Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006236.1 Hibiscus syriacus cultivar Beakdansim tig00014863_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: 110465
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:333 original size:3 final size:3
Alignment explanation
Indices: 327--377 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
317 TTTTTACCCA
*
327 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT CAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
372 TAT TAT
1 TAT TAT
378 ATATAAATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 37 0.86
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13436 original size:13 final size:13
Alignment explanation
Indices: 13418--13442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13408 TAAATTTTCA
13418 AAAAAAAAATTTT
1 AAAAAAAAATTTT
13431 AAAAAAAAATTT
1 AAAAAAAAATTT
13443 GTTTTTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAAAAATTTT
Found at i:13436 original size:14 final size:15
Alignment explanation
Indices: 13409--13439 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
13399 CAAAAATTTT
13409 AAATTTTCAAAAAAA
1 AAATTTTCAAAAAAA
13424 AAATTTT-AAAAAAA
1 AAATTTTCAAAAAAA
13438 AA
1 AA
13440 TTTGTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTTTCAAAAAAA
Found at i:22132 original size:28 final size:26
Alignment explanation
Indices: 22086--22140 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
22076 CCGAATTCGG
*
22086 TGCCCCCTTAGCAGTCGTTTTTGACT
1 TGCCCCCTTAGCAGCCGTTTTTGACT
22112 TGCCCCCTTTTAGCAGCCGTTTTTGACT
1 TGCCCCC--TTAGCAGCCGTTTTTGACT
22140 T
1 T
22141 TACAATCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.27
28 19 0.73
ACGTcount: A:0.11, C:0.31, G:0.18, T:0.40
Consensus pattern (26 bp):
TGCCCCCTTAGCAGCCGTTTTTGACT
Found at i:25295 original size:30 final size:30
Alignment explanation
Indices: 25259--25315 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
25249 GAATTCGGTG
* *
25259 CCCCCCTTTAGCAGCCGTTTTTTACTTGCC
1 CCCCCCTTTAACAGCCGTTTTTGACTTGCC
25289 CCCCCCTTTAACAGCCGTTTTTGACTT
1 CCCCCCTTTAACAGCCGTTTTTGACTT
25316 TACACACCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.39, G:0.12, T:0.37
Consensus pattern (30 bp):
CCCCCCTTTAACAGCCGTTTTTGACTTGCC
Found at i:34830 original size:206 final size:212
Alignment explanation
Indices: 34537--35111 Score: 891
Period size: 206 Copynumber: 2.7 Consensus size: 212
34527 AAATTAAATT
* ** * *
34537 TTAAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACAATTTAAAACTCC-ATTAA
1 TTAAATTTTAAAT-T-TTAAATATATTATATGGGCTCAACCCAAACCATTTAAAAC-CCAATTAA
34601 TAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAATTTATATAAAA
63 TAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAA
34665 TTTTATTTTATAATTATATTTTTAAA-TAA-TGTAA-CTGTTTTTTTAATT-AAAAA-ATTTAAT
128 TTTTATTTTATAATTATATTTTTAAATTAATTGTAACCTGTTTTTTTAATTAAAAAATATTTAAT
34725 TTTATATAAATTAATTGAAA
193 TTTATATAAATTAATTGAAA
34745 TTAAATTTTAAATTTTAAATATATTATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
1 TTAAATTTTAAATTTTAAATATATTATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
34810 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATAT-AAA-TT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
34873 TATATTTATAATTAT-TATTTAAATTAATTGTAACCTGTTTTTTTAATTAAAAAATATTTAATTT
131 TAT-TTTATAATTATATTTTTAAATTAATTGTAACCTGTTTTTTTAATTAAAAAATATTTAATTT
34937 TATATAAATTAATTGAAA
195 TATATAAATTAATTGAAA
*
34955 TTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCC
1 TTAAATTTTAAATTTT--A-A-A-TATAT-T---ATATGGGCTCAACCCAAACCATTTAAAACCC
35020 AATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAT
57 AATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAT
35085 ATAAAATTTTTATTTTATAATTATATT
122 ATAAAA-TTTTATTTTATAATTATATT
35112 AAAAGTTTGG
Statistics
Matches: 338, Mismatches: 8, Indels: 28
0.90 0.02 0.07
Matches are distributed among these distances:
205 14 0.04
206 105 0.31
207 18 0.05
208 27 0.08
209 5 0.01
210 43 0.13
212 1 0.00
213 1 0.00
214 1 0.00
215 5 0.01
216 1 0.00
219 97 0.29
220 3 0.01
221 11 0.03
222 6 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (212 bp):
TTAAATTTTAAATTTTAAATATATTATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TATTTTATAATTATATTTTTAAATTAATTGTAACCTGTTTTTTTAATTAAAAAATATTTAATTTT
ATATAAATTAATTGAAA
Found at i:35054 original size:219 final size:216
Alignment explanation
Indices: 34526--35110 Score: 964
Period size: 219 Copynumber: 2.7 Consensus size: 216
34516 TTAATTAACC
* *
34526 GAAATTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACAATTTAAA
1 GAAATTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAA
34591 ACTCC-ATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAA
66 A-TCCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA
*
34654 TTTATATAAAATTTTATTTTATAATTATATTTTTAAATAATGTAACTGTTTTTTTAATTAAAAAA
130 TTTATATAAAATTTTATTTTATAATTATATATTTAAATAATGTAACTGTTTTTTTAATTAAAAAA
34719 TTTAATTTTATATAAATTAATT
195 TTTAATTTTATATAAATTAATT
34741 GAAATTAAATTTTAAATTTT--A-A-A-TATAT-T---ATATGGGCTCAACCCAAACCATTTAAA
1 GAAATTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAA
*
34797 ACCCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
66 ATCCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
34862 TTATAT-AAA-TTTATATTTATAATTAT-TATTTAAATTAATTGTAACCTGTTTTTTTAATTAAA
131 TTATATAAAATTTTAT-TTTATAATTATATATTTAAA-TAA-TGTAA-CTGTTTTTTTAATT-AA
34924 AAATATTTAATTTTATATAAATTAATT
191 AAA-ATTTAATTTTATATAAATTAATT
34951 GAAATTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAA
1 GAAATTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAA
35016 ATCCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
66 ATCCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
35081 TTATATAAAATTTTTATTTTATAATTATAT
131 TTATATAAAA-TTTTATTTTATAATTATAT
35111 TAAAAGTTTG
Statistics
Matches: 344, Mismatches: 5, Indels: 35
0.90 0.01 0.09
Matches are distributed among these distances:
205 14 0.04
206 96 0.28
207 17 0.05
208 14 0.04
209 6 0.02
210 48 0.14
211 1 0.00
212 2 0.01
213 2 0.01
214 1 0.00
215 25 0.07
216 1 0.00
219 97 0.28
220 3 0.01
221 11 0.03
222 6 0.02
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (216 bp):
GAAATTAAATTTTAAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAA
ATCCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
TTATATAAAATTTTATTTTATAATTATATATTTAAATAATGTAACTGTTTTTTTAATTAAAAAAT
TTAATTTTATATAAATTAATT
Found at i:37032 original size:3 final size:3
Alignment explanation
Indices: 37024--37067 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
37014 TTTTTCACCA
* *
37024 TAT TAT TAT TAT TAT TAT TCT TA- TAT ATAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
37068 AATTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:37068 original size:9 final size:9
Alignment explanation
Indices: 37023--37080 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
37013 TTTTTTCACC
37023 ATATTATTA
1 ATATTATTA
*
37032 TTATTATTA
1 ATATTATTA
* *
37041 TTCTTA-TA
1 ATATTATTA
37049 TATATTATTA
1 -ATATTATTA
37059 ATATTATTA
1 ATATTATTA
37068 A-ATTA--A
1 ATATTATTA
37074 ATATTAT
1 ATATTAT
37081 AAAACCCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 2 0.05
7 4 0.10
8 6 0.15
9 27 0.66
10 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
ATATTATTA
Found at i:37077 original size:24 final size:27
Alignment explanation
Indices: 37023--37080 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
37013 TTTTTTCACC
* **
37023 ATATTATTATTATTATTATTCTTATAT
1 ATATTATTAATATTATTATAATTATAT
37050 ATATTATTAATATTATTA-AATTA-A-
1 ATATTATTAATATTATTATAATTATAT
37074 ATATTAT
1 ATATTAT
37081 AAAACCCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.25
25 1 0.04
26 3 0.11
27 17 0.61
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTATTAATATTATTATAATTATAT
Found at i:38762 original size:23 final size:24
Alignment explanation
Indices: 38730--38790 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
38720 ATTTGTAATA
38730 TTATTATTACTTTTAA-TA-TATT
1 TTATTATTACTTTTAATTATTATT
38752 TTAATTATTAC-TTTAATTATTATT
1 TT-ATTATTACTTTTAATTATTATT
*
38776 TTATTATTATTTTTA
1 TTATTATTACTTTTA
38791 TCTTAGCCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 7 0.21
23 17 0.50
