Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1175338 original size:20 final size:20
Alignment explanation
Indices: 1175290--1175348 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1175280 AATAGTTTCT
** *
1175290 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1175310 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1175330 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1175349 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1175647 original size:22 final size:22
Alignment explanation
Indices: 1175620--1175662 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1175610 TGGGAGATAG
1175620 ACGGATTTCGCCGGAGATGGGA
1 ACGGATTTCGCCGGAGATGGGA
*
1175642 ACGGATTTCGTCGGAGATGGG
1 ACGGATTTCGCCGGAGATGGG
1175663 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (22 bp):
ACGGATTTCGCCGGAGATGGGA
Found at i:1175877 original size:20 final size:20
Alignment explanation
Indices: 1175849--1176003 Score: 161
Period size: 20 Copynumber: 7.7 Consensus size: 20
1175839 GATTATGTAT
*
1175849 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1175869 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
1175889 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1175909 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
1175930 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1175950 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
1175971 TATCGCGTTGCGATAGTCAA
1 TATCGCGTTGCGAAAGTCAG
*
1175991 TATCGCATTGCGA
1 TATCGCGTTGCGA
1176004 TTTTCCCAAT
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
19 5 0.04
20 77 0.68
21 28 0.25
22 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1175995 original size:61 final size:61
Alignment explanation
Indices: 1175829--1176003 Score: 203
Period size: 61 Copynumber: 2.9 Consensus size: 61
1175819 CACTTTGAAA
* * * *
1175829 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAATATCGCGTTGCGAAAGTAAGT
* * * * *
1175890 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGT-ATTATCGCGTTGCGA--TAGTCAATATCGCGTTGCGAAAGTAAGT
* *
1175951 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAATATCGCATTGCGA
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAATATCGCGTTGCGA
1176004 TTTTCCCAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
59 3 0.03
60 16 0.17
61 57 0.61
62 16 0.17
63 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (61 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAATATCGCGTTGCGAAAGTAAGT
Found at i:1176004 original size:20 final size:19
Alignment explanation
Indices: 1175829--1176004 Score: 136
Period size: 20 Copynumber: 8.7 Consensus size: 19
1175819 CACTTTGAAA
* *
1175829 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTAGT
* *
1175850 ATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
1175870 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGT-AGT
*
1175890 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
* *
1175910 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGT
*
1175931 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
* *
1175951 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGT
*
1175972 ATCGCGTTGCGATAGTCAAT
1 ATCGCGTTGCGATAGT-AGT
*
1175992 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1176005 TTTCCCAATT
Statistics
Matches: 129, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.05
20 80 0.62
21 38 0.29
22 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAGT
Found at i:1176022 original size:41 final size:41
Alignment explanation
Indices: 1175829--1176007 Score: 254
Period size: 41 Copynumber: 4.4 Consensus size: 41
1175819 CACTTTGAAA
* * *
1175829 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
** *
1175870 ATCGCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
1175910 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
1175951 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAAT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1175992 ATCGCATTGCGATTTT
1 ATCGCGTTGCGATTTT
1176008 CCCAATTCGC
Statistics
Matches: 125, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 33 0.26
41 87 0.70
42 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1176047 original size:21 final size:21
Alignment explanation
Indices: 1175988--1176047 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
1175978 TTGCGATAGT
* *
1175988 CAATATCGCATTGCGATTTTCC
1 CAAT-TCGCATTGCGAATTTAC
*
1176010 CAATTCGCGTTGC-AATTTAC
1 CAATTCGCATTGCGAATTTAC
**
1176030 TTATTCGCATTGCGAATT
1 CAATTCGCATTGCGAATT
1176048 GGGAAAATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 15 0.48
21 12 0.39
22 4 0.13
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
CAATTCGCATTGCGAATTTAC
Found at i:1176086 original size:21 final size:22
Alignment explanation
Indices: 1176034--1176086 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1176024 ATTTACTTAT
1176034 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
1176055 TCACAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1176076 TCGCATTGCGA
1 TCGCATTGCGA
1176087 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1177162 original size:14 final size:15
Alignment explanation
Indices: 1177051--1177168 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
1177041 TAATAAGGTT
1177051 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1177066 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1177081 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1177096 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1177111 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1177130 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1177148 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1177162 ATTTATT
1 ATTTATT
1177169 AGTATGGATT
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.13
15 58 0.64
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1177186 original size:32 final size:33
Alignment explanation
Indices: 1177148--1177791 Score: 266
Period size: 32 Copynumber: 17.4 Consensus size: 33
1177138 TTTTAAAATA
1177148 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
* ** * *
1177180 ATTTATTTTAAAATATGGATTTATTTA-TTTTAAATA
1 ATTTATTTT-AAATA---ATTTATTTAGTATGGATTG
* * *
1177216 ATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATT--T-T-AAATAATTTA-TTT--AGTATGGATTG
1177256 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
1177288 ATTTATTTTAAAATGTGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTT-AAA--T--A---A--T-TTATT-TA---GTATGGATTG
1177336 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
* * * ** * *
1177368 ATTTATTATAAAATATAGATTGATTTA-TTTTAAATA
1 ATTTATT-T-TAA-ATA-ATTTATTTAGTATGGATTG
* * *
1177404 ATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATT--T-T-AAATAATTTA-TTT--AGTATGGATTG
1177444 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
*
1177476 ATTTATTTTAAAATATGGATTGATTTATTACTGTAGTTGTATGTATTG
1 ATTTATTTT--AA-AT--A---ATTTA-T--T-TA---GTATGGATTG
1177524 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
*
1177556 ATTTATTTTAAAATATGGATTGATTTATTACTGTAGTTGTATGTATTG
1 ATTTATTTT--AA-AT--A---ATTTA-T--T-TA---GTATGGATTG
*
1177604 ATTTATTTTAAATAATTTA-TTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
*
1177636 ATTTATTTTAAATAATTTA-TTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
1177668 ATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTT--AA-AT--A---A--T-TTATT-TA---GTATGGATTG
*
1177716 ATTTATTTTAAATAATTTA-TTAGTATGTATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
1177748 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTTAGTATGGATTG
1177780 ATTTATTTTAAA
1 ATTTATTTTAAA
1177792 ATATGGATTG
Statistics
Matches: 480, Mismatches: 45, Indels: 174
0.69 0.06 0.25
Matches are distributed among these distances:
32 182 0.38
33 9 0.02
34 12 0.03
35 18 0.04
36 60 0.12
37 27 0.06
38 7 0.01
39 6 0.01
40 46 0.10
42 2 0.00
43 10 0.02
44 4 0.01
45 15 0.03
46 6 0.01
47 3 0.01
48 73 0.15
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (33 bp):
ATTTATTTTAAATAATTTATTTAGTATGGATTG
Found at i:1177187 original size:22 final size:22
Alignment explanation
Indices: 1177171--1177213 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177161 AATTTATTAG
1177171 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1177193 TATGGATTTATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1177214 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1177206 original size:69 final size:67
Alignment explanation
Indices: 1177066--1177248 Score: 208
Period size: 69 Copynumber: 2.7 Consensus size: 67
1177056 TTTTAAAATA
1177066 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1177131 TG
66 TG
* ** * * * *
1177133 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATG
*
1177197 GATTT
63 GATTG
* *
1177202 ATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATA
1177249 TGGATTGATT
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
66 13 0.14
67 22 0.23
68 13 0.14
69 34 0.36
70 2 0.02
72 10 0.11
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:1177213 original size:54 final size:54
Alignment explanation
Indices: 1177148--1177819 Score: 412
Period size: 54 Copynumber: 12.3 Consensus size: 54
1177138 TTTTAAAATA
*
1177148 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1177202 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1177256 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
1177310 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * * **
1177354 ATTAGTATGGATTGATTTA-TTATAAAATATAGATTGATTTATTTT-AAATAATTTATT-
1 ATT--TAT--TTTAAATAATTTAT-TAGTATGGATTGATTTATTTTAAAAT-ATGGATTG
* * * ** * * * **
1177411 AGTATGAATTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 A-T-TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * *** *
1177467 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTACTGTAGTTGTATGTATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT--T-TA-AAATATGGATTG
1177524 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
** * * * * * *
1177578 ATTTA--TTACTGTAGTTGTA-T-GTATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTA-AATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTG
*
1177636 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1177690 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
1177748 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1177802 ATTTATTTTAAATAATTT
