Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008303.1 Hibiscus syriacus cultivar Beakdansim tig00110989_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: 1196166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1096129 original size:22 final size:22
Alignment explanation
Indices: 1096077--1096130 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
1096067 TCTGTTTTAC
* * *
1096077 TTTAGTATATATTTTTAATTTT
1 TTTATTATATATATATAATTTT
*
1096099 TTAAGATTATATATATATAATTTT
1 TT--TATTATATATATATAATTTT
1096123 TTTATTAT
1 TTTATTAT
1096131 CAGTTTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTATTATATATATATAATTTT
Found at i:1096223 original size:44 final size:43
Alignment explanation
Indices: 1096145--1096229 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
1096135 TTTATTAATT
1096145 TATATATATATATATTTACTATTTTTTAATTTA-TTTATTTTA
1 TATATATATATATATTTACTATTTTTTAATTTATTTTATTTTA
* *
1096187 TATATATATATATTATTT-TTACTTTTTTATTATTATTTTATTT
1 TATATATATATA-TATTTACTA-TTTTTTAAT-TTATTTTATTT
1096230 ATTTGTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
42 14 0.38
43 13 0.35
44 3 0.08
45 7 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (43 bp):
TATATATATATATATTTACTATTTTTTAATTTATTTTATTTTA
Found at i:1096231 original size:44 final size:43
Alignment explanation
Indices: 1096106--1096231 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 43
1096096 TTTTTAAGAT
* * * * *
1096106 TATATATATA-TAATTTTTTTATTATCAGTTTTATTAATTTATA
1 TATATATATATTTACTTTTTTATTATTA-TTTTATTTATATATA
*
1096149 TATATATATATTTACTATTTTT-TAATT-TATTTATTTTATATATA
1 TATATATATATTTACT-TTTTTATTATTAT-TTTA-TTTATATATA
*
1096193 TATATATTATTTTTACTTTTTTATTATTATTTTATTTAT
1 TATATA-TATATTTACTTTTTTATTATTATTTTATTTAT
1096232 TTGTTTTATT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
42 1 0.01
43 14 0.21
44 30 0.44
45 22 0.32
46 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (43 bp):
TATATATATATTTACTTTTTTATTATTATTTTATTTATATATA
Found at i:1096249 original size:17 final size:16
Alignment explanation
Indices: 1096112--1096254 Score: 62
Period size: 16 Copynumber: 8.8 Consensus size: 16
1096102 AGATTATATA
1096112 TATATAATTTTTTTA-T
1 TATAT-ATTTTTTTATT
* *
1096128 TATCAGT-TTTATTAATT
1 TAT-A-TATTTTTTTATT
* * *
1096145 TATATATATATATATT
1 TATATATTTTTTTATT
* *
1096161 TA-CTATTTTTTAATT
1 TATATATTTTTTTATT
* * *
1096176 TATTTATTTTATATATA
1 TATATATTTT-TTTATT
1096193 TATATATTATTTTTACTT
1 TATATATT-TTTTTA-TT
* * *
1096211 T-TTTATTATTAT-TT
1 TATATATTTTTTTATT
*
1096225 TATTTATTTGTTTTATT
1 TATATATTT-TTTTATT
1096242 TATATATTTTTTT
1 TATATATTTTTTT
1096255 CTTCTTTTTC
Statistics
Matches: 93, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
14 3 0.03
15 17 0.18
16 35 0.38
17 33 0.35
18 5 0.05
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (16 bp):
TATATATTTTTTTATT
Found at i:1096262 original size:24 final size:23
Alignment explanation
Indices: 1096193--1096262 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 23
1096183 TTTATATATA
1096193 TATATATTATTTTTACTTTTTTAT
1 TATATATT-TTTTTACTTTTTTAT
*
1096217 TAT-TATTTTATTTATTTGTTTTATT
1 TATATATTTT-TTTACTT-TTTTA-T
1096242 TATATATTTTTTT-CTTCTTTT
1 TATATATTTTTTTACTT-TTTT
1096263 TCTTCTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.05
23 10 0.26
24 14 0.36
25 7 0.18
26 6 0.15
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (23 bp):
TATATATTTTTTTACTTTTTTAT
Found at i:1096264 original size:9 final size:9
Alignment explanation
Indices: 1096250--1096275 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1096240 TTTATATATT
1096250 TTTTTCTTC
1 TTTTTCTTC
1096259 TTTTTCTTC
1 TTTTTCTTC
1096268 TTTTTCTT
1 TTTTTCTT
1096276 TATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:1096291 original size:49 final size:51
Alignment explanation
Indices: 1096159--1096293 Score: 129
Period size: 49 Copynumber: 2.7 Consensus size: 51
1096149 TATATATATA
* * *
1096159 TTTACTATT-TTTTAATTTATTTATTTTATATATATATATATTATTTTTACTTT
1 TTTATTATTATTTT-ATTTATTT-TTTT-TATATTTATATATTATTTTTACTTC
*
1096212 TTTATTATTATTTTATTTA-TTTGTTT-TATTTATATATT-TTTTT-CTTC
1 TTTATTATTATTTTATTTATTTTTTTTATATTTATATATTATTTTTACTTC
* * *
1096259 TTT-TTCTTCTTTTTCTTTATTTTTTTTATATTTAT
1 TTTATTATT-ATTTTATTTATTTTTTTTATATTTAT
1096294 TTTACTTACT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
46 4 0.06
47 14 0.20
48 11 0.16
49 18 0.26
50 1 0.01
51 3 0.04
52 2 0.03
53 13 0.19
54 4 0.06
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (51 bp):
TTTATTATTATTTTATTTATTTTTTTTATATTTATATATTATTTTTACTTC
Found at i:1100610 original size:32 final size:31
Alignment explanation
Indices: 1100574--1100693 Score: 141
Period size: 32 Copynumber: 3.7 Consensus size: 31
1100564 GGAACAATAA
1100574 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
* * *
1100606 GGGCATTTTTTTAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
* * *
1100638 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
*
1100670 GGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
1100694 CTGATGCAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
31 6 0.08
32 67 0.87
33 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Found at i:1101392 original size:106 final size:106
Alignment explanation
Indices: 1101271--1101593 Score: 423
Period size: 106 Copynumber: 3.0 Consensus size: 106
1101261 ATATCGTGCC
* *
1101271 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGACTGGTTGTTAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1101336 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * *
1101377 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAATTGGTTGTCAAGAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * *
1101442 AATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * * * * ** * **
1101483 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * * * *
1101548 AGTTCCAGAGCCAATTTTAACTTCACGGT-GGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCAC-ATCGAAGGATATTGG
1101589 ACTCG
1 ACTCG
1101594 GAACAATACA
Statistics
Matches: 187, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
106 187 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
Found at i:1102037 original size:37 final size:37
Alignment explanation
Indices: 1101962--1102048 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
1101952 ATTGAAAACA
* * * **
1101962 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
*
1101998 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
*
1102035 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1102049 TAAACATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
Found at i:1102049 original size:87 final size:87
Alignment explanation
Indices: 1101851--1102029 Score: 313
Period size: 87 Copynumber: 2.1 Consensus size: 87
1101841 GACAGTTTTT
*
1101851 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
*
1101916 CTTGAAACCAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
* * *
1101938 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
1102003 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
1102025 CTTGA
1 CTTGA
1102030 GACAGTTTCT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCC
Found at i:1102049 original size:102 final size:102
Alignment explanation
Indices: 1101938--1102177 Score: 354
Period size: 102 Copynumber: 2.4 Consensus size: 102
1101928 TTTTGTCTCC
* * *
1101938 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCA
1102003 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
** * * *
1102040 CTTGAAACATAAACATTGAAAACATTTCATTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCA
* * * *
1102105 CTTTAAATAAAATTTTGTCTCCCTTTAGATAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
1102142 CTTGAAACATAAACCTTGAAAACATTCCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
1102178 CACAAAATAT
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 122 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCA
CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:1102265 original size:37 final size:37
Alignment explanation
Indices: 1102215--1102317 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
1102205 AAAATGAGTT
*
1102215 TTGAGACAATTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
1102252 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1102288 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1102318 TGAATATATT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 35 0.56
37 27 0.44
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:1102358 original size:101 final size:102
Alignment explanation
Indices: 1102223--1102409 Score: 297
Period size: 101 Copynumber: 1.8 Consensus size: 102
1102213 TTTTGAGACA
* *
1102223 ATTTCCCTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 ATTTCCCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCCCTC
1102288 TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
66 TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
* **
1102325 ATTTTCCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCT
1 ATTTCCCTTGAAACAAAATCTT-GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCCCT
*
1102388 CTTGAGACAGTTTCTCTTGAAA
65 CTTGAGACAGTTTCCCTTGAAA
1102410 TACAAAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 2 0.03
101 63 0.81
102 13 0.17
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (102 bp):
ATTTCCCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCCCTC
TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
Found at i:1102379 original size:36 final size:36
Alignment explanation
Indices: 1102327--1102409 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 36
1102317 TTGAATATAT
1102327 TTTC-CTTGAAACAAATTTCGTCTCC-CTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTC-CCTCTTGAGACAG
* *
1102362 TTTCTTTTGAAACAAATTTTGTCCCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCCCTCTTGAGACAG
1102398 TTTCTCTTGAAA
1 TTTCTCTTGAAA
1102410 TACAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 6 0.14
36 37 0.86
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCCCTCTTGAGACAG
Found at i:1102625 original size:84 final size:85
Alignment explanation
Indices: 1102493--1102650 Score: 228
Period size: 84 Copynumber: 1.9 Consensus size: 85
1102483 CACCAAACGC
* * * *
1102493 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGC
1102558 TATCTGTCACCAAAAGACCT
66 TATCTGTCACCAAAAGACCT
** * **
1102578 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTACAGTATAACTCAAGGCAAGAAGGGC
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGC
1102642 TATCTGTCA
66 TATCTGTCA
1102651 ATAAAATTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 46 0.72
85 18 0.28
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGC
TATCTGTCACCAAAAGACCT
Found at i:1103702 original size:22 final size:22
Alignment explanation
Indices: 1103597--1103704 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 22
1103587 TCTTTTTTAC
*
1103597 TTTAGTATATAT-TTTTAATTTT
1 TTTATTATATATATTTTAA-TTT
* *
1103619 TTTAAATTATATACATATT-ATTT
1 TTT--ATTATATATATTTTAATTT
1103642 TTTATTATCAGT-T-TTATTAATTT
1 TTTATTAT-A-TATATT-TTAATTT
1103665 ATATATATATATATATATTTTAATTT
1 -T-T-TAT-TATATATATTTTAATTT
1103691 TTTATTATATATAT
1 TTTATTATATATAT
1103705 ATATATATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 26
0.69 0.05 0.26
Matches are distributed among these distances:
21 6 0.09
22 15 0.22
23 14 0.21
24 10 0.15
25 6 0.09
26 12 0.18
27 5 0.07
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTATTATATATATTTTAATTT
Found at i:1103753 original size:33 final size:34
Alignment explanation
Indices: 1103602--1103747 Score: 119
Period size: 34 Copynumber: 4.3 Consensus size: 34
1103592 TTTACTTTAG
*
1103602 TATA-TATTTTTAA-TTTTT-TTAAAT-TATATA
1 TATATTATTTTTAATTTTTTATTATATATATATA
* * *
1103632 CATATTATTTTTTATTATCAGTTTTATTAATTTATATATA
1 TATATTA-TTTTTA--AT--TTTTTATT-ATATATATATA
1103672 TATATATATATTTTAATTTTTTATTATATATATATA
1 TATAT-TAT-TTTTAATTTTTTATTATATATATATA
*
1103708 TATATTATTTTTACTTTTTTATTAT-TAT-TAT-
1 TATATTATTTTTAATTTTTTATTATATATATATA
1103739 TAT-TTATTT
1 TATATTATTT
1103748 GTTTTATTTA
Statistics
Matches: 96, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
30 9 0.09
31 5 0.05
32 9 0.09
33 3 0.03
34 17 0.18
35 3 0.03
36 15 0.16
37 11 0.11
38 2 0.02
39 4 0.04
40 11 0.11
41 7 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (34 bp):
TATATTATTTTTAATTTTTTATTATATATATATA
Found at i:1103758 original size:26 final size:23
Alignment explanation
Indices: 1103710--1103755 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1103700 TATATATATA
1103710 TATTATTTTTACTTTTTTATTAT
1 TATTATTTTTACTTTTTTATTAT
*
1103733 TATTATTATTTATTTGTTTTATT
1 TATTATT-TTTACTT-TTTTATT
1103756 TATATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (23 bp):
TATTATTTTTACTTTTTTATTAT
Found at i:1103767 original size:15 final size:13
Alignment explanation
Indices: 1103738--1103790 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
1103728 ATTATTATTA
1103738 TTATTTATTTGTT
1 TTATTTATTTGTT
1103751 TTATTTATATATGTTT
1 TTATTTAT-T-TG-TT
* *
1103767 TTCTTTATTTTTT
1 TTATTTATTTGTT
1103780 TATATTTATTT
1 T-TATTTATTT
1103791 TACTTACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 11 0.33
14 10 0.30
15 3 0.09
16 9 0.27
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (13 bp):
TTATTTATTTGTT
Found at i:1108418 original size:28 final size:28
Alignment explanation
Indices: 1108379--1108432 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1108369 TCATAAAACT
*
1108379 TAATATTATTATTTTTAAAATATTAAAA
1 TAATATTATTATTATTAAAATATTAAAA
1108407 TAAT-TTATTTATTATTAAAATATTAA
1 TAATATTA-TTATTATTAAAATATTAA
1108433 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TAATATTATTATTATTAAAATATTAAAA
Found at i:1108422 original size:20 final size:20
Alignment explanation
Indices: 1108399--1108454 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1108389 ATTTTTAAAA
*
1108399 TATTAAAATAATTTA-TTTAT
1 TATTAAAAT-ATTAATTTTAT
1108419 TATTAAAATATTAATTTTAT
1 TATTAAAATATTAATTTTAT
*
1108439 TAATAAAAATATTAAT
1 T-ATTAAAATATTAAT
1108455 ATTGGTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 15 0.47
21 13 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAAAATATTAATTTTAT
Found at i:1108449 original size:21 final size:20
