Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006423.1 Hibiscus syriacus cultivar Beakdansim tig00015498_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: 772901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:163862 original size:28 final size:23
Alignment explanation
Indices: 163802--163854 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
163792 AATCAGGAGA
163802 TGTCATGTGTTGTTGGCGACACT
1 TGTCATGTGTTGTTGGCGACACT
*
163825 TGTCATGTGTTGTTGGTGACACT
1 TGTCATGTGTTGTTGGCGACACT
163848 TGTCATG
1 TGTCATG
163855 ACATGTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.13, C:0.15, G:0.30, T:0.42
Consensus pattern (23 bp):
TGTCATGTGTTGTTGGCGACACT
Found at i:164855 original size:23 final size:23
Alignment explanation
Indices: 164804--164857 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
164794 TTTTAATCAA
*
164804 AATAT-TAATTATTAAAATATTT
1 AATATATATTTATTAAAATATTT
* *
164826 AAAATATATTTATTAATAT-TTCT
1 AATATATATTTATTAAAATATT-T
164849 AATATATAT
1 AATATATAT
164858 ATTAGTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATATATTTATTAAAATATTT
Found at i:164870 original size:19 final size:21
Alignment explanation
Indices: 164819--164876 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
164809 TAATTATTAA
** *
164819 AATATTTAAAATATATTTATT
1 AATATTTCTAATATATATATT
164840 AATATTTCTAATATATATATT
1 AATATTTCTAATATATATATT
*
164861 AGT-TTT-TAATAT-TATA
1 AATATTTCTAATATATATA
164877 ATAAATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
20 3 0.09
21 20 0.61
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATTTCTAATATATATATT
Found at i:164982 original size:8 final size:8
Alignment explanation
Indices: 164969--165024 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
164959 TACTTAATAT
164969 TAATATAA
1 TAATATAA
164977 TAATATAA
1 TAATATAA
**
164985 TAATATTT
1 TAATATAA
164993 TAATA-AA
1 TAATATAA
*
165000 TATATTTAA
1 TA-ATATAA
165009 -AATATAA
1 TAATATAA
165016 TAAT-TAA
1 TAATATAA
165023 TA
1 TA
165025 TTTTTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
7 12 0.31
8 25 0.64
9 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TAATATAA
Found at i:165012 original size:23 final size:23
Alignment explanation
Indices: 164965--165037 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
164955 TATATACTTA
*
164965 ATATTAATATAATA-ATATAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
164989 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
165012 ATAATAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
165035 ATA
1 ATA
165038 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:165038 original size:23 final size:23
Alignment explanation
Indices: 164993--165040 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
164983 AATAATATTT
164993 TAATAAATATATTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
* *
165016 TAATTAATATTTTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
165039 TA
1 TA
165041 TAACACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAA
Found at i:165167 original size:22 final size:22
Alignment explanation
Indices: 165124--165183 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
165114 TTTTAATAAT
* * *
165124 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAA-GTTTTA
*
165147 AAATTAATAATATTAAGTTTTA
1 AAATAAATAATATTAAGTTTTA
**
165169 TGATAAATAATATTA
1 AAATAAATAATATTA
165184 TTTATTATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
AAATAAATAATATTAAGTTTTA
Found at i:165168 original size:50 final size:50
Alignment explanation
Indices: 165114--165208 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
165104 AAAAATAATA
165114 TTTTAATAATAAATAA-ATTATTTTAATAT-TTTAAAATTAATAATATTAAG
1 TTTT-ATAATAAATAATATTA-TTTAATATATTTAAAATTAATAATATTAAG
* * * *
165164 TTTTATGATAAATAATATTATTTATTATATTTAATATTTATAATA
1 TTTTATAATAAATAATATTATTTAATATATTTAAAATTAATAATA
165209 AATATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 17 0.44
50 22 0.56
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (50 bp):
TTTTATAATAAATAATATTATTTAATATATTTAAAATTAATAATATTAAG
Found at i:167338 original size:11 final size:11
Alignment explanation
Indices: 167322--167350 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
167312 CCCATCCCCC
167322 CCGCCCCGTTG
1 CCGCCCCGTTG
167333 CCGCCCCGTTG
1 CCGCCCCGTTG
167344 CCGCCCC
1 CCGCCCC
167351 TACCAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.62, G:0.24, T:0.14
Consensus pattern (11 bp):
CCGCCCCGTTG
Found at i:168835 original size:3 final size:3
Alignment explanation
Indices: 168827--168854 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
168817 ATAAAACTGA
168827 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
168855 TTGCAGTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:170318 original size:32 final size:30
Alignment explanation
Indices: 170244--170326 Score: 112
Period size: 32 Copynumber: 2.7 Consensus size: 30
170234 TTCGGTATTT
170244 GGGTTGGATTTTTTTTAAAATTTAGGGATC
1 GGGTTGGATTTTTTTTAAAATTTAGGGATC
* *
170274 GGTTTAGATTTTTTTAATAAAATTTAGGGATC
1 GGGTTGGATTTTTTT--TAAAATTTAGGGATC
*
170306 GGGTTGGGTTTTTTTTTAAAA
1 GGGTT-GGATTTTTTTTAAAA
170327 AAAAAAATCG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.29
31 5 0.11
32 19 0.42
33 8 0.18
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.48
Consensus pattern (30 bp):
GGGTTGGATTTTTTTTAAAATTTAGGGATC
Found at i:170938 original size:18 final size:16
Alignment explanation
Indices: 170893--170924 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
170883 TTCAGATTCT
170893 AATTCTAATTCCTTCA
1 AATTCTAATTCCTTCA
170909 AATTCTAATTCCTTCA
1 AATTCTAATTCCTTCA
170925 CAGATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTCTAATTCCTTCA
Found at i:171868 original size:3 final size:3
Alignment explanation
Indices: 171860--171890 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
171850 CACAGCTGTA
171860 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
171891 TCCCTCTCTT
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:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:178910 original size:13 final size:13
Alignment explanation
Indices: 178894--178935 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
178884 TAGAAATGTC
178894 AACTTGAAATATG
1 AACTTGAAATATG
* *
178907 AACTT-TAAT-GG
1 AACTTGAAATATG
178918 AACTTGAAATATG
1 AACTTGAAATATG
178931 AACTT
1 AACTT
178936 TAATGGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (13 bp):
AACTTGAAATATG
Found at i:178921 original size:24 final size:24
Alignment explanation
Indices: 178894--178943 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
178884 TAGAAATGTC
178894 AACTTGAAATATGAACTTTAATGG
1 AACTTGAAATATGAACTTTAATGG
178918 AACTTGAAATATGAACTTTAATGG
1 AACTTGAAATATGAACTTTAATGG
178942 AA
1 AA
178944 TTCTCACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (24 bp):
AACTTGAAATATGAACTTTAATGG
Found at i:180703 original size:40 final size:39
Alignment explanation
Indices: 180614--180869 Score: 152
Period size: 35 Copynumber: 7.2 Consensus size: 39
180604 TTTTCTTCAT
* ** * *
180614 ATATATATATAATATAGATTTGAAAAACATGTTTGAAAAC
1 ATATATATATTATATAG-TTTTTAAAACATTTTTGAAAAA
*
180654 ATTTATATATTATATAGTTTTTAAAACATTTTTG--AAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAAA
180691 A-A-ATATATTATATAGTTTTTAAAACA-TTTTG-----
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAAA
* *** *
180722 --A-A-A-A-TATATAGTTTTTAAAAAAAAATTGAAAAC
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAAA
*
180755 ATATATATATTATATAGTTTTGAAAATCA-TTTTG--AAA
1 ATATATATATTATATAGTTTTTAAAA-CATTTTTGAAAAA
*
180792 ACATATA-A-TATATAG-TTTTAAAACA-TTTT-AAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAAA
* ** *
180826 ATATATATAATATATA-ACTTTAAAATATTTTT--AAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAAA
180862 ATATATAT
1 ATATATAT
180870 TATAGGTTTT
Statistics
Matches: 177, Mismatches: 20, Indels: 42
0.74 0.08 0.18
Matches are distributed among these distances:
27 17 0.10
28 4 0.02
29 1 0.01
30 2 0.01
33 6 0.03
34 21 0.12
35 33 0.19
36 28 0.16
37 16 0.09
38 1 0.01
39 32 0.18
40 16 0.09
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (39 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTGAAAAA
Found at i:180704 original size:35 final size:34
Alignment explanation
Indices: 180658--180873 Score: 173
Period size: 35 Copynumber: 6.3 Consensus size: 34
180648 GAAAACATTT
180658 ATATATTATATAGTTTTTAAAACATTTTTGAAAAA
1 ATATATTATATAGTTTTTAAAACA-TTTTGAAAAA
180693 ATATATTATATAGTTTTTAAAACATTTTG----A
1 ATATATTATATAGTTTTTAAAACATTTTGAAAAA
* **
180723 A-A-A-TATATAGTTTTTAAAAAAAAATTGAAAACATA
1 ATATATTATATAGTTTTT-AAAACATTTTG-AAA-A-A
* *
180758 TATATATTATATAGTTTTGAAAATCATTTTGAAAAC
1 -ATATATTATATAGTTTTTAAAA-CATTTTGAAAAA
*
180794 ATATAATATATAG-TTTTAAAACATTTT-AAAAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAAA
* * *
180826 ATATATATAATATA-TAACTTTAAAATATTTTTAAAAA
1 ATATAT-T-ATATAGT--TTTTAAAACATTTTGAAAAA
180863 TATATATTATA
1 -ATATATTATA
180874 GGTTTTGGAA
Statistics
Matches: 147, Mismatches: 14, Indels: 39
0.74 0.07 0.19
Matches are distributed among these distances:
27 12 0.08
28 9 0.06
29 1 0.01