1 ATTTATTTTAAATAATTT
1177820 TTTATTGTAG
Statistics
Matches: 501, Mismatches: 57, Indels: 120
0.74 0.08 0.18
Matches are distributed among these distances:
44 6 0.01
46 2 0.00
47 4 0.01
48 43 0.09
49 6 0.01
50 8 0.02
52 20 0.04
53 11 0.02
54 246 0.49
55 15 0.03
56 9 0.02
57 21 0.04
58 53 0.11
59 11 0.02
60 16 0.03
62 4 0.01
63 4 0.01
64 22 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1177250 original size:22 final size:22
Alignment explanation
Indices: 1177225--1177267 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177215 AATTTATTAG
1177225 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1177247 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1177268 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1177346 original size:80 final size:80
Alignment explanation
Indices: 1177247--1177396 Score: 273
Period size: 80 Copynumber: 1.9 Consensus size: 80
1177237 TATTTTAAAA
* * *
1177247 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATGTGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATAAAATATAGATTGAT
1177312 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
1177327 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATAAAATATAGATTGAT
1177392 TTATT
66 TTATT
1177397 TTAAATAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:1177348 original size:188 final size:188
Alignment explanation
Indices: 1177148--1177759 Score: 977
Period size: 188 Copynumber: 3.2 Consensus size: 188
1177138 TTTTAAAATA
*
1177148 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTTATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1177213 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
*
1177278 GTATGGATTGATTTATTTTAAAATGTGGATTGATTTATTATTGTAGTTGTATGGATTG
131 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
* *
1177336 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATAAAATATAGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1177401 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
* *
1177466 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTACTGTAGTTGTATGTATTG
131 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1177524 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA---T--
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* * *
1177584 -TACTGTAGTT-GTATGTATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAA
66 ATAATTTA-TTAGTATGAATTGATTTATTTT-AA-AA--TA-T-G---G-ATTGATTTATTTTAA
*
1177647 ATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
120 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
1177712 ATTG
185 ATTG
*
1177716 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1177760 TAATTTATTA
Statistics
Matches: 398, Mismatches: 15, Indels: 18
0.92 0.03 0.04
Matches are distributed among these distances:
182 23 0.06
183 4 0.01
184 2 0.01
185 1 0.00
186 2 0.01
187 1 0.00
188 240 0.60
191 1 0.00
192 124 0.31
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (188 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
Found at i:1177438 original size:22 final size:22
Alignment explanation
Indices: 1177413--1177455 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177403 AATTTATTAG
1177413 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1177435 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1177456 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1177481 original size:18 final size:18
Alignment explanation
Indices: 1177458--1177505 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1177448 ATTTTAAATA
*
1177458 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1177476 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1177498 ATTTATTA
1 ATTTATTA
1177506 CTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1177518 original size:26 final size:25
Alignment explanation
Indices: 1177489--1177610 Score: 79
Period size: 26 Copynumber: 4.6 Consensus size: 25
1177479 TATTTTAAAA
1177489 TATGGATTGATTTATTACTGTAGTTG
1 TATGGATTGATTTATTACTGTA-TTG
* * *
1177515 TATGTATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTA---T---TACTGTATT-G
***
1177547 TATGGATTGATTTATT--T-TAAAA
1 TATGGATTGATTTATTACTGTATTG
1177569 TATGGATTGATTTATTACTGTAGTTG
1 TATGGATTGATTTATTACTGTA-TTG
*
1177595 TATGTATTGATTTATT
1 TATGGATTGATTTATT
1177611 TTAAATAATT
Statistics
Matches: 74, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
22 16 0.22
23 2 0.03
24 2 0.03
25 2 0.03
26 29 0.39
29 2 0.03
31 2 0.03
32 19 0.26
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (25 bp):
TATGGATTGATTTATTACTGTATTG
Found at i:1177547 original size:80 final size:80
Alignment explanation
Indices: 1177435--1177647 Score: 408
Period size: 80 Copynumber: 2.7 Consensus size: 80
1177425 TATTTTAAAA
*
1177435 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1177500 TTATTACTGTAGTTG
66 TTATTACTGTAGTTG
1177515 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1177580 TTATTACTGTAGTTG
66 TTATTACTGTAGTTG
*
1177595 TATGTATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1177648 TAATTTATTA
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 131 1.00
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTACTGTAGTTG
Found at i:1177561 original size:18 final size:18
Alignment explanation
Indices: 1177538--1177585 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1177528 ATTTTAAATA
*
1177538 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1177556 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1177578 ATTTATTA
1 ATTTATTA
1177586 CTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1177623 original size:14 final size:14
Alignment explanation
Indices: 1177604--1177656 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1177594 GTATGTATTG
1177604 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1177618 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1177636 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1177650 ATTTATT
1 ATTTATT
1177657 AGTATAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1177636 original size:112 final size:112
Alignment explanation
Indices: 1177514--1177808 Score: 554
Period size: 112 Copynumber: 2.6 Consensus size: 112
1177504 TACTGTAGTT
1177514 GTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
*
1177579 TTTATTACTGTAGTTGTATGTATTGATTTATTTTAAATAATTTATTA
66 TTTATTACTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
* *
1177626 GTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGA
1 GTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
*
1177691 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
66 TTTATTACTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
1177738 GTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1177803 TTTATT
66 TTTATT
1177809 TTAAATAATT
Statistics
Matches: 177, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 177 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (112 bp):
GTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
TTTATTACTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1177641 original size:18 final size:17
Alignment explanation
Indices: 1177618--1177674 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1177608 ATTTTAAATA
1177618 ATTTATTAGTATGAATTG
1 ATTTATTAGTAT-AATTG
* *
1177636 ATTTATT--T-TAAATA
1 ATTTATTAGTATAATTG
1177650 ATTTATTAGTATAGATTG
1 ATTTATTAGTATA-ATTG
1177668 ATTTATT
1 ATTTATT
1177675 TTAAAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 2 0.06
17 2 0.06
18 16 0.52
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (17 bp):
ATTTATTAGTATAATTG
Found at i:1177787 original size:22 final size:22
Alignment explanation
Indices: 1177771--1177813 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177761 AATTTATTAG
1177771 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1177793 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1177814 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1177872 original size:31 final size:31
Alignment explanation
Indices: 1177837--1177896 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1177827 TAGTTGTATG
* *
1177837 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
1177868 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
1177897 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:1179007 original size:31 final size:31
Alignment explanation
Indices: 1178969--1179058 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 31
1178959 AAGGGAGCAA
1178969 CTCGGGGCCTGC-GAGCCTACCCAAGACAATT
1 CTCGGGGCC-GCAGAGCCTACCCAAGACAATT
* * * *
1179000 CTTGGGGCCACTA-AGACTTACCCAAGAAAATT
1 CTCGGGGCCGC-AGAG-CCTACCCAAGACAATT
*
1179032 CTCAGGGCCGCAGAGCCTACCCAAGAC
1 CTCGGGGCCGCAGAGCCTACCCAAGAC
1179059 TCGACTTAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
30 1 0.02
31 21 0.46
32 24 0.52
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (31 bp):
CTCGGGGCCGCAGAGCCTACCCAAGACAATT
Found at i:1179992 original size:29 final size:28
Alignment explanation
Indices: 1179931--1180114 Score: 323
Period size: 29 Copynumber: 6.4 Consensus size: 28
1179921 GCACCTTAAC
*
1179931 AAAAATTAATTACGAAACTAACACCTTTT
1 AAAAA-TATTTACGAAACTAACACCTTTT
1179960 AAAAATATTTACGAAACTAACACCTTTT
1 AAAAATATTTACGAAACTAACACCTTTT
1179988 AAAAATATTTACGAAACTAACACCCTTTT
1 AAAAATATTTACGAAACTAACA-CCTTTT
1180017 AAAAATATTTACGAAACTAACACCTTTT
1 AAAAATATTTACGAAACTAACACCTTTT
1180045 AAAAATATTTACGAAACTAACACCCTTTT
1 AAAAATATTTACGAAACTAACA-CCTTTT
1180074 AAAAATATTTACGAAACTAACATCCTTTT
1 AAAAATATTTACGAAACTAACA-CCTTTT
1180103 AAAAATATTTAC
1 AAAAATATTTAC
1180115 AAAAATAGCA
Statistics
Matches: 151, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
28 72 0.48
29 79 0.52
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATATTTACGAAACTAACACCTTTT
Found at i:1180020 original size:57 final size:57
Alignment explanation
Indices: 1179931--1180114 Score: 334
Period size: 57 Copynumber: 3.2 Consensus size: 57
1179921 GCACCTTAAC
*
1179931 AAAAATTAATTACGAAACTAACA-CCTTTTAAAAATATTTACGAAACTAACACCTTTT
1 AAAAA-TATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCTTTT
1179988 AAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCTTTT
1180045 AAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACATCCTTTT
1 AAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACA-CCTTTT
1180103 AAAAATATTTAC
1 AAAAATATTTAC
1180115 AAAAATAGCA
Statistics
