Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 62 of 316
Found at i:18252259 original size:23 final size:23
Alignment explanation
Indices: 18252233--18252298 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
18252223 ATACACAGAT
*
18252233 TCCAACCAAACACACC-GAAATAA
1 TCCACCCAAACACACCAG-AATAA
18252256 TCCACCCAAACACACCAGAATAA
1 TCCACCCAAACACACCAGAATAA
18252279 TCCACCCAAACACACCAGAA
1 TCCACCCAAACACACCAGAA
18252299 CAGCAATCAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.48, C:0.39, G:0.05, T:0.08
Consensus pattern (23 bp):
TCCACCCAAACACACCAGAATAA
Found at i:18253329 original size:16 final size:18
Alignment explanation
Indices: 18253303--18253335 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18253293 TGACTCTCTC
18253303 TTTCTTTTTA-TGCTTTG
1 TTTCTTTTTATTGCTTTG
18253320 TTTC-TTTTATTGCTTT
1 TTTCTTTTTATTGCTTT
18253336 TATGTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (18 bp):
TTTCTTTTTATTGCTTTG
Found at i:18253353 original size:25 final size:25
Alignment explanation
Indices: 18253308--18253363 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
18253298 CTCTCTTTCT
*
18253308 TTTTATGCTTTGTTTCTTTTATT-G
1 TTTTATGCTTTATTTCTTTTATTAG
*
18253332 CTTTTATGTTTTATTTAC-TTTATTAG
1 -TTTTATGCTTTATTT-CTTTTATTAG
18253358 TTTTAT
1 TTTTAT
18253364 AATAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (25 bp):
TTTTATGCTTTATTTCTTTTATTAG
Found at i:18263311 original size:6 final size:6
Alignment explanation
Indices: 18263300--18263454 Score: 296
Period size: 6 Copynumber: 26.2 Consensus size: 6
18263290 TAAGTAAATA
18263300 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
18263348 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
18263396 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATAT-
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
18263443 TATAT- TATATG T
1 TATATG TATATG T
18263455 TATTATAATA
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.07
6 138 0.93
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:18263828 original size:30 final size:28
Alignment explanation
Indices: 18263774--18263830 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
18263764 AATTGTAAAA
*
18263774 TAAATTGTAAATTTTGAGTATTAGGGAC
1 TAAATTGTAAATTTTGAATATTAGGGAC
18263802 TAAATTGTGAAAATTTTGAA-ATTTAGGGA
1 TAAATTGT--AAATTTTGAATA-TTAGGGA
18263831 TTTAAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 1 0.04
30 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.39
Consensus pattern (28 bp):
TAAATTGTAAATTTTGAATATTAGGGAC
Found at i:18266438 original size:42 final size:42
Alignment explanation
Indices: 18266376--18266460 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
18266366 AATTGAGTAC
* * *
18266376 GTTCAATTAATTGATTAGTGACGAATTGATGGATAAGACCAT
1 GTTCAATTAATTGATCAGTGACGAATTGACGGATAAAACCAT
*
18266418 GTTCAATTAATTGATCAGTGATGAATTGACGGATAAAACCAT
1 GTTCAATTAATTGATCAGTGACGAATTGACGGATAAAACCAT
18266460 G
1 G
18266461 GTTAAATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (42 bp):
GTTCAATTAATTGATCAGTGACGAATTGACGGATAAAACCAT
Found at i:18269752 original size:242 final size:241
Alignment explanation
Indices: 18269314--18269754 Score: 539
Period size: 242 Copynumber: 1.8 Consensus size: 241
18269304 TAATTTCATC
* * *
18269314 CCTTATTCTTATGTTTTATGACATGTTGAACATTTTTCTCTTCTATGACAACATCAAATTCTCAC
1 CCTTATTCTTATGTTTTATGACATGCTGAACATTTTTCCCTTATATGACAACATCAAATTCTCAC
* *** * **
18269379 TCTAACATGTACTTATGAACATTAGGTATTATTACCGATAATGTTGTTCTGCTCGTTTTTGCTAA
66 TCTAACATGTACTTATGAACATTAGATATTATTACCGATAATGCCATTCTACTCGTTTTCACTAA
* ** * * * * *
18269444 AAATCGCTTAGAAAAGATCATTCTCCTAACTTAAAACATTCATATTTTACCATCAAACATCAAAA
131 AAACCGAGTAGAAAAGAT-ATTCTCATAACTTAAAACACTCATATTATACCATAAAACACCAAAA
18269509 TACATGCATATCATTCATGGGTAAATTTTTAAACATAAACCCTAACT
195 TACATGCATATCATTCATGGGTAAATTTTTAAACATAAACCCTAACT
* *
18269556 CCTTATTCTTATGTTTTATGACATGCTGACCATTTTTCCCTTATATGGCAACATCAAATTCTCAC
1 CCTTATTCTTATGTTTTATGACATGCTGAACATTTTTCCCTTATATGACAACATCAAATTCTCAC
** * * *
18269621 TCTAACATGTACTTATGAGTATTAGATATTTTTACCGATTAA-GCCATTTTACTCGTTTTCACTC
66 TCTAACATGTACTTATGAACATTAGATATTATTACCGA-TAATGCCATTCTACTCGTTTTCACTA
* * **
18269685 AAAACCGAGTAGTACAAG-T-TGTCTAACATAATTTAAAAC-CTCATATTATGTCATAAAACACC
130 AAAACCGAGTAG-AAAAGATAT-TCT--CATAACTTAAAACACTCATATTATACCATAAAACACC
18269747 AAAATACA
191 AAAATACA
18269755 CAAATTTCAC
Statistics
Matches: 165, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
240 1 0.01
241 3 0.02
242 143 0.87
243 18 0.11
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (241 bp):
CCTTATTCTTATGTTTTATGACATGCTGAACATTTTTCCCTTATATGACAACATCAAATTCTCAC
TCTAACATGTACTTATGAACATTAGATATTATTACCGATAATGCCATTCTACTCGTTTTCACTAA
AAACCGAGTAGAAAAGATATTCTCATAACTTAAAACACTCATATTATACCATAAAACACCAAAAT
ACATGCATATCATTCATGGGTAAATTTTTAAACATAAACCCTAACT
Found at i:18277491 original size:38 final size:39
Alignment explanation
Indices: 18277449--18277542 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 39
18277439 CCATTTCCGT
* * *
18277449 CCAACCCAACACACCA-TGTGGGGATAGAATCAACCCAC
1 CCAACCCTACACACCAGTATGAGGATAGAATCAACCCAC
** *
18277487 CCAACCCTACACACCAAGTATGAGGATCTAATCAACCCAT
1 CCAACCCTACACACC-AGTATGAGGATAGAATCAACCCAC
18277527 CCAACCCTACACACCA
1 CCAACCCTACACACCA
18277543 ACTAGTACCG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 14 0.29
39 2 0.04
40 32 0.67
ACGTcount: A:0.37, C:0.39, G:0.11, T:0.13
Consensus pattern (39 bp):
CCAACCCTACACACCAGTATGAGGATAGAATCAACCCAC
Found at i:18281265 original size:22 final size:22
Alignment explanation
Indices: 18281218--18281314 Score: 108
Period size: 22 Copynumber: 4.3 Consensus size: 22
18281208 TGATTAATAA
*
18281218 TAAGCTCTAAT-GAGCTGGAACGG
1 TAAGCTCT-ATCGAGCT-GAACAG
18281241 TAAGCTCTATCGAGCTGAACAG
1 TAAGCTCTATCGAGCTGAACAG
* *
18281263 TAAGCTATATTGAGCTGAACAG
1 TAAGCTCTATCGAGCTGAACAG
*
18281285 TAAGCTC-ATACGAGCTGAAACAA
1 TAAGCTCTAT-CGAGCTG-AACAG
18281308 TAAGCTC
1 TAAGCTC
18281315 CAATGAGCTA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.03
22 39 0.60
23 24 0.37
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (22 bp):
TAAGCTCTATCGAGCTGAACAG
Found at i:18281277 original size:45 final size:45
Alignment explanation
Indices: 18281189--18281323 Score: 130
Period size: 45 Copynumber: 2.9 Consensus size: 45
18281179 GAACTATGAT
* * * *
18281189 CAGTAAGCTCCTCCTGAGCTGATTAATAATAAGCTCTAATGAGCTGGAA
1 CAGTAAGCTCATAC-GAGCTGA--AACAATAAGCTATAATGAGCT-GAA
* * *
18281238 CGGTAAGCTC-TATCGAGCTG-AACAGTAAGCTATATTGAGCTGAA
1 CAGTAAGCTCATA-CGAGCTGAAACAATAAGCTATAATGAGCTGAA
**
18281282 CAGTAAGCTCATACGAGCTGAAACAATAAGCTCCAATGAGCT
1 CAGTAAGCTCATACGAGCTGAAACAATAAGCTATAATGAGCT
18281324 AAAAATAGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
44 19 0.26
45 36 0.50
48 7 0.10
49 10 0.14
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (45 bp):
CAGTAAGCTCATACGAGCTGAAACAATAAGCTATAATGAGCTGAA
Found at i:18283069 original size:31 final size:31
Alignment explanation
Indices: 18283034--18283095 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
18283024 AGACATGGCC
18283034 AATGACCAATTTACCAGCTGGTACATCCTCT
1 AATGACCAATTTACCAGCTGGTACATCCTCT
* * *
18283065 AATGACTAATTTGCCAGCTGGTACATTCTCT
1 AATGACCAATTTACCAGCTGGTACATCCTCT
18283096 CGAACGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (31 bp):
AATGACCAATTTACCAGCTGGTACATCCTCT
Found at i:18283870 original size:21 final size:21
Alignment explanation
Indices: 18283818--18283875 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
18283808 AAGTTAAAAT
18283818 TAATAAGTCTTAATT-AATTAA
1 TAATAAG-CTTAATTAAATTAA
* *
18283839 -ACTAAACCTTAATTAAATTAA
1 TAAT-AAGCTTAATTAAATTAA
18283860 TAATAAGCTTAATTAA
1 TAATAAGCTTAATTAA
18283876 CATAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 9 0.30
21 19 0.63
22 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAAGCTTAATTAAATTAA
Found at i:18289128 original size:69 final size:69
Alignment explanation
Indices: 18289017--18289155 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
18289007 CGGCTCCTGG
* * *
18289017 TAATCCACCTTTTTCCTTCACTCTGATATGCTTCATCAATCTTTGCC-GAGCCTTCATCACTTTG
1 TAATCCACCTCTTTCCTTCACTCTGATAGGCTTCATCAATCTTT-CCAGAGACTTCATCACTTTG
18289081 AAGGT
65 AAGGT
* * *
18289086 TAATCCACCTCTTTCCTTCACTGTGATAGGCTTCATCGATCTTTCCAGAGACTTCTTCACTTTGA