30 2 0.01
32 9 0.06
33 7 0.05
34 17 0.12
35 37 0.25
36 16 0.11
37 8 0.05
38 14 0.10
39 15 0.10
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (34 bp):
ATATATTATATAGTTTTTAAAACATTTTGAAAAA
Found at i:180750 original size:28 final size:27
Alignment explanation
Indices: 180699--180759 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
180689 AAAAATATAT
* **
180699 TATATAGTTTTTAAAACATTTTGAAAA
1 TATATAGTTTTTAAAAAAAATTGAAAA
180726 TATATAGTTTTTAAAAAAAAATTGAAAA
1 TATATAGTTTTT-AAAAAAAATTGAAAA
*
180754 CATATA
1 TATATA
180760 TATATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (27 bp):
TATATAGTTTTTAAAAAAAATTGAAAA
Found at i:180762 original size:101 final size:101
Alignment explanation
Indices: 180646--180832 Score: 297
Period size: 101 Copynumber: 1.9 Consensus size: 101
180636 AAAAACATGT
* * *
180646 TTGAAAACATTTATATATTATATAGTTTTTAAAA-CATTTTTGAAAAAATATATTATATAGTTTT
1 TTGAAAACATATATATATTATATAGTTTTGAAAATCA-TTTTGAAAAAATATAATATATAG-TTT
*
180710 TAAAACATTTT-GAAAATATATAGTTTTTAAAAAAAAA
64 TAAAACATTTTAAAAAATATATAGTTTTTAAAAAAAAA
*
180747 TTGAAAACATATATATATTATATAGTTTTGAAAATCATTTTGAAAACATATAATATATAGTTTTA
1 TTGAAAACATATATATATTATATAGTTTTGAAAATCATTTTGAAAAAATATAATATATAGTTTTA
180812 AAACATTTTAAAAAATATATA
66 AAACATTTTAAAAAATATATA
180833 TAATATATAA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
100 14 0.18
101 63 0.80
102 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (101 bp):
TTGAAAACATATATATATTATATAGTTTTGAAAATCATTTTGAAAAAATATAATATATAGTTTTA
AAACATTTTAAAAAATATATAGTTTTTAAAAAAAAA
Found at i:180840 original size:36 final size:36
Alignment explanation
Indices: 180750--180869 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 36
180740 AAAAAAATTG
* *
180750 AAAACATATATATATTATATAGTTTTGAAAATCATTTT
1 AAAAAATATATATAATATATAGTTTT-AAAA-CATTTT
* *
180788 --GAAA-ACATATAATATATAGTTTTAAAACATTTT
1 AAAAAATATATATAATATATAGTTTTAAAACATTTT
** *
180821 AAAAAATATATATAATATATAACTTTAAAATATTTT
1 AAAAAATATATATAATATATAGTTTTAAAACATTTT
*
180857 TAAAAATATATAT
1 AAAAAATATATAT
180870 TATAGGTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
33 6 0.09
34 4 0.06
35 20 0.29
36 39 0.57
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (36 bp):
AAAAAATATATATAATATATAGTTTTAAAACATTTT
Found at i:180929 original size:18 final size:18
Alignment explanation
Indices: 180906--180956 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 18
180896 TATATATATA
*
180906 TATTATTTTAGTTTTTTT
1 TATTATTTTAGTTTTTAT
180924 TATTATTATTAACGTTTTTAT
1 TATTATT-TT-A-GTTTTTAT
180945 T-TTATTTT-GTTT
1 TATTATTTTAGTTT
180957 ATAGGTCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.14
18 7 0.24
19 4 0.14
20 6 0.21
21 8 0.28
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (18 bp):
TATTATTTTAGTTTTTAT
Found at i:182231 original size:29 final size:31
Alignment explanation
Indices: 182198--182265 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
182188 TTTTCCTTTG
182198 TTTTTTTCTA-TTTTATTATTTTCT-TTG-TA
1 TTTTTTTCTACTTTTATTATTTT-TATTGTTA
*
182227 TTTTTTT-TACTTTTGTTATTTTTATTGTTA
1 TTTTTTTCTACTTTTATTATTTTTATTGTTA
*
182257 TGTTTTTCT
1 TTTTTTTCT
182266 CTTAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 3 0.09
29 21 0.64
30 8 0.24
31 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (31 bp):
TTTTTTTCTACTTTTATTATTTTTATTGTTA
Found at i:182233 original size:14 final size:14
Alignment explanation
Indices: 182184--182233 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
182174 TATTTTAATG
182184 ATTTTTTTCCTTTG-
1 ATTTTTTT-CTTTGT
*
182198 -TTTTTTTCTATTTT
1 ATTTTTTTCT-TTGT
*
182212 ATTATTTTCTTTGT
1 ATTTTTTTCTTTGT
182226 ATTTTTTT
1 ATTTTTTT
182234 TACTTTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 2 0.07
13 9 0.31
14 10 0.34
15 8 0.28
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (14 bp):
ATTTTTTTCTTTGT
Found at i:182263 original size:30 final size:29
Alignment explanation
Indices: 182188--182265 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
182178 TTAATGATTT
182188 TTTTCCTTTGT-T-TTTTTCTATTTTATTA
1 TTTT-CTTTGTATGTTTTTCTATTTTATTA
* *
182216 TTTTCTTTGTAT-TTTTTTTACTTTTGTTA
1 TTTTCTTTGTATGTTTTTCTA-TTTTATTA
182245 TTTT-TATTGTTATGTTTTTCT
1 TTTTCT-TTG-TATGTTTTTCT
182266 CTTAATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 6 0.14
28 13 0.31
29 14 0.33
30 3 0.07
31 6 0.14
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.76
Consensus pattern (29 bp):
TTTTCTTTGTATGTTTTTCTATTTTATTA
Found at i:182305 original size:14 final size:13
Alignment explanation
Indices: 182199--182321 Score: 70
Period size: 14 Copynumber: 8.8 Consensus size: 13
182189 TTTCCTTTGT
182199 TTTTTTCTATTTTA
1 TTTTTT-TATTTTA
* *
182213 TTATTTTCTTTGTA
1 TTTTTTTATTT-TA
*
182227 TTTTTTTTACTTTTG
1 -TTTTTTTA-TTTTA
182242 TTATTTTTATTGTTA
1 TT-TTTTTATT-TTA
* * *
182257 TGTTTTTCTCTTAA
1 TTTTTTTAT-TTTA
* *
182271 TTTATTTA--ATA
1 TTTTTTTATTTTA
182282 TTTTTATTATATTTA
1 TTTTT-TTAT-TTTA
182297 TTTTTTTATTTTA
1 TTTTTTTATTTTA
182310 TTCTTTTTATTT
1 TT-TTTTTATTT
182322 GCTTTACCTT
Statistics
Matches: 82, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
11 5 0.06
12 3 0.04
13 10 0.12
14 37 0.45
15 24 0.29
16 3 0.04
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:182346 original size:16 final size:18
Alignment explanation
Indices: 182313--182350 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
182303 TATTTTATTC
*
182313 TTTTTATTTGCTTTACCT
1 TTTTTATTTGCTTAACCT
182331 TTTTTATTT-C-TAACCT
1 TTTTTATTTGCTTAACCT
182347 TTTT
1 TTTT
182351 ACTCCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 9 0.47
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTATTTGCTTAACCT
Found at i:185276 original size:94 final size:95
Alignment explanation
Indices: 185107--185289 Score: 264
Period size: 94 Copynumber: 1.9 Consensus size: 95
185097 TTATATATAC
* *
185107 AATAAAGCTTGAGTATCCCTCTAAAGCAATTGGTTAAATGCCTCGGCTTTATGAATAAGATCTAG
1 AATAAAACTTGAGTATCCCTCTAAAGCAATTGGTTAAATCCCTCGGCTTTATGAATAAGATCTAG
* *
185172 CTAACTTGATAAAGGTGATTATATCTATTT
66 CTAACCTGATAAAGATGATTATATCTATTT
* *
185202 AATAAAACTTGAGCTATCCCTCTAAGGCAATTGGTTAAA-CCCT-GGCTTTATGGATAAGAT-TC
1 AATAAAACTTGAG-TATCCCTCTAAAGCAATTGGTTAAATCCCTCGGCTTTATGAATAAGATCT-
*
185264 AGCTAACCTGATAAAGATGTTTATAT
64 AGCTAACCTGATAAAGATGATTATAT
185290 ATTGAGTTGT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
93 1 0.01
94 39 0.49
95 15 0.19
96 24 0.30
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (95 bp):
AATAAAACTTGAGTATCCCTCTAAAGCAATTGGTTAAATCCCTCGGCTTTATGAATAAGATCTAG
CTAACCTGATAAAGATGATTATATCTATTT
Found at i:186306 original size:109 final size:108
Alignment explanation
Indices: 186062--186421 Score: 482
Period size: 110 Copynumber: 3.3 Consensus size: 108
186052 TTTTACAGCT
186062 TTCAGAGTCAATTTCAACTTCACAG-AGAATGATATTGGACTCGAGACAACACAAGCTCAACTTC
1 TTCAGAGTCAATTTCAACTTCACAGCA-AATGATATTGGACTCGAGACAACACAAGCTCAACTTC
* *
186126 ACAGCGAATGAGCAACTGACTGTCAACAAACAATTTTTCAGTTTCA
65 ACAGCGAAGGGGC-ACTGA-TGTCAACAAACAATTTTTCAGTTTCA
* * *
186172 TTCAGAGTCAATTTCAACTTCACAGCAAAAGATATTGGACTCGAGACAACACAATCTCAACTTTA
1 TTCAGAGTCAATTTCAACTTCACAGCAAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
*
186237 CAGCGAAGGGGCGACTGATGTCAACAAACAAGTTTTCAGTTTCA
66 CAGCGAAGGGGC-ACTGATGTCAACAAACAATTTTTCAGTTTCA
* * *
186281 TTCAGAGTCAATTTCAACTTTACAGCGAATGATATTAGACTCGAGAC-A-ACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCAAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * * *
186344 GAGCGAAGGGGCAGCTGGCTGTCGACAAATAATTTTTCAG--T--
66 CAGCGAAGGGGCA-CT-GATGTCAACAAACAATTTTTCAGTTTCA
* *
186385 TTCAGAGTCAATTTCAACTTCACGGCAAAGGATATTG
1 TTCAGAGTCAATTTCAACTTCACAGCAAATGATATTG
186422 TCCTCGAAAC
Statistics
Matches: 224, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
104 32 0.14
106 2 0.01
107 26 0.12
108 20 0.09
109 68 0.30
110 75 0.33
111 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (108 bp):
TTCAGAGTCAATTTCAACTTCACAGCAAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCACTGATGTCAACAAACAATTTTTCAGTTTCA
Found at i:186833 original size:84 final size:84
Alignment explanation
Indices: 186549--187607 Score: 860
Period size: 84 Copynumber: 12.9 Consensus size: 84
186539 TGCCCACCAA
*
186549 ACCTTCGAGTTCGAC-ACGCTCAGC-CCAAGGCATATAATTTACA--ATAACTCAAGGCTA-AAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
186609 GGTTATCTGTCACCAAAAG
66 GGTTATCTGTCACCAAAAG
* * * * * * * *
186628 ACCTTCGAGTTTGACTACGC-CAACTCCAAGG-ATATCATTTACAGCATAGCTTAAGTCGATAAC
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
*
186691 GGCTATCTG---CC-AAAG
66 GGTTATCTGTCACCAAAAG
* * * * * * * * *
186706 ACCCTCGAGTTCGATTACACTCATCTTCGAGGGCATATCATTTACAGTATCACTCAAGGATAGAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAA
186771 GGGTTATCTGTCACCAAAAG
65 GGGTTATCTGTCACCAAAAG
* * * * *
186791 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATGATTTATAGCATAACTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
*
186856 GGCTATCTG---CC-AAAG
66 GGTTATCTGTCACCAAAAG
* * * * * *
186871 ACCCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGTTAGA
1 A-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGA
*
186935 AGGGTTAT-TGTCACTAAAAG
