Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 55 of 182
Found at i:18259635 original size:17 final size:18
Alignment explanation
Indices: 18259613--18259650 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18259603 TTTGTTTAGT
*
18259613 AATGTTTT-TATCTCAAA
1 AATGTTTTCTATCCCAAA
18259630 AATGTTTTCTATCCCAAA
1 AATGTTTTCTATCCCAAA
18259648 AAT
1 AAT
18259651 ACTTTTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (18 bp):
AATGTTTTCTATCCCAAA
Found at i:18266238 original size:28 final size:28
Alignment explanation
Indices: 18266180--18266238 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
18266170 CTTTTCACCT
**
18266180 AAATAATATAAAAAATAATTAATTATGA
1 AAATAATATAAAAAATAATTAATTACAA
*
18266208 AAATAATATAAAAACAT-GTTAATTACAA
1 AAATAATATAAAAA-ATAATTAATTACAA
18266236 AAA
1 AAA
18266239 ATAGACATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (28 bp):
AAATAATATAAAAAATAATTAATTACAA
Found at i:18266872 original size:56 final size:56
Alignment explanation
Indices: 18266804--18266934 Score: 158
Period size: 56 Copynumber: 2.3 Consensus size: 56
18266794 TTTATATTTT
18266804 TTAAAAATTAAAAAAAAATTAG-ATCTATTAAAAGTTAGTAAAAAAGTTTTAAGTCC
1 TTAAAAATT-AAAAAAAATTAGTATCTATTAAAAGTTAGTAAAAAAGTTTTAAGTCC
* ** ** *
18266860 TTAAAAGA-TAAAAAAAATTAGTATCTCTTAAAAGTTTTTAAAAAAGTTTTTTTGGCC
1 TTAAAA-ATTAAAAAAAATTAGTATCTATTAAAAGTTAGTAAAAAAG-TTTTAAGTCC
18266917 GTTAAAAATTAAAAAAAA
1 -TTAAAAATTAAAAAAAA
18266935 AATTAAACCC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 12 0.19
56 28 0.44
57 9 0.14
58 15 0.23
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (56 bp):
TTAAAAATTAAAAAAAATTAGTATCTATTAAAAGTTAGTAAAAAAGTTTTAAGTCC
Found at i:18267602 original size:48 final size:49
Alignment explanation
Indices: 18267550--18267643 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
18267540 AAAAAATGAA
18267550 TTAATTCAAATA-TTGTTAATAAGAAAAGTATT-AAAAATTATTAAATAT
1 TTAATTCAAATATTTGTTAATAAGAAAAGTATTGAAAAATT-TTAAATAT
* *
18267598 TTAATTCAAATATTTGTTAATAATAAAATTATTGAAAAATTTTAAA
1 TTAATTCAAATATTTGTTAATAAGAAAAGTATTGAAAAATTTTAAA
18267644 ATACATTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
48 12 0.29
49 23 0.55
50 7 0.17
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (49 bp):
TTAATTCAAATATTTGTTAATAAGAAAAGTATTGAAAAATTTTAAATAT
Found at i:18271236 original size:10 final size:10
Alignment explanation
Indices: 18271217--18271280 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
18271207 ACATCATTCT
18271217 AAAATTATAA
1 AAAATTATAA
*
18271227 AAAATCATAA
1 AAAATTATAA
18271237 AAAATTAT-A
1 AAAATTATAA
*
18271246 AACATTATAA
1 AAAATTATAA
* *
18271256 GAAAATCATTA
1 -AAAATTATAA
* *
18271267 CAAATTGTAA
1 AAAATTATAA
18271277 AAAA
1 AAAA
18271281 AATCATAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
9 8 0.20
10 26 0.63
11 7 0.17
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAATTATAA
Found at i:18271272 original size:30 final size:28
Alignment explanation
Indices: 18271216--18271278 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
18271206 AACATCATTC
18271216 TAAAATTATAAAAAATCATAAAAAATTA
1 TAAAATTATAAAAAATCATAAAAAATTA
* * *
18271244 TAAACATTATAAGAAAATCATTACAAATTG
1 TAAA-ATTATAA-AAAATCATAAAAAATTA
18271274 TAAAA
1 TAAAA
18271279 AAAATCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 8 0.27
30 18 0.60
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAATTATAAAAAATCATAAAAAATTA
Found at i:18271292 original size:21 final size:20
Alignment explanation
Indices: 18271226--18271292 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
18271216 TAAAATTATA
* *
18271226 AAAAATCAT-AAAAAATTAT
1 AAAAATTATAAAAAAATCAT
* *
18271245 AAACATTATAAGAAAATCATT
1 AAAAATTATAAAAAAATCA-T
* *
18271266 ACAAATTGTAAAAAAAATCAT
1 AAAAATTAT-AAAAAAATCAT
18271287 AAAAAT
1 AAAAAT
18271293 ATATTTAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 13 0.36
22 9 0.25
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAATTATAAAAAAATCAT
Found at i:18273373 original size:3 final size:3
Alignment explanation
Indices: 18273367--18273444 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
18273357 AAAAATGACA
18273367 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
18273415 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
18273445 CTTGTACGGC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:18275219 original size:23 final size:23
Alignment explanation
Indices: 18275176--18275219 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
18275166 TAGAAGCATG
**
18275176 ACTTGTATCGGTAGATGTGTCTC
1 ACTTGTATCGGTAGAACTGTCTC
18275199 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACTGTC
18275220 ATAGTAACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (23 bp):
ACTTGTATCGGTAGAACTGTCTC
Found at i:18277124 original size:21 final size:21
Alignment explanation
Indices: 18277100--18277142 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18277090 AAAAATAACA
*
18277100 TGTCTGTATATTGGAGTAATT
1 TGTCTGTATATTGAAGTAATT
18277121 TGTCTGTATATTGAAGTAATT
1 TGTCTGTATATTGAAGTAATT
18277142 T
1 T
18277143 ATATAGAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (21 bp):
TGTCTGTATATTGAAGTAATT
Found at i:18280296 original size:17 final size:16
Alignment explanation
Indices: 18280265--18280345 Score: 51
Period size: 16 Copynumber: 4.9 Consensus size: 16
18280255 CATGCTCAAT
18280265 TATTTTTTATTATTTA
1 TATTTTTTATTATTTA
*
18280281 TATTTGTTTTTTATTT-
1 TATTT-TTTATTATTTA
***
18280297 TAGCATTTATT-TTTA
1 TATTTTTTATTATTTA
*
18280312 T-TTTTTTGTTTATTTA
1 TATTTTTT-ATTATTTA
18280328 TATTGTTGTTATTTATTT
1 TATT-TT-TTA-TTATTT
18280346 TTATGTCATT
Statistics
Matches: 47, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
14 6 0.13
15 8 0.17
16 12 0.26
17 11 0.23
18 2 0.04
19 8 0.17
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (16 bp):
TATTTTTTATTATTTA
Found at i:18282246 original size:21 final size:21
Alignment explanation
Indices: 18282222--18282286 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
18282212 TCAAACAATG
18282222 ACAAAAGTATCAATACCTTTT
1 ACAAAAGTATCAATACCTTTT
* *
18282243 ACAAAAAGTATCGATACCTTGT
1 AC-AAAAGTATCAATACCTTTT
* * *
18282265 AAAAAAATATCAATAACTTTT
1 ACAAAAGTATCAATACCTTTT
18282286 A
1 A
18282287 TCAAGTATCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (21 bp):
ACAAAAGTATCAATACCTTTT
Found at i:18282251 original size:22 final size:21
Alignment explanation
Indices: 18282224--18282286 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 21
18282214 AAACAATGAC
18282224 AAAAGTATCAATACCTTTTACA
1 AAAAGTATCAATACCTTTTA-A
* *
18282246 AAAAGTATCGATACCTTGTAA
1 AAAAGTATCAATACCTTTTAA
* *
18282267 AAAAATATCAATAACTTTTA
1 AAAAGTATCAATACCTTTTA
18282287 TCAAGTATCG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (21 bp):
AAAAGTATCAATACCTTTTAA
Found at i:18286981 original size:14 final size:14
Alignment explanation
Indices: 18286944--18286982 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
18286934 TGTTTGACAG
18286944 TTTTATTAAAAATA
1 TTTTATTAAAAATA
*
18286958 TTTCAATTAAAAATA
1 TTT-TATTAAAAATA
*
18286973 TTTTGTTAAA
1 TTTTATTAAA
18286983 TTCAGATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
TTTTATTAAAAATA
Found at i:18287218 original size:15 final size:15
Alignment explanation
Indices: 18287198--18287251 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
18287188 ATACTACAAA
18287198 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
18287213 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
18287230 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
18287247 ATATT
1 ATATT
18287252 AATACTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:18287219 original size:31 final size:31
Alignment explanation
Indices: 18287184--18287262 Score: 79
Period size: 34 Copynumber: 2.4 Consensus size: 31
18287174 ATATTTTAAC
*
18287184 ATTTATACTACA-AAATATTTATTATTAATAT
1 ATTTATACTA-ATAAATATTTATTATTAAAAT
*
18287215 ATTTATAATTGTAATAAATATTTATTATTAAAAT
1 ATTTAT-A--CTAATAAATATTTATTATTAAAAT
*
18287249 ATTAATACTGAATA
1 ATTTATACT-AATA
18287263 CTTTCAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.18
32 5 0.13
33 2 0.05
34 25 0.64
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTATACTAATAAATATTTATTATTAAAAT
Found at i:18287320 original size:13 final size:14
Alignment explanation
Indices: 18287285--18287324 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
18287275 AGTGAAAAAT
18287285 ATTATTAAAATTATC
1 ATTATTAAAA-TATC
*
18287300 ATTTTTAAAAT-TC
1 ATTATTAAAATATC
18287313 ATTATTAAAATA
1 ATTATTAAAATA
18287325 AAATTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 12 0.55
14 1 0.05
15 9 0.41
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATTAAAATATC
Found at i:18287379 original size:16 final size:16
Alignment explanation
Indices: 18287333--18287382 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
18287323 TAAAATTGAA
18287333 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
18287350 A-A--AATAATAAATT
1 ATATTAATAATTTATT
18287363 ATATTAATAATTTATT
1 ATATTAATAATTTATT
18287379 ATAT
1 ATAT
18287383 AACTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:18289297 original size:49 final size:48
Alignment explanation
Indices: 18289219--18289311 Score: 141
Period size: 49 Copynumber: 1.9 Consensus size: 48
18289209 GGAGTTCTAA
* * *
18289219 CCAAATGAGTGGGAAGAAACAAAGAAAATGATAATCCAGCTATGGCAG
1 CCAAATGAGTGGAAAAAAACAAAGAAAATGAAAATCCAGCTATGGCAG
*
18289267 CCAAATGAGTGAGAAAAAAACAAAGGAAATGAAAATCCAGCTATG
1 CCAAATGAGTG-GAAAAAAACAAAGAAAATGAAAATCCAGCTATG