Alignment explanation
Indices: 1108414--1108454 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1108404 AAATAATTTA
*
1108414 TTTATTATTAAAATATTAAT
1 TTTATTATAAAAATATTAAT
1108434 TTTATTAATAAAAATATTAAT
1 TTTATT-ATAAAAATATTAAT
1108455 ATTGGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATTATAAAAATATTAAT
Found at i:1108659 original size:27 final size:25
Alignment explanation
Indices: 1108592--1108679 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 25
1108582 ATATTAATAT
*
1108592 TAAATATATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATTATT-TTTA
* *
1108619 TTAATAATTTAATAATATTATTTTTA
1 TAAATAA-TAAATAATATTATTTTTA
* *
1108645 TGAAATTAATAAATAATATAAATTTTA
1 T-AAA-TAATAAATAATATTATTTTTA
*
1108672 TTAATAAT
1 TAAATAAT
1108680 TTATTATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 36 0.72
28 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TAAATAATAAATAATATTATTTTTA
Found at i:1108730 original size:53 final size:51
Alignment explanation
Indices: 1108657--1108781 Score: 123
Period size: 53 Copynumber: 2.4 Consensus size: 51
1108647 AAATTAATAA
* *
1108657 ATAATA-TAAATT-TTATTAATAATTTATTATATATTATTA-AA-AATAAAAAT
1 ATAATATTATATTATTA-TAATAATTGATTAT-T-TTATTATAATAATAAAAAT
**
1108707 ATAATATCTTATATTATTATAATATAATTGATTATTTTATTATAATTTTAAAAAT
1 ATAATA--TTATATTATTAT-A-ATAATTGATTATTTTATTATAATAATAAAAAT
1108762 ATAATATTATATTATTATAA
1 ATAATATTATATTATTATAA
1108782 ATATTAATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
50 6 0.10
51 1 0.02
52 1 0.02
53 24 0.38
54 7 0.11
55 24 0.38
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (51 bp):
ATAATATTATATTATTATAATAATTGATTATTTTATTATAATAATAAAAAT
Found at i:1108740 original size:18 final size:18
Alignment explanation
Indices: 1108719--1108753 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1108709 AATATCTTAT
1108719 ATTATTATAATATAATTG
1 ATTATTATAATATAATTG
* *
1108737 ATTATTTTATTATAATT
1 ATTATTATAATATAATT
1108754 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTATTATAATATAATTG
Found at i:1108763 original size:32 final size:32
Alignment explanation
Indices: 1108717--1108796 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1108707 ATAATATCTT
* *
1108717 ATATTATTATAATATAATTGATTATTTTATTAT-A
1 ATATTAATA-AATATAA-T-ATTATATTATTATAA
*
1108751 ATTTTAA-AAATATAATATTATATTATTATAA
1 ATATTAATAAATATAATATTATATTATTATAA
1108782 ATATTAATAAATATA
1 ATATTAATAAATATA
1108797 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 12 0.30
31 8 0.20
32 14 0.35
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (32 bp):
ATATTAATAAATATAATATTATATTATTATAA
Found at i:1108772 original size:22 final size:23
Alignment explanation
Indices: 1108744--1108813 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
1108734 TTGATTATTT
1108744 TATTATAATTTTAAAAATA-TAA
1 TATTATAATTTTAAAAATATTAA
*
1108766 TATTAT-ATTATTATAAATATTAA
1 TATTATAATT-TTAAAAATATTAA
* * *
1108789 TA-AATATATTTTAAATATTTTAA
1 TATTATA-ATTTTAAAAATATTAA
1108812 TA
1 TA
1108814 ATTAATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.08
22 16 0.41
23 17 0.44
24 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTATAATTTTAAAAATATTAA
Found at i:1108777 original size:30 final size:31
Alignment explanation
Indices: 1108680--1108796 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 31
1108670 TATTAATAAT
* *
1108680 TTATTATATATTATTAAAAATAAAAATATAATA
1 TTATTATA-ATTATTAAAAAT-ATAATATTATA
* * *
1108713 -TCTTAT-ATTATT-ATAATATAATTGATTATT
1 TTATTATAATTATTAAAAATATAA-T-ATTATA
1108743 TTATTATAATT-TTAAAAATATAATATTATA
1 TTATTATAATTATTAAAAATATAATATTATA
*
1108773 TTATTATAAATATTAATAAATATA
1 TTATTATAATTATTAA-AAATATA
1108797 TTTTAAATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.04
29 5 0.07
30 25 0.37
31 12 0.18
32 23 0.34
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TTATTATAATTATTAAAAATATAATATTATA
Found at i:1108803 original size:21 final size:23
Alignment explanation
Indices: 1108751--1108807 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
1108741 TTTTATTATA
* *
1108751 ATTTTAAAAATATAATATTATATT
1 ATTTTAAATAT-TAATATAATATT
*
1108775 ATTATAAATATTAATA-AATA-T
1 ATTTTAAATATTAATATAATATT
1108796 ATTTTAAATATT
1 ATTTTAAATATT
1108808 TTAATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 12 0.41
22 3 0.10
23 5 0.17
24 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTAAATATTAATATAATATT
Found at i:1108858 original size:49 final size:54
Alignment explanation
Indices: 1108700--1108861 Score: 146
Period size: 53 Copynumber: 3.1 Consensus size: 54
1108690 TTATTAAAAA
* **
1108700 TAAAAATATAATATCTTATATTATTAT-AATA-TAATTGAT-TATTTTATTATAATTT
1 TAAAAATATAATA--TTATATGATTATAAATATTAATAAATATATTTTA-TA-AATTT
*
1108755 TAAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTA-AATATTT
1 TAAAAATATAATATTATATGATTATAAATATTAATAAATATATTTTATAA-ATTT
* *
1108809 TAATAAT-TAATATT-T-TGATTA-AAATGA-TATTAAA-ATATTTTATAAATTT
1 TAAAAATATAATATTATATGATTATAAAT-ATTAATAAATATATTTTATAAATTT
1108858 TAAA
1 TAAA
1108862 TTTATAAAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
49 15 0.16
50 12 0.13
51 6 0.06
52 1 0.01
53 20 0.21
54 15 0.16
55 19 0.20
56 7 0.07
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (54 bp):
TAAAAATATAATATTATATGATTATAAATATTAATAAATATATTTTATAAATTT
Found at i:1109420 original size:2 final size:2
Alignment explanation
Indices: 1109413--1109457 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1109403 AATATCAATG
1109413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1109455 AT A
1 AT A
1109458 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1109462 original size:2 final size:2
Alignment explanation
Indices: 1109457--1109481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1109447 ATATATATAT
1109457 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1109482 AATACAAGTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1116199 original size:31 final size:31
Alignment explanation
Indices: 1116164--1116238 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1116154 TTACGTAGGG
1116164 GACCATATTGCAAACGGACTAAATATTGGGA
1 GACCATATTGCAAACGGACTAAATATTGGGA
* * * *
1116195 GACCATATTGAAAATGGACTAAATGTTGGGG
1 GACCATATTGCAAACGGACTAAATATTGGGA
*
1116226 GACTATATTGCAA
1 GACCATATTGCAA
1116239 GTTTTAAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (31 bp):
GACCATATTGCAAACGGACTAAATATTGGGA
Found at i:1116522 original size:23 final size:24
Alignment explanation
Indices: 1116488--1116542 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
1116478 CATAATAAAA
*
1116488 AATTAAATATTG-ATTTTAAATTAT
1 AATTAAATATTGAATATTAAA-TAT
*
1116512 AATTAAA-ATTGAATATTGAATAT
1 AATTAAATATTGAATATTAAATAT
1116535 AATTAAAT
1 AATTAAAT
1116543 TATTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
AATTAAATATTGAATATTAAATAT
Found at i:1116586 original size:18 final size:19
Alignment explanation
Indices: 1116553--1116588 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1116543 TATTTGATAA
*
1116553 AATATAAATTTTAAAAGAT
1 AATATAAATTTAAAAAGAT
1116572 AATAT-AATTTAAAAAGA
1 AATATAAATTTAAAAAGA