64 AGGGTTATCTGTCACCAAAAG
* * *
186955 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACT-AAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
*
187019 GGTTATCTGCCAACC-AAAG
66 GGTTATCTGTC-ACCAAAAG
* * * * * * * * *
187038 ACCTTCGAATTTGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
187103 GGTTATCTG---CC-AAAG
66 GGTTATCTGTCACCAAAAG
* * * * * * * * *
187118 ACCCTCGAGTTCGATTACACCCAGCTTCGAGGGACATCATTTACAACATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
187183 GGTTATCTGTCACCAAAAG
66 GGTTATCTGTCACCAAAAG
** * * * * * * *
187202 ACCTTTAAGTTCGACTATGCTCAGCTCCAATGCATATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
*
187267 GGTTATCTGTCA-AACAAAG
66 GGTTATCTGTCACCA-AAAG
* * **** *
187286 ACCTT-GAGTTC-ATTA----CA-ATTTGGGGACATGTCATTTAC-GACATAACTCAAGGCTAGA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGG-CATATCATTTACAG-CATAACTCAAGGCTAGA
* *
187343 AGGGTTATCTGCCAAC-AAAG
64 AGGGTTATCTGTCACCAAAAG
* * * * ** * * *
187363 ACCTTCGAGTTC-ACTACGCTCAGCTCAAAGGAACATTATTTGTAGCATAGA-TTAAGTCGAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATA-ACTCAAGGCTAGAA
* *
187426 GGGCTATCTGTCA-AACAAAG
65 GGGTTATCTGTCACCA-AAAG
* * * * **** * *
187446 ACCTTCGAGTTTGATTACACTCAACTTTGGGGGCATATCATTTGCAGCATAACTCAAAGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAA
* *
187511 GGGTTATCTGCCA-AACAAAG
65 GGGTTATCTGTCACCA-AAAG
* * **
187531 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAGCTCAAGGAAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
187596 GGTTATCTGTCA
66 GGTTATCTGTCA
187608 ATAAAATTAT
Statistics
Matches: 763, Mismatches: 174, Indels: 81
0.75 0.17 0.08
Matches are distributed among these distances:
77 12 0.02
78 67 0.09
79 33 0.04
80 103 0.13
81 83 0.11
82 59 0.08
83 111 0.15
84 207 0.27
85 88 0.12
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGTCACCAAAAG
Found at i:186887 original size:165 final size:164
Alignment explanation
Indices: 186577--187031 Score: 697
Period size: 165 Copynumber: 2.8 Consensus size: 164
186567 CTCAGCCCAA
* * *
186577 GGCATATAATTTACA-ATAACTCAAGGCTA-AAGGGTTATCTGTCACCAAAAGACCTTCGAGTTT
1 GGCATATCATTTACAGATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTC
* * * *
186640 GACTACGC-CAACTCCAAGG-ATATCATTTACAGCATAGCTTAAGTCGATAACGGCTATCTGCCA
66 GACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCA
*
186703 AAGACCCTCGAGTTCGATTACACTCATCTTCGAG
131 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAG
*
186737 GGCATATCATTTACAGTATCACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTT
1 GGCATATCATTTACAG-ATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTT
* *
186802 CGACTACGCTCAGCTCCAAGGCATATGATTTATAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
65 CGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
*
186867 AAAGACCCTTGAGTTCGATTACACTCAGCTTCGAG
130 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAG
* * * *
186902 GGCACATCATTTACAGCATAACTCAAGGTTAGAAGGGTTAT-TGTCACTAAAAGACCTTTGAGTT
1 GGCATATCATTTACAG-ATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTT
*
186966 CGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAAC-TAAGTCGAGAAGGGTTATCTGCC
65 CGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
187030 AA
130 AA
187032 CCAAAGACCT
Statistics
Matches: 269, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
160 14 0.05
162 12 0.04
163 65 0.24
164 70 0.26
165 108 0.40
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (164 bp):
GGCATATCATTTACAGATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTC
GACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCA
AAGACCCTCGAGTTCGATTACACTCAGCTTCGAG
Found at i:187040 original size:247 final size:247
Alignment explanation
Indices: 186737--187604 Score: 823
Period size: 247 Copynumber: 3.5 Consensus size: 247
186727 CATCTTCGAG
* * ***
186737 GGCATATCATTTACAGTATCACTCAAGGATAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGT
1 GGCATATCATTTACAGCATAACT-AAGTCGAGAAGGGTTATCTGTCAACC-AAAGACCTTCGAGT
* * * *
186801 TCGACTACGCTCAGCTCCAAGGCATATGATTTATAGCATAACTTAAGTCGAGAAGGGCTATCTGC
64 TCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGCTATCTGC
* * * *
186866 CAAAGACCCTTGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGT
129 CAAAGACCCTCGAGTTCGATTACACCCAGCTTCGAGGG-ACATCATTTACAACATAACTCAAGGC
* *
186931 TAGAAGGGTTAT-TGTCACTAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA
193 TAGAAGGGTTATCTGTCACCAAAAGACCTTTAAGTTCGACTACGCTCAGCTCCAA
* * *
186985 GGCATATCATTTACAGCATAACTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAATTT
1 GGCATATCATTTACAGCATAACTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTC
* * * *
187050 GACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCA
66 GACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGCTATCTGCCA
187115 AAGACCCTCGAGTTCGATTACACCCAGCTTCGAGGGACATCATTTACAACATAACTCAAGGCTAG
131 AAGACCCTCGAGTTCGATTACACCCAGCTTCGAGGGACATCATTTACAACATAACTCAAGGCTAG
*
187180 AAGGGTTATCTGTCACCAAAAGACCTTTAAGTTCGACTATGCTCAGCTCCAA
196 AAGGGTTATCTGTCACCAAAAGACCTTTAAGTTCGACTACGCTCAGCTCCAA
* * * *
187232 TGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGTCAAACAAAGACCTT-GAGTT
1 GGCATATCATTTACAGCATAAC-TAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTT
* * *** * * * * *
187296 C-ATTA----CA-AT-TTGGGGACATGTCATTTAC-GACATAACTCAAGGCTAGAAGGGTTATCT
65 CGACTACGCTCAGCTCCAAGGCACA--TCATTTACAG-CATAACTTAAGTCAAGAAGGGCTATCT
* * * * * * * ** *
187353 GCCAACAAAGACCTTCGAGTTC-ACTACGCTCAGC-TCAAAGGAACATTATTTGTAGCATAGA-T
127 G-C--CAAAGACCCTCGAGTTCGATTACACCCAGCTTC-GAGGGACATCATTTACAACATA-ACT
* * * * * ** * * * * ****
187415 TAAGTCGAGAAGGGCTATCTGTCA-AACAAAGACCTTCGAGTTTGATTACACTCAACTTTGGG
187 CAAGGCTAGAAGGGTTATCTGTCACCA-AAAGACCTTTAAGTTCGACTACGCTCAGC-TCCAA
* * * * *
187477 GGCATATCATTTGCAGCATAACTCAAAG-CTAGAAGGGTTATCTGCCAAACAAAGACCTTTGAGT
1 GGCATATCATTTACAGCATAACT--AAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGT
* * * ** *
187541 TCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTG
64 TCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGCTATCTG
187605 TCAATAAAAT
Statistics
Matches: 516, Mismatches: 80, Indels: 45
0.80 0.12 0.07
Matches are distributed among these distances:
240 6 0.01
241 2 0.00
242 33 0.06
243 4 0.01
244 69 0.13
245 67 0.13
246 48 0.09
247 188 0.36
248 58 0.11
251 35 0.07
252 2 0.00
253 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (247 bp):
GGCATATCATTTACAGCATAACTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTC
GACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGCTATCTGCCA
AAGACCCTCGAGTTCGATTACACCCAGCTTCGAGGGACATCATTTACAACATAACTCAAGGCTAG
AAGGGTTATCTGTCACCAAAAGACCTTTAAGTTCGACTACGCTCAGCTCCAA
Found at i:187533 original size:329 final size:325
Alignment explanation
Indices: 186991--187608 Score: 857
Period size: 329 Copynumber: 1.9 Consensus size: 325
186981 CCAAGGCATA
* * *
186991 TCATTTACAGCATAACTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAATTTGACTAC
1 TCATTTACAGCATAACTAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAAGTTCACTAC
* * * *
187056 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACC
66 GCTCAGCTCAAAGGAACATCATTTGCAGCATAGATTAAGTCAAGAAGGGCTATCTGCCAAAGACC
* *
187121 CTCGAGTTCGATTACACCCAGCTTCGAGGGACATCATTTACAACATAACTCAAGGCTAGAAGGGT
131 CTCGAGTTCGATTACACCCAACTTCGAGGGACATCATTTACAACATAACTCAAAGCTAGAAGGGT
* * * * *
187186 TATCTGTCACCAAAAGACCTTTAAGTTCGACTATGCTCAGCTCCAATGCATATCATTTGCAGCAT
196 TATCTGCCAACAAAAGACCTTTAAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCAT
* ***
187251 AGCTTAAGTCGAGAAGGGTTATCTGTCAAACAAAGACCTTGAGTTCATTACAATTTGGGGACATG
261 AGCTCAAGGAAAGAAGGGTTATCTGTCAAACAAAGACCTTGAGTTCATTACAATTTGGGGACATG
*
187316 TCATTTAC-GACATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCG-AGTTCACT
1 TCATTTACAG-CATAACT-AAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAAGTTCACT
* * *
187378 ACGCTCAGCTCAAAGGAACATTATTTGTAGCATAGATTAAGTCGAGAAGGGCTATCTGTCAAACA
64 ACGCTCAGCTCAAAGGAACATCATTTGCAGCATAGATTAAGTCAAGAAGGGCTATCTG-C---CA
* * * * * * * *
187443 AAGACCTTCGAGTTTGATTACACTCAACTTTGGGGGCATATCATTTGCAGCATAACTCAAAGCTA
125 AAGACCCTCGAGTTCGATTACACCCAACTTCGAGGG-ACATCATTTACAACATAACTCAAAGCTA
*
187508 GAAGGGTTATCTGCCAA-ACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
189 GAAGGGTTATCTGCCAACA-AAAGACCTTTAAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
187572 TACAGCATAGCTCAAGGAAAGAAGGGTTATCTGTCAA
253 TACAGCATAGCTCAAGGAAAGAAGGGTTATCTGTCAA
187609 TAAAATTATC
Statistics
Matches: 254, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
324 58 0.23
325 28 0.11
326 22 0.09
328 33 0.13
329 113 0.44
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (325 bp):
TCATTTACAGCATAACTAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAAGTTCACTAC
GCTCAGCTCAAAGGAACATCATTTGCAGCATAGATTAAGTCAAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGATTACACCCAACTTCGAGGGACATCATTTACAACATAACTCAAAGCTAGAAGGGT
TATCTGCCAACAAAAGACCTTTAAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCAT
AGCTCAAGGAAAGAAGGGTTATCTGTCAAACAAAGACCTTGAGTTCATTACAATTTGGGGACATG
Found at i:188338 original size:32 final size:31
Alignment explanation
Indices: 188291--188420 Score: 159
