGATACAT
6293518 TGTATCGATACAT
1 TGTATCGATACAT
6293531 TG
1 TG
6293533 GCTTGTAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6300124 original size:13 final size:13
Alignment explanation
Indices: 6300106--6300131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6300096 AATTTTTTGG
6300106 TGTATCGATACAT
1 TGTATCGATACAT
6300119 TGTATCGATACAT
1 TGTATCGATACAT
6300132 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6300226 original size:20 final size:20
Alignment explanation
Indices: 6300180--6300256 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
6300170 ATCCCAATGA
***
6300180 CATGTATCGATACATATTTTT
1 CATGTATCGATACAT-TGAAT
6300201 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
6300221 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
6300241 TGTGTATCGATACATT
1 CATGTATCGATACATT
6300257 TAAGGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:6302695 original size:13 final size:13
Alignment explanation
Indices: 6302677--6302714 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
6302667 ATAATCCCCC
6302677 TGTATCGATACAG
1 TGTATCGATACAG
*
6302690 TGTATCGATACAT
1 TGTATCGATACAG
6302703 TGTATCGATACA
1 TGTATCGATACA
6302715 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:6304807 original size:15 final size:15
Alignment explanation
Indices: 6304787--6304827 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
6304777 GTTCATCGAT
6304787 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
6304802 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
6304817 CTCAATTTGGA
1 TTC-ATTTGGA
6304828 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:6306666 original size:21 final size:21
Alignment explanation
Indices: 6306637--6306681 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6306627 AAGTTTTTAT
*
6306637 TTTTCTTAG-CTAATTCATTA
1 TTTTCTTAGCCAAATTCATTA
*
6306657 TTTTCATTAGCCAAATTCTTTA
1 TTTTC-TTAGCCAAATTCATTA
6306679 TTT
1 TTT
6306682 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAAATTCATTA
Found at i:6308904 original size:21 final size:20
Alignment explanation
Indices: 6308879--6308931 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
6308869 TACAAGCCAA
**
6308879 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA-TACTTGG
6308900 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
6308919 TGTATCGATACAA
1 TGTATCGATACAA
6308932 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:6308937 original size:19 final size:18
Alignment explanation
Indices: 6308879--6308937 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 18
6308869 TACAAGCCAA
6308879 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA---TTTGG
*
6308900 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
6308919 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
6308938 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
21 12 0.35
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:6309007 original size:20 final size:20
Alignment explanation
Indices: 6308961--6309037 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
6308951 ATCCCAATGA
***
6308961 CATGTATCGATACATATTTTT
1 CATGTATCGATACAT-TGAAT
6308982 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
6309002 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
6309022 TGTGTATCGATACATT
1 CATGTATCGATACATT
6309038 TAAAGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:6312408 original size:52 final size:52
Alignment explanation
Indices: 6312263--6312388 Score: 252
Period size: 52 Copynumber: 2.4 Consensus size: 52
6312253 AATATGAAAT
6312263 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
6312315 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
6312367 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
6312389 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:6313485 original size:49 final size:48
