Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015373.1 Kokia drynarioides strain JFW-HI SEQ_130420, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 603110
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 225 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:308731 original size:15 final size:15
Alignment explanation
Indices: 308711--308741 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
308701 ATATATTGCA
308711 AAAAATAATAAAAAT
1 AAAAATAATAAAAAT
*
308726 AAAAATAATTAAAAT
1 AAAAATAATAAAAAT
308741 A
1 A
308742 TTATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAATAAAAAT
Found at i:308887 original size:15 final size:16
Alignment explanation
Indices: 308841--308888 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
308831 CTAAAAGAAG
308841 TATTTTATTATTTTTTTA
1 TATTTTATTA--TTTTTA
*
308859 TATTTTATAGATTTTTA
1 TATTTTAT-TATTTTTA
308876 T-TTTTATTATTTT
1 TATTTTATTATTTT
308889 GTTACATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.19
16 6 0.22
17 7 0.26
18 8 0.30
19 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (16 bp):
TATTTTATTATTTTTA
Found at i:308982 original size:28 final size:29
Alignment explanation
Indices: 308946--309029 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
308936 TTGTTAAAGT
* * *
308946 TAAAGATTTAAT-TTTTTTTATTATTTTAA
1 TAAA-ATTTAATAATTTTTAATAATTTTAA
* *
308975 TAAAATTTTATAATTTTTAATAATTTTAT
1 TAAAATTTAATAATTTTTAATAATTTTAA
* *
309004 TAAAATGTAATAATTTGT-ATAATTTT
1 TAAAATTTAATAATTTTTAATAATTTT
309030 TATTGATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 14 0.30
29 32 0.70
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (29 bp):
TAAAATTTAATAATTTTTAATAATTTTAA
Found at i:308985 original size:19 final size:18
Alignment explanation
Indices: 308961--309053 Score: 57
Period size: 19 Copynumber: 5.1 Consensus size: 18
308951 ATTTAATTTT
308961 TTTTATTA-TTTTAATAAAA
1 TTTTATTATTTTTAAT--AA
*
308980 TTTTATAATTTTTAATAA
1 TTTTATTATTTTTAATAA
** *
308998 TTTTATTAAAATGTAATAA
1 TTTTATT-ATTTTTAATAA
* * *
309017 TTTGTATAATTTTTATTGA
1 TTT-TATTATTTTTAATAA
*
309036 -TTT-TTATTTTTTATAA
1 TTTTATTATTTTTAATAA
309052 TT
1 TT
309054 CTTTTGTCAC
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
16 9 0.16
17 2 0.04
18 10 0.18
19 24 0.44
20 10 0.18
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATTATTTTTAATAA
Found at i:311959 original size:22 final size:22
Alignment explanation
Indices: 311929--311979 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
311919 GAACTCACAA
*
311929 CTTGTAATCTCAAACCCTTGAAC
1 CTTG-AATCTCAAACCCTTAAAC
* *
311952 CTTGAATCTCGAACTCTTAAAC
1 CTTGAATCTCAAACCCTTAAAC
*
311974 ATTGAA
1 CTTGAA
311980 CCTAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (22 bp):
CTTGAATCTCAAACCCTTAAAC
Found at i:312207 original size:20 final size:21
Alignment explanation
Indices: 312182--312226 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
312172 TGGGGTTTAA
*
312182 AGTTCAAAGTTTAAA-TTTTG
1 AGTTCAAAGTTCAAAGTTTTG
*
312202 AGTTCAAGGTTCAAAGTTTTG
1 AGTTCAAAGTTCAAAGTTTTG
312223 AGTT
1 AGTT
312227 TGAGGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTTCAAAGTTCAAAGTTTTG
Found at i:312213 original size:27 final size:28
Alignment explanation
Indices: 312169--312239 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 28
312159 AAACCTTGAG
* * *
312169 GTTTGGGGTTTAAAGTTCAAAGTTTAAA
1 GTTTGAGGTTCAAGGTTCAAAGTTTAAA
* **
312197 TTTTGA-GTTCAAGGTTCAAAGTTTTGA
1 GTTTGAGGTTCAAGGTTCAAAGTTTAAA
312224 GTTTGAGGTTCAAGGT
1 GTTTGAGGTTCAAGGT
312240 AAAATAATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.63
28 13 0.37
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.41
Consensus pattern (28 bp):
GTTTGAGGTTCAAGGTTCAAAGTTTAAA
Found at i:312223 original size:21 final size:20
Alignment explanation
Indices: 312182--312236 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
312172 TGGGGTTTAA
* *
312182 AGTTCAAAGTTTAAATTTTG
1 AGTTCAAGGTTCAAATTTTG
312202 AGTTCAAGGTTCAAAGTTTTG
1 AGTTCAAGGTTCAAA-TTTTG
**
312223 AGTTTGAGGTTCAA
1 AGTTCAAGGTTCAA
312237 GGTAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (20 bp):
AGTTCAAGGTTCAAATTTTG
Found at i:315819 original size:45 final size:44
Alignment explanation
Indices: 315768--315855 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
315758 CACCCCAACC
*
315768 TCTAAGTAAAGTTTTTAGTTTTGTGAACCTCAAAAATAAGTGTTT
1 TCTAAGTAAAGTTTTGAGTTTTGTGAACCTCAAAAATAA-TGTTT
* * *
315813 TCTAAGTAAAGTTTTGAGTTTTGTGGACCTGAAATATAATGTT
1 TCTAAGTAAAGTTTTGAGTTTTGTGAACCTCAAAAATAATGTT
315856 AGAAAAGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.10