18289312 TTATTAACGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 11 0.28
49 29 0.73
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (48 bp):
CCAAATGAGTGGAAAAAAACAAAGAAAATGAAAATCCAGCTATGGCAG
Found at i:18297709 original size:23 final size:23
Alignment explanation
Indices: 18297677--18297756 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
18297667 AAATGTCATA
*
18297677 TTTCAATTGCA-CTGAAGTGTCAC
1 TTTCAATTGCATC-GAAGTGCCAC
*
18297700 TTTCATTTGCATCGAAGTGCCAC
1 TTTCAATTGCATCGAAGTGCCAC
* *
18297723 ATTACAATAGCATCGAAGTGCCAC
1 -TTTCAATTGCATCGAAGTGCCAC
*
18297747 TTTCATTTGC
1 TTTCAATTGC
18297757 GCGCATAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (23 bp):
TTTCAATTGCATCGAAGTGCCAC
Found at i:18300714 original size:40 final size:40
Alignment explanation
Indices: 18300657--18300732 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
18300647 GAACGATTCT
*
18300657 AATATCTGTACTAAACTGGCAGTGACACTGTAAACATTAC
1 AATATCTGTACTAAACTGGCAGTGAAACTGTAAACATTAC
*
18300697 AATAT-TGATACTGAACTGGCAGTGAAACTGTAAACA
1 AATATCTG-TACTAAACTGGCAGTGAAACTGTAAACA
18300733 CTGCAGCGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (40 bp):
AATATCTGTACTAAACTGGCAGTGAAACTGTAAACATTAC
Found at i:18301310 original size:11 final size:11
Alignment explanation
Indices: 18301296--18301371 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
18301286 GATAATCACT
18301296 TTAATATTAAA
1 TTAATATTAAA
18301307 TTAATA--AAA
1 TTAATATTAAA
*
18301316 -TACTATTAAA
1 TTAATATTAAA
*
18301326 ATAAGTATTAAA
1 TTAA-TATTAAA
*
18301338 TTAATTTTAATA
1 TTAATATTAA-A
18301350 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
18301363 ATAATATTA
1 TTAATATTA
18301372 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 18 0.35
12 15 0.29
13 4 0.08
14 5 0.10
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:18301324 original size:25 final size:26
Alignment explanation
Indices: 18301270--18301324 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
18301260 TAAACATTAA
*
18301270 ATTAATTTAATATTAAGATAATCACT
1 ATTAATTTAATATTAAGAAAATCACT
*
18301296 -TTAATATTAA-ATTAATAAAAT-ACT
1 ATTAAT-TTAATATTAAGAAAATCACT
18301320 ATTAA
1 ATTAA
18301325 AATAAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 3 0.12
25 18 0.72
26 4 0.16
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTAATTTAATATTAAGAAAATCACT
Found at i:18306415 original size:18 final size:18
Alignment explanation
Indices: 18306392--18306428 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
18306382 TTTGTCAAAC
18306392 ACTATCACGGTTTAACTT
1 ACTATCACGGTTTAACTT
*
18306410 ACTATCACGTTTTAACTT
1 ACTATCACGGTTTAACTT
18306428 A
1 A
18306429 TAAACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
ACTATCACGGTTTAACTT
Found at i:18312579 original size:18 final size:18
Alignment explanation
Indices: 18312544--18312580 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
18312534 ACTTTTTAAA
* *
18312544 TTTATTTAAATTATTATT
1 TTTATTTAAATAACTATT
18312562 TTTATTTAAATAACTATT
1 TTTATTTAAATAACTATT
18312580 T
1 T
18312581 AAAACATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATTTAAATAACTATT
Found at i:18318805 original size:17 final size:17
Alignment explanation
Indices: 18318783--18318821 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18318773 CTCCACCTTG
* *
18318783 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
18318800 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
18318817 ACAAG
1 ACAAG
18318822 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:18324593 original size:85 final size:85
Alignment explanation
Indices: 18324479--18324650 Score: 285
Period size: 85 Copynumber: 2.0 Consensus size: 85
18324469 TGAAGAGACA
* *
18324479 TACTCTCCTGTGGTGGATGCAACTACTTTTAGGTTCTTGATTAGT-TAGGCAATAAGAGACA-GG
1 TACTCTCCTGTGGTGGATGCAAATACTTTTAGGTTCTTGATTAGTCT-GACAATAAGAGA-AGGG
18324542 CTTGATTTACGCCTAATGGATG
64 CTTGATTTACGCCTAATGGATG
*
18324564 TACTCTCTTGTGGTGGATGCAAATACTTTTAGGTTCTTGATTAGTCTGACAATAAGAGAAGGGCT
1 TACTCTCCTGTGGTGGATGCAAATACTTTTAGGTTCTTGATTAGTCTGACAATAAGAGAAGGGCT
18324629 TGATTTACGCCTAATGGATG
66 TGATTTACGCCTAATGGATG
18324649 TA
1 TA
18324651 GTTATAGCCT
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
84 1 0.01
85 80 0.98
86 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (85 bp):
TACTCTCCTGTGGTGGATGCAAATACTTTTAGGTTCTTGATTAGTCTGACAATAAGAGAAGGGCT
TGATTTACGCCTAATGGATG
Found at i:18325330 original size:9 final size:9
Alignment explanation
Indices: 18325316--18325345 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
18325306 TGACGTATCT
18325316 TGCTATTAG
1 TGCTATTAG
18325325 TGCTATTAG
1 TGCTATTAG
18325334 TGCTATTAG
1 TGCTATTAG
18325343 TGC
1 TGC
18325346 ATGACGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.43
Consensus pattern (9 bp):
TGCTATTAG
Found at i:18330233 original size:23 final size:23
Alignment explanation
Indices: 18330203--18330325 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 23
18330193 ACACTAGCGC
*
18330203 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCAC-TCTGCGT
* *
18330226 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTCTGCGT
* *
18330249 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTCTGCGT
* * * *
18330272 GCTCTCCGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTCTGCGT
* * * *
18330295 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTCTGCGT
18330318 GCTCTCTG
1 GCTCTCTG
18330326 TTGCCCAGCA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
22 2 0.02
23 86 0.98
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTCTGCGT
Found at i:18330317 original size:69 final size:66
Alignment explanation
Indices: 18330227--18330371 Score: 184
Period size: 69 Copynumber: 2.1 Consensus size: 66
18330217 ACGTCTCGTG
* *
18330227 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCCGATTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCCG-TTAGTACTTT
18330291 GTGTA
63 G-GTA
* *
18330296 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCCGTTAGTACTTT
18330361 GGTA
63 GGTA
18330365 CTCTCTG
1 CTCTCTG
18330372 CTTGTTCCGT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
68 2 0.03
69 38 0.56
70 11 0.16
71 12 0.18
72 5 0.07
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (66 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCCGTTAGTACTTTGGT
A
Found at i:18330326 original size:23 final size:23
Alignment explanation
Indices: 18330224--18330371 Score: 160
Period size: 23 Copynumber: 6.4 Consensus size: 23
18330214 AGCACGTCTC
18330224 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
18330247 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
18330270 GTGCTCTCCGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
18330293 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
18330316 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
18330341 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
18330362 GTACTCTCTG
1 GTGCTCTCTG
18330372 CTTGTTCCGT
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
21 13 0.12
22 4 0.04
23 71 0.66
25 14 0.13
26 5 0.05
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:18338546 original size:1 final size:1
Alignment explanation
Indices: 18338540--18338568 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
18338530 TGAGAACGAA
18338540 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
18338569 AACAACAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:18338874 original size:2 final size:2
Alignment explanation
Indices: 18338867--18338895 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18338857 AAAGGAAGGG
18338867 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
18338896 CAACAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18342664 original size:17 final size:17
Alignment explanation
Indices: 18342642--18342676 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18342632 AAAATAACAC
18342642 CCAACACGTTAGGATGT
1 CCAACACGTTAGGATGT
18342659 CCAACACGTTAGGATGT
1 CCAACACGTTAGGATGT
18342676 C
1 C
18342677 ATCCTCCGAA
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:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (17 bp):
CCAACACGTTAGGATGT
Found at i:18343238 original size:3 final size:3
Alignment explanation
Indices: 18343230--18343288 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
18343220 ACCTTCCTAC
*
18343230 TAT TAT TAT CAT 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
18343278 TAT TAT TAT TA
1 TAT TAT TAT TA
18343289 AAAACAACTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18344982 original size:22 final size:24
Alignment explanation
Indices: 18344943--18344986 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
18344933 ATTGGATCTG
18344943 AAATTTGGATATTTAATTTAAATT
1 AAATTTGGATATTTAATTTAAATT
18344967 AAATTTGG-T-TTTAATTTAAA
1 AAATTTGGATATTTAATTTAAA
18344987 ATCATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (24 bp):
AAATTTGGATATTTAATTTAAATT
Found at i:18347518 original size:18 final size:20
Alignment explanation
Indices: 18347483--18347519 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
18347473 TTTTTTAAAT
*
18347483 TATAACTTTTAATATAAGTA
1 TATAACTTTCAATATAAGTA
18347503 TATAA-TTTCAAT-TAAGT
1 TATAACTTTCAATATAAGT
18347520 GTTCTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
TATAACTTTCAATATAAGTA
Found at i:18355203 original size:19 final size:19
Alignment explanation
Indices: 18355179--18355221 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
18355169 AAACATAAAT
18355179 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