Alignment explanation
Indices: 6313367--6313662 Score: 284
Period size: 49 Copynumber: 6.1 Consensus size: 48
6313357 TATTGGACTT
* * * * *
6313367 GTGCTAATGTGCTAATTCAAGGCCAGCTAC-ATTGGACTCAAGACGGAAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGC-GCTATTGGACTTAA-A--GATAAG
* *
6313418 GTGCCAATATGCTGATTCAAGGCCAGCGCTATTGGACTTAAAAATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGCTATTGGACTTAAAGAT-AAG
** *
6313467 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGCTATTGGACTTAAAGAT-AAG
* *
6313516 GTGCCAATGTGCTGACTCAAGGCCAGCGAC-ATTGGTCTTAAAGATAAGG
1 GTGCCAATGTGCTGATTCAAGGCCAGCG-CTATTGGACTTAAAGATAA-G
* * **
6313565 GTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-AAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGCTATTGGACTTAAAGATAAG
* *
6313608 GTGCCAATGTGCTGAGTCAAGGCCAGCTAC-ATTGGACTTAAAGATAAGG
1 GTGCCAATGTGCTGATTCAAGGCCAGC-GCTATTGGACTTAAAGATAA-G
6313657 GTGCCA
1 GTGCCA
6313663 CAGACTCGTG
Statistics
Matches: 205, Mismatches: 28, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
43 34 0.17
44 2 0.01
45 1 0.00
47 1 0.00
48 4 0.02
49 127 0.62
50 2 0.01
51 34 0.17
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGCTATTGGACTTAAAGATAAG
Found at i:6313550 original size:98 final size:95
Alignment explanation
Indices: 6313367--6313662 Score: 359
Period size: 98 Copynumber: 3.1 Consensus size: 95
6313357 TATTGGACTT
* * * * *
6313367 GTGCTAATGTGCTAATTCAAGGCCAGCTACATTGGACTCAAGACGGAAAAGGTGCCAATATGCTG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAA-A--G--AAGGTGCCAATGTGCTG
* *
6313432 ATTCAAGGCCAGCG-CTATTGGACTTAAAAATGAA-G
61 ACTCAAGGCCAGCGAC-ATTGGACTTAAAGAT-AAGG
6313467 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGGGTGCCAATGTGCTGAC
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA--A-GGTGCCAATGTGCTGAC
*
6313532 TCAAGGCCAGCGACATTGGTCTTAAAGATAAGG
63 TCAAGGCCAGCGACATTGGACTTAAAGATAAGG
* * *
6313565 GTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAGGTGCCAATGTGCTGAGTCA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGCCAATGTGCTGACTCA
*
6313627 AGGCCAGCTACATTGGACTTAAAGATAAGG
66 AGGCCAGCGACATTGGACTTAAAGATAAGG
6313657 GTGCCA
1 GTGCCA
6313663 CAGACTCGTG
Statistics
Matches: 177, Mismatches: 14, Indels: 18
0.85 0.07 0.09
Matches are distributed among these distances:
92 52 0.29
93 1 0.01
95 2 0.01
96 1 0.01
97 4 0.02
98 78 0.44
99 2 0.01
100 37 0.21
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (95 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGCCAATGTGCTGACTCA
AGGCCAGCGACATTGGACTTAAAGATAAGG
Found at i:6313646 original size:141 final size:144
Alignment explanation
Indices: 6313367--6313662 Score: 393
Period size: 141 Copynumber: 2.0 Consensus size: 144
6313357 TATTGGACTT
* * *
6313367 GTGCTAATGTGCTAATTCAAGGCCAGCTACATTGGACTCAAGACGGAAAAGGTGCCAATATGCTG
1 GTGCCAATGTGCTAACTCAAGGCCAGCGACATTGGACTCAAGAC-GAAAAGGTGCCAATATGCTG
* * *
6313432 ATTCAAGGCCAGCGCTATTGGACTTAAAAATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAT
65 ATTCAAGGCCAGCGATATTGGACTT---AA-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTAC
*
6313497 ATTGGACTTAAAGATGAGG
126 ATTGGACTTAAAGATAAGG
* * * * *
6313516 GTGCCAATGTGCTGACTCAAGGCCAGCGACATTGGTCTTAA-A-GATAAGGGTGCTAATATGCTG
1 GTGCCAATGTGCTAACTCAAGGCCAGCGACATTGGACTCAAGACGA-AAAGGTGCCAATATGCTG
*
6313579 ATTCAAGGCCAGCTATATTGGACTT-A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
65 ATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
6313642 GACTTAAAGATAAGG
130 GACTTAAAGATAAGG
6313657 GTGCCA
1 GTGCCA
6313663 CAGACTCGTG
Statistics
Matches: 133, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
141 55 0.41
143 1 0.01
146 2 0.02
147 39 0.29
148 1 0.01
149 35 0.26
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (144 bp):
GTGCCAATGTGCTAACTCAAGGCCAGCGACATTGGACTCAAGACGAAAAGGTGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGG
ACTTAAAGATAAGG
Found at i:6313721 original size:35 final size:34
Alignment explanation
Indices: 6313670--6313878 Score: 203
Period size: 35 Copynumber: 6.4 Consensus size: 34
6313660 CCACAGACTC
* *
6313670 GTGGACTTAGAAGGAAAAAGAGTGCCACGAAGTT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACGAAGTT
6313704 GTGGGCTTAAAAAGGAAAAAGAGTGCCAC-AGAGTT
1 GTGGGCTT-AAAAGGAAAAAGAGTGCCACGA-AGTT
*
6313739 GTGGGCTTAAAA-G-----G-GTGCCACGGAGTT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACGAAGTT
*
6313766 GTGGACTTAAAAGGAAAAAGAGTGCCAC-AGAGTT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACGA-AGTT
*
6313800 GTGGGCTTTAAAAAGAAAAACG-GTGCCACGAAGTT
1 GTGGGC-TTAAAAGGAAAAA-GAGTGCCACGAAGTT
* * *
6313835 GTGGGCTT---CGG-AAAAGGGTGCCACGGAGTT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACGAAGTT
6313865 GTGGGCTTAAAAGG
1 GTGGGCTTAAAAGG
6313879 GTGAGGAATG
Statistics
Matches: 146, Mismatches: 11, Indels: 37
0.75 0.06 0.19
Matches are distributed among these distances:
27 22 0.15
28 2 0.01
29 1 0.01
30 24 0.16
31 1 0.01
33 4 0.03
34 30 0.21
35 60 0.41
36 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.19
Consensus pattern (34 bp):
GTGGGCTTAAAAGGAAAAAGAGTGCCACGAAGTT
Found at i:6313758 original size:27 final size:27
Alignment explanation
Indices: 6313720--6313881 Score: 110
Period size: 27 Copynumber: 5.3 Consensus size: 27
6313710 TTAAAAAGGA
*
6313720 AAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTT
* *
6313747 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTT
6313774 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAA-G-----G-GTGCCACAGAGTTGTGGGC-TT
6313809 AAAAAGAAAAACGGTGCCAC-GAAGTTGTGGGCTT
1 -AAAAG------GGTGCCACAG-AGTTGTGGGCTT
*
6313843 CGGAAAAGGGTGCCACGGAGTTGTGGGCTT
1 ---AAAAGGGTGCCACAGAGTTGTGGGCTT
6313873 AAAAGGGTG
1 AAAAGGGTG
6313882 AGGAATGTCT
Statistics
Matches: 114, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
27 37 0.32
28 1 0.01
30 20 0.18
31 1 0.01
33 1 0.01
34 20 0.18
35 20 0.18
36 14 0.12
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGGCTT
Found at i:6313801 original size:61 final size:61
Alignment explanation
Indices: 6313685--6313881 Score: 231
Period size: 61 Copynumber: 3.1 Consensus size: 61
6313675 CTTAGAAGGA
*
6313685 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGAAGTTGTGGGCTT-AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
* *
6313747 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TT
* * *
6313809 AAAAAGAAAAACGGTGCCACGAAGTTGTGGGCTT---CGG-AAAAGGGTGCCACGGAGTTGTGGG
1 -AAAAG------GGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGG
6313870 CTT
59 CTT
6313873 AAAAGGGTG
1 AAAAGGGTG
6313882 AGGAATGTCT
Statistics
Matches: 119, Mismatches: 8, Indels: 21
0.80 0.05 0.14
Matches are distributed among these distances:
57 4 0.03
61 32 0.27
62 26 0.22
63 10 0.08
64 2 0.02
65 23 0.19
66 2 0.02
69 20 0.17
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (61 bp):
AAAAGGGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
Found at i:6313818 original size:96 final size:97
Alignment explanation
Indices: 6313653--6313878 Score: 318
Period size: 96 Copynumber: 2.3 Consensus size: 97
6313643 ACTTAAAGAT
* * * *
6313653 AAGGGTGCCACAGACTCGTGGACTTAGAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAG
1 AAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAG
6313718 GAAAAA-GAGTGCCAC-AGAGTTGTGGGCTT-AA
66 GAAAAACG-GTGCCACGA-AGTTGTGGGCTTGAA
6313749 AAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCAC-AGAGTTGTGGGCTTTAAAA
1 AAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGA-AGTTGTGGGC-TTAAAA
6313813 A-GAAAAACGGTGCCACGAAGTTGTGGGCTTCGGAA
64 AGGAAAAACGGTGCCACGAAGTTGTGGGCTT--GAA
*
6313848 AAGGGTGCCACGGAGTTGTGGGCTTAAAAGG
1 AAGGGTGCCACGGAGTTGTGGACTTAAAAGG
6313879 GTGAGGAATG
Statistics