45 35 0.90
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (44 bp):
TCTAAGTAAAGTTTTGAGTTTTGTGAACCTCAAAAATAATGTTT
Found at i:320664 original size:12 final size:11
Alignment explanation
Indices: 320641--320676 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
320631 ATTTTTATAA
320641 TTTTATAATTT
1 TTTTATAATTT
320652 TTTTATAAATTT
1 TTTTAT-AATTT
320664 TGTTTATAATTT
1 T-TTTATAATTT
320676 T
1 T
320677 ATGATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.26
12 12 0.52
13 5 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:321540 original size:12 final size:12
Alignment explanation
Indices: 321525--321550 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
321515 AGAAAAAAGT
321525 TGAAAATTTTGG
1 TGAAAATTTTGG
321537 TGAAAATTTTGG
1 TGAAAATTTTGG
321549 TG
1 TG
321551 CAAGTGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (12 bp):
TGAAAATTTTGG
Found at i:323206 original size:43 final size:43
Alignment explanation
Indices: 323145--323236 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
323135 ATCTAACTCA
323145 CAAACTCCTACCAATATAAGAATTTCAGTCATGGCAACCCTCC
1 CAAACTCCTACCAATATAAGAATTTCAGTCATGGCAACCCTCC
*
323188 CAAACTCCTACCAATATAAGAATTTCAGTCATGGCAACTCTCC
1 CAAACTCCTACCAATATAAGAATTTCAGTCATGGCAACCCTCC
323231 CAAACT
1 CAAACT
323237 TTCACCATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.24
Consensus pattern (43 bp):
CAAACTCCTACCAATATAAGAATTTCAGTCATGGCAACCCTCC
Found at i:326022 original size:68 final size:66
Alignment explanation
Indices: 325945--326139 Score: 213
Period size: 68 Copynumber: 3.0 Consensus size: 66
325935 TAATTTTAAT
* *
325945 TTTAATATTAAAATTAATTTAATAGTTATCTTGATAATATTTTATTAATTTAATATTAAAGTGAT
1 TTTAATATTAAATTTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATTAAA-TGAT
326010 TA
65 TA
* * ** * *
326012 TCTTAATATTAAATTTAATTTAATATTTATATT-ATTGATAAGTGATTTA-TTAAT-TT-AAT-A
1 T-TTAATATTAAATTTAATTTAATATTTATCTTGA-TAATATTTTATTAATTTAATATTAAATGA
326072 -TA
64 TTA
* *
326074 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTGTATTAATTTAATATTAAAATGA
1 TTTAATATTAAATTTAATTTAATATTTATCTTGATAA-TATTTTATTAATTTAATATT-AAATGA
326139 T
64 T
326140 AAAGTTTAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
61 31 0.30
62 10 0.10
63 6 0.06
64 3 0.03
65 2 0.02
66 5 0.05
67 8 0.08
68 37 0.36
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (66 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATTAAATGATT
A
Found at i:326079 original size:61 final size:58
Alignment explanation
Indices: 326014--326130 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 58
326004 AGTGATTATC
*
326014 TTAATATTAAATTTAATTTAATATTTATATTATTGATAAGTGATT-TATTAATTTAATATAT
1 TTAATATTAAATTTAATCTAATA-TT-TA-TATTGATAAGT-ATTGTATTAATTTAATATAT
*
326075 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTGTATTAATTTAATAT
1 TTAATATTAAATTTAATCTAATATTTATATTGATAAGTATTGTATTAATTTAATAT
326131 TAAAATGATA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
57 3 0.06
58 24 0.45
59 2 0.04
60 2 0.04
61 22 0.42
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (58 bp):
TTAATATTAAATTTAATCTAATATTTATATTGATAAGTATTGTATTAATTTAATATAT
Found at i:332448 original size:27 final size:26
Alignment explanation
Indices: 332397--332449 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
332387 TGATTGTTTT
332397 ATTATATTTTTAATAAAATGGTTTAAA
1 ATTATATTTTTAATAAAAT-GTTTAAA
*
332424 ATTATATTATTTAGATGAAAT-TTTAA
1 ATTATATT-TTTA-ATAAAATGTTTAA
332450 TTATACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 13 0.57
28 4 0.17
29 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
ATTATATTTTTAATAAAATGTTTAAA
Found at i:335789 original size:17 final size:17
Alignment explanation
Indices: 335760--335793 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
335750 AATAAATTTT
335760 AAAACCAACCCAAAACC
1 AAAACCAACCCAAAACC
335777 AAAACACAA-CCAAAACC
1 AAAAC-CAACCCAAAACC
335794 CAATTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAACCAACCCAAAACC
Found at i:338257 original size:23 final size:23
Alignment explanation
Indices: 338229--338276 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
338219 GGGAGTACAC
338229 TTTGCCCAATCTTTTTCCATTCT
1 TTTGCCCAATCTTTTTCCATTCT
338252 TTTGCCCAATCTTTTTCCATTCT
1 TTTGCCCAATCTTTTTCCATTCT
338275 TT
1 TT
338277 ACATTTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.29, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTGCCCAATCTTTTTCCATTCT
Found at i:338266 original size:12 final size:12
Alignment explanation
Indices: 338229--338266 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
