Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008175.1 Hibiscus syriacus cultivar Beakdansim tig00110770_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: 426378
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:150 original size:18 final size:19
Alignment explanation
Indices: 113--151 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
103 ATATGTAGTG
*
113 TTATATATGGATTTTAATT
1 TTATATATGAATTTTAATT
*
132 TTATATAT-AATTTTGATT
1 TTATATATGAATTTTAATT
150 TT
1 TT
152 TGTTCACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (19 bp):
TTATATATGAATTTTAATT
Found at i:2315 original size:265 final size:266
Alignment explanation
Indices: 1838--2365 Score: 947
Period size: 265 Copynumber: 2.0 Consensus size: 266
1828 AGTCTAAAGT
1838 ATCAATAGTTGAATGTATGTGAAATTGATAGATAAGTACATGAAATAAATTACATGGTATGTGTT
1 ATCAATAGTTGAATGTATGTGAAATTGATAGATAAGTACATGAAATAAATTACATGG-ATGTGTT
*
1903 TAAGATAGATATTAAGTATGATTATTTTTTAATAGCGGAGGTGATTATAAAATAGTAATTGTTTA
65 TAAGATAAATATTAAGTATGATTATTTTTTAATAGCGGAGGTGATTATAAAATAGTAATTGTTTA
* *
1968 AAATCTTTCTTTGTTATTAACATCTATGCACCCTGCAGACACAACTGTTCAAACTCAGGATTCAT
130 AAATCTTTCTTTGTTATTAACATCTATACACCCTGCAGACACAACTGTTCAAACTCAGAATTCAT
*
2033 ATGAAGAATAATACTCTCTTCTACCACTAAAATCGCTTAATGAATTTTATTAA-ATGATTATTTG
195 ATGAAGAATAATACTCTCTTCTACCACT-AAATCGCTTAATGAATTTT-TAAATATGATTA-TTG
2097 TTAAGTGTAA
257 TTAAGTGTAA
*
2107 ATCAATAGTTGAATGTATGTGAAATTGATAGATAAGTATATGAAATAAATTACATGG-TGTGTTT
1 ATCAATAGTTGAATGTATGTGAAATTGATAGATAAGTACATGAAATAAATTACATGGATGTGTTT
2171 AAGATAAATATTAAGTATGATTA-TTTTTAATA-CGGAGGTGATTATAAAATAGTAATTGTTTAA
66 AAGATAAATATTAAGTATGATTATTTTTTAATAGCGGAGGTGATTATAAAATAGTAATTGTTTAA
2234 AATCTTTCTTTGTTATTAACATCTATACACCCTGCAGACACAACTGTTCAAACTCAGAATTCATA
131 AATCTTTCTTTGTTATTAACATCTATACACCCTGCAGACACAACTGTTCAAACTCAGAATTCATA
2299 TGAAGAATAATACTCTCTTCTACCACTAAATCGCTTAATGAATTTTTAAATATGATTATTGTTAA
196 TGAAGAATAATACTCTCTTCTACCACTAAATCGCTTAATGAATTTTTAAATATGATTATTGTTAA
2364 GT
261 GT
2366 ACTTAGTTGT
Statistics
Matches: 253, Mismatches: 5, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
263 12 0.05
264 26 0.10
265 121 0.48
266 9 0.04
267 29 0.11
269 56 0.22
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (266 bp):
ATCAATAGTTGAATGTATGTGAAATTGATAGATAAGTACATGAAATAAATTACATGGATGTGTTT
AAGATAAATATTAAGTATGATTATTTTTTAATAGCGGAGGTGATTATAAAATAGTAATTGTTTAA
AATCTTTCTTTGTTATTAACATCTATACACCCTGCAGACACAACTGTTCAAACTCAGAATTCATA
TGAAGAATAATACTCTCTTCTACCACTAAATCGCTTAATGAATTTTTAAATATGATTATTGTTAA
GTGTAA
Found at i:7205 original size:28 final size:28
Alignment explanation
Indices: 7165--7229 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
7155 TTCGTTTAGA
7165 TTATGTCGTCAAGCTAGTGCTTAAAATT
1 TTATGTCGTCAAGCTAGTGCTTAAAATT
*
7193 TTATGTCGTCAAGTTAGTGCTTAAAATT
1 TTATGTCGTCAAGCTAGTGCTTAAAATT
7221 TTATGTCGT
1 TTATGTCGT
7230 TAAGACAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (28 bp):
TTATGTCGTCAAGCTAGTGCTTAAAATT
Found at i:9631 original size:31 final size:29
Alignment explanation
Indices: 9584--9641 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
9574 GGTATGATTA
*
9584 TAAAAAAATCAAAATTTATGTACTAAAGT
1 TAAAAAAATCAAAATTTAGGTACTAAAGT
*
9613 TAAACAAAATTAATAATTTAGGTACTAAA
1 TAAA-AAAATCAA-AATTTAGGTACTAAA
9642 CAATAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 7 0.28
31 14 0.56
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
TAAAAAAATCAAAATTTAGGTACTAAAGT
Found at i:13050 original size:12 final size:12
Alignment explanation
Indices: 13035--13063 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13025 AGCAGCCTGT
13035 GATAATGCAAGA
1 GATAATGCAAGA
13047 GATAATGCAAGA
1 GATAATGCAAGA
13059 GATAA
1 GATAA
13064 GTTGCTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (12 bp):
GATAATGCAAGA
Found at i:20269 original size:15 final size:16
Alignment explanation
Indices: 20235--20272 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20225 CCTCTCAAAA
20235 ATTTTAAATTATTATAT
1 ATTTT-AATTATTATAT
*
20252 ATTTTAATT-TTTTAT
1 ATTTTAATTATTATAT
20267 ATTTTA
1 ATTTTA
20273 TAAATCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 4 0.20
17 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTAATTATTATAT
Found at i:20321 original size:27 final size:26
Alignment explanation
Indices: 20283--20334 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20273 TAAATCTATT
* *
20283 TTATCTTCTAAAAATTTTATAAATTCG
1 TTATCTCCT-AAAATTTTAAAAATTCG
*
20310 TTATCTCCTAAAGTTTTAAAAATTC
1 TTATCTCCTAAAATTTTAAAAATTC
20335 ATCCTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (26 bp):
TTATCTCCTAAAATTTTAAAAATTCG
Found at i:21134 original size:90 final size:90
Alignment explanation
Indices: 20955--21127 Score: 319
Period size: 90 Copynumber: 1.9 Consensus size: 90
20945 CGGTTTGTAA
* *
20955 TGGTAATAAAATATATTAATTTCCTATCGGAAATGAACTTAATATTTGTATTTTGAGACATTCGT
1 TGGTAATAAAATATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGT
*
21020 ATAAGACATGAGTCAAAAAGACATT
66 ATAAGACACGAGTCAAAAAGACATT
21045 TGGTAATAAAATATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGT
1 TGGTAATAAAATATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGT
21110 ATAAGACACGAGTCAAAA
66 ATAAGACACGAGTCAAAA
21128 TAACATTCTC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (90 bp):
TGGTAATAAAATATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGT
ATAAGACACGAGTCAAAAAGACATT
Found at i:23431 original size:16 final size:16
Alignment explanation
Indices: 23381--23438 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
23371 GGGTCTCCAA
*
23381 CGTTTATGTTCGTGTT
1 CGTTTATGTTCTTGTT
* *
23397 CATTTATATT-TGTGTT
1 CGTTTATGTTCT-TGTT
*
23413 CGTTTATGTTCTTGCT
1 CGTTTATGTTCTTGTT
23429 CGTTTATGTT
1 CGTTTATGTT
23439 GGTTTATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (16 bp):
CGTTTATGTTCTTGTT
Found at i:24549 original size:65 final size:66
Alignment explanation
Indices: 24474--24642 Score: 245
Period size: 65 Copynumber: 2.6 Consensus size: 66
24464 ATTGACCGTG
* * *
24474 GTACAAACATATA-TTGACATAAAAGCTGCAATCCATTTCCACATATAGATGCATTCATGCTTGT
1 GTAC-AACATATAGTTGATATAAGAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGT
24538 AT
65 AT
* *
24540 GTACAACATA-ATTTGATATAGGAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGTA
1 GTACAACATATAGTTGATATAAGAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGTA
24604 T
66 T
*
24605 GTACAA-AGATAAGTTGATATAAGAGCTGCAATCCATTT
1 GTACAACATAT-AGTTGATATAAGAGCTGCAATCCATTT
24643 AAAATGGGTC
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
64 3 0.03
65 61 0.66
66 29 0.31
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (66 bp):
GTACAACATATAGTTGATATAAGAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGTA
T
Found at i:42564 original size:22 final size:24
Alignment explanation
Indices: 42517--42564 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
42507 AAATTTGACT
*
42517 TTTGATATTTATATCTTCTATTAA
1 TTTGATATTTATATCTTCTATAAA
*
42541 TTTGATTTTTATAT-TTC-ATAAA
1 TTTGATATTTATATCTTCTATAAA
42563 TT
1 TT
42565 AAATTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 13 0.59
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTGATATTTATATCTTCTATAAA
Found at i:44198 original size:24 final size:24
Alignment explanation
Indices: 44171--44277 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
44161 AAACGGAGAT
*
44171 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
44195 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
44219 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
44243 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
44267 ATCAGAAATCA
1 ATCAGAAATCA
44278 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:44277 original size:48 final size:48
Alignment explanation
Indices: 44171--44279 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
44161 AAACGGAGAT
* * * *
44171 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
44219 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
44267 ATCAGAAATCAGA
1 ATCAGAAATCAGA
44280 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:45426 original size:18 final size:18
Alignment explanation
Indices: 45405--45440 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45395 CTTCCATCTG
*
45405 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
45423 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
45441 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:46767 original size:8 final size:8
Alignment explanation
Indices: 46747--46825 Score: 67
Period size: 8 Copynumber: 11.5 Consensus size: 8
46737 GGTCAACTCC
46747 GGTCAAC-
1 GGTCAACG
46754 GGTCAACG
1 GGTCAACG
46762 GGTCAACG
1 GGTCAACG
46770 GGT---CG
1 GGTCAACG