1 TAATCCACCTCTTTCCTTCACTCTGATAGGCTTCATCAATCTTTCCAGAGACTTCATCACTTTGA
18289151 AGGT
66 AGGT
18289155 T
1 T
18289156 GCAGATCTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (69 bp):
TAATCCACCTCTTTCCTTCACTCTGATAGGCTTCATCAATCTTTCCAGAGACTTCATCACTTTGA
AGGT
Found at i:18289387 original size:7 final size:7
Alignment explanation
Indices: 18289375--18289435 Score: 61
Period size: 7 Copynumber: 8.4 Consensus size: 7
18289365 AAAAATAATT
18289375 TTTTTTA
1 TTTTTTA
18289382 TTTTTTA
1 TTTTTTA
*
18289389 -TTTTTC
1 TTTTTTA
*
18289395 TTTTTAA
1 TTTTTTA
18289402 GTTTTTTA
1 -TTTTTTA
18289410 TTTATTTA
1 TTT-TTTA
*
18289418 CTTTTTAA
1 -TTTTTTA
18289426 TTTTTTA
1 TTTTTTA
18289433 TTT
1 TTT
18289436 GTCCTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 5 0.11
7 23 0.52
8 13 0.30
9 3 0.07
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:18289430 original size:24 final size:21
Alignment explanation
Indices: 18289375--18289435 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
18289365 AAAAATAATT
*
18289375 TTTTTTATTTTTTA-TTTTTC
1 TTTTTAATTTTTTATTTTTTC
18289395 TTTTTAAGTTTTTTATTTATTTAC
1 TTTTTAA-TTTTTTATTT-TTT-C
18289419 TTTTTAATTTTTTATTT
1 TTTTTAATTTTTTATTT
18289436 GTCCTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 6 0.17
21 7 0.19
22 2 0.06
23 13 0.36
24 8 0.22
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTAATTTTTTATTTTTTC
Found at i:18289568 original size:21 final size:20
Alignment explanation
Indices: 18289542--18289587 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
18289532 TTCTTTAAAT
18289542 TTTTTTAAAATTTAAATATTA
1 TTTTTTAAAATTTAAATA-TA
*
18289563 TTTTTTAAATTTTAAATATA
1 TTTTTTAAAATTTAAATATA
18289583 TTTTT
1 TTTTT
18289588 AAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTTAAAATTTAAATATA
Found at i:18289708 original size:21 final size:22
Alignment explanation
Indices: 18289652--18289708 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
18289642 TTTTTTTATT
*
18289652 TATTTTATAATATTTTAAATATA
1 TATTTTTTAA-ATTTTAAATATA
18289675 TATTTATTT-AATTTTAAATATA
1 TATTT-TTTAAATTTTAAATATA
18289697 -ATTTTTTAAATT
1 TATTTTTTAAATT
18289709 ATTTTTAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 3 0.10
21 8 0.26
22 12 0.39
23 6 0.19
24 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTTAAATTTTAAATATA
Found at i:18289896 original size:20 final size:21
Alignment explanation
Indices: 18289862--18289918 Score: 98
Period size: 20 Copynumber: 2.7 Consensus size: 21
18289852 GGCTTTTTTC
18289862 TAAAATATATATATTAAAAAAT
1 TAAAA-ATATATATTAAAAAAT
18289884 TAAAAAT-TATATTAAAAAAT
1 TAAAAATATATATTAAAAAAT
18289904 TAAAAATATATATTA
1 TAAAAATATATATTA
18289919 TAATTGGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.59
21 9 0.26
22 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAATATATATTAAAAAAT
Found at i:18290773 original size:20 final size:20
Alignment explanation
Indices: 18290748--18290788 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18290738 AGTTATATGG
18290748 TTGCCTTTAGTTTTAATGTT
1 TTGCCTTTAGTTTTAATGTT
18290768 TTGCCTTTAGTTTTAATGTT
1 TTGCCTTTAGTTTTAATGTT
18290788 T
1 T
18290789 AACTATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (20 bp):
TTGCCTTTAGTTTTAATGTT
Found at i:18293073 original size:5 final size:5
Alignment explanation
Indices: 18293063--18293137 Score: 57
Period size: 5 Copynumber: 15.0 Consensus size: 5
18293053 TTTGTTTTAG
* * **
18293063 ATTTT ATTTT A-TTT ATTAT -TTTT ATTTG ATGGT -TTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
*
18293110 ATTTTT ATTTTT ATTTCT AGTTT ATTTT
1 A-TTTT A-TTTT ATTT-T ATTTT ATTTT
18293138 TGGAAGTTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
4 9 0.16
5 31 0.56
6 15 0.27
ACGTcount: A:0.19, C:0.01, G:0.05, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:18293089 original size:6 final size:6
Alignment explanation
Indices: 18293064--18293138 Score: 59
Period size: 6 Copynumber: 12.7 Consensus size: 6
18293054 TTGTTTTAGA
**
18293064 TTTTA- TTTTAT TTATTAT TTTTAT TTGATGGT TTTTA- TTTTA- TTTTAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TT--TTAT TTTTAT TTTTAT TTTTAT
* *
18293112 TTTTAT TTTTAT TTCTA- GTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
18293139 GGAAGTTACG
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
5 18 0.32
6 28 0.50
7 6 0.11
8 4 0.07
ACGTcount: A:0.17, C:0.01, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:18294379 original size:27 final size:27
Alignment explanation
Indices: 18294341--18294392 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
18294331 GCTGGTTGCT
*
18294341 AGTCTTAATA-CCTAGAGAGTCGTGGGC
1 AGTCCTAATACCCT-GAGAGTCGTGGGC
*
18294368 AGTCCTAATACCCTGAGGGTCGTGG
1 AGTCCTAATACCCTGAGAGTCGTGG
18294393 ACTTTATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (27 bp):
AGTCCTAATACCCTGAGAGTCGTGGGC
Found at i:18294664 original size:92 final size:91
Alignment explanation
Indices: 18294406--18294673 Score: 356
Period size: 92 Copynumber: 2.9 Consensus size: 91
18294396 TTATTGATAA
** * * *
18294406 CAGTATAGCATATTACCGCATTGCACTGTACCGCATGTACGTTAGCTACGCTACGTACCATTAAC
1 CAGTATAGCGGATTACTGTATTGCACTGTACCGCATGTATGTTAGCTACGCTACGTACCATTAAC
*
18294471 GGAATTGGCAATCATACTAAAATCTAT
66 GG-ATTGGCAGTCATACTAAAATCTAT
* * ** *
18294498 CAGTATAGCGGATTACTGTATTGCACTGTACCGCATGTATGTAAGTTACGCTATATACCGTTAAC
1 CAGTATAGCGGATTACTGTATTGCACTGTACCGCATGTATGTTAGCTACGCTACGTACCATTAAC
* *
18294563 GGAGTTGGCAGTCTTACTACAATCTAT
66 GGA-TTGGCAGTCATACTAAAATCTAT
* *
18294590 CAGTATAGCGGATTACTGTATTGCACTGTACCGCATGTATGTTAGCTACGCTACGTACCACTATC
1 CAGTATAGCGGATTACTGTATTGCACTGTACCGCATGTATGTTAGCTACGCTACGTACCATTAAC
*
18294655 TGATCTGGCAGTTCATACT
66 GGAT-TGGCAG-TCATACT
18294674 GCATGTCTGT
Statistics
Matches: 151, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
91 2 0.01
92 143 0.95
93 6 0.04
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (91 bp):
CAGTATAGCGGATTACTGTATTGCACTGTACCGCATGTATGTTAGCTACGCTACGTACCATTAAC
GGATTGGCAGTCATACTAAAATCTAT
Found at i:18296023 original size:22 final size:23
Alignment explanation
Indices: 18295998--18296047 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
18295988 CCACCAAATA
**
18295998 AAATATTAATTTTTAAAAT-TTT
1 AAATATTAATTTAAAAAATATTT
18296020 AAATA-TAATTTAAAAAATATTT
1 AAATATTAATTTAAAAAATATTT
18296042 AAATAT
1 AAATAT
18296048 CTTTAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTAATTTAAAAAATATTT
Found at i:18296030 original size:21 final size:22
Alignment explanation
Indices: 18295998--18296055 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
18295988 CCACCAAATA
**
18295998 AAATATTAATTTTTAAAAT-TTT
1 AAATA-TAATTTAAAAAATATTT
18296020 AAATATAATTTAAAAAATATTT
1 AAATATAATTTAAAAAATATTT
*
18296042 AAATAT-CTTTAAAA
1 AAATATAATTTAAAA
18296056 GTAATTTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATATAATTTAAAAAATATTT
Found at i:18296105 original size:17 final size:18
Alignment explanation
Indices: 18296079--18296112 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18296069 TAATAATTAA
*
18296079 AAAAATATATTTGAAATT
1 AAAAATATATTTAAAATT
18296097 AAAAA-ATATTTAAAAT
1 AAAAATATATTTAAAAT
18296113 ATACACTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAAATATATTTAAAATT
Found at i:18296251 original size:23 final size:20
Alignment explanation
Indices: 18296198--18296262 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 20
18296188 ATAATATTAA
18296198 AAAATTTATATTTAAAATTT
1 AAAATTTATATTTAAAATTT
* *
18296218 AAAAATAATATTATAAAACATTT
1 AAAATTTATATT-T-AAA-ATTT
*
18296241 GAAATTTATATTTCAAAATTT
1 AAAATTTATATTT-AAAATTT
18296262 A
1 A
18296263 TAAAACTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 10 0.29
21 5 0.14
22 7 0.20
23 13 0.37
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTTATATTTAAAATTT
Found at i:18296313 original size:4 final size:4
Alignment explanation
Indices: 18296273--18296298 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18296263 TAAAACTAAT
18296273 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
18296299 GGACAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:18296337 original size:15 final size:15
Alignment explanation
Indices: 18296265--18296350 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
18296255 AAAATTTATA
*
18296265 AAACTAATAATAAAT
1 AAACTAAAAATAAAT