Matches: 124, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
56 16 0.13
57 90 0.73
58 18 0.15
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (57 bp):
AAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCTTTT
Found at i:1180144 original size:58 final size:56
Alignment explanation
Indices: 1179959--1180300 Score: 233
Period size: 58 Copynumber: 5.9 Consensus size: 56
1179949 TAACACCTTT
* * * * ***
1179959 TAAAAATATTTACGAAACTA-ACACCTTTTAAAAATATTTACGAAACTAACACCCTTT
1 TAAAATTAATTACG-AACTAGACACCTTTTAAAAATATTTACAAAAATAACA-CCGAA
* * * * ***
1180016 TAAAAATATTTACGAAACTA-ACACCTTTTAAAAATATTTACGAAACTAACACCCTTT
1 TAAAATTAATTACG-AACTAGACACCTTTTAAAAATATTTACAAAAATAACA-CCGAA
* * *
1180073 TAAAAATATTTACGAAACTA-ACATCCTTTTAAAAATATTTACAAAAATAGCACCGAA
1 TAAAATTAATTACG-AACTAGACA-CCTTTTAAAAATATTTACAAAAATAACACCGAA
* * * * * *
1180130 CAGAAATTAATTACGTATTAGGC-CTCTTTTAAAAAATATTTATAAAAATAGCACCGAA
1 TA-AAATTAATTACGAACTAGACAC-CTTTT-AAAAATATTTACAAAAATAACACCGAA
* * * * * * *
1180188 TAGAAATTAATTATGTATTAGGCACTATTTTAAAAATATTTACAAAAATATCAACGAA
1 TA-AAATTAATTACGAACTAGACAC-CTTTTAAAAATATTTACAAAAATAACACCGAA
* * * *
1180246 CATAAATTAATTACGTATTAGACACTCTTTTAAAAATATTTACAAAAATATCACC
1 TA-AAATTAATTACGAACTAGACAC-CTTTTAAAAATATTTACAAAAATAACACC
1180301 CGAGTTGTTT
Statistics
Matches: 254, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
56 1 0.00
57 91 0.36
58 156 0.61
59 6 0.02
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (56 bp):
TAAAATTAATTACGAACTAGACACCTTTTAAAAATATTTACAAAAATAACACCGAA
Found at i:1180164 original size:86 final size:86
Alignment explanation
Indices: 1179960--1180144 Score: 255
Period size: 86 Copynumber: 2.2 Consensus size: 86
1179950 AACACCTTTT
*
1179960 AAAAATATTTACGAAACTAACA-CCTTTTAAAAATATTTACGAAACTAACACCCTTTTAAAAATA
1 AAAAATAATTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCCTTTTAAAAATA
* * ****
1180024 TTTACGAAACTAACACCTTTT
66 TTTACAAAAATAACACCGAAC
* *
1180045 AAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACATCCTTTTAAAAATA
1 AAAAATAATTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCCTTTTAAAAATA
*
1180110 TTTACAAAAATAGCACCGAAC
66 TTTACAAAAATAACACCGAAC
*
1180131 AGAAATTAATTACG
1 A-AAAATAATTACG
1180145 TATTAGGCCT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 22 0.25
86 56 0.64
87 10 0.11
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (86 bp):
AAAAATAATTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCCTTTTAAAAATA
TTTACAAAAATAACACCGAAC
Found at i:1180879 original size:53 final size:53
Alignment explanation
Indices: 1180815--1180920 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
1180805 TTATGGCCCT
* * * *
1180815 GTGATTCATCCATTGT-TTACCACAAACATTTTTTTAATGTTTTAAAACC-CATG
1 GTGATTAATCCATTATCTT-CCACAAACATTTTTTAAAT-ATTTAAAACCTCATG
*
1180868 GTGATTAATCCATTATCTTCCACTAACATTTTTTAAATATTTAAAACCTCATG
1 GTGATTAATCCATTATCTTCCACAAACATTTTTTAAATATTTAAAACCTCATG
1180921 CCCCATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 9 0.20
53 35 0.76
54 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (53 bp):
GTGATTAATCCATTATCTTCCACAAACATTTTTTAAATATTTAAAACCTCATG
Found at i:1182820 original size:25 final size:24
Alignment explanation
Indices: 1182764--1182820 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1182754 TTCAGGTAAA
*
1182764 CATACTTCATAAACCAGTAAATTC
1 CATATTTCATAAACCAGTAAATTC
*
1182788 CATGATTTCATAAATCATGTACAATT-
1 CAT-ATTTCATAAACCA-GTA-AATTC
1182814 CATATTT
1 CATATTT
1182821 TTCGATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 15 0.54
26 6 0.21
27 4 0.14
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (24 bp):
CATATTTCATAAACCAGTAAATTC
Found at i:1185422 original size:22 final size:23
Alignment explanation
Indices: 1185384--1185434 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
1185374 CAACAGTCAA
* *
1185384 CGGGTCATGTCAACGGGTCGGGT
1 CGGGTCAAGTCAACGGGTCGAGT
1185407 CGGGTCAAG-CAACGGGTCGAGT
1 CGGGTCAAGTCAACGGGTCGAGT
1185429 CGGGTC
1 CGGGTC
1185435 GTGTCAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.18
Consensus pattern (23 bp):
CGGGTCAAGTCAACGGGTCGAGT
Found at i:1185999 original size:8 final size:9
Alignment explanation
Indices: 1185972--1186000 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1185962 GTTGACTGAT
1185972 AAGAGGAAA
1 AAGAGGAAA
1185981 AAGAGGAAA
1 AAGAGGAAA
1185990 AAGAGGAAA
1 AAGAGGAAA
1185999 AA
1 AA
1186001 TTCTGCAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (9 bp):
AAGAGGAAA
Found at i:1187595 original size:12 final size:12
Alignment explanation
Indices: 1187570--1187638 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
1187560 ATGGAGATAT
*
1187570 CAGAAATCAAAA
1 CAGAATTCAAAA
*
1187582 CAGAATTCAGAA
1 CAGAATTCAAAA
*
1187594 CAG-ATGTCAGAA
1 CAGAAT-TCAAAA
* *
1187606 CAGAATCCAAAT
1 CAGAATTCAAAA
*
1187618 CAGAAATCAAAA
1 CAGAATTCAAAA
1187630 CAGAATTCA
1 CAGAATTCA
1187639 TGTCATGTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.54, C:0.19, G:0.13, T:0.14
Consensus pattern (12 bp):
CAGAATTCAAAA
Found at i:1187607 original size:24 final size:24
Alignment explanation
Indices: 1187568--1187638 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
1187558 AAATGGAGAT
1187568 ATCAGAAATCAAAACAGAATTCAGA
1 ATCAGAAATCAAAACAGAATTCA-A
** * *
1187593 A-CAGATGTCAGAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAA
1187616 ATCAGAAATCAAAACAGAATTCA
1 ATCAGAAATCAAAACAGAATTCA
1187639 TGTCATGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 2 0.05
24 34 0.92
25 1 0.03
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAA
Found at i:1187674 original size:24 final size:24
Alignment explanation
Indices: 1187569--1187676 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
1187559 AATGGAGATA
*
1187569 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* ** * *
1187592 AACAGATGTCAGAACAGAATCCAAA
1 -TCAGAAATCAGAACAGAATTCAAG
* *
1187617 TCAGAAATCAAAACAGAATTCATG
1 TCAGAAATCAGAACAGAATTCAAG
*
1187641 TCATG-TATCAGAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
1187665 TC-GAAAATCAGA
1 TCAG-AAATCAGA
1187677 TAAAATATTT
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
22 1 0.02
24 60 0.95
25 2 0.03
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:1187674 original size:48 final size:48
Alignment explanation
Indices: 1187568--1187659 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
1187558 AAATGGAGAT
*
1187568 ATCAGAAATCAAAACAGAATTCAGAACAGATGTCAGAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAA
*
1187616 ATCAGAAATCAAAACAGAATTCATG-TCATG-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA-GAACA-GATATCAGAACAGAAT
1187660 TCAAGTCGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
48 38 0.95
49 2 0.05
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAA
Found at i:1192331 original size:12 final size:12
Alignment explanation
Indices: 1192306--1192374 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
1192296 ATGGAGATAT
*
1192306 CAGAAATCAAAA
1 CAGAATTCAAAA
*
1192318 CAGAATTCAGAA
1 CAGAATTCAAAA
*
1192330 CAG-ATGTCAGAA
1 CAGAAT-TCAAAA
* *
1192342 CAGAATCCAAAT
1 CAGAATTCAAAA
*
1192354 CAGAAATCAAAA
1 CAGAATTCAAAA
*
1192366 TAGAATTCA
1 CAGAATTCA
1192375 TGTCATGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAATTCAAAA
Found at i:1192333 original size:24 final size:24
Alignment explanation
Indices: 1192304--1192374 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1192294 AAATGGAGAT
1192304 ATCAGAAATCAAAACAGAATTCAGA
1 ATCAGAAATCAAAACAGAATTCA-A
** * *
1192329 A-CAGATGTCAGAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAA
*
1192352 ATCAGAAATCAAAATAGAATTCA
1 ATCAGAAATCAAAACAGAATTCA
1192375 TGTCATGTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
23 2 0.06
24 33 0.92
25 1 0.03
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAA
Found at i:1198591 original size:24 final size:24
Alignment explanation
Indices: 1198520--1198585 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
1198510 GAGATATATG
*
1198520 AAATCAAAACAGAATTCAGAACAT
1 AAATCAAAACAGAATTCAGATCAT
* * *
1198544 ATATCAAAACAGAATCCGGATCAT
1 AAATCAAAACAGAATTCAGATCAT
*
1198568 AAATCAAAACAAAATTCA
1 AAATCAAAACAGAATTCA
1198586 AGTCATGTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATCAT
Found at i:1200990 original size:16 final size:17
Alignment explanation
Indices: 1200958--1200990 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1200948 GGTCAACTGT
*
1200958 GGTCAACTCCGGTCAAC
1 GGTCAACTCCAGTCAAC
1200975 GGTCAAC-CCAGTCAAC
1 GGTCAACTCCAGTCAAC
1200991 ATTCGACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.36, G:0.21, T:0.15
Consensus pattern (17 bp):
GGTCAACTCCAGTCAAC
Found at i:1203167 original size:15 final size:15
Alignment explanation
Indices: 1203147--1203181 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1203137 CCGTAGGACC
1203147 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
1203162 ACTACGTCTCGAAGG
1 ACTACGTCCCGAAGG
1203177 ACTAC
1 ACTAC
1203182 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:1211639 original size:21 final size:21
Alignment explanation
Indices: 1211584--1211641 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 21
1211574 AAAATGACCA
1211584 ACAAAATCGCAATGCGA-AAT
1 ACAAAATCGCAATGCGATAAT
*
1211604 A-AAAATCGCAATGCGATAGT
1 ACAAAATCGCAATGCGATAAT
* *
1211624 ACAAATTCGCATTGCGAT
1 ACAAAATCGCAATGCGAT
1211642 TTTCCAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.45
20 4 0.12
21 14 0.42
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (21 bp):
ACAAAATCGCAATGCGATAAT
Found at i:1211726 original size:57 final size:57
Alignment explanation
Indices: 1211655--1211769 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
1211645 CCAGAATCGC
1211655 AACGCGAATATGAAAATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAA
1 AACGCGAATATGAAAATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAA
1211712 AACGCGAATATGAAAATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAA
1 AACGCGAATATGAAAATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAA
1211769 A
1 A
1211770 TCGCAACGCG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (57 bp):
AACGCGAATATGAAAATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAA
Found at i:1211792 original size:20 final size:20
Alignment explanation
Indices: 1211725--1211839 Score: 117
Period size: 20 Copynumber: 5.6 Consensus size: 20
1211715 GCGAATATGA
