Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007804.1 Hibiscus syriacus cultivar Beakdansim tig00110122_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: 1697051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1597198 original size:21 final size:21
Alignment explanation
Indices: 1597163--1597230 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
1597153 AAAATAAAAT
*
1597163 AAAAATAAAAGAGGAAAAAGGA
1 AAAAAGAAAA-AGGAAAAAGGA
*
1597185 AAAAGGAAAAAGGAAAAAGGA
1 AAAAAGAAAAAGGAAAAAGGA
1597206 AAAAAGAAAAA--AAAAAGAGA
1 AAAAAGAAAAAGGAAAAAG-GA
1597226 AAAAA
1 AAAAA
1597231 AATAAAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 6 0.14
20 7 0.17
21 21 0.50
22 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (21 bp):
AAAAAGAAAAAGGAAAAAGGA
Found at i:1597230 original size:14 final size:15
Alignment explanation
Indices: 1597177--1597239 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 15
1597167 ATAAAAGAGG
*
1597177 AAAAAG-GAAAAAGG
1 AAAAAGAGAAAAAGA
*
1597191 AAAAAG-GAAAAAGG
1 AAAAAGAGAAAAAGA
1597205 AAAAA-AG-AAAA-A
1 AAAAAGAGAAAAAGA
*
1597217 AAAAAGAGAAAAAAA
1 AAAAAGAGAAAAAGA
1597232 ATAAAAGA
1 A-AAAAGA
1597240 AAGGTCAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
12 5 0.12
13 6 0.14
14 24 0.56
15 2 0.05
16 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
AAAAAGAGAAAAAGA
Found at i:1597237 original size:20 final size:19
Alignment explanation
Indices: 1597177--1597243 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 19
1597167 ATAAAAGAGG
*
1597177 AAAAAGGAAAAAGGAAAAA
1 AAAAAGGAAAAAAGAAAAA
1597196 GGAAAAAGGAAAAAAGAAAAA
1 --AAAAAGGAAAAAAGAAAAA
1597217 AAAAAGAGAAAAAA-AATAAA
1 AAAAAG-GAAAAAAGAA-AAA
*
1597237 AGAAAGG
1 AAAAAGG
1597244 TCAAAGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.21
20 15 0.36
21 18 0.43
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (19 bp):
AAAAAGGAAAAAAGAAAAA
Found at i:1597237 original size:27 final size:26
Alignment explanation
Indices: 1597177--1597241 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
1597167 ATAAAAGAGG
* *
1597177 AAAAAGGAAAAAGGAAAAAGGAAAAAGG
1 AAAAAAGAAAAA--AAAAAGGAAAAAGA
1597205 AAAAAAGAAAAAAAAAAGAGAAAAA-A
1 AAAAAAGAAAAAAAAAAG-GAAAAAGA
1597231 AATAAAAGAAA
1 AA-AAAAGAAA
1597242 GGTCAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 8 0.24
27 14 0.42
28 11 0.33
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAAAGAAAAAAAAAAGGAAAAAGA
Found at i:1597317 original size:7 final size:7
Alignment explanation
Indices: 1597297--1597362 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
1597287 GATTTGGACC
1597297 TTTCTTT
1 TTTCTTT
1597304 TTT-TTT
1 TTTCTTT
1597310 TCTT-TTT
1 T-TTCTTT
1597317 TTTCTTT
1 TTTCTTT
*
1597324 TTCCTTT
1 TTTCTTT
*
1597331 TTTCCTT
1 TTTCTTT
*
1597338 TTTCCTT
1 TTTCTTT
*
1597345 TTTCCTT
1 TTTCTTT
*
1597352 TTTCCTT
1 TTTCTTT
1597359 TTTC
1 TTTC
1597363 CTCTTTTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
6 6 0.11
7 48 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTCTTT
Found at i:1597319 original size:15 final size:15
Alignment explanation
Indices: 1597306--1597375 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
1597296 CTTTCTTTTT
*
1597306 TTTTTCTTTTTTTTC
1 TTTTTCTTTTTTTCC
*
1597321 TTTTTCCTTTTTTCC
1 TTTTTCTTTTTTTCC
*
1597336 TTTTTC-CTTTTTCC
1 TTTTTCTTTTTTTCC
*
1597350 TTTTTC-CTTTTTCC
1 TTTTTCTTTTTTTCC
*
1597364 TCTTTTATTTTT
1 T-TTTTCTTTTT
1597376 ATTTTATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
14 22 0.46
15 23 0.48
16 3 0.06
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTTTTTCC
Found at i:1597354 original size:21 final size:22
Alignment explanation
Indices: 1597314--1597369 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
1597304 TTTTTTTCTT
*
1597314 TTTTTTCTTTTTCCTTTTTTCC
1 TTTTTCCTTTTTCCTTTTTTCC
1597336 TTTTTCCTTTTTCC-TTTTTCC
1 TTTTTCCTTTTTCCTTTTTTCC
1597357 TTTTTCCTCTTTT
1 TTTTTCCT-TTTT
1597370 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCCTTTTTCCTTTTTTCC
Found at i:1597363 original size:7 final size:7
Alignment explanation
Indices: 1597314--1597369 Score: 85
Period size: 7 Copynumber: 7.7 Consensus size: 7
1597304 TTTTTTTCTT
*
1597314 TTTTTTC
1 TTTTTCC
1597321 TTTTTCC
1 TTTTTCC
1597328 TTTTTTCC
1 -TTTTTCC
1597336 TTTTTCC
1 TTTTTCC
1597343 TTTTTCC
1 TTTTTCC
1597350 TTTTTCC
1 TTTTTCC
1597357 TTTTTCC
1 TTTTTCC
1597364 TCTTTT
1 T-TTTT
1597370 ATTTTTATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
7 35 0.76
8 11 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCC
Found at i:1597852 original size:17 final size:17
Alignment explanation
Indices: 1597832--1597870 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1597822 CCCTGTTGAA
1597832 GTATGTAATATAGTTCG
1 GTATGTAATATAGTTCG
1597849 GTATGTAATATAGTTCG
1 GTATGTAATATAGTTCG
1597866 GTATG
1 GTATG
1597871 CATATAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (17 bp):
GTATGTAATATAGTTCG
Found at i:1601006 original size:2 final size:2
Alignment explanation
Indices: 1601001--1601034 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1600991 TCAAAATTTC
* *
1601001 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1601035 CGGTTTTCTT
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:1602571 original size:2 final size:2
Alignment explanation
Indices: 1602564--1602588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1602554 CAAGAGGTAT
1602564 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
1602589 TACATGCATG
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:1603025 original size:11 final size:10
Alignment explanation
Indices: 1602995--1603024 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1602985 TTTAGTTTAA
1602995 ATAATTTTTT
1 ATAATTTTTT
1603005 ATAATTTTTT
1 ATAATTTTTT
*
1603015 ATTATTTTTT
1 ATAATTTTTT
1603025 TTAAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:1603075 original size:10 final size:10
Alignment explanation
Indices: 1603047--1603105 Score: 77