18296280 AAA-TAAATAAATAAAT
1 AAACT-AA-AAATAAAT
** *
18296296 AAAGGACAAATAAAT
1 AAACTAAAAATAAAT
18296311 AAAACTTAAAAAGTAAAT
1 -AAAC-TAAAAA-TAAAT
*
18296329 AAA-TAAAAA-AAAC
1 AAACTAAAAATAAAT
18296342 AAAC-AAAAA
1 AAACTAAAAA
18296351 GGAAAAAGGA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
15 19 0.33
16 14 0.25
17 7 0.12
18 5 0.09
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.17
Consensus pattern (15 bp):
AAACTAAAAATAAAT
Found at i:18296979 original size:26 final size:25
Alignment explanation
Indices: 18296939--18296988 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
18296929 ATTTTTTAGT
* *
18296939 TATAATTTAATAATTTATATAATAC
1 TATAATTTAAAAATTAATATAATAC
*
18296964 TATAATTTTAAAAATTAATTTAATA
1 TATAA-TTTAAAAATTAATATAATA
18296989 ACAAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATAATTTAAAAATTAATATAATAC
Found at i:18296998 original size:65 final size:66
Alignment explanation
Indices: 18296929--18297063 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 66
18296919 TCTATTATAG
* *
18296929 ATTTTTTAGTTATAATTTAATAATTT-ATATAATACTATAATTTTAAAAATTAATTTAATAACAA
1 ATTTTTTAGTTATAATTTAATAATTTAATATAATACTATAATTTTAAAAAATAATTTAATAAAAA
18296993 A
66 A
* * *
18296994 ATTTTTTAGTTATAATTTAATAATTTGAATATATTATTATAATTTTAAAAAATATTTTAATAAAA
1 ATTTTTTAGTTATAATTTAATAATTT-AATATAATACTATAATTTTAAAAAATAATTTAATAAAA
18297059 AA
65 AA
18297061 ATT
1 ATT
18297064 ATAAAATCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 26 0.41
67 37 0.59
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (66 bp):
ATTTTTTAGTTATAATTTAATAATTTAATATAATACTATAATTTTAAAAAATAATTTAATAAAAA
A
Found at i:18305829 original size:24 final size:24
Alignment explanation
Indices: 18305802--18305851 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
18305792 TGGCATATTT
18305802 GAGTAATTATATATTCACAATCAA
1 GAGTAATTATATATTCACAATCAA
18305826 GAGTAATTATATATTCACAATCAA
1 GAGTAATTATATATTCACAATCAA
18305850 GA
1 GA
18305852 CACAATCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (24 bp):
GAGTAATTATATATTCACAATCAA
Found at i:18307295 original size:33 final size:33
Alignment explanation
Indices: 18307249--18307403 Score: 195
Period size: 33 Copynumber: 4.7 Consensus size: 33
18307239 TCCGAGTGGT
*
18307249 AAGTATACATTTCCTTTTCATATGATATACACA
1 AAGTATACATTTCCTTTTCAAATGATATACACA
* * *
18307282 AAGTATACCTTTCCTTTTCATATGGTATACACA
1 AAGTATACATTTCCTTTTCAAATGATATACACA
**
18307315 AAGTATACATTTCCTTTTCAAATGGCATACACA
1 AAGTATACATTTCCTTTTCAAATGATATACACA
* ** *
18307348 AAGTATACCTAACATTTTCAAAT-AGTATACACA
1 AAGTATACATTTCCTTTTCAAATGA-TATACACA
*
18307381 AAGTATACATTTCCTTTGCAAAT
1 AAGTATACATTTCCTTTTCAAAT
18307404 TCGATAGCCG
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
33 105 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (33 bp):
AAGTATACATTTCCTTTTCAAATGATATACACA
Found at i:18307331 original size:66 final size:66
Alignment explanation
Indices: 18307249--18307403 Score: 229
Period size: 66 Copynumber: 2.3 Consensus size: 66
18307239 TCCGAGTGGT
* * ** * * *
18307249 AAGTATACATTTCCTTTTCATATGATATACACAAAGTATACCTTTCCTTTTCATATGGTATACAC
1 AAGTATACATTTCCTTTTCAAATGACATACACAAAGTATACCTAACATTTTCAAATAGTATACAC
18307314 A
66 A
*
18307315 AAGTATACATTTCCTTTTCAAATGGCATACACAAAGTATACCTAACATTTTCAAATAGTATACAC
1 AAGTATACATTTCCTTTTCAAATGACATACACAAAGTATACCTAACATTTTCAAATAGTATACAC
18307380 A
66 A
*
18307381 AAGTATACATTTCCTTTGCAAAT
1 AAGTATACATTTCCTTTTCAAAT
18307404 TCGATAGCCG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 80 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (66 bp):
AAGTATACATTTCCTTTTCAAATGACATACACAAAGTATACCTAACATTTTCAAATAGTATACAC
A
Found at i:18307519 original size:31 final size:31
Alignment explanation
Indices: 18307408--18307674 Score: 305
Period size: 31 Copynumber: 8.7 Consensus size: 31
18307398 GCAAATTCGA
* *
18307408 TAGCCGAAGCTATCC-CTTTTCAC-ATTC-GA
1 TAGCCGAAGCTA-CCACTTTTCACTAATCAGG
** *
18307437 TAGCCGAAGCTATCCA-TTTTCAC--ATTTGA
1 TAGCCGAAGCTA-CCACTTTTCACTAATCAGG
* *
18307466 TAGCCGAAGCTATCC-CTATTCACTGATCAGG
1 TAGCCGAAGCTA-CCACTTTTCACTAATCAGG
*
18307497 TAGCTGAAGCTACCACTTTTCACTAATCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAGG
*
18307528 TAGCCGAAGCTACTACTTTTCACTAATCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAGG
** *
18307559 TAGCCGAAGCTACCGTTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAGG
*
18307590 TAGCCGAAGCTACTACTTTTCACTAATCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAGG
**
18307621 TAGCCGAAGCTACCACTTTTCACTGGTCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAGG
* *
18307652 TAGCTGAAGCTACCAATTTTCAC
1 TAGCCGAAGCTACCACTTTTCAC
18307675 ATTGTACACA
Statistics
Matches: 208, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
28 1 0.00
29 45 0.22
30 2 0.01
31 160 0.77
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (31 bp):
TAGCCGAAGCTACCACTTTTCACTAATCAGG
Found at i:18309300 original size:22 final size:22
Alignment explanation
Indices: 18309275--18309324 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
18309265 GGGGTGGGTC
*
18309275 TTGTATATGTGGATGAAGTGAT
1 TTGTATATGTGGAGGAAGTGAT
18309297 TTGTATATGTGGAGGAAGTGAT
1 TTGTATATGTGGAGGAAGTGAT
*
18309319 CTGTAT
1 TTGTAT
18309325 GTGTCGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (22 bp):
TTGTATATGTGGAGGAAGTGAT
Found at i:18312526 original size:17 final size:19
Alignment explanation
Indices: 18312504--18312546 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
18312494 TGGAAGCTTT
*
18312504 GGAAAAC-ATTT-ATTTTA
1 GGAAAACTATTTGATCTTA
18312521 GGAAAACTATTTGATCTTA
1 GGAAAACTATTTGATCTTA
18312540 GTGAAAA
1 G-GAAAA
18312547 TCGAGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 6 0.27
20 5 0.23
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (19 bp):
GGAAAACTATTTGATCTTA
Found at i:18313406 original size:13 final size:13
Alignment explanation
Indices: 18313384--18313426 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
18313374 CACATGCCCA
*
18313384 TGTGGCCTACCCG
1 TGTGGACTACCCG
*
18313397 TGTGGACTACCTG
1 TGTGGACTACCCG
18313410 TGTGGACTA-CCG
1 TGTGGACTACCCG
18313422 TGTGG
1 TGTGG
18313427 GCCCACAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.12, C:0.26, G:0.35, T:0.28
Consensus pattern (13 bp):
TGTGGACTACCCG
Found at i:18316183 original size:139 final size:137
Alignment explanation
Indices: 18315953--18316373 Score: 444
Period size: 139 Copynumber: 3.0 Consensus size: 137
18315943 GTGCTTTTAG
* * * * * *
18315953 CCTTGAGTCCCGAGTTTAGTTTCTT-TCCTACTCACATATGTATTTTTTTCGTTTTATGTTGCTT
1 CCTTGAGTCTCAAGTTT-GATTCTTCTCCTACTCACATTTGTA--TTTTT-ATTTCATGTTGCTT
* *
18316017 CAAGCTTTTTAAATTTTTAATTCATTTTATTTAACATATTAATTTTTTGTTAGATAGTTAGATAG
62 CAAGCTTTTTAAATTTTTAATTAATTTT-TTTAACATATTAATTTTTTGTTAGATGGTTAGATAG
*
18316082 TTGCAATTATAT
126 TTGCAATTACAT
* *
18316094 CCTTGAGTCTTGAA-TTTGATTCTTCTCCTACTCACATTTGTAATTTTTATTTCATTTTGCTTCA
1 CCTTGAGTC-TCAAGTTTGATTCTTCTCCTACTCACATTTGT-ATTTTTATTTCATGTTGCTTCA
* *
18316158 AGCTTTTTAAATTTTTAATTAATTTTTTCTAACATATTAGTTCTTTTGTTAGATGGTTAAATAGT
64 AGCTTTTTAAATTTTTAATTAATTTTTT-TAACATATTAATT-TTTTGTTAGATGGTTAGATAGT
* *
18316223 TGTATTTACAT
127 TGCAATTACAT
* * * * *
18316234 CATTGAGTCTCAAGTTTGATTCCTCTACTATTCACATTTTGT-TTTTTATTTCGTGTTGCTTCAA
1 CCTTGAGTCTCAAGTTTGATTCTTCTCCTACTCACA-TTTGTATTTTTATTTCATGTTGCTTCAA
* * * *
18316298 GC--CTT---TTTTTAATTAATATTTTTAACATATTAACTCCTTTTGTTAGATGGTTAGATAATT
65 GCTTTTTAAATTTTTAATTAATTTTTTTAACATATTAA-T-TTTTTGTTAGATGGTTAGATAGTT
* *
18316358 ACGATTACAT
128 GCAATTACAT
18316368 CCTTGA
1 CCTTGA
18316374 ATTTGAGGTT
Statistics
Matches: 238, Mismatches: 33, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
133 10 0.04
134 49 0.21
137 2 0.01
138 2 0.01
139 75 0.32
140 66 0.28
141 32 0.13
142 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (137 bp):
CCTTGAGTCTCAAGTTTGATTCTTCTCCTACTCACATTTGTATTTTTATTTCATGTTGCTTCAAG
CTTTTTAAATTTTTAATTAATTTTTTTAACATATTAATTTTTTGTTAGATGGTTAGATAGTTGCA
ATTACAT
Found at i:18316502 original size:21 final size:21
Alignment explanation
Indices: 18316439--18316516 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
18316429 TTTCAAGATT
18316439 TTTTTATTTTTAATTAATGT-
1 TTTTTATTTTTAATTAATGTA
* * **
18316459 TTTGATGATGTTT--TTAAACTA
1 TTT--TTATTTTTAATTAATGTA
18316480 TTTTTATTTTTAATTAATGTA
1 TTTTTATTTTTAATTAATGTA