46775 GGTCAACG
1 GGTCAACG
46783 GGT---CG
1 GGTCAACG
46788 GGTCAACG
1 GGTCAACG
46796 GGT---CG
1 GGTCAACG
46801 GGTCAACG
1 GGTCAACG
46809 GGT---CG
1 GGTCAACG
46814 GGTCAACG
1 GGTCAACG
46822 GGTC
1 GGTC
46826 GGGTCGGGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 25
0.70 0.00 0.30
Matches are distributed among these distances:
5 20 0.34
7 7 0.12
8 32 0.54
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:46778 original size:13 final size:13
Alignment explanation
Indices: 46760--46830 Score: 142
Period size: 13 Copynumber: 5.5 Consensus size: 13
46750 CAACGGTCAA
46760 CGGGTCAACGGGT
1 CGGGTCAACGGGT
46773 CGGGTCAACGGGT
1 CGGGTCAACGGGT
46786 CGGGTCAACGGGT
1 CGGGTCAACGGGT
46799 CGGGTCAACGGGT
1 CGGGTCAACGGGT
46812 CGGGTCAACGGGT
1 CGGGTCAACGGGT
46825 CGGGTC
1 CGGGTC
46831 GGGTTGTGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.14, C:0.24, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:48981 original size:24 final size:24
Alignment explanation
Indices: 48954--49060 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
48944 AAACGGAGAT
*
48954 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
48978 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
49002 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
49026 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
49050 ATCAGAAATCA
1 ATCAGAAATCA
49061 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:49060 original size:48 final size:48
Alignment explanation
Indices: 48954--49062 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
48944 AAACGGAGAT
* * * *
48954 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
49002 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
49050 ATCAGAAATCAGA
1 ATCAGAAATCAGA
49063 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:50208 original size:18 final size:18
Alignment explanation
Indices: 50187--50222 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
50177 CTTCCATCTG
*
50187 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
50205 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
50223 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:51552 original size:8 final size:8
Alignment explanation
Indices: 51532--51610 Score: 67
Period size: 8 Copynumber: 11.5 Consensus size: 8
51522 GGTCAACTCC
51532 GGTCAAC-
1 GGTCAACG
51539 GGTCAACG
1 GGTCAACG
51547 GGTCAACG
1 GGTCAACG
51555 GGT---CG
1 GGTCAACG
51560 GGTCAACG
1 GGTCAACG
51568 GGT---CG
1 GGTCAACG
51573 GGTCAACG
1 GGTCAACG
51581 GGT---CG
1 GGTCAACG
51586 GGTCAACG
1 GGTCAACG
51594 GGT---CG
1 GGTCAACG
51599 GGTCAACG
1 GGTCAACG
51607 GGTC
1 GGTC
51611 GGGTCGGGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 25
0.70 0.00 0.30
Matches are distributed among these distances:
5 20 0.34
7 7 0.12
8 32 0.54
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:51563 original size:13 final size:13
Alignment explanation
Indices: 51545--51615 Score: 142
Period size: 13 Copynumber: 5.5 Consensus size: 13
51535 CAACGGTCAA
51545 CGGGTCAACGGGT
1 CGGGTCAACGGGT
51558 CGGGTCAACGGGT
1 CGGGTCAACGGGT
51571 CGGGTCAACGGGT
1 CGGGTCAACGGGT
51584 CGGGTCAACGGGT
1 CGGGTCAACGGGT
51597 CGGGTCAACGGGT
1 CGGGTCAACGGGT
51610 CGGGTC
1 CGGGTC
51616 GGGTTGTGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.14, C:0.24, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:53312 original size:31 final size:31
Alignment explanation
Indices: 53254--53318 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
53244 AAACTATATG
** *
53254 TTTAATATCTAAACTATTAATTTTATTTTAT
1 TTTAATATCTAAACTATTAATAATATTTAAT
* * *
53285 TTTACTATCTAAACTTTTACTAATATTTAAT
1 TTTAATATCTAAACTATTAATAATATTTAAT
53316 TTT
1 TTT
53319 TTCCTTTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTAATATCTAAACTATTAATAATATTTAAT
Found at i:59940 original size:31 final size:31
Alignment explanation
Indices: 59900--59990 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
59890 GTACGACATT
* *
59900 ATTATTTTAGTGATATGATACATATCATATC
1 ATTACTTTAGTGATATGATACATGTCATATC
*
59931 ATTACTTTAGTAATATGATACATGTCATATC
1 ATTACTTTAGTGATATGATACATGTCATATC
*
59962 ATTACTTTAGATGATATGACACATGTCAT
1 ATTACTTTAG-TGATATGATACATGTCAT
59991 GTCAATAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 38 0.70
32 16 0.30
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (31 bp):
ATTACTTTAGTGATATGATACATGTCATATC
Found at i:69764 original size:21 final size:20
Alignment explanation
Indices: 69721--69765 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
69711 GAAAGAATTG
* *
69721 TTTAGAAAAATAGTATTTAT
1 TTTAGAAAAATAATATATAT
*
69741 TTTAGAAAAATAATACTATCT
1 TTTAGAAAAATAATA-TATAT
69762 TTTA
1 TTTA
69766 TTATTTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (20 bp):
TTTAGAAAAATAATATATAT
Found at i:70594 original size:2 final size:2
Alignment explanation
Indices: 70589--70641 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
70579 AATCTCTCAA
70589 AT AT AT AT AT AT AT AT AT AT AT A- 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
70630 AT AT AT AT AT AT
1 AT AT AT AT AT AT
70642 TTTACTCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82635 original size:165 final size:164
Alignment explanation
Indices: 82313--82641 Score: 633
Period size: 166 Copynumber: 2.0 Consensus size: 164
82303 TGAAGTAGTA
82313 TTCATTCAAAAGAGAATATAAGGCTAGAACATCACATGTTTATCACAAAGGTTGTCCAGAAATCC
1 TTCATTCAAAAGAGAATATAAGGCTAGAACATCACATGTTTATCACAAAGGTTGTCCAGAAATCC
82378 ATCTATCAAACATTGCAAAACACTCTAGAGGCTTATACTCAGGAGCAGTATGTCCTCCTCCCTAC
66 ATCTATCAAACATTGCAAAACACTCTAGAGGCTTATACTCAGGAGCAGTATGTCCTCCTCCCTAC
82443 AAATTCAGCATAAAAATAAAATTTACTTTAATGTT
131 AAATTCAGCATAAAAATAAAATTTAC-TTAATGTT
82478 TTCATTCAAAAGAGAATATAAGGCTAGAACATCAACATGTTTATCACAAAGGTTGTCCAGAAATC
1 TTCATTCAAAAGAGAATATAAGGCTAGAACATC-ACATGTTTATCACAAAGGTTGTCCAGAAATC
82543 CATCTATCAAACATTGCAAAACACTCTAGAGGCTTATACTCAGGAGCAGTATGTCCTCCTCCCTA
65 CATCTATCAAACATTGCAAAACACTCTAGAGGCTTATACTCAGGAGCAGTATGTCCTCCTCCCTA
82608 CAAATTCAGCATAAAAAT-AAATTTACTTAATGTT
130 CAAATTCAGCATAAAAATAAAATTTACTTAATGTT
82642 CATGAACATG
Statistics
Matches: 163, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
164 8 0.05
165 41 0.25
166 114 0.70
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (164 bp):
TTCATTCAAAAGAGAATATAAGGCTAGAACATCACATGTTTATCACAAAGGTTGTCCAGAAATCC
ATCTATCAAACATTGCAAAACACTCTAGAGGCTTATACTCAGGAGCAGTATGTCCTCCTCCCTAC
AAATTCAGCATAAAAATAAAATTTACTTAATGTT
Found at i:82918 original size:98 final size:98
Alignment explanation
Indices: 82764--82960 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
82754 GCTTCTCCCC
82764 AACACCCCTTCTAAGAAAAAGAGAAAAAAAAGAAGAAAATTTCTGAGTCATATATATACTGACCC
1 AACACCCCTTCTAAGAAAAAGAGAAAAAAAAGAAGAAAATTTCTGAGTCATATATATACTGACCC
82829 TGCAACTTGACTTTGTACCATCCATGGTCGCCA
66 TGCAACTTGACTTTGTACCATCCATGGTCGCCA
82862 AACACCCCTTCTAAGAAAAAGAGAAAAAAAAGAAGAAAATTTCTGAGTCATATATATACTGACCC
1 AACACCCCTTCTAAGAAAAAGAGAAAAAAAAGAAGAAAATTTCTGAGTCATATATATACTGACCC
82927 TGCAACTTGACTTTGTACCATCCATGGTCGCCA
66 TGCAACTTGACTTTGTACCATCCATGGTCGCCA
82960 A
1 A
82961 TCATTAATAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (98 bp):
AACACCCCTTCTAAGAAAAAGAGAAAAAAAAGAAGAAAATTTCTGAGTCATATATATACTGACCC
TGCAACTTGACTTTGTACCATCCATGGTCGCCA
Found at i:83292 original size:21 final size:21
Alignment explanation
Indices: 83267--83313 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
83257 AATGTCCAAC
*
83267 AATAACAAAATCAGTAAAAAA
1 AATAACAAAACCAGTAAAAAA
*
83288 AATAACAAAACCAGTAAAAAT
1 AATAACAAAACCAGTAAAAAA
83309 AATAA
1 AATAA
83314 TGTTTTGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.70, C:0.11, G:0.04, T:0.15
Consensus pattern (21 bp):
AATAACAAAACCAGTAAAAAA
Found at i:85769 original size:22 final size:22
Alignment explanation
Indices: 85744--85806 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
85734 TTGATAATCG
*
85744 AATAAAAATATTATACTAATTT
1 AATAAAAATATTATAATAATTT
** *
85766 AATAACTATTTTATAATAATTT
1 AATAAAAATATTATAATAATTT
* *
85788 AAT-AATATTTTATAATAAT
1 AATAAAAATATTATAATAAT
85807 CCAATAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAAAAATATTATAATAATTT
Found at i:85797 original size:10 final size:10
Alignment explanation
Indices: 85762--85804 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
85752 TATTATACTA
85762 ATTTAATAACT
1 ATTTAATAA-T
*
85773 ATTTTATAAT
1 ATTTAATAAT
85783 AATTTAATAAT
1 -ATTTAATAAT
*
85794 ATTTTATAAT
1 ATTTAATAAT
85804 A
1 A
85805 ATCCAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 11 0.39
11 17 0.61
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTTAATAAT
Found at i:85798 original size:21 final size:22
Alignment explanation