24 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTATTACTTTTAATTATTATT
Found at i:38789 original size:12 final size:12
Alignment explanation
Indices: 38730--38791 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
38720 ATTTGTAATA
38730 TTATTATTACTT
1 TTATTATTACTT
*
38742 TTAATA-TA-TT
1 TTATTATTACTT
38752 TTAATTATTACTT
1 TT-ATTATTACTT
*
38765 TAATTATTA-TT
1 TTATTATTACTT
*
38776 TTATTATTATTT
1 TTATTATTACTT
38788 TTAT
1 TTAT
38792 CTTAGCCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 4 0.10
11 15 0.36
12 20 0.48
13 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTACTT
Found at i:42968 original size:7 final size:7
Alignment explanation
Indices: 42958--42988 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42948 TTTTGGCTCT
42958 TTCCTTC
1 TTCCTTC
42965 TTCCTTC
1 TTCCTTC
42972 TTCCTTC
1 TTCCTTC
42979 TTCCTTC
1 TTCCTTC
42986 TTC
1 TTC
42989 TTCCTCCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TTCCTTC
Found at i:48029 original size:35 final size:35
Alignment explanation
Indices: 47983--48051 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
47973 ATCTTAATCG
* *
47983 TCTATTTTGAATTATCTAACGGTCCTAAATTTGTA
1 TCTATTTTGAATTATATAACGATCCTAAATTTGTA
48018 TCTATTTTGAATTATATAACGATCCTAAATTTGT
1 TCTATTTTGAATTATATAACGATCCTAAATTTGT
48052 GTAAATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.46
Consensus pattern (35 bp):
TCTATTTTGAATTATATAACGATCCTAAATTTGTA
Found at i:48427 original size:30 final size:28
Alignment explanation
Indices: 48393--48453 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
48383 AAATTGCTCT
48393 TATTTTAATCAC-TCTAATTTATTTTATTAA
1 TATTTTAATCACATC--ATTT-TTTTATTAA
* *
48423 TATTTTTATGACATCATTTTTTTATTAA
1 TATTTTAATCACATCATTTTTTTATTAA
48451 TAT
1 TAT
48454 ATAACTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.43
29 4 0.14
30 10 0.36
31 2 0.07
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (28 bp):
TATTTTAATCACATCATTTTTTTATTAA
Found at i:50515 original size:16 final size:16
Alignment explanation
Indices: 50471--50518 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
50461 ATACAAAAAA
**
50471 AGGAAAATAATCGAAT
1 AGGAAAATAATTAAAT
* *
50487 GGGCAAA-AATTAAAT
1 AGGAAAATAATTAAAT
50502 AGGAAAATAATTAAAT
1 AGGAAAATAATTAAAT
50518 A
1 A
50519 AAAAGAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (16 bp):
AGGAAAATAATTAAAT
Found at i:52298 original size:138 final size:138
Alignment explanation
Indices: 52049--52441 Score: 454
Period size: 138 Copynumber: 2.8 Consensus size: 138
52039 TTATTCTCTG
* * * * *
52049 TGAGTTCTTCTCATTATGAACTCTTCATTTATCCACCTTCTTGTGTGATGGAC-AATCCCAAGTT
1 TGAGTTCTTCTCATTATGAACTCCTCATTTATCCACCTCCTTGTGCGATAGACGAAT-CCAGGTT
* * * * * * *
52113 GAAC-AGACTTTTCTCATTACGAGCTTCTTCTACCTCGTTGGATGAGTTCTTCTTATGATGAACC
65 GAACAAG-CTCTTCTCATTACGAACTTCTTCTTCCTTGTTGGACGAGTTCTTCTCATGACGAACC
*
52177 CTTCATCGGGA
129 CTTCATC-AGA
* * * *
52188 -GAGTTCTTCTCATTATGAACTCCTCATTTACCCACCTCCTTGTGGGATAAACGACTCCAGGTTG
1 TGAGTTCTTCTCATTATGAACTCCTCATTTATCCACCTCCTTGTGCGATAGACGAATCCAGGTTG
* *
52252 AACAAGCTCTTCTCATTACGAACTTCTTCTTCCTTGTTGGACGAGTTATTCTCATTACGAACCCT
66 AACAAGCTCTTCTCATTACGAACTTCTTCTTCCTTGTTGGACGAGTTCTTCTCATGACGAACCCT
*
52317 TCGTCAGA
131 TCATCAGA
* * * * * *
52325 TGAGTTATTCTCATTATGAACTCCTCATTTATCTATCTCCTTATGCAATAGACGATTCCAGGTTG
1 TGAGTTCTTCTCATTATGAACTCCTCATTTATCCACCTCCTTGTGCGATAGACGAATCCAGGTTG
* *
52390 AACAATCTCTTCTCATTACGAACTTCTTC-TCCTT-TCTCGGACAAGTTCTTCT
66 AACAAGCTCTTCTCATTACGAACTTCTTCTTCCTTGT-T-GGACGAGTTCTTCT
52442 AATTACGAGC
Statistics
Matches: 218, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
136 1 0.00
137 8 0.04
138 205 0.94
139 4 0.02
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (138 bp):
TGAGTTCTTCTCATTATGAACTCCTCATTTATCCACCTCCTTGTGCGATAGACGAATCCAGGTTG
AACAAGCTCTTCTCATTACGAACTTCTTCTTCCTTGTTGGACGAGTTCTTCTCATGACGAACCCT
TCATCAGA
Found at i:53435 original size:17 final size:18
Alignment explanation
Indices: 53413--53446 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53403 GAACCCTTAT
53413 TTTCTTT-TTTTTTTCTA
1 TTTCTTTATTTTTTTCTA
53430 TTTCTTTATTTTTTTCT
1 TTTCTTTATTTTTTTCT