1116589 AAATGAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AATATAAATTTAAAAAGAT
Found at i:1117185 original size:3 final size:3
Alignment explanation
Indices: 1117177--1117218 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1117167 AAGCTTAATT
1117177 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1117219 GGGTAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1117288 original size:29 final size:29
Alignment explanation
Indices: 1117249--1117311 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
1117239 CACTAAACTT
* * *
1117249 TTTTAAAACTTTCATTTAAGTCCCCCAAC
1 TTTTAAAACTTACAATAAAGTCCCCCAAC
1117278 TTTTAAAACTTACAATAAAGTCCCCCAAC
1 TTTTAAAACTTACAATAAAGTCCCCCAAC
*
1117307 ATTTA
1 TTTTA
1117312 GTCCGTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTTAAAACTTACAATAAAGTCCCCCAAC
Found at i:1119087 original size:32 final size:31
Alignment explanation
Indices: 1119046--1119131 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 31
1119036 ATGCACGTCC
1119046 CCAACACAGGTCGCCATGCACTCCCCAACACA
1 CCAACACAGGTCGCCATGCACTCCCCAAC-CA
* *
1119078 CCAACACAGGTCGCCATGCACT-CCCAGCGA
1 CCAACACAGGTCGCCATGCACTCCCCAACCA
*
1119108 CCTACA-AGGTCGCCATGCACTCCC
1 CCAACACAGGTCGCCATGCACTCCC
1119132 AGCAACCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 15 0.30
30 8 0.16
31 5 0.10
32 22 0.44
ACGTcount: A:0.27, C:0.45, G:0.16, T:0.12
Consensus pattern (31 bp):
CCAACACAGGTCGCCATGCACTCCCCAACCA
Found at i:1119127 original size:29 final size:30
Alignment explanation
Indices: 1119049--1119139 Score: 130
Period size: 29 Copynumber: 3.0 Consensus size: 30
1119039 CACGTCCCCA
* *
1119049 ACACAGGTCGCCATGCACTCCCCAACACACCA
1 ACACAGGTCGCCATGCACT-CCCAGCA-ACCT
*
1119081 ACACAGGTCGCCATGCACTCCCAGCGACCT
1 ACACAGGTCGCCATGCACTCCCAGCAACCT
1119111 ACA-AGGTCGCCATGCACTCCCAGCAACCT
1 ACACAGGTCGCCATGCACTCCCAGCAACCT
1119140 TGTAGGTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
29 25 0.45
30 6 0.11
31 5 0.09
32 19 0.35
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.12
Consensus pattern (30 bp):
ACACAGGTCGCCATGCACTCCCAGCAACCT
Found at i:1119653 original size:29 final size:26
Alignment explanation
Indices: 1119566--1119649 Score: 125
Period size: 26 Copynumber: 3.3 Consensus size: 26
1119556 ACATAAAAGA
* *
1119566 AAGAAAGGGAGAAGAGATTACAGCTG
1 AAGAAAGGGAGAAGAGATTGCAGCAG
1119592 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAGATTGCAGCAG
* *
1119618 AAGAAAGGGAGAAGAAATTGCAGCCG
1 AAGAAAGGGAGAAGAGATTGCAGCAG
1119644 -AGAAAG
1 AAGAAAG
1119650 AAAGAAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
25 6 0.11
26 48 0.89
ACGTcount: A:0.48, C:0.08, G:0.36, T:0.08
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAGATTGCAGCAG
Found at i:1120168 original size:16 final size:16
Alignment explanation
Indices: 1120136--1120182 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1120126 TTTAAAAAGT
*
1120136 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
1120152 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
1120168 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
1120183 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:1120177 original size:15 final size:14
Alignment explanation
Indices: 1120157--1120187 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1120147 GTTTATTAGT
1120157 TTATTATATTATAAG
1 TTATTATATTA-AAG
1120172 TTATTATATTAAAG
1 TTATTATATTAAAG
1120186 TT
1 TT
1120188 TAGTGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:1122418 original size:14 final size:14
Alignment explanation
Indices: 1122399--1122436 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1122389 TTCAAGTCGT
1122399 AAATCATTACA-ATC
1 AAATCATTA-ATATC
1122413 AAATCATTAATATC
1 AAATCATTAATATC
1122427 AAATCATTAA
1 AAATCATTAA
1122437 ATATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:1122451 original size:21 final size:21
Alignment explanation
Indices: 1122413--1122514 Score: 56
Period size: 21 Copynumber: 5.0 Consensus size: 21
1122403 CATTACAATC
1122413 AAATCATTAAT-ATCAAATCATT
1 AAAT-ATTAATAAT-AAATCATT
1122435 AAATATTAATAATAAAT--TT
1 AAATATTAATAATAAATCATT
* * * * *
1122454 --TTATTACTAAT-CATTACT
1 AAATATTAATAATAAATCATT
**
1122472 -AATCATTAATATCAAATCATT
1 AAAT-ATTAATAATAAATCATT
*
1122493 AAATATTAATAATAAATTATT
1 AAATATTAATAATAAATCATT
1122514 A
1 A
1122515 TTACTAATCA
Statistics
Matches: 59, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
16 2 0.03
17 9 0.15
18 1 0.02
19 3 0.05
20 6 0.10
21 29 0.49
22 9 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATTAATAATAAATCATT
Found at i:1122493 original size:24 final size:25
Alignment explanation
Indices: 1122462--1122534 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 25
1122452 TTTTATTACT
*
1122462 AATCATTACTAATCATTAAT-ATCA
1 AATCATTACTAATCATTAATAATAA
1122486 AATCATTA--AAT-ATTAATAATAA
1 AATCATTACTAATCATTAATAATAA
* *
1122508 ATTATTATTACTAATCATTACTAATAA
1 A--ATCATTACTAATCATTAATAATAA
1122535 TTACTATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
24 14 0.35
26 3 0.08
27 10 0.25
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (25 bp):
AATCATTACTAATCATTAATAATAA
Found at i:1122620 original size:60 final size:60
Alignment explanation
Indices: 1122413--1123042 Score: 400
Period size: 60 Copynumber: 10.2 Consensus size: 60
1122403 CATTACAATC
1122413 AAATCATTAATATCAAATCATTAAATATTAATAATAAATTT--TTATTACTAATCATTACT
1 AAATCATTAATATCAAATCATTAAATATTAATAAT-AATTTCATTATTACTAATCATTACT
*
1122472 -AATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACT
1 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
* * *
1122530 -AATAATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
*
1122589 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAATCATTATT
1 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT-AATCATTACT
* * ** * ** * * * * **
1122650 ATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAA--ACATTGTTCATTGTT
1 A-AA--TCATTAATA-TCAAATCA-TTAAATA---TTAA-T-AA-TAATTTCATTATT-ACTAAT
*
1122713 CAAGT-CGT
54 C-ATTAC-T
* * * * *
1122721 AAATCATTACTATCAAATCATTACTAAATCATTAAT-ATCAA-ATAATTAAATATTAAT-A--A-
1 AAATCATTAATATCAAATCA-T--TAAAT-ATTAATAAT-AATTTCATT-ATTACTAATCATTAC
1122780 T
60 T
* * * * * * ** * * *
1122781 AAATTATTATTA-CTAATCATT-ACTA-TCA-AATCATTAAAAATTAATAATAATTTCATTATT
1 AAATCATTAATATCAAATCATTAAATATTAATAATAATT--TCATTATTACTAA--TCATTACT
* *
1122841 ACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
1 A--AATCATTA--ATATCA--AATCATTAAAT-ATT--A-A-TAA---TAATTTCATTATTACTA
1122905 ATCATTACT
52 ATCATTACT
* *
1122914 AAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATCATTACT
1 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1122974 AAATCATTAATAT-ATAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1 AAATCATTAATATCA-AATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1123034 AAATCATTA
1 AAATCATTA
1123043 TTATAATTTC
Statistics
Matches: 450, Mismatches: 66, Indels: 109
0.72 0.11 0.17
Matches are distributed among these distances:
52 1 0.00
53 4 0.01
54 8 0.02
55 6 0.01
56 2 0.00
57 5 0.01
58 88 0.20
59 27 0.06
60 149 0.33
61 10 0.02
62 9 0.02
63 4 0.01
64 13 0.03
65 13 0.03
66 9 0.02
