Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 30
Found at i:3031632 original size:176 final size:176
Alignment explanation
Indices: 3031332--3031658 Score: 478
Period size: 176 Copynumber: 1.9 Consensus size: 176
3031322 GTATTTTTTG
*
3031332 GAATCATGTTTAGGAGGTCAAGGGCTTTGATTTAGTATAGTTTGGTATTTTTCGGCCACCACTCA
1 GAATCATGTTTAGGAGGTCAAGGGCTTTGATTTAGTATAGTTTGGTATTTTTCGGCCACCACCCA
* * * * * *
3031397 GCGGCTATCGGTAATGGCACATGGTGGTCGGCCGGTGATCGATCTCCCTCCGACGAGGGATTCTA
66 GCGACTATAGCTAACGGCACATGGTGGCCGGCCGGTGATCAATCTCCCTCCGACGAGGGATTCTA
* *
3031462 GAGGGAGTTGAGAGTTTCTCTATCTTTTTAGTAGAAAAGAGGCTCA
131 GAGAGAGTTGAGAGCTTCTCTATCTTTTTAGTAGAAAAGAGGCTCA
* *
3031508 GAATCGTGTTTAGGAGGTCAAGGGCTTTGATTTAGTGTAGTTTGGTATTTTTCGGCCACCACCC-
1 GAATCATGTTTAGGAGGTCAAGGGCTTTGATTTAGTATAGTTTGGTATTTTTCGGCCACCACCCA
* ** * *
3031572 GACGATTATTAGCT-ACGGCGTATGGTGGCCTGCCTGTGATCAATCTCCCTCCGACGAGGGATTC
66 G-CGACTA-TAGCTAACGGCACATGGTGGCCGGCCGGTGATCAATCTCCCTCCGACGAGGGATTC
3031636 TAGAGAGAGTTGAGAGCTTCTCT
129 TAGAGAGAGTTGAGAGCTTCTCT
3031659 CTCTAAAGAG
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
175 1 0.01
176 129 0.97
177 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (176 bp):
GAATCATGTTTAGGAGGTCAAGGGCTTTGATTTAGTATAGTTTGGTATTTTTCGGCCACCACCCA
GCGACTATAGCTAACGGCACATGGTGGCCGGCCGGTGATCAATCTCCCTCCGACGAGGGATTCTA
GAGAGAGTTGAGAGCTTCTCTATCTTTTTAGTAGAAAAGAGGCTCA
Found at i:3032048 original size:16 final size:17
Alignment explanation
Indices: 3032029--3032061 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3032019 TTAGGATTAT
3032029 TAATTT-ACATATTTTA
1 TAATTTAACATATTTTA
*
3032045 TAATTTAACCTATTTTA
1 TAATTTAACATATTTTA
3032062 ATATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTTAACATATTTTA
Found at i:3039178 original size:25 final size:26
Alignment explanation
Indices: 3039150--3039199 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
3039140 GGATTTATAG
*
3039150 AAATGCCCTAAAGTGT-AAATGACTA
1 AAATACCCTAAAGTGTAAAATGACTA
3039175 AAATACCCTAAAGTGTAAAATGACT
1 AAATACCCTAAAGTGTAAAATGACT
3039200 TAAAGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (26 bp):
AAATACCCTAAAGTGTAAAATGACTA
Found at i:3041567 original size:21 final size:23
Alignment explanation
Indices: 3041543--3041585 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
3041533 TTTTTGTTAA
*
3041543 TTAACAAGTTAAT-TT-AAAACC
1 TTAACAAGATAATATTGAAAACC
3041564 TTAACAAGATAATATTGAAAAC
1 TTAACAAGATAATATTGAAAAC
3041586 TCCTCGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (23 bp):
TTAACAAGATAATATTGAAAACC
Found at i:3043876 original size:2 final size:2
Alignment explanation
Indices: 3043869--3043896 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3043859 AATAAAATAA
3043869 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
3043897 GAAATCGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3046115 original size:19 final size:19
Alignment explanation
Indices: 3046088--3046135 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
3046078 AGTATATATA
* **
3046088 TATATATATATGGTTGAAT
1 TATAAATATATGGTAAAAT
*
3046107 TATAAATATAGGGTAAAAT
1 TATAAATATATGGTAAAAT
3046126 TATAAA-ATAT
1 TATAAATATAT
3046136 TATAATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (19 bp):
TATAAATATATGGTAAAAT
Found at i:3048296 original size:12 final size:12
Alignment explanation
Indices: 3048262--3048301 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3048252 TTCAAAGAAA
3048262 TTAAAA-TTATT
1 TTAAAATTTATT
*
3048273 TT--AATATATT
1 TTAAAATTTATT
3048283 TTAAAATTTATT
1 TTAAAATTTATT
3048295 TTAAAAT
1 TTAAAAT
3048302 ATGGATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 2 0.08
10 6 0.25
11 2 0.08
12 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:3048296 original size:22 final size:21
Alignment explanation
Indices: 3048262--3048303 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3048252 TTCAAAGAAA
*
3048262 TTAAAATTATTTTAATATATT
1 TTAAAATTATTTTAAAATATT
3048283 TTAAAATTTATTTTAAAATAT
1 TTAAAA-TTATTTTAAAATAT
3048304 GGATTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAATTATTTTAAAATATT
Found at i:3048313 original size:22 final size:22
Alignment explanation
Indices: 3048288--3048765 Score: 769
Period size: 22 Copynumber: 21.7 Consensus size: 22
3048278 ATATTTTAAA
3048288 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3048310 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
3048332 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
3048354 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3048376 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
3048398 ATTTCTTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
3048420 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3048442 ATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3048464 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3048486 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
3048508 ATTTATTTAAAAATATGGATTT
1 ATTTATTTTAAAATATGGATTG
***
3048530 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
3048552 ATTTATTTTAAAATATGGATAT-
1 ATTTATTTTAAAATATGGAT-TG
3048574 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3048596 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
3048618 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3048640 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3048662 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
3048684 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
3048706 ATTTATTTTAAAATATCGATTT
1 ATTTATTTTAAAATATGGATTG
*
3048728 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
3048750 ATTTATTTTAAAATAT
1 ATTTATTTTAAAATAT
3048766 TTATTATTGT
Statistics
Matches: 420, Mismatches: 34, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
21 1 0.00
22 419 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:3050768 original size:44 final size:44
Alignment explanation
Indices: 3050640--3050770 Score: 146
Period size: 44 Copynumber: 3.1 Consensus size: 44
3050630 TGTTATATTG
* * *
3050640 AAAAATTAGAGACCTCAATTATAAAAGTAAAAATTGAGA---AT
1 AAAAATTAGGGACCTCAATTATAAAAGTAAAAAGTGAGATTGAA
* * * * **
3050681 AAAATTTAGGG-CTTCAATTA-AAAGGTAGATTGTGAGATTGAA
1 AAAAATTAGGGACCTCAATTATAAAAGTAAAAAGTGAGATTGAA
3050723 AAAAATTAGGGACCTCAATTATAAAAGTAAAAAGTGAGATTGAA
1 AAAAATTAGGGACCTCAATTATAAAAGTAAAAAGTGAGATTGAA
3050767 AAAA
1 AAAA
3050771 TTAAAGGTTG
Statistics
Matches: 70, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
39 12 0.17
40 8 0.11
41 9 0.13
42 11 0.16
43 8 0.11
44 22 0.31
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (44 bp):
AAAAATTAGGGACCTCAATTATAAAAGTAAAAAGTGAGATTGAA
Found at i:3050773 original size:43 final size:42
Alignment explanation
Indices: 3050620--3050769 Score: 153
Period size: 42 Copynumber: 3.6 Consensus size: 42
3050610 TAAACTAAAA
* * * *
3050620 AAAAGTAAAATGTTATATTGAAAAATTAGAGACCTCAATTAT
1 AAAAGTAAAAAGTGAGATTGAAAAATTAGGGACCTCAATTAT
* * * *
3050662 AAAAGTAAAAATTGAGAAT-AAAATTTAGGG-CTTCAATTA-
1 AAAAGTAAAAAGTGAGATTGAAAAATTAGGGACCTCAATTAT
* * **
3050701 AAAGGTAGATTGTGAGATTGAAAAAAATTAGGGACCTCAATTAT
1 AAAAGTAAAAAGTGAGATTG--AAAAATTAGGGACCTCAATTAT
3050745 AAAAGTAAAAAGTGAGATTGAAAAA
1 AAAAGTAAAAAGTGAGATTGAAAAA
3050770 ATTAAAGGTT
Statistics
Matches: 83, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
39 13 0.16
40 8 0.10
41 9 0.11
42 29 0.35
43 8 0.10
44 16 0.19
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (42 bp):
AAAAGTAAAAAGTGAGATTGAAAAATTAGGGACCTCAATTAT
Found at i:3050900 original size:88 final size:89
Alignment explanation
Indices: 3050781--3051043 Score: 236
Period size: 88 Copynumber: 3.0 Consensus size: 89
3050771 TTAAAGGTTG
* * * * * *
3050781 AAAAAATTAGGAGCCTCAATTATAAATGTAAAAAAATGATATT-AAAAAATTTAGGGCTTCAATT
1 AAAAAATAAGGAGCCTCAATAATAAAAGT-AAAAAATGAGATTAAAAAAAATTAGAGCTTCAATT
* * * *
3050845 GTAATGGTGAAAGGAGAGATTGAAA
65 ATAAAGGTAAAAAGAGAGATTGAAA
* *
3050870 AAAAAATAAGG-GCCTTAATAATAAAAGTAAAAAGTGAGATTAAAAAAAATTAGAGCTTCAATTA
1 AAAAAATAAGGAGCCTCAATAATAAAAGTAAAAAATGAGATTAAAAAAAATTAGAGCTTCAATTA
* *
3050934 TAAAGGTAAAAATAGGGATTG---
66 TAAAGGTAAAAAGAGAGATTGAAA
* * * * * * *
3050955 AAAAAATTAGGAGTCTCAGTTATAAAGGTAAAAAGTGAGATT--AAAAAATTAGATACTTCAATT
1 AAAAAATAAGGAGCCTCAATAATAAAAGTAAAAAATGAGATTAAAAAAAATTAGA-GCTTCAATT
* *
3051018 ATAAAGCTACAAAGTA-AGATTGAAA
65 ATAAAGGTAAAAAG-AGAGATTGAAA
3051043 A
1 A
3051044 TGTTAGGGGC
Statistics
Matches: 142, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
84 11 0.08
85 34 0.24
86 26 0.18
87 11 0.08
88 50 0.35
89 10 0.07
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.25
Consensus pattern (89 bp):
AAAAAATAAGGAGCCTCAATAATAAAAGTAAAAAATGAGATTAAAAAAAATTAGAGCTTCAATTA
TAAAGGTAAAAAGAGAGATTGAAA
Found at i:3050937 original size:43 final size:42
Alignment explanation
Indices: 3050781--3051258 Score: 251
Period size: 43 Copynumber: 11.1 Consensus size: 42
3050771 TTAAAGGTTG
* * * *
3050781 AAAAAATTAGGAGCCTCAATTATAAATGTAAAAAAATGATATTA
1 AAAAAATTA-GAGCTTCAATTATAAAAGT-AAAAAGTGAGATTA
* * * ** * * *
3050825 AAAAATTTAGGGCTTCAATTGTAATGGTGAAAGGAGAGATTGAAA
1 AAAAAATTAGAGCTTCAATTATAAAAGTAAAAAGTGAGATT---A
* * *
3050870 AAAAAATAAGGGCCTT-AATAATAAAAGTAAAAAGTGAGATTAA
1 AAAAAATTAGAG-CTTCAATTATAAAAGTAAAAAGTGAGATT-A
* * *
3050913 AAAAAATTAGAGCTTCAATTATAAAGGTAAAAA-TAGGGATTG
1 AAAAAATTAGAGCTTCAATTATAAAAGTAAAAAGT-GAGATTA
* *
3050955 AAAAAATTAGGAG-TCTCAGTTATAAAGGTAAAAAGTGAGATT-
1 AAAAAATTA-GAGCT-TCAATTATAAAAGTAAAAAGTGAGATTA
* * * *
3050997 AAAAAATTAGATACTTCAATTAT-AAAGCTACAAAGTAAGATTG
1 AAAAAATTAGA-GCTTCAATTATAAAAG-TAAAAAGTGAGATTA
** * * * * *
3051040 AAAATGTTAGGGGCCTT-ATTTATAAATA-TAAAAA-TGGGACTG
1 AAAAAATTA-GAG-CTTCAATTATAAA-AGTAAAAAGTGAGATTA
* ** * * *
3051082 AAAAAATTAGGAGCCTCAATTATAAATTTAAAAGGTGATACTA
1 AAAAAATTA-GAGCTTCAATTATAAAAGTAAAAAGTGAGATTA
* * *
3051125 AAAAAATTAGGGACTTCAATTGT-AAAGCTAAAAAGTGAGATTG
1 AAAAAATTAGAG-CTTCAATTATAAAAG-TAAAAAGTGAGATTA
* * *
3051168 AAAAAATTAGGGGCCTT-AATTAT-AAAGATAAAAAATGAGATTG
1 AAAAAATTA-GAG-CTTCAATTATAAAAG-TAAAAAGTGAGATTA
* * *
3051211 AAAAAATTAGAGACCTCAATTAT-AAAGGAAAATGGTGAGATTA
1 AAAAAATTAGAG-CTTCAATTATAAAAGTAAAA-AGTGAGATTA
3051254 AAAAA
1 AAAAA
3051259 TTAAGGCTCT
Statistics
Matches: 337, Mismatches: 72, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
41 7 0.02
42 90 0.27
43 186 0.55
44 21 0.06
45 30 0.09
46 3 0.01
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAAATTAGAGCTTCAATTATAAAAGTAAAAAGTGAGATTA
Found at i:3050991 original size:86 final size:84
Alignment explanation
Indices: 3050778--3051258 Score: 350
Period size: 85 Copynumber: 5.6 Consensus size: 84
3050768 AAATTAAAGG
* * * * *
3050778 TTGAAAAAATTAGGAGCCTCAATTATAAATGTAAAAAAATGATATTAAAAAATTTAGGGCTTCAA
1 TTGAAAAAATTAGGAGCCTCAATTATAAAGGT-AAAAAGTGAGATTAAAAAAATTAGAGCTTCAA
* * **
3050843 TTGTAATGGTGAAAGGAGAGA
65 TTATAAAGGT-AAAAAAGAGA
* * * *
3050864 TTGAAAAAAAAATAAGG-GCCTTAATAATAAAAGTAAAAAGTGAGATTAAAAAAAATTAGAGCTT
1 TTG---AAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAAAATTAGAGCTT
*
3050928 CAATTATAAAGGTAAAAATAGGGA
62 CAATTATAAAGGTAAAAA-AGAGA
* * *
3050952 TTGAAAAAATTAGGAGTCTCAGTTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGATACTTCAA
1 TTGAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGA-GCTTCAA
* *
3051016 TTATAAAGCT-ACAAAGTAAGA
65 TTATAAAGGTAAAAAAG--AGA
** * * * ** * * * *
3051037 TTGAAAATGTTAGGGGCCTTATTTATAAATATAAAAA-TGGGACTGAAAAAATTAGGAGCCTCAA
1 TTGAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTA-GAGCTTCAA
* * * *
3051101 TTATAAA-TTTAAAAGGTGA
65 TTATAAAGGTAAAAAAGAGA
* * * * * *
3051120 TACTAAAAAAATTAGG-GACTTCAATTGTAAAGCTAAAAAGTGAGATTGAAAAAATTAGGGGCCT
1 T--TGAAAAAATTAGGAG-CCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTA-GAG-CT
*
3051184 T-AATTATAAAGATAAAAAATGAGA
61 TCAATTATAAAGGTAAAAAA-GAGA
*
3051208 TTGAAAAAATTA-GAGACCTCAATTATAAAGG-AAAATGGTGAGATTAAAAAA
1 TTGAAAAAATTAGGAG-CCTCAATTATAAAGGTAAAA-AGTGAGATTAAAAAA
3051259 TTAAGGCTCT
Statistics
Matches: 312, Mismatches: 62, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
83 5 0.02
84 21 0.07
85 111 0.36
86 94 0.30
87 21 0.07
88 50 0.16
89 10 0.03
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (84 bp):
TTGAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGCTTCAAT
TATAAAGGTAAAAAAGAGA
Found at i:3051072 original size:128 final size:128
Alignment explanation
Indices: 3050778--3051261 Score: 441
Period size: 128 Copynumber: 3.8 Consensus size: 128
3050768 AAATTAAAGG