53447 TTCTTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTTTATTTTTTTCTA
Found at i:53449 original size:16 final size:16
Alignment explanation
Indices: 53413--53452 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
53403 GAACCCTTAT
53413 TTTCTTTTTTTTTTCTA
1 TTTCTTTTTTTTTTC-A
53430 TTTCTTTATTTTTTTC-
1 TTTCTTT-TTTTTTTCA
53446 TTTCTTT
1 TTTCTTT
53453 CTTGTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 8 0.36
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTTTTTCA
Found at i:56134 original size:5 final size:5
Alignment explanation
Indices: 56124--56148 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56114 ATTCATATAC
56124 TTCAT TTCAT TTCAT TTCAT TTCAT
1 TTCAT TTCAT TTCAT TTCAT TTCAT
56149 ATATAGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCAT
Found at i:57249 original size:21 final size:22
Alignment explanation
Indices: 57216--57270 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
57206 TCGAAGTTCC
57216 ATGGTAT-GTATACC-C-TCCAT
1 ATGGTATCG-ATACCTCTTCCAT
*
57236 ATAGGTATCGATACCTCTTTCAT
1 AT-GGTATCGATACCTCTTCCAT
57259 ATGGTATCGATA
1 ATGGTATCGATA
57271 GTTTTCATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.07
21 10 0.33
22 12 0.40
23 6 0.20
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (22 bp):
ATGGTATCGATACCTCTTCCAT
Found at i:61563 original size:18 final size:17
Alignment explanation
Indices: 61536--61580 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
61526 TCAGTATTCG
*
61536 TCCCGTAGGACTCCTACA
1 TCCCGAAGGACT-CTACA
61554 TCCCGAAGGA--CTACA
1 TCCCGAAGGACTCTACA
61569 TCCCGAAGGACT
1 TCCCGAAGGACT
61581 ACGTCCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 15 0.62
18 9 0.38
ACGTcount: A:0.27, C:0.36, G:0.20, T:0.18
Consensus pattern (17 bp):
TCCCGAAGGACTCTACA
Found at i:61569 original size:15 final size:15
Alignment explanation
Indices: 61549--61596 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
61539 CGTAGGACTC
61549 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
61564 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
61579 CTACGTCCCGAATGA
1 CTACATCCCGAAGGA
61594 CTA
1 CTA
61597 TTATACCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:61727 original size:29 final size:29
Alignment explanation
Indices: 61676--61758 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
61666 TTATATTTCA
*
61676 TATGTTCATGTA-CTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
61704 TATGATCATGTAGCTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
*
61733 TGTGATCATGTAGCTCATGTCATTTC
1 TATGATCATGTAGCTCATGTCATTTC
61759 ATATCATGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
28 11 0.21
29 41 0.79
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.46
Consensus pattern (29 bp):
TATGATCATGTAGCTCATGTCATTTCTCT
Found at i:61787 original size:12 final size:12
Alignment explanation
Indices: 61770--61815 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
61760 TATCATGTTC
*
61770 TCATATCACAGG
1 TCATATCACAGA
*
61782 TCATATCACATA
1 TCATATCACAGA
*
61794 TCATATCACATA
1 TCATATCACAGA
*
61806 GCATATCACA
1 TCATATCACA
61816 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:61801 original size:24 final size:24
Alignment explanation
Indices: 61770--61816 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
61760 TATCATGTTC
*
61770 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
61794 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
61817 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:61816 original size:12 final size:12
Alignment explanation
Indices: 61783--61816 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
61773 TATCACAGGT
*
61783 CATATCACATAT
1 CATATCACATAG
61795 CATATCACATAG
1 CATATCACATAG
61807 CATATCACAT
1 CATATCACAT
61817 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:62233 original size:64 final size:64
Alignment explanation
Indices: 62125--62301 Score: 178
Period size: 64 Copynumber: 2.8 Consensus size: 64
62115 TAATGAAGAT
* * * ** ** * * **
62125 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
* * *
62189 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATACATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