Matches: 118, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
95 1 0.01
96 76 0.64
97 9 0.08
99 32 0.27
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (97 bp):
AAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAG
GAAAAACGGTGCCACGAAGTTGTGGGCTTGAA
Found at i:6315327 original size:11 final size:11
Alignment explanation
Indices: 6315311--6315389 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 11
6315301 ATCCGGACCC
6315311 TTTTTGTTGTT
1 TTTTTGTTGTT
6315322 TTTTTG-T-TT
1 TTTTTGTTGTT
*
6315331 TTTTTGTCTTTT
1 TTTTTGT-TGTT
6315343 TTTTTGTT-TT
1 TTTTTGTTGTT
*
6315353 TTTTT-CTGTT
1 TTTTTGTTGTT
*
6315363 TTTTTCTTG-T
1 TTTTTGTTGTT
6315373 TTTTTGTTTGTT
1 TTTTTG-TTGTT
6315385 TTTTT
1 TTTTT
6315390 CTTTCTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
9 9 0.16
10 21 0.36
11 13 0.22
12 15 0.26
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTGTTGTT
Found at i:6315333 original size:10 final size:10
Alignment explanation
Indices: 6315311--6315389 Score: 95
Period size: 11 Copynumber: 7.3 Consensus size: 10
6315301 ATCCGGACCC
6315311 TTTTTGTTGTT
1 TTTTTGTT-TT
6315322 TTTTTGTTTT
1 TTTTTGTTTT
*
6315332 TTTTGTCTTTT
1 TTTT-TGTTTT
6315343 TTTTTGTTTTT
1 TTTTTG-TTTT
6315354 TTTTCTGTTTT
1 TTTT-TGTTTT
6315365 TTTCTTGTTTT
1 TTT-TTGTTTT
6315376 TTGTTTGTTTT
1 TT-TTTGTTTT
6315387 TTT
1 TTT
6315390 CTTTCTTTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
10 8 0.13
11 49 0.80
12 4 0.07
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:6315335 original size:12 final size:12
Alignment explanation
Indices: 6315328--6315399 Score: 76
Period size: 12 Copynumber: 6.2 Consensus size: 12
6315318 TGTTTTTTTG
*
6315328 TTTTTTTTGTCT
1 TTTTTTTTGTTT
6315340 TTTTTTTTGTTT
1 TTTTTTTTGTTT
*
6315352 TTTTTTCTG-TT
1 TTTTTTTTGTTT
*
6315363 TTTTTCTTG-TT
1 TTTTTTTTGTTT
*
6315374 TTTTGTTTGTTT
1 TTTTTTTTGTTT
* *
6315386 TTTTCTTTCTTT
1 TTTTTTTTGTTT
6315398 TT
1 TT
6315400 CGGAGGACGC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
11 18 0.35
12 33 0.65
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:6315353 original size:22 final size:21
Alignment explanation
Indices: 6315311--6315399 Score: 99
Period size: 23 Copynumber: 4.0 Consensus size: 21
6315301 ATCCGGACCC
*
6315311 TTTTTGTTGTTTTTTTG-TTT
1 TTTTTGTTTTTTTTTTGTTTT
6315331 TTTTTGTCTTTTTTTTTGTTTTT
1 TTTTTGT-TTTTTTTTTG-TTTT
*
6315354 TTTTCTGTTTTTTTCTTGTTTT
1 TTTT-TGTTTTTTTTTTGTTTT
*
6315376 TTGTTTGTTTTTTTCTTTCTTTT
1 TT-TTTGTTTTTTT-TTTGTTTT
6315399 T
1 T
6315400 CGGAGGACGC
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.12
21 9 0.15
22 15 0.25
23 25 0.42
24 3 0.05
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (21 bp):
TTTTTGTTTTTTTTTTGTTTT
Found at i:6315398 original size:11 final size:10
Alignment explanation
Indices: 6315320--6315400 Score: 83
Period size: 10 Copynumber: 7.8 Consensus size: 10
6315310 CTTTTTGTTG
*
6315320 TTTTTTTGTT
1 TTTTTTTCTT
6315330 TTTTTTGTCTT
1 TTTTTT-TCTT
*
6315341 TTTTTTTGTT
1 TTTTTTTCTT
*
6315351 TTTTTTTCTG
1 TTTTTTTCTT
6315361 TTTTTTTCTT
1 TTTTTTTCTT
6315371 GTTTTTTGT-TT
1 -TTTTTT-TCTT
6315382 GTTTTTTTCTT
1 -TTTTTTTCTT
*
6315393 TCTTTTTC
1 TTTTTTTC
6315401 GGAGGACGCC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
10 34 0.56
11 26 0.43
12 1 0.02
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:6315400 original size:32 final size:30
Alignment explanation
Indices: 6315311--6315400 Score: 110
Period size: 32 Copynumber: 2.9 Consensus size: 30
6315301 ATCCGGACCC
* *
6315311 TTTTTGTTGTTTTTTTGTTTTTTTTGTCTTTT
1 TTTTTGTTGTTTTTTT-CTTTTTTT-TCTTGT
6315343 TTTTTGTT-TTTTTTTCTGTTTTTTTCTTGT
1 TTTTTGTTGTTTTTTTCT-TTTTTTTCTTGT
6315373 TTTTTGTTTGTTTTTTTCTTTCTTTTTC
1 TTTTTG-TTGTTTTTTTCTTT-TTTTTC
6315401 GGAGGACGCC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
30 12 0.23
31 17 0.33
32 23 0.44