338219 GGGAGTACAC
338229 TTTGCCCAATCT
1 TTTGCCCAATCT
* *
338241 TTT-TCCATTCT
1 TTTGCCCAATCT
338252 TTTGCCCAATCT
1 TTTGCCCAATCT
338264 TTT
1 TTT
338267 TCCATTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.13, C:0.29, G:0.05, T:0.53
Consensus pattern (12 bp):
TTTGCCCAATCT
Found at i:349674 original size:19 final size:19
Alignment explanation
Indices: 349632--349675 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
349622 CAAAGGTTTT
**
349632 TTTTCAATATATTAATATTT
1 TTTT-AATATATTAATATGA
349652 TTTTAATATATTAATATGA
1 TTTTAATATATTAATATGA
349671 TTTTA
1 TTTTA
349676 TGATAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTAATATATTAATATGA
Found at i:349674 original size:21 final size:20
Alignment explanation
Indices: 349629--349668 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
349619 TTACAAAGGT
349629 TTTTTTTCAATATATTAATA
1 TTTTTTTCAATATATTAATA
349649 TTTTTTT-AATATATTAATA
1 TTTTTTTCAATATATTAATA
349668 T
1 T
349669 GATTTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTCAATATATTAATA
Found at i:350257 original size:22 final size:23
Alignment explanation
Indices: 350226--350268 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
350216 AATCTTAATT
*
350226 TTTATAAAATATAAAAAAAAATG
1 TTTATAAAATACAAAAAAAAATG
*
350249 TTTA-AAAATCCAAAAAAAAA
1 TTTATAAAATACAAAAAAAAA
350269 ATTCTTACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (23 bp):
TTTATAAAATACAAAAAAAAATG
Found at i:350718 original size:13 final size:13
Alignment explanation
Indices: 350700--350726 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
350690 ATTTTGGGGG
350700 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
350713 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
350726 A
1 A
350727 CATTCATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:353992 original size:15 final size:17
Alignment explanation
Indices: 353973--354047 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 17
353963 CATGATTACA
353973 ATTATTTTTTTATT-TT
1 ATTATTTTTTTATTGTT
*
353989 -TTATTTTTTTGTTGTT
1 ATTATTTTTTTATTGTT
**
354005 ATTATTTTTTAGTATCATT
1 ATTATTTTTT--TATTGTT
*
354024 GATTAATTTTATTATTGTT
1 -ATT-ATTTTTTTATTGTT
354043 ATTAT
1 ATTAT
354048 CATGATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.26
16 2 0.04
17 11 0.24
18 3 0.07
19 9 0.20
20 3 0.07
21 6 0.13
ACGTcount: A:0.21, C:0.01, G:0.07, T:0.71
Consensus pattern (17 bp):
ATTATTTTTTTATTGTT
Found at i:354009 original size:3 final size:3
Alignment explanation
Indices: 354003--354137 Score: 59
Period size: 3 Copynumber: 46.3 Consensus size: 3
353993 TTTTTTGTTG
* * *
354003 TTA TTA TT- TT- TTA GTA TCA TTGA TTAA TT- TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TTA TTA TTA
* * * * *
354047 TCA TGA TAA TTA -TA TTA TTA TTT TTA TTA TCT- TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * * * * * *
354091 TTC TTG TT- TTA TTG TT- TTA TTA CTA GTA TTA TTA TTG TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
354137 T
1 T
354138 GAATTTACTA
Statistics
Matches: 99, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
2 13 0.13
3 79 0.80
4 7 0.07
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:354035 original size:29 final size:27
Alignment explanation
Indices: 354003--354070 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
353993 TTTTTTGTTG
354003 TTATTATTTTTTAGTATCATTGATTAATT
1 TTATTATTTTTTAGTATCA-TGA-TAATT
* *
354032 TTATTA-TTGTTATTATCATGATAATT
1 TTATTATTTTTTAGTATCATGATAATT
*
354058 ATATTATTATTTT
1 TTATTATT-TTTT
354071 TATTATCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 10 0.30
27 4 0.12
28 13 0.39
29 6 0.18
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (27 bp):
TTATTATTTTTTAGTATCATGATAATT
Found at i:354073 original size:26 final size:27
Alignment explanation
Indices: 354004--354073 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 27
353994 TTTTTGTTGT
*
354004 TATTATTTTTTAGTATCATTGATTAATTT
1 TATTATTTTTT--TATCATTGATTAATTA
*
354033 TATTATTGTTATTATCA-TGA-TAATTA
1 TATTATT-TTTTTATCATTGATTAATTA
354059 TATTATTATTTTTAT
1 TATTATT-TTTTTAT
354074 TATCTTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 18 0.50
27 3 0.08
28 5 0.14
29 7 0.19
30 3 0.08
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (27 bp):
TATTATTTTTTTATCATTGATTAATTA
Found at i:354074 original size:29 final size:28
Alignment explanation
Indices: 354003--354089 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 28
353993 TTTTTTGTTG
*
354003 TTATTATTTTTTAGTATCATTGATTAA-T-T
1 TTATTA-TTTTTATTATCA-TGA-TAATTAT
*
354032 TTATTATTGTTATTATCATGATAATTAT
1 TTATTATTTTTATTATCATGATAATTAT
