Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 14
Found at i:784297 original size:42 final size:41
Alignment explanation
Indices: 784238--784360 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 41
784228 ATGAATCGGG
784238 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAGGGGC
* * *
784280 CTCTTGAACGGTGGGAGGGGCCTCTTAAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGGGC
* *
784322 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGACAGG
784361 TGAATCTGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGGGC
Found at i:784724 original size:21 final size:21
Alignment explanation
Indices: 784669--784743 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
784659 GTAAAGTAGA
*
784669 TACCTCACCACGTAAAG-CAC
1 TACCTCACCACGTAAAGACCC
** * *
784689 TATTGTCATCGCGTAAA-ACCTC
1 TA-CCTCACCACGTAAAGACC-C
*
784711 TACCTCACCACGTAAAGACCG
1 TACCTCACCACGTAAAGACCC
*
784732 TACCTCATCACG
1 TACCTCACCACG
784744 CCATGCACCA
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
20 2 0.05
21 32 0.80
22 6 0.15
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.21
Consensus pattern (21 bp):
TACCTCACCACGTAAAGACCC
Found at i:784989 original size:18 final size:18
Alignment explanation
Indices: 784966--785014 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
784956 CGGCTCGATC
784966 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
784984 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
785002 AGGTGATGGCTCT
1 AGGTGATGGCTCT
785015 CGAAATGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.12, C:0.12, G:0.47, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:786524 original size:20 final size:20
Alignment explanation
Indices: 786501--786566 Score: 100
Period size: 19 Copynumber: 3.4 Consensus size: 20
786491 TCTGAAACTT
*
786501 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
786521 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
786540 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
786559 AAAATCGC
1 AAAATCGC
786567 GTTGCGATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 27 0.63
20 16 0.37
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:786855 original size:25 final size:26
Alignment explanation
Indices: 786811--786859 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
786801 TTAAATATGA
*
786811 AAAACTAATAATAATAAAAAAAATTC
1 AAAACTAAAAATAATAAAAAAAATTC
*
786837 AAAA-TAAAAATAATTAAAAAAAT
1 AAAACTAAAAATAATAAAAAAAAT
786860 AACCCTCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAACTAAAAATAATAAAAAAAATTC
Found at i:786856 original size:16 final size:16
Alignment explanation
Indices: 786810--786856 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
786800 TTTAAATATG
*
786810 AAAAACTAA-TAATAAT
1 AAAAA-TAATTAAAAAT
* *
786826 AAAAAAAATTCAAAAT
1 AAAAATAATTAAAAAT
786842 AAAAATAATTAAAAA
1 AAAAATAATTAAAAA
786857 AATAACCCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAATTAAAAAT
Found at i:787091 original size:19 final size:20
Alignment explanation
Indices: 787069--787106 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
787059 AATACTGTGT
787069 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
787088 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
787107 CGCACTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:787142 original size:20 final size:20
Alignment explanation
Indices: 787117--787161 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
787107 CGCACTTTGA
787117 GAATTTAACTTATGTGTTGC
1 GAATTTAACTTATGTGTTGC
* *
787137 GAATTTGACTTCTGTGTTGC
1 GAATTTAACTTATGTGTTGC
787157 GAATT
1 GAATT
787162 ACAAATTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (20 bp):
GAATTTAACTTATGTGTTGC
Found at i:787211 original size:20 final size:20
Alignment explanation
Indices: 787152--787232 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
787142 TGACTTCTGT
** *
787152 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTTGAAAATCGC
* * *
787172 GTTACG-ATTTGCAGATTCGC
1 GTTGCGAATTTG-AAAATCGC
787192 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
*
787212 ATTGC-AGATTTGGAAAATCGC
1 GTTGCGA-ATTT-GAAAATCGC
787233 AACGCGAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
19 4 0.08
20 31 0.63
21 14 0.29
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:788094 original size:64 final size:65
Alignment explanation
Indices: 788012--788145 Score: 200
Period size: 65 Copynumber: 2.1 Consensus size: 65
788002 ACACTCTAAT
* * * *
788012 TCGAATGCATTTTGTGTACCGATGCAC-AACCATGCATCGATGCACTCCT-GGTTTTATTGGAAC
1 TCGAACGCATTTTATGTACCGATGCACAAACCATGCATCGATGCACTCCTGGGTCTT-TTGAAAC
788075 A
65 A
*
788076 TCGAACGCATTTTATGTACCGATGCACAAACCATGCATTGATGCACTCCTGGGTCTTTTGAAACA
1 TCGAACGCATTTTATGTACCGATGCACAAACCATGCATCGATGCACTCCTGGGTCTTTTGAAACA
788141 TCGAA
1 TCGAA
788146 TGTAATTAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
64 25 0.40
65 33 0.52
66 5 0.08
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (65 bp):
TCGAACGCATTTTATGTACCGATGCACAAACCATGCATCGATGCACTCCTGGGTCTTTTGAAACA
Found at i:793574 original size:44 final size:44
Alignment explanation
Indices: 793498--793599 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
793488 TTTGTGCAAA
* *
793498 ATGCATCGATACACCATGAAAGTGTACTGATGCATTCCTTGAAT
1 ATGCATCGATACACCATGAAAGTGCACCGATGCATTCCTTGAAT
* *
793542 ATGCATTGATACACCAT-TAAGATGCACCGATGCATTCCTTGAAT
1 ATGCATCGATACACCATGAAAG-TGCACCGATGCATTCCTTGAAT
* *
793586 GTGCATCAATACAC
1 ATGCATCGATACAC
793600 TATACAGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 3 0.06
44 47 0.94
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (44 bp):
ATGCATCGATACACCATGAAAGTGCACCGATGCATTCCTTGAAT
Found at i:795363 original size:13 final size:14
Alignment explanation
Indices: 795333--795368 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
795323 AGGGGGAGTA
795333 ATTTTCAAA-ATTG
1 ATTTTCAAAGATTG
795346 A-TTTCAAAGA-TG
1 ATTTTCAAAGATTG
795358 ATTTTCAAAGA
1 ATTTTCAAAGA
795369 AAATCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (14 bp):
ATTTTCAAAGATTG
Found at i:795774 original size:64 final size:66
Alignment explanation
Indices: 795700--795858 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 66
795690 GCACACCCTA
* * *
795700 ATTCGAATGCATTTTGTGTACCGATGCACA-ACCATGCATTGATGCACTCCT-AATTTTATTGAA
1 ATTCAAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATCTT-TTGAA
795763 AC
65 AC
* **
795765 A-TCAAATGCATTTTATGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTCTTTTGAAA
1 ATTCAAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATCTTTTGAAA
*
795829 T
66 C
* *
795830 ATTCAAATGTATTTAGTGTACCGATGCAC
1 ATTCAAATGCATTTTGTGTACCGATGCAC
795859 CCCAAGTGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
64 26 0.32
65 28 0.35
66 27 0.33
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (66 bp):
ATTCAAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATCTTTTGAAA
C
Found at i:801158 original size:21 final size:21
Alignment explanation
Indices: 801121--801201 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
801111 GACTATCGCA
* * *
801121 TTGCGATTTCCCAAATTTGTG
1 TTGCGATTTTCCTAATTCGTG
**
801142 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTTCCTAATTCGTG
* *
801163 TTGCGATTTACGT-ATTCGTG
1 TTGCGATTTTCCTAATTCGTG
801183 TTGCGATTTTCCTAATTCG
1 TTGCGATTTTCCTAATTCG
801202 CAACGCGATT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 16 0.33
21 32 0.67
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (21 bp):
TTGCGATTTTCCTAATTCGTG
Found at i:801193 original size:41 final size:41
Alignment explanation
Indices: 801116--801216 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
801106 ATTCTGACTA
* ** *
801116 TCGCATTGCGATTTCCCAAATTTGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTT-ACGTATTCGTGTTGCGATTTTCCTAAT
801158 TCGCATTGCGATTTACGTATTCGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTATTCGTGTTGCGATTTTCCTAAT
**
801199 TCGCAACGCGA-TTACGTA
1 TCGCATTGCGATTTACGTA
801217 AATCGCAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 7 0.13
41 32 0.60
42 14 0.26
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGTGTTGCGATTTTCCTAAT
Found at i:801229 original size:41 final size:41
Alignment explanation
Indices: 801143--801270 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 41
801133 AAATTTGTGT
** * ***
801143 TGCGATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGTGT
1 TGCGATTTTCCTAATTCGCAACGCGA-TTACGTAAATCGCAA
801184 TGCGATTTTCCTAATTCGCAACGCGATTACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAACGCGATTACGTAAATCGCAA
* **** * *
801225 TGCGAATTAGGAAAATCGCAACGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAACGCGATTACGTAAATCGCAA
801266 TGCGA
1 TGCGA
801271 ATTAGGAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 6 0.08
41 67 0.92
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAACGCGATTACGTAAATCGCAA
Found at i:801240 original size:21 final size:21
Alignment explanation
Indices: 801199--801296 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 21
801189 TTTTCCTAAT
* *
801199 TCGCAACGCG-ATTACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
801219 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
801240 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
801260 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
801281 TCGCAATGCGATTTAC
1 TCGCAATGCGAATTAC
801297 ATAGCGCCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
20 26 0.40
21 39 0.60
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:801271 original size:41 final size:41
Alignment explanation
Indices: 801199--801291 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
801189 TTTTCCTAAT
*
801199 TCGCAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
801240 TCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
*
801281 TCGCAATGCGA
1 TCGCAACGCGA
801292 TTTACATAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
Found at i:802621 original size:14 final size:14
Alignment explanation
Indices: 802602--802637 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
802592 ATTGTTTAAT
802602 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
802616 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
802630 TGATTTGT
1 TGATTTGT
802638 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:802803 original size:19 final size:18
Alignment explanation
Indices: 802744--802803 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
802734 AAAAATGACT
*
802744 ATCGCAATGCGAAATGAAA
1 ATCGCAACGC-AAATGAAA
*
802763 ATCGCAACG---A-GAGA
1 ATCGCAACGCAAATGAAA
802777 ATCGCAACGCAAAATGAAA
1 ATCGCAACGC-AAATGAAA
802796 ATCGCAAC
1 ATCGCAAC
802804 AACAAAATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 12 0.36
15 1 0.03
18 1 0.03
19 19 0.58
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (18 bp):
ATCGCAACGCAAATGAAA
Found at i:802813 original size:33 final size:33
Alignment explanation
Indices: 802744--802819 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
802734 AAAAATGACT
* * * * *
802744 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCAAAATGAAAATCGCAACAACAAA
802777 ATCGCAACGCAAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCAAAATGAAAATCGCAACAACAAA
*
802810 ATCGTAACGC
1 ATCGCAACGC
802820 GAAACTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCAAAATGAAAATCGCAACAACAAA
Found at i:802851 original size:19 final size:19
Alignment explanation
Indices: 802829--802946 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
802819 CGAAACTAAA
802829 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
802848 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
802863 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
802881 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
802896 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
802914 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
802933 TTACGCGTTGCGAT
1 TT-CGCGTTGCGAT
802947 AGACATTAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 35 0.47
20 10 0.14
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:802875 original size:33 final size:33
Alignment explanation
Indices: 802833--802926 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
802823 ACTAAATTCG
*
802833 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
802866 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
802899 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
802927 AGTCATTTAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:802945 original size:20 final size:20
Alignment explanation
Indices: 802899--802992 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
802889 GCGATTCTCT
**
802899 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTACG
*
802918 CATTGCGATAGTCATTTACG
1 CGTTGCGATAGTCATTTACG
* *
802938 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTACG
* * *
802957 ATGATTGCGAAAGTCATTTCCG
1 -CG-TTGCGATAGTCATTTACG
*
802979 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
802993 AATGAATGCC
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
19 18 0.31
20 26 0.44
21 12 0.20
22 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTACG
Found at i:806172 original size:22 final size:22
Alignment explanation
Indices: 806112--806172 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
806102 TGCCGGATGG
*
806112 GGAA-GGATGTCGTTAGATATA
1 GGAACGGATGTCGTTGGATATA
806133 GGAACGGATGTCGTTGGATATA
1 GGAACGGATGTCGTTGGATATA
*
806155 GGAACGGATGTCGCTGGA
1 GGAACGGATGTCGTTGGA
806173 GAGAGTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 4 0.11
22 33 0.89
ACGTcount: A:0.28, C:0.10, G:0.38, T:0.25
Consensus pattern (22 bp):
GGAACGGATGTCGTTGGATATA
Found at i:806366 original size:20 final size:20
Alignment explanation
Indices: 806343--806436 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
806333 GTCAGAATCT
806343 CGTTGCGATTTATAG-ATTCA
1 CGTTGCGATTTA-AGTATTCA
* * *
806363 CGTTGCAATTTACGTATTCG
1 CGTTGCGATTTAAGTATTCA
* *
806383 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTAAGTATTCA
** * * *
806403 TATTGCGAATTACGTATTCC
1 CGTTGCGATTTAAGTATTCA
*
806423 CGTTGCGAATTAAG
1 CGTTGCGATTTAAG
806437 AAAATCGCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
19 1 0.02
20 61 0.98
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTAAGTATTCA
Found at i:806453 original size:21 final size:21
Alignment explanation
Indices: 806427--806472 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
806417 TATTCCCGTT
806427 GCGAATTAAGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
** * *
806448 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
806469 GCGA
1 GCGA
806473 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:806570 original size:21 final size:21
Alignment explanation
Indices: 806544--806756 Score: 174
Period size: 20 Copynumber: 10.4 Consensus size: 21
806534 TTATCGATCG
**
806544 CGTTGCGATTTTACGTATTTT
1 CGTTGCGATTTTACGTATACT
806565 CGTTGCGATTTTACGTATTA-T
1 CGTTGCGATTTTACGTA-TACT
* *
806586 CGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTTACGTATACT
* *
806606 CATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTTACGTATACT
806626 CGTTGCGATTTATA-G-ATA-T
1 CGTTGCGATTT-TACGTATACT
*
806645 GCGTTGCGA-TTTACGTATTCT
1 -CGTTGCGATTTTACGTATACT
* * *
806666 CGTTGCGA-TTTACGGACACA
1 CGTTGCGATTTTACGTATACT
* * **
806686 CGTTACAATTTTACGTATTGT
1 CGTTGCGATTTTACGTATACT
* * *
806707 CGTTGC-AATTTACGGATACG
1 CGTTGCGATTTTACGTATACT
*
806727 CGTTGCGATTTTACGGATACT
1 CGTTGCGATTTTACGTATACT
806748 CGTTGCGAT
1 CGTTGCGAT
806757 AGTCAGAATC
Statistics
Matches: 153, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 79 0.52
21 63 0.41
22 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTTACGTATACT
Found at i:806629 original size:40 final size:41
Alignment explanation
Indices: 806565--806756 Score: 253
Period size: 40 Copynumber: 4.7 Consensus size: 41
806555 TACGTATTTT
*
806565 CGTTGCGATTTTACGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* ** *
806606 CATTGCGA-TTTACGTATTCTCGTTGCGATTTATAGATATG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* *
806646 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGACACA
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * * *
806686 CGTTACAATTTTACGTATTGTCGTTGCAATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* *
806727 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTTACGTATTCTCGTTGCGAT
806757 AGTCAGAATC
Statistics
Matches: 127, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 68 0.54
41 59 0.46
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:806651 original size:121 final size:122
Alignment explanation
Indices: 806524--806756 Score: 301
Period size: 121 Copynumber: 1.9 Consensus size: 122
806514 ACCGGAGATC
* **** * *
806524 GCGTTGCGAATTATCG-A-TCGCGTTGCGATTTTACGTATTTTCGTTGCGATTTTACGTATTATC
1 GCGTTGCGAATTA-CGTATTCGCGTTGCGA-TTTACGGACACACGTTACAATTTTACGTATTATC
* * *
806587 GTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCGTTGCGATTTATAGATAT
64 GTTGCAATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCGATTTATAGATAT
* * *
806645 GCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGACACACGTTACAATTTTACGTATTGTCGT
1 GCGTTGCGAATTACGTATTCGCGTTGCGATTTACGGACACACGTTACAATTTTACGTATTATCGT
*
806710 TGCAATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
66 TGCAATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCGAT
806757 AGTCAGAATC
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
120 2 0.02
121 64 0.67
122 29 0.31
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (122 bp):
GCGTTGCGAATTACGTATTCGCGTTGCGATTTACGGACACACGTTACAATTTTACGTATTATCGT
TGCAATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCGATTTATAGATAT
Found at i:806675 original size:60 final size:61
Alignment explanation
Indices: 806525--806756 Score: 240
Period size: 61 Copynumber: 3.8 Consensus size: 61
806515 CCGGAGATCG
* *
806525 CGTTGCGAATTATC-GAT-CGCGTTGCGATTTTACGTATTTTCGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTA-CGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTTACGTATTAT
*
806586 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTATA-G-A-TAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTT-TACGTATTAT
* * * * ** * * * *
806645 GCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGACACACGTTACAATTTTACGTATTGT
1 -CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTTACGTATTAT
* * *
806707 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGAT
806757 AGTCAGAATC
Statistics
Matches: 141, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
59 5 0.04
60 44 0.31
61 62 0.44
62 30 0.21
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (61 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTTACGTATTAT
Found at i:806916 original size:20 final size:21
Alignment explanation
Indices: 806893--807102 Score: 182
Period size: 20 Copynumber: 10.3 Consensus size: 21
806883 CGATAGTCAG
*
806893 AATCTCATTGCGATTTAC-TA
1 AATCGCATTGCGATTTACGTA
* * *
806913 AATCACAATGC-AATTACGTA
1 AATCGCATTGCGATTTACGTA
* * * *
806933 AATCGCAATGCGAATTAGGAA
1 AATCGCATTGCGATTTACGTA
* *
806954 AATCGCAATGCGA-ATACGT-
1 AATCGCATTGCGATTTACGTA
*
806973 AATCGCATTGCTATTTACGT-
1 AATCGCATTGCGATTTACGTA
* *
806993 AATCGCATTGCGATTTTCCTA
1 AATCGCATTGCGATTTACGTA
*
807014 ATTCGCATTGCGATTTACGT-
1 AATCGCATTGCGATTTACGTA
* *
807034 AATCGCATTGCGATTTTCCTA
1 AATCGCATTGCGATTTACGTA
*
807055 ATTCGCATTGCGATTTACGT-
1 AATCGCATTGCGATTTACGTA
* * * *
807075 ATTCGCATTGCGAATTAGGAA
1 AATCGCATTGCGATTTACGTA
807096 AATCGCA
1 AATCGCA
807103 ACGCGAATTT
Statistics
Matches: 156, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
19 16 0.10
20 80 0.51
21 60 0.38
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (21 bp):
AATCGCATTGCGATTTACGTA
Found at i:806956 original size:21 final size:21
Alignment explanation
Indices: 806912--807129 Score: 88
Period size: 21 Copynumber: 10.7 Consensus size: 21
806902 GCGATTTACT
* *
806912 AAATCACAATGC-AATTACGT
1 AAATCGCAATGCGAATTACGA
*
806932 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTACGA
806953 AAATCGCAATGCGAA-TACG-
1 AAATCGCAATGCGAATTACGA
* * * *
806972 TAATCGCATTGCTATTTACG-
1 AAATCGCAATGCGAATTACGA
* * * * **
806992 TAATCGCATTGCGATTTTCCT
1 AAATCGCAATGCGAATTACGA
* * *
807013 AATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * * * **
807033 TAATCGCATTGCGATTTTCCT
1 AAATCGCAATGCGAATTACGA
* * *
807054 AATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * * *
807074 TATTCGCATTGCGAATTAGGA
1 AAATCGCAATGCGAATTACGA
* ** *
807095 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTACGA
*
807116 AAATCGCAAAGCGA
1 AAATCGCAATGCGA
807130 TAGTCAGAAT
Statistics
Matches: 160, Mismatches: 33, Indels: 9
0.79 0.16 0.04
Matches are distributed among these distances:
19 11 0.07
20 68 0.43
21 81 0.51
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (21 bp):
AAATCGCAATGCGAATTACGA
Found at i:807030 original size:41 final size:41
Alignment explanation
Indices: 806975--807087 Score: 208
Period size: 41 Copynumber: 2.8 Consensus size: 41
806965 GAATACGTAA
*
806975 TCGCATTGCTATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
807016 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
*
807057 TCGCATTGCGATTTACGTATTCGCATTGCGA
1 TCGCATTGCGATTTACGTAATCGCATTGCGA
807088 ATTAGGAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:807040 original size:61 final size:61
Alignment explanation
Indices: 806968--807087 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 61
806958 GCAATGCGAA
* * *
806968 TACGTAATCGCATTGCTATTTACGTAA-TCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TACGTAATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACCT-ATTCGCATTGCGATT
* *
807029 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCATTGCGA
1 TACGTAATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACCTATTCGCATTGCGA
807088 ATTAGGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 37 0.70
62 16 0.30
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (61 bp):
TACGTAATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACCTATTCGCATTGCGATT
Found at i:807897 original size:44 final size:43
Alignment explanation
Indices: 807846--807932 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
807836 TGTAAATTAA
** * * *
807846 AATTTGATACATTGTTAATAAAAATATGGCAAAATGTCTAAATT
1 AATTTGATACATTAATAATAAAAACATGAC-AAATATCTAAATT
*
807890 AATTTGATATATTAATAATAAAAACATGACAAATATCTAAATT
1 AATTTGATACATTAATAATAAAAACATGACAAATATCTAAATT
807933 TTAATTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 12 0.32
44 25 0.68
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (43 bp):
AATTTGATACATTAATAATAAAAACATGACAAATATCTAAATT
Found at i:808879 original size:20 final size:20
Alignment explanation
Indices: 808856--808945 Score: 60
Period size: 20 Copynumber: 4.5 Consensus size: 20
808846 GCAACTAGAT
*
808856 TTTCTAATTT-GCAAAGTGAG
1 TTTC-AATTTCGCAAAGTGAA
*
808876 TTTCAATTTCGCAACGTGAA
1 TTTCAATTTCGCAAAGTGAA
** *
808896 TTTCGTTTTCGC-AACTGAA
1 TTTCAATTTCGCAAAGTGAA
* *
808915 TTTTCTAA-TTCGCAACGCGAA
1 -TTTC-AATTTCGCAAAGTGAA
*
808936 TTTAAATTTC
1 TTTCAATTTC
808946 AAAAATCATC
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
19 12 0.23
20 37 0.70
21 4 0.08
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (20 bp):
TTTCAATTTCGCAAAGTGAA
Found at i:808944 original size:60 final size:60
Alignment explanation
Indices: 808817--808945 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 60
808807 CAACTCAATT
* * * * *
808817 TTTAAA-TTCGCAACACGAGTTTTGTTTTCGCAACTAGATTTTCTAATTTGCAAAGTGAG
1 TTTAAATTTCGCAACACGAATTTCGTTTTCGCAACTAGATTTTCTAATTCGCAAAGCGAA
* ** *
808876 TTTCAATTTCGCAACGTGAATTTCGTTTTCGCAACT-GAATTTTCTAATTCGCAACGCGAA
1 TTTAAATTTCGCAACACGAATTTCGTTTTCGCAACTAG-ATTTTCTAATTCGCAAAGCGAA
808936 TTTAAATTTC
1 TTTAAATTTC
808946 AAAAATCATC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 6 0.10
60 52 0.90
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (60 bp):
TTTAAATTTCGCAACACGAATTTCGTTTTCGCAACTAGATTTTCTAATTCGCAAAGCGAA
Found at i:809082 original size:22 final size:22
Alignment explanation
Indices: 809057--809111 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
809047 TCTCTCACTC
*
809057 TCTCCGGCGACATCCTTCCCCA
1 TCTCCGGCGACATCCGTCCCCA
*
809079 TCTCCGACGACATCCGTCCCCA
1 TCTCCGGCGACATCCGTCCCCA
809101 TCTCCGGCGAC
1 TCTCCGGCGAC
809112 CCCCTCCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.15, C:0.49, G:0.16, T:0.20
Consensus pattern (22 bp):
TCTCCGGCGACATCCGTCCCCA
Found at i:809512 original size:34 final size:34
Alignment explanation
Indices: 809471--809543 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
809461 CAAGAAACTT
*
809471 AAATTTGCAACATGAAAATCGCAACTCGAAAATG
1 AAATTTGCAACACGAAAATCGCAACTCGAAAATG
809505 AAATTTGCAACACGAAAATCGCAACTCGAAAATG
1 AAATTTGCAACACGAAAATCGCAACTCGAAAATG
809539 AAATT
1 AAATT
809544 CGAGTTGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.21
Consensus pattern (34 bp):
AAATTTGCAACACGAAAATCGCAACTCGAAAATG
Found at i:809541 original size:20 final size:20
Alignment explanation
Indices: 809482--809523 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
809472 AATTTGCAAC
*
809482 ATGAAAATCGCAACTCGAAA
1 ATGAAAATCGCAACACGAAA
* *
809502 ATGAAATTTGCAACACGAAA
1 ATGAAAATCGCAACACGAAA
809522 AT
1 AT
809524 CGCAACTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (20 bp):
ATGAAAATCGCAACACGAAA
Found at i:809575 original size:20 final size:20
Alignment explanation
Indices: 809539--809576 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
809529 CTCGAAAATG
**
809539 AAATTCGAGTTGTGAATTCA
1 AAATTCGAGTTACGAATTCA
809559 AAATTCGAGTTACGAATT
1 AAATTCGAGTTACGAATT
809577 TCATTTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATTCGAGTTACGAATTCA
Found at i:811139 original size:39 final size:41
Alignment explanation
Indices: 811057--811157 Score: 125
Period size: 39 Copynumber: 2.5 Consensus size: 41
811047 TCTTTACTTT
* *
811057 GACACCGAGACCCATCACCTCATAGAGCCGATTCTACATCTC
1 GACACCGAGATCCATCACCTCATA-AGCCGATTCTACACCTC
* *
811099 GACACTGAGATCCATCACCTC-T-AGTCGATTCTACACCTC
1 GACACCGAGATCCATCACCTCATAAGCCGATTCTACACCTC
* *
811138 GACACCAAGATCTATCACCT
1 GACACCGAGATCCATCACCT
811158 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 32 0.62
41 1 0.02
42 19 0.37
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.22
Consensus pattern (41 bp):
GACACCGAGATCCATCACCTCATAAGCCGATTCTACACCTC
Found at i:811290 original size:21 final size:21
Alignment explanation
Indices: 811258--811387 Score: 118