67 19 0.04
68 16 0.04
69 13 0.03
70 12 0.03
71 16 0.04
72 3 0.01
73 8 0.02
74 2 0.00
75 9 0.02
77 4 0.01
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (60 bp):
AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
Found at i:1122659 original size:14 final size:14
Alignment explanation
Indices: 1122622--1122661 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1122612 AATATTAATA
1122622 ATAATTTCATTATT
1 ATAATTTCATTATT
*
1122636 ACTAA-ATCATTATT
1 A-TAATTTCATTATT
1122650 ATAATTTCATTA
1 ATAATTTCATTA
1122662 CTAGTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTTCATTATT
Found at i:1122740 original size:14 final size:14
Alignment explanation
Indices: 1122721--1122768 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1122711 TTCAAGTCGT
1122721 AAATCATTACTATC
1 AAATCATTACTATC
1122735 AAATCATTAC--T-
1 AAATCATTACTATC
*
1122746 AAATCATTAATATC
1 AAATCATTACTATC
*
1122760 AAATAATTA
1 AAATCATTA
1122769 AATATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1122784 original size:21 final size:22
Alignment explanation
Indices: 1122720--1122826 Score: 67
Period size: 25 Copynumber: 4.6 Consensus size: 22
1122710 GTTCAAGTCG
* *
1122720 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAAT-A--AT
1122745 TAAATCATTAATATCAAATAAT
1 TAAATCATTAATATCAAATAAT
1122767 TAAAT-ATTAATAAT-AAATTATTAT
1 TAAATCATTAAT-ATCAAA-TA--AT
* *
1122791 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATAAT
*
1122815 TAAA-AATTAATA
1 TAAATCATTAATA
1122827 ATAATTTCAT
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
21 15 0.22
22 12 0.18
24 9 0.13
25 18 0.26
26 6 0.09
27 8 0.12
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATATCAAATAAT
Found at i:1122862 original size:21 final size:21
Alignment explanation
Indices: 1122838--1123042 Score: 78
Period size: 21 Copynumber: 10.2 Consensus size: 21
1122828 TAATTTCATT
*
1122838 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
1122859 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
1122880 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
1122898 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* * *
1122919 ATTACT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
1122940 ATTAATAATAATT--T-TATT
1 ATTAATAATCATTACTAAATC
*
1122958 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* * *
1122979 ATTAATATATAATCATTAAAT-
1 ATTAATA-ATCATTACTAAATC
* * *
1123000 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
1123018 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
1123039 ATTA
1 ATTA
1123043 TTATAATTTC
Statistics
Matches: 135, Mismatches: 30, Indels: 38
0.67 0.15 0.19
Matches are distributed among these distances:
17 6 0.04
18 36 0.27
20 18 0.13
21 45 0.33
22 30 0.22
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:1122944 original size:120 final size:120
Alignment explanation
Indices: 1122789--1123373 Score: 614
Period size: 120 Copynumber: 5.1 Consensus size: 120
1122779 ATAAATTATT
* *
1122789 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1122853 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
1122908 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1122973 TAAATCATTAATAT-ATAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCA-AATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * * * * **
1123028 ATTACTAAATCATTATTAT-AATTTCATTACTAGTTATGTAACGAA-AATATGGTTAATTGAACC
1 ATTACTAAATCATTAATATCAA-ATCATTA--A-ATAT-TAA-TAATAATTTCATT-ATT--A-C
* * * * * *
1123091 AAAT-ATTA-T---TCATT-GT-TCAAGTC-GT-AA-A-TCAT--T-A---C--TA-T-CAAATC
56 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
1123135 ATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATT-ATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* *
1123199 T--ATC---AA-ATC----C-TTAAAAAATAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1123243 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
*
1123308 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1123363 ATTACTAAATC
1 ATTACTAAATC
1123374 TTAGAAATAC
Statistics
Matches: 388, Mismatches: 33, Indels: 89
0.76 0.06 0.17
Matches are distributed among these distances:
95 2 0.01
96 2 0.01
97 1 0.00
98 7 0.02
99 7 0.02
100 2 0.01
101 6 0.02
102 4 0.01
103 6 0.02
104 4 0.01
105 1 0.00
106 2 0.01
107 29 0.07
108 52 0.13
109 21 0.05
111 4 0.01
114 2 0.01
115 4 0.01
117 3 0.01
118 1 0.00
119 12 0.03
120 177 0.46
121 4 0.01
122 3 0.01
123 8 0.02
124 9 0.02
125 5 0.01
126 1 0.00
127 5 0.01
128 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (120 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:1122948 original size:322 final size:321
Alignment explanation
Indices: 1122317--1122971 Score: 1050
Period size: 325 Copynumber: 2.0 Consensus size: 321
1122307 TTTTAGTATC
1122317 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
1 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
*
1122382 TTCATTGTTCAAGTCGTAAATCATTACAATCAAATCATTAATATCAAATCATTAAATATTAATAA
66 TTCATTGTTCAAGTCGTAAATCATTACAATCAAATCATTAATATCAAATCATTAAATATAAATAA
* * * *
1122447 TAAATTTTTATTACTAATCATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTA
131 TAAATTTTAATAAATAATCATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTA
*
1122512 TTATTACTAATCATTACTAATAATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTA
196 TTATTACTAATCATTACTAATAATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTA
1122577 CTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
261 CTAATCATTACTAAATCATTAATATCAAATCATTAAATATT-ATAATAATTTCATTATTACT
1122639 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
1 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
* *
1122704 TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATT-A-CT-AAATCATT-AATATCAAATA
66 TTCATTGTTCAAGTCGTAAATCATTACAATCAAATCATTAATATCAAATCATTAAATAT-AAATA
* * *
1122765 ATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATA
130 A-TAAAT-TT--TAATAAATAATCATTACTAATCATTAATATCAAATCATTAAAAATTAATAATA
* * *
1122830 ATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC
191 AATT-ATTATTACTAATCATTACT-AATAATTAATATCAAATCATTAAAAATTAATAATAATTTC
* *
1122895 ATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTAT
254 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATT-ATAATAATTTCATTAT
1122960 TACT
318 TACT
1122964 -AATCATTA
1 AAATCATTA
1122972 CTAAATCATT
Statistics
Matches: 310, Mismatches: 16, Indels: 12
0.92 0.05 0.04
Matches are distributed among these distances:
318 5 0.02
319 13 0.04
320 6 0.02
321 3 0.01
322 103 0.33
323 49 0.16
324 27 0.09
325 104 0.34
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (321 bp):
AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
TTCATTGTTCAAGTCGTAAATCATTACAATCAAATCATTAATATCAAATCATTAAATATAAATAA
TAAATTTTAATAAATAATCATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTA
TTATTACTAATCATTACTAATAATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTA
CTAATCATTACTAAATCATTAATATCAAATCATTAAATATTATAATAATTTCATTATTACT
Found at i:1123031 original size:13 final size:12
Alignment explanation
Indices: 1122955--1123049 Score: 56
Period size: 11 Copynumber: 7.9 Consensus size: 12