* *
354060 ATTATTATTTTTATTATCTTTATAATTAT
1 -TTATTATTTTTATTATCATGATAATTAT
354089 T
1 T
354090 ATTCTTGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.06
27 4 0.08
28 12 0.24
29 31 0.62
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (28 bp):
TTATTATTTTTATTATCATGATAATTAT
Found at i:354100 original size:29 final size:29
Alignment explanation
Indices: 354004--354103 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
353994 TTTTTGTTGT
* *
354004 TATTATT--TTTTAGTATCATTGATTAATTT
1 TATTATTAGTTTTATTATCA-TGA-TAATTA
354033 TATTATT-G--TTATTATCATGATAATTA
1 TATTATTAGTTTTATTATCATGATAATTA
* * *
354059 TATTATTATTTTTATTATCTTTATAATTA
1 TATTATTAGTTTTATTATCATGATAATTA
*
354088 TTATTCTT-GTTTTATT
1 -TATTATTAGTTTTATT
354104 GTTTTATTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 12 0.20
27 3 0.05
28 8 0.14
29 30 0.51
30 6 0.10
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (29 bp):
TATTATTAGTTTTATTATCATGATAATTA
Found at i:356188 original size:20 final size:20
Alignment explanation
Indices: 356163--356205 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
356153 TTGTTAATGA
356163 AAGATTAAGTCAATATAATT
1 AAGATTAAGTCAATATAATT
* *
356183 AAGATTAAGTTAATTTAATT
1 AAGATTAAGTCAATATAATT
356203 AAG
1 AAG
356206 CAATTAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (20 bp):
AAGATTAAGTCAATATAATT
Found at i:369952 original size:53 final size:52
Alignment explanation
Indices: 369872--370063 Score: 280
Period size: 53 Copynumber: 3.7 Consensus size: 52
369862 CATAAATGCG
*
369872 AAAGGTCCGATGACTCTGTATCATCTTGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTAC-GATT
* * * *
369925 AAAGGTCCGATGACTTTGTGTCATCTTGAGTTATATAAATCCTATTACAGATT
1 AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTAC-GATT
369978 AAAGGTCCGATGACTC--TATCATCGTGAGTTATATGAATCCTATTACGAGTT
1 AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTACGA-TT
*
370029 AAAGGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 AAA-GGTCCGATGACTCTGTATCATCGTGAGTTAT
370064 CAAACGTGAA
Statistics
Matches: 126, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 32 0.25
52 13 0.10
53 64 0.51
54 15 0.12
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (52 bp):
AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTACGATT
Found at i:373338 original size:20 final size:20
Alignment explanation
Indices: 373306--373365 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
373296 AATTTGAAGT
*
373306 GTTAAAATGATTTTAACTTG
1 GTTAAAATTATTTTAACTTG
* * *
373326 GTTCAAATTATTTTGACTTA
1 GTTAAAATTATTTTAACTTG
* *
373346 TTTAAAATTATTTAAACTTG
1 GTTAAAATTATTTTAACTTG
373366 ATTTTAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (20 bp):
GTTAAAATTATTTTAACTTG
Found at i:376308 original size:7 final size:7
Alignment explanation
Indices: 376296--376326 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
376286 TAATTTACAA
376296 TGCCCAC
1 TGCCCAC
376303 TGCCCAC
1 TGCCCAC
376310 TGCCCAC
1 TGCCCAC
376317 TGCCCAC
1 TGCCCAC
376324 TGC
1 TGC
376327 TTCATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.55, G:0.16, T:0.16
Consensus pattern (7 bp):
TGCCCAC
Found at i:379025 original size:4 final size:4
Alignment explanation
Indices: 379016--379045 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
379006 TCGTAACAAC
379016 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
379046 AACTAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:379273 original size:2 final size:2
Alignment explanation
Indices: 379266--379290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
379256 ACCACCAAAT
379266 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
379291 AATGGAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:389417 original size:25 final size:22
Alignment explanation
Indices: 389378--389423 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
389368 TGTATATAAA
*
389378 AAAATATCTCTAGAGATTTTTT
1 AAAATATCTCTAGAGAATTTTT
389400 AAAATAATCTCTTCAGAGAATTTT
1 AAAAT-ATCTC-T-AGAGAATTTT
389424 CTCTCTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 5 0.25
24 1 0.05
25 9 0.45
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (22 bp):
AAAATATCTCTAGAGAATTTTT
Found at i:392478 original size:52 final size:52
Alignment explanation
Indices: 392409--392648 Score: 167
Period size: 52 Copynumber: 4.6 Consensus size: 52
392399 AAAAGGGGTT
*
392409 CGATGATTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATGAAAAGGTC
1 CGATGAATAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATGAAAAGGTC
* * * * **
392461 CGATGAATAAGTTTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTC
1 CGATGAATAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATGAAAAGGTC
* * * * * ** * * *
392513 GGATGACTAAGTGTCGTCGTGAGCATATGGGTCCTTTACA-AATTAAGAGGTC
1 CGATGAATAAGTGTCATCGTGAGTAAATGAATCCTTTA-AGGATGAAAAGGTC
* ** * * * *** * *
392565 CGATGACTCTGTGTCATCGTGAGTATACGAATCCCTCGTGGATTATAAGGTC
1 CGATGAATAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATGAAAAGGTC
* ** * *
392617 CGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 CGATGAATAAGTGTCATCGTGAGTAAATGAAT
392649 GAAGTGAAAT
Statistics
Matches: 150, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
52 150 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (52 bp):
CGATGAATAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATGAAAAGGTC
Found at i:392590 original size:104 final size:104
Alignment explanation
Indices: 392416--392645 Score: 248
Period size: 104 Copynumber: 2.2 Consensus size: 104
392406 GTTCGATGAT
* * ** * * * *
392416 TAAGTGTCATCGTGAGTAAATGAATCCTTTA-AGGATGAAAAGGTCCGATGAATAAGTTTCATCG
1 TAAGTGTCATCGTGAGCATATGGGTCCTTTACA-AATTAAGAGGTCCGATGAATAAGTGTCATCG
* * * *
392480 TGAGTATATGAATCCTTTATGGATTATGAGGT-CGGATGAC
65 TGAGTATACGAATCCCTCATGGATTATAAGGTCCGG-TGAC
* * **
392520 TAAGTGTCGTCGTGAGCATATGGGTCCTTTACAAATTAAGAGGTCCGATGACTCTGTGTCATCGT
1 TAAGTGTCATCGTGAGCATATGGGTCCTTTACAAATTAAGAGGTCCGATGAATAAGTGTCATCGT
* *
392585 GAGTATACGAATCCCTCGTGGATTATAAGGTCCGGTGGC
66 GAGTATACGAATCCCTCATGGATTATAAGGTCCGGTGAC
* *
392624 TATGTGTCATCGTGAGTATATG
1 TAAGTGTCATCGTGAGCATATG
392646 AATGAAGTGA
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
104 99 0.96
105 4 0.04
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (104 bp):
TAAGTGTCATCGTGAGCATATGGGTCCTTTACAAATTAAGAGGTCCGATGAATAAGTGTCATCGT
GAGTATACGAATCCCTCATGGATTATAAGGTCCGGTGAC
Found at i:399799 original size:52 final size:52
Alignment explanation
Indices: 399599--399788 Score: 245
Period size: 52 Copynumber: 3.7 Consensus size: 52
399589 AAAAGGGGTT
* * * * *
399599 CGATGATTAAGTGTCATCGTGAGTAAATGAATCATTTACGGATAAAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTC
* * *
399651 CGATGAATAAGTTTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTC
* * * *
399703 GGATGACTAAGTGTCGTCGTGAGTATATGGATCCTTTACAGATTAAGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTC
** *
399755 CGATGACTCTGTGTCATCGTGAGTATACGAATCC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCC
399789 CTCGTGGATT
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (52 bp):
CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTC
Found at i:399806 original size:52 final size:52
Alignment explanation
Indices: 399599--399838 Score: 241
Period size: 52 Copynumber: 4.6 Consensus size: 52
399589 AAAAGGGGTT
* * * * *
399599 CGATGATTAAGTGTCATCGTGAGTAAATGAATCATTTACGGATAAAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTC
* * *
399651 CGATGAATAAGTTTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTC
* * * *
399703 GGATGACTAAGTGTCGTCGTGAGTATATGGATCCTTTACAGATTA-AGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA-AGGTC
** * * ***
399755 CGATGACTCTGTGTCATCGTGAGTATACGAATCCCTCGTGGATTATAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTC
* * * *
399807 CGGTGGCTATA-TGTTATCGTGAGTGTATGAAT
1 CGATGACTA-AGTGTCATCGTGAGTATATGAAT
399839 GAAGTGAAAT
Statistics
Matches: 153, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
52 152 0.99
53 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (52 bp):
CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTC
Found at i:401286 original size:15 final size:15
Alignment explanation
Indices: 401251--401286 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
401241 ATAATCATTT
*
401251 AAAGTAGATGAGTTA
1 AAAGTTGATGAGTTA
401266 AAAGTTGATGAGTTA
1 AAAGTTGATGAGTTA
401281 AAAGTT
1 AAAGTT
401287 ATCTTTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (15 bp):
AAAGTTGATGAGTTA
Found at i:402513 original size:20 final size:20
Alignment explanation
Indices: 402490--402531 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
402480 AGAAACATAC
402490 TTGTATCAGTAGAACTGAAG
1 TTGTATCAGTAGAACTGAAG
* *
402510 TTGTATCGGTAGAAGTGAAG
1 TTGTATCAGTAGAACTGAAG
402530 TT
1 TT
402532 CTACTGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (20 bp):
TTGTATCAGTAGAACTGAAG
Found at i:406866 original size:3 final size:3
Alignment explanation
Indices: 406858--406889 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
406848 TCTTTCATCC
406858 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
406890 CTTTTCTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:409517 original size:21 final size:21