18316501 TTTTTATTTTTAATTA
1 TTTTTATTTTTAATTA
18316517 TTTTTATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
19 6 0.13
20 8 0.18
21 25 0.56
22 6 0.13
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTTTATTTTTAATTAATGTA
Found at i:18316619 original size:22 final size:21
Alignment explanation
Indices: 18316593--18316667 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
18316583 AAGAAAAGAG
18316593 TTAAAAATAAAAAATACATTAA
1 TTAAAAATAAAAAATA-ATTAA
18316615 TTAAAAAT-AAAAATAATT-A
1 TTAAAAATAAAAAATAATTAA
*
18316634 --AAAAATCACTAAAAT-ATTAA
1 TTAAAAAT-A-AAAAATAATTAA
18316654 TTAAAAATAAAAAA
1 TTAAAAATAAAAAA
18316668 GCTTGAAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
17 6 0.13
19 4 0.09
20 13 0.29
21 8 0.18
22 14 0.31
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAAAAATAAAAAATAATTAA
Found at i:18318091 original size:22 final size:21
Alignment explanation
Indices: 18318010--18318113 Score: 65
Period size: 22 Copynumber: 4.9 Consensus size: 21
18318000 TTCTTTTACA
*
18318010 TTTTT-TTATTTTATTATTAACT
1 TTTTTCTTATTTTATT-TT-ATT
* * *
18318032 TTTGTC-T-TTTTCTTTAATT
1 TTTTTCTTATTTTATTTTATT
18318051 TTTTTCTT-TTTTAAGTTTTATAT
1 TTTTTCTTATTTT-A-TTTTAT-T
*
18318074 TTTTTCTTATTTTATTTTGTT
1 TTTTTCTTATTTTATTTTATT
18318095 TATTTAT-TTATTTTATTTT
1 T-TTT-TCTTATTTTATTTT
18318114 TTGTTATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
19 7 0.11
20 6 0.09
21 8 0.12
22 30 0.45
23 11 0.17
24 4 0.06
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTTCTTATTTTATTTTATT
Found at i:18318200 original size:32 final size:34
Alignment explanation
Indices: 18318155--18318220 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
18318145 TTATAATATA
18318155 TATTTTTTAAAATTTTAAATATTA-TTTTTAAAT
1 TATTTTTTAAAATTTTAAATATTATTTTTTAAAT
18318188 TATTTTTT-AAATTTTAAATATTATTTTTTAAAT
1 TATTTTTTAAAATTTTAAATATTATTTTTTAAAT
18318221 ATTAAATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTTTTTAAAATTTTAAATATTATTTTTTAAAT
Found at i:18318212 original size:21 final size:21
Alignment explanation
Indices: 18318178--18318237 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
18318168 TTTAAATATT
*
18318178 ATTTTTAA-ATTATTTTTTAA
1 ATTTTAAATATTATTTTTTAA
18318198 ATTTTAAATATTATTTTTTAA
1 ATTTTAAATATTATTTTTTAA
*
18318219 ATATTAAATATGTATTTTT
1 ATTTTAAATAT-TATTTTT
18318238 AATAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.19
21 22 0.61
22 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTTAAATATTATTTTTTAA
Found at i:18318218 original size:14 final size:14
Alignment explanation
Indices: 18318167--18318224 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
18318157 TTTTTTAAAA
18318167 TTTTAAATATTA-T
1 TTTTAAATATTATT
*
18318180 TTTTAAATTATTTTTT
1 TTTTAAA-TA-TTATT
18318196 AAATTTTAAATATTATT
1 ---TTTTAAATATTATT
18318213 TTTTAAATATTA
1 TTTTAAATATTA
18318225 AATATGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
13 7 0.19
14 14 0.38
15 2 0.05
16 1 0.03
17 4 0.11
18 2 0.05
19 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAAATATTATT
Found at i:18318244 original size:23 final size:21
Alignment explanation
Indices: 18318186--18318253 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 21
18318176 TTATTTTTAA
*
18318186 ATTATTTTTTAAATTTTAAAT
1 ATTATTTTTTAAATATTAAAT
18318207 ATTATTTTTTAAATATTAAAT
1 ATTATTTTTTAAATATTAAAT
* *
18318228 ATGTATTTTTAATAATATAAAAT
1 AT-TATTTTTTA-AATATTAAAT
18318251 ATT
1 ATT
18318254 TAAATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 22 0.52
22 9 0.21
23 11 0.26
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
ATTATTTTTTAAATATTAAAT
Found at i:18318337 original size:14 final size:14
Alignment explanation
Indices: 18318320--18318385 Score: 51
Period size: 15 Copynumber: 4.5 Consensus size: 14
18318310 ATATTATTTA
*
18318320 ATTTAATTTATAAT
1 ATTTAAATTATAAT
*
18318334 ATTTTAAATTATGAT
1 A-TTTAAATTATAAT
*
18318349 TTTTAAATTATATAT
1 ATTTAAATTATA-AT
* **
18318364 ATTGAAAAAATATAT
1 ATTTAAATTATA-AT
18318379 ATTTAAA
1 ATTTAAA
18318386 ATTTAAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.27
15 30 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTTAAATTATAAT
Found at i:18318339 original size:15 final size:15
Alignment explanation
Indices: 18318299--18318366 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
18318289 ATTAGTTTTT
18318299 TAATATTTTTAATATTA
1 TAATA-TTTTAA-ATTA
* * *
18318316 T-TTAATTTAATTTA
1 TAATATTTTAAATTA
18318330 TAATATTTTAAATTA
1 TAATATTTTAAATTA
*
18318345 TGAT-TTTTAAATTA
1 TAATATTTTAAATTA
18318359 TATATATT
1 TA-ATATT
18318367 GAAAAAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
14 15 0.38
15 20 0.50
16 4 0.10
17 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (15 bp):
TAATATTTTAAATTA
Found at i:18318350 original size:22 final size:22
Alignment explanation
Indices: 18318303--18318343 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18318293 GTTTTTTAAT
* *
18318303 ATTTTTAATATTATTTAATTTA
1 ATTTATAATATTATTAAATTTA
18318325 ATTTATAATATT-TTAAATT
1 ATTTATAATATTATTAAATT
18318344 ATGATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTATAATATTATTAAATTTA
Found at i:18318463 original size:10 final size:10
Alignment explanation
Indices: 18318438--18318483 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
18318428 CAAGTTTTAT
*
18318438 AAAATTAATA
1 AAAATAAATA
*
18318448 ATAATAAATA
1 AAAATAAATA
18318458 AAAATAAAT-
1 AAAATAAATA
18318467 -AAATAAATA
1 AAAATAAATA
*
18318476 AAGATAAA
1 AAAATAAA
18318484 GACATGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 8 0.27
10 22 0.73
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAATAAATA
Found at i:18318768 original size:22 final size:21
Alignment explanation
Indices: 18318743--18318808 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 21
18318733 TTTTTAAATG
18318743 TTTAAATATTATTAAAAAT-ATA
1 TTTAAATA-T-TTAAAAATAATA
*
18318765 TTT-AATATTTAAGAATAATA
1 TTTAAATATTTAAAAATAATA
* *
18318785 TTTAAAT-TTAAAAAAAAATGA
1 TTTAAATATTTAAAAATAAT-A
18318806 TTT
1 TTT
18318809 CAAAAATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 7 0.19
20 16 0.43
21 11 0.30
22 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTAAATATTTAAAAATAATA
Found at i:18318781 original size:19 final size:19
Alignment explanation
Indices: 18318754--18318798 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
18318744 TTAAATATTA
18318754 TTAAAAAT-ATATTTAATAT
1 TTAAAAATAATATTTAA-AT
*
18318773 TTAAGAATAATATTTAAAT
1 TTAAAAATAATATTTAAAT
18318792 TTAAAAA
1 TTAAAAA
18318799 AAAATGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAAAAATAATATTTAAAT
Found at i:18318888 original size:32 final size:33
Alignment explanation
Indices: 18318838--18318904 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
18318828 CTTATAAGAC
18318838 ATAATTTAAAAAAATAATATTCAAAAGTTGAAAA
1 ATAATTT-AAAAAATAATATTCAAAAGTTGAAAA
* * *
18318872 ATAATTT-AAAAATAATATTTAAAATTTTAAAA
1 ATAATTTAAAAAATAATATTCAAAAGTTGAAAA
18318904 A
1 A
18318905 ATATATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 23 0.77
34 7 0.23
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (33 bp):
ATAATTTAAAAAATAATATTCAAAAGTTGAAAA
Found at i:18318964 original size:10 final size:9
Alignment explanation
Indices: 18318951--18319037 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 9
18318941 TTTTAAAATT
18318951 AATAACAAAA
1 AATAA-AAAA
*
18318961 AATAAATAA
1 AATAAAAAA
18318970 AATAAATAAA
1 AATAAA-AAA
* *
18318980 CA-AAATAA
1 AATAAAAAA
18318988 AATAAGAAAA
1 AATAA-AAAA
*
18318998 AATATAAAA
1 AATAAAAAA
**
18319007 CTTAAAAAA
1 AATAAAAAA
**
18319016 AGGAAAAAA
1 AATAAAAAA
18319025 AATTAAAGAAA
1 AA-TAAA-AAA
18319036 AA
1 AA
18319038 GACAAAAGTT
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
8 3 0.05
9 31 0.54
10 18 0.32
11 5 0.09
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:18318973 original size:9 final size:9
Alignment explanation
Indices: 18318959--18318992 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
18318949 TTAATAACAA
18318959 AAAATAAAT
1 AAAATAAAT
18318968 AAAATAAAT
1 AAAATAAAT
18318977 AAACA-AAAT
1 AAA-ATAAAT
18318986 AAAATAA
1 AAAATAA
18318993 GAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:18318976 original size:13 final size:13
Alignment explanation