* *
62253 ATGCATCGATGCACTACTTATACATCGATGTATGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGT
62302 TTTTATTTTA
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.02
64 92 0.98
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:62322 original size:64 final size:64
Alignment explanation
Indices: 62188--62333 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 64
62178 TTATTGCTGG
* * * *
62188 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATACATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
* * * *
62252 GATGCATCGATGCACTACTTATACATCGATGTA-TGAATTGCATTCGATGTTTTTA-TTTTAAA-
1 GATGCATCGATGCACTACTTATACATCGATGCACCG-ATTGCATTCGATG-TTTCACTATTAAAG
62314 A
64 A
*
62315 GAGTGCATCTATGCACTAC
1 GA-TGCATCGATGCACTAC
62334 CAATGCATCG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 63 0.90
65 4 0.06
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATACATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:67527 original size:15 final size:15
Alignment explanation
Indices: 67503--67550 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
67493 CGTAGGACTC
*
67503 CTACATCCCGAAGGA
1 CTACAGCCCGAAGGA
67518 CTACAGCCCGAAGGA
1 CTACAGCCCGAAGGA
*
67533 CTAC-GTCCTGAAGGA
1 CTACAG-CCCGAAGGA
67548 CTA
1 CTA
67551 TTATACCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (15 bp):
CTACAGCCCGAAGGA
Found at i:67677 original size:29 final size:29
Alignment explanation
Indices: 67635--67712 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
67625 TTTCATATGT
67635 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
67663 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
67692 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
67713 ATATCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:67741 original size:12 final size:12
Alignment explanation
Indices: 67724--67769 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
67714 TATCATGTTC
*
67724 TCATATCACAGG
1 TCATATCACAGA
*
67736 TCATATCACATA
1 TCATATCACAGA
*
67748 TCATATCACATA
1 TCATATCACAGA
*
67760 GCATATCACA
1 TCATATCACA
67770 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:67755 original size:24 final size:24
Alignment explanation
Indices: 67724--67770 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
67714 TATCATGTTC
*
67724 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
67748 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
67771 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:67770 original size:12 final size:12
Alignment explanation
Indices: 67737--67770 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
67727 TATCACAGGT
*
67737 CATATCACATAT
1 CATATCACATAG
67749 CATATCACATAG
1 CATATCACATAG
67761 CATATCACAT
1 CATATCACAT
67771 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:68258 original size:64 final size:63
Alignment explanation
Indices: 68081--68259 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 63
68071 TAATGAAGAT
* * * ** * * **
68081 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGTATTCGATGT-TTACTATTAATGGG
* * *
68145 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-TGAATTGTATTCGATGTTT-ACTATTAATGGG
68209 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGTATTCGATGTTT
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGTATTCGATGTTT
68260 TTATTTTAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.02
64 95 0.98
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGTATTCGATGTTTACTATTAATGGG
Found at i:68278 original size:64 final size:64
Alignment explanation
Indices: 68144--68305 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
68134 TTATTGCTGG
* * *
68144 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
* * * *
68208 GATGCATCGATGCACTACTTATGCATCGATGCA-TGAATTGTATTCGATGTTTTTA-TTTTAAA-
1 GATGCATCGATGCACTACTTATGCATCGATGCACCG-ATTGCATTCGATG-TTTCACTATTAAAG
68270 A
64 A
** *
68271 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
68306 ATTCAAACAA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.04
64 77 0.92
65 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:72933 original size:64 final size:64