Period size: 9 Copynumber: 5.9 Consensus size: 10
1603037 CCTTTTACTT
1603047 TTTTATTTTA
1 TTTTATTTTA
*
1603057 -TTCATTTTA
1 TTTTATTTTA
1603066 TTTTATTTTA
1 TTTTATTTTA
1603076 TTTTATTTTTA
1 TTTTA-TTTTA
1603087 TTTTTATTTT-
1 -TTTTATTTTA
1603097 TTTTATTTT
1 TTTTATTTT
1603106 CATTATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 17 0.39
10 13 0.30
11 9 0.20
12 5 0.11
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:1603078 original size:15 final size:15
Alignment explanation
Indices: 1603047--1603105 Score: 77
Period size: 14 Copynumber: 3.9 Consensus size: 15
1603037 CCTTTTACTT
*
1603047 TTTTATTTTA-TTCA
1 TTTTATTTTATTTTA
1603061 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
1603076 TTTTATTTTTATTTTTA
1 TTTTA-TTTTA-TTTTA
1603093 TTTT-TTTTATTTT
1 TTTTATTTTATTTT
1603106 CATTATTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
14 14 0.34
15 13 0.32
16 5 0.12
17 9 0.22
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:1603101 original size:9 final size:9
Alignment explanation
Indices: 1603045--1603131 Score: 66
Period size: 9 Copynumber: 9.0 Consensus size: 9
1603035 ACCCTTTTAC
1603045 TTTTTTATT
1 TTTTTTATT
* *
1603054 TTATTCATT
1 TTTTTTATT
1603063 TTATTTTATT
1 TT-TTTTATT
1603073 TTATTTTATTTT
1 TT-TTTTA--TT
1603085 TATTTTTATT
1 T-TTTTTATT
1603095 TTTTTTATT
1 TTTTTTATT
**
1603104 TTCATTATT
1 TTTTTTATT
**
1603113 TTCATTATT
1 TTTTTTATT
1603122 TTTGTTTATT
1 TTT-TTTATT
1603132 ATCTTTTTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
9 35 0.54
10 21 0.32
12 8 0.12
13 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTTTATT
Found at i:1603105 original size:6 final size:5
Alignment explanation
Indices: 1603047--1603105 Score: 77
Period size: 5 Copynumber: 11.8 Consensus size: 5
1603037 CCTTTTACTT
*
1603047 TTTTA TTTTA -TTCA TTTTA TTTTA TTTTA TTTTA TTTTTA TTTTTA TTTT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA
1603097 TTTTA TTTT
1 TTTTA TTTT
1603106 CATTATTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
4 7 0.14
5 31 0.63
6 11 0.22
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1603114 original size:15 final size:15
Alignment explanation
Indices: 1603078--1603114 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1603068 TTATTTTATT
*
1603078 TTATTTTTATTTTTA
1 TTATTTTTATTTTCA
*
1603093 TTTTTTTTATTTTCA
1 TTATTTTTATTTTCA
1603108 TTATTTT
1 TTATTTT
1603115 CATTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
TTATTTTTATTTTCA
Found at i:1604992 original size:18 final size:19
Alignment explanation
Indices: 1604971--1605015 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1604961 ATTTAGACAT
1604971 TTTGCATTTT-TTAGTTTC
1 TTTGCATTTTGTTAGTTTC
*
1604989 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTAGTTTC
1605008 TTTGCATT
1 TTTGCATT
1605016 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTAGTTTC
Found at i:1608403 original size:106 final size:106
Alignment explanation
Indices: 1608216--1609119 Score: 1558
Period size: 106 Copynumber: 8.5 Consensus size: 106
1608206 TTCAAGCCAG
* *
1608216 AGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1608281 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * * *
1608322 ATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACGACTTCTCAATTTCAGAGCTAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
*
1608387 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
1608428 AGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
*
1608493 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
1608534 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
*
1608599 TTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
1608640 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* *
1608705 TTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACACA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
1608746 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* *
1608811 TTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1608852 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
*
1608917 TTCAACCTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
1608958 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGTCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* * *
1609023 TTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
1609064 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTT-TCAACTTCA
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCA
1609120 CGACGAAGGG
Statistics
Matches: 757, Mismatches: 41, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 8 0.01
106 749 0.99
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
Found at i:1609118 original size:44 final size:44
Alignment explanation
Indices: 1609066--1609168 Score: 197
Period size: 44 Copynumber: 2.3 Consensus size: 44
1609056 ACAACGCAAG
*
1609066 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
1609110 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
1609154 TTCAACTTCACGACG
1 TTCAACTTCACGACG
1609169 GAGGATATTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (44 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
Found at i:1610942 original size:24 final size:24
Alignment explanation
Indices: 1610915--1610973 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1610905 AAACTAACCC
1610915 TTTTACTT-TTTTTTATTCA-TTTTA
1 TTTTA-TTATTTTTT-TTCATTTTTA
*
1610939 TTTTATTATTTTTTTTTATTTTTA
1 TTTTATTATTTTTTTTCATTTTTA
1610963 TTTT-TTATTTT
1 TTTTATTATTTT
1610974 CATTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTATTATTTTTTTTCATTTTTA
Found at i:1610944 original size:14 final size:12
Alignment explanation
Indices: 1610921--1610998 Score: 61
Period size: 13 Copynumber: 6.1 Consensus size: 12
1610911 ACCCTTTTAC
1610921 TTTTTTTTATTCA
1 TTTTTTTTATT-A
1610934 TTTTATTTTATTA
1 TTTT-TTTTATTA
*
1610947 TTTTTTTTTATTT
1 -TTTTTTTTATTA
1610960 TTATTTTTTATT-
1 TT-TTTTTTATTA
1610972 TTCATTATTTTATTA
1 TT--TT-TTTTATTA
*
1610987 -TTTGTTTATTA
1 TTTTTTTTATTA
1610998 T
1 T