Indices: 85754--85806 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
85744 AATAAAAATA
*
85754 TTATACTAATTTAATAACTATT
1 TTATAATAATTTAATAACTATT
85776 TTATAATAATTTAATAA-TATT
1 TTATAATAATTTAATAACTATT
85797 TTATAATAAT
1 TTATAATAAT
85807 CCAATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATAATAATTTAATAACTATT
Found at i:85812 original size:21 final size:22
Alignment explanation
Indices: 85766--85813 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
85756 ATACTAATTT
**
85766 AATAACTATTTTATAATAATTT
1 AATAACTATTTTATAATAATCC
85788 AATAA-TATTTTATAATAATCC
1 AATAACTATTTTATAATAATCC
85809 AATAA
1 AATAA
85814 ATTAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAACTATTTTATAATAATCC
Found at i:87119 original size:22 final size:25
Alignment explanation
Indices: 87095--87140 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
87085 TAATTCTACA
87095 TTTA-TGACACATTTTT-TCTTTAT
1 TTTAGTGACACATTTTTGTCTTTAT
*
87118 TTTAGTGACATATTTTTGTCTTT
1 TTTAGTGACACATTTTTGTCTTT
87141 TTTGTCGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.61
Consensus pattern (25 bp):
TTTAGTGACACATTTTTGTCTTTAT
Found at i:93252 original size:24 final size:23
Alignment explanation
Indices: 93242--93366 Score: 117
Period size: 24 Copynumber: 5.2 Consensus size: 23
93232 CATAATTCAC
93242 ATCAAGTATCATATCAAAATCCA
1 ATCAAGTATCATATCAAAATCCA
* *
93265 GGTCAAGTATCATATCAGAATCCA
1 -ATCAAGTATCATATCAAAATCCA
*
93289 AGTCAAGTATCATATCAGAATCCA
1 A-TCAAGTATCATATCAAAATCCA
* *
93313 TGTC-AGATATCATATCAGAATCCA
1 -ATCAAG-TATCATATCAAAATCCA
* * *
93337 TGTCAAGTATCAGATCAGAAATCAA
1 -ATCAAGTATCATATCA-AAATCCA
93362 ATCAA
1 ATCAA
93367 AAATCAGGTA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
23 2 0.02
24 79 0.90
25 7 0.08
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (23 bp):
ATCAAGTATCATATCAAAATCCA
Found at i:93311 original size:48 final size:48
Alignment explanation
Indices: 93243--93356 Score: 176
Period size: 48 Copynumber: 2.4 Consensus size: 48
93233 ATAATTCACA
*
93243 TCAAGTATCATATCAAAATCCAGGTCA-AGTATCATATCAGAATCCAAG
1 TCAAGTATCATATCAGAATCCAGGTCAGA-TATCATATCAGAATCCAAG
* *
93291 TCAAGTATCATATCAGAATCCATGTCAGATATCATATCAGAATCCATG
1 TCAAGTATCATATCAGAATCCAGGTCAGATATCATATCAGAATCCAAG
*
93339 TCAAGTATCAGATCAGAA
1 TCAAGTATCATATCAGAA
93357 ATCAAATCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (48 bp):
TCAAGTATCATATCAGAATCCAGGTCAGATATCATATCAGAATCCAAG
Found at i:107968 original size:26 final size:26
Alignment explanation
Indices: 107939--107993 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
107929 TTAAAAGCCC
107939 ATTTTCACTTCT-TTAAAATTTTACAA
1 ATTTT-ACTTCTCTTAAAATTTTACAA
* *
107965 A-TTTATTTCTCCTTAAAATTTTATAA
1 ATTTTACTTCT-CTTAAAATTTTACAA
107991 ATT
1 ATT
107994 CGTTCCTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
24 5 0.21
25 3 0.12
26 15 0.62
27 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTTACTTCTCTTAAAATTTTACAA
Found at i:115784 original size:31 final size:31
Alignment explanation
Indices: 115749--115817 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
115739 ATAAGTAACT
* **
115749 ACATCTTAATTAAATAAAAACGAACTTGATC
1 ACATCTTAATGAAATAAAAACGAAAGTGATC
*
115780 ACATCTTAATGAAATAAAAATGAAAGTGATC
1 ACATCTTAATGAAATAAAAACGAAAGTGATC
115811 A-ATCTTA
1 ACATCTTA
115818 GTTTACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (31 bp):
ACATCTTAATGAAATAAAAACGAAAGTGATC
Found at i:116476 original size:169 final size:171
Alignment explanation
Indices: 116197--116536 Score: 657
Period size: 169 Copynumber: 2.0 Consensus size: 171
116187 GAAATCAATG
116197 TTTGTATAAGGTTGCATCATCCTTCCGTATAGTATATAAGTGATTGGCAATTATCATTCTATTGG
1 TTTGTATAAGGTTGCATCATCCTTCCGTATAGTATATAAGTGATTGGCAATTATCATTCTATTGG
116262 TTGAATATATTTTATTAGAACGATTACAGTCTTGTAAAATGAAAAGAGGATCCCACATTGTTT-C
66 TTGAATATATTTTATTAGAACGATTACAGTCTTGTAAAATGAAAAGAGGATCCCACATTGTTTCC
116326 CAGGACAGAGCATCTAGTCAAAA-GGAGATAATATGATAAA
131 CAGGACAGAGCATCTAGTCAAAATGGAGATAATATGATAAA
*
116366 TTTGTATAAGTTTGCATCATCCTTCCGTATAGTATATAAGTGATTGGCAATTATCATTCTATTGG
1 TTTGTATAAGGTTGCATCATCCTTCCGTATAGTATATAAGTGATTGGCAATTATCATTCTATTGG
116431 TTGAATATATTTTATTAGAACGATTACAGTCTTGTAAAATGAAAAGAGGATCCCACATTGTTTCC
66 TTGAATATATTTTATTAGAACGATTACAGTCTTGTAAAATGAAAAGAGGATCCCACATTGTTTCC
116496 CAGGACAGAGCATCTAGTCAAAATGGAGATAATATGATAAA
131 CAGGACAGAGCATCTAGTCAAAATGGAGATAATATGATAAA
116537 CACACCATGT
Statistics
Matches: 168, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
169 127 0.76
170 24 0.14
171 17 0.10
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (171 bp):
TTTGTATAAGGTTGCATCATCCTTCCGTATAGTATATAAGTGATTGGCAATTATCATTCTATTGG
TTGAATATATTTTATTAGAACGATTACAGTCTTGTAAAATGAAAAGAGGATCCCACATTGTTTCC
CAGGACAGAGCATCTAGTCAAAATGGAGATAATATGATAAA
Found at i:124502 original size:6 final size:6
Alignment explanation
Indices: 124491--124519 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
124481 TTTACCTTGA
124491 GAATGG GAATGG GAATGG GAATGG GAATG
1 GAATGG GAATGG GAATGG GAATGG GAATG
124520 ATGATAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
GAATGG
Found at i:130705 original size:20 final size:20
Alignment explanation
Indices: 130663--130721 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
130653 CGATATTAAG
* *
130663 CCCTTTAGTATCAATACTAA
1 CCCTTCAGTATCAATACCAA
* *
130683 CCCTTCAGTATCGATACCCA
1 CCCTTCAGTATCAATACCAA
* *
130703 CCCTTGA-TACCAATACCAA
1 CCCTTCAGTATCAATACCAA
130722 AATTGTATTC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (20 bp):
CCCTTCAGTATCAATACCAA
Found at i:132038 original size:69 final size:68
Alignment explanation
Indices: 131937--132064 Score: 238
Period size: 69 Copynumber: 1.9 Consensus size: 68
131927 TCAAGACACA
*
131937 TGCATCGTGGACACAGTATTGTTAGACAACTGATCTCAACTAGAGTTATCTATATATGATAAGTC
1 TGCATCGTGGACACAATATTGTTAGACAACTGATCTCAACTAGAGTTATCTATAT-TGATAAGTC
132002 AACG
65 AACG
132006 TGCATCGTGGACACAATATTGTTAGACAACTGATCTCAACTAGAGTTATCTATATTGAT
1 TGCATCGTGGACACAATATTGTTAGACAACTGATCTCAACTAGAGTTATCTATATTGAT
132065 TTTGTAAAGT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 4 0.07
69 54 0.93
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (68 bp):
TGCATCGTGGACACAATATTGTTAGACAACTGATCTCAACTAGAGTTATCTATATTGATAAGTCA
ACG
Found at i:139551 original size:16 final size:17
Alignment explanation
Indices: 139525--139557 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
139515 GGAATTAGAC
139525 AGAGAAAGGGGAAGGGG
1 AGAGAAAGGGGAAGGGG
*
139542 AGAG-AAGGGGATGGGG
1 AGAGAAAGGGGAAGGGG
139558 TAATGGCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (17 bp):
AGAGAAAGGGGAAGGGG
Found at i:139723 original size:12 final size:12
Alignment explanation
Indices: 139706--139731 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
139696 TGCACCGGTC
139706 CTGTCTCTCTCT
1 CTGTCTCTCTCT
139718 CTGTCTCTCTCT
1 CTGTCTCTCTCT
139730 CT
1 CT
139732 CCTTTTCGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (12 bp):
CTGTCTCTCTCT
Found at i:140402 original size:2 final size:2
Alignment explanation
Indices: 140395--140424 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
140385 TATTGACATG
140395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
140425 GTTGTATTAT
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):
TA
Found at i:141252 original size:40 final size:40
Alignment explanation
Indices: 141197--141275 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
141187 GTCAACACAC
141197 TGACATAATATTTTCATATGTTTCTCTTTCCATGTTTTAT
1 TGACATAATATTTTCATATGTTTCTCTTTCCATGTTTTAT
141237 TGACATAATATTTTCATATGTTTCTCTTTCCATGTTTTA
1 TGACATAATATTTTCATATGTTTCTCTTTCCATGTTTTA
141276 CTTATGTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (40 bp):
TGACATAATATTTTCATATGTTTCTCTTTCCATGTTTTAT
Found at i:142676 original size:15 final size:17
Alignment explanation
Indices: 142639--142675 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
142629 AATTTTATTA
142639 TTTTTAGTATATTTACT
1 TTTTTAGTATATTTACT
142656 TTTTTAGTA-ATTTACT
1 TTTTTAGTATATTTACT
142672 TTTT
1 TTTT
142676 ATTTTTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTAGTATATTTACT
Found at i:142680 original size:21 final size:21
Alignment explanation
Indices: 142646--142716 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
142636 TTATTTTTAG
142646 TATATTTACTTTTTTAGTA-ATT
1 TATATTTA--TTTTTAGTATATT
* *
142668 TACTTTTTATTTTTAGTATTTT
1 TA-TATTTATTTTTAGTATATT
*
142690 TATATTTATTTTT-GAATATT
1 TATATTTATTTTTAGTATATT
*
142710 TAAATTT
1 TATATTT
142717 TTATATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 11 0.27
21 19 0.46
22 6 0.15
23 5 0.12
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (21 bp):
TATATTTATTTTTAGTATATT