Indices: 18318946--18318988 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18318936 AAATTTTTTA
* *
18318946 AAATTAATAACAAA
1 AAATAAATAA-AAT
18318960 AAATAAATAAAAT
1 AAATAAATAAAAT
*
18318973 AAATAAACAAAAT
1 AAATAAATAAAAT
18318986 AAA
1 AAA
18318989 ATAAGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:18318990 original size:23 final size:24
Alignment explanation
Indices: 18318944--18319001 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
18318934 TCAAATTTTT
*
18318944 TAAAATTAAT-AACAAAAAATAAA
1 TAAAATAAATAAACAAAAAATAAA
*
18318967 TAAAATAAATAAACAAAATA-AAA
1 TAAAATAAATAAACAAAAAATAAA
*
18318990 TAAGAAAAAATA
1 TAA-AATAAATA
18319002 TAAAACTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (24 bp):
TAAAATAAATAAACAAAAAATAAA
Found at i:18319284 original size:14 final size:15
Alignment explanation
Indices: 18319265--18319297 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
18319255 ATCTTTAAAA
18319265 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
18319279 ATAATTTAAAATATT
1 ATAATTTAAAATATT
18319294 ATAA
1 ATAA
18319298 AACAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:18319425 original size:33 final size:33
Alignment explanation
Indices: 18319385--18319447 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
18319375 TTTTATATTA
*
18319385 TTAAAAATATATATTTAATA-TTTAAAAAATAAT
1 TTAAAAATA-ATATTTAAAATTTTAAAAAATAAT
18319418 TTAAAAATAATATTTAAAATTTTAAAAAAT
1 TTAAAAATAATATTTAAAATTTTAAAAAAT
18319448 TTATATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TTAAAAATAATATTTAAAATTTTAAAAAATAAT
Found at i:18319504 original size:9 final size:9
Alignment explanation
Indices: 18319490--18319523 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
18319480 TTAATAACAA
18319490 AAAATAAAT
1 AAAATAAAT
18319499 AAAATAAAT
1 AAAATAAAT
18319508 AAACA-AAAT
1 AAA-ATAAAT
18319517 AAAATAA
1 AAAATAA
18319524 GAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:18319507 original size:13 final size:13
Alignment explanation
Indices: 18319477--18319519 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18319467 AAATTTTTTA
* *
18319477 AAATTAATAACAAA
1 AAATAAATAA-AAT
18319491 AAATAAATAAAAT
1 AAATAAATAAAAT
*
18319504 AAATAAACAAAAT
1 AAATAAATAAAAT
18319517 AAA
1 AAA
18319520 ATAAGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:18319521 original size:23 final size:24
Alignment explanation
Indices: 18319475--18319532 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
18319465 TCAAATTTTT
*
18319475 TAAAATTAAT-AACAAAAAATAAA
1 TAAAATAAATAAACAAAAAATAAA
*
18319498 TAAAATAAATAAACAAAATA-AAA
1 TAAAATAAATAAACAAAAAATAAA
*
18319521 TAAGAAAAAATA
1 TAA-AATAAATA
18319533 TAAAACTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (24 bp):
TAAAATAAATAAACAAAAAATAAA
Found at i:18319537 original size:22 final size:22
Alignment explanation
Indices: 18319512--18319558 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
18319502 ATAAATAAAC
18319512 AAAA-TAAAATAAG-AAAAAATAT
1 AAAACTAAAA-AAGTAAAAAAT-T
*
18319534 AAAACTTAAAAAGTAAAAAATT
1 AAAACTAAAAAAGTAAAAAATT
18319556 AAA
1 AAA
18319559 GAAAAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAACTAAAAAAGTAAAAAATT
Found at i:18320391 original size:30 final size:31
Alignment explanation
Indices: 18320323--18320393 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
18320313 CTATTTCGCA
* *
18320323 TTTATTTCTTTTTGAATAATTTGATATATTT
1 TTTATTTATTTTTGAATAATATGATATATTT
* *
18320354 TTT-TTTATTTTTTAAT-ATAT-ATATTTTT
1 TTTATTTATTTTTGAATAATATGATATATTT
18320382 GTTTATTTATTT
1 -TTTATTTATTT
18320394 ATACTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 18 0.53
31 3 0.09
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (31 bp):
TTTATTTATTTTTGAATAATATGATATATTT
Found at i:18323297 original size:15 final size:15
Alignment explanation
Indices: 18323279--18323310 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18323269 CATTTTATTA
*
18323279 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
18323294 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
18323309 TT
1 TT
18323311 TGCATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:18325021 original size:21 final size:21
Alignment explanation
Indices: 18324926--18325052 Score: 94
Period size: 21 Copynumber: 6.0 Consensus size: 21
18324916 TTTAACTCTC
* * * *
18324926 ATGAGCTTCTGTTTAACTCAT
1 ATGAGTTTCTGTTCAACCCTT
* *
18324947 ATGAGTTTCCGTTCAACCCTA
1 ATGAGTTTCTGTTCAACCCTT
* * * * *
18324968 ATGGGTTTCTATACAGCTC-T
1 ATGAGTTTCTGTTCAACCCTT
*
18324988 ATTGAGCTTCTGTTCAACCCTT
1 A-TGAGTTTCTGTTCAACCCTT
* * *
18325010 ATGGGTTTCTGTTCAGCTCTT
1 ATGAGTTTCTGTTCAACCCTT
*
18325031 ATGAGCTTCTGTTCAACCCTT
1 ATGAGTTTCTGTTCAACCCTT
18325052 A
1 A
18325053 CAGGTTTCTG
Statistics
Matches: 77, Mismatches: 27, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
20 1 0.01
21 74 0.96
22 2 0.03
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGAGTTTCTGTTCAACCCTT
Found at i:18325061 original size:21 final size:20
Alignment explanation
Indices: 18324995--18325064 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
18324985 TCTATTGAGC
*
18324995 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAACCCTTA-AGGT
* * * *
18325016 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAACCCTTAAG-GT
18325037 TTCTGTTCAACCCTTACAGGT
1 TTCTGTTCAACCCTTA-AGGT
18325058 TTCTGTT
1 TTCTGTT
18325065 TAGCACTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (20 bp):
TTCTGTTCAACCCTTAAGGT
Found at i:18325062 original size:42 final size:42
Alignment explanation
Indices: 18324932--18325075 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 42
18324922 TCTCATGAGC
* * * * * *
18324932 TTCTGTTTAACTCATATGAGTTTCCGTTCAACCCTAATGGGT
1 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
* *
18324974 TTCTATACAGCTC-TATTGAGCTTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCTTA-TGAGCTTCTGTTCAACCCTTATGGGT
**
18325016 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTACAGGT
1 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
* *
18325058 TTCTGTTTAGCACTTATG
1 TTCTGTTCAGCTCTTATG
18325076 TGTTTTTATT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.02
42 83 0.95
43 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (42 bp):
TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
Found at i:18325080 original size:21 final size:20
Alignment explanation
Indices: 18324995--18325080 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 20
18324985 TCTATTGAGC
* *
18324995 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAGCACTTAT-GGT
* *
18325016 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCACTTATG-GT
* * *
18325037 TTCTGTTCAACCCTTACAGGT
1 TTCTGTTCAGCACTTA-TGGT
*
18325058 TTCTGTTTAGCACTTATGTGT
1 TTCTGTTCAGCACTTATG-GT
18325079 TT
1 TT
18325081 TTATTTAGCC
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.04
21 48 0.94
22 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (20 bp):
TTCTGTTCAGCACTTATGGT
Found at i:18327424 original size:48 final size:48
Alignment explanation
Indices: 18327366--18327462 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
18327356 ATTCTAAAAA
*
18327366 TAATATTATTTTAATAGTTTAATATTAAATTTAATTTAATACTTATCT
1 TAATAGTATTTTAATAGTTTAATATTAAATTTAATTTAATACTTATCT
* * **
18327414 TAATAGTATTTTATTAGTTTGATATTAAATTTAATTTAATGTTTATCT
1 TAATAGTATTTTAATAGTTTAATATTAAATTTAATTTAATACTTATCT
18327462 T
1 T
18327463 GTAGATAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (48 bp):
TAATAGTATTTTAATAGTTTAATATTAAATTTAATTTAATACTTATCT
Found at i:18336494 original size:6 final size:6
Alignment explanation
Indices: 18336485--18336512 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18336475 TTTTGGTTTT
18336485 GGTAGA GGTAGA GGTAGA GGTAGA GGTA
1 GGTAGA GGTAGA GGTAGA GGTAGA GGTA
18336513 AGGCTATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
GGTAGA
Found at i:18337634 original size:18 final size:19
Alignment explanation
Indices: 18337613--18337661 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
18337603 TATTATTTTT
18337613 AAAAA-TATAAAATA-ATA
1 AAAAATTATAAAATATATA
18337630 AAAAATTATAAAA-ATATA
1 AAAAATTATAAAATATATA
*
18337648 AAGAATTATAAAAT
1 AAAAATTATAAAAT
18337662 TTTATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATTATAAAATATATA
Found at i:18337670 original size:26 final size:26
Alignment explanation
Indices: 18337609--18337673 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
18337599 TGTATATTAT
18337609 TTTTAAAAATATAAAATAATAAAAAA
1 TTTTAAAAATATAAAATAATAAAAAA
* * *
18337635 TTATAAAAATATAAAGA-ATTATAAAA
1 TTTTAAAAATATAAA-ATAATAAAAAA
*
18337661 TTTTATAAATATA
1 TTTTAAAAATATA
18337674 TTACCATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTTAAAAATATAAAATAATAAAAAA
Found at i:18341605 original size:20 final size:18
Alignment explanation
Indices: 18341555--18341606 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
18341545 TATTAAGATA
18341555 AATAGTAAATTAA-ATTT
1 AATAGTAAATTAATATTT
*
18341572 AATATTAAGA-TAATCACTTT
1 AATAGTAA-ATTAAT-A-TTT
18341592 AATAGTAAATTAATA
1 AATAGTAAATTAATA
18341607 AAATACAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAGTAAATTAATATTT
Found at i:18347246 original size:25 final size:25
Alignment explanation
Indices: 18347218--18347282 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
18347208 CACACCACAA
18347218 CTCGCATGAGCTTCCCGTTATTCAG
1 CTCGCATGAGCTTCCCGTTATTCAG
* *
18347243 CTCGCATGAACTTCCCGTTATTTAG
1 CTCGCATGAGCTTCCCGTTATTCAG
*
18347268 CTCACATGAGCTTCC
1 CTCGCATGAGCTTCC
18347283 TATTTACAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (25 bp):
CTCGCATGAGCTTCCCGTTATTCAG
Found at i:18350765 original size:16 final size:14
Alignment explanation
Indices: 18350741--18350777 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
18350731 AAAACAAGAA
18350741 AAAGAAATAGAGAAG
1 AAAGAAATAGA-AAG
18350756 AAACGAAATAGAAAG
1 AAA-GAAATAGAAAG
18350771 AAAGAAA
1 AAAGAAA
18350778 GAAGAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.70, C:0.03, G:0.22, T:0.05
Consensus pattern (14 bp):
AAAGAAATAGAAAG
Found at i:18350803 original size:26 final size:26
Alignment explanation
Indices: 18350741--18350793 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
18350731 AAAACAAGAA
* * *
18350741 AAAGAAATAGAGAAGAAACGAAATAG
1 AAAGAAAGAAAGAAGAAAAGAAATAG
18350767 AAAGAAAGAAAGAAGAAAAGAAA-AG
1 AAAGAAAGAAAGAAGAAAAGAAATAG
18350792 AA
1 AA
18350794 GAAGGAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.04
Consensus pattern (26 bp):
AAAGAAAGAAAGAAGAAAAGAAATAG
Found at i:18352755 original size:40 final size:39
Alignment explanation
Indices: 18352719--18352934 Score: 162
Period size: 39 Copynumber: 5.5 Consensus size: 39
18352709 AAAGCCTACG
* *
18352719 GGACTTTAAGCCCAGATATAGTACCAGTACGAAGCCTGT
1 GGACCTTAAGCCCAGATATAGTACCAGCACGAAGCCTGT
* * *
18352758 GGACCTTAAGTCCGGATATAGTACCAGCACGAAGCCTGC
1 GGACCTTAAGCCCAGATATAGTACCAGCACGAAGCCTGT
* * * * * * *
18352797 GGATCTTAAGTCCGGATACAATTCCAGCACGAAGCCTGC
1 GGACCTTAAGCCCAGATATAGTACCAGCACGAAGCCTGT
* * * * * * * *
18352836 GAGTCTTTAAGCCCGGATACAATTCCAGCATGAAGCCTGC
1 G-GACCTTAAGCCCAGATATAGTACCAGCACGAAGCCTGT
* * * * * * *
18352876 GGACCTTAAGTCCGGATACAATTCCAGAACGAAGCCTGC
1 GGACCTTAAGCCCAGATATAGTACCAGCACGAAGCCTGT
* *
18352915 GGACCTTAAGTCCGGATATA
1 GGACCTTAAGCCCAGATATA
18352935 CATCAAATAT
Statistics
Matches: 156, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
39 122 0.78
40 34 0.22
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (39 bp):
GGACCTTAAGCCCAGATATAGTACCAGCACGAAGCCTGT
Found at i:18352776 original size:39 final size:39
Alignment explanation
Indices: 18352742--18352932 Score: 274
Period size: 39 Copynumber: 4.9 Consensus size: 39
18352732 AGATATAGTA
* * * * *
18352742 CCAGTACGAAGCCTGTGGACCTTAAGTCCGGATATAGTA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
*
18352781 CCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* * *
18352820 CCAGCACGAAGCCTGCGAGTCTTTAAGCCCGGATACAATT
1 CCAGCACGAAGCCTGCG-GACCTTAAGTCCGGATACAATT
*
18352860 CCAGCATGAAGCCTGCGGACCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
*
18352899 CCAGAACGAAGCCTGCGGACCTTAAGTCCGGATA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA
18352933 TACATCAAAT
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
39 101 0.75
40 34 0.25
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
Found at i:18352852 original size:79 final size:78
Alignment explanation
Indices: 18352742--18352934 Score: 278
Period size: 79 Copynumber: 2.5 Consensus size: 78
18352732 AGATATAGTA
* * * *
18352742 CCAGTACGAAGCCTGTGGACCTTAAGTCCGGATATAGTACCAGCACGAAGCCTGCGGATCTTAAG
1 CCAGAACGAAGCCTGCGGACCTTAAGTCCGGATATAATACCAGCACGAAGCCTGCGGACCTTAAG
18352807 TCCGGATACAATT
66 TCCGGATACAATT
* * * * * * *
18352820 CCAGCACGAAGCCTGCGAGTCTTTAAGCCCGGATACAATTCCAGCATGAAGCCTGCGGACCTTAA
1 CCAGAACGAAGCCTGCG-GACCTTAAGTCCGGATATAATACCAGCACGAAGCCTGCGGACCTTAA
18352885 GTCCGGATACAATT
65 GTCCGGATACAATT
18352899 CCAGAACGAAGCCTGCGGACCTTAAGTCCGGATATA
1 CCAGAACGAAGCCTGCGGACCTTAAGTCCGGATATA
18352935 CATCAAATAT
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 30 0.30
79 69 0.70
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (78 bp):
CCAGAACGAAGCCTGCGGACCTTAAGTCCGGATATAATACCAGCACGAAGCCTGCGGACCTTAAG
TCCGGATACAATT
Found at i:18353506 original size:24 final size:24
Alignment explanation
Indices: 18353494--18353585 Score: 157
Period size: 24 Copynumber: 3.8 Consensus size: 24
18353484 TTGACATTCC
18353494 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
18353518 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
* *
18353542 AATTCGCACACATAGTGCCATTCA
1 AATCCGCACACATAGTGCCATACA
*
18353566 AATTCGCACACATAGTGCCA
1 AATCCGCACACATAGTGCCA
18353586 AAATCATTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.20
Consensus pattern (24 bp):
AATCCGCACACATAGTGCCATACA
Found at i:18353555 original size:72 final size:72
Alignment explanation
Indices: 18353449--18353585 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
18353439 CCATGTTAAC
* ** * * *
18353449 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCCAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
18353514 TACAAAT
66 TACAAAT
* * *
18353521 CCGCACACATAGTGCCATACAAATTCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
18353586 AAATCATTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (72 bp):
CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
TACAAAT
Found at i:18353583 original size:48 final size:48
Alignment explanation
Indices: 18353449--18353585 Score: 161
Period size: 48 Copynumber: 2.9 Consensus size: 48
18353439 CCATGTTAAC
* * * * * *
18353449 CCGCACACATAGTGCC-TT-AGTAATTCACATACATATTGACATTCCAAT
1 CCGCACACATAGTGCCATTCA--AATTCGCACACATAGTGCCATACAAAT
* *
18353497 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCATACAAAT
*
18353545 TCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
18353586 AAATCATTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 74 0.97
49 1 0.01
50 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (48 bp):
CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCATACAAAT
Found at i:18354793 original size:17 final size:17
Alignment explanation
Indices: 18354761--18354794 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18354751 CCCCACTTAA
**
18354761 TATATTATAACTTATTT
1 TATATTATAAAATATTT
18354778 TATATTATAAAATATTT
1 TATATTATAAAATATTT
18354795 CAATTATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAAAATATTT
Found at i:18358564 original size:39 final size:39
Alignment explanation
Indices: 18358530--18358720 Score: 265
Period size: 39 Copynumber: 4.9 Consensus size: 39
18358520 AGATATAGTA
* * * *
18358530 CCAGTACGAAGCCTGCGGACCTTAAGTCCGGATATAGTA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* *
18358569 CCAGCACGAAGCCTACGGATCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* * * *
18358608 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGAATACAATT
1 CCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATACAATT
* *
18358648 CCAGCATGAAGCCTGCGGGCCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
18358687 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA
18358721 TACATCAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
39 99 0.75
40 33 0.25
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
Found at i:18359461 original size:24 final size:24
Alignment explanation
Indices: 18359449--18359540 Score: 157
Period size: 24 Copynumber: 3.8 Consensus size: 24
18359439 TTGACATTCC
18359449 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