Alignment explanation
Indices: 409493--409536 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
409483 TTCTCTTCAA
*
409493 ATTTTGTTTT-AGATTATATCT
1 ATTTT-TTTTAAGATAATATCT
409514 ATTTTTTTTGAAGATAATATCT
1 ATTTTTTTT-AAGATAATATCT
409536 A
1 A
409537 GAACTACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (21 bp):
ATTTTTTTTAAGATAATATCT
Found at i:411327 original size:30 final size:30
Alignment explanation
Indices: 411266--411329 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
411256 ATATTATCGA
*
411266 TTTTAACAATCCAATGATTTAAATTAAAAC
1 TTTTAACAATCCAATGATCTAAATTAAAAC
* **
411296 TTTTGAACAATTCAATG-TCTAAATTGTAAC
1 TTTT-AACAATCCAATGATCTAAATTAAAAC
411326 TTTT
1 TTTT
411330 CAATTAAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (30 bp):
TTTTAACAATCCAATGATCTAAATTAAAAC
Found at i:417086 original size:52 final size:52
Alignment explanation
Indices: 417008--417114 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
416998 GACGACATAA
*
417008 TACTGTTTTTTAGTATTTGAATCAAATGCTCACTTTGATTCTTTTATGGGAT
1 TACTGTTTTTTAGTATTTGAATCAAATGCTCACTTTGATTCTTTTACGGGAT
417060 TACTGTTTTTTAGTATTTGAATCAAATGCTCACTTTGATTCTTTTACGGGAT
1 TACTGTTTTTTAGTATTTGAATCAAATGCTCACTTTGATTCTTTTACGGGAT
417112 TAC
1 TAC
417115 AGACTCATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (52 bp):
TACTGTTTTTTAGTATTTGAATCAAATGCTCACTTTGATTCTTTTACGGGAT
Found at i:423990 original size:28 final size:29
Alignment explanation
Indices: 423675--423990 Score: 273
Period size: 30 Copynumber: 10.8 Consensus size: 29
423665 CGAACTTCCA
* * * *
423675 AAAATCACATTTTGACTCTCGAACTTTTCA
1 AAAATCACATTTTAACCCT-AAACTTTTCT
* * * *
423705 AAAATCATATTTTGACCCTCAAACTTCTCA
1 AAAATCACATTTTAACCCT-AAACTTTTCT
* *
423735 AAAATCATATTTTAACTCCTAAACCTTTCT
1 AAAATCACATTTTAAC-CCTAAACTTTTCT
*
423765 AAAATCACATTTTGACCCCTAAACTTTTCT
1 AAAATCACATTTT-AACCCTAAACTTTTCT
*
423795 AAAATTACATTTTAACCCTCAAACTTTT-T
1 AAAATCACATTTTAACCCT-AAACTTTTCT
* * *
423824 AAAATCACATTTTCACCCCAAACTTCTCT
1 AAAATCACATTTTAACCCTAAACTTTTCT
* * *
423853 AAAATCACATTTTGACCACCAAAC-CTTCTT
1 AAAATCACATTTTAACC-CTAAACTTTTC-T
* * *
423883 AAAATCACA-TTTGACCCCAAACTTCTCT
1 AAAATCACATTTTAACCCTAAACTTTTCT
* * *
423911 AAAATCACATTTTAACCCCAAAC-TTCCC
1 AAAATCACATTTTAACCCTAAACTTTTCT
* * *
423939 AAAATTACATTTTATCCTTAAACTTTTC-
1 AAAATCACATTTTAACCCTAAACTTTTCT
* *
423967 AAAATTACATTTTAACCCTGAACT
1 AAAATCACATTTTAACCCTAAACT
423991 CTCCAAAACT
Statistics
Matches: 243, Mismatches: 34, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
28 65 0.27
29 65 0.27
30 108 0.44
31 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATCACATTTTAACCCTAAACTTTTCT
Found at i:423997 original size:28 final size:28
Alignment explanation
Indices: 423713--424007 Score: 148
Period size: 28 Copynumber: 10.2 Consensus size: 28
423703 CAAAAATCAT
* * * *
423713 ATTTTGACCCTCAAACTTCTCAAAAATCAT
1 ATTTTAACCCT-AAAC-TCTCCAAAATTAC
* * *
423743 ATTTTAACTCCTAAACCTTTCTAAAATCAC
1 ATTTTAAC-CCTAAA-CTCTCCAAAATTAC
* * *
423773 ATTTTGACCCCTAAACTTTTCTAAAATTAC
1 ATTTT-AACCCTAAAC-TCTCCAAAATTAC
* ** *
423803 ATTTTAACCCTCAAACTTTTTAAAATCAC
1 ATTTTAACCCT-AAACTCTCCAAAATTAC
* * * *
423832 ATTTTCACCCCAAACTTCTCTAAAATCAC
1 ATTTTAACCCTAAAC-TCTCCAAAATTAC
* * * *
423861 ATTTTGACCACCAAAC-CTTCTTAAAATCAC
1 ATTTTAACC-CTAAACTC-TC-CAAAATTAC
* * * *
423891 A-TTTGACCCCAAACTTCTCTAAAATCAC
1 ATTTTAACCCTAAAC-TCTCCAAAATTAC
*
423919 ATTTTAACCCCAAACT-TCCCAAAATTAC
1 ATTTTAACCCTAAACTCT-CCAAAATTAC
* * * *
423947 ATTTTATCCTTAAACTTTTCAAAATTAC
1 ATTTTAACCCTAAACTCTCCAAAATTAC
*
423975 ATTTTAACCCTGAACTCTCCAAAACTT-C
1 ATTTTAACCCTAAACTCTCCAAAA-TTAC
424003 ATTTT
1 ATTTT
424008 CGACCCCACT
Statistics
Matches: 224, Mismatches: 26, Indels: 32
0.79 0.09 0.11
Matches are distributed among these distances:
27 1 0.00
28 77 0.34
29 71 0.32
30 69 0.31
31 6 0.03
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (28 bp):
ATTTTAACCCTAAACTCTCCAAAATTAC
Found at i:423997 original size:56 final size:57
Alignment explanation
Indices: 423725--424007 Score: 159
Period size: 58 Copynumber: 4.9 Consensus size: 57
423715 TTTGACCCTC
* * * * * * * *
423725 AAACTTCTCAAAAATCATATTTTAACTCCTAAACCTTTCTAAAA-TCACATTTTGACCCCT
1 AAACTTCTCTAAAATCACATTTTAAC-CCCAAA-CTTCCCAAAACT-TCATTTT-ATCCTT
* * *** * **
423785 AAACTTTTCTAAAATTACATTTTAACCCTCAAACTTTTTAAAA-TCACATTTTCA-CCCC
1 AAACTTCTCTAAAATCACATTTTAACCC-CAAACTTCCCAAAACT-TCATTTT-ATCCTT
* ** * * **
423843 AAACTTCTCTAAAATCACATTTTGACCACCAAACCTTCTTAAAA-TCACATTTGA-CCCC
1 AAACTTCTCTAAAATCACATTTTAACC-CCAAA-CTTCCCAAAACT-TCATTTTATCCTT
423901 AAACTTCTCTAAAATCACATTTTAACCCCAAACTTCCCAAAA-TTACATTTTATCCTT