1610999 CTTTCTTCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
11 7 0.12
12 6 0.11
13 24 0.43
14 19 0.34
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTTTTTTATTA
Found at i:1610949 original size:13 final size:13
Alignment explanation
Indices: 1610921--1610989 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 13
1610911 ACCCTTTTAC
1610921 TTTT-TTTTATTCA
1 TTTTATTTTATT-A
1610934 TTTTATTTTATTA
1 TTTTATTTTATTA
*
1610947 TTTTTTTTTATT-
1 TTTTATTTTATTA
*
1610959 TTTATTTTTTATT-
1 TTT-TATTTTATTA
1610972 TTCATTATTTTATTA
1 TT--TTATTTTATTA
1610987 TTT
1 TTT
1610990 GTTTATTATC
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
12 3 0.06
13 28 0.57
14 15 0.31
15 3 0.06
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:1610995 original size:8 final size:7
Alignment explanation
Indices: 1610923--1610996 Score: 58
Period size: 8 Copynumber: 9.3 Consensus size: 7
1610913 CCTTTTACTT
1610923 TTTTTTA
1 TTTTTTA
1610930 TTCATTTTA
1 TT--TTTTA
1610939 TTTTATTA
1 TTTT-TTA
*
1610947 TTTTTTTT
1 -TTTTTTA
1610955 TATTTTTA
1 T-TTTTTA
1610963 TTTTTTA
1 TTTTTTA
1610970 TTTTCATTA
1 TTTT--TTA
1610979 TTTTATTA
1 TTTT-TTA
1610987 TTTGTTTA
1 TTT-TTTA
1610995 TT
1 TT
1610997 ATCTTTCTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
7 15 0.26
8 23 0.40
9 19 0.33
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:1610996 original size:16 final size:15
Alignment explanation
Indices: 1610934--1610989 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
1610924 TTTTTATTCA
1610934 TTTTATTTTATTATT
1 TTTTATTTTATTATT
* *
1610949 TTTTTTTATTTTTATT
1 TTTTATT-TTATTATT
1610965 TTTTATTTTCATTATT
1 TTTTATTTT-ATTATT
1610981 TTATTATTT
1 TT-TTATTT
1610990 GTTTATTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.24
16 20 0.59
17 6 0.18
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTATT
Found at i:1611933 original size:186 final size:186
Alignment explanation
Indices: 1611619--1611999 Score: 744
Period size: 186 Copynumber: 2.0 Consensus size: 186
1611609 ATAATAATTA
*
1611619 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATGTAAATTTCTAAAGGTTATA
1 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATATAAATTTCTAAAGGTTATA
1611684 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
66 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
1611749 AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
131 AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
1611805 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATATAAATTTCTAAAGGTTATA
1 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATATAAATTTCTAAAGGTTATA
1611870 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
66 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
*
1611935 AGATCCGGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
131 AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
1611991 TTATATTTT
1 TTATATTTT
1612000 ATTCAACTAA
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 193 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (186 bp):
TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATATAAATTTCTAAAGGTTATA
AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
Found at i:1615806 original size:36 final size:36
Alignment explanation
Indices: 1615765--1615840 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
1615755 ATTTTCGGGA
*
1615765 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1615801 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1615837 TTTT
1 TTTT
1615841 TTTTGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:1616284 original size:15 final size:15
Alignment explanation
Indices: 1616264--1616293 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1616254 TATCACAATC
1616264 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
1616279 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
1616294 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:1620812 original size:36 final size:36
Alignment explanation
Indices: 1620771--1620846 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
1620761 ATTTTCGGGA
*
1620771 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1620807 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1620843 TTTT
1 TTTT
1620847 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:1626177 original size:13 final size:13
Alignment explanation
Indices: 1626159--1626205 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
1626149 ATGGTCAAAT
1626159 TTTGAAAACTATG
1 TTTGAAAACTATG
1626172 TTTGAAAACTATG
1 TTTGAAAACTATG
*
1626185 TTTGAAAACAATG
1 TTTGAAAACTATG
1626198 TTTGAAAA
1 TTTGAAAA
1626206 TCAATATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (13 bp):
TTTGAAAACTATG
Found at i:1626719 original size:23 final size:21
Alignment explanation
Indices: 1626668--1626743 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 21
1626658 GTCTTGACAG
* *
1626668 GGGGTATCGGTAC-CCTT-AA
1 GGGGTATCGATACACATTAAA
*
1626687 GGGGTTTCGATACACATTCAAA
1 GGGGTATCGATACACATT-AAA
* *
1626709 TGGGGTATCGATACACGTTGAA
1 -GGGGTATCGATACACATTAAA
1626731 GGGGTATCGATAC
1 GGGGTATCGATAC
1626744 CTAGTGCACA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.23
20 3 0.06
21 13 0.28
22 4 0.09
23 16 0.34
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (21 bp):
GGGGTATCGATACACATTAAA
Found at i:1630576 original size:21 final size:20
Alignment explanation
Indices: 1630550--1630600 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1630540 GAGATTATTT
*
1630550 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTT-AAAAA
**
1630571 TCATTTTTTTATTTTAAAAA
1 TCATTTTTCAATTTTAAAAA
*
1630591 TAATTTTTCA
1 TCATTTTTCA
1630601 TAATCCGAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (20 bp):
TCATTTTTCAATTTTAAAAA
Found at i:1634441 original size:22 final size:22
Alignment explanation
Indices: 1634415--1634457 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1634405 GCAATAGGTA
*
1634415 TTGATATTTAGCAATGTTTGTG
1 TTGATATTTAGCAACGTTTGTG
*
1634437 TTGATATTTAGCGACGTTTGT