* * ** * *
3050778 TTGAAAAAATTAGGAGCCTCAATTATAAATG-TAAAAA-AATGATATTAAAAAATTTAGG-GCTT
1 TTGAAAAAATTAGGGGCCTTAATTATAAA-GATAAAAATAGGGAT-TGAAAAAA-TTAGGAGCCT
* * * * * * * *
3050840 CAATTGTAATGGTGAAAGGAGAGATTGAAAAAAAAATAAGGGCCTT-AATAATAAAAG-TAAAAA
63 CAATTATAAAGGTAAAAGGTGAGATT----AAAAAATTAGAGACTTCAATTAT-AAAGCTAAAAA
*
3050903 GTGAGA
123 GTAAGA
* * * *
3050909 TTAAAAAAAATTA-GAG-CTTCAATTATAAAGGTAAAAATAGGGATTGAAAAAATTAGGAGTCTC
1 TT-GAAAAAATTAGGGGCCTT-AATTATAAAGATAAAAATAGGGATTGAAAAAATTAGGAGCCTC
* * * *
3050972 AGTTATAAAGGTAAAAAGTGAGATTAAAAAATTAGATACTTCAATTATAAAGCTACAAAGTAAGA
64 AATTATAAAGGTAAAAGGTGAGATTAAAAAATTAGAGACTTCAATTATAAAGCTAAAAAGTAAGA
** * * *
3051037 TTGAAAATGTTAGGGGCCTTATTTATAAATATAAAAAT-GGGACTGAAAAAATTAGGAGCCTCAA
1 TTGAAAAAATTAGGGGCCTTAATTATAAAGATAAAAATAGGGATTGAAAAAATTAGGAGCCTCAA
** * * * * *
3051101 TTATAAATTTAAAAGGTGATACTAAAAAAATTAGGGACTTCAATTGTAAAGCTAAAAAGTGAGA
66 TTATAAAGGTAAAAGGTGAGA-TTAAAAAATTAGAGACTTCAATTATAAAGCTAAAAAGTAAGA
*
3051165 TTGAAAAAATTAGGGGCCTTAATTATAAAGATAAAAA-ATGAGATTGAAAAAATTA-GAGACCTC
1 TTGAAAAAATTAGGGGCCTTAATTATAAAGATAAAAATA-GGGATTGAAAAAATTAGGAG-CCTC
3051228 AATTATAAAGG-AAAATGGTGAGATTAAAAAATTA
64 AATTATAAAGGTAAAA-GGTGAGATTAAAAAATTA
3051262 AGGCTCTCAA
Statistics
Matches: 289, Mismatches: 50, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
127 63 0.22
128 120 0.42
129 36 0.12
130 8 0.03
131 49 0.17
132 13 0.04
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (128 bp):
TTGAAAAAATTAGGGGCCTTAATTATAAAGATAAAAATAGGGATTGAAAAAATTAGGAGCCTCAA
TTATAAAGGTAAAAGGTGAGATTAAAAAATTAGAGACTTCAATTATAAAGCTAAAAAGTAAGA
Found at i:3051285 original size:43 final size:43
Alignment explanation
Indices: 3051159--3051285 Score: 107
Period size: 43 Copynumber: 3.0 Consensus size: 43
3051149 AAGCTAAAAA
* * * * * **
3051159 GTGAGATTGAAAAAATTAGGGGCCTTAATTATAAA-GATAAAAA
1 GTGAGATTGAAAAAATTAGAGACCTCAAATACAAAGGA-AAATG
* * *
3051202 ATGAGATTGAAAAAATTAGAGACCTCAATTATAAAGGAAAATG
1 GTGAGATTGAAAAAATTAGAGACCTCAAATACAAAGGAAAATG
*
3051245 GTGAGATT-AAAAAATTA-AGGCTCTCAAATACAAAGAGAAAA
1 GTGAGATTGAAAAAATTAGAGAC-CTCAAATACAAAG-GAAAA
3051286 AATTAAATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.04
42 20 0.28
43 46 0.65
44 2 0.03
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (43 bp):
GTGAGATTGAAAAAATTAGAGACCTCAAATACAAAGGAAAATG
Found at i:3051301 original size:86 final size:86
Alignment explanation
Indices: 3051123--3051301 Score: 202
Period size: 85 Copynumber: 2.1 Consensus size: 86
3051113 AAGGTGATAC
* * * * * * *
3051123 TAAAAAAATTAGGGACTTCAATTGTAAAGCTAAAAAGTGAGATTGAAAAAATTAGGGGCCTTAAT
1 TAAAAAAATTAGAGACCTCAATTATAAAGCGAAAAAGTGAGATTGAAAAAATTAGAGGCCTCAAA
* * *
3051188 TATAAAGATAAAAAATGAGAT
66 TACAAAGAGAAAAAATGAAAT
* *
3051209 TGAAAAAATTAGAGACCTCAATTATAAAG-GAAAATGGTGAGATT-AAAAAATTA-AGGCTCTCA
1 TAAAAAAATTAGAGACCTCAATTATAAAGCGAAAA-AGTGAGATTGAAAAAATTAGAGGC-CTCA
*
3051271 AATACAAAGAGAAAAAATTAAAT
64 AATACAAAGAGAAAAAATGAAAT
3051294 TAAAAAAA
1 TAAAAAAA
3051302 GTAAATATCT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
84 3 0.04
85 41 0.53
86 33 0.43
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (86 bp):
TAAAAAAATTAGAGACCTCAATTATAAAGCGAAAAAGTGAGATTGAAAAAATTAGAGGCCTCAAA
TACAAAGAGAAAAAATGAAAT
Found at i:3051514 original size:40 final size:40
Alignment explanation
Indices: 3051470--3051556 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
3051460 GACTCCAATT
*
3051470 TCGCAAC-CCAGTTTCCAAATTCGCAACGCGAATCTGTAAA
1 TCGCAACGCCAATTTCCAAA-TCGCAACGCGAATCTGTAAA
* ** *
3051510 TCGCAACGCGAATTTGTAAATCGCAACGCGAATTTGTAAA
1 TCGCAACGCCAATTTCCAAATCGCAACGCGAATCTGTAAA
3051550 TCGCAAC
1 TCGCAAC
3051557 ACAAAAGTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 33 0.80
41 8 0.20
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
TCGCAACGCCAATTTCCAAATCGCAACGCGAATCTGTAAA
Found at i:3051573 original size:20 final size:20
Alignment explanation
Indices: 3051550--3051698 Score: 131
Period size: 20 Copynumber: 7.4 Consensus size: 20
3051540 AATTTGTAAA
3051550 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
**
3051570 TCGCAACACTGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
3051590 TCGCAGCACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * **
3051610 TTGCAACGCGAATCTGT-AAA-
1 TCGCAACAC-AA-AAGTCAAAT
* *
3051630 TCGCAATACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
3051650 TCGCAATACAGAAGTCAAAAT
1 TCGCAACACAAAAGTC-AAAT
* * *
3051671 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
3051691 TCGCAACA
1 TCGCAACA
3051699 TTGAATTTCA
Statistics
Matches: 101, Mismatches: 23, Indels: 10
0.75 0.17 0.07
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 73 0.72
21 20 0.20
22 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:3051574 original size:40 final size:40
Alignment explanation
Indices: 3051485--3051655 Score: 181
Period size: 40 Copynumber: 4.3 Consensus size: 40
3051475 ACCCAGTTTC
* **
3051485 CAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACAC-AA-AAGT
*
3051527 -AAA-TCGCAACGCGAATTTGTAAATCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGT
* *
3051565 CAAATTCGCAACACTGAA---GTCAAATTCGCAGCACAAAAGT
1 CAAATTCGCAACGC-GAATCTGT-AAA-TCGCAACACAAAAGT
* * *
3051605 CAAATTTGCAACGCGAATCTGTAAATCGCAATACATAAGT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGT
3051645 CAAATTCGCAA
1 CAAATTCGCAA
3051656 TACAGAAGTC
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
38 4 0.04
39 11 0.10
40 83 0.76
41 9 0.08
42 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGT
Found at i:3051594 original size:80 final size:82
Alignment explanation
Indices: 3051530--3051697 Score: 234
Period size: 80 Copynumber: 2.1 Consensus size: 82
3051520 AATTTGTAAA
* *
3051530 TCGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACACTGAAGTC-AAATTCGC
1 TCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACACAGAAGTCAAAATTCGC
* *
3051594 AGCAC-AAAAGTCAAAT
66 AACGCGAAAAGTCAAAT
* * * *
3051610 TTGCAACGCGAATCTGTAAATCGCAATACATAAGTCAAATTCGCAATACAGAAGTCAAAATTCGC
1 TCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACACAGAAGTCAAAATTCGC
*
3051675 AACGCG-ATAGTCAAAT
66 AACGCGAAAAGTCAAAT
3051691 TCGCAAC
1 TCGCAAC
3051698 ATTGAATTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
80 50 0.66
81 26 0.34
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (82 bp):
TCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACACAGAAGTCAAAATTCGC
AACGCGAAAAGTCAAAT
Found at i:3051634 original size:60 final size:61
Alignment explanation
Indices: 3051562--3051718 Score: 178
Period size: 60 Copynumber: 2.6 Consensus size: 61
3051552 GCAACACAAA
* *
3051562 AGTCAAATTCGCAACACTGAAGTCAAATTCGCAGCACAAAAGTC-AAATTTGCAACGCGAAT
1 AGTCAAATTCGCAACACTGAAGTCAAATTCGCAACACAAAAGTCAAAATTCGCAACGCG-AT
* * * *
3051623 CTGT-AAA-TCGCAATACAT-AAGTCAAATTCGCAATACAGAAGTCAAAATTCGCAACGCGAT
1 -AGTCAAATTCGCAACAC-TGAAGTCAAATTCGCAACACAAAAGTCAAAATTCGCAACGCGAT
* *
3051683 AGTCAAATTCGCAACATTGAATTTCAAATTCGCAAC
1 AGTCAAATTCGCAACACTGAA-GTCAAATTCGCAAC
3051719 TGAATTTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
59 2 0.03
60 36 0.46
61 26 0.33
62 14 0.18
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (61 bp):
AGTCAAATTCGCAACACTGAAGTCAAATTCGCAACACAAAAGTCAAAATTCGCAACGCGAT
Found at i:3051724 original size:19 final size:20
Alignment explanation
Indices: 3051685--3051757 Score: 105
Period size: 19 Copynumber: 3.7 Consensus size: 20
3051675 AACGCGATAG
3051685 TCAAATTCGCAACATTGAATT
1 TCAAATTCGCAACA-TGAATT
3051706 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACATGAATT
*
3051725 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAACATGAATT
*
3051745 T-AATTTCGCAACA
1 TCAAATTCGCAACA
3051758 GGTTTTAGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 30 0.61
20 6 0.12
21 13 0.27
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (20 bp):
TCAAATTCGCAACATGAATT
Found at i:3051745 original size:20 final size:20
Alignment explanation
Indices: 3051485--3051757 Score: 129
Period size: 20 Copynumber: 13.7 Consensus size: 20
3051475 ACCCAGTTTC
*
3051485 CAAATTCGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
*
3051507 -AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* *
3051525 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* * **
3051545 GTAAA-TCGCAACACAAAAGT
1 -CAAATTCGCAACACGAATTT
*
3051565 CAAATTCGCAACACTGAA-GT
1 CAAATTCGCAACAC-GAATTT
* * **
3051585 CAAATTCGCAGCACAAAAGT
1 CAAATTCGCAACACGAATTT
* *
3051605 CAAATTTGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
* **
3051627 -AAA-TCGCAATAC-ATAAGT
1 CAAATTCGCAACACGA-ATTT
* *
3051645 CAAATTCGCAATACAGAA-GT
1 CAAATTCGCAACAC-GAATTT
* *
3051665 CAAAATTCGCAACGCG-ATAGT
1 C-AAATTCGCAACACGAAT-TT
*
3051686 CAAATTCGCAACATTGAATTT
1 CAAATTCGCAACA-CGAATTT
*
3051707 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
3051726 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
3051746 -AATTTCGCAACA
1 CAAATTCGCAACA
3051758 GGTTTTAGTT
Statistics
Matches: 207, Mismatches: 26, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.01
19 41 0.20
20 123 0.59
21 37 0.18
22 4 0.02
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:3051932 original size:14 final size:15
Alignment explanation
Indices: 3051913--3051950 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3051903 TCCCCATCTC
3051913 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
3051927 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
3051943 TAATTTTT
1 TAATTTTT
3051951 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:3052676 original size:24 final size:24
Alignment explanation
Indices: 3052649--3052702 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3052639 GTATTTGAAA
3052649 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3052673 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3052697 TTTGAT
1 TTTGAT
3052703 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3052894 original size:12 final size:12
Alignment explanation
Indices: 3052877--3052901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3052867 ATATAACCCT
3052877 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3052889 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3052901 G
1 G
3052902 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3054985 original size:18 final size:18
Alignment explanation
Indices: 3054962--3054997 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3054952 AAGCAAAAGG
*
3054962 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3054980 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3054998 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3055454 original size:66 final size:65
Alignment explanation
Indices: 3055372--3055547 Score: 237
Period size: 66 Copynumber: 2.6 Consensus size: 65
3055362 AATTTAAAAC
3055372 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATC-AATT
3055437 A
65 A
* * *
3055438 AACAAATCAACTTTTACAAATCAATTAAACAAG-CAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATCAATTA
* **
3055502 AACAAATAAACTTTCAGTGTAAATTTCAATTAAACAAGAAAAAAAA
1 AACAAATCAACTTT---TACAAA--TCAATTAAACAAGAAAAAAAA
3055548 GTGTACCCCA
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
64 18 0.19
65 23 0.24
66 33 0.34
67 4 0.04
69 13 0.13
70 6 0.06
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:3056941 original size:42 final size:42
Alignment explanation
Indices: 3056875--3056993 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
3056865 GTGAATCGGG
* * *
3056875 CTCTTGAACGGTGGGCGGGACCTCTTGAACGATGACATGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
* *
3056917 CTCTTGAACGGTGGGAGGGGCCTCTTCG-ATGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTT-GAATGATGACAGGGGC
* * * *
3056959 CTATTGAACGATAGGAGGCACCTCTTGAATGATGA
1 CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGA
3056994 TAGGTACATC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.02
42 63 0.97
43 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
Found at i:3056976 original size:21 final size:20
Alignment explanation
Indices: 3056875--3056992 Score: 78
Period size: 21 Copynumber: 5.7 Consensus size: 20
3056865 GTGAATCGGG
*
3056875 CTCTTGAACGGTGG-GCGGGAC
1 CTCTTGAACGATGGAG-GGG-C
* *
3056896 CTCTTGAACGATGACATGGGC
1 CTCTTGAACGATG-GAGGGGC
*
3056917 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGAT-GGAGGGGC
*
3056938 CTCTTCG-ATGATGAGAGGGGC
1 CTCTT-GAACGATG-GAGGGGC
* **
3056959 CTATTGAACGATAGGAGGCAC