Found at i:142719 original size:22 final size:21
Alignment explanation
Indices: 142671--142736 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
142661 AGTAATTTAC
* **
142671 TTTTTATTTTTAGTATTTTTA
1 TTTTTATTTTTAATATTTAAA
*
142692 TATTTATTTTTGAATATTTAAA
1 TTTTTATTTTT-AATATTTAAA
* *
142714 TTTTTATATTTAAAATTTTAAA
1 TTTTTATTTTTAATA-TTTAAA
142736 T
1 T
142737 AGTTTTTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.36
22 23 0.64
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTTATTTTTAATATTTAAA
Found at i:142729 original size:15 final size:14
Alignment explanation
Indices: 142671--142733 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
142661 AGTAATTTAC
* *
142671 TTTTTATTTTTAGTA
1 TTTTTATATTTA-AA
142686 TTTTTATATTT--A
1 TTTTTATATTTAAA
142698 TTTTTGAATATTTAAA
1 TTTTT--ATATTTAAA
142714 TTTTTATATTTAAA
1 TTTTTATATTTAAA
*
142728 ATTTTA
1 TTTTTA
142734 AATAGTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 6 0.14
14 20 0.48
15 10 0.24
16 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTTTATATTTAAA
Found at i:145275 original size:222 final size:219
Alignment explanation
Indices: 144890--145312 Score: 616
Period size: 222 Copynumber: 1.9 Consensus size: 219
144880 TGTGTAATTT
* * * * *
144890 TTAAACATTAATTTATACAAGATTAAAATAAAATTAAATTTAAGTTTTACACATGATTAAAATCA
1 TTAAACATTAATTTATACAAAATTAAAAAAAAACTAAATTTAAGATTTACACATAATTAAAATCA
* ** *
144955 ATTCCTAATTACACATTTTAATTATACAAATTAATAAAAAACAATTAAAATATAAATGATTCATA
66 ATTCCTAATTACACATTTTAACTATACAAAACAATAAAAAACAATTAAAATATAAATGATCCATA
* *
145020 TATTTTATTTTTCAATAAAAATAAAATTATTAATTAAATTAAAACGAGTATCAATTTTTTGACTT
131 TATTTTATTTTTCAATAAAAATAAAATTATTAATTAAATTAAAA--AGTATCAATTTTTAGACTA
145085 TATCTATAATCATTAAATTATAAATG
194 TATCTATAATCATTAAATTATAAATG
* *
145111 TTAAACATTAGTTTATACAAAATTAAAAGAAAAACTAAATTTAAGATTTACACATAATTAAATTC
1 TTAAACATTAATTTATACAAAATTAAAA-AAAAACTAAATTTAAGATTTACACATAATTAAAATC
* ** **
145176 GACTT-CTAATTACACATTTTAACTATGTAAAACAATAAAAATTTAATTAAAATATAAATGATCC
65 -AATTCCTAATTACACATTTTAACTATACAAAACAATAAAAA-ACAATTAAAATATAAATGATCC
*
145240 ATATATTTTATTTTTTAATAAAAA-AAAATTATTAATTAAATTAAAAAGTATCAATTTTTAGACT
128 ATATATTTTATTTTTCAATAAAAATAAAATTATTAATTAAATTAAAAAGTATCAATTTTTAGACT
145304 ATATCTATA
193 ATATCTATA
145313 TATATACAAA
Statistics
Matches: 180, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
220 25 0.14
221 26 0.14
222 84 0.47
223 45 0.25
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (219 bp):
TTAAACATTAATTTATACAAAATTAAAAAAAAACTAAATTTAAGATTTACACATAATTAAAATCA
ATTCCTAATTACACATTTTAACTATACAAAACAATAAAAAACAATTAAAATATAAATGATCCATA
TATTTTATTTTTCAATAAAAATAAAATTATTAATTAAATTAAAAAGTATCAATTTTTAGACTATA
TCTATAATCATTAAATTATAAATG
Found at i:146243 original size:31 final size:31
Alignment explanation
Indices: 146208--146287 Score: 160
Period size: 31 Copynumber: 2.6 Consensus size: 31
146198 GGAGCCATAC
146208 AAATATCTTCTTCTCTTTTGCTCCATCTTAT
1 AAATATCTTCTTCTCTTTTGCTCCATCTTAT
146239 AAATATCTTCTTCTCTTTTGCTCCATCTTAT
1 AAATATCTTCTTCTCTTTTGCTCCATCTTAT
146270 AAATATCTTCTTCTCTTT
1 AAATATCTTCTTCTCTTT
146288 ACTATTAGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.20, C:0.25, G:0.03, T:0.53
Consensus pattern (31 bp):
AAATATCTTCTTCTCTTTTGCTCCATCTTAT
Found at i:146620 original size:20 final size:20
Alignment explanation
Indices: 146597--146706 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
146587 ACAAGTTTCA
*
146597 AAATCGCAATGCGAATAGGT
1 AAATCGCAACGCGAATAGGT
* * * ****
146617 AAATCGCAATGTGATTTTCC
1 AAATCGCAACGCGAATAGGT
* *
146637 AAATTCGTAACGCGAATAGTT
1 AAA-TCGCAACGCGAATAGGT
146658 AAATCGCAACGCGAATAGGT
1 AAATCGCAACGCGAATAGGT
* *
146678 AAATTGCAACGCGAATATGT
1 AAATCGCAACGCGAATAGGT
146698 AAATCGCAA
1 AAATCGCAA
146707 TACAAAAGTC
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 58 0.83
21 12 0.17
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (20 bp):
AAATCGCAACGCGAATAGGT
Found at i:146727 original size:40 final size:42
Alignment explanation
Indices: 146636--146733 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 42
146626 TGTGATTTTC
* * *
146636 CAAATTCGTAACGCGAATAGTTAAATCGCAACGCGAATAGGT
1 CAAATTCGCAACGCGAATAGTTAAATCGCAACACGAATAAGT
*
146678 -AAATT-GCAACGCGAATA-TGTAAATCGCAATAC-AA-AAGT
1 CAAATTCGCAACGCGAATAGT-TAAATCGCAACACGAATAAGT
*
146716 CAAATTCGCAACGTGAAT
1 CAAATTCGCAACGCGAAT
146734 TTATTTTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.06
39 8 0.17
40 32 0.67
41 5 0.10
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (42 bp):
CAAATTCGCAACGCGAATAGTTAAATCGCAACACGAATAAGT
Found at i:146807 original size:20 final size:20
Alignment explanation
Indices: 146781--146848 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
146771 ATTTTCTAAA
146781 TCGCAACACGAATTTTGATT
1 TCGCAACACGAATTTTGATT
* * *
146801 TCACAACTC-AATTTTCGAAT
1 TCGCAACACGAATTTT-GATT
*
146821 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
146841 TCGCAACA
1 TCGCAACA
146849 ACTTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.15
20 27 0.69
21 6 0.15
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:146815 original size:40 final size:40
Alignment explanation
Indices: 146771--146847 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
146761 TCGCAACAAG
* *
146771 ATTTTCTAAATCGCAACACGAATTTTGATTTCACAACTCA
1 ATTTTCGAAATCGCAACACGAATTTTAATTTCACAACTCA
* *
146811 ATTTTCGAATTCGCAACACGAATTTTAATTTCGCAAC
1 ATTTTCGAAATCGCAACACGAATTTTAATTTCACAAC
146848 AACTTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (40 bp):
ATTTTCGAAATCGCAACACGAATTTTAATTTCACAACTCA
Found at i:150947 original size:20 final size:20
Alignment explanation
Indices: 150922--150959 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
150912 GTTTTCCTTG
150922 AATTCGCAACGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
150942 AATTCGCAACGCGAAAGT
1 AATTCGCAACGCGAAAGT
150960 ATACCTTCAA
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:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
AATTCGCAACGCGAAAGTCA
Found at i:152486 original size:21 final size:21
Alignment explanation
Indices: 152438--152539 Score: 87
Period size: 21 Copynumber: 4.9 Consensus size: 21
152428 GTGAATCAGG
* ** *
152438 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGACAGGGGC
*
152459 CTCTTGAACGATGACAGTGGC
1 CTCTTGAACGATGACAGGGGC
* * * **
152480 CTATTGAATGGTGGTAGGGGC
1 CTCTTGAACGATGACAGGGGC
* * *
152501 CTCTTAAAGGATGATAGGGGC
1 CTCTTGAACGATGACAGGGGC
152522 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
152540 TGAATCAGGC
Statistics
Matches: 62, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGGC
Found at i:152504 original size:42 final size:42
Alignment explanation
Indices: 152441--152531 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 42
152431 AATCAGGCTC
* *
152441 TTGAACGGTGGGAGGGACCTCTTGAACGATGACAGTGGCCTA
1 TTGAACGGTGGGAGGGACCTCTTAAACGATGACAGGGGCCTA
* * * * * *
152483 TTGAATGGTGGTAGGGGCCTCTTAAAGGATGATAGGGGCCTC
1 TTGAACGGTGGGAGGGACCTCTTAAACGATGACAGGGGCCTA
152525 TTGAACG
1 TTGAACG
152532 ATGACAGGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.24
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGACCTCTTAAACGATGACAGGGGCCTA
Found at i:152969 original size:21 final size:21
Alignment explanation
Indices: 152945--152985 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
152935 GTCTTCACAT
* *
152945 AAAGTATCGACCTCCTCACGC
1 AAAGCATCGACCTCATCACGC
*
152966 AAAGCATTGACCTCATCACG
1 AAAGCATCGACCTCATCACG
152986 TAACTCCCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAGCATCGACCTCATCACGC
Found at i:154664 original size:19 final size:18
Alignment explanation
Indices: 154640--154675 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
154630 TCTGAAACTT
154640 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGC-AAATG
154659 AAAATCGCAACGCAAAT
1 AAAATCGCAACGCAAAT
154676 TTCATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCAAATG
Found at i:154717 original size:20 final size:20
Alignment explanation
Indices: 154689--154728 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
154679 ATTTTAGTAA
* *
154689 CGTTGCGATTTTCATTTTCG
1 CGTTACGATTTACATTTTCG
154709 CGTTACGATTTACATTTTCG
1 CGTTACGATTTACATTTTCG
154729 TGTTGCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (20 bp):
CGTTACGATTTACATTTTCG
Found at i:155099 original size:22 final size:22
Alignment explanation
Indices: 155074--155116 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
155064 TAGAGGGGGG
* *
155074 TCGCCAGATATGTGGACGGATT
1 TCGCCAGAGATGGGGACGGATT
*
155096 TCGCCGGAGATGGGGACGGAT
1 TCGCCAGAGATGGGGACGGAT
155117 GTCACCGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
TCGCCAGAGATGGGGACGGATT