1 TTGATATTTAGCAACGTTTGT
1634458 CAAAAAAATA
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:0.07, G:0.23, T:0.49
Consensus pattern (22 bp):
TTGATATTTAGCAACGTTTGTG
Found at i:1634498 original size:43 final size:43
Alignment explanation
Indices: 1634437--1634535 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
1634427 AATGTTTGTG
*
1634437 TTGATATTTAGCGACGTTTGTCAAAAAAATACTGCAGTAAGTA
1 TTGATATTTAGCGACGTTTGTCAAAAAAATACTGCAATAAGTA
* * * *
1634480 TTGATATTTAGC-AGCGTTTGTCATAAAAATGCTGCAATAGGTG
1 TTGATATTTAGCGA-CGTTTGTCAAAAAAATACTGCAATAAGTA
1634523 TTGATATTTAGCG
1 TTGATATTTAGCG
1634536 GCATTTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.02
43 48 0.98
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (43 bp):
TTGATATTTAGCGACGTTTGTCAAAAAAATACTGCAATAAGTA
Found at i:1634600 original size:43 final size:42
Alignment explanation
Indices: 1634470--1634713 Score: 181
Period size: 43 Copynumber: 5.7 Consensus size: 42
1634460 AAAAAATACT
* * * * ** * *
1634470 GCAGTAAGTATTGATATTTAGCAGCGTTTGTCATAAAAATGCT
1 GCAGTAGGT-TTGATGTTTAGCGGCGTTTTTCCCACAAATGCC
* * * *** *
1634513 GCAATAGGTGTTGATATTTAGCGGCATTTTTTAGACAAACGCC
1 GCAGTAGGT-TTGATGTTTAGCGGCGTTTTTCCCACAAATGCC
* *
1634556 GCAATAGGTTATGATGTTTAGCGGCGTTTTTCTCTA-AAATGCC
1 GCAGTAGGTT-TGATGTTTAGCGGCGTTTTTC-CCACAAATGCC
* * * *
1634599 GCAGTAGGTGATAATGTTTTGCGGCG-TTTTCCCACAAACGCC
1 GCAGTAGGT-TTGATGTTTAGCGGCGTTTTTCCCACAAATGCC
*
1634641 GCAGTAGGTGTTGATGTTTTA-CGACG-TTTTCCCACAAATGCC
1 GCAGTAGGT-TTGATG-TTTAGCGGCGTTTTTCCCACAAATGCC
*
1634683 GCAGTAGGTTTTGATGTTTTGCGGCGTTTTT
1 GCAGTAGG-TTTGATGTTTAGCGGCGTTTTT
1634714 GCTAAAAATA
Statistics
Matches: 163, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
41 5 0.03
42 63 0.39
43 94 0.58
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (42 bp):
GCAGTAGGTTTGATGTTTAGCGGCGTTTTTCCCACAAATGCC
Found at i:1634643 original size:42 final size:42
Alignment explanation
Indices: 1634547--1634712 Score: 199
Period size: 42 Copynumber: 3.9 Consensus size: 42
1634537 CATTTTTTAG
* * * *
1634547 ACAAACGCCGCAATAGGTTATGATGTTTAGCGGCGTTTTTCTCT
1 ACAAACGCCGCAGTAGGTGATGATGTTTTGCGGCG-TTTTC-CC
* *
1634591 A-AAATGCCGCAGTAGGTGATAATGTTTTGCGGCGTTTTCCC
1 ACAAACGCCGCAGTAGGTGATGATGTTTTGCGGCGTTTTCCC
* * *
1634632 ACAAACGCCGCAGTAGGTGTTGATGTTTTACGACGTTTTCCC
1 ACAAACGCCGCAGTAGGTGATGATGTTTTGCGGCGTTTTCCC
* **
1634674 ACAAATGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTT
1 ACAAACGCCGCAGTAGGTGATGATGTTTTGCGGCGTTTT
1634713 TGCTAAAAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.02
42 75 0.71
43 28 0.26
44 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (42 bp):
ACAAACGCCGCAGTAGGTGATGATGTTTTGCGGCGTTTTCCC
Found at i:1634705 original size:84 final size:85
Alignment explanation
Indices: 1634547--1634712 Score: 223
Period size: 84 Copynumber: 2.0 Consensus size: 85
1634537 CATTTTTTAG
* *
1634547 ACAAACGCCGCAATAGGTTATGATGTTTAGCGGCGTTTTTCTCTAAAATGCCGCAGTAGGTGATA
1 ACAAACGCCGCAATAGGTTATGATGTTTAGCGACGTTTTTCTCCAAAATGCCGCAGTAGGTGATA
1634612 ATGTTTTGCGGCGTTTTCCC
66 ATGTTTTGCGGCGTTTTCCC
* *
1634632 ACAAACGCCGCAGTAGGTGT-TGATGTTTTA-CGACG-TTTTC-CCACAAATGCCGCAGTAGGTT
1 ACAAACGCCGCAATAGGT-TATGATG-TTTAGCGACGTTTTTCTCCA-AAATGCCGCAGTAGGTG
* *
1634693 TTGATGTTTTGCGGCGTTTT
63 ATAATGTTTTGCGGCGTTTT
1634713 TGCTAAAAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
83 2 0.03
84 39 0.54
85 26 0.36
86 5 0.07
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (85 bp):
ACAAACGCCGCAATAGGTTATGATGTTTAGCGACGTTTTTCTCCAAAATGCCGCAGTAGGTGATA
ATGTTTTGCGGCGTTTTCCC
Found at i:1635144 original size:21 final size:21
Alignment explanation
Indices: 1635120--1635170 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1635110 CTGTTGATAT
1635120 GCTGCTTCTCTCTATGTTGCC
1 GCTGCTTCTCTCTATGTTGCC
* *
1635141 GCTGCTTCTCTCTGTGTTGTC
1 GCTGCTTCTCTCTATGTTGCC
*
1635162 ACTGCTTCT
1 GCTGCTTCT
1635171 TTCTCTGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.31, G:0.20, T:0.45
Consensus pattern (21 bp):
GCTGCTTCTCTCTATGTTGCC
Found at i:1644575 original size:41 final size:41
Alignment explanation
Indices: 1644530--1644608 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
1644520 AACACAGCTA
*
1644530 AAGTACATGGATATTGAGGCGTTTGATCACAAACGCCAGAT
1 AAGTACAAGGATATTGAGGCGTTTGATCACAAACGCCAGAT
* * **
1644571 AAGTACAAGGCTATTGTGGCGTTTTCTCACAAACGCCA
1 AAGTACAAGGATATTGAGGCGTTTGATCACAAACGCCA
1644609 CTAAATTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
AAGTACAAGGATATTGAGGCGTTTGATCACAAACGCCAGAT
Found at i:1651637 original size:13 final size:13
Alignment explanation
Indices: 1651619--1651653 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1651609 TACAATCACT
1651619 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
1651632 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
1651645 -AGAAAAGAA
1 CA-AAAAGAA
1651654 ATTGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (13 bp):
CAAAAAGAAGAAA
Found at i:1658933 original size:59 final size:59
Alignment explanation
Indices: 1658841--1658967 Score: 227
Period size: 59 Copynumber: 2.2 Consensus size: 59
1658831 ACATGTGATA
*
1658841 ATTCCACCTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
1 ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
1658900 ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
1 ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
* *
1658959 TTTGCACTT
1 ATTCCACTT
1658968 TACATTTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (59 bp):
ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
Found at i:1671000 original size:42 final size:41
Alignment explanation
Indices: 1670954--1671118 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 41
1670944 AAATTAACGG
1670954 CGTTTATACCACAAACGCCGCAATAG-ATTACA-CATATAGTGA
1 CGTTTATACCACAAACGCCGCAATAGTA-TA-ATCA-ATAGTGA
* * * *
1670996 CGTTTATTCCTCAAATGCCGCAATAGTGATAATCAATAGTGG
1 CGTTTATACCACAAACGCCGCAATAGT-ATAATCAATAGTGA
* * * *
1671038 CGTTTTTA-GACAAACGCCGCAATAGTTTTAATCAATAGTGG