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (30 bp):
TTTTTGTTGTTTTTTTCTTTTTTTTCTTGT
Found at i:6315415 original size:1 final size:1
Alignment explanation
Indices: 6315320--6315399 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
6315310 CTTTTTGTTG
* * * * * * * * * *
6315320 TTTTTTTGTTTTTTTTGTCTTTTTTTTTGTTTTTTTTTCTGTTTTTTTCTTGTTTTTTGTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
6315385 TTTTTCTTTCTTTTT
1 TTTTTTTTTTTTTTT
6315400 CGGAGGACGC
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:6329489 original size:52 final size:52
Alignment explanation
Indices: 6329240--6329469 Score: 433
Period size: 52 Copynumber: 4.4 Consensus size: 52
6329230 AATATGAAAT
*
6329240 TTTGTCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
6329292 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
6329344 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* *
6329396 TTTGCCTGCATGTATCGATACATTTCATAGTATATCGATACATCTAGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
6329448 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
6329470 AAGATCAGTG
Statistics
Matches: 175, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 175 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:6329496 original size:13 final size:13
Alignment explanation
Indices: 6329478--6329502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6329468 CAAAGATCAG
6329478 TGTATCGATACAA
1 TGTATCGATACAA
6329491 TGTATCGATACA
1 TGTATCGATACA
6329503 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6329976 original size:13 final size:13
Alignment explanation
Indices: 6329958--6329985 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6329948 TACACTTTCA
6329958 ATTGTATCGATAC
1 ATTGTATCGATAC
6329971 ATTGTATCGATAC
1 ATTGTATCGATAC
6329984 AT
1 AT
6329986 GACAAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:6329977 original size:33 final size:31
Alignment explanation
Indices: 6329940--6330006 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
6329930 AACCCTTAAA
** *
6329940 TGTATCGATACACTTTCAATTGTATCGATACAT
1 TGTATCGATACA-TGACAAATGTATCGATAC-T
6329973 TGTATCGATACATGACAAATGTATCGATACT
1 TGTATCGATACATGACAAATGTATCGATACT
6330004 TGT
1 TGT
6330007 TAAGAATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 4 0.13
32 15 0.48
33 12 0.39
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (31 bp):
TGTATCGATACATGACAAATGTATCGATACT
Found at i:6329997 original size:19 final size:20
Alignment explanation
Indices: 6329973--6330024 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
6329963 ATCGATACAT
6329973 TGTATCGATACATG-ACA-AA
1 TGTATCGATACATGTA-AGAA
*
6329992 TGTATCGATACTTGTTAAGAA
1 TGTATCGATACATG-TAAGAA
6330013 TGTATCGATACA
1 TGTATCGATACA
6330025 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 14 0.50
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGTAAGAA
Found at i:6330092 original size:13 final size:13
Alignment explanation
Indices: 6330074--6330099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6330064 ACACACAATA
6330074 TGTATCGATACAT
1 TGTATCGATACAT
6330087 TGTATCGATACAT
1 TGTATCGATACAT
6330100 CCTAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6335965 original size:8 final size:8
Alignment explanation
Indices: 6335952--6335982 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
6335942 ATTTGATTAA
6335952 ATTTTGTG
1 ATTTTGTG
6335960 ATTTTGTG
1 ATTTTGTG
6335968 ATTTTGTG
1 ATTTTGTG
6335976 ATGTTTG
1 AT-TTTG
6335983 ATGTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (8 bp):
ATTTTGTG
Found at i:6338627 original size:13 final size:13
Alignment explanation
Indices: 6338609--6338633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6338599 ATATTGCACA
6338609 GTATCGATACATT
1 GTATCGATACATT
6338622 GTATCGATACAT
1 GTATCGATACAT
6338634 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Done.