1 AAACTTCTCTAAAATCACATTTTAACCCCAAACTTCCCAAAACTT-CATTTTATCCTT
* * **
423958 AAACTTTTC-AAAATTACATTTTAACCCTGAAC-TCTCCAAAACTTCATTTT
1 AAACTTCTCTAAAATCACATTTTAACCCCAAACTTC-CCAAAACTTCATTTT
424008 CGACCCCACT
Statistics
Matches: 192, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
55 2 0.01
56 47 0.24
57 17 0.09
58 62 0.32
59 39 0.20
60 25 0.13
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.35
Consensus pattern (57 bp):
AAACTTCTCTAAAATCACATTTTAACCCCAAACTTCCCAAAACTTCATTTTATCCTT
Found at i:433363 original size:3 final size:3
Alignment explanation
Indices: 433355--433381 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
433345 TTATGATATT
433355 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
433382 AGGGATGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:435858 original size:78 final size:78
Alignment explanation
Indices: 435640--436036 Score: 397
Period size: 78 Copynumber: 5.1 Consensus size: 78
435630 AATCAAGAAG
* * * * ** ** *
435640 GGCAGATTTCAGCCATCCGATCTCTTACCCCGAGCCCGATACAAATCACCATCAGCCAATCTCTT
1 GGCAGATTGCAACCATCCGATCTTTTACCTCGAGCTTGGGACAGATCACCATCAGCCAATCTCTT
*
435705 ACCCCGAG-CTTA
66 ACCCCGAGCCTGA
* * * *
435717 GGGCAGATT-CAGCTATCCGATCTCTTACCCCGAGCTTGGGACAGATCACCATCAGCCAATCTCT
1 -GGCAGATTGCAACCATCCGATCTTTTACCTCGAGCTTGGGACAGATCACCATCAGCCAATCTCT
435781 TACCCCGAGCCTGA
65 TACCCCGAGCCTGA
* * ** * * *
435795 GGTAGATTGCAACTATCTAATCTTGTACCTCGAGCTTGAGG-CAAATCACCATCAGTCAATCTCT
1 GGCAGATTGCAACCATCCGATCTTTTACCTCGAGCTTG-GGACAGATCACCATCAGCCAATCTCT
* ** *
435859 TAACTAGAGCCTGG
65 TACCCCGAGCCTGA
* * **
435873 GGCAGATTGCAACCATCTGATCTTTTACCTTGAGCTTGGGACAGATCATTATCAGCCAATCTCTT
1 GGCAGATTGCAACCATCCGATCTTTTACCTCGAGCTTGGGACAGATCACCATCAGCCAATCTCTT
*
435938 ACCCCGAGCCTGG
66 ACCCCGAGCCTGA
* * * ** *
435951 GGTAGATTACAGCCATCCGATCTTTTACCTCGAGCCTAAGG-TAGATCACCATCAGCCAATCTCT
1 GGCAGATTGCAACCATCCGATCTTTTACCTCGAG-CTTGGGACAGATCACCATCAGCCAATCTCT
* *
436015 TACCTCGAGCTTGA
65 TACCCCGAGCCTGA
436029 GGCAGATT
1 GGCAGATT
436037 ACAGTAAGCC
Statistics
Matches: 268, Mismatches: 46, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
77 67 0.25
78 195 0.73
79 6 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (78 bp):
GGCAGATTGCAACCATCCGATCTTTTACCTCGAGCTTGGGACAGATCACCATCAGCCAATCTCTT
ACCCCGAGCCTGA
Found at i:436037 original size:78 final size:78
Alignment explanation
Indices: 435640--436116 Score: 396
Period size: 78 Copynumber: 6.1 Consensus size: 78
435630 AATCAAGAAG
* * * * ** *
435640 GGCAGATTTCAGCCATCCGATCTCTTACCCCGAGCCCGATACAAATCACCATCAGCCAATCTCTT
1 GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTT
*
435705 ACCCCGAG-CTTA
66 ACCCCGAGCCTGA
* * * *
435717 GGGCAGATT-CAGCTATCCGATCTCTTACCCCGAGCTTG-GGACAGATCACCATCAGCCAATCTC
1 -GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGG-CAGATCACCATCAGCCAATCTC
435780 TTACCCCGAGCCTGA
64 TTACCCCGAGCCTGA
* * * * ** * * * *
435795 GGTAGATTGCAACTATCTAATCTTGTACCTCGAGCTTGAGGCAAATCACCATCAGTCAATCTCTT
1 GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTT
* ** *
435860 AACTAGAGCCTGG
66 ACCCCGAGCCTGA
* * * * * **
435873 GGCAGATTGCAACCATCTGATCTTTTACCTTGAGCTTG-GGACAGATCATTATCAGCCAATCTCT
1 GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGG-CAGATCACCATCAGCCAATCTCT
*
435937 TACCCCGAGCCTGG
65 TACCCCGAGCCTGA
* * *
435951 GGTAGATTACAGCCATCCGATCTTTTACCTCGAGCCTAAGGTAGATCACCATCAGCCAATCTCTT
1 GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTT
* *
436016 ACCTCGAGCTTGA
66 ACCCCGAGCCTGA
** * * * *
436029 GGCAGATTACAGTAAGCCAATCTCTTACCTTGAGCCT-AGTGCAGATTGCAGCCATTC-G---AT
1 GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAG-GCAGA-T-CA-CCA-TCAGCCAAT
* *
436089 CTTTTACCTCGAGCCTGA
61 CTCTTACCCCGAGCCTGA
436107 GGCAGATTAC
1 GGCAGATTAC
436117 CATCAGCCAA
Statistics
Matches: 333, Mismatches: 55, Indels: 22
0.81 0.13 0.05
Matches are distributed among these distances:
77 68 0.20
78 252 0.76
79 5 0.02
80 2 0.01
81 4 0.01
82 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (78 bp):
GGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTT
ACCCCGAGCCTGA
Found at i:436047 original size:117 final size:117
Alignment explanation
Indices: 435693--436154 Score: 335
Period size: 117 Copynumber: 4.0 Consensus size: 117
435683 AATCACCATC
* * * * **
435693 AGCCAATCTCTTACCCCGAGCTTAGGGCAGATT-CAGCTATCCGATCTCTTACCCCGAG-CTTGG
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTAAG
* * *
435756 GACAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-GAGGTAGATTGCAACT-
66 G-CAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATTAC-AGTA
* * * * * * * * *