1122945 TAATAATTTT
1122955 ATTATTACTAATC
1 ATTATTA-TAATC
*
1122968 ATTACTA-AATC
1 ATTATTATAATC
* *
1122979 ATTAATAT-ATA
1 ATTATTATAATC
*
1122990 ATCATTA-AAT-
1 ATTATTATAATC
*
1123000 ATTAATAATAATTTC
1 ATT-ATTATAA--TC
1123015 ATTATTACTAATC
1 ATTATTA-TAATC
*
1123028 ATTACTA-AATC
1 ATTATTATAATC
1123039 ATTATTATAAT
1 ATTATTATAAT
1123050 TTCATTACTA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
10 2 0.03
11 32 0.51
12 5 0.08
13 14 0.22
14 4 0.06
15 6 0.10
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTATTATAATC
Found at i:1123130 original size:395 final size:385
Alignment explanation
Indices: 1122414--1123373 Score: 1680
Period size: 395 Copynumber: 2.5 Consensus size: 385
1122404 ATTACAATCA
* *
1122414 AATCATTAATATCAAATCATTAAATATTAATAATAAATTT--TTATTACTAATCATTACT-AATC
1 AATCATTACTATCAAATCATTAAAAATTAATAAT-AATTTCATTATTACTAATCATTACTAAATC
* *
1122476 ATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACT-AATAATTAC
65 ATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
*
1122539 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCA
130 TATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCA
1122604 AATCATTAAATATTAATAATAATTTCATTATTACTAAATCATTATTATAATTTCATTACTAGTTA
195 AATCATTAAATATTAATAATAATTTCATTATTACTAAATCATTATTATAATTTCATTACTAGTTA
*
1122669 TGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTACTAT
260 TGTAACGAAAATATGGTTAATTGAACCAAACATTATTCATTGTTCAAGTCGTAAATCATTACTAT
1122734 CAAATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATTATTATTACT
325 CAAATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATTATTATTACT
1122795 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1122860 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
66 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
*
1122925 ATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATCATTACTAAATCATTAATAT-AT
131 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCA-
1122989 AATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATTATAATTTCA
195 AATCATTAAATATTAATAATAATTTC------A-T--T-ATTACTAAATCATTATTATAATTTCA
*
1123054 TTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAATATTATTCATTGTTCAAGTCGTAAA
250 TTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTATTCATTGTTCAAGTCGTAAA
1123119 TCATTACTATCAAATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATTATT
315 TCATTACTATCAAATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATTATT
1123184 ATTACT
380 ATTACT
* *
1123190 AATCATTACTATCAAATCCTTAAAAAATAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1123255 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
66 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
1123320 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATC
131 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATC
1123374 TTAGAAATAC
Statistics
Matches: 552, Mismatches: 11, Indels: 18
0.95 0.02 0.03
Matches are distributed among these distances:
380 5 0.01
381 32 0.06
382 18 0.03
383 38 0.07
384 20 0.04
385 95 0.17
391 1 0.00
392 1 0.00
394 1 0.00
395 341 0.62
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.41
Consensus pattern (385 bp):
AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAA
ATCATTAAATATTAATAATAATTTCATTATTACTAAATCATTATTATAATTTCATTACTAGTTAT
GTAACGAAAATATGGTTAATTGAACCAAACATTATTCATTGTTCAAGTCGTAAATCATTACTATC
AAATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATTATTATTACT
Found at i:1123135 original size:14 final size:14
Alignment explanation
Indices: 1123116--1123163 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1123106 TTCAAGTCGT
1123116 AAATCATTACTATC
1 AAATCATTACTATC
1123130 AAATCATTAC--T-
1 AAATCATTACTATC
*
1123141 AAATCATTAATATC
1 AAATCATTACTATC
*
1123155 AAATAATTA
1 AAATCATTA
1123164 AATATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1123143 original size:25 final size:25
Alignment explanation
Indices: 1123115--1123163 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1123105 GTTCAAGTCG
* *
1123115 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATAATTAC
1123140 TAAATCATTAATATCAAATAATTA
1 TAAATCATTAATATCAAATAATTA
1123164 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATAATTAC
Found at i:1123179 original size:21 final size:22
Alignment explanation
Indices: 1123115--1123173 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 22
1123105 GTTCAAGTCG
* *
1123115 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAAT-A--AT
1123140 TAAATCATTAATATCAAATAAT
1 TAAATCATTAATATCAAATAAT
1123162 TAAAT-ATTAATA
1 TAAATCATTAATA
1123174 ATAAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.22
22 6 0.19
24 1 0.03
25 18 0.56
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATAAT
Found at i:1123184 original size:21 final size:22
Alignment explanation
Indices: 1123115--1123184 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
1123105 GTTCAAGTCG
* *
1123115 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
1123140 TAAATCATTAATATCAAATAAT
1 TAAATCATTAATATCAAATTAT
1123162 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
1123183 TA
1 TA
1123185 TTACTAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:1123188 original size:49 final size:54
Alignment explanation
Indices: 1123132--1123373 Score: 226
Period size: 60 Copynumber: 4.3 Consensus size: 54
1123122 TTACTATCAA
*
1123132 ATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAAT-A-AATTA-T
1 ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATAATTACT
* * * *
1123183 -T-ATTACT-AATCATTACTATCAAATCCTTAAAAAATAATAATAATTTCATTATTACT
1 ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA--T-A--ATTACT
1123239 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA--T-A--ATTACT
*
1123299 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA--T-A--ATTACT
1123359 AATCATTACTAAATC
1 -ATCATTACTAAATC
1123374 TTAGAAATAC
Statistics
Matches: 169, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
48 29 0.17
49 7 0.04
50 1 0.01
53 1 0.01
55 4 0.02
56 1 0.01
58 1 0.01
59 6 0.04
60 119 0.70
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (54 bp):
ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATAATTACT
Found at i:1123257 original size:21 final size:21
Alignment explanation
Indices: 1123233--1123320 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
1123223 TAATTTCATT
1123233 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
1123254 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
1123275 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
1123293 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
1123314 ATTACTA
1 ATTACTA
1123321 TCAAATCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
17 2 0.04
18 12 0.24
20 6 0.12
21 20 0.40
22 10 0.20
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:1123263 original size:60 final size:60
Alignment explanation
Indices: 1123184--1123373 Score: 337
Period size: 60 Copynumber: 3.2 Consensus size: 60
1123174 ATAAATTATT
* * *
1123184 ATTACT-AATCATTACTATCAAATCCTTAAAAAATAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