* *
1211725 AAATCGCAACGCG-ATTCTT
1 AAATCGCAACGCGTATCCGT
* *
1211744 ACTATCGCAACGAGTATCCGT
1 A-AATCGCAACGCGTATCCGT
1211765 AAAAATCGCAACGCGTATCCGT
1 --AAATCGCAACGCGTATCCGT
* *
1211787 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
1211807 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1211828 AAATCGCAACGC
1 AAATCGCAACGC
1211840 AATTTTTAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.01
20 39 0.49
21 21 0.27
22 17 0.22
23 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1211823 original size:41 final size:42
Alignment explanation
Indices: 1211724--1211842 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 42
1211714 CGCGAATATG
* * * ** *
1211724 AAAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATCCGTA
1 AAAATCGCAACGCGTATCCGTA-AATCGCAACGACAATACGTA
1211766 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT-
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
1211807 AAAATCGCAACGCGTATCCGTAAATCGCAACG-CAAT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAAT
1211843 TTTTAAAGCG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
40 4 0.06
41 32 0.46
42 29 0.41
43 5 0.07
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (42 bp):
AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
Found at i:1214033 original size:93 final size:92
Alignment explanation
Indices: 1213874--1214065 Score: 305
Period size: 93 Copynumber: 2.1 Consensus size: 92
1213864 CTTAGATGCT
* * *
1213874 AAGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATGTTTATTCTTTAACACTGTGAAGTTAGT
1 AAGTAAATTTATTCGGTTACTGCCAATACTGCTAAATGTGTATTCTTTAACACTGTGAAGATAGT
1213939 ATTTGTCTTTTGTTTTGTCTTTTGGTTG
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTG
* *
1213967 AAGTAAATTTATTCGGTTACTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA-ATAG
1 AAGTAAATTTATTCGGTTACTGCCAATACTGCTAAA-TGTGTATTCTTTAACACTGTGAAGATAG
1214031 TATTTGTCTTTGTTTTGTCTTTTGGTTG
65 TATTTGTCTTTGTTTTGTCTTTTGGTTG
*
1214059 AACTAAA
1 AAGTAAA
1214066 CTGTGTATTC
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
92 26 0.28
93 44 0.48
94 22 0.24
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (92 bp):
AAGTAAATTTATTCGGTTACTGCCAATACTGCTAAATGTGTATTCTTTAACACTGTGAAGATAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTG
Found at i:1214076 original size:63 final size:63
Alignment explanation
Indices: 1213998--1214123 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
1213988 GTCAATTCTG
*
1213998 CTAAACTGTGTATTCTTTAACACTGTGAA-ATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAGATAG-ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1214061 CTAAACTGTGTATTCTTTAATACTCTGAAGTTAGATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAGATAGATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1214124 GTAATGCAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 56 0.95
64 3 0.05
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.50
Consensus pattern (63 bp):
CTAAACTGTGTATTCTTTAACACTCTGAAGATAGATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1214231 original size:19 final size:19
Alignment explanation
Indices: 1214175--1214308 Score: 99
Period size: 19 Copynumber: 7.4 Consensus size: 19
1214165 TATTTTACTT
* *
1214175 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
1214195 TCGCAACGTGAAAAATGACAA
1 TCGCAACGCG--AAATGAAAA
1214216 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1214235 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
1214249 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1214268 TCGCAA--CG--AT-AGAA
1 TCGCAACGCGAAATGAAAA
*
1214282 TCGCAACACGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1214301 TCGCAACG
1 TCGCAACG
1214309 ACAAAATCGC
Statistics
Matches: 89, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
14 19 0.21
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 34 0.38
20 8 0.09
21 13 0.15
22 3 0.03
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1214252 original size:14 final size:14
Alignment explanation
Indices: 1214233--1214288 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1214223 GCGAAATGAA
1214233 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1214247 AATCGCAACGAGAAATG
1 AATCGCAACGAG--A-G
*
1214264 AAAATCGCAACGATAG
1 --AATCGCAACGAGAG
1214280 AATCGCAAC
1 AATCGCAAC
1214289 ACGAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 21 0.58
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1214334 original size:33 final size:33
Alignment explanation
Indices: 1214214--1214327 Score: 183
Period size: 33 Copynumber: 3.5 Consensus size: 33
1214204 GAAAAATGAC
*
1214214 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
1214247 AATCGCAACGAGAAATGAAAATCGCAACGATAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
1214280 AATCGCAACACGAAATGAAAATCGCAACGACAA
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1214313 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
1214328 CCAAAATAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1214706 original size:42 final size:42
Alignment explanation
Indices: 1214655--1214748 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
1214645 CCACTCCTAT
* * *
1214655 CATTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCTCCTCCCAC
1 CATTCAAGAGGCCACTATCA-TCATCGAAGAGGTC-CCTCCCAC
* * *
1214697 CGTTCAAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCAC
1214739 CATTCAAGAG
1 CATTCAAGAG
1214749 CTCGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.09
42 36 0.84
43 3 0.07
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (42 bp):
CATTCAAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCAC
Found at i:1216117 original size:83 final size:83
Alignment explanation
Indices: 1215969--1216145 Score: 320
Period size: 83 Copynumber: 2.1 Consensus size: 83
1215959 GTATGGTTGC
1215969 AAAAGTTGATTCAATAGTAGATGAGAAAATAGAATTAATGCTTATTTTTTGATTGTTTAATTGA-
1 AAAAGTTGATTCAATAGTAGATGAGAAAATAGAATTAATGCTTATTTTTTGATTGTTTAATTGAT
1216033 TTGTAAAAGATGATTTGT
66 TTGTAAAAGATGATTTGT
* *
1216051 AAAAGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGA
1 AAAAGTTGATTCAATAGTAGATGAGAAAAT-AGAATTAATGCTTATTTTTTGATTGTTTAATTGA
1216116 TTTGTAAAAGATGATTTGT
65 TTTGTAAAAGATGATTTGT
1216135 AAAAGTTGATT
1 AAAAGTTGATT
1216146 TGTTTAATTG
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
82 29 0.32
83 33 0.36
84 29 0.32
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (83 bp):
AAAAGTTGATTCAATAGTAGATGAGAAAATAGAATTAATGCTTATTTTTTGATTGTTTAATTGAT
TTGTAAAAGATGATTTGT
Found at i:1216132 original size:14 final size:14
Alignment explanation
Indices: 1216113--1216148 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1216103 ATTGTTTAAT
1216113 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1216127 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1216141 TGATTTGT
1 TGATTTGT
1216149 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:1216327 original size:33 final size:33
Alignment explanation
Indices: 1216285--1216835 Score: 775
Period size: 33 Copynumber: 16.2 Consensus size: 33
1216275 TCGCAACGAG
1216285 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216318 TGCGATTCTCTCGTTGCGA-TTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
*
1216350 TGTGATTCTCTCGTTGCGATTTT-ATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216382 TGCGATTCTCTCGTTGCGA-TTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216414 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
*
1216447 TGCGATAGTCATTTCCGCGTTGCGATTTTCATTTCGCAT
1 TGCGAT--TC---T-CTCGTTGCGATTTTCATTTCGCAT
*
1216486 TGCGATTCTCTCGTTGTGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216519 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216552 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216585 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
*
1216618 TGCGATAGTCATTTCCGCGTTGCGATTTTCATTTCGCAT
1 TGCGAT--TC---T-CTCGTTGCGATTTTCATTTCGCAT
1216657 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216690 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
* * * *
1216723 TGCGATAGTCATTTCCGCGTTGCGATATTAATATTCGCGT
1 TGCGAT--TC---T-CTCGTTGCGATTTTCAT-TTCGCAT
* *
1216763 TGCGATTTTCACGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
* * * *
1216796 TGCGATTCTCTCGTTGCAATTGTAATTTTCGCGT
1 TGCGATTCTCTCGTTGCGATTTTCA-TTTCGCAT
1216830 TGCGAT
1 TGCGAT
1216836 AGTCAAATGA
Statistics
Matches: 472, Mismatches: 23, Indels: 45
0.87 0.04 0.08
Matches are distributed among these distances:
31 3 0.01
32 86 0.18
33 255 0.54
34 29 0.06
35 7 0.01
37 4 0.01
38 4 0.01
39 72 0.15
40 12 0.03
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
Found at i:1216471 original size:20 final size:19
Alignment explanation
Indices: 1216298--1216802 Score: 352
Period size: 19 Copynumber: 29.4 Consensus size: 19
1216288 GATTCTCTCG
1216298 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216317 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216331 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1216349 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216363 TTGCGATTTT-ATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216381 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216395 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216413 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216427 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1216446 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1216466 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216485 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1216499 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216518 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216532 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216551 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216565 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216584 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216598 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1216617 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1216637 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216656 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216670 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1216689 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1216703 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1216722 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