Found at i:155280 original size:20 final size:20
Alignment explanation
Indices: 155255--155310 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
155245 ATTCGCGTTG
**
155255 CGAATTTGACTTATGTGTTA
1 CGAATTTGACTTATGCATTA
*
155275 CGAATTTGACTTATGCATTG
1 CGAATTTGACTTATGCATTA
155295 CGAATTTGACTTATGC
1 CGAATTTGACTTATGC
155311 GTTGTGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (20 bp):
CGAATTTGACTTATGCATTA
Found at i:155339 original size:20 final size:20
Alignment explanation
Indices: 155316--155380 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
155306 TATGCGTTGT
155316 GATTTATCTATTCGCGTTAC
1 GATTTATCTATTCGCGTTAC
*
155336 GATTTATCTATTCACGTTAC
1 GATTTATCTATTCGCGTTAC
* *
155356 GATTTAACTATTCGCGTTGC
1 GATTTATCTATTCGCGTTAC
155376 GATTT
1 GATTT
155381 TGGAACCTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (20 bp):
GATTTATCTATTCGCGTTAC
Found at i:161703 original size:40 final size:40
Alignment explanation
Indices: 161643--161727 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
161633 CGTCGCGAAG
*
161643 TCGAATCCATCTTGAAATGATATGGAATTGAAGCCGCAGA
1 TCGAGTCCATCTTGAAATGATATGGAATTGAAGCCGCAGA
161683 TCGAGTCCATCTTGAAATGATATGGAATTGAAGCCGCAGA
1 TCGAGTCCATCTTGAAATGATATGGAATTGAAGCCGCAGA
161723 TCGAG
1 TCGAG
161728 ATTTGAATCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (40 bp):
TCGAGTCCATCTTGAAATGATATGGAATTGAAGCCGCAGA
Found at i:162787 original size:63 final size:63
Alignment explanation
Indices: 162710--162844 Score: 225
Period size: 63 Copynumber: 2.1 Consensus size: 63
162700 TCCTCCGCCG
* *
162710 TGAAGTTGAAATTGGTTCTGGAACTGGGAAATGATTTGTTGACAGTCAGCCGCCCCTTCGCTA
1 TGAAGTTGAAATTGGCTCTGAAACTGGGAAATGATTTGTTGACAGTCAGCCGCCCCTTCGCTA
* * *
162773 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCTG
1 TGAAGTTGAAATTGGCTCTGAAACTGGGAAATGATTTGTTGACAGTCAGCCGCCCCTTCGCTA
162836 TGAAGTTGA
1 TGAAGTTGA
162845 GCTTGTGCTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (63 bp):
TGAAGTTGAAATTGGCTCTGAAACTGGGAAATGATTTGTTGACAGTCAGCCGCCCCTTCGCTA
Found at i:168566 original size:38 final size:36
Alignment explanation
Indices: 168494--168591 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 36
168484 CTTATATATA
* *
168494 AAAATATTTTCAAAAAC-ATATAATATATAAATTTTT
1 AAAATATTTTTAAAAACTATAT-ATATATAAATTTTC
168530 AAAATATTTTTTAAAAACTATATAT-TATACATATTTTC
1 AAAATA-TTTTTAAAAACTATATATATATA-A-ATTTTC
*
168568 AAAACATTTTTAAGAAACTATATA
1 AAAATATTTTTAA-AAACTATATA
168592 ATAAAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
36 10 0.19
37 20 0.37
38 24 0.44
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (36 bp):
AAAATATTTTTAAAAACTATATATATATAAATTTTC
Found at i:195002 original size:22 final size:22
Alignment explanation
Indices: 194971--195019 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
194961 CCCCACTGCA
*
194971 TGCA-GGCGACCTCTTCCGACG
1 TGCATGGCGACCTCTTACGACG
*
194992 TGCATGGCGACCTCTTATGACG
1 TGCATGGCGACCTCTTACGACG
195014 TGCATG
1 TGCATG
195020 TCGCATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (22 bp):
TGCATGGCGACCTCTTACGACG
Found at i:195061 original size:31 final size:31
Alignment explanation
Indices: 195026--195084 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
195016 CATGTCGCAT
*
195026 GCAAAGCTTT-ATCCTCTCACCACAGCTCTTA
1 GCAAAG-TTTCATCCTATCACCACAGCTCTTA
* *
195057 GCAAAGTTTCATTCTATCGCCACAGCTC
1 GCAAAGTTTCATCCTATCACCACAGCTC
195085 GTATAGAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.25, C:0.34, G:0.12, T:0.29
Consensus pattern (31 bp):
GCAAAGTTTCATCCTATCACCACAGCTCTTA
Found at i:195426 original size:17 final size:18
Alignment explanation
Indices: 195389--195431 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
195379 TTATTGTAAC
195389 TTTAATAATTAAATCTTA
1 TTTAATAATTAAATCTTA
* *
195407 TTTAGTAATT-AATTTTA
1 TTTAATAATTAAATCTTA
195424 TTTAATAA
1 TTTAATAA
195432 AATAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAATAATTAAATCTTA
Found at i:195579 original size:16 final size:16
Alignment explanation
Indices: 195544--195584 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
195534 GTTTACTTCA
*
195544 GAATGATT-AAGTGCT
1 GAATGATTCAACTGCT
*
195559 GAATGATTCAACTGTT
1 GAATGATTCAACTGCT
195575 GAATGATTCA
1 GAATGATTCA
195585 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAACTGCT
Found at i:196126 original size:18 final size:18
Alignment explanation
Indices: 196100--196157 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
196090 TTATATTAAT
196100 TTTAATAATTAAATATTA
1 TTTAATAATTAAATATTA
* *
196118 TTTAGTAATTAGAT-TTA
1 TTTAATAATTAAATATTA
*
196135 TTTAATAAAGTAAATATTTA
1 TTTAAT-AATTAAATA-TTA
196155 TTT
1 TTT
196158 TAGACAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 8 0.25
18 18 0.56
20 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
TTTAATAATTAAATATTA
Found at i:215401 original size:125 final size:125
Alignment explanation
Indices: 215265--215511 Score: 458
Period size: 125 Copynumber: 2.0 Consensus size: 125
215255 CTCTTGTTGG
*
215265 TCCCTGCTAGGGGTGAAATTATAAAATTTTACAGATAGTAAACTTGTAAAATTTTATAAGTAATA
1 TCCCTGCTAGGGGTGAAATTATAAAATTTTACAGAGAGTAAACTTGTAAAATTTTATAAGTAATA
*
215330 ATATATTATTAATAAAAATATCTAAAATATAAGAGGATTAAAAAATTTAAGGGAGAATGT
66 ATATATTATGAATAAAAATATCTAAAATATAAGAGGATTAAAAAATTTAAGGGAGAATGT
*
215390 TCCCTGCTAGGGGTGAAATTATAAAATTTTACAGAGAGTGAACTTGTAAAATTTTATAAGTAATA
1 TCCCTGCTAGGGGTGAAATTATAAAATTTTACAGAGAGTAAACTTGTAAAATTTTATAAGTAATA
*
215455 ATATATTATGAATAAAAATATCTAAAATATAAGAGGATTAAAAATTTTAAGGGAGAA
66 ATATATTATGAATAAAAATATCTAAAATATAAGAGGATTAAAAAATTTAAGGGAGAA
215512 GACGACTACC
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (125 bp):
TCCCTGCTAGGGGTGAAATTATAAAATTTTACAGAGAGTAAACTTGTAAAATTTTATAAGTAATA
ATATATTATGAATAAAAATATCTAAAATATAAGAGGATTAAAAAATTTAAGGGAGAATGT
Found at i:224797 original size:27 final size:27
Alignment explanation
Indices: 224766--224820 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
224756 ATCAACGGCT
224766 CGTGATTCTTCAATTATTGGTGCATGG
1 CGTGATTCTTCAATTATTGGTGCATGG
*
224793 CGTGATTCTTCAATTATTGGTGCGTGG
1 CGTGATTCTTCAATTATTGGTGCATGG
224820 C
1 C
224821 AGCCGACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.40
Consensus pattern (27 bp):
CGTGATTCTTCAATTATTGGTGCATGG
Found at i:225031 original size:17 final size:17
Alignment explanation
Indices: 225009--225044 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
224999 TTAATAGTTT
225009 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
225026 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
225043 GT
1 GT
225045 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:225251 original size:30 final size:30
Alignment explanation
Indices: 225182--225287 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
225172 TTTAGTTAAT
* *
225182 TAGTTTTTTAGTAGTGAA-TTATAATTAAAAAA
1 TAGTTTATTAGT--TGAAGTTAT-ATTAAAGAA
* *
225214 TATTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
225244 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
225274 TAGTTTATTAGTTG
1 TAGTTTATTAGTTG
225288 TTTAAAGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 53 0.79
31 4 0.06
32 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:225282 original size:15 final size:16
Alignment explanation
Indices: 225229--225283 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
225219 TATTAGTTTA
225229 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
225245 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
225259 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
225275 AGTT-TATTA
1 AGTTATATTA
225284 GTTGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:225368 original size:15 final size:16
Alignment explanation
Indices: 225340--225373 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
225330 GTTTGTTACT
225340 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
225356 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
225371 TTA
1 TTA
225374 AATATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:227580 original size:60 final size:60
Alignment explanation
Indices: 227511--227819 Score: 537
Period size: 60 Copynumber: 5.1 Consensus size: 60
227501 ATTTATAATA
*
227511 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* * *
227571 AATCATTACTAAATTATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
227631 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
227691 AATCATTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
227751 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
227811 AAATCATTA
1 -AATCATTA
227820 ATATCAAATC
Statistics
Matches: 238, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
60 230 0.97
61 8 0.03