Alignment explanation
Indices: 72845--73115 Score: 236
Period size: 64 Copynumber: 4.2 Consensus size: 64
72835 CAATGAAGGT
* * * *
72845 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTTGATGTT-TCCTTATTAATGA
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTATCATT-TTAATGA
72908 G
64 G
* * * *
72909 ATGCATCGATGCA-TACCTTATGCATCGATGCACTAATTGCATTTGATGTTCT-ATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATT-TTAATGA
72972 G
64 G
* * * * *
72973 ATGCATTGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAA-AAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATTTTAATGA-
73036 G
64 G
* * * * *
73037 ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTC-TTTTAAAG-
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTT-ATCATTTTAATGA
73099 G
64 G
73100 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
73116 TATGAATGTG
Statistics
Matches: 174, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
63 4 0.02
64 162 0.93
65 8 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTATCATTTTAATGAG
Found at i:79117 original size:535 final size:535
Alignment explanation
Indices: 78108--79176 Score: 2066
Period size: 535 Copynumber: 2.0 Consensus size: 535
78098 TCACCCTCTA
78108 GTATTACGATACTAAATATGAAACTAAATGTAGGTTCTAAGTATCCTAATTAGATCATATTTTAA
1 GTATTACGATACTAAATATGAAACTAAATGTAGGTTCTAAGTATCCTAATTAGATCATATTTTAA
78173 TTCAATTATTAGTTCAAGGACTAAATGGTGAAAATTCTAAAGTCTAGGCACTAATCTAACAAATT
66 TTCAATTATTAGTTCAAGGACTAAATGGTGAAAATTCTAAAGTCTAGGCACTAATCTAACAAATT
78238 AAGGCTCTAATAACCTATTTAATTACTGAAAATTAAAGAACTAATCCTAAGTGGGCTTTAAAATT
131 AAGGCTCTAATAACCTATTTAATTACTGAAAATTAAAGAACTAATCCTAAGTGGGCTTTAAAATT
78303 AATCAATAAGTAACCAATTATTTGATTTGAACAAATAACTCGAATAATCGGGCATTGAAGCGAAA
196 AATCAATAAGTAACCAATTATTTGATTTGAACAAATAACTCGAATAATCGGGCATTGAAGCGAAA
78368 ATTCGAATCAAATTGCTCTTTGATAATTAGCTGAAAACCTAGACATCTAACCACATAATTTATTT
261 ATTCGAATCAAATTGCTCTTTGATAATTAGCTGAAAACCTAGACATCTAACCACATAATTTATTT
*
78433 TTAAATTGAACTATTTATCTAAAGGGTGAATCCTCAACTAAAACAATATAAAATTAACTACATAA
326 TTAAAGTGAACTATTTATCTAAAGGGTGAATCCTCAACTAAAACAATATAAAATTAACTACATAA
78498 AGATGCAAACACAGATAACAAGTAGAAAATTTAAAACCATTAACTAACCAAAATAAAAAATGGTT
391 AGATGCAAACACAGATAACAAGTAGAAAATTTAAAACCATTAACTAACCAAAATAAAAAATGGTT
* * *
78563 GTCCCTTGTTCCCATATATAATGGGGTAAAGGGAGGTAATATAGTAGGCTACCCCCAACACCAGG
456 GTCCCTTATTCCCATATATAATGGGGTAAAGGGAGATAAGATAGTAGGCTACCCCCAACACCAGG
78628 TTGAGAGCAGCTTCC
521 TTGAGAGCAGCTTCC
*
78643 GTATTACGATACTAAATATGAAACTAAATTTAGGTTCTAAGTATCCTAATTAGATCATATTTTAA
1 GTATTACGATACTAAATATGAAACTAAATGTAGGTTCTAAGTATCCTAATTAGATCATATTTTAA
78708 TTCAATTATTAGTTCAAGGACTAAATGGTGAAAATTCTAAAGTCTAGGCACTAATCTAACAAATT
66 TTCAATTATTAGTTCAAGGACTAAATGGTGAAAATTCTAAAGTCTAGGCACTAATCTAACAAATT
78773 AAGGCTCTAATAACCTATTTAATTACTGAAAATTAAAGAACTAATCCTAAGTGGGCTTTAAAATT
131 AAGGCTCTAATAACCTATTTAATTACTGAAAATTAAAGAACTAATCCTAAGTGGGCTTTAAAATT
78838 AATCAATAAGTAACCAATTATTTGATTTGAACAAATAACTCGAATAATCGGGCATTGAAGCGAAA
196 AATCAATAAGTAACCAATTATTTGATTTGAACAAATAACTCGAATAATCGGGCATTGAAGCGAAA
78903 ATTCGAATCAAATTGCTCTTTGATAATTAGCTGAAAACCTAGACATCTAACCACATAATTTATTT
261 ATTCGAATCAAATTGCTCTTTGATAATTAGCTGAAAACCTAGACATCTAACCACATAATTTATTT
78968 TTAAAGTGAACTATTTATCTAAAGGGTGAATCCTCAACTAAAACAATATAAAATTAACTACATAA
326 TTAAAGTGAACTATTTATCTAAAGGGTGAATCCTCAACTAAAACAATATAAAATTAACTACATAA
*
79033 AGATGCAAACACAGATAACAAGTAGAAAATTTAAAACCATTAACTAACCAAAATAAATAATGGTT
391 AGATGCAAACACAGATAACAAGTAGAAAATTTAAAACCATTAACTAACCAAAATAAAAAATGGTT
* *
79098 GTCCCTTATTCCCATATATAATGGGGTAAGGGGAGATAAGATAGTAGGCTGCCCCCAACACCAGG
456 GTCCCTTATTCCCATATATAATGGGGTAAAGGGAGATAAGATAGTAGGCTACCCCCAACACCAGG
79163 TTGAGAGCAGCTTC
521 TTGAGAGCAGCTTC
79177 TGTAGAAGAC
Statistics
Matches: 526, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
535 526 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (535 bp):
GTATTACGATACTAAATATGAAACTAAATGTAGGTTCTAAGTATCCTAATTAGATCATATTTTAA
TTCAATTATTAGTTCAAGGACTAAATGGTGAAAATTCTAAAGTCTAGGCACTAATCTAACAAATT
AAGGCTCTAATAACCTATTTAATTACTGAAAATTAAAGAACTAATCCTAAGTGGGCTTTAAAATT
AATCAATAAGTAACCAATTATTTGATTTGAACAAATAACTCGAATAATCGGGCATTGAAGCGAAA