Period size: 32 Copynumber: 4.3 Consensus size: 31
188281 TTTGAAAATT
188291 AAAATA-ATATATAGTTTTTAAAACATTTTTG
1 AAAATATATATATAGTTTTTAAAACA-TTTTG
188322 AAAATATATATATAGTTTTTAAAACATTTTG
1 AAAATATATATATAGTTTTTAAAACATTTTG
188353 --AA-A-ATATATAGTTTTTAAAAAAACATTTTG
1 AAAATATATATATAGTTTTT---AAAACATTTTG
188383 AAAATATATATATAG--TTTAAAACATTTT-
1 AAAATATATATATAGTTTTTAAAACATTTTG
*
188411 AAATTATATA
1 AAAATATATA
188421 GTTTTAAACA
Statistics
Matches: 90, Mismatches: 1, Indels: 19
0.82 0.01 0.17
Matches are distributed among these distances:
27 13 0.14
28 10 0.11
29 12 0.13
30 11 0.12
31 11 0.12
32 24 0.27
33 1 0.01
34 8 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (31 bp):
AAAATATATATATAGTTTTTAAAACATTTTG
Found at i:188365 original size:59 final size:56
Alignment explanation
Indices: 188296--188433 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 56
188286 AAATTAAAAT
188296 AATATATAGTTTTTAAAACATTTTTGAAAATATATATATAGTTTTTAAAACATTTTGAA
1 AATATATAGTTTTTAAAACATTTTTGAAAATATATATATAG--TTTAAAACATTTT-AA
188355 AATATATAGTTTTTAAAAAAACA-TTTTGAAAATATATATATAGTTTAAAACATTTTAA
1 AATATATAGTTTTT---AAAACATTTTTGAAAATATATATATAGTTTAAAACATTTTAA
*
188413 ATTATATAG-TTTT-AAACATTT
1 AATATATAGTTTTTAAAACATTT
188434 AAATATATAA
Statistics
Matches: 74, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
53 5 0.07
54 2 0.03
57 4 0.05
58 10 0.14
59 27 0.36
61 20 0.27
62 6 0.08
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (56 bp):
AATATATAGTTTTTAAAACATTTTTGAAAATATATATATAGTTTAAAACATTTTAA
Found at i:188419 original size:24 final size:22
Alignment explanation
Indices: 188390--188442 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 22
188380 TTGAAAATAT
188390 ATATATAGTTTAAAACATTTTAA
1 ATATATAGTTTAAAACA-TTTAA
*
188413 ATTATATAGTTTTAAACATTTAA
1 A-TATATAGTTTAAAACATTTAA
188436 ATATATA
1 ATATATA
188443 ATTAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 6 0.21
23 7 0.25
24 15 0.54
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATATAGTTTAAAACATTTAA
Found at i:188467 original size:13 final size:14
Alignment explanation
Indices: 188431--188480 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
188421 GTTTTAAACA
188431 TTTAAATATATAA-
1 TTTAAATATATAAT
*
188444 TTAAAATATATAAT
1 TTTAAATATATAAT
188458 TTTAAA-ATAT--T
1 TTTAAATATATAAT
*
188469 TTTAAAAATATA
1 TTTAAATATATA
188481 TTATATATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 7 0.22
12 4 0.12
13 16 0.50
14 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTAAATATATAAT
Found at i:189859 original size:14 final size:15
Alignment explanation
Indices: 189821--189869 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
189811 TCCCTTGTGT
*
189821 TTTTTTCTATT-TTA
1 TTTTTTCTTTTGTTA
189835 TTATTTTC-TTTG-TA
1 TT-TTTTCTTTTGTTA
189849 TTTTTTACTTTTGTTA
1 TTTTTT-CTTTTGTTA
189865 TTTTT
1 TTTTT
189870 ATTGTTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.14
14 9 0.31
15 9 0.31
16 7 0.24
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTTTCTTTTGTTA
Found at i:189874 original size:27 final size:27
Alignment explanation
Indices: 189818--189883 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
189808 TTTTCCCTTG
189818 TGTT-TTTTTCTATTTTATTATTTTCTT
1 TGTTATTTTT-TATTTTATTATTTTCTT
*
189845 TG-TATTTTTTACTTTTGTTATTTT-TAT
1 TGTTATTTTTTA-TTTTATTATTTTCT-T
189872 TGTTATGTTTTT
1 TGTTAT-TTTTT
189884 TCTCTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 4 0.12
27 21 0.64
28 3 0.09
29 5 0.15
ACGTcount: A:0.12, C:0.05, G:0.08, T:0.76
Consensus pattern (27 bp):
TGTTATTTTTTATTTTATTATTTTCTT
Found at i:189912 original size:3 final size:3
Alignment explanation
Indices: 189904--189932 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
189894 TATTTAATAT
189904 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
189933 TTTCTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:190800 original size:19 final size:19
Alignment explanation
Indices: 190766--190802 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
190756 TCATCATTAT
* *
190766 ATTACTAAATTTACTTTAA
1 ATTACTAAAATGACTTTAA
190785 ATTACTAAAATGACTTTA
1 ATTACTAAAATGACTTTA
190803 TATATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTACTAAAATGACTTTAA
Found at i:191348 original size:22 final size:22
Alignment explanation
Indices: 191323--191386 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
191313 TGATTTCTAA
*
191323 TCAGCATTCAGACCAAGTCCAG
1 TCAGCATTCATACCAAGTCCAG
191345 TCAGCATTCATACCAAGTCCAG
1 TCAGCATTCATACCAAGTCCAG
*
191367 CCAGCATTCATACCAA-TCCA
1 TCAGCATTCATACCAAGTCCA
191387 ATCAATGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.20
Consensus pattern (22 bp):
TCAGCATTCATACCAAGTCCAG
Found at i:192560 original size:37 final size:34
Alignment explanation
Indices: 192495--192578 Score: 87
Period size: 37 Copynumber: 2.4 Consensus size: 34
192485 AATTAGCATC
* * *
192495 AAAATTCTGAAAATAAAAATAAAATAAAATAGTT
1 AAAATTATAAAAATAAAAATAAAATAAAATAATT
* * *
192529 AGAATTTTAAAAATAAAATAATCAAATTAAAATAATT
1 AAAATTATAAAAAT-AAA-AAT-AAAATAAAATAATT
192566 AAAATTATAAAAA
1 AAAATTATAAAAA
192579 AAATCGACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 11 0.28
35 3 0.08
36 3 0.08
37 23 0.57
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (34 bp):
AAAATTATAAAAATAAAAATAAAATAAAATAATT
Found at i:200771 original size:38 final size:38
Alignment explanation
Indices: 200720--200794 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
200710 ACACAAATGT
200720 AAGAGTTAAAGTTTATTCCACAAAACCTTTCTCAGAAC
1 AAGAGTTAAAGTTTATTCCACAAAACCTTTCTCAGAAC
200758 AAGAGTTAAAGTTTATTCCACAAAACCTTTCTCAGAA
1 AAGAGTTAAAGTTTATTCCACAAAACCTTTCTCAGAA
200795 ATGCCATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (38 bp):
AAGAGTTAAAGTTTATTCCACAAAACCTTTCTCAGAAC
Found at i:204593 original size:2 final size:2
Alignment explanation
Indices: 204586--204629 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
204576 AATATGAAAG
204586 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
204628 AT
1 AT
204630 TATGGTTAGA
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
Found at i:205955 original size:39 final size:40
Alignment explanation
Indices: 205912--206003 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
205902 ACTATTTTCT
205912 GGTGTAAGTTAGTCCTTT-TCCCTCAAACTTATTTACACC
1 GGTGTAAGTTAGTCCTTTCTCCCTCAAACTTATTTACACC
* * * *
205951 GGTGTAAGTTTGGCCTTTCTCCTTCATACTTATTTACACC
1 GGTGTAAGTTAGTCCTTTCTCCCTCAAACTTATTTACACC
205991 GGTGTAAGTTAGT
1 GGTGTAAGTTAGT
206004 TGGAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 16 0.35
40 30 0.65
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (40 bp):
GGTGTAAGTTAGTCCTTTCTCCCTCAAACTTATTTACACC
Found at i:211802 original size:18 final size:18
Alignment explanation
Indices: 211779--211828 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
211769 GATACTTTTG
* *
211779 AGGGGTGGCACTTGGATT
1 AGGGGTGACACTTGAATT
211797 AGGGGTGACACTTGAATT
1 AGGGGTGACACTTGAATT
211815 AGGGGTGACACTTG
1 AGGGGTGACACTTG
211829 TGGAGGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.40, T:0.26
Consensus pattern (18 bp):
AGGGGTGACACTTGAATT
Found at i:212340 original size:51 final size:50
Alignment explanation
Indices: 212282--212405 Score: 149
Period size: 56 Copynumber: 2.3 Consensus size: 50
212272 TTCGTTTTCT
* *
212282 CAACGCGAATTTCGCAACATTAATTACTGATATAGGTAAACACAACTATCG
1 CAACGCGAATTTCGCAACACT-ATTACCGATATAGGTAAACACAACTATCG
*
212333 CAACGCGAATTTCGTTTTCGCAACGCTATTACCGATATAGGTAAACACAACTATCG
1 CAACGCGAA------TTTCGCAACACTATTACCGATATAGGTAAACACAACTATCG
*
212389 CGACGCGAATTTCGCAA
1 CAACGCGAATTTCGCAA
212406 ATCGAATTCG
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
50 8 0.13
51 9 0.14
56 36 0.57
57 10 0.16
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (50 bp):
CAACGCGAATTTCGCAACACTATTACCGATATAGGTAAACACAACTATCG
Found at i:216261 original size:21 final size:20
Alignment explanation
Indices: 216234--216351 Score: 76
Period size: 21 Copynumber: 5.8 Consensus size: 20
216224 AATCAGTTTC
*
216234 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-AT
* * * *
216255 GAAAATCGCAATGCGATAGAA
1 CAAAATCGCAACGCGAT-TAT
* ** *
216276 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTAT
*
216296 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTAT
* **
216317 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGATTAT
216336 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
216352 TATCCGTAAA
Statistics
Matches: 75, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.01
20 30 0.40
21 44 0.59
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTAT
Found at i:216361 original size:20 final size:20
Alignment explanation
Indices: 216299--216491 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
216289 CGATTTTCCA
* ** *
216299 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
216319 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
216339 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
216359 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
216379 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
216399 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