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (60 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:227585 original size:21 final size:22
Alignment explanation
Indices: 227561--228051 Score: 112
Period size: 21 Copynumber: 24.0 Consensus size: 22
227551 ATAATAATTT
227561 AATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
* *
227582 AATTATTACT-ATCAAATCATTA
1 AATTATTACTAATC-AATTACTA
*
227604 AA-TATTAATAA-CAATT--T-
1 AATTATTACTAATCAATTACTA
*
227621 CATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
* * *
227642 AATCATTACT-ATCAAATCATTA
1 AATTATTACTAATC-AATTACTA
*
227664 AA-TATTAATAA-CAATT--T-
1 AATTATTACTAATCAATTACTA
* *
227681 CATTATTACTAATC-ATTATTA
1 AATTATTACTAATCAATTACTA
* * *
227702 AATCATTACT-ATCAAATCATTA
1 AATTATTACTAATC-AATTACTA
* *
227724 AA-AATTAATAAT-AATT--T-
1 AATTATTACTAATCAATTACTA
*
227741 CATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
* * *
227762 AATCATTACT-ATCAAATCATTA
1 AATTATTACTAATC-AATTACTA
* *
227784 AA-AATTAATAAT-AATT--T-
1 AATTATTACTAATCAATTACTA
* * *
227801 CATCATTACTAAATC-ATTAATATCA
1 AATTATTACT-AATCAATT-A-CT-A
* ** * *
227826 AATCATTAAAAATTAATAATACTTT
1 AATTATTACTAATCAAT--TAC-TA
227851 AATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
* * *
227872 AATCATTACT-ATCAAATCATTA
1 AATTATTACTAATC-AATTACTA
*
227894 AA-TATTAAT-ATCAATT--T-
1 AATTATTACTAATCAATTACTA
*
227911 TATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
* * *
227932 AATCATTACT-ATCAAATCATTA
1 AATTATTACTAATC-AATTACTA
*
227954 AA-TATTAATAA-CAATT--T-
1 AATTATTACTAATCAATTACTA
*
227971 TATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
* *
227992 AATCATTACT-ATCAAATTATTA
1 AATTATTACTAATC-AATTACTA
*
228014 AA-TATTAATAA-CAATT--T-
1 AATTATTACTAATCAATTACTA
*
228031 CATTATTACTAATC-ATTACTA
1 AATTATTACTAATCAATTACTA
228052 TCAAATCATT
Statistics
Matches: 338, Mismatches: 69, Indels: 126
0.63 0.13 0.24
Matches are distributed among these distances:
17 7 0.02
18 76 0.22
19 13 0.04
20 49 0.14
21 103 0.30
22 62 0.18
23 1 0.00
24 5 0.01
25 19 0.06
26 2 0.01
27 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTATTACTAATCAATTACTA
Found at i:227661 original size:25 final size:25
Alignment explanation
Indices: 227631--227833 Score: 90
Period size: 25 Copynumber: 8.3 Consensus size: 25
227621 CATTATTACT
*
227631 AATCATTACTAAATCATTACTATCA
1 AATCATTACTAAATCATTAATATCA
*
227656 AATCA-T--TAAAT-ATTAATAACA
1 AATCATTACTAAATCATTAATATCA
* *
227677 ATTTCATTATTACTAATCATT-AT-T-A
1 A-ATCATTACTA--AATCATTAATATCA
227702 AATCATTACTATCAAATCATT-A-A--A
1 AATCATTAC--T-AAATCATTAATATCA
* * * * * *
227726 AATTAATAATAATTTCATTATTA-CT
1 AATCATTACTAA-ATCATTAATATCA
*
227751 AATCATTACTAAATCATTACTATCA
1 AATCATTACTAAATCATTAATATCA
* * * **
227776 AATCATTA-AAAATTAATAATAATTT
1 AATCATTACTAAATCATTAAT-ATCA
*
227801 CATCATTACTAAATCATTAATATCA
1 AATCATTACTAAATCATTAATATCA
227826 AATCATTA
1 AATCATTA
227834 AAAATTAATA
Statistics
Matches: 129, Mismatches: 31, Indels: 36
0.66 0.16 0.18
Matches are distributed among these distances:
21 11 0.09
22 14 0.11
23 1 0.01
24 31 0.24
25 53 0.41
26 10 0.08
27 6 0.05
28 3 0.02
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
AATCATTACTAAATCATTAATATCA
Found at i:227674 original size:120 final size:120
Alignment explanation
Indices: 227511--228110 Score: 874
Period size: 120 Copynumber: 5.1 Consensus size: 120
227501 ATTTATAATA
*
227511 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCA
* *
227576 TTACTAAATTATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
227631 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCA
* *
227696 TTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
227751 AATCATTACTAAATCATTACTATCAAATCATTAAA-A--ATTAATAA--TAA-T-TT-C--ATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCA
* * * *
227806 TTACTAAATCATTAATATCAAATCATTAAAAATTAATAATACTTTAATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
227861 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT-ATCAATTTTATTATTACTAATC
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAAT-AATTTAATTATTACTAATC
* *
227925 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTTATTATTACT
65 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
227981 AATCATTACTAAATCATTACTATCAAATTATTAAATATTAATAACAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCA
* * *
228046 TTACT--ATCA--AATCATTAAAT-ATT-AATATTAATAATAATTTCATCATTACT
66 TTACTAAATCATTACT-ATCAAATCATTAAATATTAATAATAATTTCATTATTACT
228096 AATCATTACTAAATC
1 AATCATTACTAAATC
228111 TTATAAATAC
Statistics
Matches: 438, Mismatches: 29, Indels: 31
0.88 0.06 0.06
Matches are distributed among these distances:
110 90 0.21
111 1 0.00
112 3 0.01
113 6 0.01
114 1 0.00
115 43 0.10
116 6 0.01
117 14 0.03
118 5 0.01
119 1 0.00
120 267 0.61
121 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (120 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCA
TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:227866 original size:60 final size:60
Alignment explanation
Indices: 227802--228110 Score: 443
Period size: 60 Copynumber: 5.2 Consensus size: 60
227792 TAATAATTTC
* * * *
227802 ATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATACTTTAATTATTACTA
1 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
*
227862 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT-ATCAATTTTATTATTACTA
1 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAAT-AATTTCATTATTACTA
* *
227922 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTTATTATTACTA
1 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
* *
227982 ATCATTACTAAATCATTACTATCAAATTATTAAATATTAATAACAATTTCATTATTACTA
1 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
* * *
228042 ATCATTACT--ATCA--AATCATTAAAT-ATT-AATATTAATAATAATTTCATCATTACTA
1 ATCATTACTAAATCATTACT-ATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
228097 ATCATTACTAAATC
1 ATCATTACTAAATC
228111 TTATAAATAC
Statistics
Matches: 233, Mismatches: 11, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
55 35 0.15
56 5 0.02
57 9 0.04
58 4 0.02
59 2 0.01
60 177 0.76
61 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
Found at i:228032 original size:290 final size:285
Alignment explanation
Indices: 227512--228103 Score: 999
Period size: 290 Copynumber: 2.1 Consensus size: 285
227502 TTTATAATAA
*
227512 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCAT
1 ATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCAT
*
227577 TACTAAATTATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTA
66 TACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTA
*
227642 AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTATTAAATCA
131 AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCA
* *
227707 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC-ATTAC
196 TTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTACT--ATCAAAT-C
227771 TATCAAATCATTAAAAATTAATAATAATTTC
258 -ATCAAAT-ATT-AAAATTAATAATAATTTC
*
227802 ATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATACTTTAATTATTACTAATCAT
1 ATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCAT
* *
227867 TACTAAATCATTACTATCAAATCATTAAATATTAATATCAATTTTATTATTACTAATCATTACTA
66 TACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTA
*
227932 AATCATTACTATCAAATCATTAAATATTAATAACAATTTTATTATTACTAATCATTACTAAATCA
131 AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCA
* * *
227997 TTACTATCAAATTATTAAATATTAATAACAATTTCATTATTACTAATCATTACTATCAAATCATT
196 TTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTACTATCAAATCATC
*
228062 AAATATTAATATTAATAATAATTTC
261 AAATATTAAAATTAATAATAATTTC
228087 ATCATTACT-AATCATTA
1 ATCATTACTAAATCATTA
228104 CTAAATCTTA
Statistics
Matches: 288, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
284 8 0.03
285 26 0.09
286 3 0.01
287 6 0.02
288 4 0.01
289 2 0.01
290 239 0.83
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (285 bp):
ATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCAT
TACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTA
AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCA
TTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTACTATCAAATCATC
AAATATTAAAATTAATAATAATTTC
Found at i:231022 original size:26 final size:24
Alignment explanation
Indices: 230962--231022 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
230952 TACTAATATT
*
230962 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
230986 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
231013 ATTTAATAAT
1 A-TTAATAAT
231023 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:231752 original size:42 final size:48
Alignment explanation
Indices: 231706--231811 Score: 134