1 CGTTTATACCACAAACGCCGCAATAG-TATAATCAATAGTGA
* * *
1671079 CGTTTTTA--ACAAACGCCACAATAGTGTAATCAATAGTGA
1 CGTTTATACCACAAACGCCGCAATAGTATAATCAATAGTGA
1671118 C
1 C
1671119 TTTTTTTGTA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.13
40 15 0.14
41 35 0.33
42 37 0.35
43 4 0.04
44 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (41 bp):
CGTTTATACCACAAACGCCGCAATAGTATAATCAATAGTGA
Found at i:1671063 original size:41 final size:40
Alignment explanation
Indices: 1670964--1671140 Score: 171
Period size: 41 Copynumber: 4.3 Consensus size: 40
1670954 CGTTTATACC
* **
1670964 ACAAACGCCGCAATAGAT-TACA-CATATAGTGACGTTTATTCC
1 ACAAACGCCGCAATAG-TGTA-ATCA-ATAGTGGCGTTT-TTAG
* *
1671006 TCAAATGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAG
1 ACAAACGCCGCAATAGTG-TAATCAATAGTGGCGTTTTTAG
*
1671047 ACAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTA-
1 ACAAACGCCGCAATAG-TGTAATCAATAGTGGCGTTTTTAG
* * * *
1671087 ACAAACGCCACAATAGTGTAATCAATAGTGACTTTTTTTG
1 ACAAACGCCGCAATAGTGTAATCAATAGTGGCGTTTTTAG
*
1671127 TATAAACGCCGCAA
1 -ACAAACGCCGCAA
1671141 AATGTTAAAT
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
39 19 0.17
40 15 0.13
41 49 0.43
42 27 0.24
43 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (40 bp):
ACAAACGCCGCAATAGTGTAATCAATAGTGGCGTTTTTAG
Found at i:1671076 original size:83 final size:81
Alignment explanation
Indices: 1670964--1671140 Score: 198
Period size: 83 Copynumber: 2.2 Consensus size: 81
1670954 CGTTTATACC
** * *
1670964 ACAAACGCCGCAATAGATTACACATATAGTGACGTTTATTCCTCAAATGCCGCAATAGTGATAAT
1 ACAAACGCCGCAATAGATTACACATATAGTGACGTTT-TT-AACAAACGCCACAATAGTG-TAAT
*
1671029 CAATAGTGGCGTTTTTAG-
63 CAATAGTGACGTTTTTAGT
* *
1671047 ACAAACGCCGCAATAGTTTTA-ATCA-ATAGTGGCGTTTTTAACAAACGCCACAATAGTGTAATC
1 ACAAACGCCGCAATAG-ATTACA-CATATAGTGACGTTTTTAACAAACGCCACAATAGTGTAATC
* *
1671110 AATAGTGACTTTTTTTGT
64 AATAGTGACGTTTTTAGT
*
1671128 ATAAACGCCGCAA
1 ACAAACGCCGCAA
1671141 AATGTTAAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
80 19 0.23
81 27 0.33
82 2 0.02
83 28 0.35
84 5 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (81 bp):
ACAAACGCCGCAATAGATTACACATATAGTGACGTTTTTAACAAACGCCACAATAGTGTAATCAA
TAGTGACGTTTTTAGT
Found at i:1675893 original size:20 final size:20
Alignment explanation
Indices: 1675870--1675921 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1675860 AACGCGATCC
1675870 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1675890 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1675910 CCAAAATCGCAA
1 CCAGAATCGCAA
1675922 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1675938 original size:21 final size:20
Alignment explanation
Indices: 1675911--1676009 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1675901 AATCAGTTTC
1675911 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1675932 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1675953 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1675973 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1675994 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1676010 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1676038 original size:20 final size:20
Alignment explanation
Indices: 1675976--1676169 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1675966 CGATTTTCCA
* ** *
1675976 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1675996 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1676016 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1676036 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1676056 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1676076 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1676096 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1676116 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1676136 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1676157 AAATCGCAACGCG
1 AAATCGCAACGCG
1676170 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1676060 original size:60 final size:60
Alignment explanation
Indices: 1675976--1676169 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1675966 CGATTTTCCA
* ** * *
1675976 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1676036 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1676096 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1676157 AAATCGCAACGCG
1 AAATCGCAACGCG
1676170 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1676585 original size:33 final size:33
Alignment explanation
Indices: 1676546--1676616 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1676536 TTCACTTAGA
*
1676546 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1676579 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1676612 TTTCA
1 TTTCA
1676617 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1676802 original size:31 final size:32
Alignment explanation
Indices: 1676737--1676805 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
1676727 AGAATGACTG
***
1676737 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAAC-AGAGAATCGCAACGCGAAACCAAAA
1676770 TCGCAAC-GAGAATCGCAACGCGAAACCAAAA
1 TCGCAACAGAGAATCGCAACGCGAAACCAAAA
1676801 TCGCA
1 TCGCA
1676806 TTGCGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 26 0.79
33 7 0.21
ACGTcount: A:0.42, C:0.26, G:0.23, T:0.09
Consensus pattern (32 bp):
TCGCAACAGAGAATCGCAACGCGAAACCAAAA
Found at i:1676823 original size:19 final size:19
Alignment explanation
Indices: 1676801--1676898 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1676791 GAAACCAAAA
*
1676801 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1676820 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1676834 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1676853 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1676867 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1676886 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1676899 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1676842 original size:14 final size:14