18355198 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
18355217 TAAAT
1 TAAAT
18355222 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:18355921 original size:107 final size:106
Alignment explanation
Indices: 18355774--18355975 Score: 291
Period size: 107 Copynumber: 1.9 Consensus size: 106
18355764 TATTTTGTGA
* *
18355774 TTTTTTTCCTTTTTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACCCA
1 TTTTTTTCCTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCA
* *
18355839 AGCACTCCATCTCGGTTACTCAGCCTAACATGCTCTCAATT
66 AGCACTCCACCCCGGTTACTCAGCCTAACATGCTCTCAATT
* * *
18355880 TTTTTCTTCTCTTTTTTTTT-TTGT-AGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAA
1 TTTTT-TTC-CTTTTTTTTTCTT-TAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAA
*
18355943 CCAAGCACTCCACCCCGGTTACTCAGTCTAACA
63 CCAAGCACTCCACCCCGGTTACTCAGCCTAACA
18355976 CATTTCGAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
106 5 0.06
107 69 0.81
108 11 0.13
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (106 bp):
TTTTTTTCCTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCA
AGCACTCCACCCCGGTTACTCAGCCTAACATGCTCTCAATT
Found at i:18356003 original size:107 final size:108
Alignment explanation
Indices: 18355783--18356004 Score: 263
Period size: 107 Copynumber: 2.1 Consensus size: 108
18355773 ATTTTTTTCC
* * *
18355783 TTTTTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACCCAAGCACTCCA
1 TTTTTTTTTCTGTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCA
* * * * *
18355848 TCTCGGTTACTCAGCCTAACATGCTCTCAATTTTTTTCTTCTCT
66 CCCCGGTTACTCAGCCTAACA-GCTCTCAATTTATTTATTATCT
* * *
18355892 TTTTTTTTT-TGT-AGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAACCAAGCACTCCA
1 TTTTTTTTTCTGTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCA
* *
18355955 CCCCGGTTACTCAGTCTAACA-CATTTCGAATTTATTTATTAT-T
66 CCCCGGTTACTCAGCCTAACAGC-TCTC-AATTTATTTATTATCT
*
18355998 ATTTTTT
1 TTTTTTT
18356005 ATTCGAGTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
105 1 0.01
106 10 0.10
107 75 0.77
108 2 0.02
109 9 0.09
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (108 bp):
TTTTTTTTTCTGTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCA
CCCCGGTTACTCAGCCTAACAGCTCTCAATTTATTTATTATCT
Found at i:18356660 original size:22 final size:22
Alignment explanation
Indices: 18356633--18356685 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
18356623 AGTTTCCTGG
18356633 AAAAAAATAA-ATA-AATAAATA
1 AAAAAAATAAGATAGAA-AAATA
*
18356654 AATAAAATAAGATAGAAAAATA
1 AAAAAAATAAGATAGAAAAATA
18356676 AAAAAAATAA
1 AAAAAAATAA
18356686 TTAGGTTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.32
22 17 0.61
23 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAAAAATAAGATAGAAAAATA
Found at i:18360742 original size:21 final size:21
Alignment explanation
Indices: 18360718--18360757 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18360708 ATAGATGCCT
*
18360718 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
*
18360739 CAGTTTGCTTTTGGAAATC
1 CAGTTTGCTTTTGAAAATC
18360758 TATAGATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:18360767 original size:21 final size:21
Alignment explanation
Indices: 18360725--18360768 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
18360715 CCTCAGTTTT
*
18360725 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAGATTG
* * *
18360746 CTTTTGGAAATCTATAGATTG
1 CTTTTGAAAATCCACAGATTG
18360767 CT
1 CT
18360769 GCTGAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTTTGAAAATCCACAGATTG
Found at i:18361722 original size:73 final size:73
Alignment explanation
Indices: 18361603--18361752 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
18361593 ATCCTCAGTT
18361603 ACCCCCTGAGGTTTCATACTCAAACAAACCATATGAAATTCCTTCAGATGTTTATGTGGATTCTC
1 ACCCCCTGAGGTTTCATACTCAAACAAACCATATGAAATTCCTTCAGATGTTTATGTGGATTCTC
18361668 ATTCTGCA
66 ATTCTGCA
18361676 ACCCCCTGAGGTTTCATACTCAAACAAACCATATGAAATTCCTTCAGATGTTTATGTGGATTCTC
1 ACCCCCTGAGGTTTCATACTCAAACAAACCATATGAAATTCCTTCAGATGTTTATGTGGATTCTC
18361741 ATTCTGCA
66 ATTCTGCA
18361749 ACCC
1 ACCC
18361753 ACGAAAATCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (73 bp):
ACCCCCTGAGGTTTCATACTCAAACAAACCATATGAAATTCCTTCAGATGTTTATGTGGATTCTC
ATTCTGCA
Found at i:18362424 original size:21 final size:22
Alignment explanation
Indices: 18362378--18362438 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
18362368 TGACCTAAGG
* *
18362378 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAACT
18362399 AAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
18362421 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
18362439 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:18362429 original size:15 final size:16
Alignment explanation
Indices: 18362404--18362433 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18362394 GAATTAAAAA
18362404 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
18362420 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
18362434 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:18381605 original size:23 final size:22
Alignment explanation
Indices: 18381554--18381605 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
18381544 TAGGGGTCGA
* *
18381554 AATT-AAATTATAATTTTTACG
1 AATTAAAAATATAATTTTTAAG
*
18381575 ATAATAAAAATATAATTTTTAAAG
1 A-ATTAAAAATATAATTTTT-AAG
18381599 AATTAAA
1 AATTAAA
18381606 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 2 0.08
23 18 0.75
24 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTAAAAATATAATTTTTAAG
Found at i:18384794 original size:19 final size:19
Alignment explanation
Indices: 18384684--18384795 Score: 68
Period size: 20 Copynumber: 5.8 Consensus size: 19
18384674 ACTATAAAAA
* *
18384684 ATAAAAATTATTAGA-TTT
1 ATAAAAATTATAAAATTTT
18384702 -TAAAAATATATAAAA-TTT
1 ATAAAAAT-TATAAAATTTT
* ***
18384720 ATTAAAAATTAGATTTTTTT
1 A-TAAAAATTATAAAATTTT
* *
18384740 ATAAAAATCGTAAAAAATTAT
1 ATAAAAAT--TATAAAATTTT
* *
18384761 AAAAACAATTGTAAAATTTT
1 ATAAA-AATTATAAAATTTT
18384781 ATAAAAATTATAAAA
1 ATAAAAATTATAAAA
18384796 ATGCATAAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
17 7 0.10
18 8 0.11
19 19 0.27
20 23 0.33
21 10 0.14
22 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
ATAAAAATTATAAAATTTT
Found at i:18385965 original size:29 final size:30
Alignment explanation
Indices: 18385909--18385966 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
18385899 TTAAGCCATC
**
18385909 AAATTTAAATATTTTTATAGTTTATTATTA
1 AAATTTAAATATTTTTATAACTTATTATTA
18385939 AAATTT-AATAATTTTTATAACTT-TTATT
1 AAATTTAAAT-ATTTTTATAACTTATTATT
18385967 GTTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (30 bp):
AAATTTAAATATTTTTATAACTTATTATTA
Found at i:18386252 original size:89 final size:89
Alignment explanation
Indices: 18386046--18386252 Score: 237
Period size: 89 Copynumber: 2.3 Consensus size: 89
18386036 ATTAGGGGTG
*
18386046 GTTCAAATACCCAATTGAGTGC-TAAAAAATCAGTGGCTTAATTGCTTTCTTTGAAAAAGTTTGA
1 GTTCAAATACCCAATTGAGTGCAAAAAAAATCAGTGGCTTAATTGCTTTCTTTGAAAAAGTTTGA
* *
18386110 GAGCTTTTTTGATGCATTTTGAAA
66 GAACCTTTTTGATGCATTTTGAAA
* ** *
18386134 GTTCAAGTATTCAATTGGGTGCAAAAAAAAT-A-TAAGGACTTAATTGCTGTT-TTTGAAAAAGT
1 GTTCAAATACCCAATTGAGTGCAAAAAAAATCAGT--GG-CTTAATTGCT-TTCTTTGAAAAAGT
*
18386196 TTGAGAACCTTTTT-ATGCATTTTTG-TA
62 TTGAGAACCTTTTTGATGCA-TTTTGAAA
* *
18386223 GTTTAAATACCCAATTGAATGCAAAAAAAA
1 GTTCAAATACCCAATTGAGTGCAAAAAAAA
18386253 AAAAACAGAA
Statistics
Matches: 99, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
87 1 0.01
88 19 0.19
89 39 0.39
90 38 0.38
91 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (89 bp):
GTTCAAATACCCAATTGAGTGCAAAAAAAATCAGTGGCTTAATTGCTTTCTTTGAAAAAGTTTGA
GAACCTTTTTGATGCATTTTGAAA
Found at i:18386569 original size:25 final size:25
Alignment explanation
Indices: 18386518--18386569 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
18386508 TTAGATAGCA
* *
18386518 TTGAATTTTTGAATTTTTTATATTT
1 TTGAATTTATGAATTTTTTATAATT
*
18386543 TTGAATTTAT-AATTTCTTTTTAATT
1 TTGAATTTATGAATTT-TTTATAATT
18386568 TT
1 TT
18386570 AAACAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (25 bp):
TTGAATTTATGAATTTTTTATAATT
Found at i:18386995 original size:13 final size:14
Alignment explanation
Indices: 18386967--18386996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18386957 TAATTATTTT
18386967 ACCTTGAATCTCGA
1 ACCTTGAATCTCGA
18386981 ACCTTGAAT-TCGA
1 ACCTTGAATCTCGA
18386994 ACC
1 ACC
18386997 CTAAACCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (14 bp):
ACCTTGAATCTCGA
Found at i:18387150 original size:21 final size:20
Alignment explanation
Indices: 18387124--18387177 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
18387114 TTAGGCTTAA
*
18387124 GGGTTTAGGGTTATAAGTTTT
1 GGGTTTAGGGTT-TAAGGTTT
* *
18387145 GGGTTTTGAGTTTAAGGTTT
1 GGGTTTAGGGTTTAAGGTTT
*
18387165 AGGTTTAAGGGTT
1 GGGTTT-AGGGTT
18387178 CGTAGCTATG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (20 bp):
GGGTTTAGGGTTTAAGGTTT
Found at i:18388869 original size:37 final size:36
Alignment explanation
Indices: 18388819--18388889 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
18388809 CGAATTGATT
* *
18388819 TGATATCTCTATCATATTAATCCAAAATATTGTCATG
1 TGATAACTCTATCATATCAATCC-AAATATTGTCATG
*
18388856 TGATAACTCTATCATGTCAATCCAAATATTGTCA
1 TGATAACTCTATCATATCAATCCAAATATTGTCA
18388890 CGGTTGGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (36 bp):
TGATAACTCTATCATATCAATCCAAATATTGTCATG
Found at i:18392753 original size:46 final size:44