216419 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
216439 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
216459 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
216479 AAATCGCAACGCG
1 AAATCGCAACGCG
216492 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:216912 original size:33 final size:33
Alignment explanation
Indices: 216873--216943 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
216863 TTCACTTAGA
216873 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
216906 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
216939 TTTCA
1 TTTCA
216944 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:217080 original size:41 final size:41
Alignment explanation
Indices: 217022--217099 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
217012 TTGCAGAAGA
*
217022 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
217063 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
217100 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:217096 original size:21 final size:21
Alignment explanation
Indices: 217023--217098 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
217013 TGCAGAAGAG
*
217023 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
217044 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
217064 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
217085 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
217099 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:217102 original size:14 final size:14
Alignment explanation
Indices: 217083--217139 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
217073 GAGAAATGAA
217083 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
217097 AATCGCAACGCGAAATTAA
1 AATCGCAA--CG--A-GAG
217116 AATCGCAACGAGAG
1 AATCGCAACGAGAG
217130 AATCGCAACG
1 AATCGCAACG
217140 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:217118 original size:33 final size:33
Alignment explanation
Indices: 217075--217155 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
217065 CGCAACGAGA
*
217075 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATCAAAATCGCAACGAGAGAATCGCAACGC
*
217108 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATCAAAATCGCAACGAGAGAATCGCAACGC
*
217141 GAAACCAAAATCGCA
1 GAAATCAAAATCGCA
217156 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATCAAAATCGCAACGAGAGAATCGCAACGC
Found at i:217173 original size:19 final size:19
Alignment explanation
Indices: 217151--217248 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
217141 GAAACCAAAA
*
217151 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
217170 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
217184 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
217203 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
217217 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
217236 TCGCGTTGCGATT
1 TCGCGTTGCGATT
217249 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:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:217192 original size:14 final size:14
Alignment explanation
Indices: 217173--217262 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
217163 TTTCATTTCG
217173 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
217187 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
217206 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
217220 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
217239 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
217253 CGTTGCGATT
1 CGTTGCGATT
217263 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:217198 original size:33 final size:33
Alignment explanation
Indices: 217156--217270 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
217146 CAAAATCGCA
217156 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
217189 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
217222 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
217255 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
217271 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:219271 original size:92 final size:93
Alignment explanation
Indices: 218968--219341 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
218958 TAGATTGCTT
*
218968 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
219033 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
219061 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
219126 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
219154 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
219218 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
219246 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
219310 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
219337 AGTAA
1 AGTAA
219342 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 6 0.02
92 125 0.45
93 148 0.53
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:219281 original size:185 final size:184
Alignment explanation
Indices: 218968--219341 Score: 714
Period size: 185 Copynumber: 2.0 Consensus size: 184
218958 TAGATTGCTT
218968 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
219033 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
219098 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
219154 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
219218 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
219283 GTGTATTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
131 GTGTATTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
219337 AGTAA
1 AGTAA
219342 TGCAATCCAT
Statistics
Matches: 187, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
183 6 0.03
184 33 0.18
185 97 0.52
186 51 0.27
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:219429 original size:19 final size:19
Alignment explanation
Indices: 219389--219498 Score: 105
Period size: 19 Copynumber: 6.3 Consensus size: 19
219379 TAGTTTACTT
* *
219389 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
219409 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
219428 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
219442 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
219461 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
219475 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
219494 TCGCA
1 TCGCA
219499 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 29 0.39
20 13 0.18
ACGTcount: A:0.45, C:0.30, G:0.16, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:219449 original size:33 final size:32
Alignment explanation
Indices: 219406--219498 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 32
219396 ACGAAACTTA
219406 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
219438 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
219471 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
219499 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
32 2 0.03
33 57 0.97
ACGTcount: A:0.46, C:0.30, G:0.17, T:0.06
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:219516 original size:19 final size:19
Alignment explanation
Indices: 219494--219612 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
219484 GAAACCAAAA
*
219494 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
219513 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
219529 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
219546 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
219562 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
219579 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
219598 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
219613 AAGTTTCATG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:219535 original size:14 final size:14
Alignment explanation
Indices: 219516--219572 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
219506 TTTCATTTCG
219516 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
219530 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
219547 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
219563 CGTTGCGATT
1 CGTTGCGATT
219573 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:219541 original size:33 final size:33
Alignment explanation
Indices: 219499--219591 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
219489 CAAAATCGCA
*
219499 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
219532 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
219565 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
219592 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:219628 original size:20 final size:19
Alignment explanation
Indices: 219563--219619 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
219553 GCGATTCTGT
219563 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
219582 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
219601 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATTTT-AGTTTC
219620 ATGTTGCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 29 0.85
20 5 0.15
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:221561 original size:14 final size:14
Alignment explanation
Indices: 221542--221577 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