Alignment explanation
Indices: 1676823--1676912 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1676813 TTTCATTTCG
1676823 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1676837 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1676856 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1676870 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1676887 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1676903 CGTTGCGATT
1 CGTTGCGATT
1676913 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1676848 original size:33 final size:33
Alignment explanation
Indices: 1676806--1676920 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1676796 CAAAATCGCA
1676806 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1676839 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1676872 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1676905 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1676921 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1678829 original size:185 final size:183
Alignment explanation
Indices: 1678599--1678977 Score: 715
Period size: 185 Copynumber: 2.1 Consensus size: 183
1678589 TAGATTGCTT
1678599 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1678664 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1678729 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTG--TTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
*
1678784 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1678849 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1678914 GTGTTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
131 GTGTTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
1678967 AGTAAATTTAT
1 AGTAAATTTAT
1678978 CCATTCAAGT
Statistics
Matches: 191, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 40 0.21
184 19 0.10
185 132 0.69
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (183 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
Found at i:1678913 original size:93 final size:93
Alignment explanation
Indices: 1678599--1678975 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
1678589 TAGATTGCTT
*
1678599 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1678664 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1678692 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1678756 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1678784 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1678849 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1678877 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTG--TTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1678940 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1678967 AGTAAATTT
1 AGTAAATTT
1678976 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
90 19 0.07
91 40 0.14
92 92 0.33
93 131 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1679059 original size:19 final size:19
Alignment explanation
Indices: 1679019--1679147 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1679009 TAGTTTACTT
* *
1679019 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1679039 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1679058 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1679077 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1679091 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1679110 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1679124 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1679143 TCGCA
1 TCGCA
1679148 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1679098 original size:33 final size:32
Alignment explanation
Indices: 1679055--1679147 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1679045 CGCGAAACCA
**
1679055 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1679087 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1679120 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1679148 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1679145 original size:52 final size:52
Alignment explanation
Indices: 1679019--1679147 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1679009 TAGTTTACTT
**
1679019 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1679071 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1679124 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1679148 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1679165 original size:19 final size:19
Alignment explanation
Indices: 1679143--1679276 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1679133 GAAACCAAAA
*
1679143 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1679162 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1679178 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1679195 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1679211 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1679228 TCGCGTTGCGA-TTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1679246 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1679266 TCGTGTTGCGA
1 TCGCGTTGCGA
1679277 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
18 16 0.17
19 29 0.31
20 12 0.13
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1679184 original size:14 final size:14
Alignment explanation
Indices: 1679165--1679221 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1679155 TTTCATTTCG
1679165 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1679179 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1679196 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1679212 CGTTGCGATT
1 CGTTGCGATT
1679222 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1679190 original size:33 final size:33
Alignment explanation
Indices: 1679148--1679276 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
1679138 CAAAATCGCA
1679148 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
1679181 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