Alignment explanation
Indices: 18392655--18392753 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
18392645 TATTACATAA
* *
18392655 TCTATTTCATTCAACCAAACACAAGAATACTATTACAGTTTTAT
1 TCTATTTCATTCAACCAAACACAAGAATACTATTACAATTCTAT
* * * *
18392699 TCCATTTCATTTAACCAAACA-ATTGAATTATTGATTACAATTCTAT
1 TCTATTTCATTCAACCAAACACA-AGAA-TACT-ATTACAATTCTAT
18392745 TCTATTTCA
1 TCTATTTCA
18392754 ATTTTATTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 3 0.07
46 19 0.42
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (44 bp):
TCTATTTCATTCAACCAAACACAAGAATACTATTACAATTCTAT
Found at i:18398723 original size:28 final size:28
Alignment explanation
Indices: 18398683--18398741 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
18398673 TCTATACGAC
18398683 TAACTGTTAAAGGATTAAAAAATTCGGT
1 TAACTGTTAAAGGATTAAAAAATTCGGT
18398711 TAACTGTTAAAGGATTAAAAAATTCGGT
1 TAACTGTTAAAGGATTAAAAAATTCGGT
18398739 TAA
1 TAA
18398742 TACTAATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (28 bp):
TAACTGTTAAAGGATTAAAAAATTCGGT
Found at i:18404856 original size:7 final size:7
Alignment explanation
Indices: 18404844--18404875 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
18404834 CGGTGGAGGG
18404844 CTAAACC
1 CTAAACC
18404851 CTAAACC
1 CTAAACC
18404858 CTAAACC
1 CTAAACC
18404865 CTAAACC
1 CTAAACC
18404872 CTAA
1 CTAA
18404876 TCCACAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:18405054 original size:38 final size:39
Alignment explanation
Indices: 18404984--18405060 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
18404974 CAGCAAGCTG
18404984 TCTATATTAAAATATACCAAAAAACTTTTCTGAATTTCA
1 TCTATATTAAAATATACCAAAAAACTTTTCTGAATTTCA
* *
18405023 TCTATATTGAAATCTACC-AAAAACTTTTCTGAATTTCA
1 TCTATATTAAAATATACCAAAAAACTTTTCTGAATTTCA
18405061 ACCATTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 20 0.56
39 16 0.44
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (39 bp):
TCTATATTAAAATATACCAAAAAACTTTTCTGAATTTCA
Found at i:18413222 original size:36 final size:36
Alignment explanation
Indices: 18413123--18413506 Score: 204
Period size: 36 Copynumber: 10.5 Consensus size: 36
18413113 CCGACCTTTG
* ** * *
18413123 AAAAAGGTTGAGATAGGTCTTATCTAAGGCAACCTTTT
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC--TT
* * * *
18413161 AAAAAAAGTTGGGATTGA-CTCGTCTAAAGCAATCTT
1 -AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTT
* * **
18413197 AAAAATGTTGGGATAAACCTTGTCTAAAATAACCTTT
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC-TT
* * * *
18413234 AAAAAAGGTTGGGATAAACCTTATTTAAGGCAACCTT
1 -AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTT
* * * *
18413271 AAAAATGTTGGAATATACCTTGTC-AAAGGTAACCTTT
1 AAAAAGGTTGGGATAGACCTTGTCTAAA-GCAACC-TT
* * * *
18413308 AAAAAAGGTTGGAATAGA-CATGTTTAAAGCAATCTT
1 -AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTT
* * *
18413344 GAAAAGGTTGGGATAGATCTTGTTTAAAGCAACCTTTT
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC--TT
* * * * *
18413382 AAAAAGGTT-GGATAGACCTTATTTAAGGTAACTTT
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTT
** ** * * *
18413417 AAAAAAATTGGGATAGAGTTTATCTAAGGCAACTTTT
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAAC-CTT
* * **
18413454 AAAAAAAGTT-GGATAGA-CTCGTCTAAAATAACCTT
1 -AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTT
* *
18413489 AAAAAGGTTAGGAAAGAC
1 AAAAAGGTTGGGATAGAC
18413507 ACATTTAAAG
Statistics
Matches: 270, Mismatches: 60, Indels: 33
0.74 0.17 0.09
Matches are distributed among these distances:
34 8 0.03
35 48 0.18
36 82 0.30
37 43 0.16
38 76 0.28
39 13 0.05
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (36 bp):
AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTT
Found at i:18413378 original size:73 final size:72
Alignment explanation
Indices: 18413123--18413506 Score: 272
Period size: 73 Copynumber: 5.2 Consensus size: 72
18413113 CCGACCTTTG
* ** * * * * *
18413123 AAAAAGGTTGAGATAGGTCTTATCTAAGGCAACCTTTTAAAAAAAGTTGGGATTGACTCGTCTAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC-TTTAAAAAAGGTTGGGATAGACT-GTTTAA
18413188 AGCAATCTT
64 AGCAATCTT
* * ** * *
18413197 AAAAATGTTGGGATAAACCTTGTCTAAAATAACCTTTAAAAAAGGTTGGGATAAACCTTATTTAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTTAAAAAAGGTTGGGATAGA-C-TGTTTAA
* *
18413262 GGCAACCTT
64 AGCAATCTT
* * * * *
18413271 AAAAATGTTGGAATATACCTTGTC-AAAGGTAACCTTTAAAAAAGGTTGGAATAGACATGTTTAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAA-GCAACCTTTAAAAAAGGTTGGGATAGAC-TGTTTAA
18413335 AGCAATCTT
64 AGCAATCTT
* * * * *
18413344 GAAAAGGTTGGGATAGATCTTGTTTAAAGCAACCTTTTAAAAAGGTT-GGATAGACCTTATTTAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTTAAAAAAGGTTGGGATAGA-C-TGTTTAA
* *
18413408 GGTAA-CTTT
64 AGCAATC-TT
** ** * * * * *
18413417 AAAAAAATTGGGATAGAGTTTATCTAAGGCAACTTTTAAAAAAAGTT-GGATAGACTCGTCTAAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTTAAAAAAGGTTGGGATAGACT-GTTTAAA
** *
18413481 ATAACCTT
65 GCAATCTT
* *
18413489 AAAAAGGTTAGGAAAGAC
1 AAAAAGGTTGGGATAGAC
18413507 ACATTTAAAG
Statistics
Matches: 244, Mismatches: 58, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
71 1 0.00
72 30 0.12
73 126 0.52
74 86 0.35
75 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (72 bp):
AAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTTAAAAAAGGTTGGGATAGACTGTTTAAAG
CAATCTT
Found at i:18414000 original size:36 final size:36
Alignment explanation
Indices: 18413814--18414005 Score: 145
Period size: 36 Copynumber: 5.3 Consensus size: 36
18413804 TGCTCTAAAA
* * * *
18413814 TAAAGAGGTTCGGATAGACCTTATTTGAAGCAACCTT
1 TAAAAAGGTTGGGATAGACCTTATCTAAAGCAACC-T
* * * *
18413851 TAAAAAAGGTTGGGATAAACCTTGTCTAAGGCAACTT
1 T-AAAAAGGTTGGGATAGACCTTATCTAAAGCAACCT
* * * * ***
18413888 TAAAAAAGCTGGGGTAGGCCTCGCCTAAAGCAACCT
1 TAAAAAGGTTGGGATAGACCTTATCTAAAGCAACCT
* * * * *
18413924 TAAAAAAGTTTGAATAGACTCGT-T-TAAGGCAACCT
1 TAAAAAGGTTGGGATAGAC-CTTATCTAAAGCAACCT
* *
18413959 TAAAAAGGTTGGGATAAACCTTATCTAAAACAACCT
1 TAAAAAGGTTGGGATAGACCTTATCTAAAGCAACCT
18413995 TAAAAAGGTTG
1 TAAAAAGGTTG
18414006 AGACAATTTA
Statistics
Matches: 118, Mismatches: 33, Indels: 9
0.74 0.21 0.06
Matches are distributed among these distances:
34 2 0.02
35 26 0.22
36 60 0.51
37 4 0.03
38 26 0.22
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (36 bp):
TAAAAAGGTTGGGATAGACCTTATCTAAAGCAACCT
Found at i:18414104 original size:36 final size:35
Alignment explanation
Indices: 18414016--18414354 Score: 294
Period size: 36 Copynumber: 9.5 Consensus size: 35
18414006 AGACAATTTA
* *
18414016 AAAAAAGTTAGGATAGACCTTGTATAAGGGAACCTT
1 AAAAAAGTT-GGATAGACCTTGTCTAAGGCAACCTT
* *
18414052 -----GGTTGGGATAGACCTTGTCTAAAGCAACCTT
1 AAAAAAGTT-GGATAGACCTTGTCTAAGGCAACCTT
* *
18414083 AAAAAAGTTAGGATAGACCTTGTCTAAAGTAACCTT
1 AAAAAAGTT-GGATAGACCTTGTCTAAGGCAACCTT
* * *
18414119 AAAAAAGTTTGGGTAGA-GTCGTCTAAGGCAACCTT
1 AAAAAAG-TTGGATAGACCTTGTCTAAGGCAACCTT
* *
18414154 AAAAAAGTTGAGATAAACCTTGTATAAGGCAACCTT
1 AAAAAAGTTG-GATAGACCTTGTCTAAGGCAACCTT
* ** **
18414190 AAAAAGGTTGTGATAGATTTTGTCTAAAACAACCTT
1 AAAAAAGTTG-GATAGACCTTGTCTAAGGCAACCTT
*
18414226 AAAAAAGTTAGGGTAGACCTTGTCTAAGGCAACCTT
1 AAAAAAGTT-GGATAGACCTTGTCTAAGGCAACCTT
* * * *
18414262 AAAAAAGTTGAGATATACCTTATCTGAGACAACCTTT
1 AAAAAAGTTG-GATAGACCTTGTCTAAGGCAACC-TT
* * * *
18414299 AAAAAAAGTTGGGACAGACCTTATCTAAGGTAATCTT
1 -AAAAAAGTT-GGATAGACCTTGTCTAAGGCAACCTT
*
18414336 AAAAATGTTGGGATAGACC
1 AAAAAAGTT-GGATAGACC
18414355 CGTCTAATGC
Statistics
Matches: 245, Mismatches: 45, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
31 26 0.11
34 3 0.01
35 26 0.11
36 156 0.64
37 7 0.03
38 26 0.11
39 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (35 bp):
AAAAAAGTTGGATAGACCTTGTCTAAGGCAACCTT
Found at i:18414190 original size:107 final size:107
Alignment explanation
Indices: 18414053--18414361 Score: 354
Period size: 107 Copynumber: 2.9 Consensus size: 107
18414043 GGGAACCTTG
* * *
18414053 GTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAAGTTAGGATAGACCTTGTCTAAAGTAACCT
1 GTTGAGATAAACCTTGTCTAAGGCAACCTTAAAAAAGTT-GGATAGACCTTGTCTAAAGTAACCT
* *
18414118 TAAAAAAGTTTGGGTAGA-GTCGTCTAAGGCAACCTTAAAAAA
65 TAAAAAAGTTAGGGTAGACCTCGTCTAAGGCAACCTTAAAAAA
* * ** **
18414160 GTTGAGATAAACCTTGTATAAGGCAACCTTAAAAAGGTTGTGATAGATTTTGTCTAAAACAACCT
1 GTTGAGATAAACCTTGTCTAAGGCAACCTTAAAAAAGTTG-GATAGACCTTGTCTAAAGTAACCT
*
18414225 TAAAAAAGTTAGGGTAGACCTTGTCTAAGGCAACCTTAAAAAA
65 TAAAAAAGTTAGGGTAGACCTCGTCTAAGGCAACCTTAAAAAA
* * * * * * * *
18414268 GTTGAGATATACCTTATCTGAGACAACCTTTAAAAAAAGTTGGGACAGACCTTATCTAAGGTAAT
1 GTTGAGATAAACCTTGTCTAAGGCAACC-TT-AAAAAAGTT-GGATAGACCTTGTCTAAAGTAAC
*
18414333 CTTAAAAATGTT-GGGATAGACC-CGTCTAA
63 CTTAAAAAAGTTAGGG-TAGACCTCGTCTAA
18414362 TGCTGGGATA
Statistics
Matches: 168, Mismatches: 28, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
106 1 0.01
107 71 0.42
108 45 0.27
109 11 0.07
110 39 0.23
111 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (107 bp):
GTTGAGATAAACCTTGTCTAAGGCAACCTTAAAAAAGTTGGATAGACCTTGTCTAAAGTAACCTT
AAAAAAGTTAGGGTAGACCTCGTCTAAGGCAACCTTAAAAAA
Found at i:18414233 original size:143 final size:138
Alignment explanation
Indices: 18414016--18414270 Score: 368
Period size: 143 Copynumber: 1.8 Consensus size: 138
18414006 AGACAATTTA
* * *
18414016 AAAAAAGTTAGGATAGACCTTGTATAAGGGAACCTTGGTTGGGATAGACCTTGTCTAAAGCAACC
1 AAAAAAGTTAGGATAAACCTTGTATAAGGCAACCTTGGTTGGGATAGACCTTGTCTAAAACAACC
*
18414081 TTAAAAAAGTTAGGATAGACCTTGTCTAAAGTAACCTTAAAAAAGTTTGGGTAGAGTCGTCTAAG
66 TTAAAAAAGTTAGGATAGACCTTGTCTAAAGCAACCTTAAAAAAGTTTGGGTAGAGTCGTCTAAG