221532 ATTGTTTAAT
221542 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
221556 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
221570 TGATTTGT
1 TGATTTGT
221578 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:221700 original size:19 final size:19
Alignment explanation
Indices: 221684--221780 Score: 150
Period size: 19 Copynumber: 5.4 Consensus size: 19
221674 AAAAATGACT
221684 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
221703 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
221722 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
221736 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
221755 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
221774 ATCGCAA
1 ATCGCAA
221781 CGGGATAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 55 0.77
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:221762 original size:52 final size:52
Alignment explanation
Indices: 221684--221794 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 52
221674 AAAAATGACT
221684 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
221736 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGGGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
221788 ATCGCAA
1 ATCGCAA
221795 CGGGATTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:221792 original size:14 final size:14
Alignment explanation
Indices: 221773--221800 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
221763 GCGAAATGAA
221773 AATCGCAACGGGAT
1 AATCGCAACGGGAT
221787 AATCGCAACGGGAT
1 AATCGCAACGGGAT
221801 TTTCATTTCG
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:0.36, C:0.21, G:0.29, T:0.14
Consensus pattern (14 bp):
AATCGCAACGGGAT
Found at i:221820 original size:19 final size:19
Alignment explanation
Indices: 221798--221991 Score: 203
Period size: 19 Copynumber: 11.2 Consensus size: 19
221788 ATCGCAACGG
221798 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
221817 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
221831 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
221850 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
221869 GA--TTC-TATCG--TTGC
1 GATTTTCATTTCGCATTGC
221883 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
221902 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
221921 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
221935 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
*
221955 GATTTTCA--T-G--TTGG
1 GATTTTCATTTCGCATTGC
221969 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
221988 GATT
1 GATT
221992 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 8, Indels: 42
0.74 0.04 0.21
Matches are distributed among these distances:
14 29 0.20
16 23 0.16
17 20 0.14
18 3 0.02
19 59 0.40
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:221845 original size:52 final size:52
Alignment explanation
Indices: 221798--221963 Score: 314
Period size: 52 Copynumber: 3.2 Consensus size: 52
221788 ATCGCAACGG
221798 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
*
221850 GATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
221902 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGC
221955 GATTTTCAT
1 GATTTTCAT
221964 GTTGGGATTT
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 94 0.85
53 17 0.15
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
Found at i:222013 original size:33 final size:33
Alignment explanation
Indices: 221798--222005 Score: 226
Period size: 33 Copynumber: 6.1 Consensus size: 33
221788 ATCGCAACGG
221798 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
221831 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGC
* * * * *
221869 GATTCTATCGTTGCG-ATTTTC-ATT-TCGCATTGC
1 GATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGC
221902 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
* *
221935 GATTTTCATTTCCGCATTGCGATTTTCAT-GTTGG
1 GATTTTCATTT-CGCATTGCGATTCTC-TCGTTGC
221969 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
222002 GATT
1 GATT
222006 GTAATTTCCG
Statistics
Matches: 145, Mismatches: 16, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 69 0.48
34 29 0.20
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
Found at i:224514 original size:24 final size:24
Alignment explanation
Indices: 224480--224526 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
224470 CTGAAACATC
224480 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
224504 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
224527 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:225236 original size:20 final size:20
Alignment explanation
Indices: 225208--225417 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
225198 AAATTTCAGT
* * * *
225208 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
225228 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* *
225248 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATACGC
* *
225268 GTTGCGATTTATGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
225288 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
225308 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
225328 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
225348 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
225368 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
225388 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
225408 GTTGCGATTT
1 GTTGCGATTT
225418 TGGAAAATCG
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:225434 original size:21 final size:21
Alignment explanation
Indices: 225404--225486 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
225394 ATTTATGTGT
*
225404 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
225425 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
225446 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
225467 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
225487 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:230268 original size:2 final size:2
Alignment explanation
Indices: 230261--230323 Score: 84
Period size: 2 Copynumber: 34.5 Consensus size: 2
230251 TATTAATAAT
230261 TA TA TA TA TA -A TA -A T- TA TA TA TA TA -A TA -A T- 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
230297 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
230324 TCATAAACTA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:230274 original size:15 final size:15
Alignment explanation
Indices: 230254--230318 Score: 103
Period size: 15 Copynumber: 4.1 Consensus size: 15
230244 ATATTTTTAT
230254 TAATAATTATATATA
1 TAATAATTATATATA
230269 TAATAATTATATATA
1 TAATAATTATATATA
230284 TAATAATTATATATA
1 TAATAATTATATATA
230299 TATATATATATATATATA
1 TA-ATA-AT-TATATATA
230317 TA
1 TA
230319 TATATTCATA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
15 32 0.68
16 3 0.06
17 2 0.04
18 10 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATAATTATATATA
Found at i:231447 original size:23 final size:23
Alignment explanation
Indices: 231421--231489 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
231411 CACCACAGCT
*
231421 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
231444 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
231467 CATAGAATTGCATCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
231490 TATAAGATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:238341 original size:24 final size:23
Alignment explanation
Indices: 238314--238383 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
238304 CACCACAGCT
* *
238314 CGTATAAATGCACTGAAAGTGCCA
1 CGTAGAAATGCACCG-AAGTGCCA
* *
238338 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
238361 CGTAGAATTGCATCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
238384 TATAAGATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 27 0.69
24 12 0.31
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:238364 original size:23 final size:23
Alignment explanation
Indices: 238330--238383 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
238320 AATGCACTGA
238330 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
* *
238353 AAGTGCCGCGTAGAATTGCATCG
1 AAGTGCCACGTAGAATTGCACCG
*
238376 TAGTGCCA
1 AAGTGCCA
238384 TATAAGATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:238435 original size:2 final size:2
Alignment explanation
Indices: 238428--238457 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
238418 CTTAAGAATC
238428 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
238458 GTTAAGGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242040 original size:23 final size:22
Alignment explanation
Indices: 241992--242040 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
241982 ACAGAATGTC
241992 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
242013 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
242036 AAGGA
1 AAGGA
242041 AAAATATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:242987 original size:31 final size:31
Alignment explanation
Indices: 242949--243135 Score: 304
Period size: 31 Copynumber: 6.0 Consensus size: 31
242939 AGGGTCGAGG