1 CTCTTGAACGAT-GGAGGGGC
*
3056980 CTCTTGAATGATG
1 CTCTTGAACGATG
3056993 ATAGGTACAT
Statistics
Matches: 76, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
20 3 0.04
21 67 0.88
22 6 0.08
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGATGGAGGGGC
Found at i:3058875 original size:222 final size:220
Alignment explanation
Indices: 3058437--3058878 Score: 866
Period size: 222 Copynumber: 2.0 Consensus size: 220
3058427 GGTGGGAGAT
3058437 ACCACTAGTGTACCGGGTTACATCATCGTGTCCGAAGCGTAGACTAGTTATTAAGCAAAACTCCT
1 ACCACTAGTGTACCGGGTTACATCATCGTGTCCGAAGCGTAGACTAGTTATTAAGCAAAACTCCT
3058502 CCCACCCAAAACAAGTATACGCCGGAGGAAAATGAAACCATATCTTCATCACCACGTTGTATCAT
66 CCCACCCAAAACAAGTATACGCCGGAGGAAAATGAAACCATATCTTCATCACCACGTTGTATCAT
3058567 CTCGGGTAGATCGTTAGTCATGGTCTGAAGAAATAAATGTGTCAACATAGTATCTCCACCCGAAT
131 CTCGGGTAGATCGTTAGTCATGGTCTGAAGAAATAAATGTGTCAACATAGTATCTCCACCCGAAT
3058632 GTTGTACTTTCAGCCATGGCCCGAA
196 GTTGTACTTTCAGCCATGGCCCGAA
3058657 ACCACTAGTGTACCGGGTTACATCATCGTGTCCGAAGCGTAGACTAGTTATTAAGCAAAACTCCT
1 ACCACTAGTGTACCGGGTTACATCATCGTGTCCGAAGCGTAGACTAGTTATTAAGCAAAACTCCT
3058722 CCCACCCAAAACAAGTATACGCCGGAGGAAAATGAAACCATATCTCTTCATCACCACGTTGTATC
66 CCCACCCAAAACAAGTATACGCCGGAGGAAAATGAAACCATA--TCTTCATCACCACGTTGTATC
3058787 ATCTCGGGTAGATCGTTAGTCATGGTCTGAAGAAATAAATGTGTCAACATAGTATCTCCACCCGA
129 ATCTCGGGTAGATCGTTAGTCATGGTCTGAAGAAATAAATGTGTCAACATAGTATCTCCACCCGA
3058852 ATGTTGTACTTTCAGCCATGGCCCGAA
194 ATGTTGTACTTTCAGCCATGGCCCGAA
3058879 GCAAGTATCC
Statistics
Matches: 220, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
220 107 0.49
222 113 0.51
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (220 bp):
ACCACTAGTGTACCGGGTTACATCATCGTGTCCGAAGCGTAGACTAGTTATTAAGCAAAACTCCT
CCCACCCAAAACAAGTATACGCCGGAGGAAAATGAAACCATATCTTCATCACCACGTTGTATCAT
CTCGGGTAGATCGTTAGTCATGGTCTGAAGAAATAAATGTGTCAACATAGTATCTCCACCCGAAT
GTTGTACTTTCAGCCATGGCCCGAA
Found at i:3059395 original size:20 final size:20
Alignment explanation
Indices: 3059367--3059413 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3059357 CTAAAATTGC
3059367 GTTGCGAATTTGAATTATGT
1 GTTGCGAATTTGAATTATGT
* * *
3059387 GTTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGAATTATGT
3059407 GTTGCGA
1 GTTGCGA
3059414 TTTACAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGAATTATGT
Found at i:3059438 original size:20 final size:20
Alignment explanation
Indices: 3059413--3059469 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
3059403 CTGTGTTGCG
*
3059413 ATTTACAGATTCACGTTACA
1 ATTTACAGATTCGCGTTACA
* *
3059433 ATTTACAGATTCGCGTTTCG
1 ATTTACAGATTCGCGTTACA
3059453 ATTTACAGATTCGCGTT
1 ATTTACAGATTCGCGTT
3059470 GCGAATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTTACAGATTCGCGTTACA
Found at i:3059496 original size:20 final size:20
Alignment explanation
Indices: 3059467--3059595 Score: 163
Period size: 20 Copynumber: 6.5 Consensus size: 20
3059457 ACAGATTCGC
3059467 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTCAGT
* *
3059487 GTTGCAAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCAGT
*
3059507 ATTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTCAGT
*
3059527 GTTGCGAATTCGACTTCAGT
1 GTTGCGAATTTGACTTCAGT
*
3059547 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCAGT
* *
3059567 GTTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCAGT
3059587 GTTGCGAAT
1 GTTGCGAAT
3059596 GGAAACTGGG
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.04
20 85 0.91
21 4 0.04
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCAGT
Found at i:3059542 original size:60 final size:60
Alignment explanation
Indices: 3059467--3059595 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
3059457 ACAGATTCGC
*
3059467 GTTGCGAATTTGACTTCAGTGTTGCAAATTTGACTATCGCATTGCGAATTTGACTTCAGT
1 GTTGCGAATTCGACTTCAGTGTTGCAAATTTGACTATCGCATTGCGAATTTGACTTCAGT
* * * *
3059527 GTTGCGAATTCGACTTCAGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCTGT
1 GTTGCGAATTCGACTTCAGTGTTGCAAATTTGACTATCGCATTGCGAATTTGACTTCAGT
3059587 GTTGCGAAT
1 GTTGCGAAT
3059596 GGAAACTGGG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTCGACTTCAGTGTTGCAAATTTGACTATCGCATTGCGAATTTGACTTCAGT
Found at i:3060629 original size:21 final size:21
Alignment explanation
Indices: 3060603--3060649 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3060593 TGTTCTTTCT
3060603 TCTTCTTCTTTAAAGCAATCA
1 TCTTCTTCTTTAAAGCAATCA
3060624 TCTTCTTCTTTAAAGCAATCA
1 TCTTCTTCTTTAAAGCAATCA
3060645 TCTTC
1 TCTTC
3060650 AGTTTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.45
Consensus pattern (21 bp):
TCTTCTTCTTTAAAGCAATCA
Found at i:3065404 original size:102 final size:102
Alignment explanation
Indices: 3065255--3065444 Score: 301
Period size: 102 Copynumber: 1.9 Consensus size: 102
3065245 AAGTCTCTGA
*
3065255 TTCCAGTGGTGTTGCCACCATCTCCTCCATCCGCGCGAACCCAAAATACAGCTCCGCCACCATTC
1 TTCCAGTGGTGTTGCCACCATCTCCTCCATCCGCGCGAACCCAAAATACAACTCCGCCACCATTC
3065320 CCTATTGAAGAAAATTTACCATCATTGGCTGCAAGTT
66 CCTATTGAAGAAAATTTACCATCATTGGCTGCAAGTT
* * * * *
3065357 TTCCAGTGGTGTTAG-CACCATTTCCTCCATCCGCGCGAACCCGAAATACAACTCTGTCACTATT
1 TTCCAGTGGTGTT-GCCACCATCTCCTCCATCCGCGCGAACCCAAAATACAACTCCGCCACCATT
*
3065421 CCCTATTGAAGAACATTTACCATC
65 CCCTATTGAAGAAAATTTACCATC
3065445 CTTTGTACAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 79 0.99
103 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.27
Consensus pattern (102 bp):
TTCCAGTGGTGTTGCCACCATCTCCTCCATCCGCGCGAACCCAAAATACAACTCCGCCACCATTC
CCTATTGAAGAAAATTTACCATCATTGGCTGCAAGTT
Found at i:3068465 original size:15 final size:15
Alignment explanation
Indices: 3068445--3068474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3068435 TGATCCTTCA
*
3068445 GTACTAAATAATGGT
1 GTACTAAACAATGGT
3068460 GTACTAAACAATGGT
1 GTACTAAACAATGGT
3068475 CTCTTGCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (15 bp):
GTACTAAACAATGGT
Found at i:3076582 original size:26 final size:26
Alignment explanation
Indices: 3076553--3076605 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3076543 TTTACATATT
3076553 TGTAAAATACATTTAAATAATTACTA
1 TGTAAAATACATTTAAATAATTACTA
3076579 TGTAAAATACATTTAAATAATTACTA
1 TGTAAAATACATTTAAATAATTACTA
3076605 T
1 T
3076606 CTCATTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (26 bp):
TGTAAAATACATTTAAATAATTACTA
Found at i:3083214 original size:90 final size:92
Alignment explanation
Indices: 3083113--3083296 Score: 336
Period size: 90 Copynumber: 2.0 Consensus size: 92
3083103 GAGTTTATGA
3083113 TTCTTGACGAAAAATTAATTTTATGTTCAAATCGTTTAAAGATTAATTG-ATTGTTTGAACATGA
1 TTCTTGACGAAAAATTAATTTTATGTTCAAATCGTTTAAAGATTAATTGAATTGTTTGAACATGA
3083177 TTAATTTTC-ATATGAGTTGCCAATAC
66 TTAATTTTCAATATGAGTTGCCAATAC
3083203 TTCTTGACGAAAAATTAATTTTATGTTCAAATCGTTTAAAGATTAATTGAATTGTTTGAACATGA
1 TTCTTGACGAAAAATTAATTTTATGTTCAAATCGTTTAAAGATTAATTGAATTGTTTGAACATGA
3083268 TTAATTTTCAATATATGAGTTGCCAATAC
66 TTAATTTTC-A-ATATGAGTTGCCAATAC
3083297 CACTAGAGGA
Statistics
Matches: 90, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
90 49 0.54
91 24 0.27
94 17 0.19
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (92 bp):
TTCTTGACGAAAAATTAATTTTATGTTCAAATCGTTTAAAGATTAATTGAATTGTTTGAACATGA
TTAATTTTCAATATGAGTTGCCAATAC
Found at i:3083440 original size:20 final size:21
Alignment explanation
Indices: 3083401--3083445 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3083391 CCCCTTTTGA
*
3083401 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
* *
3083422 AGGGGAATCGA-TACCCCCAT
1 AGGGGAACCGATTACCCCCAC
3083442 AGGG
1 AGGG
3083446 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.11
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:3086992 original size:9 final size:9
Alignment explanation
Indices: 3086978--3087011 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
3086968 AGTGCTTATG
3086978 CAAATTTCT
1 CAAATTTCT
3086987 CAAATTTCT
1 CAAATTTCT
3086996 CAAATTTCT
1 CAAATTTCT
3087005 CAAATTT
1 CAAATTT
3087012 TGGTCTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (9 bp):
CAAATTTCT
Found at i:3087781 original size:30 final size:30
Alignment explanation
Indices: 3087725--3087783 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3087715 TTTTATTTTG
* * *
3087725 GGGATTAAATTGAAATTTTGATTAAATTTA
1 GGGATTAAAATGAAATTTTAAGTAAATTTA
3087755 GGGATTAAAAT-AAATATTTAAGTAAATTT
1 GGGATTAAAATGAAAT-TTTAAGTAAATTT
3087784 GGATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (30 bp):
GGGATTAAAATGAAATTTTAAGTAAATTTA
Found at i:3095990 original size:269 final size:262
Alignment explanation
Indices: 3095497--3096029 Score: 955
Period size: 269 Copynumber: 2.0 Consensus size: 262
3095487 TGTGTTTTGA
3095497 TTCGAAAGAAAACTGAGAAGTTTTTGGCCAATGAATGGGGGCGTTTTCGAGATCTATTTTTGTAG
1 TTCGAAAGAAAACTGAGAAGTTTTTGGCCAATGAATGGGGGCGTTTTCGAGATCTATTTTTGTAG
3095562 ATCTATACCCGAAGGCTTGTATTTTTTGAAAAACTATTCAGATTTTTATAAACGGGTCGTGTGGA
66 ATCTATACCCGAAGGCTTGTATTTTTTGAAAAACTATTCAGATTTTTATAAACGGGTCGTGTGGA
3095627 TCTGTGTGTTTGCCTCTACAGTGGGTTAATGCCCATTTCGGTCCCCCTGATTTTAAATACACGCA
131 TCTGTGTGTTTGCCTCTACAGTGGGTTAATGCCCATTTCGGTCCCCCTGATTTTAAATACACGCA
3095692 GATTCGTTTTTCTTCAATTGGGCTTTTAATTTCGACCCCTAATTCA-TTTTTA-TTTAATTTAAC
196 GATTCGTTTTTCTTCAATTGGGCTTTTAATTTCGACCCCTAATTCATTTTTTATTTTAATTTAAC
3095755 CC
261 CC
3095757 TTCGAAAGAAAACTGAGAGAAGTGTTTTTGGCCAATGAATGGGGGCGTTTTCGAGATCTATTTTT
1 TTCGAAAGAAAACT--GAGAA--GTTTTTGGCCAATGAATGGGGGCGTTTTCGAGATCTATTTTT
3095822 GTAGATCTATACCCCCCGAAGGCTTGTATTTTTTTGAAAAACTATTCAGATTTTTATAAACGGGT
62 GTAGATCTATA---CCCGAAGGCTTGTA-TTTTTTGAAAAACTATTCAGATTTTTATAAACGGGT
3095887 CGTGTGGATCTGTGTGTTTTGCCTCTACAGTGGGTTAATGCCCATTTCGGTCCCCCTGATTTTAA
123 CGTGTGGATCTGTGTG-TTTGCCTCTACAGTGGGTTAATGCCCATTTCGGTCCCCCTGATTTTAA
3095952 ATACACGCAGATTCGTTTTTTCTTCAATT-GGCTTTTAATTTCGACCCCTAATTCATTTTTTATT
187 ATACACGCAGATTCG-TTTTTCTTCAATTGGGCTTTTAATTTCGACCCCTAATTCATTTTTTATT
3096016 TTAATTTAACCC
251 TTAATTTAACCC
3096028 TT
1 TT
3096030 AATATTTATA
Statistics
Matches: 261, Mismatches: 0, Indels: 13
0.95 0.00 0.05
Matches are distributed among these distances:
260 14 0.05
262 5 0.02
264 53 0.20
267 14 0.05
268 52 0.20
269 89 0.34
270 19 0.07
271 15 0.06
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (262 bp):
TTCGAAAGAAAACTGAGAAGTTTTTGGCCAATGAATGGGGGCGTTTTCGAGATCTATTTTTGTAG
ATCTATACCCGAAGGCTTGTATTTTTTGAAAAACTATTCAGATTTTTATAAACGGGTCGTGTGGA
TCTGTGTGTTTGCCTCTACAGTGGGTTAATGCCCATTTCGGTCCCCCTGATTTTAAATACACGCA
GATTCGTTTTTCTTCAATTGGGCTTTTAATTTCGACCCCTAATTCATTTTTTATTTTAATTTAAC
CC
Found at i:3096054 original size:2 final size:2
Alignment explanation
Indices: 3096031--3096091 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
3096021 TTAACCCTTA
* *
3096031 AT AT TT AT AT GT AT AT AT -T 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
3096072 AT AT AT AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3096092 TATTTTTAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:3096207 original size:24 final size:24
Alignment explanation
Indices: 3096180--3096262 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
3096170 ATATTTTATC
3096180 TTCATTTATTTTATTTTATTCAAT
1 TTCATTTATTTTATTTTATTCAAT
* * * *
3096204 TTCATTTTTTTTGTTTCATGCAA-
1 TTCATTTATTTTATTTTATTCAAT
**
3096227 TT-ATTTTATGTTTATTATTATT-GGT
1 TTCA-TTTAT-TTTATT-TTATTCAAT
3096252 TTCATTTATTT
1 TTCATTTATTT
3096263 CCTTGGTTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
22 1 0.02
23 6 0.14
24 26 0.59
25 10 0.23
26 1 0.02
ACGTcount: A:0.20, C:0.07, G:0.06, T:0.66
Consensus pattern (24 bp):
TTCATTTATTTTATTTTATTCAAT
Found at i:3099202 original size:13 final size:14
Alignment explanation
Indices: 3099153--3099210 Score: 70
Period size: 13 Copynumber: 4.4 Consensus size: 14
3099143 CAAAAAGGGA
3099153 AAAAAGAAAAGAATC
1 AAAAAGAAAAGAA-C
*
3099168 --AAA-AAAAGAAA
1 AAAAAGAAAAGAAC
3099179 AAAAAGAAAAGAAC
1 AAAAAGAAAAGAAC
3099193 AAAAAG-AAAGAAC
1 AAAAAGAAAAGAAC
3099206 AAAAA
1 AAAAA
3099211 TCGAAAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.18
13 18 0.47
14 13 0.34
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAGAAC
Found at i:3099209 original size:26 final size:25
Alignment explanation
Indices: 3099139--3099209 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
3099129 AGATTCAATC
*
3099139 AGAACAAAAAG--GGAAAAAAGAAA
1 AGAACAAAAAGAAAGAAAAAAGAAA
*
3099162 AGAATCAAAAA-AAGAAAAAAAAGAAA
1 AGAA-CAAAAAGAA-AGAAAAAAGAAA
3099188 AGAACAAAAAGAAAGAACAAAA
1 AGAACAAAAAGAAAGAA-AAAA