Period size: 50 Copynumber: 2.3 Consensus size: 48
231696 GTTTAAAGAC
*
231706 ACTAACAAATTAATTAA-TA-TTTTTT-TATAT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAACTATTTTTTTATATATATATATATAACTTAA
*
231748 ACTAATAAACTAATTAACTATTTTTTTTATATATATAATATATAACTTAA
1 ACTAACAAACTAATTAACTA-TTTTTTTATATATAT-ATATATAACTTAA
231798 ACTAACAAACTAAT
1 ACTAACAAACTAAT
231812 AATTTATACT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 15 0.28
43 2 0.04
45 6 0.11
46 5 0.09
47 1 0.02
49 2 0.04
50 22 0.42
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (48 bp):
ACTAACAAACTAATTAACTATTTTTTTATATATATATATATAACTTAA
Found at i:231822 original size:21 final size:21
Alignment explanation
Indices: 231789--231837 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
231779 TATATAATAT
231789 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
231810 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
231831 ATTAACT
1 A-TAACT
231838 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:232398 original size:37 final size:37
Alignment explanation
Indices: 232345--232417 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
232335 TGATGCAGAC
*
232345 CTACCATGTCGTCGGGACTCCATGGCGACCTACCATT
1 CTACCATGTCGCCGGGACTCCATGGCGACCTACCATT
232382 CTACCATGTCGCCGGGACTCCATGGCGACCTACCAT
1 CTACCATGTCGCCGGGACTCCATGGCGACCTACCAT
232418 GTCGCCGGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.37, G:0.22, T:0.22
Consensus pattern (37 bp):
CTACCATGTCGCCGGGACTCCATGGCGACCTACCATT
Found at i:232437 original size:25 final size:27
Alignment explanation
Indices: 232382--232439 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 27
232372 ACCTACCATT
*
232382 CTACCATGTCGCCGGGACTCCATGGCGAC
1 CTACCATGTCGCCGGGA--CCATGGCAAC
232411 CTACCATGTCGCC-GG-CCATGGCAAC
1 CTACCATGTCGCCGGGACCATGGCAAC
232436 CTAC
1 CTAC
232440 GATAGAACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.46
28 2 0.07
29 13 0.46
ACGTcount: A:0.19, C:0.40, G:0.24, T:0.17
Consensus pattern (27 bp):
CTACCATGTCGCCGGGACCATGGCAAC
Found at i:232730 original size:29 final size:30
Alignment explanation
Indices: 232647--232731 Score: 147
Period size: 29 Copynumber: 2.9 Consensus size: 30
232637 AAAGAATGTT
232647 GGACGCCGGGCGTGCATGGCGACCT-TATA
1 GGACGCCGGGCGTGCATGGCGACCTATATA
*
232676 GGACGTCGGGCGTGCATGGCGACCTATA-A
1 GGACGCCGGGCGTGCATGGCGACCTATATA
232705 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
232732 GCTGTCACTG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 51 0.96
30 2 0.04
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.16
Consensus pattern (30 bp):
GGACGCCGGGCGTGCATGGCGACCTATATA
Found at i:234851 original size:22 final size:23
Alignment explanation
Indices: 234826--234868 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
234816 TGATAGATAA
234826 TTATTTA-AATTATGAATCAAAT
1 TTATTTATAATTATGAATCAAAT
* *
234848 TTATTTATTATTTTGAATCAA
1 TTATTTATAATTATGAATCAA
234869 TAGATCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (23 bp):
TTATTTATAATTATGAATCAAAT
Found at i:235176 original size:3 final size:3
Alignment explanation
Indices: 235163--235212 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
235153 TCTATGTACA
235163 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
235210 TAT
1 TAT
235213 ATATGTTGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:244776 original size:15 final size:15
Alignment explanation
Indices: 244756--244797 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
244746 AATATAAGGT
*
244756 TATTTTGAATTTTGA
1 TATTTTGAATTTGGA
244771 TATTTT-AGATTTGGA
1 TATTTTGA-ATTTGGA
244786 TGATTTTGAATT
1 T-ATTTTGAATT
244798 AATTTGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 13 0.57
16 8 0.35
17 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
TATTTTGAATTTGGA
Found at i:251358 original size:49 final size:49
Alignment explanation
Indices: 251286--251383 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
251276 CGAAGGATGT
*
251286 CGCAGCATTGTTGCCTATCAAAATTAACAAAACAAACTTTAAAACACCA
1 CGCAGCATTGTGGCCTATCAAAATTAACAAAACAAACTTTAAAACACCA
* *
251335 CGCAGCGTTGTGGCCTATCAAAATTAACAAAACAAACTTTGAAACACCA
1 CGCAGCATTGTGGCCTATCAAAATTAACAAAACAAACTTTAAAACACCA
251384 AGATGACAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.21
Consensus pattern (49 bp):
CGCAGCATTGTGGCCTATCAAAATTAACAAAACAAACTTTAAAACACCA
Found at i:256542 original size:2 final size:2
Alignment explanation
Indices: 256535--256575 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
256525 CCGCCCAGAT
256535 TA TA TA TA TA TA TA TA TA TA T- TA -A T- TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256573 TA T
1 TA T
256576 TTTATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:256602 original size:13 final size:13
Alignment explanation
Indices: 256551--256603 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
256541 TATATATATA
*
256551 TATATTAATTATA
1 TATATTAATTATT
256564 TATATATAA-TATT
1 TATAT-TAATTATT
256577 T-TA-T-ATT-TT
1 TATATTAATTATT
256586 TATATTAATTATT
1 TATATTAATTATT
256599 TATAT
1 TATAT
256604 AATATATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 1 0.03
12 5 0.15
13 16 0.48
14 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTAATTATT
Found at i:259874 original size:24 final size:23
Alignment explanation
Indices: 259842--259886 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
259832 ATAAACATGT
**
259842 TTAGAATTATTTTTATTGAATTA
1 TTAGAATTAAGTTTATTGAATTA
259865 TTAGAGATTAAGTTTATTGAAT
1 TTAGA-ATTAAGTTTATTGAAT
259887 AATTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (23 bp):
TTAGAATTAAGTTTATTGAATTA
Found at i:260013 original size:29 final size:26
Alignment explanation
Indices: 259958--260009 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
259948 TTTTTATTTT
*
259958 TTTTATTTTTTTTGAAAGATCATATA
1 TTTTATTTTTTTTGAAAGATCAAATA
259984 TTTTATTTATTTTTTGAAAGATCAAA
1 TTTTA-TT-TTTTTTGAAAGATCAAA
260010 ATATCATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 2 0.09
28 16 0.70
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (26 bp):
TTTTATTTTTTTTGAAAGATCAAATA
Found at i:261977 original size:42 final size:42
Alignment explanation
Indices: 261894--261989 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
261884 ACCACTCCTT
* * *
261894 AAGAATCACATATATATTCCAAAGGACCAAATATGTGTCCCG
1 AAGAACCACATATATATTCCAAAGGACCAAATATATATCCCG
* ** *
261936 AAGAACCACATATATTTTCCAAAGGATTACATATATATCCCG
1 AAGAACCACATATATATTCCAAAGGACCAAATATATATCCCG
261978 AATG-ACCACATA
1 AA-GAACCACATA
261990 GAACTATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (42 bp):
AAGAACCACATATATATTCCAAAGGACCAAATATATATCCCG
Found at i:261988 original size:21 final size:21
Alignment explanation
Indices: 261900--261989 Score: 72
Period size: 21 Copynumber: 4.3 Consensus size: 21
261890 CCTTAAGAAT
*
261900 CACATATATATTCCAAAGGAC
1 CACATATATATCCCAAAGGAC
* * * * *
261921 CAAATATGTGTCCCGAAGAAC
1 CACATATATATCCCAAAGGAC
* * *
261942 CACATATATTTTCCAAAGGAT
1 CACATATATATCCCAAAGGAC
* * *
261963 TACATATATATCCCGAATGAC
1 CACATATATATCCCAAAGGAC
261984 CACATA
1 CACATA
261990 GAACTATTTA
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (21 bp):
CACATATATATCCCAAAGGAC
Found at i:262494 original size:20 final size:20
Alignment explanation
Indices: 262471--262522 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
262461 AACGCGATCC
262471 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
262491 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
262511 CCAAAATCGCAA
1 CCAGAATCGCAA
262523 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:262639 original size:20 final size:20
Alignment explanation
Indices: 262616--262770 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
262606 CGCAAACACA
262616 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
262636 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
262656 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
262676 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
262696 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
262716 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
262736 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
262757 TAAATCGCAACGCG
1 TAAATCGCAACGCG
262771 ATATTTAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.85
21 15 0.13
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:262661 original size:60 final size:60
Alignment explanation
Indices: 262578--262770 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
262568 GATTTTCCAT
* ** * *
262578 AATCGCAACGCGAATATGAAAATCGCAACGCAAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCAAATACATAAATCGCAACGCGTATCCGTA
* ** *** *