* * *
1216742 TTGCGATATTAATATTCGCG
1 TTGCGATTTTCAT-TTCGCA
1216762 TTGCGATTTTCA---CG--
1 TTGCGATTTTCATTTCGCA
1216776 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1216795 TTGCGATT
1 TTGCGATT
1216803 CTCTCGTTGC
Statistics
Matches: 385, Mismatches: 43, Indels: 116
0.71 0.08 0.21
Matches are distributed among these distances:
14 70 0.18
15 6 0.02
16 79 0.21
17 57 0.15
18 17 0.04
19 94 0.24
20 60 0.16
21 2 0.01
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1216535 original size:105 final size:99
Alignment explanation
Indices: 1216285--1216835 Score: 775
Period size: 105 Copynumber: 5.4 Consensus size: 99
1216275 TCGCAACGAG
1216285 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCA
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
1216349 TTGTGATTCTCTCGTTGCGATTTT-ATTTCGCAT
66 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1216382 TGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
1216446 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTTCGCAT
66 TTGCGAT--TC---T-CTCGTTGCGATTTTCATTTCGCAT
*
1216486 TGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1216551 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
66 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
*
1216585 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATTTTCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CTCGTTGCGATTTTCAT
1216650 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
60 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
* * *
1216690 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATATTAAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CTCGTTGCGATTTTCAT
* * *
1216755 ATTCGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCAT
60 -TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
* * * *
1216796 TGCGATTCTCTCGTTGCAATTGTAATTTTCGCGTTGCGAT
1 TGCGATTCTCTCGTTGCGATTTTCA-TTTCGCATTGCGAT
1216836 AGTCAAATGA
Statistics
Matches: 422, Mismatches: 15, Indels: 24
0.92 0.03 0.05
Matches are distributed among these distances:
96 32 0.08
97 37 0.09
99 63 0.15
100 1 0.00
101 2 0.00
102 1 0.00
103 15 0.04
104 28 0.07
105 171 0.41
106 59 0.14
107 13 0.03
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (99 bp):
TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
Found at i:1216537 original size:14 final size:14
Alignment explanation
Indices: 1216485--1216605 Score: 71
Period size: 14 Copynumber: 7.6 Consensus size: 14
1216475 TCATTTCGCA
1216485 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
* *
1216499 TTGTGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1216516 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1216532 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1216549 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1216565 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1216582 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1216598 TTGCGATT
1 TTGCGATT
1216606 TTCATTTCGC
Statistics
Matches: 84, Mismatches: 8, Indels: 30
0.69 0.07 0.25
Matches are distributed among these distances:
14 25 0.30
16 21 0.25
17 21 0.25
19 17 0.20
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1216609 original size:171 final size:171
Alignment explanation
Indices: 1216296--1216801 Score: 856
Period size: 171 Copynumber: 2.9 Consensus size: 171
1216286 GCGATTCTCT
*
1216296 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGTGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1216360 TCGTTGCGATTTT-ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTCT
66 TCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
1216423 CTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
131 CTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
*
1216464 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1216529 TCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
66 TCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
1216594 CTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
131 CTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1216635 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
* * * *
1216700 TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATATTAATATTCGCGTTG
66 TCGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CTCGTTGCGATTTTCAT-TTCGCATTG
* *
1216765 CGATTTTCACGTTGCGATTTTCATTTCGCATTGCGAT
124 CGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1216802 TCTCTCGTTG
Statistics
Matches: 319, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
168 40 0.13
169 35 0.11
170 28 0.09
171 156 0.49
173 2 0.01
176 1 0.00
177 14 0.04
178 43 0.13
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (171 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
TCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
CTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
Found at i:1216675 original size:14 final size:14
Alignment explanation
Indices: 1216656--1216710 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1216646 TCATTTCGCA
1216656 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1216670 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1216687 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1216703 TTGCGATT
1 TTGCGATT
1216711 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1216779 original size:14 final size:14
Alignment explanation
Indices: 1216760--1216787 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1216750 TTAATATTCG
1216760 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1216774 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1216788 TTTCGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:1219337 original size:24 final size:24
Alignment explanation
Indices: 1219303--1219356 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1219293 CTGAAACATC
1219303 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1219327 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1219351 ATCAAA
1 ATCAAA
1219357 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1219370 original size:24 final size:24
Alignment explanation
Indices: 1219303--1219370 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1219293 CTGAAACATC
* * *
1219303 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1219327 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1219351 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1219371 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1219503 original size:12 final size:12
Alignment explanation
Indices: 1219482--1219515 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1219472 GGTTGTAGGT
*
1219482 TTTGAGATTGTG
1 TTTGATATTGTG
1219494 TTTGATATTGTG
1 TTTGATATTGTG
*
1219506 TTTGGTATTG
1 TTTGATATTG
1219516 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1220202 original size:20 final size:20
Alignment explanation
Indices: 1220177--1220488 Score: 242
Period size: 20 Copynumber: 15.4 Consensus size: 20
1220167 AAATTTAAGT
1220177 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
1220197 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
*
1220217 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACAGATTCTC
1220237 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* * *
1220257 GTTACGATTAAC-GTATTCTG
1 GTTGCGATTTACAG-ATTCTC
* * *
1220277 GTTGCGA-TAATCAGAATCGC
1 GTTGCGATTTA-CAGATTCTC
1220297 GTTGCGATTTTAC-GTATTCTC
1 GTTGCGA-TTTACAG-ATTCTC
** * *
1220318 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACAGATTCTC
1220338 GTTGCGATTTTAC-GTATTCTC
1 GTTGCGA-TTTACAG-ATTCTC
* * *
1220359 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
*
1220379 GTTGCGATTTTAC-GTATTGTC
1 GTTGCGA-TTTACAG-ATTCTC
* * *
1220400 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
* * *
1220420 GTTGCGATAGT-CAGAATCAC
1 GTTGCGAT-TTACAGATTCTC
*
1220440 GTTGCGATTTATATG-TTCTC
1 GTTGCGATTTACA-GATTCTC
* * *
1220460 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACAGATTCTC
1220480 GTTGCGATT
1 GTTGCGATT
1220489 CTGGAAAATC
Statistics
Matches: 234, Mismatches: 41, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.02
20 179 0.76
21 48 0.21
22 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCTC
Found at i:1220234 original size:40 final size:41
Alignment explanation
Indices: 1220177--1220427 Score: 275
Period size: 41 Copynumber: 6.2 Consensus size: 41
1220167 AAATTTAAGT
*
1220177 GTTGCGA-TTTACAG-ATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTTAC-GTATTCTCGTTGCGATTTACGGATTAGC
* * **
1220217 GTTGCGA-TTTACGGATTCTCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATTAGC
* * * * * * *
1220257 GTTACGA-TTAACGTATTCTGGTTGCGA-TAATCAGAATCGC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTA-CGGATTAGC
*
1220297 GTTGCGATTTTACGTATTCTCGTTGCGATTTATGGA-TACGC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATTA-GC
1220338 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGA-TACGC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATTA-GC
*
1220379 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGA-TACGC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATTA-GC
1220420 GTTGCGAT
1 GTTGCGAT
1220428 AGTCAGAATC
Statistics
Matches: 188, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 73 0.39
41 110 0.59
42 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATTAGC
Found at i:1225291 original size:2 final size:2
Alignment explanation
Indices: 1225284--1225315 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1225274 TTGTTGATGC
1225284 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
1225316 GTAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1225323 original size:10 final size:10
Alignment explanation
Indices: 1225284--1225338 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1225274 TTGTTGATGC
*
1225284 ATATATATAT
1 ATATAAATAT
*
1225294 ATATATATAT
1 ATATAAATAT
*
1225304 ATATATATAT
1 ATATAAATAT
*
1225314 ATGTAAATAT
1 ATATAAATAT
1225324 -TATGAAA-AT
1 ATAT-AAATAT
1225333 ATATAA
1 ATATAA
1225339 GTTATGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
9 6 0.15
10 34 0.85
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (10 bp):
ATATAAATAT
Found at i:1225541 original size:2 final size:2
Alignment explanation