ATTCGAATCAAATTGCTCTTTGATAATTAGCTGAAAACCTAGACATCTAACCACATAATTTATTT
TTAAAGTGAACTATTTATCTAAAGGGTGAATCCTCAACTAAAACAATATAAAATTAACTACATAA
AGATGCAAACACAGATAACAAGTAGAAAATTTAAAACCATTAACTAACCAAAATAAAAAATGGTT
GTCCCTTATTCCCATATATAATGGGGTAAAGGGAGATAAGATAGTAGGCTACCCCCAACACCAGG
TTGAGAGCAGCTTCC
Found at i:81496 original size:67 final size:67
Alignment explanation
Indices: 81418--81548 Score: 208
Period size: 67 Copynumber: 2.0 Consensus size: 67
81408 AAAGCGTCGT
* * *
81418 TGTTCCTGCTACACCAAAATAAGGAGAAATAGTAAGCTATAATGGTTCAAAGAATTCAAGCAAAG
1 TGTTCCCGCTACACCAAAACAAGGAGAAATAGTAAGCCATAATGGTTCAAAGAATTCAAGCAAAG
81483 TA
66 TA
* * *
81485 TGTTCCCGCTACACTAAAACAAGGAGAAATGGTAAGCCATGATGGTTCAAAGAATTCAAGCAAA
1 TGTTCCCGCTACACCAAAACAAGGAGAAATAGTAAGCCATAATGGTTCAAAGAATTCAAGCAAA
81549 ACATTATTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (67 bp):
TGTTCCCGCTACACCAAAACAAGGAGAAATAGTAAGCCATAATGGTTCAAAGAATTCAAGCAAAG
TA
Found at i:91209 original size:17 final size:17
Alignment explanation
Indices: 91187--91221 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
91177 AAGTAGAGAG
91187 TGGAAACAAAATAAAAC
1 TGGAAACAAAATAAAAC
91204 TGGAAACAAAATAAAAC
1 TGGAAACAAAATAAAAC
91221 T
1 T
91222 CTTGCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.14
Consensus pattern (17 bp):
TGGAAACAAAATAAAAC
Found at i:95054 original size:22 final size:22
Alignment explanation
Indices: 95029--95070 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
95019 TATACAAAAT
95029 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAATATTTTTGG
* *
95051 TATTTTTATTTAATTTTTTT
1 TATTTTTATTAAATATTTTT
95071 AAAAATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TATTTTTATTAAATATTTTTGG
Found at i:96581 original size:2 final size:2
Alignment explanation
Indices: 96576--96619 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
96566 TTTTATTAAA
96576 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
96618 AT
1 AT
96620 TTTTAGGAAC
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:96960 original size:51 final size:51
Alignment explanation
Indices: 96880--97097 Score: 230
Period size: 51 Copynumber: 4.3 Consensus size: 51
96870 TTCATACTAC
* * * *
96880 AAAAAAATGTAGCA-TTAACACATATTTACACCGGTGTAAG-ACAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTA-AATAAAAT
* * ** *
96930 AAACAAGTGTAACACTTAATACATACTTACACATTTGTAAGTAAATAAAAC
1 AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTAAATAAAAT
* * *
96981 AAAAAA-TGTAACACTTAACACATA-ATACACAAGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTAAATAAAAT
* *
97030 AAAAAAAAGTGTAGCACTTAATACATACTTACA-ACGGTGTAAGTAAATAAAAT
1 --AAAAAAGTGTAACACTTAACACATACTTACACA-GGTGTAAGTAAATAAAAT
*
97083 AAAAAAGTGCAACAC
1 AAAAAAGTGTAACAC
97098 GTTGAAGACA
Statistics
Matches: 138, Mismatches: 23, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
49 20 0.14
50 28 0.20
51 52 0.38
52 18 0.13
53 20 0.14
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (51 bp):
AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTAAATAAAAT
Found at i:97071 original size:102 final size:101
Alignment explanation
Indices: 96881--97097 Score: 269
Period size: 102 Copynumber: 2.1 Consensus size: 101
96871 TCATACTACA
* * ** *
96881 AAAAAATGTAGCA-TTAACACATATTTACACCGGTGTAAGACAATAAAATAAACAAGTGTAACAC
1 AAAAAATGTAACACTTAACACATATATACACAAGTGTAAGACAATAAAATAAAAAAGTGTAACAC
**
96945 TTAATACATACTTACACATTTGTAAGTAAATAAAAC
66 TTAATACATACTTACACAGGTGTAAGTAAATAAAAC
** *
96981 AAAAAATGTAACACTTAACACATA-ATACACAAGTGTAAGTGAATAAAATAAAAAAAAGTGTAGC
1 AAAAAATGTAACACTTAACACATATATACACAAGTGTAAGACAATAAAAT--AAAAAAGTGTAAC
*
97045 ACTTAATACATACTTACA-ACGGTGTAAGTAAATAAAAT
64 ACTTAATACATACTTACACA-GGTGTAAGTAAATAAAAC
*
97083 AAAAAAGTGCAACAC
1 AAAAAA-TGTAACAC
97098 GTTGAAGACA
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
100 32 0.32
101 11 0.11
102 50 0.50
103 7 0.07
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.24
Consensus pattern (101 bp):
AAAAAATGTAACACTTAACACATATATACACAAGTGTAAGACAATAAAATAAAAAAGTGTAACAC
TTAATACATACTTACACAGGTGTAAGTAAATAAAAC
Found at i:97148 original size:2 final size:2
Alignment explanation