3099210 ATCGAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.10
24 6 0.15
25 9 0.23
26 20 0.51
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.01
Consensus pattern (25 bp):
AGAACAAAAAGAAAGAAAAAAGAAA
Found at i:3099210 original size:14 final size:14
Alignment explanation
Indices: 3099168--3099210 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3099158 GAAAAGAATC
3099168 AAAA-AAAGAA-AA
1 AAAAGAAAGAACAA
3099180 AAAAGAAAAGAAC-A
1 AAAAG-AAAGAACAA
3099194 AAAAGAAAGAACAA
1 AAAAGAAAGAACAA
3099208 AAA
1 AAA
3099211 TCGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 16 0.59
ACGTcount: A:0.84, C:0.05, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAACAA
Found at i:3099881 original size:22 final size:22
Alignment explanation
Indices: 3099853--3099907 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3099843 GCTACCCCAT
*
3099853 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAACATCAAATGC
3099875 CAAACCTTTGAACATCAAATGC
1 CAAACCTTTGAACATCAAATGC
3099897 CAAACCTTTGA
1 CAAACCTTTGA
3099908 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAACATCAAATGC
Found at i:3100828 original size:106 final size:106
Alignment explanation
Indices: 3100641--3100972 Score: 558
Period size: 106 Copynumber: 3.1 Consensus size: 106
3100631 GAGAGTGGAT
*
3100641 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
3100706 CAACTTCACAAT-GAAGGATATTGGACTCGAGACAACACTAG
66 CAACTTCAC-ATCGAAGGATATTGGACTCGAGACAACACAAG
* * *
3100747 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
3100812 CAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAG
* *
3100853 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAAAGCCAATTT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
3100918 CAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAG
66 CAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAG
3100959 TTCAACTTCACAAC
1 TTCAACTTCACAAC
3100973 CAGCTTTTAG
Statistics
Matches: 209, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
105 2 0.01
106 207 0.99
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAG
Found at i:3101351 original size:106 final size:106
Alignment explanation
Indices: 3101146--3102078 Score: 1429
Period size: 106 Copynumber: 8.8 Consensus size: 106
3101136 GATTTCAGCA
* * *
3101146 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
3101211 ACAGCGAAGGATATTGGACTCGAGAAAACATAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
*
3101252 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * * **
3101317 ACATCGAAGGATATTGGAGTCCAGACAACGTAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* * *
3101358 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
*
3101423 ACAGCGAAGGATATTAGACTCGAGACAACACAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
3101464 TCA-AACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
3101528 ACATCGAAGG-TATTGGACTCTAGACAACGCAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* * * * *
3101568 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTGCCCAATTTCATAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
3101633 ACAACAAAGGATATTGGACTTGAGACAACACAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* * *
3101674 TCACAACGAAGGGTCGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTT
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
3101739 ACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* * *
3101780 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
*
3101845 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* *
3101886 TCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
3101951 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* * * * * *
3101992 TCACAACGAAGGGACGGCTGGTTGCCAATAAACAAATTCCCAGTTCCAGAACCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
3102057 ACGGCGGAGGATATTGGTCTCG
66 ACAGCGAAGGATATTGGACTCG
3102079 GAACAGTACA
Statistics
Matches: 751, Mismatches: 74, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
104 30 0.04
105 131 0.17
106 590 0.79
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
Found at i:3101413 original size:498 final size:498
Alignment explanation
Indices: 3100475--3101466 Score: 1815
Period size: 498 Copynumber: 2.0 Consensus size: 498
3100465 TAATCTTTTA
*
3100475 CAGCTTTTAGAGTCAAGTTTCGACTTCAAGACGAAGGATACTCGATTCAAAAGAACCTTTAAAGA
1 CAGCTTTTAGAGTCAAGTTTCGACTTCAAGACGAAGGATACTCAATTCAAAAGAACCTTTAAAGA
3100540 TTCATGTTGCTTGCTTAACTCAGCAGCAAGAAGCTACACTTCGACCAACTCGACAGATTGAAAGT
66 TTCATGTTGCTTGCTTAACTCAGCAGCAAGAAGCTACACTTCGACCAACTCGACAGATTGAAAGT
*
3100605 TTCTCTCGAAACAACACAATTTGCTCGAGAGTGGATTTCAACTTCACGACGAAGGGACCGCTGGT
131 TTCTCTCGAAACAACACAATTTGCTCGAGAGTGGATTTCAACATCACGACGAAGGGACCGCTGGT
*
3100670 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCG
196 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
* * *
3100735 AGACAACACTAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAATTT
261 AGAAAACACTAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATTT
3100800 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
326 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3100865 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAAC
391 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAAC
*
3100930 GAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAAC
456 GAAGGATATTAGACTCGAGACAACACAAGTTCAACTTCACAAC
*
3100973 CAGCTTTTAGAGTCAAGTTTCGACTTCAAGACGAAGGATACTCAATTCAAAAGCACCTTTAAAGA
1 CAGCTTTTAGAGTCAAGTTTCGACTTCAAGACGAAGGATACTCAATTCAAAAGAACCTTTAAAGA
*
3101038 TTCATGTTGGTTGCTTAACTCAGCAGCAAGAAGCTACACTTCGACCAACTCGACAGATTGAAAGT
66 TTCATGTTGCTTGCTTAACTCAGCAGCAAGAAGCTACACTTCGACCAACTCGACAGATTGAAAGT
*
3101103 TTCTCTCGAAACAACACAATTTGCTCGAGAGTGGATTTCAGCATCACGACGAAGGGACCGCTGGT
131 TTCTCTCGAAACAACACAATTTGCTCGAGAGTGGATTTCAACATCACGACGAAGGGACCGCTGGT
*
3101168 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
196 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
3101233 AGAAAACA-TAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATT
261 AGAAAACACT-AGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATT
* *
3101297 TCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGAGTCCAGACAACGTAAGTTCAACTTCAC
325 TCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * * *
3101362 GACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
390 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAA
3101427 CGAAGGATATTAGACTCGAGACAACACAAGTTCAACTTCA
455 CGAAGGATATTAGACTCGAGACAACACAAGTTCAACTTCA
3101467 AACGAAGGGA
Statistics
Matches: 476, Mismatches: 17, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
497 1 0.00
498 475 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (498 bp):
CAGCTTTTAGAGTCAAGTTTCGACTTCAAGACGAAGGATACTCAATTCAAAAGAACCTTTAAAGA
TTCATGTTGCTTGCTTAACTCAGCAGCAAGAAGCTACACTTCGACCAACTCGACAGATTGAAAGT
TTCTCTCGAAACAACACAATTTGCTCGAGAGTGGATTTCAACATCACGACGAAGGGACCGCTGGT
TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
AGAAAACACTAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATTT
CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAAC
GAAGGATATTAGACTCGAGACAACACAAGTTCAACTTCACAAC
Found at i:3102404 original size:83 final size:83
Alignment explanation
Indices: 3102265--3102605 Score: 362
Period size: 83 Copynumber: 4.1 Consensus size: 83
3102255 AAAGAAGGAG
* * ** *
3102265 TATCTGTCAGCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGTGCATCATTTACAGCATA
1 TATCTGTCAGCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATA
*
3102330 GCTCAAGGCTAAAAGGGT
66 ACTCAAGGCTAAAAGGGT
* * *
3102348 TATCTGTCAGCAAAGACCTTCGAGTTTGACTACACTCAGCTCCAAGGCACATCATTTGCAACATA
1 TATCTGTCAGCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATA
*
3102413 ACTCAAGGC-AATAAGGGC
66 ACTCAAGGCTAA-AAGGGT
* * * * * ** *
3102431 TATTTGCCAACAAAAGACCTTCGAGTTCGACTA-AGCTTAACTCCAAGGCATATCATTTGTAGCA
1 TATCTGTCAGC-AAAGACCTTCGAGTTCGACTACA-CTCAACTCCAAGGCACATCATTTACAACA
*
3102495 TAACTCAAGGCTAGAAGGGT
64 TAACTCAAGGCTAAAAGGGT
* * * * * * *
3102515 GATCTGTCATCAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCAAATTAAATTTACAACA
1 TATCTGTCAGCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACA-T-CATTTACAACA
* * *
3102580 TAACTCAAGACGAGAAGGGT
64 TAACTCAAGGCTAAAAGGGT
3102600 TATCTG
1 TATCTG
3102606 CCATCAAAAT
Statistics
Matches: 216, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
82 2 0.01
83 114 0.53
84 69 0.32
85 31 0.14
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (83 bp):
TATCTGTCAGCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATA
ACTCAAGGCTAAAAGGGT
Found at i:3103181 original size:37 final size:37
Alignment explanation
Indices: 3103079--3103183 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
3103069 CCTTTTCGTC
* *
3103079 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAGTT
3103116 CTACTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAGTT
* *
3103153 CTACTATGATTCAAACTCCCAAAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
3103184 CCACAAGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAGTT
Found at i:3103640 original size:2 final size:2
Alignment explanation
Indices: 3103633--3103685 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3103623 CCTTATTATT
3103633 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
3103675 TA TA TA TA TA T
1 TA TA TA TA TA T
3103686 TTAATTATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3103762 original size:2 final size:2
Alignment explanation
Indices: 3103755--3103783 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3103745 ATTATTTTCC
3103755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3103784 TTTTTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3109881 original size:394 final size:394
Alignment explanation
Indices: 3109140--3109915 Score: 1194
Period size: 394 Copynumber: 2.0 Consensus size: 394
3109130 AATACTTTCT
**
3109140 AATCCAGGAGACATGATATACCTCGGTGTGGGTTACCCAAAGACTCAGACAATACATGTTGGCTA
1 AATCCAGGAGACATGATATACCTCGGCATGGGTTACCCAAAGACTCAGACAATACATGTTGGCTA
* ** * * *
3109205 ATAGCCAGATTTGATCCTCTAAAGTTCTTGATGGAATCAATGGTTTTGATAAGTATATTGGCTAG
66 ATAACCAGATTTGATCCTCTAAAGTTCTTGATGGAATCAACAGTTTTGACAAGAAGATTGGCTAG
* *
3109270 ATGGTAGATGTTGTTATCCGAGTTTGACATCGGGTATGAAAGCGATAAAAATGAATGCCATAATA
131 ATGGTAGATGTTGTTATCCGAGTTTGACATCGGGTATGAAAGCAATAAAAAAGAATGCCATAATA
**
3109335 GATCCTCTAACAAGACGGGCATCAGACGATTATGAGTCCCTAGGTTTTAATTTTTCCAAATGAGG
196 GATCCTCTAACAAGACGACCATCAGACGATTATGAGTCCCTAGGTTTTAATTTTTCCAAATGAGG
* **
3109400 ATTTATTGTGTATCTTTACTGAAGAAGAAATTAAAGAAGCTGACGAATCCTAGAAGCTTTAATGG
261 ATTTATTGTGCATCTTTACTGAAGAAGAAATTAAAGAAGCTGAAAAATCCTAGAAGCTTTAATGG
* * *
3109465 GGCATACAATGCTTTTGGATGAGAATTTGGGGCAGTGATGATTTCTTTAGAAAATGTCTTTTACC
326 AGCATACAACGCTTTGGGATGAGAATTTGGGGCAGTGATGATTTCTTTAGAAAATGTCTTTTACC
3109530 TGCC
391 TGCC
* * * * *
3109534 AATCCATGAGACATGATATGCCTTGGCATGGGTTATCCGAAGACTCAGACAATACATGTTGGCTA
1 AATCCAGGAGACATGATATACCTCGGCATGGGTTACCCAAAGACTCAGACAATACATGTTGGCTA
* *
3109599 ATAACCATATTTGATCCTCTAAAGTTCTTGATGGAATCAACAGTTTTGACAAGAAGATTGGCTCG
66 ATAACCAGATTTGATCCTCTAAAGTTCTTGATGGAATCAACAGTTTTGACAAGAAGATTGGCTAG
*
3109664 ATGTTAGATGTTGTTATCCGAGTTTGACATCGGGTATGAAAGCAATAAAAAAGAATGCCATAATA
131 ATGGTAGATGTTGTTATCCGAGTTTGACATCGGGTATGAAAGCAATAAAAAAGAATGCCATAATA
* * * ** * * *
3109729 GATCTTCTAGCAATACGACCATTTGATGATTATGTGTCCCTAGGTTTTAATTTTTCTAAATGAGG
196 GATCCTCTAACAAGACGACCATCAGACGATTATGAGTCCCTAGGTTTTAATTTTTCCAAATGAGG
* *
3109794 ATTTATTGTGCGTCTTTACTGAAGAAGAAATTAAAGCAAG-TGAAAAATCCTGGAAGCTTTAATG
261 ATTTATTGTGCATCTTTACTGAAGAAGAAATTAAAG-AAGCTGAAAAATCCTAGAAGCTTTAATG
* *
3109858 GAGCATCCAACGCTTTGGGATGAGAATTTGTGGCAGTGATGATTTCTTTAGAAAATGT
325 GAGCATACAACGCTTTGGGATGAGAATTTGGGGCAGTGATGATTTCTTTAGAAAATGT
3109916 ATGTTATCCT
Statistics
Matches: 343, Mismatches: 38, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
394 340 0.99
395 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (394 bp):
AATCCAGGAGACATGATATACCTCGGCATGGGTTACCCAAAGACTCAGACAATACATGTTGGCTA
ATAACCAGATTTGATCCTCTAAAGTTCTTGATGGAATCAACAGTTTTGACAAGAAGATTGGCTAG
ATGGTAGATGTTGTTATCCGAGTTTGACATCGGGTATGAAAGCAATAAAAAAGAATGCCATAATA
GATCCTCTAACAAGACGACCATCAGACGATTATGAGTCCCTAGGTTTTAATTTTTCCAAATGAGG
ATTTATTGTGCATCTTTACTGAAGAAGAAATTAAAGAAGCTGAAAAATCCTAGAAGCTTTAATGG
AGCATACAACGCTTTGGGATGAGAATTTGGGGCAGTGATGATTTCTTTAGAAAATGTCTTTTACC
TGCC
Found at i:3110450 original size:14 final size:14
Alignment explanation
Indices: 3110428--3110517 Score: 55
Period size: 14 Copynumber: 6.4 Consensus size: 14