18414146 GCAACCTT
131 GCAACCTT
* **
18414154 AAAAAAGTT-GAGATAAACCTTGTATAAGGCAACCTTAAAAAGGTTGTGATAGATTTTGTCTAAA
1 AAAAAAGTTAG-GATAAACCTTGTATAAGGCAACCTT-----GGTTGGGATAGACCTTGTCTAAA
* *
18414218 ACAACCTTAAAAAAGTTAGGGTAGACCTTGTCTAAGGCAACCTTAAAAAAGTT
60 ACAACCTTAAAAAAGTTAGGATAGACCTTGTCTAAAGCAACCTTAAAAAAGTT
18414271 GAGATATACC
Statistics
Matches: 102, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
137 1 0.01
138 32 0.31
143 69 0.68
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (138 bp):
AAAAAAGTTAGGATAAACCTTGTATAAGGCAACCTTGGTTGGGATAGACCTTGTCTAAAACAACC
TTAAAAAAGTTAGGATAGACCTTGTCTAAAGCAACCTTAAAAAAGTTTGGGTAGAGTCGTCTAAG
GCAACCTT
Found at i:18414246 original size:72 final size:72
Alignment explanation
Indices: 18414016--18414354 Score: 334
Period size: 72 Copynumber: 4.8 Consensus size: 72
18414006 AGACAATTTA
* * * *
18414016 AAAAAAGTTAGGATAGACCTTGTATAAGGGAACCTT-----GGTTGGGATAGACCTTGTCTAAAG
1 AAAAAAGTTAGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGTTGGGATAGACCTTGTCTAAAA
18414076 CAACCTT
66 CAACCTT
* * * * *
18414083 AAAAAAGTTAGGATAGACCTTGTCTAAAGTAACCTTAAAAAAGTTTGGG-TAGA-GTCGTCTAAG
1 AAAAAAGTTAGGATAGACCTTGTCTAAGGCAACCTTAAAAAAG-TTGGGATAGACCTTGTCTAAA
*
18414146 GCAACCTT
65 ACAACCTT
* * * * **
18414154 AAAAAAGTT-GAGATAAACCTTGTATAAGGCAACCTTAAAAAGGTTGTGATAGATTTTGTCTAAA
1 AAAAAAGTTAG-GATAGACCTTGTCTAAGGCAACCTTAAAAAAGTTGGGATAGACCTTGTCTAAA
18414218 ACAACCTT
65 ACAACCTT
* * * * * *
18414226 AAAAAAGTTAGGGTAGACCTTGTCTAAGGCAACCTTAAAAAAGTTGAGATATACCTTATCTGAGA
1 AAAAAAGTTAGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGTTGGGATAGACCTTGTCTAAAA
18414291 CAACCTTT
66 CAACC-TT
* * * * * *
18414299 AAAAAAAGTTGGGACAGACCTTATCTAAGGTAATCTTAAAAATGTTGGGATAGACC
1 -AAAAAAGTTAGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGTTGGGATAGACC
18414355 CGTCTAATGC
Statistics
Matches: 223, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
67 33 0.15
70 5 0.02
71 55 0.25
72 76 0.34
73 8 0.04
74 46 0.21
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (72 bp):
AAAAAAGTTAGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGTTGGGATAGACCTTGTCTAAAA
CAACCTT
Found at i:18415049 original size:14 final size:14
Alignment explanation
Indices: 18414978--18415050 Score: 53
Period size: 14 Copynumber: 5.1 Consensus size: 14
18414968 TATGTTTATG
*
18414978 TTTAGGGTTTAAGGAT
1 TTTA-GGTTTATGG-T
18414994 TTTAGG-TTATGGGT
1 TTTAGGTTTAT-GGT
*
18415008 TTGAGGTTTAT-G-
1 TTTAGGTTTATGGT
**
18415020 TTTAGAGTTTGGGGT
1 TTTAG-GTTTATGGT
18415035 TTTAGGTTTATGGT
1 TTTAGGTTTATGGT
18415049 TT
1 TT
18415051 ACGGTTCGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
12 4 0.09
13 5 0.11
14 19 0.42
15 13 0.29
16 4 0.09
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (14 bp):
TTTAGGTTTATGGT
Found at i:18415627 original size:141 final size:140
Alignment explanation
Indices: 18415327--18415640 Score: 448
Period size: 141 Copynumber: 2.2 Consensus size: 140
18415317 AACACTTAGG
*
18415327 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
** * * * *
18415392 CCAATTCTTATACAAAGAGTTGGCCAAAGCGTATGCCGATAAGTCTACCCCAGCACTTAGGAAAG
66 CCAACCCTTATAAAAAGAGTTGGCAAAAGCGTATGCCGACAAGTCTACCCCAACACTTAGGAAAG
18415457 TGTCGGCCCA
131 TGTCGGCCCA
** * ** *
18415467 AAAGTGTCATCATAATGTTGGACAAAGCTGACTCTTATTTAAGCGTTGCCTTAGGCATGCGTATC
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
* * *
18415532 CCAACCCTTATATAAAAGAGTTGGCAAAAGCGTATGTCGACAAGTTTATCCCAACACTTAGGAAA
66 CCAACCCTTATA-AAAAGAGTTGGCAAAAGCGTATGCCGACAAGTCTACCCCAACACTTAGGAAA
* *
18415597 GTGTCGTCTCA
130 GTGTCGGCCCA
*
18415608 AAAGTGTCGGCATAGTGTTGGACAAAGTCAACT
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACT
18415641 TGTTAGGATT
Statistics
Matches: 149, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
140 68 0.46
141 81 0.54
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (140 bp):
AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
CCAACCCTTATAAAAAGAGTTGGCAAAAGCGTATGCCGACAAGTCTACCCCAACACTTAGGAAAG
TGTCGGCCCA
Found at i:18415809 original size:19 final size:19
Alignment explanation
Indices: 18415767--18415810 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
18415757 TCCAACTAAC
*
18415767 TTAACTACTTTTAACAGCA
1 TTAACTACTTCTAACAGCA
* **
18415786 GTAACTACTTCTAACTTCA
1 TTAACTACTTCTAACAGCA
18415805 TTAACT
1 TTAACT
18415811 GCATATAACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (19 bp):
TTAACTACTTCTAACAGCA
Found at i:18429019 original size:3 final size:3
Alignment explanation
Indices: 18429013--18429047 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18429003 AAGGGTTAAT
18429013 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18429048 GCGGTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18429863 original size:13 final size:13
Alignment explanation
Indices: 18429845--18429869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18429835 CATTTAAAGC
18429845 ATATAATAAAAAT
1 ATATAATAAAAAT
18429858 ATATAATAAAAA
1 ATATAATAAAAA
18429870 AAAAGGCAAT
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):
ATATAATAAAAAT
Found at i:18446928 original size:36 final size:36
Alignment explanation
Indices: 18446874--18446956 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
18446864 AAAAGGTATG
*
18446874 ATTAGTCTTTGAGGAGATGAAAGGGCATGT-TTCTTC
1 ATTAGTCTTTGAGGAGATGAAAGAGCATGTCTT-TTC
* **
18446910 ATTTGTCTTTGATTAGATGAAAGAGCATGTCTTTTC
1 ATTAGTCTTTGAGGAGATGAAAGAGCATGTCTTTTC
18446946 ATTAGTCTTTG
1 ATTAGTCTTTG
18446957 GATAGTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
36 39 0.95
37 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (36 bp):
ATTAGTCTTTGAGGAGATGAAAGAGCATGTCTTTTC
Found at i:18447552 original size:50 final size:52
Alignment explanation
Indices: 18447439--18447552 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 52
18447429 TTACTAAATG
* * *
18447439 CATGACTTGT-TTTAATGATGCATACTTAACAAATCATGAGAGTTACATAATG
1 CATGACTT-TATTTAATGATGCATACTTAACAAATCATGAAAATTACATAATA
* * * **
18447491 CATGTCATTATTT-ATGATGTATACTTAATTAA-CATGAAAATTACATAATA
1 CATGACTTTATTTAATGATGCATACTTAACAAATCATGAAAATTACATAATA
18447541 CATGACTTTATT
1 CATGACTTTATT
18447553 AGATGCAGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
50 25 0.49
51 17 0.33
52 9 0.18
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (52 bp):
CATGACTTTATTTAATGATGCATACTTAACAAATCATGAAAATTACATAATA
Found at i:18447605 original size:33 final size:35
Alignment explanation
Indices: 18447553--18447624 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
18447543 TGACTTTATT
* * *
18447553 AGATGCAGATTACATAATGCATGTCA-TAATTAAA
1 AGATACAGATTACATAATGCAAGACATTAATTAAA
*
18447587 AGATACAGATTA-ATAATGCAAGACATTAATTTAA
1 AGATACAGATTACATAATGCAAGACATTAATTAAA
18447621 AGAT
1 AGAT
18447625 GCTAACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (35 bp):
AGATACAGATTACATAATGCAAGACATTAATTAAA
Found at i:18448988 original size:20 final size:20
Alignment explanation
Indices: 18448963--18449003 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18448953 AGGAAGGAGT
* *
18448963 TAACATGTACCCATGATACA
1 TAACATCTACCAATGATACA
*
18448983 TAACATCTATCAATGATACA
1 TAACATCTACCAATGATACA
18449003 T
1 T
18449004 GAGTATTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (20 bp):
TAACATCTACCAATGATACA
Found at i:18457717 original size:25 final size:24
Alignment explanation
Indices: 18457689--18457751 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
18457679 GAGTGAGATT
*
18457689 AAATTATATATTTTTATTATAATAA
1 AAATT-TATATTTTTATCATAATAA
**
18457714 AAATTTA-A-TTTTATCATTTTAA
1 AAATTTATATTTTTATCATAATAA
*
18457736 TAATTTATATTTTTAT
1 AAATTTATATTTTTAT
18457752 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 17 0.53
23 2 0.06
24 8 0.25
25 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATTTATATTTTTATCATAATAA
Found at i:18457753 original size:15 final size:16
Alignment explanation
Indices: 18457723--18457756 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18457713 AAAATTTAAT
18457723 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
18457739 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
18457754 TTT
1 TTT
18457757 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:18458254 original size:24 final size:23
Alignment explanation
Indices: 18458227--18458291 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
18458217 AGTTTTTATT
*
18458227 TGCCTTTGTGGCATGTTTTTTCTC
1 TGCC-TTGTGGCATGTTTTTTCTA
*
18458251 TGCCTTGTGGCATGCTTTTTCTA
1 TGCCTTGTGGCATGTTTTTTCTA
* *
18458274 TGTCTTGTGGCACGTTTT
1 TGCCTTGTGGCATGTTTT
18458292 CGTTACCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.06, C:0.20, G:0.23, T:0.51
Consensus pattern (23 bp):
TGCCTTGTGGCATGTTTTTTCTA
Found at i:18459172 original size:17 final size:18
Alignment explanation
Indices: 18459147--18459182 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18459137 TCTTTTAAAA
18459147 ATTATAAAAATATAAATT
1 ATTATAAAAATATAAATT
*
18459165 ATTA-AAAATTATAAATT
1 ATTATAAAAATATAAATT
18459182 A
1 A
18459183 ATTTCGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTATAAAAATATAAATT
Found at i:18479388 original size:17 final size:17
Alignment explanation
Indices: 18479353--18479434 Score: 65
Period size: 17 Copynumber: 4.5 Consensus size: 17
18479343 GATCTTTAGG
*
18479353 TTTAAATTCATTATTAAA
1 TTTAAATTTATT-TTAAA
18479371 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
18479388 TTTAAAAATATTTGAAATAAA
1 TTTAAATTTATTT----TAAA
* *
18479409 TTTAAAATTTAATTAAAA
1 TTT-AAATTTATTTTAAA
18479427 TTTAAATT
1 TTTAAATT