242949 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
242980 GTTTACCTATGTTCTTGGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
243011 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
243042 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
243073 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
243104 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
243135 G
1 G
243136 GTCCTTTGGG
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 146 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:244270 original size:19 final size:19
Alignment explanation
Indices: 244246--244335 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
244236 TTTAAGGGAG
244246 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
244265 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
**
244284 ATGCATCGATGCACT-AAT
1 ATGCATCGATGCACTCCTT
* *
244302 -TGCATTTGATGCACTTCTT
1 ATGCA-TCGATGCACTCCTT
244321 ATGCATCGATGCACT
1 ATGCATCGATGCACT
244336 AATTGCATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.06
18 10 0.16
19 44 0.71
20 4 0.06
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:244314 original size:18 final size:18
Alignment explanation
Indices: 244291--244349 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
244281 CTTATGCATC
244291 GATGCACTAATTGCATTT
1 GATGCACTAATTGCATTT
** *
244309 GATGCACTTCTTATGCA-TC
1 GATGCAC-TAAT-TGCATTT
244328 GATGCACTAATTGCATTT
1 GATGCACTAATTGCATTT
244346 GATG
1 GATG
244350 TTCATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 4 0.12
18 14 0.44
19 10 0.31
20 4 0.12
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (18 bp):
GATGCACTAATTGCATTT
Found at i:244322 original size:37 final size:37
Alignment explanation
Indices: 244246--244349 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
244236 TTTAAGGGAG
** *
244246 ATGCATCGATGCACTCCTTATGCA-TCGATGCACTCCTT
1 ATGCATCGATGCACT-AAT-TGCATTTGATGCACTCCTT
*
244284 ATGCATCGATGCACTAATTGCATTTGATGCACTTCTT
1 ATGCATCGATGCACTAATTGCATTTGATGCACTCCTT
244321 ATGCATCGATGCACTAATTGCATTTGATG
1 ATGCATCGATGCACTAATTGCATTTGATG
244350 TTCATTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
36 4 0.07
37 42 0.69
38 15 0.25
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (37 bp):
ATGCATCGATGCACTAATTGCATTTGATGCACTCCTT
Found at i:245905 original size:21 final size:21
Alignment explanation
Indices: 245850--245894 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
245840 CGTTAAGATG
245850 GTTGCAAAGAAATTTTAAAGA
1 GTTGCAAAGAAATTTTAAAGA
245871 GTTGCAAAGAAATTTTAAAGA
1 GTTGCAAAGAAATTTTAAAGA
245892 GTT
1 GTT
245895 TCGCAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (21 bp):
GTTGCAAAGAAATTTTAAAGA
Found at i:246108 original size:29 final size:30
Alignment explanation
Indices: 246076--246145 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
246066 AGCTTTTTAG
* *
246076 TAGTGACCAAAATATATATTTTG-AAAGTT
1 TAGTGACCAAAATATAAATTTGGAAAAGTT
* *
246105 TAGT-AGCTAAATATAAATTTGGAAAAGTT
1 TAGTGACCAAAATATAAATTTGGAAAAGTT
*
246134 TAGGGACCAAAA
1 TAGTGACCAAAA
246146 ATGTAATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 14 0.44
29 13 0.41
30 5 0.16
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.31
Consensus pattern (30 bp):
TAGTGACCAAAATATAAATTTGGAAAAGTT
Found at i:255777 original size:21 final size:21
Alignment explanation
Indices: 255751--255790 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
255741 CCCCCTTTGA
*
255751 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
255772 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
255791 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:259584 original size:61 final size:61
Alignment explanation
Indices: 259490--259608 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 61
259480 TCATATTTAA
*
259490 ATGGTACATAAATTATTTTATGATTTTACACGATTAACG-AAAAATTTAAAAGTTGAACAT
1 ATGGTACATAAAATATTTTATGATTTTACACGATTAACGAAAAAATTTAAAAGTTGAACAT
259550 ATGGTACATAAAAATATTTTATGATTTTACACGATTAACGAAAAAATTTAAAAGTTGAA
1 ATGGTACAT-AAAATATTTTATGATTTTACACGATTAACGAAAAAATTTAAAAGTTGAA
259609 AAGAAAGATT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
60 9 0.16
61 29 0.52
62 18 0.32
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (61 bp):
ATGGTACATAAAATATTTTATGATTTTACACGATTAACGAAAAAATTTAAAAGTTGAACAT
Found at i:263288 original size:20 final size:21
Alignment explanation
Indices: 263230--263288 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
263220 TCCAGAACCT
*
263230 GGGGGTATCGATTCCC-TCAA
1 GGGGGTATCAATTCCCTTCAA
* *
263250 GGAGGGAATCAGTTCCCCTTCAA
1 GG-GGGTATCAATT-CCCTTCAA
263273 -GGGGTATCAATTCCCT
1 GGGGGTATCAATTCCCT
263289 CTGCCCTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 6 0.19
21 17 0.55
22 4 0.13
23 4 0.13
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
GGGGGTATCAATTCCCTTCAA
Found at i:269744 original size:20 final size:21
Alignment explanation
Indices: 269711--269763 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
269701 CACAACAGCT
* * *
269711 GATTCTGATTCCATATCC-CC
1 GATTCAGATGCCATACCCGCC
269731 GATTCAGATGCCATACCCGCC
1 GATTCAGATGCCATACCCGCC
*
269752 TATTCAGATGCC
1 GATTCAGATGCC
269764 TCCACTGCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (21 bp):
GATTCAGATGCCATACCCGCC
Found at i:273251 original size:16 final size:16
Alignment explanation
Indices: 273230--273264 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
273220 TAAAAGCCAT
273230 TTTGAGAATTTGAAAG
1 TTTGAGAATTTGAAAG
* *
273246 TTTGAGAGTTTGATAG
1 TTTGAGAATTTGAAAG
273262 TTT
1 TTT
273265 CAAGTTATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (16 bp):
TTTGAGAATTTGAAAG
Found at i:282684 original size:65 final size:65
Alignment explanation
Indices: 282580--282723 Score: 209
Period size: 65 Copynumber: 2.2 Consensus size: 65
282570 TTCAAAAATT
*
282580 CTTTGAATTATGGGCAATTTCATCCCTACTTTTAGCAAAGACCTTGGTACCACCTT-GACGCTTA
1 CTTTGAATTATGGGCAACTTCATCCCTACTTTTAGCAAAGACCTTGGTACCA-CTTCGACGCTTA
282644 C
65 C
** * *
282645 CTTTGAATTATGGGCAACTTCATCTTTGCTTTTAGCAAAGACCTTGGTACCACTTCGACGCTTAT
1 CTTTGAATTATGGGCAACTTCATCCCTACTTTTAGCAAAGACCTTGGTACCACTTCGACGCTTAC
**
282710 CGCTGAATTATGGG
1 CTTTGAATTATGGG
282724 ATATTAGCGA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
64 3 0.04
65 68 0.96
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (65 bp):
CTTTGAATTATGGGCAACTTCATCCCTACTTTTAGCAAAGACCTTGGTACCACTTCGACGCTTAC
Found at i:284603 original size:14 final size:14
Alignment explanation
Indices: 284584--284613 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
284574 TTAAATGATA
284584 AACGAACACAAATG
1 AACGAACACAAATG
*
284598 AACGAACATAAATG
1 AACGAACACAAATG
284612 AA
1 AA
284614 TGAGTCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:284638 original size:23 final size:23
Alignment explanation
Indices: 284598--284663 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
284588 AACACAAATG
* *
284598 AACGAACATAAATGAATGAGTC-TA
1 AACGAACA-AAATAAATGA-ACATA
284622 AACGAACAAAATAAATGAACATA
1 AACGAACAAAATAAATGAACATA
* *
284645 AATGAACACAATAAATGAA
1 AACGAACAAAATAAATGAA
284664 TGAAAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.03
23 28 0.76
24 8 0.22
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (23 bp):
AACGAACAAAATAAATGAACATA
Found at i:284708 original size:23 final size:23
Alignment explanation
Indices: 284682--284730 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
284672 AACATGTACA
* *
284682 AACATAACAAATGAACATAATCG
1 AACACAACAAATGAACATAAACG
* *
284705 AACACAATAAATGAACGTAAACG
1 AACACAACAAATGAACATAAACG
284728 AAC
1 AAC
284731 GTAAACAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (23 bp):
AACACAACAAATGAACATAAACG
Found at i:285079 original size:40 final size:37
Alignment explanation
Indices: 285022--285095 Score: 103
Period size: 40 Copynumber: 1.9 Consensus size: 37
285012 AATGAGACAT
* *
285022 TTGTTCGTGTTCGTTCATTTAATTAAATGAACATAAAATC
1 TTGTTCATGTTCATTCATTTAA-TAAAT-AA-ATAAAATC
285062 TTGTTCATGTTCATTCATTTAATAAATAAATAAA
1 TTGTTCATGTTCATTCATTTAATAAATAAATAAA
285096 TATAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 5 0.16
38 2 0.06
39 5 0.16
40 20 0.62
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (37 bp):
TTGTTCATGTTCATTCATTTAATAAATAAATAAAATC
Found at i:293267 original size:24 final size:24
Alignment explanation
Indices: 293235--293320 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
293225 GATATCAGAA
*
293235 ATCAAAACAGAATTCAGATAAGAT
1 ATCATAACAGAATTCAGATAAGAT
* * * *
293259 ATCATAACATAATCCAGATCAGAA
1 ATCATAACAGAATTCAGATAAGAT
* * *
293283 ATCAGAACATAATTCAGGTAATG-T
1 ATCATAACAGAATTCAGATAA-GAT
293307 ATCATAACAGAATT
1 ATCATAACAGAATT
293321 AAAGTCGAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCATAACAGAATTCAGATAAGAT
Found at i:295971 original size:16 final size:17
Alignment explanation
Indices: 295941--295973 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
295931 AAACCGATCC
295941 AAAAAACCGATAACCGA
1 AAAAAACCGATAACCGA
*
295958 AAAAAATCGA-AACCGA
1 AAAAAACCGATAACCGA
295974 TTTAGTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAACCGATAACCGA
Found at i:297201 original size:23 final size:23