3110418 AGAAAAGAAG
*
3110428 GAAATAAAAAATAA
1 GAAAAAAAAAATAA
3110442 -AAACAAAAAAATAA
1 GAAA-AAAAAAATAA
*
3110456 GAAAAAAGAAAATGA
1 GAAAAAA-AAAATAA
*
3110471 GAAAGGAAAAAAT--
1 GAAA-AAAAAAATAA
*
3110484 GAATAAAAAGAAA-AG
1 GAA-AAAAA-AAATAA
3110499 GAAAAAATAAAATAA
1 GAAAAAA-AAAATAA
3110514 -AAAA
1 GAAAA
3110518 GAGAGAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
13 9 0.15
14 27 0.44
15 23 0.38
16 2 0.03
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (14 bp):
GAAAAAAAAAATAA
Found at i:3110467 original size:15 final size:14
Alignment explanation
Indices: 3110435--3110532 Score: 58
Period size: 15 Copynumber: 6.8 Consensus size: 14
3110425 AAGGAAATAA
3110435 AAAATAAAAACAAA-
1 AAAATAAAAA-AAAG
3110449 AAAATAAGAAAAAAG
1 AAAATAA-AAAAAAG
**
3110464 AAAATGAGAAAGGAA-
1 AAAAT-A-AAAAAAAG
*
3110479 AAAATGAATAAAAAG
1 AAAAT-AAAAAAAAG
** *
3110494 AAAA-GGAAAAAAT
1 AAAATAAAAAAAAG
*
3110507 AAAATAAAAAAGAG
1 AAAATAAAAAAAAG
3110521 AGAAATAAAAAA
1 A-AAATAAAAAA
3110533 GAAAATTGAA
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
13 9 0.14
14 20 0.31
15 29 0.45
16 5 0.08
17 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (14 bp):
AAAATAAAAAAAAG
Found at i:3110502 original size:23 final size:24
Alignment explanation
Indices: 3110425--3110516 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 24
3110415 TGAAGAAAAG
* *
3110425 AAGGAAATAA-AAAATAAAAACAA
1 AAGGAAAAAATAAAATAAAAAGAA
* * *
3110448 AA--AAATAAGAAAAAAGAAAATGAGA
1 AAGGAAA-AA-ATAAAATAAAAAGA-A
*
3110473 AAGGAAAAAAT-GAATAAAAAGAA
1 AAGGAAAAAATAAAATAAAAAGAA
3110496 AAGGAAAAAATAAAATAAAAA
1 AAGGAAAAAATAAAATAAAAA
3110517 AGAGAGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
21 3 0.06
22 1 0.02
23 15 0.28
24 25 0.47
25 4 0.08
26 2 0.04
27 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.09
Consensus pattern (24 bp):
AAGGAAAAAATAAAATAAAAAGAA
Found at i:3110537 original size:20 final size:20
Alignment explanation
Indices: 3110472--3110537 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 20
3110462 AGAAAATGAG
3110472 AAAGGAAAAAATGAATAAAAAGA
1 AAAGGAAAAAAT--A-AAAAAGA
3110495 AAAGGAAAAAATAAAATAA-A
1 AAAGGAAAAAATAAAA-AAGA
*
3110515 AAA-GAGAGAAATAAAAAAGA
1 AAAGGA-AAAAATAAAAAAGA
3110535 AAA
1 AAA
3110538 TTGAAAGGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 3 0.08
23 12 0.31
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAGGAAAAAATAAAAAAGA
Found at i:3112774 original size:36 final size:35
Alignment explanation
Indices: 3112708--3112775 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
3112698 GATATGAAAA
* **
3112708 AATTTATCTCACTTGAGATTGTTTTTCTTAAAATC
1 AATTTATCTCACTTGAGATAGTTTCCCTTAAAATC
*
3112743 AATTTCATCTCGCTTGAGATAGTTTCCCTTAAA
1 AATTT-ATCTCACTTGAGATAGTTTCCCTTAAA
3112776 GCACAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 5 0.18
36 23 0.82
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (35 bp):
AATTTATCTCACTTGAGATAGTTTCCCTTAAAATC
Found at i:3112902 original size:101 final size:101
Alignment explanation
Indices: 3112706--3112921 Score: 245
Period size: 101 Copynumber: 2.1 Consensus size: 101
3112696 TAGATATGAA
* * * *
3112706 AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAATCAATTTCATCTCGCTTGAGATAGTTTCCC
1 AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTCATCTCACTTGAGACAGTTTCAC
* * * *
3112771 TTAAAGCACAAATTTTGGATTTGATGCACTCGAAAC
66 TTAAAGCACAAAATTTGAAATTGATGCACTCAAAAC
* * * * * *
3112807 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTCGTCTTACTTGTGACGGTTTTTA
1 AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTCATCTCACTTGAGACAG-TTTCA
* * * *
3112872 CTTGAAGCATAAAATTTGAAATTG-TTCACTCAAAAT
65 CTTAAAGCACAAAATTTGAAATTGATGCACTCAAAAC
3112908 AAAATTTTATCTCA
1 AAAA-TTTATCTCA
3112922 ACTAATATAG
Statistics
Matches: 94, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
101 63 0.67
102 31 0.33
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (101 bp):
AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTCATCTCACTTGAGACAGTTTCAC
TTAAAGCACAAAATTTGAAATTGATGCACTCAAAAC
Found at i:3113681 original size:163 final size:162
Alignment explanation
Indices: 3113189--3113761 Score: 740
Period size: 163 Copynumber: 3.5 Consensus size: 162
3113179 TATAACAGAT
* *
3113189 GGAGGTGGATCAACATTTCTAATGGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAA
1 GGAGATGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAA
* * * * * * *
3113254 GAAGTTCGTAATGAAAAGAACTTGTTCACCCTTTTAG-TCGACTCTATCGTATAAGGAGATAAAT
66 GAAGTTCATAATGAGAAGAACTTGTTCA-ACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGAT
* * * * *
3113318 AAGCATAAGCATTTTGATCGAATCCATCACAGAA
130 CAGCATCAGCATTTTGTTCG-ATTCATCATAGAA
* ** * *
3113352 GGAGGTGGATCGTCATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCAACCGAAGAGAAAGAA
1 GGAGATGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAA
* * * *
3113417 GAAGTTCATAAT--G-AGAACTTGTTTAACTTTTTGCTCAACTCCATCGCAGTAGGAGATAGATC
66 GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATC
* *
3113479 AACATCATCATTTTGTTCGATTCAATCATAGAA
131 AGCATCAGCATTTTGTTCGATTC-ATCATAGAA
* * * *
3113512 GGAGATGTATCAACATTTCTAATGGAAGGGTTCATAATTAGAAGAACTCATCCGAAGAGGAAGAA
1 GGAGATGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAA
* * * *
3113577 GAAATTCATAATGAGAATAACTTGTTCAACTTTTTGCTCGACTATATTGCAGAAGGAGATAGATC
66 GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATC
* *
3113642 TGCATCAGCATTTTGTTTGATTTCATCATAGAA
131 AGCATCAGCATTTTGTTCGA-TTCATCATAGAA
* * *
3113675 GGAGATGGATCAACATTTCCAATGGAAGGGTTCATAATAATAAGAACTCATCCGAAGAGGAAGAA
1 GGAGATGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAA
3113740 GAAGTTCATAATGAGAAGAACT
66 GAAGTTCATAATGAGAAGAACT
3113762 CATCCTATGA
Statistics
Matches: 354, Mismatches: 50, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
159 9 0.03
160 122 0.34
162 1 0.00
163 219 0.62
164 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (162 bp):
GGAGATGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAA
GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATC
AGCATCAGCATTTTGTTCGATTCATCATAGAA
Found at i:3113747 original size:39 final size:39
Alignment explanation
Indices: 3113704--3113800 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 39
3113694 CAATGGAAGG
*
3113704 GTTCATAATAATAAGAACTCATCCGAAG-AGGAAGAAGAA
1 GTTCATAATAAGAAGAACTCATCCGAAGAAGG-AGAAGAA
* * * *
3113743 GTTCATAATGAGAAGAACTCATCCTATGAATGAGAAGAA
1 GTTCATAATAAGAAGAACTCATCCGAAGAAGGAGAAGAA
* *
3113782 GTTCATAATGAGAATAACT
1 GTTCATAATAAGAAGAACT
3113801 TGTTCGATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 49 0.96
40 2 0.04
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (39 bp):
GTTCATAATAAGAAGAACTCATCCGAAGAAGGAGAAGAA
Found at i:3113758 original size:17 final size:17
Alignment explanation
Indices: 3113736--3113795 Score: 66
Period size: 17 Copynumber: 3.2 Consensus size: 17
3113726 CCGAAGAGGA
3113736 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
*
3113753 AGAAGAACTCATCCTATGAATG
1 AGAAGAAGT--T-C-AT-AATG
3113775 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
3113792 AGAA
1 AGAA
3113796 TAACTTGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 16 0.44
18 2 0.06
19 2 0.06
20 2 0.06
21 2 0.06
22 12 0.33
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:3119015 original size:45 final size:45
Alignment explanation
Indices: 3118957--3119155 Score: 319
Period size: 45 Copynumber: 4.4 Consensus size: 45
3118947 CATTTATCGT
*
3118957 ATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATACC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATACC
* *
3119002 ATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATACC
3119047 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATACC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATACC
* * **
3119092 ATAAGCTCGTAAGTTTATTTTACCAATATACTTTCCA-TTATTTC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATACC
*
3119136 ATAAGCTCGTAAGTTTATTT
1 ATAAGCTCGTAAGCTTATTT
3119156 GCCCAATAGC
Statistics
Matches: 145, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
44 25 0.17
45 120 0.83
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATACC
Found at i:3119025 original size:24 final size:25
Alignment explanation
Indices: 3118993--3119116 Score: 71
Period size: 25 Copynumber: 5.4 Consensus size: 25
3118983 TATACTTACC
3118993 ATTTATACCATAAGCTCGTAAGCTT
1 ATTTATACCATAAGCTCGTAAGCTT
*
3119018 ATTT-TACCAATACA-CT--T-A-C-C
1 ATTTATACC-ATA-AGCTCGTAAGCTT
*
3119038 ATTTATTCCATAAGCTCGTAAGCTT
1 ATTTATACCATAAGCTCGTAAGCTT
*
3119063 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTATACC-ATA-AGCTCGTAAGCTT
*
3119083 ATTTATACCATAAGCTCGTAAGTTT
1 ATTTATACCATAAGCTCGTAAGCTT
3119108 ATTT-TACCA
1 ATTTATACCA
3119117 ATATACTTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 37
0.63 0.06 0.31
Matches are distributed among these distances:
19 2 0.03
20 18 0.24
21 9 0.12
22 4 0.05
23 4 0.05
24 13 0.18
25 22 0.30
26 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (25 bp):
ATTTATACCATAAGCTCGTAAGCTT
Found at i:3119265 original size:40 final size:40
Alignment explanation
Indices: 3119221--3119342 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
3119211 ACCATAGTGC
*
3119221 TACACATAAGGTCGTGCCCACAATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3119261 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
3119301 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3119341 TA
1 TA
3119343 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:3121269 original size:30 final size:30
Alignment explanation
Indices: 3121229--3121295 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
3121219 TTTGGTCCCT
*
3121229 AAACTATTTAAAGTTTATACTTTGTTTACC
1 AAACTTTTTAAAGTTTATACTTTGTTTACC
3121259 AAACTTTTTAAAGTTTATACTTTGTTTACC
1 AAACTTTTTAAAGTTTATACTTTGTTTACC
3121289 AAACTTT
1 AAACTTT
3121296 ACCAAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (30 bp):
AAACTTTTTAAAGTTTATACTTTGTTTACC
Found at i:3121306 original size:30 final size:30
Alignment explanation
Indices: 3121238--3121312 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
3121228 TAAACTATTT
**
3121238 AAAGTTTATACTTTGTTTACCAAACTTTTT
1 AAAGTTTATACTTTGTTTACCAAACTTTCC
3121268 AAAGTTTATACTTTGTTTACCAAACTTTACC
1 AAAGTTTATACTTTGTTTACCAAACTTT-CC
*
3121299 AAA-TTTATAATTTG
1 AAAGTTTATACTTTG
3121313 GTCACTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 38 0.93
31 3 0.07
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (30 bp):
AAAGTTTATACTTTGTTTACCAAACTTTCC
Found at i:3124507 original size:15 final size:15
Alignment explanation
Indices: 3124487--3124515 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3124477 CGGCTGCGGT
3124487 GGTTTCAAACCCTAG
1 GGTTTCAAACCCTAG
3124502 GGTTTCAAACCCTA
1 GGTTTCAAACCCTA
3124516 CGTATTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (15 bp):
GGTTTCAAACCCTAG
Found at i:3124578 original size:21 final size:21
Alignment explanation
Indices: 3124554--3124604 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3124544 GGGCTTTGTT
3124554 GTTGGGCTTCAATTTGGGCTG
1 GTTGGGCTTCAATTTGGGCTG
*
3124575 GTTGGGCTTTAATTTGGGCTG
1 GTTGGGCTTCAATTTGGGCTG
3124596 GTTGGGCTT
1 GTTGGGCTT
3124605 GCTAATTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.08, C:0.12, G:0.39, T:0.41
Consensus pattern (21 bp):
GTTGGGCTTCAATTTGGGCTG
Found at i:3124692 original size:3 final size:3
Alignment explanation
Indices: 3124684--3124746 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
3124674 CTGAAAACAA
* *
3124684 AAT AAT AAT AAT AAT AAAT AAAT AAT ATT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3124731 AAT AAT -AT AAT GAT AA
1 AAT AAT AAT AAT AAT AA
3124747 ATTAGAACAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 43 0.83
4 7 0.13
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3125377 original size:134 final size:133
Alignment explanation
Indices: 3124930--3125378 Score: 514
Period size: 134 Copynumber: 3.4 Consensus size: 133
3124920 ACGTTGACTT
* * * * ** *
3124930 ATTCCACTGTT-CTTCAGGGAATATTGAATCTAGGTATACTTGTTTGACTGTCACTCAAGGAATA
1 ATTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGGATA
* * * ** * *
3124994 CCAAATTTTAAAAGAGAGTGAACTATTCGGCTTCTTCTTGAGGGTAAATTATATCTGGGGACTTT
65 TCAAATCTTGAAAGAGAGTGATTTATTC-GCTTCTTCTTGAGGGAAAATCATATCTGGGGACTTT
3125059 GATTC
129 GATTC
* * * * * *
3125064 ATTCCATTTTTACTCAGGGAAGATTAAATCGAGGTAGACTTGTTCTAGTGTCACTC-AGGGAATA