18479435 AAAAGTCCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
17 21 0.40
18 17 0.33
21 7 0.13
22 7 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:18479434 original size:12 final size:12
Alignment explanation
Indices: 18479405--18479438 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
18479395 ATATTTGAAA
18479405 TAAATTTAAAATT
1 TAAA-TTAAAATT
18479418 T-AATTAAAATT
1 TAAATTAAAATT
18479429 TAAATTAAAA
1 TAAATTAAAA
18479439 GTCCAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 10 0.50
13 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTAAAATT
Found at i:18480150 original size:25 final size:27
Alignment explanation
Indices: 18480101--18480154 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
18480091 AAAACGTAAC
*
18480101 AAATAAATTGTTTTAATAAATATTAAT
1 AAATAAATTGTTTTAATAAAAATTAAT
*
18480128 AAATATATT-TTTTAA-AAAAATTAAT
1 AAATAAATTGTTTTAATAAAAATTAAT
18480153 AA
1 AA
18480155 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.44
26 6 0.24
27 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AAATAAATTGTTTTAATAAAAATTAAT
Found at i:18481240 original size:59 final size:59
Alignment explanation
Indices: 18481174--18481771 Score: 758
Period size: 59 Copynumber: 10.2 Consensus size: 59
18481164 CTGAATTGTC
* * * * * *
18481174 CAAAAATTATCATTTTACCCCTAAACTTTCTAAAACTCCATTTTTAACGCTGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * * * *
18481233 CGAAAATTATCGTTTTATCCCTAAACTTTCTAAAACTCCATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
18481292 CAAAAAAATACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCAT
1 C-AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
18481352 CAAAAATTACTATTTT-CCCCTAAACTTTTCAAAATTCCATTTTTAACCTCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
18481410 CAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAA-CCCTAGTTTCAT
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAT
** *
18481469 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * *
18481528 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAA-CCCTAGTTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAT
** * * * *
18481587 CAAAAATTATAATATTACCCCTAAACTTTCCAAAATTTCA-TTTTAACCCCAATGTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** * **
18481645 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCTTGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
18481704 TAAAAATTACCATTTTA-CCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
18481763 CAAAAATTA
1 CAAAAATTA
18481772 TTATTTTGCC
Statistics
Matches: 471, Mismatches: 58, Indels: 20
0.86 0.11 0.04
Matches are distributed among these distances:
58 111 0.24
59 302 0.64
60 58 0.12
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
Found at i:18481799 original size:176 final size:177
Alignment explanation
Indices: 18481174--18481784 Score: 818
Period size: 176 Copynumber: 3.5 Consensus size: 177
18481164 CTGAATTGTC
* * * * * *
18481174 CAAAAATTATCATTTTACCC-CTAAACTTTCTAAAACTCCATTTTTAACGCTGATTTCACCGAAA
1 CAAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * * * *
18481238 ATTATCGTTTTATCCCTAAACTTTCTAAAACTCCATTTTTAACCCCGATTTCATCAAAAAAATAC
65 ATTATCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCATC-AAAAATTAC
**
18481303 CATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCAT
129 CATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCAT
* * * * *
18481352 CAAAAATTACTATTTTCCCCT-AAACTTTTCAAAATTCCATTTTTAACCTCGATTTCATCAAAAA
1 CAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* * * *
18481416 TTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCTAGTTTCATCAAAAATTACC
66 TTATCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCATCAAAAATTACC
* *
18481480 ATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAT
130 ATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCAT
* * *
18481528 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAA-CCCTAGTTTCACCAAAA
1 CAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACCAAAA
* * * *
18481592 ATTATAATATTACCCCTAAACTTTCCAAAATTTCA-TTTTAACCCCAATGTCATCAAAAATTACC
65 ATTATCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCATCAAAAATTACC
**
18481656 ATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCTTGATTTCAT
130 ATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCAT
*
18481704 TAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
1 CAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* *
18481769 TTATTATTTTGCCCCT
66 TTATCATTTTACCCCT
18481785 CGCGTATCCA
Statistics
Matches: 376, Mismatches: 51, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
176 217 0.58
177 138 0.37
178 21 0.06
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (177 bp):
CAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
TTATCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCATCAAAAATTACCA
TTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCAT
Found at i:18481821 original size:28 final size:29
Alignment explanation
Indices: 18481765--18481825 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
18481755 GATTTCACCA
*
18481765 AAAATTATTATTTTGCCCCTCGCGTATCC
1 AAAATTATCATTTTGCCCCTCGCGTATCC
*
18481794 AAAATTATCATTTTG-CCCTCGGGTATCC
1 AAAATTATCATTTTGCCCCTCGCGTATCC
18481822 AAAA
1 AAAA
18481826 GTCCCATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (29 bp):
AAAATTATCATTTTGCCCCTCGCGTATCC
Found at i:18481833 original size:28 final size:29
Alignment explanation
Indices: 18481774--18481835 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
18481764 AAAAATTATT
* *
18481774 ATTTTGCCCCTCGCGTATCCAAAATTATC
1 ATTTTGCCCCTCGCGTATCCAAAAGTACC
* *
18481803 ATTTTG-CCCTCGGGTATCCAAAAGTCCC
1 ATTTTGCCCCTCGCGTATCCAAAAGTACC
18481831 ATTTT
1 ATTTT
18481836 CAACCCCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (29 bp):
ATTTTGCCCCTCGCGTATCCAAAAGTACC
Found at i:18494125 original size:77 final size:76
Alignment explanation
Indices: 18493948--18494249 Score: 541
Period size: 76 Copynumber: 3.9 Consensus size: 76
18493938 TCAGATCAAA
18493948 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
18494013 TGAAGTAAGAG
66 TGAAGTAAGAG
* * * *
18494024 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTTATCTCCGAAA
1 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTC-TTTATCTCTGAAA
18494089 TTGAAGTAAGAG
65 TTGAAGTAAGAG
18494101 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
18494166 TGAAGTAAGAG
66 TGAAGTAAGAG
*
18494177 CAAAATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTTGAAA
1 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC-TGAAA
18494242 TTGAAGTA
65 TTGAAGTA
18494250 GAGTTGGATA
Statistics
Matches: 215, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
76 130 0.60
77 85 0.40
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (76 bp):
CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:18494226 original size:153 final size:153
Alignment explanation
Indices: 18493948--18494249 Score: 543
Period size: 153 Copynumber: 2.0 Consensus size: 153
18493938 TCAGATCAAA
18493948 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
* * *
18494013 TGAAGTAAGAGCAAGATTATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
66 TGAAGTAAGAGCAAAATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTC-TT
18494078 TATCTC-CGAAATTGAAGTAAGAG
130 TATCTCTCGAAATTGAAGTAAGAG
18494101 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
*
18494166 TGAAGTAAGAGCAAAATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTT
66 TGAAGTAAGAGCAAAATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTT
*
18494231 ATCTCTTGAAATTGAAGTA
131 ATCTCTCGAAATTGAAGTA
18494250 GAGTTGGATA
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
152 8 0.06
153 135 0.94
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (153 bp):
CAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
TGAAGTAAGAGCAAAATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTT
ATCTCTCGAAATTGAAGTAAGAG
Found at i:18494293 original size:191 final size:192
Alignment explanation
Indices: 18494041--18494439 Score: 694
Period size: 191 Copynumber: 2.1 Consensus size: 192
18494031 ATTTCCTATC
18494041 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTTATCTCCGAAATTGAAGTAAGAGCAAGA
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTTATCTCCGAAATTGAAGTAAGAGCAAGA
* *
18494106 TTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAG
66 TTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAG
* *
18494171 TAAGAGCAAAATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
131 TAAGAGCAAAATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTTAT
18494233 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTC-TTTATCTCCGAAATTGAAGTAAGAGCAAGA
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTTATCTCCGAAATTGAAGTAAGAGCAAGA
* *
18494297 TTATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAG
66 TTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAG
* * * *
18494362 TAAGAGCAAGATCATTTCTTATCCTCTTGAAATTGAAGTACAGTTGGATATCAAATCTTTAT
131 TAAGAGCAAAATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTTAT
18494424 CTC-TGAAATTGAAGTA
1 CTCTTGAAATTGAAGTA
18494440 AGAGCAAGAT
Statistics
Matches: 197, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
190 13 0.07
191 150 0.76
192 34 0.17
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (192 bp):
CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTTATCTCCGAAATTGAAGTAAGAGCAAGA
TTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAG
TAAGAGCAAAATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTTAT
Found at i:18494326 original size:76 final size:76
Alignment explanation
Indices: 18494233--18494525 Score: 496
Period size: 76 Copynumber: 3.9 Consensus size: 76
18494223 AAGTCTTTAT
18494233 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
*
18494298 TATTTCCTATC
66 CATTTCCTATC
18494309 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
*
18494374 CATTTCTTATC
66 CATTTCCTATC
* * * *
18494385 CTCTTGAAATTGAAGTACAGTTGGATATCAAATCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
18494450 CATTTCCTATC
66 CATTTCCTATC
* * * *
18494461 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
18494526 GAATCCTCGA
Statistics
Matches: 207, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 207 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (76 bp):
CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATC
Found at i:18494858 original size:12 final size:12
Alignment explanation
Indices: 18494829--18494862 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
18494819 ATATTTGAAA
18494829 TAAATTTAAAATT
1 TAAA-TTAAAATT
18494842 T-AATTAAAATT
1 TAAATTAAAATT
18494853 TAAATTAAAA
1 TAAATTAAAA
18494863 GTCCAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 10 0.50
13 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTAAAATT
Found at i:18495228 original size:27 final size:25
Alignment explanation
Indices: 18495197--18495250 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
18495187 AAAACATAAC
*
18495197 AAATAAATGGTTTTAATAAATATTAAT
1 AAATAAATAGTTTTAA-AAA-ATTAAT
* *
18495224 AAATATATATTTTTAAAAAATTAAT
1 AAATAAATAGTTTTAAAAAATTAAT
18495249 AA
1 AA
18495251 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 3 0.12
27 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AAATAAATAGTTTTAAAAAATTAAT
Found at i:18495255 original size:20 final size:21
Alignment explanation
Indices: 18495225--18495263 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
18495215 AATATTAATA
18495225 AATATATATTTTTAAAAAATT
1 AATATATATTTTTAAAAAATT
18495246 AATA-ATATTTTTAAAAAA
1 AATATATATTTTTAAAAAA
18495264 AGGAGTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATATATTTTTAAAAAATT
Found at i:18496296 original size:30 final size:29
Alignment explanation
Indices: 18496260--18496415 Score: 81
Period size: 31 Copynumber: 5.3 Consensus size: 29
18496250 TTATAGGTCT
18496260 CTAAACTGTCTAAAAATTACCATTTTACCC
1 CTAAACT-TCTAAAAATTACCATTTTACCC
* * *
18496290 CTAAACTT-TCAAAACT-CCATTTTCAACC
1 CTAAACTTCTAAAAATTACCATTTT-ACCC
* * *
18496318 CT-AATTTCACCAAAAATTACCGTTTTACCC
1 CTAAACTT--CTAAAAATTACCATTTTACCC
* * *
18496348 CTAAACTT-TCCAAAACT-CCATTTTTAACC
1 CTAAACTTCT-AAAAATTACCA-TTTTACCC
* * *
18496377 CT-GATTTCACAAAAAAATTACCATTTTACCC
1 CTAAACTT--C-TAAAAATTACCATTTTACCC
18496408 CTAAACTT
1 CTAAACTT
18496416 TCCAAAACTC
Statistics
Matches: 89, Mismatches: 23, Indels: 26
0.64 0.17 0.19
Matches are distributed among these distances:
27 11 0.12
28 16 0.18
29 15 0.17
30 17 0.19
31 24 0.27
32 6 0.07
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
CTAAACTTCTAAAAATTACCATTTTACCC
Found at i:18496392 original size:59 final size:58
Alignment explanation
Indices: 18496271--18496822 Score: 655
Period size: 59 Copynumber: 9.4 Consensus size: 58
18496261 TAAACTGTCT
* * **
18496271 AAAAATTACCATTTTACCCCTAAACTTT-CAAAACTCCATTTTCAACCCTAATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
* * *
18496329 AAAAATTACCGTTTTACCCCTAAACTTTCCAAAACTCCATTTTTAACCCTGATTTCAC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* *
18496387 AAAAAAATTACCATTTTACCCCTAAACTTTCCAAAACTCCATTTTTAACCCTGATTTCATC
1 --AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
* * * * *
18496448 AAAAATTATCATTTTA-CCCTCGAACTTTCCAAAATTCTATTTTTAACCCCTATTTAATC
1 AAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
** ** * *
18496507 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTTAATTTTTAACCCCAATTTCGTC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTC-AC
** **
18496566 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTTAATTTTTAACCCC-AGTTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA-C
* ** *
18496625 AAAAATTACCATATTACCCCTAAACTTTATAAAATTCTATTTTTAACCCCGATATT-ATC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGAT-TTCA-C
* * *
18496684 AAAAATTACCATTTTACCCTTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCATC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
18496743 AAAAATTACCATTTTA-CCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-C
*
18496802 AAAAATTACCATTTTGCCCCT
1 AAAAATTACCATTTTACCCCT
18496823 CGCGTGTCCA
Statistics
Matches: 443, Mismatches: 37, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
58 38 0.09
59 338 0.76
60 66 0.15
61 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:18496821 original size:29 final size:29
Alignment explanation
Indices: 18496321--18496821 Score: 116
Period size: 29 Copynumber: 17.0 Consensus size: 29
18496311 TTCAACCCTA
* *
18496321 ATTTCACCAAAAATTACCGTTTTACCCCTAA
1 ATTTCACCAAAAATTACCATTTTACCCC--G
* *
18496352 ACTTT--CC-AAAACT-CCATTTTTAACCCTG
1 A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
* *
18496380 ATTTCACAAAAAAATTACCATTTTACCCCTAA
1 ATTTCAC-CAAAAATTACCATTTTACCCC--G
* *
18496412 ACTTT--CC-AAAACT-CCATTTTTAACCCTG
1 A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
* *
18496440 ATTTCATCAAAAATTATCATTTTACCCTCG
1 ATTTCACCAAAAATTACCATTTTACCC-CG
* *
18496470 AACTTT--CC-AAAATT-CTATTTTTAACCCCT
1 -A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
* *
18496499 ATTTAATCAAAAATTACCATTTTACCCCCG
1 ATTTCACCAAAAATTACCATTTTA-CCCCG
* *
18496529 AACTTT--CCAAAATTTA--ATTTTTAACCCCA
1 -A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
**
18496558 ATTTCGTCAAAAATTACCATTTTACCCCCG
1 ATTTCACCAAAAATTACCATTTTA-CCCCG
*
18496588 AACTTT--CCAAAATTTA--ATTTTTAACCCC-
1 -A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
* *
18496616 AGTTTCACCAAAAATTACCATATTACCCCTAA
1 A-TTTCACCAAAAATTACCATTTTACCCC--G
* *
18496648 ACTTT-A--TAAAATT-CTATTTTTAACCCCG
1 A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
* *
18496676 ATATT-ATCAAAAATTACCATTTTACCCTTG
1 AT-TTCACCAAAAATTACCATTTTACCC-CG
*
18496706 AACTTT---CTAAAATT-CCATTTTTAACCCCG
1 -A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
* *
18496735 ATTTCATCAAAAATTACCATTTTACCCTCAA
1 ATTTCACCAAAAATTACCATTTTACCC-C-G
18496766 ACTTT--CC-AAAATT-CCATTTTTAACCCCG
1 A-TTTCACCAAAAATTACCA-TTTT-ACCCCG
*
18496794 ATTTCACCAAAAATTACCATTTTGCCCC
1 ATTTCACCAAAAATTACCATTTTACCCC
18496822 TCGCGTGTCC
Statistics
Matches: 350, Mismatches: 49, Indels: 144
0.64 0.09 0.27
Matches are distributed among these distances:
27 23 0.07
28 26 0.07
29 122 0.35
30 119 0.34
31 33 0.09
32 24 0.07
33 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTCACCAAAAATTACCATTTTACCCCG
Found at i:18499962 original size:18 final size:18
Alignment explanation
Indices: 18499936--18499970 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18499926 CAAATAATAA
* *
18499936 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
18499954 AATAATATTATTAATTA
1 AATAATATTATTAATTA
18499971 ATATATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:18499962 original size:21 final size:20
Alignment explanation
Indices: 18499932--18499975 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
18499922 ATATCAAATA
* *
18499932 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
18499952 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
18499973 ATA
1 ATA
18499976 TTTTTGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Found at i:18500010 original size:30 final size:29
Alignment explanation
Indices: 18499928--18500011 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 29
18499918 TATAATATCA
* *
18499928 AATAATAAAATATTATTATTTATTATAAT
1 AATAATAAAAAATTATTATTTTTTATAAT
* ** *
18499957 AAT-ATTATTAATTAATATATTTTTGATAAT
1 AATAATAAAAAATT-AT-TATTTTTTATAAT
*
18499987 AATAATAAAAAATCATTATTTTTTA
1 AATAATAAAAAATTATTATTTTTTA
18500012 AAGTAATGGT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
28 6 0.15
29 13 0.32
30 16 0.39
31 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
AATAATAAAAAATTATTATTTTTTATAAT
Found at i:18500809 original size:29 final size:29
Alignment explanation
Indices: 18500746--18500810 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
18500736 GTCACATTTG
* *
18500746 AATTTTTGGAAAATTCGAGGGTAAAACTT
1 AATTTTTGGAAAATTAGAGGGTAAAACAT
*
18500775 AGATTTTTGGAAAGTTAG-GGGTCAAAACAT
1 A-ATTTTTGGAAAATTAGAGGGT-AAAACAT
18500805 AATTTT
1 AATTTT
18500811 AAAATAAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (29 bp):
AATTTTTGGAAAATTAGAGGGTAAAACAT
Found at i:18500955 original size:11 final size:12
Alignment explanation
Indices: 18500928--18500954 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18500918 GGCCAAATTG
18500928 AAAATAACAAAA
1 AAAATAACAAAA
18500940 AAAATAACAAAA
1 AAAATAACAAAA
18500952 AAA
1 AAA
18500955 TTAAGGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAATAACAAAA
Found at i:18503202 original size:13 final size:13
Alignment explanation
Indices: 18503184--18503208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18503174 TACGAGTAAT
18503184 AAATATATAAAAC
1 AAATATATAAAAC
18503197 AAATATATAAAA
1 AAATATATAAAA
18503209 ATAAAAATAA
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:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATATATAAAAC
Found at i:18503417 original size:30 final size:30
Alignment explanation
Indices: 18503376--18503535 Score: 125
Period size: 30 Copynumber: 5.4 Consensus size: 30