1679214 TTGCGATTTTCATTTCGCGTTGCGATTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TT-CTTT--CG
* *
1679251 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
1679277 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
33 57 0.66
34 2 0.02
35 2 0.02
37 13 0.15
38 12 0.14
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:1681115 original size:37 final size:37
Alignment explanation
Indices: 1681082--1681152 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1681072 ATTGATTGTT
1681082 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
*
1681119 TTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATT
1681153 TGTAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (37 bp):
TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
Found at i:1681151 original size:14 final size:14
Alignment explanation
Indices: 1681134--1681169 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1681124 ATTGTTTAAT
1681134 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1681148 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1681162 TGATTTGT
1 TGATTTGT
1681170 GTAATTGATG
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:1681291 original size:19 final size:19
Alignment explanation
Indices: 1681275--1681376 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1681265 AAAAATGACT
1681275 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1681294 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1681313 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1681327 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1681346 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1681366 ATCGCAATGCG
1 ATCGCAATGCG
1681377 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1681429 original size:19 final size:19
Alignment explanation
Indices: 1681405--1681797 Score: 476
Period size: 19 Copynumber: 22.4 Consensus size: 19
1681395 GATTATCTCG
1681405 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681424 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681443 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1681457 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681476 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681495 TTGCGATTTTCATTT--CA
1 TTGCGATTTTCATTTCGCA
1681512 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1681526 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681544 TTGCGATTTTCATTT-GCA
1 TTGCGATTTTCATTTCGCA
*
1681562 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1681581 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1681619 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1681633 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681652 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1681671 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1681685 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1681704 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1681723 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1681737 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1681757 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1681771 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1681790 TTGCGATT
1 TTGCGATT
1681798 GTATTTTCCG
Statistics
Matches: 328, Mismatches: 12, Indels: 68
0.80 0.03 0.17
Matches are distributed among these distances:
14 44 0.13
15 6 0.02
16 36 0.11
17 36 0.11
18 27 0.08
19 167 0.51
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1681445 original size:52 final size:49
Alignment explanation
Indices: 1681383--1681797 Score: 375
Period size: 52 Copynumber: 7.9 Consensus size: 49
1681373 TGCGTTTATA
* *
1681383 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCATTGCGA-TTTCATTTCGCGTTGCGATTTTC
* *
1681435 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-T-TTTCATTGCGA-TTTCATTTCGCGTTGCGATTTTC
* * **
1681487 ATTTCGCATTGCGATTTTCATTTC-ATTGCGATTCTTTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTTTCATTGCGATTTC-ATT-TCGCGTTGCGATTTTC
** *
1681536 ATTTCGCATTGCGATTTTCATTTGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA---T--TTT-CATTGCGA-TTTCATTTCGCGTTGCGATTTTC
* * *
1681592 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * *
1681644 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * *
1681696 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
*
1681748 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTCA--TTGCGA-TTTCATTTCGCGTTGCGATT
1681798 GTATTTTCCG
Statistics
Matches: 320, Mismatches: 23, Indels: 39
0.84 0.06 0.10
Matches are distributed among these distances:
48 3 0.01
49 22 0.07
50 24 0.08
51 8 0.03
52 182 0.57
53 31 0.10
54 8 0.03
55 18 0.06
56 21 0.07
57 3 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (49 bp):
ATTTCGCATTGCGATTTTCATTGCGATTTCATTTCGCGTTGCGATTTTC
Found at i:1681741 original size:33 final size:33
Alignment explanation
Indices: 1681424--1681797 Score: 363
Period size: 33 Copynumber: 10.8 Consensus size: 33
1681414 TCATTTCGCA
1681424 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1681457 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
1681493 CATTGCGATTTTCATTT--CATTGCGATTCTTTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
*
1681526 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTT-CG
* *
1681562 TTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG
*
1681598 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1681633 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
*
1681669 CATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
*
1681702 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1681737 TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTTTC--G
* *
1681771 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1681798 GTATTTTCCG
Statistics
Matches: 298, Mismatches: 14, Indels: 57
0.81 0.04 0.15
Matches are distributed among these distances:
30 8 0.03
31 6 0.02
32 11 0.04
33 105 0.35
34 32 0.11
35 24 0.08
36 37 0.12
37 24 0.08
38 51 0.17