1 ATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGG-ATA
* *
3125128 TCAAATCTTGAAAGAGAGTGATATGT-TTCGCTTCTTCTTGAGGGAAAATCATATATGAGGACTT
65 TCAAATCTTGAAAGAGAGTGAT-T-TATTCGCTTCTTCTTGAGGGAAAATCATATCTGGGGACTT
3125192 TGATTC
128 TGATTC
* * *
3125198 ATTCCACTGTTACTCAGGGAAGATTGAATCAAGACAGGCTTGTTCCACTGTCACTCAAGGGATAT
1 ATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGGATAT
* *
3125263 CAAATCTTGAAAGAGAGGGGTTTATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGA-TGTT
66 CAAATCTTGAAAGAGAGTGATTTATTC-GCTTCTTCTTGAGGGAAAATCATATCTGGGGACT-TT
3125327 GAATT-
129 G-ATTC
* *
3125332 ATTCCACTCTT-CTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
1 ATTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
3125379 TTGTTCCTCA
Statistics
Matches: 268, Mismatches: 37, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
132 1 0.00
133 9 0.03
134 246 0.92
135 11 0.04
136 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (133 bp):
ATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGGATAT
CAAATCTTGAAAGAGAGTGATTTATTCGCTTCTTCTTGAGGGAAAATCATATCTGGGGACTTTGA
TTC
Found at i:3125402 original size:134 final size:133
Alignment explanation
Indices: 3124930--3125498 Score: 501
Period size: 134 Copynumber: 4.2 Consensus size: 133
3124920 ACGTTGACTT
* * * * * **
3124930 ATTCCACTGTT-CTTCAGGGAATATTGAATCTAGGTATACTTGTTTGACTGTCACTCAAGGAATA
1 ATTCCACTATTAC-TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTC-AGGAATA
* * * * ** * * *
3124994 CCAAATTTTAAAAGAGAGTGAACTATTCGGCTTCTTCTTGAGGGTAAATTATATCTGGGGACTTT
64 TCAAATCTTGAAAGAGAGCGATTTATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGACTTT
3125059 GATTC
129 GATTC
* * * * * *
3125064 ATTCCATTTTTACTCAGGGAAGATTAAATCGAGGTAGACTTGTTCTAGTGTCACTCAGGGAATAT
1 ATTCCACTATTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCA-GGAATAT
* * *
3125129 CAAATCTTGAAAGAGAGTGATATGT-TTC-GCTTCTTCTTGAGGGAAAATCATATATGAGGACTT
65 CAAATCTTGAAAGAGAGCGAT-T-TATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGACTT
3125192 TGATTC
128 TGATTC
* * * * *
3125198 ATTCCACTGTTACTCAGGGAAGATTGAATCAAGACAGGCTTGTTCCACTGTCACTCAAGGGATAT
1 ATTCCACTATTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTC-AGGAATAT
* *
3125263 CAAATCTTGAAAGAGAGGGGTTTATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGA-TGTT
65 CAAATCTTGAAAGAGAGCGATTTATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGACT-TT
3125327 GAATT-
129 G-ATTC
* * * *
3125332 ATTCCACTCTT-CTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTGTTC-CTCAGTGAAG
1 ATTCCACTATTAC-TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTG-TCACTCAG-GAAT
* * * * * * * * * * *
3125395 ATTAAATCTGGAAAAAAGAGCAATTTGTTCTGCTGCTTCTTGAGGGAAGACCAGATCT-GGAAAT
63 ATCAAATCTTG-AAAGAGAGCGATTTATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGACT
3125459 GTTGATTC
127 -TTGATTC
* *
3125467 AGTCCACTATT-CTTCA-AGAAGATTGAATCGAG
1 ATTCCACTATTAC-TCAGGGAAGATTGAATCGAG
3125499 TTCGATTTGC
Statistics
Matches: 364, Mismatches: 56, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
132 1 0.00
133 9 0.02
134 288 0.79
135 65 0.18
136 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (133 bp):
ATTCCACTATTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGAATATC
AAATCTTGAAAGAGAGCGATTTATTCTGCTTCTTCTTGAGGGAAAATCATATCTGGGGACTTTGA
TTC
Found at i:3125490 original size:268 final size:268
Alignment explanation
Indices: 3124976--3125495 Score: 588
Period size: 268 Copynumber: 1.9 Consensus size: 268
3124966 TACTTGTTTG
* * *
3124976 ACTGTCACTCAAGGAATACCAAATTTTAAAAGAGAGTGAACTATTCGGCTTCTTCTTGAGGGTAA
1 ACTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGAACTATTCGGCTTCTTCTTGAGGGAAA
* * * *
3125041 ATTATATCTGGGGACTTTGATTCATTCCATTTTTACTCAGGGAAGATTAAATCGAGGTAGACTTG
66 ATCATATCTGGGGACTTTGATTCATTCCACTCTTACTCAGGGAAGATTAAATCGAGGCAGACTTG
* * * * ** *
3125106 TTCTAGTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGTGATATGTTTCGCTTCTTCTTGAGG
131 TTCCAGTGTCACTCAGGGAAGATCAAATCTGGAAAAAGAGCAATATGTTTCGCTGCTTCTTGAGG
* * * * * * *
3125171 GAAAATCATATATGAGGACTTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCAAGACAGG
196 GAAAACCAGATATGAGAAATTTGATTCAGTCCACTATTACTCAGAGAAGATTGAATCAAGACAGG
3125236 CTTGTTCC
261 CTTGTTCC
* * * *** *
3125244 ACTGTCACTCAAGGGATATCAAATCTTGAAAGAGAGGGGTTTATTCTGCTTCTTCTTGAGGGAAA
1 ACTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGAACTATTCGGCTTCTTCTTGAGGGAAA
* *
3125309 ATCATATCTGGGGA-TGTTGAATT-ATTCCACTCTT-CTTTAGGGAAGATTGAATCGAGGCAGAC
66 ATCATATCTGGGGACT-TTG-ATTCATTCCACTCTTAC-TCAGGGAAGATTAAATCGAGGCAGAC
* * * *
3125371 TTGTTCCATTGTTC-CTCAGTGAAGATTAAATCTGGAAAAAAGAGCAATTTG-TTCTGCTGCTTC
128 TTGTTCCAGTG-TCACTCAGGGAAGATCAAATCTGG-AAAAAGAGCAATATGTTTC-GCTGCTTC
* *
3125434 TTGAGGGAAGACCAGATCTG-GAAATGTTGATTCAGTCCACTATT-CTTCA-AGAAGATTGAATC
190 TTGAGGGAAAACCAGATATGAGAAAT-TTGATTCAGTCCACTATTAC-TCAGAGAAGATTGAATC
3125496 GAGTTCGATT
Statistics
Matches: 208, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
267 2 0.01
268 148 0.71
269 58 0.28
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (268 bp):
ACTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGAACTATTCGGCTTCTTCTTGAGGGAAA
ATCATATCTGGGGACTTTGATTCATTCCACTCTTACTCAGGGAAGATTAAATCGAGGCAGACTTG
TTCCAGTGTCACTCAGGGAAGATCAAATCTGGAAAAAGAGCAATATGTTTCGCTGCTTCTTGAGG
GAAAACCAGATATGAGAAATTTGATTCAGTCCACTATTACTCAGAGAAGATTGAATCAAGACAGG
CTTGTTCC
Found at i:3126308 original size:233 final size:230
Alignment explanation
Indices: 3125965--3126386 Score: 598
Period size: 233 Copynumber: 1.8 Consensus size: 230
3125955 ACTTTTTTCA
*
3125965 TTTTCAAAAATTTCAATTTTCAGAATTAAATGAGAAACTTTTTCATTTTCGAAAACATGTGAAAA
1 TTTTCAAAAATTTCAATTTTCAGAATTAAATGAGAAACTTTCTCATTTTCGAAAACATGTGAAAA
* * *
3126030 CATTCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTGGCTCAAAAGACTTA-AGA
66 CATTCTACCCAAAGGTCTTATGGATGACCCCAAGGACTTATCATCTGGCTCAAAAGACTTACAG-
* * * * *
3126094 ATGACCCGAAGGATTTAAGCGTCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAACT
130 ATAACCCAAAGGATTTAAGCATCAGGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAACT
3126159 TTGGAAATAGTTTACTTGGTAAGAAACTTTCCTTAC
195 TTGGAAATAGTTTACTTGGTAAGAAACTTTCCTTAC
* * * *
3126195 TTTTCAAAAACTTT-AATTTTCATATTTAAATGAGAAACTTTCCTCATTTTTTGAGAGACATGTG
1 TTTTCAAAAA-TTTCAATTTTCAGAATTAAATGAGAAACTTT-CTCA-TTTTCGA-AAACATGTG
* * * * *
3126259 AAAACA-TCTTACCCAAAGGTCTTGTTGATGACCCCAAGGACTTATCATCTTGCTCGAAATACTT
62 AAAACATTC-TACCCAAAGGTCTTATGGATGACCCCAAGGACTTATCATCTGGCTCAAAAGACTT
*
3126323 ACAGATAACCCAAAGGATTTAAGCATCAGGCTCAAAAGACTTATTGATGGCCCGAAGGACTTAC
126 ACAGATAACCCAAAGGATTTAAGCATCAGGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAC
3126387 TAAGTAAAAA
Statistics
Matches: 167, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
230 35 0.21
231 6 0.04
232 8 0.05
233 116 0.69
234 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (230 bp):
TTTTCAAAAATTTCAATTTTCAGAATTAAATGAGAAACTTTCTCATTTTCGAAAACATGTGAAAA
CATTCTACCCAAAGGTCTTATGGATGACCCCAAGGACTTATCATCTGGCTCAAAAGACTTACAGA
TAACCCAAAGGATTTAAGCATCAGGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAACTT
TGGAAATAGTTTACTTGGTAAGAAACTTTCCTTAC
Found at i:3129742 original size:29 final size:31
Alignment explanation
Indices: 3129707--3129775 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
3129697 TATAGCGTAG
*
3129707 TATATATAGT-ATACAGTACA-TTTTTGAAA
1 TATATATAGTAATACAGTACATTTTTTAAAA
* *
3129736 TATATATA-TAATATAGTAGATTTTTTAAAA
1 TATATATAGTAATACAGTACATTTTTTAAAA
*
3129766 CATATATAGT
1 TATATATAGT
3129776 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 16 0.48
30 15 0.45
31 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (31 bp):
TATATATAGTAATACAGTACATTTTTTAAAA
Found at i:3129843 original size:16 final size:17
Alignment explanation
Indices: 3129818--3129849 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3129808 TACTTGAAAA
3129818 TATATATATAATATATG
1 TATATATATAATATATG
3129835 TATAT-TATAATATAT
1 TATATATATAATATAT
3129850 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATATATAATATATG
Found at i:3129895 original size:22 final size:21
Alignment explanation
Indices: 3129835--3129895 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
3129825 ATAATATATG
3129835 TATATTATAATATATTTAAAAAAA
1 TATATTAT-AT-TA-TTAAAAAAA
* *
3129859 TATGTTATAGTATTAAAAAATA
1 TATATTATATTATTAAAAAA-A
3129881 TATATTATATTATTA
1 TATATTATATTATTA
3129896 TTAATGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.25
22 16 0.50
23 1 0.03
24 7 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TATATTATATTATTAAAAAAA
Found at i:3129916 original size:11 final size:11
Alignment explanation
Indices: 3129883--3129925 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3129873 AAAAAATATA
*
3129883 TATTATATTAT
1 TATTATTTTAT
*
3129894 TATTAATGTTAT
1 TATT-ATTTTAT
3129906 TATTATTTTAT
1 TATTATTTTAT
*
3129917 TTTTATTTT
1 TATTATTTT
3129926 CGGGTTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:3136963 original size:23 final size:23
Alignment explanation
Indices: 3136919--3136965 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3136909 AACATATTGT
**
3136919 GTAGCGCTTATATAATGTAATAG
1 GTAGCGCTTATATAATAAAATAG
3136942 GTAGCGCTTATATAATAAAATAG
1 GTAGCGCTTATATAATAAAATAG
3136965 G
1 G
3136966 CATTTAACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAG
Found at i:3137027 original size:87 final size:87
Alignment explanation
Indices: 3136879--3137041 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 87
3136869 TATGTTATAT
* * *
3136879 CATTTAACCGGAAATATTATCAAGCACAATAACATATTGTGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACATATTGTGTAGCACTTATATAATATAATAGAT
3136944 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
3136966 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAG-GTAGCACTTATATAATATAATAGA
1 CATTTAACCGGAAATATTATCAAGCACAATAACATATT-GTGTAGCACTTATATAATATAATAGA
3137030 TAGCGCTTATAT
65 TAGCGCTTATAT
3137042 TGATATATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 70 0.99
88 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGCACAATAACATATTGTGTAGCACTTATATAATATAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:3137514 original size:22 final size:22
Alignment explanation
Indices: 3137472--3137529 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
3137462 GACGTTTTTA
*
3137472 GTATCGACAC-TTGTTGTAAAT
1 GTATCGACACTTTGTTGCAAAT
3137493 GTATCGACACTTTGTTGCAAAT
1 GTATCGACACTTTGTTGCAAAT
3137515 GTATCGACACTTTGT
1 GTATCGACACTTTGT
3137530 CATGCACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 10 0.29
22 25 0.71
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (22 bp):
GTATCGACACTTTGTTGCAAAT
Found at i:3137942 original size:201 final size:201
Alignment explanation
Indices: 3137617--3138362 Score: 1201
Period size: 201 Copynumber: 3.7 Consensus size: 201
3137607 ACGAATTTAA
* * *
3137617 AAAGTATCGATACATTATGTT-GA-CTGGTTTTCTCATAAAACCGGTAAATTTAAACCAGTTACA
1 AAAGTGTCGATACATTAT-TTAGACCT-ATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACA
* * * *
3137680 TTGTAAAGTGACCTATTACATTATAATTTTTGGTTTCGAAGTATTTGGGGTCGATACTTTTTATA
64 TTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGACACTTTTTATA
* * *
3137745 AATTTATCGACACTTTATGCGTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACAC
129 AATGTATCGACACTTTATGCTTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACGC
3137810 AAATAAAT
194 AAATAAAT
*
3137818 AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACTGGTTACATT
1 AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATT
*
3137883 GTAAAGTGACCTATTACATTATAATTTTCGATCTCGATGTATTTGGGGTCGACACTTTTTATAAA
66 GTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGACACTTTTTATAAA
3137948 TGTATCGACACTTTATGCTTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACGCAA
131 TGTATCGACACTTTATGCTTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACGCAA
3138013 ATAAAT
196 ATAAAT
*
3138019 AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACTGGTAAATTTAAACCGGTTACATT
1 AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATT
* *
3138084 GTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGATACTTTTAATAAA
66 GTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGACACTTTTTATAAA
* * * *
3138149 TGTATCGACAATGTATGTTTACACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACGCAA
131 TGTATCGACACTTTATGCTTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACGCAA
*
3138214 AAAAAT
196 ATAAAT
*
3138220 AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATT
1 AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATT
* * * * * *
3138285 G-AAAGTGACCTATTACATTATAATTATAGGTTTCGATGTATTTGGGATCGACACATGTTATAAA
66 GTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGACACTTTTTATAAA
*
3138349 TGTATCAACACTTT
131 TGTATCGACACTTT
3138363 TTTGTGAACT
Statistics
Matches: 508, Mismatches: 35, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
200 68 0.13
201 438 0.86
202 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (201 bp):
AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATT
GTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGACACTTTTTATAAA
TGTATCGACACTTTATGCTTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATCGACGCAA
ATAAAT
Found at i:3142715 original size:200 final size:200
Alignment explanation
Indices: 3142161--3142889 Score: 971
Period size: 200 Copynumber: 3.6 Consensus size: 200
3142151 GTTGACCGAG
** ** * * ** *
3142161 TTTCTCATAAAACCGGTAAATTTAAACCGATTACATTGTAAAGTGACCTATTACATTATAATTAT
1 TTTCTCAT-AAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTATAATTAT
* * * *
3142226 AGGTTTCGATGTATTTGGGATCGAAACATGTTATAAATGTATCGACACTTTTTTGTACACTTGGT
65 AGGTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCGACACTTTTTCGTGCACTTGGT
3142291 TTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGTAGTTGTGTCGATACTTTATGTAT
130 TTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGTAGTTGTGTCGATACTTTATGTAT
*
3142356 ACCTGT
195 ACATGT
** ** * ** *
3142362 TTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTAT
1 TTTCTCAT-AAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTATAATTAT
* * * *
3142427 AGGTTTTGATGTATTTGGGATCGATACATGTTATAAATGTATCGACACTTTTTTGTGCACTTGGT
65 AGGTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCGACACTTTTTCGTGCACTTGGT
* * *
3142492 TTGGAAAATAAATTCTGGACAAAAAGTATCTACACTTGTTGTAGTTATGTCGATACTTTATGTAT
130 TTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGTAGTTGTGTCGATACTTTATGTAT
3142557 ACATGT
195 ACATGT
*
3142563 TTTCTCATAAACCGGTGTATTTAGGCCAGTTACATTGTTATTTTACCTATTACATTAT-ATCTAT
1 TTTCTCATAAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTATAAT-TAT
* * * * *
3142627 -GTGTTTCAATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTTTCGTCCACTTGG
65 AG-GTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCGACACTTTTTCGTGCACTTGG
*
3142691 TTTGGAAAATACATTCTAGACAAAAAGTATCGACACTTGTTGTAGTTGTGTCGATACTTTATGTA
129 TTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGTAGTTGTGTCGATACTTTATGTA
*
3142756 TACTTGT
194 TACATGT
*
3142763 TTTCTCATAAACCGGTGTATTTAGGTCGGTTACATTGTTATTTTACCTATTACATTAT-ATCTAT
1 TTTCTCATAAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTATAAT-TAT
* * ** * * *
3142827 -GTGTTTCGATGTTTTTAGTATAAACACTTGTTATAAATGTATCGACACTCTGTCGTGCACTTG
65 AG-GTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCGACACTTTTTCGTGCACTTG
3142890 TTATAAATGG
Statistics
Matches: 487, Mismatches: 39, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
199 3 0.01
200 283 0.58
201 201 0.41
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (200 bp):
TTTCTCATAAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTATAATTATA
GGTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTT
TGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGTAGTTGTGTCGATACTTTATGTATA
CATGT
Found at i:3144381 original size:12 final size:12
Alignment explanation
Indices: 3144364--3144398 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3144354 ACTTGTTTGG
*
3144364 ATCATCATCATC
1 ATCATCTTCATC
3144376 ATCATCTTCATC
1 ATCATCTTCATC
*
3144388 GTCATCTTCAT
1 ATCATCTTCAT
3144399 TGACCGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (12 bp):
ATCATCTTCATC
Found at i:3146396 original size:199 final size:199
Alignment explanation
Indices: 3145946--3147248 Score: 2025
Period size: 199 Copynumber: 6.6 Consensus size: 199
3145936 GTTTCAAATT
* * ** * * * ** * *
3145946 AAACCGGTATATTTATACCGGTTAAATTGCAAAATGACTTATTACATTAAAATTTTGGGTTTCAA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
* * * * * *
3146011 TATTCTTAGGATCGATACTTGTTATAAATGTATCGACACTTTTTCCTGCACTTGGTTTT-GAAAT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTT-GTTTTAGAAAT
*
3146075 TCATTCTGGACCAAAAGTATCGACACTTGTTTTA----T-T---T--TTTTTGTACACCTATTTT
130 TCATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
3146130 CTCAA
195 CTCAA
3146135 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
* *
3146200 TATTTTTGGGATCGACACTTATTATAAATGTATCGACATTTTTTCGTGCACTTGTTTTAGAAATT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
* * * *
3146265 CATTCTGGACCAAAAGTATCGACACTTATTTTATTTGTGCCGATACCTTTTGTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
3146330 TCAA
196 TCAA
* * *
3146334 AAACCGGTATATTTAGACCAGTTACAATGTTAATTTACCTATTACATCCTAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
* * *
3146399 TGTTTTTGGGATCGACGCTTATTATAAATGTATCGACATTTTTTCGTGCACTTGTTTAAGAAATT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
*
3146464 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACGTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
3146529 TCAA
196 TCAA
* *
3146533 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACTTATTACATTCTAATTATGGATTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
3146598 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
* * * *
3146663 AATTCTGGACCAAAAGTATCGACACTTGTGTTATTTGTGTCGATAATTTTTGTACATCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
3146728 TCAA
196 TCAA
* * * * *
3146732 AAATCGGTATATTTAAACCGGTTACATTGTTAATTTAACTGTTACATTCTAATTATAGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
*
3146797 TGTTTTTGGGATCGACACTTATTATAAATGTATTGACACTTTTTCGTGCACTTGTTTTAGAAATT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
3146862 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
3146927 TCAA
196 TCAA
*
3146931 AAATCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
* *
3146996 TATTTTTGGGATCGACACTTATTATAAATGTATCGATACTTTTTCGTGCACTTGTTTTAGAAATT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
*
3147061 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
3147126 TCAA
196 TCAA
* * * * *
3147130 AAACCGATATATTTAAACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCTA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
* * *
3147195 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACATTTTTTCGTGCACTTG
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTG
3147249 GTATATTTTA
Statistics
Matches: 1027, Mismatches: 76, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
188 5 0.00
189 139 0.14
193 1 0.00
197 1 0.00
199 881 0.86
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTCTAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATT
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
TCAA
Found at i:3147571 original size:176 final size:175
Alignment explanation
Indices: 3147248--3147595 Score: 592
Period size: 176 Copynumber: 2.0 Consensus size: 175
3147238 TCGTGCACTT
*
3147248 GGTATATTTTACCTATTAATTTTGGAAACCATACTTGGACAAAATATTGGAATCAAATCTTTCTG
1 GGTATATTTTACCTATTAAGTTTGGAAACCATACTTGGACAAAATATTGGAATCAAATCTTTCTG
*
3147313 TTTATTAATTTTGTCATTATTATATTCTATTTTTTACCACCTACATTGTAAATTTATCTATTACT
66 TTTATTAATTTTGTCATTATTATATTCTATTTTTTACCACCTACATTGTAAATTTACCTATTACT
*
3147378 TTAAAGTTATTGCATTTTGTAGTTATTGAACATACCTAAATATACC
131 TTAAAGTTATGGCATTTTGTAGTTATTGAACATACC-AAATATACC
* * *
3147424 GGTATATTTTACCTATTAAGTTT-GAGAACCATACTTGGAGAAAATTTTGGAATCAAATCTTTGT
1 GGTATATTTTACCTATTAAGTTTGGA-AACCATACTTGGACAAAATATTGGAATCAAATCTTTCT
3147488 GTTTATTAATTTTGTCATTATTATATTCTATTTTTT-CCACCTACATTGTAAATTTACCTATTAC
65 GTTTATTAATTTTGTCATTATTATATTCTATTTTTTACCACCTACATTGTAAATTTACCTATTAC
*
3147552 TTTAAAGTTAGTGGCATTTTGTAGTTATTGAACTTACCAAATAT
130 TTTAAAGTTA-TGGCATTTTGTAGTTATTGAACATACCAAATAT
3147596 GGAATAATGC
Statistics
Matches: 163, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
175 45 0.28
176 118 0.72
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (175 bp):
GGTATATTTTACCTATTAAGTTTGGAAACCATACTTGGACAAAATATTGGAATCAAATCTTTCTG
TTTATTAATTTTGTCATTATTATATTCTATTTTTTACCACCTACATTGTAAATTTACCTATTACT
TTAAAGTTATGGCATTTTGTAGTTATTGAACATACCAAATATACC
Found at i:3147742 original size:19 final size:19
Alignment explanation
Indices: 3147718--3147767 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
3147708 TTACATTCAC
*
3147718 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
**
3147737 ATACAAAATTAAAAATTTT
1 ATACAAAATTAAAAATCGT
3147756 ATACAAAATTAA
1 ATACAAAATTAA
3147768 CCCTACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:3149260 original size:18 final size:18
Alignment explanation
Indices: 3149237--3149274 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3149227 TTCTCCCTAT
*
3149237 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTCTCTTC
3149255 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTCTCTTC
3149273 TT
1 TT
3149275 GAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (18 bp):
TTCCTCCATCTTCTCTTC
Found at i:3149963 original size:22 final size:21
Alignment explanation
Indices: 3149935--3149990 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
3149925 AACCTGCATT
*
3149935 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
3149957 TATAATAACTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
3149981 TATAAAAAAA
1 TATAATAAAA
3149991 ACAAAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:3150993 original size:18 final size:18
Alignment explanation
Indices: 3150953--3150994 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3150943 TACTGTCAAC
*
3150953 ATTTAAAATTTGTAATTA
1 ATTTAAAATTTGTAAATA
3150971 ATTTAAAATTCT-TAAATA
1 ATTTAAAATT-TGTAAATA
*
3150989 CTTTAA
1 ATTTAA
3150995 TCCAATTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTTAAAATTTGTAAATA
Found at i:3151284 original size:18 final size:18
Alignment explanation
Indices: 3151243--3151309 Score: 98
Period size: 19 Copynumber: 3.6 Consensus size: 18
3151233 CATTTATACA
*
3151243 ACCTAAAATATCATTTTCT
1 ACCTATAATATCATTTT-T
3151262 ACCTATAATATCATTTTT
1 ACCTATAATATCATTTTT
3151280 ACCTATAATATCATTTTTT
1 ACCTATAATATCA-TTTTT
*
3151299 ACGTATAATAT
1 ACCTATAATAT
3151310 TAAATAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.31
19 31 0.69
ACGTcount: A:0.36, C:0.16, G:0.01, T:0.46
Consensus pattern (18 bp):
ACCTATAATATCATTTTT
Found at i:3151341 original size:58 final size:58
Alignment explanation
Indices: 3151279--3151423 Score: 245
Period size: 58 Copynumber: 2.5 Consensus size: 58
3151269 ATATCATTTT
* * *
3151279 TACCTATAATATCATTTTTTACGTATAATATTAAATAAAAGTATCGATATTTATCATC
1 TACCTAGAATATCACTTTTTACATATAATATTAAATAAAAGTATCGATATTTATCATC
*
3151337 TACCTAGAATATCACTTTTTACCTATAATATTAAATAAAAGTATCGATATTTATCATC
1 TACCTAGAATATCACTTTTTACATATAATATTAAATAAAAGTATCGATATTTATCATC
*
3151395 TACCTAGAATATCACTTTCTACATATAAT
1 TACCTAGAATATCACTTTTTACATATAAT
3151424 CGTTCCCAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 82 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (58 bp):
TACCTAGAATATCACTTTTTACATATAATATTAAATAAAAGTATCGATATTTATCATC
Found at i:3151853 original size:20 final size:20
Alignment explanation
Indices: 3151828--3151881 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3151818 GTAGCGCTTT
3151828 ACCGGTTTTGTCATTTTGAG
1 ACCGGTTTTGTCATTTTGAG
3151848 ACCGGTTTTGTCATTTTGAG
1 ACCGGTTTTGTCATTTTGAG
*
3151868 ACCGGTTTTTTCAT
1 ACCGGTTTTGTCAT
3151882 ATTTTTACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
ACCGGTTTTGTCATTTTGAG
Found at i:3155795 original size:19 final size:20
Alignment explanation
Indices: 3155767--3155804 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3155757 TGGAGAGAAA
3155767 GAGAAGGAAG-AAGTGAAGT
1 GAGAAGGAAGAAAGTGAAGT
*
3155786 GAGAATGAAGAAAGTGAAG
1 GAGAAGGAAGAAAGTGAAG
3155805 AGAAGACGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (20 bp):
GAGAAGGAAGAAAGTGAAGT
Found at i:3156562 original size:23 final size:24
Alignment explanation
Indices: 3156520--3156564 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3156510 AATTACTCAT
* *
3156520 TTATTCTGAGTTTAAGTCTAAAAA
1 TTATTCTGAATTTAAATCTAAAAA
3156544 TTATTCT-AATTTAAATCTAAA
1 TTATTCTGAATTTAAATCTAAA
3156565 TATATTACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (24 bp):
TTATTCTGAATTTAAATCTAAAAA
Found at i:3157214 original size:31 final size:32
Alignment explanation
Indices: 3157179--3157248 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
3157169 CTAACCCTCT
*