Period size: 21 Copynumber: 6.2 Consensus size: 21
811248 CCTCCATGGT
* *
811258 ATGAGTTAGGTGTTTTACGTG
1 ATGAGGTAGGTGCTTTACGTG
* *
811279 ATGAGGTCGGTGCTTTACATG
1 ATGAGGTAGGTGCTTTACGTG
* * * *
811300 ATGAGGTCGATGTTTTATGTG
1 ATGAGGTAGGTGCTTTACGTG
** *
811321 ATGA-CAATGGTGCTTTATGTG
1 ATGAGGTA-GGTGCTTTACGTG
811342 ATGAGGTAGGTGCTTTACGTG
1 ATGAGGTAGGTGCTTTACGTG
* * *
811363 GTGAGGTAGCTGCTTTACATG
1 ATGAGGTAGGTGCTTTACGTG
811384 ATGA
1 ATGA
811388 CAATTGTGCT
Statistics
Matches: 87, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
21 86 0.99
22 1 0.01
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.37
Consensus pattern (21 bp):
ATGAGGTAGGTGCTTTACGTG
Found at i:811386 original size:63 final size:63
Alignment explanation
Indices: 811266--811416 Score: 185
Period size: 63 Copynumber: 2.4 Consensus size: 63
811256 GTATGAGTTA
* * * **
811266 GGTGTTTTACGTGATGAGGTCGGTGCTTTACATGATGAGGTCGATGTTTTATGTGATGACAAT
1 GGTGCTTTACGTGATGAGGTCGGTGCTTTACATGATGAGGTAGATGCTTTACATGATGACAAT
* * * * *
811329 GGTGCTTTATGTGATGAGGTAGGTGCTTTACGTGGTGAGGTAGCTGCTTTACATGATGACAAT
1 GGTGCTTTACGTGATGAGGTCGGTGCTTTACATGATGAGGTAGATGCTTTACATGATGACAAT
* * *
811392 TGTGCTCTACGTGATAAGGTCGGTG
1 GGTGCTTTACGTGATGAGGTCGGTG
811417 TTTCATCGTT
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.20, C:0.11, G:0.33, T:0.36
Consensus pattern (63 bp):
GGTGCTTTACGTGATGAGGTCGGTGCTTTACATGATGAGGTAGATGCTTTACATGATGACAAT
Found at i:811818 original size:21 final size:21
Alignment explanation
Indices: 811742--811818 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
811732 GAAGAAGTAT
* *
811742 GATCCACATACCATTGTTCAG
1 GATCCACATTCCATCGTTCAG
*
811763 GATCCAC-CTCTCATCGTTCAG
1 GATCCACATTC-CATCGTTCAG
* *
811784 GATCCACCTCCCATCGTTCAG
1 GATCCACATTCCATCGTTCAG
*
811805 GATCCGCATTCCAT
1 GATCCACATTCCAT
811819 ACTATGTAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.27
Consensus pattern (21 bp):
GATCCACATTCCATCGTTCAG
Found at i:816447 original size:24 final size:24
Alignment explanation
Indices: 816419--816520 Score: 150
Period size: 24 Copynumber: 4.2 Consensus size: 24
816409 CTGAAACATC
* *
816419 ATCAAAATCCTAGTATTGACCAAT
1 ATCAAAGTCCGAGTATTGACCAAT
* *
816443 ATCAAAGTCTGGGTATTGACCAAT
1 ATCAAAGTCCGAGTATTGACCAAT
*
816467 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAGTCCGAGTATTGACCAAT
*
816491 ATCAAAGTTCGAGTATTGACCAAT
1 ATCAAAGTCCGAGTATTGACCAAT
816515 ATCAAA
1 ATCAAA
816521 TTTCGAATAC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (24 bp):
ATCAAAGTCCGAGTATTGACCAAT
Found at i:817356 original size:20 final size:20
Alignment explanation
Indices: 817331--817391 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
817321 CCCAAAACAT
817331 TTGTGTTGCGAAATTAAAAA
1 TTGTGTTGCGAAATTAAAAA
** *
817351 TTGTGTTGTAAAATTAAAAT
1 TTGTGTTGCGAAATTAAAAA
*
817371 TTGCGTTGCG-AATTCAAAAA
1 TTGTGTTGCGAAATT-AAAAA
817391 T
1 T
817392 CGAGTTACGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGTGTTGCGAAATTAAAAA
Found at i:817477 original size:20 final size:20
Alignment explanation
Indices: 817395--817477 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 20
817385 CAAAAATCGA
* *
817395 GTTACGAAAATGAAATTCCT
1 GTTACGAAAATGAAACTCGT
* * *
817415 GTTGCAAAAATGAAACTCGC
1 GTTACGAAAATGAAACTCGT
* * **
817435 GTTACG-AATTAGAAAATTTT
1 GTTACGAAAAT-GAAACTCGT
*
817455 GTTACGAAAAGGAAACTCGT
1 GTTACGAAAATGAAACTCGT
817475 GTT
1 GTT
817478 GTGAATTTAA
Statistics
Matches: 44, Mismatches: 17, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
19 3 0.07
20 39 0.89
21 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (20 bp):
GTTACGAAAATGAAACTCGT
Found at i:817580 original size:20 final size:19
Alignment explanation
Indices: 817527--817586 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
817517 TGTGAAATTG
817527 TCAAATTCGAGTTGCGAAT
1 TCAAATTCGAGTTGCGAAT
* * *
817546 TCGACTTCTGTGTTGCGAAT
1 TCAAATTC-GAGTTGCGAAT
817566 TCCAAATTCGAGTTGCGAAT
1 T-CAAATTCGAGTTGCGAAT
817586 T
1 T
817587 TGGAAACTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.18
20 22 0.67
21 5 0.15
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (19 bp):
TCAAATTCGAGTTGCGAAT
Found at i:817597 original size:40 final size:40
Alignment explanation
Indices: 817528--817604 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
817518 GTGAAATTGT
**
817528 CAAATTCGAGTTGCGAATTCGACTTCTGTGTTGCGAATTC
1 CAAATTCGAGTTGCGAATTCGACAACTGTGTTGCGAATTC
*
817568 CAAATTCGAGTTGCGAATTTGGA-AACTGTGTTGCGAA
1 CAAATTCGAGTTGCGAA-TTCGACAACTGTGTTGCGAA
817605 ATTGGAGTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (40 bp):
CAAATTCGAGTTGCGAATTCGACAACTGTGTTGCGAATTC
Found at i:824291 original size:18 final size:18
Alignment explanation
Indices: 824268--824308 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
824258 TATGCTCTCT
824268 TGAAGGTTGTGCAAGTCA
1 TGAAGGTTGTGCAAGTCA
824286 TGAAGGTTGTGCAAGTCA
1 TGAAGGTTGTGCAAGTCA
824304 TGAAG
1 TGAAG
824309 CTGTGCTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.34, T:0.27
Consensus pattern (18 bp):
TGAAGGTTGTGCAAGTCA
Found at i:833069 original size:2 final size:2
Alignment explanation
Indices: 833062--833091 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
833052 TTATCTCTTT
833062 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
833092 AAAGTCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:837430 original size:23 final size:23
Alignment explanation
Indices: 837404--837468 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
837394 CACATATGGA
837404 AGAAATACATGATTTTAAATTAC
1 AGAAATACATGATTTTAAATTAC
*
837427 AGAAATACATTATTTTAAATTAC
1 AGAAATACATGATTTTAAATTAC
* *
837450 ATAAATACTTGATTTTAAA
1 AGAAATACATGATTTTAAA
837469 CGACCGTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (23 bp):
AGAAATACATGATTTTAAATTAC
Found at i:837702 original size:24 final size:24
Alignment explanation
Indices: 837674--837720 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
837664 AAGAAAATCA
*
837674 GATAAATG-AGTTTATAAACGAGCC
1 GATAAATGAAGTGT-TAAACGAGCC
837698 GATAAATGAAGTGTTAAACGAGC
1 GATAAATGAAGTGTTAAACGAGC
837721 TTGTTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (24 bp):
GATAAATGAAGTGTTAAACGAGCC
Found at i:839890 original size:17 final size:18
Alignment explanation
Indices: 839865--839903 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
839855 ACACTGTAAC
*
839865 AAAATATTTCTCAGCAA-
1 AAAACATTTCTCAGCAAT
*
839882 AAAACATTTTTCAGCAAT
1 AAAACATTTCTCAGCAAT
839900 AAAA
1 AAAA
839904 AAAGAGGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAACATTTCTCAGCAAT
Found at i:845554 original size:30 final size:30
Alignment explanation
Indices: 845497--845564 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
845487 ATGCATAAGT
* **
845497 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
845527 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
845557 ATATGCAT
1 AAATGCAT
845565 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:853714 original size:39 final size:40
Alignment explanation
Indices: 853660--853763 Score: 124
Period size: 39 Copynumber: 2.6 Consensus size: 40
853650 CATCAGCTGG
* * *
853660 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCC-G-A
1 CCAGATCTCCTCATCACGTAGGAGTCGTGTCA-CCCCAGAA
853699 CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCAGATAA
1 CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCAG--AA
853741 CCAG-TCGTCCTCATCACGTAGGA
1 CCAGATC-TCCTCATCACGTAGGA
853764 ACCATGTTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
38 4 0.07
39 30 0.53
41 2 0.04
42 21 0.37
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCAGAA
Found at i:853798 original size:47 final size:45
Alignment explanation
Indices: 853728--853823 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 45
853718 AGGAGTCGTG
853728 TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
1 TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
*
853773 TCACCCCATAGATAACCAG-CTGTCCTCATCACGTAGGAACCGTGTTA
1 TCACCCC--AGATAACCAGTC-GTCCTCATCACGTAGGAACCATGTTA
853820 TCAC
1 TCAC
853824 ATCTCCTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 7 0.15
46 1 0.02
47 39 0.83
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (45 bp):
TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
Found at i:853953 original size:43 final size:40
Alignment explanation
Indices: 853842--853958 Score: 103
Period size: 43 Copynumber: 2.9 Consensus size: 40
853832 AAGATGGCCA
*
853842 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCACGACC
* * * * *
853882 AGATA-TCCTCATCATGTAGGATCCGTGTCA-CCCTTAGACGACC
1 AGA-ACTCTTCATCACGTATGAGCAGTGTCATCCC----ACGACC
* *
853925 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
853959 CAACAACCAA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
39 3 0.05
40 23 0.40
41 1 0.02
42 1 0.02
43 26 0.46
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCACGACC
Found at i:854114 original size:3 final size:3
Alignment explanation
Indices: 854106--854138 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
854096 GTCTTTTTAT
854106 TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
854139 TTGTTGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:856780 original size:35 final size:35
Alignment explanation
Indices: 856734--856811 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
856724 AAAATTTCTC
856734 ATGAACATACAAACAAATATCTT-AGCAAACACTAA
1 ATGAACATACAAACAAATATCTTCA-CAAACACTAA
* *
856769 ATGAACATACAAACAAATATTTTCACAAACATTAA
1 ATGAACATACAAACAAATATCTTCACAAACACTAA
856804 ATGAACAT
1 ATGAACAT
856812 GTTGGCGATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (35 bp):
ATGAACATACAAACAAATATCTTCACAAACACTAA
Found at i:857619 original size:53 final size:54
Alignment explanation
Indices: 857544--857658 Score: 169
Period size: 53 Copynumber: 2.1 Consensus size: 54
857534 ATTTGGCTTG
* * **
857544 AACTCGAACTCGAACTAAATTTCTTAACGAGCTAAAGTGAGTTATTTGGCATCC
1 AACTCGAACTCAAACTAAATTTCTTAACGAACTAAAACGAGTTATTTGGCATCC
* *
857598 AACTCGAACT-AAACTTAATTTCTTAACGAACTAAAACGAGTTATTTGGTATCC
1 AACTCGAACTCAAACTAAATTTCTTAACGAACTAAAACGAGTTATTTGGCATCC
857651 AACTCGAA
1 AACTCGAA
857659 AAACACATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
53 45 0.82
54 10 0.18
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.30
Consensus pattern (54 bp):
AACTCGAACTCAAACTAAATTTCTTAACGAACTAAAACGAGTTATTTGGCATCC
Found at i:864920 original size:2 final size:2
Alignment explanation
Indices: 864913--864948 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
864903 GTACTTAGAC
864913 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
864949 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:866665 original size:41 final size:40
Alignment explanation
Indices: 866613--866730 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 40
866603 GCCTAGATGT
* * *
866613 AACTATTAATAATCTATATGCCACTATTCGAACCTAGACCC
1 AACTATCAATAATCT-TATACCTCTATTCGAACCTAGACCC
*
866654 AACTATCAATAATCTTCTTACCTCTATTCGAACCTAGACCC
1 AACTATCAATAATCTT-ATACCTCTATTCGAACCTAGACCC
*
866695 AACTATCAATAATCTTTATATCTCTATTCGAACCTA
1 AACTATCAATAATC-TTATACCTCTATTCGAACCTA
866731 TAAACTATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.01
41 66 0.96
42 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (40 bp):
AACTATCAATAATCTTATACCTCTATTCGAACCTAGACCC
Found at i:870122 original size:21 final size:21
Alignment explanation
Indices: 870078--870122 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
870068 GTTGACCATT
* *
870078 ACGGTGCTGATGTGACAGTTC
1 ACGGTGCTGACGTGACAGTCC
**
870099 ACGGTGCTGACGTGGTAGTCC
1 ACGGTGCTGACGTGACAGTCC
870120 ACG
1 ACG
870123 ATACTGACAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (21 bp):
ACGGTGCTGACGTGACAGTCC
Found at i:872914 original size:22 final size:22
Alignment explanation
Indices: 872886--872937 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
872876 GGTTCAACCT
*
872886 AATTTTTTTTG-ATTTGTTATTA
1 AATTTTTTTGGTATTT-TTATTA
*
872908 AATTTTTTTGGTATTTTTATTT
1 AATTTTTTTGGTATTTTTATTA
872930 AATTTTTT
1 AATTTTTT
872938 AAATAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (22 bp):
AATTTTTTTGGTATTTTTATTA
Found at i:873513 original size:2 final size:2
Alignment explanation
Indices: 873506--873534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
873496 TTAATTGAAA
873506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
873535 GGGGTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:873857 original size:2 final size:2
Alignment explanation
Indices: 873850--873905 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
873840 CCCATTTTGT
873850 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
873892 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
873906 GATCAATTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:875111 original size:31 final size:31
Alignment explanation
Indices: 875074--875138 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
875064 TGACCACGTC
** * *
875074 TTAATTAAATAAAAATGAAAGTGATCATATA
1 TTAATTAAATAAAAACAAAAATGACCATATA
*
875105 TTAATTAAATATAAACAAAAATGACCATATA
1 TTAATTAAATAAAAACAAAAATGACCATATA
875136 TTA
1 TTA
875139 TGTTTTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAATGACCATATA
Found at i:876388 original size:16 final size:18
Alignment explanation
Indices: 876356--876390 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
876346 ATATAAAAAC
876356 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
876374 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
876390 A
1 A
876391 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:876415 original size:17 final size:17
Alignment explanation
Indices: 876324--876418 Score: 50
Period size: 17 Copynumber: 5.2 Consensus size: 17
876314 TAATGCAAAT
*
876324 AAATAAATAAAACAAGTA
1 AAATATATAAAA-AAGTA
*
876342 AAAGATATAAAAACA-TA
1 AAATATATAAAAA-AGTA
* *
876359 AAATATAGGATAAATA-TAA
1 AAATATA-TA-AAAAAGT-A
*
876378 AAATAGATAAATAAATGAGTA
1 AAATATAT-AA-AAA--AGTA
876399 AAATATATAAAAAAGTA
1 AAATATATAAAAAAGTA
876416 AAA
1 AAA
876419 GCATATATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
17 16 0.27
18 15 0.25
19 16 0.27
20 2 0.03
21 9 0.15
22 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.21
Consensus pattern (17 bp):
AAATATATAAAAAAGTA
Found at i:876500 original size:2 final size:2
Alignment explanation
Indices: 876493--876517 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
876483 AAAATAGGAA
876493 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
876518 ATAACACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:877002 original size:37 final size:36
Alignment explanation
Indices: 876959--877060 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
876949 ATAGTATAAC
876959 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
876996 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
877030 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
877061 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:877903 original size:105 final size:105
Alignment explanation
Indices: 877606--878537 Score: 1434
Period size: 105 Copynumber: 9.0 Consensus size: 105
877596 CATTGTTCCA
* * * ** * * * *
877606 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-GTTGTTGACAAG
* * * * * *
877671 CAGCCGTCCCTTCGTTGTGACGTTGAACTTGTGTTATCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
877712 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
877772 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
877812 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
877877 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATT-TCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
877916 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
877981 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
878021 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
878086 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
878126 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
878191 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
878231 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
878293 AGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
878332 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
878397 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
878437 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
** * * *
878502 CAGTTGTCCATTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
878538 CCTCGAGTGC
Statistics
Matches: 776, Mismatches: 39, Indels: 22
0.93 0.05 0.03
Matches are distributed among these distances:
100 82 0.11
101 82 0.11
102 22 0.03
103 4 0.01
104 124 0.16
105 388 0.50
106 74 0.10
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:878414 original size:206 final size:208
Alignment explanation
Indices: 877605--878537 Score: 1387
Period size: 206 Copynumber: 4.5 Consensus size: 208
877595 GCATTGTTCC
* * * ** * *
877605 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-T-GTTGTTGACAA
* * * * * * *
877670 CCAGCCGTCCCTTCGTTGTGACGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTCGTTGTGAA
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* **
877735 GTTAAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
128 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
877795 GAACTTGCGTTGTCTG
193 GAACTTGCGTTGTCTG
* * * *
877811 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAG
*
877876 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATT-TCTGGAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
877940 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
878005 AACTTGCGTTGTCTG
194 AACTTGCGTTGTCTG
878020 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAG
878085 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
878150 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
878215 AACTTGCGTTGTCTG
194 AACTTGCGTTGTCTG
* * *
878230 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA-GTTGTTGACAGGCA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
* *
878294 GCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
*
878358 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
878423 CTTGCGTTGTCTG
196 CTTGCGTTGTCTG
*
878436 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TG-TTGTTGACAA
* ** * * *
878501 CCAGTTGTCCATTCGTTGTGAAGTTGAACTTGTGTTG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
878538 CCTCGAGTGC
Statistics
Matches: 671, Mismatches: 44, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
204 40 0.06
205 43 0.06
206 225 0.34
207 20 0.03
208 2 0.00
209 147 0.22
210 169 0.25
211 25 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (208 bp):
AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTG
Found at i:878427 original size:311 final size:313
Alignment explanation
Indices: 877605--878537 Score: 1425
Period size: 311 Copynumber: 3.0 Consensus size: 313
877595 GCATTGTTCC
* * * * ** * *
877605 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-T-GTTGTTGACAA
* * * * * *
877670 CCAGCCGTCCCTTCGTTGTGACGTTGAACTTGTGTTATCTCG-AGTCCAATATCCTTCGTTGTGA
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGA
* **
877734 AGTTAAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
127 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* * *
877794 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGGG
192 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
877859 AAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATT-TCTG
257 AAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
877915 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAG
877980 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
878045 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
878110 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
194 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
878175 GTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
259 GTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
878230 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA-GTTGTTGACAGGCA
1 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
*
878294 GCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
*
878358 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
878423 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
196 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
* ** * * *
878488 TGTTTGTTGACAACCAGTTGTCCATTCGTTGTGAAGTTGAACTTGTGTTG
261 TG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
878538 CCTCGAGTGC
Statistics
Matches: 579, Mismatches: 35, Indels: 16
0.92 0.06 0.03
Matches are distributed among these distances:
308 1 0.00
309 82 0.14
310 45 0.08
311 192 0.33
312 61 0.11
313 2 0.00
314 147 0.25
315 49 0.08
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (313 bp):
AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
TGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:879308 original size:67 final size:66
Alignment explanation
Indices: 879173--879326 Score: 186
Period size: 68 Copynumber: 2.3 Consensus size: 66
879163 AAGATATCTG
* * * **
879173 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTAAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
879238 TT
65 TT
* *
879240 TGTGTTTCAAGAGCAACTGTCTAAAGGGAGAA-AAAATT-TGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTAAAGGGA-AACAAAATTATGTTTTAAGGGAAATAAATTCAAAG
*
879303 GTT
64 ATT
*
879306 TTGTTTCAAGGGAAACTGTCT
1 TTGTTTCAAGAGAAACTGTCT
879327 CAAGATAGAC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 18 0.24
66 3 0.04
67 23 0.31
68 29 0.39
69 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTAAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:879357 original size:36 final size:35
Alignment explanation
Indices: 879306--879586 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
879296 TTCAAAGGTT
* *
879306 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
879342 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
879377 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
879415 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
879444 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
879479 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
879516 TTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
879551 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
879587 CTCTTATAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 132 0.65
37 33 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:879415 original size:138 final size:137
Alignment explanation
Indices: 879248--879567 Score: 419
Period size: 138 Copynumber: 2.3 Consensus size: 137
879238 TTTGTGTTTC
* * * * * * *
879248 AAGAGCAACTGTCTAAAGGGAGAAAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTC
* *
879313 AAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
66 AAGGGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
879377 CTTAGTTCCA
130 -TTAGTT-CA
* * * * *
879387 AA-AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTC
* * *
879451 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
66 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
* *
879516 TTGTTTA
131 TAGTTCA
*
879523 AAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
879568 TGTCTCAAGA
Statistics
Matches: 156, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
136 3 0.02
137 47 0.30
138 104 0.67
139 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (137 bp):
AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTC
AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
TAGTTCA
Found at i:879530 original size:102 final size:102
Alignment explanation
Indices: 879342--879530 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
879332 TAGACGAAAA
*
879342 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
*
879407 GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
66 GACGAAATTTGTTTAAAAGAAAACATATTCAAATATT
* * * ** *
879444 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
879508 GACGAAATTTGTTTAAAGAGAAA
66 GACGAAATTTGTTTAAA-AGAAA
879531 CTGTCTCAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 36 0.46
102 42 0.54
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTAAAAGAAAACATATTCAAATATT
Found at i:880543 original size:22 final size:22
Alignment explanation
Indices: 880517--880565 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
880507 TTGTGTTTGG
* *
880517 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
880539 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
880561 TCAAA
1 TCAAA
880566 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:880572 original size:22 final size:22
Alignment explanation
Indices: 880529--880572 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
880519 AAAGGTTTGG
* * *
880529 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
880551 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
880573 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:881235 original size:16 final size:17
Alignment explanation
Indices: 881216--881261 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
881206 TCTTTTTGAT
*
881216 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
881232 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
881249 TTTTTCT-TTGTTT
1 TTTTGCTCTTGTTT
881262 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:881272 original size:14 final size:15
Alignment explanation
Indices: 881249--881301 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
881239 CTTGTTTCTC
881249 TTTTTCTTTG-TTTT
1 TTTTTCTTTGCTTTT
*
881263 TTTTTTTTTGCTTTT
1 TTTTTCTTTGCTTTT
* *
881278 TTGCTTCTTTTCTTTT
1 TT-TTTCTTTGCTTTT
*
881294 TTGTTCTT
1 TTTTTCTT
881302 GATTGGATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.28
15 11 0.34
16 12 0.38
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTGCTTTT
Found at i:881292 original size:16 final size:16
Alignment explanation
Indices: 881255--881301 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
881245 TCTCTTTTTC
*
881255 TTTG-TTTTTT-TTTT
1 TTTGCTTTTTTGTTCT
881269 TTTGCTTTTTTGCTTCT
1 TTTGCTTTTTTG-TTCT
881286 TTT-CTTTTTTGTTCT
1 TTTGCTTTTTTGTTCT
881301 T
1 T
881302 GATTGGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
16 8 0.28
17 6 0.21
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTGCTTTTTTGTTCT
Found at i:885135 original size:37 final size:36
Alignment explanation
Indices: 885092--885193 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
885082 ATAGTATAAC
*