1123243 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1123303 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1123363 ATTACTAAATC
1 ATTACTAAATC
1123374 TTAGAAATAC
Statistics
Matches: 125, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
59 6 0.05
60 119 0.95
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:1123388 original size:10 final size:10
Alignment explanation
Indices: 1123375--1123406 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1123365 TACTAAATCT
1123375 TAGAAATACA
1 TAGAAATACA
*
1123385 TAGAAATTCA
1 TAGAAATACA
1123395 TAGAAATACA
1 TAGAAATACA
1123405 TA
1 TA
1123407 TATCATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (10 bp):
TAGAAATACA
Found at i:1127120 original size:28 final size:30
Alignment explanation
Indices: 1127072--1127133 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
1127062 TTTTTTTATA
1127072 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1127102 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1127130 TAAT
1 TAAT
1127134 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1127583 original size:23 final size:23
Alignment explanation
Indices: 1127553--1127596 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1127543 GCTTGGCTAC
1127553 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
1127576 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
1127597 ACGCATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:1127647 original size:26 final size:26
Alignment explanation
Indices: 1127611--1127662 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1127601 ATGCACGAGG
1127611 GAGCAGGGTTAAGTTTGGTCGCCAGC
1 GAGCAGGGTTAAGTTTGGTCGCCAGC
1127637 GAGCAGGGTTAAGTTTGGTCGCCAGC
1 GAGCAGGGTTAAGTTTGGTCGCCAGC
1127663 TTGGTCGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (26 bp):
GAGCAGGGTTAAGTTTGGTCGCCAGC
Found at i:1127769 original size:32 final size:33
Alignment explanation
Indices: 1127708--1127777 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
1127698 GCTGGGAGTA
1127708 CATGGCGACCTGTGTTGGGGTGTTAGGGACGTG
1 CATGGCGACCTGTGTTGGGGTGTTAGGGACGTG
* * *
1127741 CATGGTGACTTGTGTT-GGGTGTTGGGGACGTG
1 CATGGCGACCTGTGTTGGGGTGTTAGGGACGTG
1127773 CATGG
1 CATGG
1127778 AACATGCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.11, C:0.13, G:0.46, T:0.30
Consensus pattern (33 bp):
CATGGCGACCTGTGTTGGGGTGTTAGGGACGTG
Found at i:1128241 original size:20 final size:18
Alignment explanation
Indices: 1128216--1128254 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1128206 ATTACGTGTT
*
1128216 ATTTTATAGTTATAACTATA
1 ATTTTAT-GTCATAA-TATA
1128236 ATTTTATGTCATAATATA
1 ATTTTATGTCATAATATA
1128254 A
1 A
1128255 AGCAGTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTTATGTCATAATATA
Found at i:1130669 original size:23 final size:22
Alignment explanation
Indices: 1130638--1130709 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
1130628 TCTACGCAGT
1130638 CATTCGGGACAATTCTATGTGGA
1 CATT-GGGACAATTCTATGTGGA
* * * *
1130661 CTTTTGGGATAATTCTACGTGGT
1 C-ATTGGGACAATTCTATGTGGA
*
1130684 CATTGTGGACAAATCTATGTGG-
1 CATTG-GGACAATTCTATGTGGA
1130706 CATT
1 CATT
1130710 TCGGTGCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 7 0.18
23 30 0.77
24 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (22 bp):
CATTGGGACAATTCTATGTGGA
Found at i:1130750 original size:24 final size:24
Alignment explanation
Indices: 1130702--1130755 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1130692 ACAAATCTAT
* * *
1130702 GTGGCATTTCGGTGCATATTCTAC
1 GTGGCACTTCGGTGCAAATTATAC
1130726 GTGGCACTTCGGTGCAAATTATAC
1 GTGGCACTTCGGTGCAAATTATAC
*
1130750 GCGGCA
1 GTGGCA
1130756 GTTTCGACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (24 bp):
GTGGCACTTCGGTGCAAATTATAC
Found at i:1135648 original size:11 final size:11
Alignment explanation
Indices: 1135632--1135661 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1135622 TGTAACATCC
1135632 CCGACCCGTAT
1 CCGACCCGTAT
1135643 CCGACCCGTAT
1 CCGACCCGTAT
1135654 CCGACCCG
1 CCGACCCG
1135662 GATTCGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (11 bp):
CCGACCCGTAT
Found at i:1136384 original size:22 final size:21
Alignment explanation
Indices: 1136359--1136402 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1136349 CCGAAGTTCA
1136359 ACATATAATATCCCGAAGGACC
1 ACATA-AATATCCCGAAGGACC
* *
1136381 ACATAGATGTCCCGAAGGACC
1 ACATAAATATCCCGAAGGACC
1136402 A
1 A
1136403 TGTAGAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
ACATAAATATCCCGAAGGACC
Found at i:1136395 original size:21 final size:23
Alignment explanation
Indices: 1136369--1136423 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 23
1136359 ACATATAATA
1136369 TCCCGAAGGACCACATAG-A-TG
1 TCCCGAAGGACCACATAGAATTG
**
1136390 TCCCGAAGGACCATGTAGAATTG
1 TCCCGAAGGACCACATAGAATTG
1136413 TCCCGAAGGAC
1 TCCCGAAGGAC
1136424 TGCGTAGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.53
22 1 0.03
23 13 0.43
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGAATTG
Found at i:1136430 original size:23 final size:23
Alignment explanation
Indices: 1136369--1136432 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
1136359 ACATATAATA
*
1136369 TCCCGAAGGACCACATAG-A-TG
1 TCCCGAAGGACCACGTAGAATTG
*
1136390 TCCCGAAGGACCATGTAGAATTG
1 TCCCGAAGGACCACGTAGAATTG
**
1136413 TCCCGAAGGACTGCGTAGAA
1 TCCCGAAGGACCACGTAGAA
1136433 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 16 0.44
22 1 0.03
23 19 0.53
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (23 bp):
TCCCGAAGGACCACGTAGAATTG
Found at i:1149081 original size:18 final size:18
Alignment explanation
Indices: 1149058--1149114 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 18
1149048 TATATTTTCC
*
1149058 AACAATTGGTATCTTTTT
1 AACAATTGATATCTTTTT
1149076 AACAATTGATATCCTTTTGTT
1 AACAATTGATAT-C-TTT-TT
1149097 AACAATTGATATCTTTTT
1 AACAATTGATATCTTTTT
1149115 CATTAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (18 bp):
AACAATTGATATCTTTTT
Found at i:1149366 original size:20 final size:20
Alignment explanation
Indices: 1149341--1149404 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
1149331 TGAACATTAA
*
1149341 TGAACAGTACCAATATTGTG
1 TGAACAGTACCAATACTGTG
* *
1149361 TGAACAGTATCGATACTGTG
1 TGAACAGTACCAATACTGTG
* * *
1149381 TGAACAATATCGATACTGTG
1 TGAACAGTACCAATACTGTG
1149401 TGAA
1 TGAA
1149405 TGGTGATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (20 bp):
TGAACAGTACCAATACTGTG
Found at i:1150619 original size:22 final size:24
Alignment explanation
Indices: 1150576--1150630 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 24
1150566 TCTAATTACT
1150576 TAATATGTATATCAAAACATATTA-A
1 TAATATGTATATC--AACATATTATA
1150601 CTAATATGTATATC-A-ATATTATA
1 -TAATATGTATATCAACATATTATA
1150624 TAATATG
1 TAATATG
1150631 AAAACCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 13 0.46
23 2 0.07
26 13 0.46
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (24 bp):
TAATATGTATATCAACATATTATA
Found at i:1155985 original size:18 final size:18
Alignment explanation
Indices: 1155962--1156006 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1155952 ATTATTGTTT