3157179 AAAATTTT-TAAAATTATTATTTAA-TCTTTTA
1 AAAATTTTATAAAATGATTA-TTAAGTCTTTTA
3157210 AAAATTTTATAAAATGATTATTAAGTCTTTTA
1 AAAATTTTATAAAATGATTATTAAGTCTTTTA
*
3157242 AATATTT
1 AAAATTT
3157249 AAACAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 12 0.34
32 23 0.66
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (32 bp):
AAAATTTTATAAAATGATTATTAAGTCTTTTA
Found at i:3159498 original size:44 final size:44
Alignment explanation
Indices: 3159433--3159522 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
3159423 GGTGTTAACA
3159433 TCGAGTTTAGGAGCTTCCTACACTGCCTCCACCACTCTGTTTGT
1 TCGAGTTTAGGAGCTTCCTACACTGCCTCCACCACTCTGTTTGT
*
3159477 TCGAGTTTAGGAGCTTGCTACACTGCCTCCACCACTCTGTTTGT
1 TCGAGTTTAGGAGCTTCCTACACTGCCTCCACCACTCTGTTTGT
3159521 TC
1 TC
3159523 ATCCGTTCCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.16, C:0.31, G:0.19, T:0.34
Consensus pattern (44 bp):
TCGAGTTTAGGAGCTTCCTACACTGCCTCCACCACTCTGTTTGT
Found at i:3159680 original size:3 final size:3
Alignment explanation
Indices: 3159667--3159734 Score: 100
Period size: 3 Copynumber: 21.3 Consensus size: 3
3159657 GTATGGTAGG
3159667 TAA TAA TTAA TAA TTAA TAA TTAA TAA TTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA -TAA TAA -TAA TAA -TAA TAA TAA TAA TAA TAA TAA
3159716 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
3159735 GTTTTTTAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
3 49 0.80
4 12 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3160622 original size:32 final size:31
Alignment explanation
Indices: 3160580--3160664 Score: 91
Period size: 34 Copynumber: 2.6 Consensus size: 31
3160570 CATGATATCC
*
3160580 TTCGTCGTGAAGTTGAAATTG-TGGATGGCTCA
1 TTCGTTGTGAAGTTGAAATTGATGGAT-G-TCA
* *
3160612 TTCGTTGTGAAGTTGAGATTTGAATTGGATGTCC
1 TTCGTTGTGAAGTTGA-AATTG-A-TGGATGTCA
3160646 TTCGTTGTGAAGTTGAAAT
1 TTCGTTGTGAAGTTGAAAT
3160665 CCAATCTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
32 15 0.33
33 6 0.13
34 18 0.40
35 1 0.02
36 5 0.11
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.39
Consensus pattern (31 bp):
TTCGTTGTGAAGTTGAAATTGATGGATGTCA
Found at i:3165041 original size:19 final size:19
Alignment explanation
Indices: 3165000--3165042 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
3164990 TTGTAATACC
3165000 CCAAAAATTCAGATAATGA
1 CCAAAAATTCAGATAATGA
3165019 -CAAAAATTCAGATAATGA
1 CCAAAAATTCAGATAATGA
3165037 CCAAAA
1 CCAAAA
3165043 TGAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (19 bp):
CCAAAAATTCAGATAATGA
Found at i:3167725 original size:2 final size:2
Alignment explanation
Indices: 3167713--3167745 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3167703 ATATTATAGT
*
3167713 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3167746 CTTATTCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3169958 original size:2 final size:2
Alignment explanation
Indices: 3169953--3169980 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3169943 AAAATTATGA
3169953 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
3169981 TGTATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3172867 original size:54 final size:54
Alignment explanation
Indices: 3172802--3173201 Score: 575
Period size: 54 Copynumber: 7.4 Consensus size: 54
3172792 TCCTTGGTTT
* * * *
3172802 TTGCAGACATAGTTCCAATACGGTAATTCACAAACTAATCATAAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
* * * *
3172856 TTGCACACATAGTGCCAATATGGTAATTCACAAACAAATTATTAATTACTTAAG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
* *
3172910 TTGCACACACAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
* * * *
3172964 TTGCACACATAGTACCAATATGGTAATTCACAAACAAATTATGAATTACTTAAG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
*
3173018 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATTAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
* * * * *
3173072 TTGCACACATAGTACCATTACGGAAATTCACAAACAAATTATGAATTACTTAAG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
* ** *
3173126 TTGCACACATAGTGTCAATACAATAATTCACAAACTAATTATGAGTTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
*
3173180 TTGCACACATAGTGACAATACG
1 TTGCACACATAGTGCCAATACG
3173202 ATTTTCAAAA
Statistics
Matches: 305, Mismatches: 41, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 305 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGG
Found at i:3172991 original size:108 final size:108
Alignment explanation
Indices: 3172802--3173192 Score: 638
Period size: 108 Copynumber: 3.6 Consensus size: 108
3172792 TCCTTGGTTT
* * * * *
3172802 TTGCAGACATAGTTCCAATACGGTAATTCACAAACTAATCATAAATTACTTAGGTTGCACACATA
1 TTGCACACATAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATA
* *
3172867 GTGCCAATATGGTAATTCACAAACAAATTATTAATTACTTAAG
66 GTACCAATATGGTAATTCACAAACAAATTATGAATTACTTAAG
*
3172910 TTGCACACACAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATA
1 TTGCACACATAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATA
3172975 GTACCAATATGGTAATTCACAAACAAATTATGAATTACTTAAG
66 GTACCAATATGGTAATTCACAAACAAATTATGAATTACTTAAG
* *
3173018 TTGCACACATAGTGCCAATACGGTAATTCACAAACTAATTATTAATTACTTAGGTTGCACACATA
1 TTGCACACATAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATA
* * *
3173083 GTACCATTACGGAAATTCACAAACAAATTATGAATTACTTAAG
66 GTACCAATATGGTAATTCACAAACAAATTATGAATTACTTAAG
* * *
3173126 TTGCACACATAGTGTCAATACAATAATTCACAAACTAATTATGAGTTACTTAGGTTGCACACATA
1 TTGCACACATAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATA
3173191 GT
66 GT
3173193 GACAATACGA
Statistics
Matches: 264, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 264 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (108 bp):
TTGCACACATAGTGCCAATACAGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATA
GTACCAATATGGTAATTCACAAACAAATTATGAATTACTTAAG
Found at i:3174006 original size:24 final size:24
Alignment explanation
Indices: 3173979--3174030 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3173969 CAACTCGTAT
*
3173979 AAATTGCACCGAAGTGCCGCATAG
1 AAATTGCACCGAAGTGCCACATAG
* *
3174003 AAATTGCACTGAAGTGCCACATAT
1 AAATTGCACCGAAGTGCCACATAG
3174027 AAAT
1 AAAT
3174031 CTTCCAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAG
Found at i:3174067 original size:23 final size:23
Alignment explanation
Indices: 3174037--3174097 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3174027 AAATCTTCCA
3174037 AAGGACCGCGTAGAATTATCCCG
1 AAGGACCGCGTAGAATTATCCCG
*
3174060 AAGGACCGCGTAGAATTGTCCCG
1 AAGGACCGCGTAGAATTATCCCG
*
3174083 AAGGACCACGTAGAA
1 AAGGACCGCGTAGAA
3174098 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.15
Consensus pattern (23 bp):
AAGGACCGCGTAGAATTATCCCG
Found at i:3180140 original size:22 final size:23
Alignment explanation
Indices: 3180091--3180170 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
3180081 AGAAATTACA
*
3180091 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAATTGTC
*
3180114 CCGAAGGACCACATAGTATT-TC
1 CCGAAGGACCACATAGAATTGTC
3180136 CCGAAGGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAATTGTC
3180159 CCGAAGGACCAC
1 CCGAAGGACCAC
3180171 GTATAACCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
22 22 0.42
23 30 0.58
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTGTC
Found at i:3181124 original size:20 final size:20
Alignment explanation
Indices: 3181099--3181148 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3181089 TTTTAGACTG
3181099 AATAGTATCGATACCCCTCC
1 AATAGTATCGATACCCCTCC
3181119 AATAGTATCGATACCCCTCC
1 AATAGTATCGATACCCCTCC
* *
3181139 TATGGTATCG
1 AATAGTATCG
3181149 GTACTTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (20 bp):
AATAGTATCGATACCCCTCC
Found at i:3185910 original size:23 final size:23
Alignment explanation
Indices: 3185895--3185939 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3185885 GGTGTTGATG
3185895 ATGAAATGAAGATGGTGGTGAAA
1 ATGAAATGAAGATGGTGGTGAAA
* *
3185918 ATGAAATGGAGATGATGGTGAA
1 ATGAAATGAAGATGGTGGTGAA
3185940 GTCGTATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (23 bp):
ATGAAATGAAGATGGTGGTGAAA
Found at i:3185934 original size:26 final size:24
Alignment explanation
Indices: 3185881--3185937 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
3185871 TGGAATATGT
* **
3185881 TGATGGTGTTGATGATGAAATGAA
1 TGATGGTGGTGAAAATGAAATGAA
3185905 -GATGGTGGTGAAAATGAAATGGAGA
1 TGATGGTGGTGAAAATGAAAT-GA-A
3185930 TGATGGTG
1 TGATGGTG
3185938 AAGTCGTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 17 0.63
24 2 0.07
25 1 0.04
26 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.28
Consensus pattern (24 bp):
TGATGGTGGTGAAAATGAAATGAA
Found at i:3190486 original size:23 final size:23
Alignment explanation
Indices: 3190448--3190507 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3190438 GGAATGTGTT
* *
3190448 GATGGTGTTGATGATGAAATGAA
1 GATGGTGGTGAAGATGAAATGAA
*
3190471 GATGGTGGTGAAGATGAAATGGA
1 GATGGTGGTGAAGATGAAATGAA
*
3190494 GATAGTGGTGAAGA
1 GATGGTGGTGAAGA
3190508 CTAATCTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.25
Consensus pattern (23 bp):
GATGGTGGTGAAGATGAAATGAA
Found at i:3192271 original size:54 final size:54
Alignment explanation
Indices: 3192205--3192613 Score: 570
Period size: 54 Copynumber: 7.6 Consensus size: 54
3192195 GTGGTTTTTA
** * *
3192205 CACACATAGTGCCAATACGACAATTCACAAACTAAGTATGAATTAATTAGGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
** * *
3192259 TGCACATAGTGCCAATACGGTAATTCATAAA-TAAATTATGAATTACTTAAGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACT-AATTATGAATTACTTAGGTTG
**
3192313 CACACATAGTGCCAATACATTAATTCACAAACTAATTATGAATTACTTAGGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
* * * * *
3192367 CACAAATAGTGCCACTACGGTAATTCATAAACAAATTATGAATTACTTAAGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
* * ** * *
3192421 CACACATAATGTCAATACAATAATTCACAAACTGATTATGAATTAATTAGGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
* * *
3192475 CACACATAGTGTCAATACGGTAATTCACAAACAAATTATGAATTACTTAAGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
*
3192529 CACACATAGTGCCAATAAGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
1 CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
3192583 CACACATAGTGCCAATACGGTAATTCA-AAAC
1 CACACATAGTGCCAATACGGTAATTCACAAAC
3192614 ATATACATTA
Statistics
Matches: 309, Mismatches: 44, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
53 5 0.02
54 303 0.98
55 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (54 bp):
CACACATAGTGCCAATACGGTAATTCACAAACTAATTATGAATTACTTAGGTTG
Found at i:3192394 original size:108 final size:107
Alignment explanation
Indices: 3192205--3192614 Score: 635
Period size: 108 Copynumber: 3.8 Consensus size: 107
3192195 GTGGTTTTTA
* * **
3192205 CACACATAGTGCCAATACGACAATTCACAAACTAAGTATGAATTAATTAGGTTGTGCACATAGTG
1 CACACATAGTGCCAATAC-ATAATTCACAAACTAATTATGAATTAATTAGGTTGCACACATAGTG
*
3192270 CCAATACGGTAATTCATAAATAAATTATGAATTACTTAAGTTG
65 CCAATACGGTAATTCATAAACAAATTATGAATTACTTAAGTTG
* *
3192313 CACACATAGTGCCAATACATTAATTCACAAACTAATTATGAATTACTTAGGTTGCACAAATAGTG
1 CACACATAGTGCCAATACA-TAATTCACAAACTAATTATGAATTAATTAGGTTGCACACATAGTG
*
3192378 CCACTACGGTAATTCATAAACAAATTATGAATTACTTAAGTTG
65 CCAATACGGTAATTCATAAACAAATTATGAATTACTTAAGTTG
* * *
3192421 CACACATAATGTCAATACAATAATTCACAAACTGATTATGAATTAATTAGGTTGCACACATAGTG
1 CACACATAGTGCCAATAC-ATAATTCACAAACTAATTATGAATTAATTAGGTTGCACACATAGTG
* *
3192486 TCAATACGGTAATTCACAAACAAATTATGAATTACTTAAGTTG
65 CCAATACGGTAATTCATAAACAAATTATGAATTACTTAAGTTG
*
3192529 CACACATAGTGCCAATA-AGGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATAGT
1 CACACATAGTGCCAATACA--TAATTCACAAACTAATTATGAATTAATTAGGTTGCACACATAGT
3192593 GCCAATACGGTAATTCA-AAACA
64 GCCAATACGGTAATTCATAAACA
3192615 TATACATTAA
Statistics
Matches: 277, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
106 1 0.00
107 6 0.02
108 269 0.97
109 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (107 bp):
CACACATAGTGCCAATACATAATTCACAAACTAATTATGAATTAATTAGGTTGCACACATAGTGC
CAATACGGTAATTCATAAACAAATTATGAATTACTTAAGTTG
Found at i:3199319 original size:23 final size:23
Alignment explanation
Indices: 3199293--3199350 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
3199283 CTAGGTATCG
3199293 ATACCCCCTTTGAATGGGTACCA
1 ATACCCCCTTTGAATGGGTACCA
* *
3199316 ATACCCACTTTGAATGGGTACCG
1 ATACCCCCTTTGAATGGGTACCA
3199339 ATACCCCCTTTG
1 ATACCCCCTTTG
3199351 GGTTTTAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (23 bp):
ATACCCCCTTTGAATGGGTACCA
Done.