Indices: 1225536--1225562 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1225526 TATTTTTTAC
1225536 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 A
1225563 ATTAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1232133 original size:33 final size:33
Alignment explanation
Indices: 1232078--1232195 Score: 159
Period size: 33 Copynumber: 3.6 Consensus size: 33
1232068 AAGCAATAGA
* *
1232078 GGGCATATTTGAAGATTCAACATCAAAAATTTG
1 GGGCATCTTTGGAGATTCAACATCAAAAATTTG
* * **
1232111 GGGTATCTTTGGAGATTTAACATCAAATGTTT-
1 GGGCATCTTTGGAGATTCAACATCAAAAATTTG
1232143 GGGCATCTTTGGAGATTCAACATC-AAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAAAAT-TTG
1232176 GGGCATCTTTGGAGATTCAA
1 GGGCATCTTTGGAGATTCAA
1232196 TATCGAATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 3 0.04
32 24 0.33
33 46 0.63
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (33 bp):
GGGCATCTTTGGAGATTCAACATCAAAAATTTG
Found at i:1232213 original size:65 final size:65
Alignment explanation
Indices: 1232078--1232213 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
1232068 AAGCAATAGA
* * *
1232078 GGGCATATTTGAAGATTCAACATCAAAAATTTGGGGTATCTTTGGAGATTTAACATCAAATGTTT
1 GGGCATATTTGAAGATTCAACATCAAAAATTTGGGGCATCTTTGGAGATTCAACATCAAATGATT
* * * *
1232143 GGGCATCTTTGGAGATTCAACATC-AAAATGTTGGGGCATCTTTGGAGATTCAATATCGAAT-AT
1 GGGCATATTTGAAGATTCAACATCAAAAAT-TTGGGGCATCTTTGGAGATTCAACATCAAATGAT
1232206 T
65 T
1232207 GCGGCAT
1 G-GGCAT
1232214 TCAAATCCTG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 8 0.13
65 54 0.87
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (65 bp):
GGGCATATTTGAAGATTCAACATCAAAAATTTGGGGCATCTTTGGAGATTCAACATCAAATGATT
Found at i:1232400 original size:34 final size:34
Alignment explanation
Indices: 1232324--1232409 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
1232314 AATTTTTTTG
*
1232324 TCTCACTTGAGATAATTTCTCAAAACAAAATTAA
1 TCTCGCTTGAGATAATTTCTCAAAACAAAATTAA
* **
1232358 TCTCGCTTGAGACAATTTCTCAAAAC-AAATTCCG
1 TCTCGCTTGAGATAATTTCTCAAAACAAAATT-AA
*
1232392 TCTTGCTTGAGATAATTT
1 TCTCGCTTGAGATAATTT
1232410 TTCTCTGAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 5 0.11
34 40 0.89
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (34 bp):
TCTCGCTTGAGATAATTTCTCAAAACAAAATTAA
Found at i:1232674 original size:40 final size:40
Alignment explanation
Indices: 1232628--1232723 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1232618 ATTTCATTTG
*
1232628 ACTCAAGATTGTTTTTCTTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
1232668 ATTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATTTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1232708 ACTCAAGATTGTTTTT
1 ACTCAAGATTGTTTTT
1232724 AAAGAAGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (40 bp):
ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
Found at i:1232825 original size:36 final size:36
Alignment explanation
Indices: 1232731--1232968 Score: 280
Period size: 36 Copynumber: 6.5 Consensus size: 36
1232721 TTTAAAGAAG
* * * * *
1232731 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAGCAGAAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAA--A-CAA
* *
1232770 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * *
1232806 ATTTTGCCTCTCTTAAGACAATTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* *
1232842 ATTTTGTCTCTCTTGAGACAGTTTCTCTTTAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1232878 ATTTTGTCT-TCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCT-CTTGAGACAGTTTCCCTTGAAACAA
* * *
1232914 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
*
1232950 ATTTTTGTCTCCCTTGAGA
1 A-TTTTGTCTCTCTTGAGA
1232969 TTATTAAAAC
Statistics
Matches: 177, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.01
36 129 0.73
37 18 0.10
39 29 0.16
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1233112 original size:61 final size:61
Alignment explanation
Indices: 1232992--1233111 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
1232982 ATTCGTCTCA
* * *
1232992 CTTGAGACATTTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTTTTTTAAAAACC
1 CTTGAGACAATTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTCTCTTAAAAACC
1233053 CTTGAGACAATTTT-CCTTCGAAACAAAATTTATCTCACTTGAGA-GAGCTTCTCTTAAAA
1 CTTGAGACAATTTTCCCTT-GAAACAAAATTTATCTCACTTGAGATG-G-TTCTCTTAAAA
1233112 CAAGTTTCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
60 5 0.09
61 39 0.74
62 9 0.17
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (61 bp):
CTTGAGACAATTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTCTCTTAAAAACC
Found at i:1233591 original size:136 final size:136
Alignment explanation
Indices: 1233351--1233933 Score: 956
Period size: 136 Copynumber: 4.3 Consensus size: 136
1233341 TAAACAGATC
* *
1233351 AACATTTCCACTTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
* *
1233416 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAACCAGTGACGCCTCGCTTGA
66 TAAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1233481 GGGATC
131 GGGATT
1233487 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1233552 TAAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
66 TAAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1233617 GGTATT
131 GGGATT
* * *
1233623 AACATTTCCAATGGAGAGTTCATAATGAGAATAACTTATCCGATAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
*
1233688 TGAA-AAGAGCTTGTTCGACTTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTG
66 T-AAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTG
*
1233752 AGGTATT
130 AGGGATT
* * *
1233759 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAACTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
* * *
1233824 TGAGAAGAGCTTGTTCGACCTATCACTTGATTCATGGCATTTCGAATCAGTGACGCCTCGCTTGA
66 TAAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1233889 AGGATT
131 GGGATT
* *
1233895 GACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCC
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
1233934 TAAAGAAGAA
Statistics
Matches: 424, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
134 27 0.06
135 2 0.00
136 393 0.93
137 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (136 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
TAAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
GGGATT
Found at i:1234094 original size:76 final size:76
Alignment explanation
Indices: 1233997--1234139 Score: 225
Period size: 76 Copynumber: 1.9 Consensus size: 76
1233987 AAGGAGGTGG
*
1233997 ATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
1234062 AACAACATGGC
66 AACAACATGGC
* * * *
1234073 ATCAACATTTCCAGATG-AGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAGACGAAGTTCA
1 ATCAACATTTCCAG-TGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCA
1234137 TAA
65 TAA
1234140 TGAGAAGAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 59 0.97
77 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (76 bp):
ATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
AACAACATGGC
Found at i:1234265 original size:91 final size:91
Alignment explanation
Indices: 1234071--1234269 Score: 303
Period size: 91 Copynumber: 2.2 Consensus size: 91
1234061 TAACAACATG
* *
1234071 GCATCAACATTTCCAGATGAGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAGACGAAGTTC
1 GCATCAACATTTCCAGATGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTC
1234136 ATAATGAGAAGAACTTGTTCAACCAT
66 ATAATGAGAAGAACTTGTTCAACCAT
* * *
1234162 GCTTCAAGATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTT
1 GCATCAACATTTCCAGAT-GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTT
*
1234226 CATAATGAGAAGAACTTGTTCAACCTT
65 CATAATGAGAAGAACTTGTTCAACCAT
*
1234253 AG-ATCAATATTTCCAGA
1 -GCATCAACATTTCCAGA
1234270 AGAACCTGCA
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
90 1 0.01
91 95 0.98
92 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (91 bp):
GCATCAACATTTCCAGATGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCAT
Found at i:1236081 original size:2 final size:2
Alignment explanation
Indices: 1236074--1236109 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1236064 TTGTTGATGC
1236074 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
1236110 GTAAATATTA
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):
AT
Found at i:1241605 original size:2 final size:2
Alignment explanation
Indices: 1241587--1241620 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1241577 TCATTTATCC
* *
1241587 AT AT AT GT AT AT GT 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
1241621 CCCTAGTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1241820 original size:15 final size:14
Alignment explanation
Indices: 1241802--1241849 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
1241792 CAAAATGAGA
1241802 AAAAAAAGAGAAAAG
1 AAAAAAAGA-AAAAG
*
1241817 AAAAAAA-ACAAAG
1 AAAAAAAGAAAAAG
1241830 AAAAAAAGAAAAAAG
1 AAAAAAAG-AAAAAG
1241845 AAAAA
1 AAAAA
1241850 GGGACGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 11 0.38
14 1 0.03
15 17 0.59
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:1241849 original size:7 final size:7
Alignment explanation
Indices: 1241803--1241849 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
1241793 AAAATGAGAA
1241803 AAAAAAG
1 AAAAAAG
*
1241810 AGAAAAG
1 AAAAAAG
1241817 AAAAAA-
1 AAAAAAG
*
1241823 AACAAAG
1 AAAAAAG
1241830 AAAAAAAG
1 -AAAAAAG
1241838 AAAAAAG
1 AAAAAAG
1241845 AAAAA
1 AAAAA
1241850 GGGACGATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 5 0.15
7 23 0.68
8 6 0.18
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1242933 original size:33 final size:33
Alignment explanation
Indices: 1242878--1242995 Score: 159
Period size: 33 Copynumber: 3.6 Consensus size: 33
1242868 AAGCAATAGA
* *
1242878 GGGCATATTTGAAGATTCAACATCAAAAATTTG
1 GGGCATCTTTGGAGATTCAACATCAAAAATTTG
* * **
1242911 GGGTATCTTTGGAGATTTAACATCAAATGTTT-
1 GGGCATCTTTGGAGATTCAACATCAAAAATTTG
1242943 GGGCATCTTTGGAGATTCAACATC-AAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAAAAT-TTG
1242976 GGGCATCTTTGGAGATTCAA
1 GGGCATCTTTGGAGATTCAA
1242996 TATCGAATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 3 0.04
32 24 0.33
33 46 0.63
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (33 bp):
GGGCATCTTTGGAGATTCAACATCAAAAATTTG
Found at i:1243013 original size:65 final size:65
Alignment explanation
Indices: 1242878--1243013 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