Alignment explanation
Indices: 297169--297214 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
297159 TCGGTTCGTC
*
297169 GATCGAAGGTCGGACGACGAGTA
1 GATCGAAGGTCAGACGACGAGTA
* *
297192 GATCGGAGGTCAGACGGCGAGTA
1 GATCGAAGGTCAGACGACGAGTA
297215 TATCAGAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.41, T:0.13
Consensus pattern (23 bp):
GATCGAAGGTCAGACGACGAGTA
Found at i:298602 original size:2 final size:2
Alignment explanation
Indices: 298595--298629 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
298585 TATTCTTTTA
298595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
298630 CCCCATCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:302216 original size:2 final size:2
Alignment explanation
Indices: 302209--302248 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
302199 TGTGAAAATA
*
302209 AT AT AT AT AC 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
302249 GCCTTATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:303462 original size:14 final size:13
Alignment explanation
Indices: 303432--303482 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
303422 GTAAAAATAT
*
303432 TAAATATTAAATAA
1 TAAATA-TAATTAA
303446 TAAATATAATTATA
1 TAAATATAATTA-A
*
303460 TAATTATAATTAA
1 TAAATATAATTAA
*
303473 AAAATA-AATT
1 TAAATATAATT
303483 TGAGGTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 10 0.31
14 18 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:314684 original size:16 final size:16
Alignment explanation
Indices: 314663--314699 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
314653 TCGAAGTTTC
314663 TTTTCCTTTTGATTTA
1 TTTTCCTTTTGATTTA
*
314679 TTTTCCTTTTGATTTC
1 TTTTCCTTTTGATTTA
314695 TTTTC
1 TTTTC
314700 AAGTTCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTTCCTTTTGATTTA
Found at i:320579 original size:20 final size:20
Alignment explanation
Indices: 320556--320605 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
320546 GCAAATTTGG
* *
320556 AATTCGCAAGACAGAAGTCA
1 AATTCGCAACACAAAAGTCA
320576 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
320596 AATTCGCAAC
1 AATTCGCAAC
320606 TCGATTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:320662 original size:20 final size:21
Alignment explanation
Indices: 320639--320728 Score: 79
Period size: 20 Copynumber: 4.6 Consensus size: 21
320629 CATATTTCTT
*
320639 TTTCACAACACGATTTTT-AA
1 TTTCGCAACACGATTTTTGAA
*
320659 TTTCGCAACTCGATTTTTGAA
1 TTTCGCAACACGATTTTTGAA
*
320680 -TTCGCAACACGAATTTT---
1 TTTCGCAACACGATTTTTGAA
*
320697 TTTCGCAACTCGATTTCTT---
1 TTTCGCAACACGATTT-TTGAA
320716 TTTCGCAACACGA
1 TTTCGCAACACGA
320729 ATTGTTTGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
18 13 0.22
19 14 0.23
20 31 0.52
21 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (21 bp):
TTTCGCAACACGATTTTTGAA
Found at i:320730 original size:37 final size:38
Alignment explanation
Indices: 320632--320731 Score: 132
Period size: 38 Copynumber: 2.6 Consensus size: 38
320622 CGTAACACAT
* *
320632 ATTTCTTTTTCACAACACGATTTTTAATTTCGCAACTCG
1 ATTTCTTTTTCGCAACACGAATTTT-ATTTCGCAACTCG
*
320671 ATTT-TTGAATTCGCAACACGAATTTT-TTTCGCAACTCG
1 ATTTCTT--TTTCGCAACACGAATTTTATTTCGCAACTCG
320709 ATTTCTTTTTCGCAACACGAATT
1 ATTTCTTTTTCGCAACACGAATT
320732 GTTTGGGTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 15 0.28
38 18 0.33
39 6 0.11
40 15 0.28
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (38 bp):
ATTTCTTTTTCGCAACACGAATTTTATTTCGCAACTCG
Found at i:321663 original size:24 final size:24
Alignment explanation
Indices: 321636--321682 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
321626 AGTCAGTATT
321636 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
*
321660 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
321683 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:321694 original size:24 final size:24
Alignment explanation
Indices: 321641--321687 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
321631 GTATTCGAAA
*
321641 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
321665 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
321688 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:321912 original size:3 final size:3
Alignment explanation
Indices: 321869--321897 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
321859 ATATAACCCT
321869 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
321898 GTCCCAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:323961 original size:21 final size:20
Alignment explanation
Indices: 323937--324007 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 20
323927 ATGTGGATCC
323937 TGAACGATGGGAGGGGATTCT
1 TGAACGATGGGAGGGG-TTCT
*
323958 TGAACGATGGGAGGAGGCTCT
1 TGAACGATGGGAGG-GGTTCT
*
323979 TGAACGATGGGATGGGTCTCT
1 TGAACGATGGGAGGGGT-TCT
324000 TGAACGAT
1 TGAACGAT
324008 AAGAGCTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.39, T:0.24
Consensus pattern (20 bp):
TGAACGATGGGAGGGGTTCT
Found at i:324024 original size:21 final size:21
Alignment explanation
Indices: 324000--324049 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
323990 ATGGGTCTCT
*
324000 TGAACGATAAGAGCTGAATCC
1 TGAACAATAAGAGCTGAATCC
** *
324021 TGAACAATGGGAGGTGAATCC
1 TGAACAATAAGAGCTGAATCC
324042 TGAACAAT
1 TGAACAAT
324050 GGTAGGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (21 bp):
TGAACAATAAGAGCTGAATCC
Found at i:324025 original size:42 final size:42
Alignment explanation
Indices: 323933--324034 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
323923 TTGAATGTGG
** * *
323933 ATCCTGAACGATGGGAGGGGATTCTTGAACGATGGGAGGAGG
1 ATCCTGAACGATGGGAGGGGATTCTTGAACGATAAGAGCAGA
* * * *
323975 CTCTTGAACGATGGGATGGG-TCTCTTGAACGATAAGAGCTGA
1 ATCCTGAACGATGGGAGGGGAT-TCTTGAACGATAAGAGCAGA
*
324017 ATCCTGAACAATGGGAGG
1 ATCCTGAACGATGGGAGG
324035 TGAATCCTGA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (42 bp):
ATCCTGAACGATGGGAGGGGATTCTTGAACGATAAGAGCAGA
Found at i:324050 original size:21 final size:21
Alignment explanation
Indices: 324014--324057 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
324004 CGATAAGAGC
324014 TGAATCCTGAACAATGGGAGG
1 TGAATCCTGAACAATGGGAGG
*
324035 TGAATCCTGAACAATGGTAGG
1 TGAATCCTGAACAATGGGAGG
324056 TG
1 TG
324058 GATCAGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.23
Consensus pattern (21 bp):
TGAATCCTGAACAATGGGAGG
Found at i:324395 original size:21 final size:20
Alignment explanation
Indices: 324371--324454 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 20
324361 CCTCGTCACA
324371 TAAAACAACTACCTCACCACG
1 TAAAAC-ACTACCTCACCACG
* ** *
324392 TAAAACACCATTGTCATCACG
1 TAAAACACTA-CCTCACCACG
324413 TAAAACAACTACCTCACCACG
1 TAAAAC-ACTACCTCACCACG
* *
324434 TAAAGACCCTACCTCATCACG
1 TAAA-ACACTACCTCACCACG
324455 CCATGCATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
20 3 0.06
21 42 0.84
22 5 0.10
ACGTcount: A:0.39, C:0.36, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAACACTACCTCACCACG
Found at i:324454 original size:42 final size:41
Alignment explanation
Indices: 324346--324454 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 41
324336 GAAATAATCT
* * * *
324346 CACGTAGAGCACCGACCTCGTCACATAAAACAACTACCTCAC
1 CACGTAAAACACC-ACCTCATCACGTAAAACAACTACCTCAC
**
324388 CACGTAAAACACCATTGTCATCACGTAAAACAACTACCTCAC
1 CACGTAAAACACCA-CCTCATCACGTAAAACAACTACCTCAC
324430 CACGTAAAGAC-CCTACCTCATCACG
1 CACGTAAA-ACACC-ACCTCATCACG
324455 CCATGCATCA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 52 0.93
43 3 0.05
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.17
Consensus pattern (41 bp):
CACGTAAAACACCACCTCATCACGTAAAACAACTACCTCAC
Found at i:325467 original size:44 final size:44
Alignment explanation
Indices: 325401--325507 Score: 162
Period size: 44 Copynumber: 2.4 Consensus size: 44
325391 ATGCAATATT
*
325401 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTT-AT-CCATAAGCTCGTAAGCTTATTTTACCAATACAC
325447 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
*
325491 TTGCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
325508 CCATATACCA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
43 3 0.05
44 44 0.76
45 2 0.03
46 9 0.16
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
Found at i:327949 original size:15 final size:16
Alignment explanation
Indices: 327920--327953 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
327910 TAGTGATAAT
327920 AATATGATCACTGATA
1 AATATGATCACTGATA
*
327936 AATATGTTCA-TGATA
1 AATATGATCACTGATA
327951 AAT
1 AAT
327954 GTATATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (16 bp):
AATATGATCACTGATA
Found at i:333518 original size:22 final size:22
Alignment explanation
Indices: 333493--333569 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
333483 ATGGAGGGGG
* *
333493 GTCGCCGGATATGGGGACGAAT
1 GTCGCCGGAGATGGGGACGGAT
333515 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
* *
333537 GTCGTCGGAGATGTGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
333559 GTCGCCGGAGA
1 GTCGCCGGAGA
333570 GAGTGAGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.45, T:0.17
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Done.