262638 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCAAATACATAAATCGCAACGCGTATCCGTA
*
262698 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCA-AATACAT-AAATCGCAACGCGTATCCGTA
262759 AATCGCAACGCG
1 AATCGCAACGCG
262771 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
60 79 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCAAATACATAAATCGCAACGCGTATCCGTA
Found at i:263192 original size:33 final size:33
Alignment explanation
Indices: 263153--263223 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
263143 TTCACTTAGA
*
263153 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
263186 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
263219 TTTCA
1 TTTCA
263224 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:263345 original size:20 final size:19
Alignment explanation
Indices: 263303--263387 Score: 90
Period size: 20 Copynumber: 4.6 Consensus size: 19
263293 TGCAGAAGAG
263303 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
*
263324 TCGCAACGAGAGAATGACAA
1 TCGCAACGAGA-AATGAAAA
263344 TCGCAAC--GAAA-G--AA
1 TCGCAACGAGAAATGAAAA
*
263358 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
263377 TCGCAACGAGA
1 TCGCAACGAGA
263388 GAATCGCAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
14 9 0.16
16 5 0.09
17 3 0.05
18 2 0.04
19 13 0.23
20 14 0.25
21 10 0.18
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:263361 original size:14 final size:14
Alignment explanation
Indices: 263342--263398 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
263332 AGAGAATGAC
263342 AATCGCAACGAAAG
1 AATCGCAACGAAAG
263356 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
*
263373 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
263389 AATCGCAACG
1 AATCGCAACG
263399 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 6 0.16
17 5 0.14
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:263379 original size:33 final size:33
Alignment explanation
Indices: 263322--263414 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
263312 GATAAATGAA
* *
263322 AATCGCAACGAGAGAATGACAATCGCAACGAAAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGAAAG
*
263356 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
263389 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
263415 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 42 0.78
34 12 0.22
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:263432 original size:19 final size:19
Alignment explanation
Indices: 263410--263507 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
263400 GAAACCAAAA
*
263410 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
263429 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
263443 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
263462 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
263476 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
263495 TCGCGTTGCGATT
1 TCGCGTTGCGATT
263508 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:263451 original size:14 final size:14
Alignment explanation
Indices: 263432--263521 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
263422 TTTCATTTCG
263432 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
263446 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
263465 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
263479 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
263496 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
263512 CGTTGCGATT
1 CGTTGCGATT
263522 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:263457 original size:33 final size:33
Alignment explanation
Indices: 263415--263529 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
263405 CAAAATCGCA
263415 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
263448 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
263481 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
263514 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
263530 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:264355 original size:30 final size:31
Alignment explanation
Indices: 264304--264365 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
264294 TACAACCATT
*
264304 CCCAAATTTTCCAAAATTAACA-AATTGGTCC
1 CCCAAATTTTCCAAAAATAACAGAA-TGGTCC
*
264335 CCCAACTTTT-CAAAAATAACAGAATGGTCC
1 CCCAAATTTTCCAAAAATAACAGAATGGTCC
264365 C
1 C
264366 TGATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (31 bp):
CCCAAATTTTCCAAAAATAACAGAATGGTCC
Found at i:264451 original size:11 final size:11
Alignment explanation
Indices: 264418--264451 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
264408 CCAGACCTTA
264418 TATAATTTTTC
1 TATAATTTTTC
*
264429 CATAATTTTTC
1 TATAATTTTTC
*
264440 TATAAATTTTC
1 TATAATTTTTC
264451 T
1 T
264452 CATCCTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (11 bp):
TATAATTTTTC
Found at i:265374 original size:30 final size:29
Alignment explanation
Indices: 265313--265377 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
265303 ACCCGTATAT
* * * *
265313 AACTTTTTAAAATTATATTTTGGTCCCTA
1 AACTTTTTAAAATTATACTCTAGTCACTA
*
265342 AACTTTTTAAAATTTATACTCTAGTCATTA
1 AACTTTTTAAAA-TTATACTCTAGTCACTA
265372 AACTTT
1 AACTTT
265378 ACTAAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.48
Consensus pattern (29 bp):
AACTTTTTAAAATTATACTCTAGTCACTA
Found at i:266647 original size:18 final size:16
Alignment explanation
Indices: 266626--266660 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
266616 TAAACATCTC
266626 TCATCTTTTTTTTCATTT
1 TCAT-TTTTTTTT-ATTT
266644 TCATTTTTTTTTATTT
1 TCATTTTTTTTTATTT
266660 T
1 T
266661 TTTATTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (16 bp):
TCATTTTTTTTTATTT
Found at i:266662 original size:12 final size:12
Alignment explanation
Indices: 266647--266706 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 12
266637 TTCATTTTCA
*
266647 TTTTTTTTT-AT
1 TTTTTTTTTCTT
*
266658 TTTTTTATTCTT
1 TTTTTTTTTCTT
*
266670 TTTCTTATTTCTT
1 TTT-TTTTTTCTT
*
266683 TCTTTTTTTCTT
1 TTTTTTTTTCTT
266695 TTTCTTTTTTCT
1 TTT-TTTTTTCT
266707 AGCTCTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 8 0.21
12 14 0.36
13 17 0.44
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:266663 original size:28 final size:28
Alignment explanation
Indices: 266631--266691 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
266621 ATCTCTCATC
*
266631 TTTTTT-TTCATTTTCATT-TTTTTTTAT
1 TTTTTTATTCATTTTC-TTATTTCTTTAT
* *
266658 TTTTTTATTCTTTTTCTTATTTCTTTCT
1 TTTTTTATTCATTTTCTTATTTCTTTAT
266686 TTTTTT
1 TTTTTT
266692 CTTTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTTTATTCATTTTCTTATTTCTTTAT
Found at i:266680 original size:7 final size:6
Alignment explanation
Indices: 266634--266703 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
266624 TCTCATCTTT
* * * *
266634 TTTTTC ATTTTC ATTTT- TTTTTA TTTTT- TTATTC TTTTTC TTATTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC
266681 TTTCTT- TTTTTC TTTTTC TTTTT
1 TTT-TTC TTTTTC TTTTTC TTTTT
266704 TCTAGCTCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 10 0.18
6 37 0.67
7 8 0.15
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:266694 original size:25 final size:26
Alignment explanation
Indices: 266632--266706 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 26
266622 TCTCTCATCT
* * *
266632 TTTTTTTCATTTTCATTTTTTTTTATT
1 TTTTTTTCTTTTTC-TTTTTTCTTATC
*
266659 TTTTTATTCTTTTTCTTATTTCTT-TC
1 TTTTT-TTCTTTTTCTTTTTTCTTATC
266685 TTTTTTTCTTTTTCTTTTTTCT
1 TTTTTTTCTTTTTCTTTTTTCT
266707 AGCTCTTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 16 0.38
26 6 0.14
27 12 0.29
28 8 0.19
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTTCTTTTTCTTTTTTCTTATC
Found at i:269277 original size:31 final size:31
Alignment explanation
Indices: 269230--269293 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
269220 GCACATATAC
* *
269230 AATACTGATATCTTTTATAATCCCAGGTATT
1 AATACTGAGATCTTTTATAAGCCCAGGTATT
* *
269261 AATATTGAGATCTTTTATAAGCCCATGTATT
1 AATACTGAGATCTTTTATAAGCCCAGGTATT
269292 AA
1 AA
269294 CCCATGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (31 bp):
AATACTGAGATCTTTTATAAGCCCAGGTATT
Found at i:270967 original size:30 final size:31
Alignment explanation
Indices: 270911--270978 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
270901 AATCATTCTC
* *
270911 AACTTTTCCAAAATTACCAAATTGGTCCCTA
1 AACTTTTCAAAAATTACCAAATTGGTCCCCA
*
270942 AACTTTTCAAAAATTA-TAGAA-TGGTCCCCA
1 AACTTTTCAAAAATTACCA-AATTGGTCCCCA
*
270972 AAGTTTT
1 AACTTTT
270979 TTTTCTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (31 bp):
AACTTTTCAAAAATTACCAAATTGGTCCCCA
Done.