1155962 AATATAAAAATTATTTAA
1 AATATAAAAATTATTTAA
1155980 AATATAAAAATTATTTAA
1 AATATAAAAATTATTTAA
1155998 AATATAAAA
1 AATATAAAA
1156007 TAAAAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAAAAATTATTTAA
Found at i:1156549 original size:15 final size:16
Alignment explanation
Indices: 1156529--1156561 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1156519 ATATCACTTT
1156529 ATTATTTTAT-TTTTA
1 ATTATTTTATATTTTA
1156544 ATTATTTTATATTTTA
1 ATTATTTTATATTTTA
1156560 AT
1 AT
1156562 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATTTTATATTTTA
Found at i:1162177 original size:3 final size:3
Alignment explanation
Indices: 1162169--1162228 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
1162159 GGCCTGTTTG
**
1162169 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
1162214 TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA
1162229 AAAATGGGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1176178 original size:20 final size:18
Alignment explanation
Indices: 1176133--1176169 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1176123 AATTCTCACG
*
1176133 CTTGTTATTGATATAATA
1 CTTGTTATTGAGATAATA
*
1176151 CTTGTTATTGAGATGATA
1 CTTGTTATTGAGATAATA
1176169 C
1 C
1176170 ATATGTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (18 bp):
CTTGTTATTGAGATAATA
Found at i:1176537 original size:33 final size:33
Alignment explanation
Indices: 1176500--1176567 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1176490 ATATATATGA
* *
1176500 AATCATTA-AAAAATAATTTAATATTCAAATTAT
1 AATCATAAGAAAAAT-ATTTAAAATTCAAATTAT
1176533 AATCATAAGAAAAATATTTAAAATTCAAATTAT
1 AATCATAAGAAAAATATTTAAAATTCAAATTAT
1176566 AA
1 AA
1176568 ATTTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (33 bp):
AATCATAAGAAAAATATTTAAAATTCAAATTAT
Found at i:1178602 original size:16 final size:16
Alignment explanation
Indices: 1178581--1178611 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1178571 TAATAAATAA
1178581 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1178597 ACGAACATAAACGAA
1 ACGAACATAAACGAA
1178612 ATTTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1181479 original size:22 final size:21
Alignment explanation
Indices: 1181437--1181479 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1181427 AATTGTTTTG
** *
1181437 AATTCAATTTTTTTTCCTTAA
1 AATTCAAAGTTTTTTCATTAA
1181458 AATTCAAAGTTTTTTCTATTAA
1 AATTCAAAGTTTTTTC-ATTAA
1181480 TATATGTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTCAAAGTTTTTTCATTAA
Found at i:1181518 original size:18 final size:18
Alignment explanation
Indices: 1181495--1181533 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1181485 GTATGTGCCC
1181495 ATCCTAAAATTTTATCGT
1 ATCCTAAAATTTTATCGT
1181513 ATCCTAAAATTTTATCGT
1 ATCCTAAAATTTTATCGT
1181531 ATC
1 ATC
1181534 TATTTATAAA
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:0.18, G:0.05, T:0.44
Consensus pattern (18 bp):
ATCCTAAAATTTTATCGT
Found at i:1184650 original size:23 final size:23
Alignment explanation
Indices: 1184624--1184672 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1184614 TTATTATAAA
*
1184624 ATATAT-TTTATTTGTATTTTATT
1 ATATATATTTA-TTATATTTTATT
*
1184647 ATATTTATTTATTATATTTTATT
1 ATATATATTTATTATATTTTATT
1184670 ATA
1 ATA
1184673 GTTTAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATATATATTTATTATATTTTATT
Found at i:1184667 original size:10 final size:10
Alignment explanation
Indices: 1184625--1184677 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
1184615 TATTATAAAA
1184625 TATATTTTATT
1 TATATTTTA-T
*
1184636 TGTATTTTAT
1 TATATTTTAT
1184646 TATATTTATTTAT
1 TATA--T-TTTAT
1184659 TATATTTTAT
1 TATATTTTAT
*
1184669 TATAGTTTA
1 TATATTTTA
1184678 AATTGATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 17 0.47
11 9 0.25
12 1 0.03
13 9 0.25
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1184671 original size:13 final size:13
Alignment explanation
Indices: 1184641--1184665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184631 TTATTTGTAT
1184641 TTTATTATATTTA
1 TTTATTATATTTA
1184654 TTTATTATATTT
1 TTTATTATATTT
1184666 TATTATAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTATATTTA
Found at i:1184686 original size:23 final size:22
Alignment explanation
Indices: 1184625--1184733 Score: 61
Period size: 23 Copynumber: 4.9 Consensus size: 22
1184615 TATTATAAAA
* *
1184625 TATATTT-TATTTGTATTTTAT
1 TATATTTATAATTATATTTTAT
*
1184646 TATATTTATTTATTATATTTTAT
1 TATATTTA-TAATTATATTTTAT
1184669 TATAGTTTA-AATTGATATATTTCA-
1 TATA-TTTATAATT-ATAT-TTT-AT
*
1184693 TATA-TAATAA-TAT-TTTTAAAT
1 TATATTTATAATTATATTTT--AT
1184714 T-TATTTATAATATATATTTT
1 TATATTTATAAT-TATATTTT
1184734 TATTTTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 23
0.69 0.07 0.23
Matches are distributed among these distances:
19 3 0.04
20 4 0.06
21 15 0.22
22 6 0.09
23 24 0.35
24 15 0.22
25 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (22 bp):
TATATTTATAATTATATTTTAT
Found at i:1184715 original size:25 final size:25
Alignment explanation
Indices: 1184687--1184735 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1184677 AAATTGATAT
1184687 ATTTCATATATAATA-ATATTTTTAA
1 ATTT-ATATATAATATATATTTTTAA
*
1184712 ATTTATTTATAATATATATTTTTA
1 ATTTATATATAATATATATTTTTA
1184736 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTATATATAATATATATTTTTAA
Found at i:1189379 original size:24 final size:24
Alignment explanation
Indices: 1189347--1189394 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1189337 CAATCATTTT
1189347 TAAGGTAAGATTGGTGTAGCACCC
1 TAAGGTAAGATTGGTGTAGCACCC
1189371 TAAGGTAAGATTGGTGTAGCACCC
1 TAAGGTAAGATTGGTGTAGCACCC
1189395 AAATTCGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (24 bp):
TAAGGTAAGATTGGTGTAGCACCC
Found at i:1190458 original size:22 final size:20
Alignment explanation
Indices: 1190426--1190487 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1190416 TTTGTAAAAA
1190426 TTCCTT-GGTATCGATACCC
1 TTCCTTGGGTATCGATACCC
* *
1190445 TTTTCTTGGGGTATTGATACTCC
1 -TTCCTT-GGGTATCGATAC-CC
1190468 -TCCTTGGGTATCGATACCC
1 TTCCTTGGGTATCGATACCC
1190487 T
1 T
1190488 GATGAACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.06
20 16 0.47
21 4 0.12
22 10 0.29
23 2 0.06
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (20 bp):
TTCCTTGGGTATCGATACCC
Found at i:1195427 original size:32 final size:32
Alignment explanation
Indices: 1195353--1195487 Score: 227
Period size: 32 Copynumber: 4.2 Consensus size: 32
1195343 AAGTTAGCGG
* *
1195353 GTTAGTTTGAACAATAAAATAAAATGTTAGTAA
1 GTTAGTATGAACAATAAAATAAAA-GTTAGTAT
*
1195386 GTTAGTATGAACAATAAAATAAAAGTGAGTAT
1 GTTAGTATGAACAATAAAATAAAAGTTAGTAT
1195418 GTTAGTATGAACAATAAAATAAAAGTTAGTAT
1 GTTAGTATGAACAATAAAATAAAAGTTAGTAT
1195450 GTTAGTATGAACAATAAAATAAAAGTTAGTAT
1 GTTAGTATGAACAATAAAATAAAAGTTAGTAT
1195482 G-TAGTA
1 GTTAGTA
1195488 GTTAATATAA
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 5 0.05
32 70 0.71
33 23 0.23
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (32 bp):
GTTAGTATGAACAATAAAATAAAAGTTAGTAT
Done.