1242868 AAGCAATAGA
* * *
1242878 GGGCATATTTGAAGATTCAACATCAAAAATTTGGGGTATCTTTGGAGATTTAACATCAAATGTTT
1 GGGCATATTTGAAGATTCAACATCAAAAATTTGGGGCATCTTTGGAGATTCAACATCAAATGATT
* * * *
1242943 GGGCATCTTTGGAGATTCAACATC-AAAATGTTGGGGCATCTTTGGAGATTCAATATCGAAT-AT
1 GGGCATATTTGAAGATTCAACATCAAAAAT-TTGGGGCATCTTTGGAGATTCAACATCAAATGAT
1243006 T
65 T
1243007 GCGGCAT
1 G-GGCAT
1243014 TCAATATCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 8 0.13
65 54 0.87
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (65 bp):
GGGCATATTTGAAGATTCAACATCAAAAATTTGGGGCATCTTTGGAGATTCAACATCAAATGATT
Found at i:1243168 original size:34 final size:33
Alignment explanation
Indices: 1243124--1243203 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 33
1243114 ATTTTTTTTG
*
1243124 TCTCACTTGAGATAATTTCTCAAAACAAAATTCA
1 TCTCACTTGAGACAATTTCTCAAAA-AAAATTCA
* *
1243158 TCTCGCTTGAGACAATTTCTCAAAAAAAATTCCG
1 TCTCACTTGAGACAATTTCTCAAAAAAAATT-CA
*
1243192 TCTTACTTGAGA
1 TCTCACTTGAGA
1243204 TAACTTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.15
34 34 0.85
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (33 bp):
TCTCACTTGAGACAATTTCTCAAAAAAAATTCA
Found at i:1243470 original size:79 final size:80
Alignment explanation
Indices: 1243379--1243525 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
1243369 CATTTGAAAC
* * * *
1243379 AGATTTTGTCTCACTT-GAGACTG-TTTTACTTGAAAGA-AGACATTTCATTTGACTCAAGATTG
1 AGATTTTATCTCA-TTCAAGACTGTTTTTACTTGAAACATA-ACATTTCATTTCACTCAAGATTG
1243441 TTTTTCTTTGAAACAGA
64 TTTTTCTTTGAAACAGA
* * * *
1243458 AGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATTTCACTCAAGATTGTT
1 AGATTTTATCTCATTCAAGACTGTTTTTACTTGAAACATAACATTTCATTTCACTCAAGATTGTT
1243523 TTT
66 TTT
1243526 AAAGAAGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
78 2 0.04
79 17 0.30
80 37 0.65
81 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (80 bp):
AGATTTTATCTCATTCAAGACTGTTTTTACTTGAAACATAACATTTCATTTCACTCAAGATTGTT
TTTCTTTGAAACAGA
Found at i:1243476 original size:40 final size:40
Alignment explanation
Indices: 1243430--1243525 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1243420 ATTTCATTTG
*
1243430 ACTCAAGATTGTTTTTCTTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
1243470 ATTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATTTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1243510 ACTCAAGATTGTTTTT
1 ACTCAAGATTGTTTTT
1243526 AAAGAAGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (40 bp):
ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
Found at i:1243627 original size:36 final size:36
Alignment explanation
Indices: 1243533--1243770 Score: 280
Period size: 36 Copynumber: 6.5 Consensus size: 36
1243523 TTTAAAGAAG
* * * * *
1243533 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAGCAGAAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAA--A-CAA
* *
1243572 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * *
1243608 ATTTTGCCTCTCTTAAGACAATTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* *
1243644 ATTTTGTCTCTCTTGAGACAGTTTCTCTTTAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1243680 ATTTTGTCT-TCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCT-CTTGAGACAGTTTCCCTTGAAACAA
* * *
1243716 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
*
1243752 ATTTTTGTCTCCCTTGAGA
1 A-TTTTGTCTCTCTTGAGA
1243771 TTATTAAAAC
Statistics
Matches: 177, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.01
36 129 0.73
37 18 0.10
39 29 0.16
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1243913 original size:62 final size:62
Alignment explanation
Indices: 1243794--1243914 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
1243784 ATTCGTCTCA
* * *
1243794 CTTGAGACATCTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTTTTTTTAAAAACC
1 CTTGAGACATCTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGATTCTCTTAAAAACC
1243856 CTTGAGACAAT-TTT-CCTTCGAAACAAAATTTATCTCACTTGAGA-GAGATTCTCTTAAAA
1 CTTGAGAC-ATCTTTCCCTT-GAAACAAAATTTATCTCACTTGAGATG-GATTCTCTTAAAA
1243915 CAAGTTTCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 5 0.09
62 46 0.87
63 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (62 bp):
CTTGAGACATCTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGATTCTCTTAAAAACC
Found at i:1244394 original size:136 final size:136
Alignment explanation
Indices: 1244154--1244732 Score: 982
Period size: 136 Copynumber: 4.3 Consensus size: 136
1244144 TAAACAGATC
* *
1244154 AACATTTCCACTTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
*
1244219 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAACCAGTGACGCCTCGCTTGA
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1244284 GGGATC
131 GGGATT
1244290 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1244355 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1244420 GGTATT
131 GGGATT
* *
1244426 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
1244491 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1244556 GGTATT
131 GGGATT
* * *
1244562 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAACTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
* * * *
1244627 TGAGAAGTGCTTGTTCGACCTATCACTTGATTCATGACATTTCGAATCAGTGACGCCTCGCTTGA
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
*
1244692 AGGATT
131 GGGATT
* *
1244698 GACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTC
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
1244733 GTCCTAAAGA
Statistics
Matches: 426, Mismatches: 17, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
134 23 0.05
135 1 0.00
136 402 0.94
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (136 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGA
GGGATT
Found at i:1244882 original size:20 final size:20
Alignment explanation
Indices: 1244819--1244883 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1244809 TCCAGTGAAG
1244819 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1244839 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
1244858 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1244878 TGTTCA
1 AGTTCA
1244884 ACATGGCATC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1245068 original size:91 final size:92
Alignment explanation
Indices: 1244800--1245086 Score: 413
Period size: 91 Copynumber: 3.2 Consensus size: 92
1244790 AAGGAGGTGG
* * *
1244800 ATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
1 ATCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
1244865 AATGAGAAGAACTTGTTCAA-CATGGC
66 AATGAGAAGAACTTGTTCAACCATGGC
* *
1244891 ATC-AGCATTTCCAGAT-GAGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAGAAGAAGTTC
1 ATCAAG-ATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTC
1244954 ATAATGAGAAGAACTTGTTCAACCAT-GC
64 ATAATGAGAAGAACTTGTTCAACCATGGC
* * * *
1244982 TTCAAGATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGTAGAATAAGTTCAT
1 ATCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
* *
1245047 AATGAGAAGAACTTGTTCAACCTTAG-
66 AATGAGAAGAACTTGTTCAACCATGGC
*
1245073 ATCAATATTTCCAG
1 ATCAAGATTTCCAG
1245087 AAGAACCCGC
Statistics
Matches: 176, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
90 2 0.01
91 167 0.95
92 7 0.04
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (92 bp):
ATCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCATGGC
Found at i:1251529 original size:2 final size:2
Alignment explanation
Indices: 1251522--1251546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1251512 AAAGATATGG
1251522 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1251547 TAACTATTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1251564 original size:12 final size:13
Alignment explanation
Indices: 1251544--1251572 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1251534 TATATATATA
1251544 TATTAACTATTAC
1 TATTAACTATTAC
1251557 TATT-ACTATTAC
1 TATTAACTATTAC
1251569 TATT
1 TATT
1251573 TATTTCTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTAACTATTAC
Found at i:1255236 original size:17 final size:19
Alignment explanation
Indices: 1255214--1255251 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1255204 ATATATTGCA
1255214 TTTTATA-TTT-CATGTTT
1 TTTTATATTTTCCATGTTT
1255231 TTTTATATTTTCCATGTTT
1 TTTTATATTTTCCATGTTT
1255250 TT
1 TT
1255252 ACATTCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 9 0.47
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTATATTTTCCATGTTT
Found at i:1262175 original size:7 final size:7
Alignment explanation
Indices: 1262163--1262205 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
1262153 GTCCTAAGTC
1262163 AGAAAAA
1 AGAAAAA
1262170 AGAAAAA
1 AGAAAAA
1262177 AG-AAAA
1 AGAAAAA
1262183 AGAAAAA
1 AGAAAAA
1262190 ATGAAAAA
1 A-GAAAAA
1262198 GAGAAAAA
1 -AGAAAAA
1262206 CGTTTAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.18
7 14 0.42
8 12 0.36
9 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AGAAAAA
Found at i:1262182 original size:14 final size:14
Alignment explanation
Indices: 1262163--1262205 Score: 61
Period size: 13 Copynumber: 3.0 Consensus size: 14
1262153 GTCCTAAGTC
1262163 AGAAAAAAGAAAAA
1 AGAAAAAAGAAAAA
1262177 AG-AAAAAGAAAAA
1 AGAAAAAAGAAAAA
1262190 ATGAAAAAGAGAAAAA
1 A-GAAAAA-AGAAAAA
1262206 CGTTTAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 4 0.15
16 7 0.27
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AGAAAAAAGAAAAA
Found at i:1262260 original size:6 final size:6
Alignment explanation
Indices: 1262244--1262314 Score: 67
Period size: 6 Copynumber: 11.8 Consensus size: 6
1262234 CCTAAATTGA
*
1262244 AAAAAG AAAAAAG AAAAAG AGAAA- AAAAAG AAAAAG AAAAAGG AGAAAA-
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G A-AAAAG
* *
1262293 AAGAA- CAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAA
1262315 CAAGGTGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
5 10 0.19
6 32 0.59
7 8 0.15
8 4 0.07
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1262269 original size:9 final size:8
Alignment explanation
Indices: 1262243--1262308 Score: 66
Period size: 8 Copynumber: 8.5 Consensus size: 8
1262233 CCCTAAATTG
1262243 AAAAAAG-
1 AAAAAAGA
1262250 AAAAAAGA
1 AAAAAAGA
*
1262258 AAAAGAGA
1 AAAAAAGA
1262266 AAAAAA-A
1 AAAAAAGA
*
1262273 GAAAAAG-
1 AAAAAAGA
*
1262280 AAAAAGGA
1 AAAAAAGA
1262288 GAAAAAAGA
1 -AAAAAAGA
*
1262297 ACAAAAGA