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
Found at i:1684316 original size:24 final size:23
Alignment explanation
Indices: 1684282--1684327 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1684272 CTGAAACATC
*
1684282 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCG-ATATTGACCAAT
*
1684306 ATCAAAGTCCGATATTGACCAA
1 ATCAAAATCCGATATTGACCAA
1684328 GACCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAAAATCCGATATTGACCAAT
Found at i:1685025 original size:20 final size:20
Alignment explanation
Indices: 1684997--1685405 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
1684987 AAATTTCAGT
* * * *
1684997 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1685017 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1685037 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1685057 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1685077 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1685097 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1685117 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1685137 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1685157 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1685177 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1685197 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1685217 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1685237 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1685257 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1685277 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1685297 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1685317 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1685337 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1685357 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1685377 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1685397 GTTGCGATT
1 GTTGCGATT
1685406 ATGGAAAATC
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 331 0.97
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1691105 original size:21 final size:21
Alignment explanation
Indices: 1691079--1691191 Score: 102
Period size: 21 Copynumber: 5.4 Consensus size: 21
1691069 AGCAGAAATT
1691079 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGCGGAAGCAGAGAGA
* * **
1691100 GCAGCAGCGAAAGCAGCCAGA
1 GAAGCAGCGGAAGCAGAGAGA
* *
1691121 GAAGCAGTGGAAGCAGAGAAA
1 GAAGCAGCGGAAGCAGAGAGA
* *
1691142 GAAGCAGCGGCAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * *
1691163 GAAGAAGCGGTAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
*
1691184 AAAGCAGC
1 GAAGCAGC
1691192 ATATCAGCAG
Statistics
Matches: 73, Mismatches: 18, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
20 2 0.03
21 71 0.97
ACGTcount: A:0.43, C:0.18, G:0.37, T:0.02
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:1691113 original size:42 final size:42
Alignment explanation
Indices: 1691066--1691150 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
1691056 TGGCTAACTT
** * *
1691066 GAAAGCAGAAATTGAAGCAAG-GGAAGCAGAGAGAGCAGCAGC
1 GAAAGCAGAAAGAGAAGC-AGTGGAAGCAGAGAAAGAAGCAGC
**
1691108 GAAAGCAGCCAGAGAAGCAGTGGAAGCAGAGAAAGAAGCAGC
1 GAAAGCAGAAAGAGAAGCAGTGGAAGCAGAGAAAGAAGCAGC
1691150 G
1 G
1691151 GCAGCACAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.45, C:0.15, G:0.36, T:0.04
Consensus pattern (42 bp):
GAAAGCAGAAAGAGAAGCAGTGGAAGCAGAGAAAGAAGCAGC
Found at i:1691597 original size:43 final size:43
Alignment explanation
Indices: 1691506--1691621 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 43
1691496 ATTATATGTT
*
1691506 ATTTAGCGGCGTTTGTAAAAAATAACGCCGCAATATACCATAC
1 ATTTAGCGGCGTTTGTAAAAAATAACGCCGCAATACACCATAC
* * *
1691549 ATTTAGCGGCGTTTGTATACTAGA-AACGCCGCGATACACCGA-AC
1 ATTTAGCGGCGTTTGTA-A-AAAATAACGCCGCAATACACC-ATAC
* * *
1691593 -TTTAGTGGTGTTTGTAAGAAA-AACGCCGC
1 ATTTAGCGGCGTTTGTAAAAAATAACGCCGC
1691622 TAAATCTCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
41 10 0.16
42 1 0.02
43 31 0.50
44 17 0.27
45 3 0.05
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTAAAAAATAACGCCGCAATACACCATAC
Found at i:1691693 original size:43 final size:43
Alignment explanation
Indices: 1691611--1691714 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
1691601 TGTTTGTAAG
** *
1691611 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTTCAAT
1 AAAAACGCCGCTAAATCTCAACACCTATTGCAACATTTTCAAT
* * *
1691654 AAAAACGTCGCTAATTCTCAAC-CCTGATTGCAACATTTTCGAT
1 AAAAACGCCGCTAAATCTCAACACCT-ATTGCAACATTTTCAAT
* *
1691697 ACAAACACCGCTAAATCT
1 AAAAACGCCGCTAAATCT
1691715 GAAAATCTAC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 3 0.06
43 47 0.94
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.26
Consensus pattern (43 bp):
AAAAACGCCGCTAAATCTCAACACCTATTGCAACATTTTCAAT
Found at i:1691777 original size:43 final size:43
Alignment explanation
Indices: 1691730--1691988 Score: 190
Period size: 43 Copynumber: 6.1 Consensus size: 43
1691720 TCTACTACGA
* * *
1691730 CGTTTGTGGGGAAAACACCGCTAAACATCATCACCTATTGCGG
1 CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
** * * * * *
1691773 CGTTTGT-GAAAAAATGCCAC-AAA-AT-ATCAACTATTGTGG
1 CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
* * * * *
1691812 TGTTTGTAAGTAAAACGCCGCTAAATC-TCAAAACCTACTGCGG
1 CGTTTGTAGGGAAAACGCCGCTAAA-CATCAACACCTATTGCGG
* * *
1691855 CGTTTGTAGGGAAAACTCCGCTAAACATCAACACTTATTGCAG
1 CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
* * * * *
1691898 CGTTT-TTGTGACAAATGCCGCTAAATAACAACACCTATTGCGG
1 CGTTTGTAGGGA-AAACGCCGCTAAACATCAACACCTATTGCGG
* * * *
1691941 C-TTTGTTGTGGCAAACGCCGCTAAATAACAACACCTATTGCGG
1 CGTTTGTAG-GGAAAACGCCGCTAAACATCAACACCTATTGCGG
*
1691984 TGTTT
1 CGTTT
1691989 TTTGTTAAAA
Statistics
Matches: 168, Mismatches: 38, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
39 18 0.11
40 10 0.06
41 6 0.04
42 17 0.10
43 113 0.67
44 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (43 bp):
CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
Done.