18503366 AAAATGAAAG
* *
18503376 TTTGAAAAGTTTGGGGGCCAAAT-TCAAATT
1 TTTGGAAAGTTTGAGGGCCAAATCT-AAATT
18503406 TTTGGAAAGTTTGAGGGCCAAATCTAAA-T
1 TTTGGAAAGTTTGAGGGCCAAATCTAAATT
* **
18503435 TTTGGAAAGTTAGAGGGTTAAATCTAAATT
1 TTTGGAAAGTTTGAGGGCCAAATCTAAATT
* * *
18503465 TTT-GAGAAGTTT-AGGGGTCAAATTTAAAAT
1 TTTGGA-AAGTTTGA-GGGCCAAATCTAAATT
* * * *
18503495 TTTGG-AAG-TTAAGGAGTCAAAACTTAATT
1 TTTGGAAAGTTTGAGG-GCCAAATCTAAATT
*
18503524 TTTGAAAAGTTT
1 TTTGGAAAGTTT
18503536 AGGAGTCAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.04
29 47 0.44
30 52 0.49
31 4 0.04
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.36
Consensus pattern (30 bp):
TTTGGAAAGTTTGAGGGCCAAATCTAAATT
Found at i:18503450 original size:29 final size:30
Alignment explanation
Indices: 18503376--18503505 Score: 108
Period size: 29 Copynumber: 4.4 Consensus size: 30
18503366 AAAATGAAAG
* * * *
18503376 TTTGAAAAGTTTGGGGGCCAAAT-TCAAATT
1 TTTGGAAAGTTAGAGGGCCAAATCT-AAAAT
*
18503406 TTTGGAAAGTTTGAGGGCCAAATCT-AAAT
1 TTTGGAAAGTTAGAGGGCCAAATCTAAAAT
**
18503435 TTTGGAAAGTTAGAGGGTTAAATCT-AAAT
1 TTTGGAAAGTTAGAGGGCCAAATCTAAAAT
* * *
18503464 TTTTGAGAAGTTTAG-GGGTCAAATTTAAAAT
1 TTTGGA-AAG-TTAGAGGGCCAAATCTAAAAT
18503495 TTTGG-AAGTTA
1 TTTGGAAAGTTA
18503506 AGGAGTCAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.03
29 37 0.43
30 33 0.38
31 13 0.15
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (30 bp):
TTTGGAAAGTTAGAGGGCCAAATCTAAAAT
Found at i:18503540 original size:30 final size:30
Alignment explanation
Indices: 18503461--18503555 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
18503451 GTTAAATCTA
* *
18503461 AATTTTTGAGAAGTTTAGGGGTC-AAATTT
1 AATTTTTGAGAAGTTTAGGAGTCAAAACTT
* *
18503490 AAAATTTTG-GAAGTTAAGGAGTCAAAACTT
1 -AATTTTTGAGAAGTTTAGGAGTCAAAACTT
* *
18503520 AATTTTTGAAAAGTTTAGGAGTCAAAACAT
1 AATTTTTGAGAAGTTTAGGAGTCAAAACTT
18503550 AATTTT
1 AATTTT
18503556 AAAATATTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.35
30 36 0.65
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (30 bp):
AATTTTTGAGAAGTTTAGGAGTCAAAACTT
Found at i:18503544 original size:59 final size:58
Alignment explanation
Indices: 18503401--18503545 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 58
18503391 GGCCAAATTC
* * * *
18503401 AAATTTTTGGAAAGTTTGAGGGCCAAATCTAAATTTTGGAAAGTTAGAGGGTTAAATCT
1 AAATTTTTGAAAAGTTT-AGGGTCAAATCTAAATTTTGGAAAGTTAGAGGGTCAAAACT
* *
18503460 AAATTTTTGAGAAGTTTAGGGGTCAAATTTAAAATTTTGG-AAGTTA-AGGAGTCAAAACT
1 AAATTTTTGAAAAGTTTA-GGGTCAAATCT-AAATTTTGGAAAGTTAGAGG-GTCAAAACT
*
18503519 TAATTTTTGAAAAGTTTAGGAGTCAAA
1 AAATTTTTGAAAAGTTTAGG-GTCAAA
18503546 ACATAATTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
58 6 0.08
59 59 0.80
60 9 0.12
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (58 bp):
AAATTTTTGAAAAGTTTAGGGTCAAATCTAAATTTTGGAAAGTTAGAGGGTCAAAACT
Found at i:18505463 original size:31 final size:32
Alignment explanation
Indices: 18505417--18505487 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
18505407 TATTTAAAAA
* * * *
18505417 TTTAGATTAATTTAAATTTTATATATCATTAT
1 TTTAAATTAATTTAAATATCACATATCATTAT
*
18505449 TTTAAATT-ATTTAAATATCACATATTATTAT
1 TTTAAATTAATTTAAATATCACATATCATTAT
*
18505480 TTAAAATT
1 TTTAAATT
18505488 TTAAAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (32 bp):
TTTAAATTAATTTAAATATCACATATCATTAT
Found at i:18505495 original size:30 final size:31
Alignment explanation
Indices: 18505439--18505496 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
18505429 TAAATTTTAT
* *
18505439 ATATCATTATTTTAAATTATTTAAATATCAC
1 ATATCATTATTTAAAATTATTAAAATATCAC
*
18505470 ATATTATTATTTAAAATT-TTAAAATAT
1 ATATCATTATTTAAAATTATTAAAATAT
18505497 TTTATGTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (31 bp):
ATATCATTATTTAAAATTATTAAAATATCAC
Found at i:18506950 original size:19 final size:19
Alignment explanation
Indices: 18506910--18506960 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
18506900 ATCCAAAAAA
**
18506910 TTATATTTTTTAAATTAAT
1 TTATATTTTTTAAAAGAAT
*
18506929 TTATATTTTTTAAAAGATT
1 TTATATTTTTTAAAAGAAT
*
18506948 TTAAATTTTTTAA
1 TTATATTTTTTAA
18506961 TATCTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATTTTTTAAAAGAAT
Found at i:18509320 original size:9 final size:8
Alignment explanation
Indices: 18509304--18509329 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
18509294 AGTAAATATA
18509304 TATTTTTT
1 TATTTTTT
18509312 TATTTTTT
1 TATTTTTT
18509320 TATTTTTT
1 TATTTTTT
18509328 TA
1 TA
18509330 AATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:18509835 original size:16 final size:16
Alignment explanation
Indices: 18509814--18509845 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18509804 CATTCAAAAC
18509814 ATTTTTAAAATTTTTT
1 ATTTTTAAAATTTTTT
*
18509830 ATTTTTATAATTTTTT
1 ATTTTTAAAATTTTTT
18509846 GTGTTACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTAAAATTTTTT
Found at i:18513262 original size:60 final size:60
Alignment explanation
Indices: 18513167--18513341 Score: 188
Period size: 59 Copynumber: 3.0 Consensus size: 60
18513157 AATTTAGGTG
* *
18513167 CCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAGGAAAAAAATGTCAAGTTCAAGTA
1 CCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAAG-AAAAAATATCAAGTTCAAGTA
* *
18513228 TCAAATT-AGATCT-AAAAAAGTTTAGGA-ATCAAATTAAGAAAAAATATCAAGTTCAAGTA
1 CCAAATTGA-ATCTAAAAAAAGTTTA-GATACCAAATTAAGAAAAAATATCAAGTTCAAGTA
* * *
18513287 CCAAATTGGA--TAAAAAAA-TTTA-AGTACCAAATT-A-AAAAAATATTAAGTTTAAGTA
1 CCAAATTGAATCTAAAAAAAGTTTAGA-TACCAAATTAAGAAAAAATATCAAGTTCAAGTA
18513342 TCAATTGTTA
Statistics
Matches: 99, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
55 20 0.20
56 1 0.01
57 12 0.12
58 6 0.06
59 27 0.27
60 21 0.21
61 12 0.12
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (60 bp):
CCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAAGAAAAAATATCAAGTTCAAGTA
Found at i:18514758 original size:24 final size:24
Alignment explanation
Indices: 18514731--18514778 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
18514721 AAAAAAAGAG
*
18514731 AAAAAAATTTGTTTACCAAAACAA
1 AAAAAAATTTGTTTAACAAAACAA
*
18514755 AAAAAAGTTTGTTTAACAAAACAA
1 AAAAAAATTTGTTTAACAAAACAA
18514779 GAGAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.25
Consensus pattern (24 bp):
AAAAAAATTTGTTTAACAAAACAA
Found at i:18516728 original size:15 final size:16
Alignment explanation
Indices: 18516708--18516737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18516698 GAATATAGTA
18516708 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
18516723 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
18516738 ATATACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:18518220 original size:4 final size:4
Alignment explanation
Indices: 18518213--18518239 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18518203 TATATATATA
18518213 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
18518240 ATTTTTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:18519433 original size:29 final size:28
Alignment explanation
Indices: 18519401--18519459 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
18519391 TTACTTCAGG
**
18519401 TTACATTTTAGTCTTTTATGTTTAAAATA
1 TTACATTTTAGTCACTTATG-TTAAAATA
* *
18519430 TTACGTTTTAGTCACTTATGTTAACATA
1 TTACATTTTAGTCACTTATGTTAAAATA
18519458 TT
1 TT
18519460 GTAATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (28 bp):
TTACATTTTAGTCACTTATGTTAAAATA
Found at i:18520686 original size:31 final size:31
Alignment explanation
Indices: 18520615--18520678 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
18520605 TAAGGGTGAA
18520615 TTTAA-AAGAAAT-AAAATAAAAAGGTTAAAT
1 TTTAACAA-AAATAAAAATAAAAAGGTTAAAT
* *
18520645 TTTAACAAAAATAAAAATAAAAAGATTTAAT
1 TTTAACAAAAATAAAAATAAAAAGGTTAAAT
18520676 TTT
1 TTT
18520679 TTAAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (31 bp):
TTTAACAAAAATAAAAATAAAAAGGTTAAAT
Found at i:18520692 original size:31 final size:31
Alignment explanation
Indices: 18520627--18520692 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
18520617 TAAAAGAAAT
*
18520627 AAAATAAAAAGGTTAAATTTTAACAAAAATA
1 AAAATAAAAAGGTTAAATTTTAACAAAAAGA
* * *
18520658 AAAATAAAAAGATTTAATTTTTTA-AAAAAGA
1 AAAATAAAAAG-GTTAAATTTTAACAAAAAGA
18520689 AAAA
1 AAAA
18520693 ATGGGGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (31 bp):
AAAATAAAAAGGTTAAATTTTAACAAAAAGA
Found at i:18521446 original size:11 final size:11
Alignment explanation
Indices: 18521430--18521470 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
18521420 CCCTAGATCC
18521430 TTTTATTTTCT
1 TTTTATTTTCT
18521441 TTTTATTTTC-
1 TTTTATTTTCT
18521451 -TTTATTTT-T
1 TTTTATTTTCT
18521460 TATTTATTTTC
1 T-TTTATTTTC
18521471 AAAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCT
Found at i:18521456 original size:20 final size:20
Alignment explanation
Indices: 18521431--18521470 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18521421 CCTAGATCCT
18521431 TTTATTTTCTT-TTTATTTTC
1 TTTATTTT-TTATTTATTTTC
18521451 TTTATTTTTTATTTATTTTC
1 TTTATTTTTTATTTATTTTC
18521471 AAAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTATTTTTTATTTATTTTC
Found at i:18522150 original size:14 final size:13
Alignment explanation
Indices: 18522128--18522161 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
18522118 TTTTGAGCAA
*
18522128 TTTAATTTTTTTC
1 TTTATTTTTTTTC
18522141 TTTTATTTTTTTTC
1 -TTTATTTTTTTTC
18522155 TTTATTT
1 TTTATTT
18522162 CCATTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTTTTTC
Done.