885092 TCTATCCTATTTTTAGGAGTTTAAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
885129 TTTATCCTATTTTTAAGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
885163 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
885194 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 32 0.55
37 26 0.45
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:888532 original size:114 final size:114
Alignment explanation
Indices: 888327--888533 Score: 360
Period size: 114 Copynumber: 1.8 Consensus size: 114
888317 ATAGAACAAG
* *
888327 ACAGGTCATAATCATCTACAAACACAAGGCATAACTACACAAGCTTGCACAATCTCAGTTACAGC
1 ACAGATCATAATCATCTACAAACACAAGGCATAACTACACAAGCTTGCACAATCTCAGTCACAGC
*
888392 AGTGTTACGGTTTAAACATTTCTGATTACCTATTGAACATGAGTTCAAA
66 AGTGTTACGGTTTAAAAATTTCTGATTACCTATTGAACATGAGTTCAAA
* *
888441 ACAGATCATAATCATCTACAAACACAAGGCATAACTACACAAGTTTGCACAATTTCAGTCACAGC
1 ACAGATCATAATCATCTACAAACACAAGGCATAACTACACAAGCTTGCACAATCTCAGTCACAGC
*
888506 AGTGTTATGGTTTAAAAATTTCTGATTA
66 AGTGTTACGGTTTAAAAATTTCTGATTA
888534 ATCCGACAAC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 87 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (114 bp):
ACAGATCATAATCATCTACAAACACAAGGCATAACTACACAAGCTTGCACAATCTCAGTCACAGC
AGTGTTACGGTTTAAAAATTTCTGATTACCTATTGAACATGAGTTCAAA
Found at i:890843 original size:35 final size:35
Alignment explanation
Indices: 890797--890887 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
890787 TTATCAGTAG
890797 AACTGGAATTCTAAACCTGCTAGATATCGGCTCTT
1 AACTGGAATTCTAAACCTGCTAGATATCGGCTCTT
* *
890832 AACTGGAATTCT-AAGCTGGCTATATATCGGCTCTT
1 AACTGGAATTCTAAACCT-GCTAGATATCGGCTCTT
* *
890867 AACT--AATTCCAAGCCTGCTAG
1 AACTGGAATTCTAAACCTGCTAG
890888 TTGTCGACTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
33 9 0.19
34 7 0.15
35 32 0.67
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (35 bp):
AACTGGAATTCTAAACCTGCTAGATATCGGCTCTT
Found at i:901959 original size:19 final size:19
Alignment explanation
Indices: 901918--901959 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
901908 AGAACACAAC
* *
901918 AATTTGAATTTTTTTTAAT
1 AATTTGAAATTTTTTGAAT
901937 AATTTCGAAATTTTTTGAA-
1 AATTT-GAAATTTTTTGAAT
901956 AATT
1 AATT
901960 CTTGTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTGAAATTTTTTGAAT
Found at i:902353 original size:22 final size:22
Alignment explanation
Indices: 902321--902409 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
902311 CAGAACCTCC
*
902321 AGGGGGTATCGATTCCCCTACA
1 AGGGGGAATCGATTCCCCTACA
* *
902343 GGGGGGAATCG-TTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTAC-A
* * *
902365 AGGGGGAATTGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTACA
* *
902387 AGGGGGTATCAATTCCCTCTACA
1 AGGGGGAATCGATTCCC-CTACA
902410 CTAAAACTGA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
21 8 0.15
22 33 0.61
23 13 0.24
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTACA
Found at i:902368 original size:23 final size:23
Alignment explanation
Indices: 902333--902392 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
902323 GGGGTATCGA
*
902333 TTCCCCTAC-AGGGGGGAA-TCG
1 TTCCCCTTCAAGGGGGGAATTCG
* *
902354 TTCCCCTTCAAAGGGGGAATTGG
1 TTCCCCTTCAAGGGGGGAATTCG
902377 TTCCCCTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
902393 TATCAATTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.24
22 8 0.24
23 17 0.52
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
TTCCCCTTCAAGGGGGGAATTCG
Found at i:905095 original size:21 final size:21
Alignment explanation
Indices: 905069--905111 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
905059 TTTCTGGGTT
* *
905069 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
905090 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
905111 A
1 A
905112 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:905186 original size:67 final size:69
Alignment explanation
Indices: 905091--905243 Score: 229
Period size: 67 Copynumber: 2.2 Consensus size: 69
905081 ACCCATTCAA
* *
905091 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
905154 GGGG
66 GGGG
* * * *
905158 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
905223 GGGG
66 GGGG
*
905227 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
905244 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
67 26 0.34
68 26 0.34
69 25 0.32
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGGG
Found at i:905668 original size:30 final size:30
Alignment explanation
Indices: 905610--905668 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
905600 GTTATATGGG
* *
905610 CTATGTGATAAAGGTATTAAATTGATATGT
1 CTATGTGATAAAGGTATGAAATTAATATGT
905640 CTATGTGATAAAGGTATGGAAA-TAATATG
1 CTATGTGATAAAGGTAT-GAAATTAATATG
905669 ACTACGCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAATTAATATGT
Found at i:905956 original size:22 final size:22
Alignment explanation
Indices: 905882--905948 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
905872 TTATGGACAT
905882 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
905904 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
905926 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
905948 A
1 A
905949 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:911169 original size:21 final size:21
Alignment explanation
Indices: 911143--911185 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
911133 TTTCTGGGTT
* *
911143 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
911164 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
911185 A
1 A
911186 CGAATATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:911245 original size:66 final size:68
Alignment explanation
Indices: 911165--911315 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 68
911155 ACCCATTCAA
* *
911165 GGGGAACCGATACCCCTTCAACGAATAT-AATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
911228 GGG
66 GGG
* * * *
911231 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
911296 GGG
66 GGG
*
911299 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
911316 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 25 0.33
67 27 0.36
68 24 0.32
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:911740 original size:30 final size:30
Alignment explanation
Indices: 911682--911740 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
911672 GTTATATGGG
* *
911682 CTATGTGATAAAGGTATTAAATTGATATGT
1 CTATGTGATAAAGGTATGAAATTAATATGT
911712 CTATGTGATAAAGGTATGGAAA-TAATATG
1 CTATGTGATAAAGGTAT-GAAATTAATATG
911741 ACTACGCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAATTAATATGT
Found at i:912028 original size:22 final size:22
Alignment explanation
Indices: 911954--912020 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
911944 TTATGGACAT
911954 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
911976 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
911998 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
912020 A
1 A
912021 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:914781 original size:20 final size:20
Alignment explanation
Indices: 914756--914794 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
914746 GAATGCTAGA
*
914756 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
914776 GGGGAACCGATTCCCCCAG
1 GGGGAACCGATACCCCCAG
914795 ATAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.33, T:0.10
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:921518 original size:21 final size:21
Alignment explanation
Indices: 921476--921518 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
921466 TTTCTGGGCT
* *
921476 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
921497 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
921518 A
1 A
921519 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:934797 original size:32 final size:32
Alignment explanation
Indices: 934761--934825 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
934751 GCACAGCTAT
934761 CTCGAATAATGAAAGTCTATCAAAGCTCATTA
1 CTCGAATAATGAAAGTCTATCAAAGCTCATTA
934793 CTCGAATAATGAAAGTCTATCAAAGCTCATTA
1 CTCGAATAATGAAAGTCTATCAAAGCTCATTA
934825 C
1 C
934826 CGACTTCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (32 bp):
CTCGAATAATGAAAGTCTATCAAAGCTCATTA
Found at i:938440 original size:19 final size:20
Alignment explanation
Indices: 938416--938463 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
938406 AATGATTTTC
* *
938416 TTTTGAAAGCCAAAA-TAGA
1 TTTTGAAAACCAAAATTAAA
938435 TTTTGAAAACCAAAATTAAA
1 TTTTGAAAACCAAAATTAAA
938455 TTTTGAAAA
1 TTTTGAAAA
938464 AGGATTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATTAAA
Found at i:941736 original size:20 final size:20
Alignment explanation
Indices: 941711--941748 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
941701 TTTGGTTCAC
941711 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