Indices: 97136--97188 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
97126 AATCACAAAT
* * *
97136 TA TA CA TA TA TA TA -A TG T- TA TA AA T- TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97174 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
97189 GAGTTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:98228 original size:2 final size:2
Alignment explanation
Indices: 98221--98255 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
98211 TTCATCAATT
98221 TA TA TA TA 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 TA TA TA TA T
98256 TATTTATTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98439 original size:30 final size:32
Alignment explanation
Indices: 98388--98446 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
98378 TACTTTTTTA
*
98388 TTTTCTCTTATGTTATTTTCATT-TTTATTCC
1 TTTTCTCTTATCTTATTTTCATTCTTTATTCC
*
98419 TTTTCT-TTATCTTTTTTTCATTCTTTAT
1 TTTTCTCTTATCTTATTTTCATTCTTTAT
98447 ATTTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (32 bp):
TTTTCTCTTATCTTATTTTCATTCTTTATTCC
Found at i:99287 original size:20 final size:20
Alignment explanation
Indices: 99262--99299 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
99252 GGACTAAGGG
99262 TCTGGCAGGCCCAAGGGGTC
1 TCTGGCAGGCCCAAGGGGTC
99282 TCTGGCAGGCCCAAGGGG
1 TCTGGCAGGCCCAAGGGG
99300 GCACCGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.29, G:0.42, T:0.13
Consensus pattern (20 bp):
TCTGGCAGGCCCAAGGGGTC
Found at i:99308 original size:20 final size:20
Alignment explanation
Indices: 99265--99308 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
99255 CTAAGGGTCT
* * *
99265 GGCAGGCCCAAGGGGTCTCT
1 GGCAGGCCCAAGGGGGCACC
99285 GGCAGGCCCAAGGGGGCACC
1 GGCAGGCCCAAGGGGGCACC
99305 GGCA
1 GGCA
99309 AGGAGAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.43, T:0.07
Consensus pattern (20 bp):
GGCAGGCCCAAGGGGGCACC
Found at i:108637 original size:71 final size:70
Alignment explanation
Indices: 108527--108680 Score: 197
Period size: 71 Copynumber: 2.2 Consensus size: 70
108517 AATACTTCGC
*
108527 TTAGGATGAAAACCTGAGAGAGCGTCTTAAGTCAAAAAAAGAGAAAAA-AAAAAC-AAAAAGAAG
1 TTAGGGTGAAAACCTGAGAGAGCGTCTTAAGTCAAAAAAAGAGAAAAATAAAAACGAAAAA-AA-
108590 AAAACGT
64 AAAACGT
* *
108597 TTAGGGGTGAAAACCTGAGAG-GTGTCTTAAGTCGAGAAAAAGAGAAAAATTAAAAACGAAAAAA
1 TTA-GGGTGAAAACCTGAGAGAGCGTCTTAAGTC-AAAAAAAGAGAAAAA-TAAAAACGAAAAAA
* *
108661 AAGAATGT
63 AAAAACGT
108669 TTAGGGTGAAAA
1 TTAGGGTGAAAA
108681 TCCGAAAGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
70 14 0.19
71 39 0.53
72 8 0.11
73 8 0.11
74 5 0.07
ACGTcount: A:0.53, C:0.08, G:0.23, T:0.16
Consensus pattern (70 bp):
TTAGGGTGAAAACCTGAGAGAGCGTCTTAAGTCAAAAAAAGAGAAAAATAAAAACGAAAAAAAAA
AACGT
Found at i:108716 original size:8 final size:8
Alignment explanation
Indices: 108703--108757 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
108693 CCCTAAATTG
108703 GAAAAAAA
1 GAAAAAAA
108711 GAAAAAAA
1 GAAAAAAA
108719 GAGAAAAGGAA
1 GA-AAAA--AA
108730 -AAAAAAA
1 GAAAAAAA
*
108737 GAACAAAA
1 GAAAAAAA
*
108745 GAAAAATA
1 GAAAAAAA
108753 GAAAA
1 GAAAA
108758 GAAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 2 0.05
8 27 0.68
9 8 0.20
10 1 0.03
11 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (8 bp):
GAAAAAAA
Found at i:108756 original size:26 final size:26
Alignment explanation
Indices: 108704--108763 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
108694 CCTAAATTGG
*
108704 AAAAAAAGAAAAAAAGAGAAAAGGAA
1 AAAAAAAGAAAAAAAGAGAAAAAGAA
*
108730 AAAAAAAGAACAAAAGA-AAAATAGAA
1 AAAAAAAGAAAAAAAGAGAAAA-AGAA
108756 AAGAAAAA
1 AA-AAAAA
108764 TAAAGAGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 21 0.70
27 5 0.17
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (26 bp):
AAAAAAAGAAAAAAAGAGAAAAAGAA
Found at i:108757 original size:13 final size:13
Alignment explanation
Indices: 108741--108765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
108731 AAAAAAGAAC
108741 AAAAGAAAAATAG
1 AAAAGAAAAATAG
108754 AAAAGAAAAATA
1 AAAAGAAAAATA
108766 AAGAGGGTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAAGAAAAATAG
Done.