18359473 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
* *
18359497 AATTCGCACACATAGTGCCATTCA
1 AATCCGCACACATAGTGCCATACA
*
18359521 AATTCGCACACATAGTGCCA
1 AATCCGCACACATAGTGCCA
18359541 AAATCATTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.20
Consensus pattern (24 bp):
AATCCGCACACATAGTGCCATACA
Found at i:18359510 original size:72 final size:72
Alignment explanation
Indices: 18359404--18359540 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
18359394 CCATGTTAAC
* ** * * *
18359404 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCCAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
18359469 TACAAAT
66 TACAAAT
* * *
18359476 CCGCACACATAGTGCCATACAAATTCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
18359541 AAATCATTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (72 bp):
CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
TACAAAT
Found at i:18359538 original size:48 final size:48
Alignment explanation
Indices: 18359404--18359540 Score: 161
Period size: 48 Copynumber: 2.9 Consensus size: 48
18359394 CCATGTTAAC
* * * * * *
18359404 CCGCACACATAGTGCC-TT-AGTAATTCACATACATATTGACATTCCAAT
1 CCGCACACATAGTGCCATTCA--AATTCGCACACATAGTGCCATACAAAT
* *
18359452 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCATACAAAT
*
18359500 TCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
18359541 AAATCATTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 74 0.97
49 1 0.01
50 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (48 bp):
CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCATACAAAT
Found at i:18360739 original size:17 final size:17
Alignment explanation
Indices: 18360717--18360750 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18360707 CCCCATTTAA
18360717 TATATTATAACATATTT
1 TATATTATAACATATTT
18360734 TATATTATAACATATTT
1 TATATTATAACATATTT
18360751 CAATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:18367068 original size:25 final size:25
Alignment explanation
Indices: 18367031--18367098 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
18367021 GGACACACCA
18367031 CAACTCGTATGAGCTTCCAGTTATT
1 CAACTCGTATGAGCTTCCAGTTATT
* * * *
18367056 GAGCTCGCATGAGCTTCCTGTTATT
1 CAACTCGTATGAGCTTCCAGTTATT
*
18367081 CAACTCATATGAGCTTCC
1 CAACTCGTATGAGCTTCC
18367099 CATTTACAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (25 bp):
CAACTCGTATGAGCTTCCAGTTATT
Found at i:18371399 original size:10 final size:10
Alignment explanation
Indices: 18371371--18371410 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
18371361 TCAATTTAAT
18371371 TAAATAAATTA
1 TAAA-AAATTA
18371382 TAAAAAAATTA
1 T-AAAAAATTA
18371393 TAAAAAATTA
1 TAAAAAATTA
*
18371403 TTAAAAAT
1 TAAAAAAT
18371411 AGAGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 16 0.59
11 8 0.30
12 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:18372271 original size:31 final size:29
Alignment explanation
Indices: 18372244--18372322 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 29
18372234 ATTTTTTAAA
*
18372244 AATTTTAAAATATTAAAAATATGTTTTTTAT
1 AATTTTAAAAT-TTAAAAATAT-CTTTTTAT
* *
18372275 AATTTTAATGATTTTAAAATATCTTTTTAT
1 AATTTTAA-AATTTAAAAATATCTTTTTAT
*
18372305 AATTTTTAAATTTAAAAA
1 AATTTTAAAATTTAAAAA
18372323 ATTAATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 8 0.20
30 14 0.34
31 17 0.41
32 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (29 bp):
AATTTTAAAATTTAAAAATATCTTTTTAT
Found at i:18376396 original size:20 final size:20
Alignment explanation
Indices: 18376359--18376397 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18376349 TAAATTGGAA
*
18376359 TGAAATTGTGATATTGAATG
1 TGAAATTATGATATTGAATG
18376379 TGAAATTAT-ATATATGAAT
1 TGAAATTATGATAT-TGAAT
18376398 TGGATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (20 bp):
TGAAATTATGATATTGAATG
Found at i:18379580 original size:14 final size:14
Alignment explanation
Indices: 18379561--18379593 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
18379551 ACGAAGTTGG
*
18379561 TGATTTCTTTTTGT
1 TGATTTCCTTTTGT
18379575 TGATTTCCTTTTGT
1 TGATTTCCTTTTGT
18379589 TGATT
1 TGATT
18379594 AAATGACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.67
Consensus pattern (14 bp):
TGATTTCCTTTTGT
Found at i:18384052 original size:16 final size:16
Alignment explanation
Indices: 18384031--18384069 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18384021 TATGAATGTT
*
18384031 TTTGAATGATTTTTGA
1 TTTGAATGATATTTGA
*
18384047 TTTGAATGGTATTTGA
1 TTTGAATGATATTTGA
18384063 TTATGAA
1 TT-TGAA
18384070 ATGTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTGAATGATATTTGA
Found at i:18385169 original size:13 final size:13
Alignment explanation
Indices: 18385121--18385172 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
18385111 CTTAGGACAT
*
18385121 GGCCGTGTGGCCA
1 GGCCGTGGGGCCA
*
18385134 GCCCGTGGGGTTCCCA
1 GGCCGTGGGG---CCA
18385150 TGGCCGTGGGGCCA
1 -GGCCGTGGGGCCA
18385164 GGCCGTGGG
1 GGCCGTGGG
18385173 CAGATCTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 17 0.53
14 3 0.09
16 3 0.09
17 9 0.28
ACGTcount: A:0.06, C:0.31, G:0.48, T:0.15
Consensus pattern (13 bp):
GGCCGTGGGGCCA
Found at i:18386909 original size:16 final size:15
Alignment explanation
Indices: 18386877--18386911 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18386867 AAACCCTATT
18386877 TTTCCTTTATTTTTC
1 TTTCCTTTATTTTTC
*
18386892 TTTCCTTTTTTCTTTC
1 TTTCCTTTATT-TTTC
18386908 TTTC
1 TTTC
18386912 TTTCCTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCCTTTATTTTTC
Found at i:18387001 original size:8 final size:8
Alignment explanation
Indices: 18386952--18387014 Score: 56
Period size: 8 Copynumber: 7.9 Consensus size: 8
18386942 TCCTTGTTCT
*
18386952 TTATTATT
1 TTATTATA
18386960 TTATTAT-
1 TTATTATA
* *
18386967 TTCTTTTA
1 TTATTATA
18386975 TTATTATA
1 TTATTATA
**
18386983 ACATATATA
1 TTAT-TATA
18386992 TTATTATA
1 TTATTATA
*
18387000 TTATTAAA
1 TTATTATA
18387008 TTATTAT
1 TTATTAT
18387015 TATTTACTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
7 5 0.12
8 32 0.74
9 6 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATTATA
Found at i:18393773 original size:6 final size:6
Alignment explanation
Indices: 18393757--18393809 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
18393747 ATGGAATTTT
* *
18393757 AAAT-A AAATAG AAATAG AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
18393804 AAATAA
1 AAATAA
18393810 TAGTAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 4 0.09
6 41 0.91
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:18395672 original size:6 final size:6
Alignment explanation
Indices: 18395661--18395687 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18395651 TAAGATACAC
18395661 AGAGGA AGAGGA AGAGGA AGAGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGA
18395688 CATTCACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:18436206 original size:31 final size:31
Alignment explanation
Indices: 18436171--18436233 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
18436161 TGTCAAAGGT
18436171 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
1 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
18436202 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
1 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
18436233 T
1 T
18436234 CTAACCCCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.21
Consensus pattern (31 bp):
TAGGAAACTTAAGCTAGAAAAATGAAATGCC
Found at i:18436326 original size:19 final size:19
Alignment explanation
Indices: 18436302--18436341 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
18436292 CTTTTGTCTC
*
18436302 ATCATACGATAACGTTTAA
1 ATCATACGATAACATTTAA
18436321 ATCATACGATAACATTTAA
1 ATCATACGATAACATTTAA
18436340 AT
1 AT
18436342 TTTAGTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (19 bp):
ATCATACGATAACATTTAA
Found at i:18437883 original size:6 final size:7
Alignment explanation
Indices: 18437866--18437896 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
18437856 TACTTTAGCC
18437866 TTTTTTA
1 TTTTTTA
18437873 TTTTTTA
1 TTTTTTA
18437880 TTTTTTTA
1 -TTTTTTA
18437888 TTTTTTA
1 TTTTTTA
18437895 TT
1 TT
18437897 ACATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:18437886 original size:15 final size:15
Alignment explanation