941731 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
941749 AGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:946800 original size:18 final size:18
Alignment explanation
Indices: 946777--946830 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
946767 CTTGACAAGT
**
946777 TCACCCTTCCACTGACGA
1 TCACCCTTCCACCAACGA
*
946795 TCACCCTCCCACCAACGA
1 TCACCCTTCCACCAACGA
* *
946813 TCACCTTTCCATCAACGA
1 TCACCCTTCCACCAACGA
946831 ATGGTCAAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.26, C:0.46, G:0.07, T:0.20
Consensus pattern (18 bp):
TCACCCTTCCACCAACGA
Found at i:954204 original size:16 final size:16
Alignment explanation
Indices: 954185--954218 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
954175 ACTCGAACAA
954185 AAAATAAACAGAACTG
1 AAAATAAACAGAACTG
* *
954201 AAAATAATCTGAACTG
1 AAAATAAACAGAACTG
954217 AA
1 AA
954219 TTTAACTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAATAAACAGAACTG
Found at i:954554 original size:32 final size:32
Alignment explanation
Indices: 954498--954560 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
954488 ACCGATCCGA
* *
954498 TATTGACCGGACCCGAAATCTAACCAATCTGG
1 TATTAACCGGACCCAAAATCTAACCAATCTGG
*
954530 TATTAACCGGACCCAAAAAT-TAACCGATCTG
1 TATTAACCGGACCC-AAAATCTAACCAATCTG
954561 ATACTAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (32 bp):
TATTAACCGGACCCAAAATCTAACCAATCTGG
Found at i:969639 original size:39 final size:39
Alignment explanation
Indices: 969585--969665 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
969575 ATTGACGTGC
969585 AAACAACTGGGGAAAGATTCATGCTTTCAAGTAGCAATG
1 AAACAACTGGGGAAAGATTCATGCTTTCAAGTAGCAATG
969624 AAACAACTGGGGAAAGATTCATGCTTTCAAGTAGCAATG
1 AAACAACTGGGGAAAGATTCATGCTTTCAAGTAGCAATG
969663 AAA
1 AAA
969666 ATAAGAACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (39 bp):
AAACAACTGGGGAAAGATTCATGCTTTCAAGTAGCAATG
Found at i:974373 original size:18 final size:18
Alignment explanation
Indices: 974350--974388 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
974340 CGTTGCGATG
974350 ATCGCTCATATTTCACAA
1 ATCGCTCATATTTCACAA
974368 ATCGCTCATATTTCACAA
1 ATCGCTCATATTTCACAA
974386 ATC
1 ATC
974389 AACTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (18 bp):
ATCGCTCATATTTCACAA
Found at i:984765 original size:15 final size:15
Alignment explanation
Indices: 984745--984774 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
984735 CGTCTGAGCA
984745 ATGGAGATGGTGGCT
1 ATGGAGATGGTGGCT
984760 ATGGAGATGGTGGCT
1 ATGGAGATGGTGGCT
984775 GATGTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.47, T:0.27
Consensus pattern (15 bp):
ATGGAGATGGTGGCT
Found at i:987449 original size:52 final size:52
Alignment explanation
Indices: 987361--987543 Score: 271
Period size: 52 Copynumber: 3.5 Consensus size: 52
987351 GGTACTGAAA
*
987361 GAACAATATCGATA-TTGTTCATA-TGATAGCTTAAAAACAATAGAGTTTAGGAG
1 GAACAATATCGATACTTCTTCA-AGT-A-AGCTTAAAAACAATAGAGTTTAGGAG
* * **
987414 GAACAATATCAATACTTCTTCAAGTAAGCTTAAAAACTATAGAGTTTAGTTG
1 GAACAATATCGATACTTCTTCAAGTAAGCTTAAAAACAATAGAGTTTAGGAG
987466 GAACAATATCGATACTTCTTCAAGTAAGCTTAAAAACAATAGAGTTTAGGAG
1 GAACAATATCGATACTTCTTCAAGTAAGCTTAAAAACAATAGAGTTTAGGAG
*
987518 GAACAATATTGATACTTCTTCAAGTA
1 GAACAATATCGATACTTCTTCAAGTA
987544 GTATCAATAC
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
52 96 0.81
53 15 0.13
54 7 0.06
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (52 bp):
GAACAATATCGATACTTCTTCAAGTAAGCTTAAAAACAATAGAGTTTAGGAG
Found at i:990385 original size:22 final size:22
Alignment explanation
Indices: 990359--990404 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
990349 GGGTATATTA
990359 GTCCTTCGAGACGCATCCAGTG
1 GTCCTTCGAGACGCATCCAGTG
* * * *
990381 GTCCTTTGGGATGTATCCAGTG
1 GTCCTTCGAGACGCATCCAGTG
990403 GT
1 GT
990405 ATTTCGGGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.30
Consensus pattern (22 bp):
GTCCTTCGAGACGCATCCAGTG
Found at i:992716 original size:3 final size:3
Alignment explanation
Indices: 992710--992792 Score: 102
Period size: 3 Copynumber: 27.7 Consensus size: 3
992700 TTCATTTAAA
992710 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT ATAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
992755 TAT TA- TAT ATAT TAT TA- TAT GTAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
992793 AAAAAATTAC
Statistics
Matches: 72, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
2 7 0.10
3 55 0.76
4 10 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:994928 original size:26 final size:27
Alignment explanation
Indices: 994876--994933 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
994866 TAATTCTTTC
*
994876 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
994904 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
994930 TTTT
1 TTTT
994934 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:998247 original size:15 final size:15
Alignment explanation
Indices: 998227--998258 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
998217 ATTAATACCT
998227 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
998242 TTTTGCATACATTCA
1 TTTTGCATACATGCA
998257 TT
1 TT
998259 ATTCATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1006815 original size:94 final size:93
Alignment explanation
Indices: 1006606--1006889 Score: 473
Period size: 93 Copynumber: 3.0 Consensus size: 93
1006596 CGTAGACCCA
1006606 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCC-TAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCATAAAAACCA
1006670 ATCATTGAATTTGGAAGATGAATGTGCTC
66 ATCATTGAATTT-GAAGATGAATGTGCTC
* *
1006699 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAACCCAAAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCATAAAAACCA
1006764 ATCATTGAATTTAGAAGATGAATGTGCTC
66 ATCATTGAATTT-GAAGATGAATGTGCTC
* *
1006793 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGTATGAA-CCATAAAAACAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCATAAAAACCA
* *
1006857 ATCATTGGATTTGAAAGATGAATGTGATC
66 ATCATTGAATTTG-AAGATGAATGTGCTC
1006886 ATAG
1 ATAG
1006890 TAGAAATAAG
Statistics
Matches: 180, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
92 1 0.01
93 93 0.52
94 86 0.48
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCATAAAAACCA
ATCATTGAATTTGAAGATGAATGTGCTC
Found at i:1008202 original size:116 final size:113
Alignment explanation
Indices: 1007680--1008192 Score: 670
Period size: 113 Copynumber: 4.5 Consensus size: 113
1007670 GCAAAGATTC
* * * * * * *
1007680 AAATCCATCAATTGATGGATCAGCATTACCAGTTCGAGTTCATAATAACAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1007745 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * * *
1007793 AAATTCATTATTTGATGGATTAACATTGCCAGAAAGAGTTCATAATAAGAAGAACTCATCTAAAG
1 AAATTCATCATTTGATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1007858 -A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * * * *
1007904 GAATTTATCATTTGATGGATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1007969 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *
1008017 AAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCATTTGATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAA--C-TCATCTG
*
1008082 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * * *
1008133 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATC
1 AAATTCATCATTTGATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATC
1008193 ATCTGAAGAA
Statistics
Matches: 345, Mismatches: 50, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
111 95 0.28
112 2 0.01
113 145 0.42
114 1 0.00
115 1 0.00
116 101 0.29
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATTCATCATTTGATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:1008468 original size:3 final size:3
Alignment explanation
Indices: 1008462--1008531 Score: 90
Period size: 3 Copynumber: 22.7 Consensus size: 3
1008452 TTCATTTAAA
1008462 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT ATAT ATAT TAT TA-
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT
1008508 TAT GTAT TAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TAT TAT TA
1008532 AAAAATTACA
Statistics
Matches: 62, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.05
3 48 0.77
4 11 0.18
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1008940 original size:24 final size:25
Alignment explanation
Indices: 1008895--1008955 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
1008885 TTCCCCTGCA
*
1008895 AACAAAAAAAAACCAGCAAAAGCAGAG
1 AACAAAAAAAAACCAG-AAAAGCA-AC
1008922 AACAAAAAAAAA-CAG-AAAGCAAC
1 AACAAAAAAAAACCAGAAAAGCAAC
1008945 AA-AAAAAAAAA
1 AACAAAAAAAAA
1008956 GCTTACCGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 9 0.27
23 3 0.09
24 6 0.18
26 3 0.09
27 12 0.36
ACGTcount: A:0.75, C:0.15, G:0.10, T:0.00
Consensus pattern (25 bp):
AACAAAAAAAAACCAGAAAAGCAAC
Done.