1 AAAAAAGA
1262305 AAAA
1 AAAA
1262309 GAAAAACAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
7 18 0.38
8 22 0.47
9 7 0.15
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1262275 original size:24 final size:24
Alignment explanation
Indices: 1262243--1262314 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
1262233 CCCTAAATTG
1262243 AAAAAAGAAAAAAGAAAAAGAGAA
1 AAAAAAGAAAAAAGAAAAAGAGAA
*
1262267 AAAAAAG-AAAAAGAAAAAG-GAG
1 AAAAAAGAAAAAAGAAAAAGAGAA
1262289 AAAAAAGAACAAAAGAAAAAGA-AA
1 AAAAAAGAA-AAAAGAAAAAGAGAA
1262313 AA
1 AA
1262315 CAAGGTGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.21
23 13 0.30
24 21 0.49
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAAAAGAAAAAGAGAA
Found at i:1262278 original size:30 final size:29
Alignment explanation
Indices: 1262243--1262314 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
1262233 CCCTAAATTG
1262243 AAAAAAGAAAAAAGAAAAAGAG--AAAA--
1 AAAAAAG-AAAAAGAAAAAGAGAAAAAAGA
1262269 --AAAAGAAAAAGAAAAAGGAGAAAAAAGA
1 AAAAAAGAAAAAGAAAAA-GAGAAAAAAGA
*
1262297 ACAAAAGAAAAAGAAAAA
1 AAAAAAGAAAAAGAAAAA
1262315 CAAGGTGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
23 11 0.28
24 8 0.21
26 4 0.10
30 16 0.41
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (29 bp):
AAAAAAGAAAAAGAAAAAGAGAAAAAAGA
Found at i:1262282 original size:79 final size:79
Alignment explanation
Indices: 1262130--1262284 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
1262120 AATACTTCGC
* * * *
1262130 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTCAGAAAAAAGAAAAAAGAAAAAGAAAAAATGAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAGAAAAAAGAAAAAAGAAAAAGAAAAAATAAA
*
1262195 AAAGAGAAAAACGT
66 AAAAAGAAAAACGT
* * *
1262209 TTAGGGTGTAAACCCGAAAGGGCGCCCTAAAT-TGAAAAAAGAAAAAAGAAAAAGAGAAAAA-AA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAGAAAAAAGAAAAAAGAAAAAGA-AAAAATAA
1262272 AGAAAAAGAAAAA
65 A-AAAAAGAAAAA
1262285 GGAGAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 24 0.36
79 42 0.64
ACGTcount: A:0.59, C:0.10, G:0.22, T:0.10
Consensus pattern (79 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAGAAAAAAGAAAAAAGAAAAAGAAAAAATAAA
AAAAAGAAAAACGT
Found at i:1265443 original size:3 final size:3
Alignment explanation
Indices: 1265435--1265465 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1265425 TTTCTGTGTA
1265435 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1265466 TCATTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1266345 original size:21 final size:21
Alignment explanation
Indices: 1266306--1266345 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1266296 ATTTCAATGA
*
1266306 TACCAGCAGAGTTGACACATG
1 TACCAACAGAGTTGACACATG
1266327 TACCAACACGAGTTG-CACA
1 TACCAACA-GAGTTGACACA
1266346 AGAGAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (21 bp):
TACCAACAGAGTTGACACATG
Found at i:1277305 original size:17 final size:17
Alignment explanation
Indices: 1277255--1277315 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
1277245 GGGGTGAAAC
1277255 TATAAAAGTGTTTATAAA
1 TATAAAAGTGTTTA-AAA
* * *
1277273 AATAAAATTAACTTTAAAA
1 TATAAAAGT--GTTTAAAA
*
1277292 TATAAAAGTGTTTAAAT
1 TATAAAAGTGTTTAAAA
1277309 TATAAAA
1 TATAAAA
1277316 ATAATAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 13 0.38
18 7 0.21
19 10 0.29
20 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (17 bp):
TATAAAAGTGTTTAAAA
Found at i:1278059 original size:55 final size:55
Alignment explanation
Indices: 1277975--1278083 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
1277965 TAGAAGGTTA
*
1277975 GGAAAGAGGGAAATGATGCAATTATGGGCTTTTGTCTCATAGATATTATGATTTT
1 GGAAAGAGGGAAATGATGAAATTATGGGCTTTTGTCTCATAGATATTATGATTTT
*
1278030 GGAAAGAGGGAAATGATGAAATTATGGGCTTTTGTCTTATAGATATTATGATTT
1 GGAAAGAGGGAAATGATGAAATTATGGGCTTTTGTCTCATAGATATTATGATTT
1278084 CTCCCTTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (55 bp):
GGAAAGAGGGAAATGATGAAATTATGGGCTTTTGTCTCATAGATATTATGATTTT
Found at i:1279733 original size:15 final size:15
Alignment explanation
Indices: 1279710--1279756 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1279700 TAAATTATTT
*
1279710 TAATCAATTAAAATA
1 TAATAAATTAAAATA
*
1279725 TAATAAATTAATATA
1 TAATAAATTAAAATA
*
1279740 TATATATATT-AAATA
1 TA-ATAAATTAAAATA
1279755 TA
1 TA
1279757 TTATTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAATTAAAATA
Found at i:1282651 original size:40 final size:40
Alignment explanation
Indices: 1282602--1282714 Score: 133
Period size: 39 Copynumber: 2.9 Consensus size: 40
1282592 AAAATAAAAA
* * *
1282602 AAAAAACTCTTCATCTTCCAAGA-ACTCTTAAATTCACAAT
1 AAAAAACTCTT-AACTCCCAAGAGAATCTTAAATTCACAAT
* *
1282642 AAAATACTC-TAACTCCCAAGAGAATCTTAATTTCACAAT
1 AAAAAACTCTTAACTCCCAAGAGAATCTTAAATTCACAAT
* *
1282681 AAAACACTC-TAACTCCCAAGTGAATCTTAAATTC
1 AAAAAACTCTTAACTCCCAAGAGAATCTTAAATTC
1282715 CCCCATTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.14
39 47 0.73
40 8 0.12
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.28
Consensus pattern (40 bp):
AAAAAACTCTTAACTCCCAAGAGAATCTTAAATTCACAAT
Found at i:1282671 original size:39 final size:39
Alignment explanation
Indices: 1282622--1282714 Score: 150
Period size: 39 Copynumber: 2.4 Consensus size: 39
1282612 TCATCTTCCA
*
1282622 AGAACTCTTAAATTCACAATAAAATACTCTAACTCCCAAG
1 AGAA-TCTTAAATTCACAATAAAACACTCTAACTCCCAAG
*
1282662 AGAATCTTAATTTCACAATAAAACACTCTAACTCCCAAG
1 AGAATCTTAAATTCACAATAAAACACTCTAACTCCCAAG
*
1282701 TGAATCTTAAATTC
1 AGAATCTTAAATTC
1282715 CCCCATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 45 0.92
40 4 0.08
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.28
Consensus pattern (39 bp):
AGAATCTTAAATTCACAATAAAACACTCTAACTCCCAAG
Found at i:1283914 original size:14 final size:16
Alignment explanation
Indices: 1283875--1283916 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
1283865 GAAATTCCCA
1283875 AATTCTTTTATGTTAT
1 AATTCTTTTATGTTAT
*
1283891 AGATTTTTTTATGTT-T
1 A-ATTCTTTTATGTTAT
1283907 -ATTCTTTTAT
1 AATTCTTTTAT
1283917 ATTTCATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.39
16 2 0.09
17 12 0.52
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (16 bp):
AATTCTTTTATGTTAT
Found at i:1285668 original size:22 final size:22
Alignment explanation
Indices: 1285643--1285685 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1285633 CTAGGTGTTG
*
1285643 ACTGGATGTTGAACGGGCGTTA
1 ACTGGATGTTGAACGAGCGTTA
*
1285665 ACTGGATGTTGACCGAGCGTT
1 ACTGGATGTTGAACGAGCGTT
1285686 GACTAGGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.28
Consensus pattern (22 bp):
ACTGGATGTTGAACGAGCGTTA
Found at i:1285698 original size:22 final size:21
Alignment explanation
Indices: 1285672--1285754 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 21
1285662 TTAACTGGAT
*
1285672 GTTGACCGAGCGTTGACTAGGC
1 GTTGACCGACCGTTGACT-GGC
* * *
1285694 ATTGATC-AGGCGTTGACTGGC
1 GTTGACCGA-CCGTTGACTGGC
* * *
1285715 TGTTGACCAACCGTTAACTGTC
1 -GTTGACCGACCGTTGACTGGC
1285737 GTTGACCGACCGTTGACT
1 GTTGACCGACCGTTGACT
1285755 TTTTCCAAGA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 20 0.41
22 28 0.57
23 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (21 bp):
GTTGACCGACCGTTGACTGGC
Found at i:1286662 original size:26 final size:26
Alignment explanation
Indices: 1286630--1286685 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1286620 AAATAACATA
*
1286630 AAATACCCCCAAGC-CTTGGAATGACT
1 AAATACCCCCAAGCTC-TGGAATGAAT
**
1286656 AAATACCCTTAAGCTCTGGAATGAAT
1 AAATACCCCCAAGCTCTGGAATGAAT
1286682 AAAT
1 AAAT
1286686 CTACCTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (26 bp):
AAATACCCCCAAGCTCTGGAATGAAT
Found at i:1287751 original size:32 final size:32
Alignment explanation
Indices: 1287715--1287792 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
1287705 TAAGGTGACA
*
1287715 CTTGGGTAGGCTCTGAA-GCCCCAAGGTATTTC
1 CTTGGGTAGGCTCT-AAGGCCCCAAGGTATTCC
* *
1287747 CTTGGGTAGGCTCTAAGGCGCTAAGGTATTCC
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
1287779 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
1287793 TATGACCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 2 0.05
32 40 0.95
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (32 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
Found at i:1288918 original size:98 final size:97
Alignment explanation
Indices: 1288743--1288935 Score: 289
Period size: 98 Copynumber: 2.0 Consensus size: 97
1288733 TACGTAATAG
* *
1288743 GTATACCAAAGTATTTTATTTGTTATGACTCAATCTGTGCAAAAAAAAGGAATATTGTCAGTATT
1 GTATACCAAAGTATCTTATCTGTTATGACTCAATCTGTGCAAAAAAAAGGAATATTGTCAGTATT
1288808 CGACCCAATTTGGAAGTTACCCCACGAGTAAAA
66 CGACCCAATTTGGAAGTTA-CCCACGAGTAAAA
* * * *
1288841 GTATACCAAATTATCTTATCTGTTATGACTCAATTTGTGC-AAAAAAGGGAATATTGTTAGTATT
1 GTATACCAAAGTATCTTATCTGTTATGACTCAATCTGTGCAAAAAAAAGGAATATTGTCAGTATT
* *
1288905 CGTCCCAATTTTGGAAGTTACCCGCGAGTAA
66 CGACCCAA-TTTGGAAGTTACCCACGAGTAA
1288936 TGTGGGAGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
97 39 0.45
98 47 0.55
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (97 bp):
GTATACCAAAGTATCTTATCTGTTATGACTCAATCTGTGCAAAAAAAAGGAATATTGTCAGTATT
CGACCCAATTTGGAAGTTACCCACGAGTAAAA
Found at i:1290357 original size:2 final size:2
Alignment explanation
Indices: 1290352--1290398 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1290342 TCAGTTCGAT
1290352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1290394 TA TA T
1 TA TA T
1290399 TGTTTACTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1291314 original size:21 final size:19
Alignment explanation
Indices: 1291290--1291344 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
1291280 AATTAGGTCC
*
1291290 TTATTTTATGTTCATTTATTT
1 TTATTTTATGTT--TTTATTG
*
1291311 TTATTCTATGTTTTTATTG
1 TTATTTTATGTTTTTATTG
1291330 TT-TTTTAT-TTTTTAT
1 TTATTTTATGTTTTTAT
1291345 AATTTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 7 0.23
18 5 0.16
19 8 0.26
21 11 0.35
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (19 bp):
TTATTTTATGTTTTTATTG
Found at i:1299051 original size:2 final size:2
Alignment explanation
Indices: 1299044--1299087 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1299034 ATCCTTTCAA
1299044 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
1299086 AT
1 AT
1299088 TCCTTGTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.