Indices: 18437866--18437896 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18437856 TACTTTAGCC
18437866 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
18437881 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
18437896 T
1 T
18437897 ACATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:18445749 original size:15 final size:16
Alignment explanation
Indices: 18445717--18445749 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18445707 TCAAACACAC
*
18445717 TCCTTTTTTTTTCCTT
1 TCCTTTTTTTTTCATT
18445733 TCCTTTTTTTTT-ATT
1 TCCTTTTTTTTTCATT
18445748 TC
1 TC
18445750 TTTCCCCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TCCTTTTTTTTTCATT
Found at i:18446778 original size:28 final size:28
Alignment explanation
Indices: 18446712--18446868 Score: 215
Period size: 29 Copynumber: 5.5 Consensus size: 28
18446702 CATGAGATTG
* * **
18446712 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
18446741 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
18446769 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
*
18446798 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
18446827 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
18446855 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
18446869 GACTTACTAT
Statistics
Matches: 118, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
28 45 0.38
29 73 0.62
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:18446801 original size:57 final size:58
Alignment explanation
Indices: 18446712--18446867 Score: 219
Period size: 57 Copynumber: 2.7 Consensus size: 58
18446702 CATGAGATTG
* * * *
18446712 GCACTAAGTGTGCGGGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATAT-A
1 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCAAGTTTGATTATATAA
* *
18446769 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATAA
*
18446827 GCACTAAGTGTGCGAGTTTGATTATATAA-CACTAAGTGTGC
1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGC
18446868 GGACTTACTA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 58 0.64
58 32 0.36
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATAA
Found at i:18450422 original size:4 final size:4
Alignment explanation
Indices: 18450413--18450459 Score: 67
Period size: 4 Copynumber: 11.2 Consensus size: 4
18450403 TTTCTTGTAC
*
18450413 ATAA ATAA ATAA ATAA ATAAA ATTAA AAAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA AT-AA A-TAA ATAA ATAA ATAA ATAA ATAA A
18450460 GGATCAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 32 0.82
5 6 0.15
6 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:18450439 original size:22 final size:22
Alignment explanation
Indices: 18450414--18450455 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18450404 TTCTTGTACA
*
18450414 TAAATAAATAAATAAATAAAAT
1 TAAAAAAATAAATAAATAAAAT
18450436 TAAAAAAATAAATAAATAAA
1 TAAAAAAATAAATAAATAAA
18450456 TAAAGGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAAAATAAATAAATAAAAT
Found at i:18451030 original size:6 final size:6
Alignment explanation
Indices: 18450997--18451023 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18450987 AGGTTATAAG
18450997 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
18451024 TGTTTTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:18475552 original size:18 final size:19
Alignment explanation
Indices: 18475517--18475552 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18475507 TTTCAAACCA
*
18475517 CCAATATCAAAAAGCATAT
1 CCAACATCAAAAAGCATAT
18475536 CCAACATCAAAAA-CATA
1 CCAACATCAAAAAGCATA
18475553 GAGATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (19 bp):
CCAACATCAAAAAGCATAT
Found at i:18476366 original size:14 final size:14
Alignment explanation
Indices: 18476347--18476373 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18476337 AATATAATTA
18476347 TTACTATTATTATT
1 TTACTATTATTATT
18476361 TTACTATTATTAT
1 TTACTATTATTAT
18476374 CTAATATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTACTATTATTATT
Found at i:18476445 original size:3 final size:3
Alignment explanation
Indices: 18476431--18476688 Score: 92
Period size: 3 Copynumber: 85.3 Consensus size: 3
18476421 TTAACGTGTC
* * * ** *
18476431 ATT ATT ACT ATT ATT TTT ATT TTT ATT ACC ATT ATT ATT ATC A-T ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * *
18476479 -GT ATT -TAT ATT -TT TTT ATT -TT AAT ATT ATT ATT ATT ACT ACTT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
18476522 CCATT ATT -TT -TT ATT -TCT AACT ATT ATT ATT TTT ATGT ATAT ATT
1 --ATT ATT ATT ATT ATT AT-T -ATT ATT ATT ATT ATT AT-T AT-T ATT
* * * *
18476567 ATT AATT A-T ATT ATT GTT ATT ATT ACT ATT ATT AAAT ATT CTT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * * *
18476613 ATT ACT ATT ATT -TT CATT CCTT -TT ATT ATT GTTT ATT ATC ATT -GT
1 ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT -ATT ATT ATT ATT ATT
*
18476658 ATT ATT ATT ATT ACTT -CT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A
18476689 CTTTCTTTGT
Statistics
Matches: 187, Mismatches: 43, Indels: 50
0.67 0.15 0.18
Matches are distributed among these distances:
2 20 0.11
3 140 0.75
4 24 0.13
5 2 0.01
6 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:18480944 original size:2 final size:2
Alignment explanation
Indices: 18480939--18480967 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18480929 TTCTCTCTTT
18480939 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18480968 ATACTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18481232 original size:5 final size:5
Alignment explanation
Indices: 18481222--18481248 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18481212 ATAAATATTC
18481222 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
18481249 TTTAAAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:18485880 original size:17 final size:18
Alignment explanation
Indices: 18485841--18485881 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
18485831 TTTCAAATAT
* *
18485841 GATTGTTTTTTCGTGTAC
1 GATTGTTTTTTCATGCAC
18485859 GATTGTTTTTTCATGCAC
1 GATTGTTTTTTCATGCAC
18485877 -ATTGT
1 GATTGT
18485882 GCGTATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.54
Consensus pattern (18 bp):
GATTGTTTTTTCATGCAC
Found at i:18487694 original size:24 final size:26
Alignment explanation
Indices: 18487658--18487720 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
18487648 ATATACTTTT
18487658 TATTAT-ATATTTTATTATA-TAAATA
1 TATTATAAT-TTTTATTATATTAAATA
* *
18487683 TATT-TAATTTTTTTTATATTATATA
1 TATTATAATTTTTATTATATTAAATA
18487708 TATTAATAATTTT
1 TATT-ATAATTTT
18487721 ACCATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 10 0.31
25 15 0.47
27 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTATAATTTTTATTATATTAAATA
Found at i:18487717 original size:27 final size:24
Alignment explanation
Indices: 18487667--18487720 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
18487657 TTATTATATA
18487667 TTTTATTATATAAATATATTTAAT
1 TTTTATTATATAAATATATTTAAT
* *
18487691 TTTTTTTATATTATATATATTAATAAT
1 TTTTATTATA-TAAATATATT--TAAT
18487718 TTT
1 TTT
18487721 ACCATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 9 0.36
27 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTATTATATAAATATATTTAAT
Found at i:18487761 original size:11 final size:11
Alignment explanation
Indices: 18487745--18487801 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
18487735 TGCAAAATAC
18487745 TTATTATATTA
1 TTATTATATTA
*
18487756 TTATTATTTTA
1 TTATTATATTA
18487767 -TATTATATT-
1 TTATTATATTA
18487776 TCT-TTATATT-
1 T-TATTATATTA
*
18487786 TTAGTCATATTA
1 TTA-TTATATTA
18487798 TTAT
1 TTAT
18487802 ACATAACTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 1 0.03
10 16 0.42
11 18 0.47
12 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTATATTA
Found at i:18487769 original size:16 final size:15
Alignment explanation
Indices: 18487748--18487785 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
18487738 AAAATACTTA
18487748 TTATATTATTATTAT-T
1 TTATATTA-TATT-TCT
18487764 TTATATTATATTTCT
1 TTATATTATATTTCT
18487779 TTATATT
1 TTATATT
18487786 TTAGTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 8 0.38
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATATTATATTTCT
Done.