435809 ATCTAATCT-TGTACCTCGAG-CTTGAGGCA-AAT-CA-CCATCAGTCAATCTCTTAACTAGAGC
1 AGCCAATCTCT-TACCCCGAGCCTAG-GGCAGATTACAGCCATC---CGATCTTTTACCTCGAGC
** * * ** * *
435869 CTGGGGCAGATTGCAACCATCTG---ATCTTTTACCTTGAG-CTTGGGACAGA-T-CATTA
61 CTAAGGCAGA-T-C-ACCATCAGCCAATCTCTTACCCCGAGCCTAGGG-CAGATTACAGTA
* *
435924 TCAGCCAATCTCTTACCCCGAGCCTGGGGTAGATTACAGCCATCCGATCTTTTACCTCGAGCCTA
1 --AGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTA
* * *
435989 AGGTAGATCACCATCAGCCAATCTCTTACCTCGAG-CTTGAGGCAGATTACAGTA
64 AGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATTACAGTA
** * * * *
436043 AGCCAATCTCTTACCTTGAGCCTAGTGCAGATTGCAGCCATTCGATCTTTTACCTCGAGCCTGAG
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTAAG
*
436108 GCAGATTACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTA
66 GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTA
436155 TAACCATTCG
Statistics
Matches: 273, Mismatches: 47, Indels: 51
0.74 0.13 0.14
Matches are distributed among these distances:
114 13 0.05
115 9 0.03
116 25 0.09
117 189 0.69
118 18 0.07
119 7 0.03
120 12 0.04
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (117 bp):
AGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCTCGAGCCTAAG
GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGTA
Found at i:436074 original size:156 final size:154
Alignment explanation
Indices: 435643--436063 Score: 484
Period size: 156 Copynumber: 2.7 Consensus size: 154
435633 CAAGAAGGGC
* * * * **
435643 AGATTTCAGCCATCCGATCTCTTACCCCGAGCCCGATACAAATCACCATCAGCCAATCTCTTACC
1 AGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAAATCACCATCAGCCAATCTCTTACC
* **
435708 CCGAGCTT-AGGGCAGATTCAGCTATCCGATCTCTTACCCCGAGCTTGGGACAGATCACCATCAG
66 TCGAGCTTGA-GGCAGATTCAG-TATCCGATCTCTTACCTTGAGCTTGGGACAGATCACCATCAG
435772 CCAATCTCTTACCCCGAGCCTGAGGT
129 CCAATCTCTTACCCCGAGCCTGAGGT
* * * ** * * * *
435798 AGATTGCAACTATCTAATCTTGTACCTCGAGCTTGAGGCAAATCACCATCAGTCAATCTCTTAAC
1 AGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAAATCACCATCAGCCAATCTCTTACC
* * * ** * * **
435863 TAGAGCCTGGGGCAGATTGCAACCATCTGATCTTTTACCTTGAGCTTGGGACAGATCATTATCAG
66 TCGAGCTTGAGGCAGATT-C-AGTATCCGATCTCTTACCTTGAGCTTGGGACAGATCACCATCAG
*
435928 CCAATCTCTTACCCCGAGCCTGGGGT
129 CCAATCTCTTACCCCGAGCCTGAGGT
* * *
435954 AGATTACAGCCATCCGATCTTTTACCTCGAGCCTAAGGTAGATCACCATCAGCCAATCTCTTACC
1 AGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAAATCACCATCAGCCAATCTCTTACC
* *
436019 TCGAGCTTGAGGCAGATTACAGTAAGCCAATCTCTTACCTTGAGC
66 TCGAGCTTGAGGCAGATT-CAGT-ATCCGATCTCTTACCTTGAGC
436064 CTAGTGCAGA
Statistics
Matches: 213, Mismatches: 49, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
155 65 0.31
156 147 0.69
157 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (154 bp):
AGATTACAGCCATCCGATCTTTTACCTCGAGCCTGAGGCAAATCACCATCAGCCAATCTCTTACC
TCGAGCTTGAGGCAGATTCAGTATCCGATCTCTTACCTTGAGCTTGGGACAGATCACCATCAGCC
AATCTCTTACCCCGAGCCTGAGGT
Found at i:436125 original size:78 final size:78
Alignment explanation
Indices: 436009--436239 Score: 313
Period size: 78 Copynumber: 3.0 Consensus size: 78
435999 CCATCAGCCA
* * * *
436009 ATCTCTTACCTCGAGCTTGAGGCAGATTA-CAGTAAGCCAATCTCTTACCTTGAGCCTAGTGCAG
1 ATCTTTTACCTCGAGCTTGAGGCAGATTACCA-TCAGCCAATCTCTTACCCTGAGCCTAGGGCAG
*
436073 ATTGCAGCCATTCG
65 ATTGCAACCATTCG
* *
436087 ATCTTTTACCTCGAGCCTGAGGCAGATTACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
1 ATCTTTTACCTCGAGCTTGAGGCAGATTACCATCAGCCAATCTCTTACCCTGAGCCTAGGGCAGA
**
436152 TTATAACCATTCG
66 TTGCAACCATTCG
* * * *
436165 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCTGAGCC-AGGGACAG
1 ATCTTTTACCTCGAGCTTGAGGCAGATTACCATCAGCCAATCTCTTACCCTGAGCCTAGGG-CAG
436229 ATTGCAACCAT
65 ATTGCAACCAT
436240 CCAATATCTT
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
77 4 0.03
78 128 0.96
79 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTTTTACCTCGAGCTTGAGGCAGATTACCATCAGCCAATCTCTTACCCTGAGCCTAGGGCAGA
TTGCAACCATTCG
Found at i:436150 original size:39 final size:39
Alignment explanation
Indices: 435687--436231 Score: 263
Period size: 39 Copynumber: 14.0 Consensus size: 39
435677 GATACAAATC
*
435687 ACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
* * * * *
435726 --CAGCTATCCGATCTCTTACCCCGAG-CTTGGGACAGATC
1 ACCATC-AGCCAATCTCTTACCCCGAGCCTAGGG-CAGATT
*
435764 ACCATCAGCCAATCTCTTACCCCGAGCCT-GAGGTAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATT
* * * * * * * *
435803 -GCAACTATCTAATCT-TGTACCTCGAG-CTTGAGGCAAATC
1 ACCATC-AGCCAATCTCT-TACCCCGAGCCTAG-GGCAGATT
* * ** *
435842 ACCATCAGTCAATCTCTTAACTAGAGCCTGGGGCAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
* * * * ** * ** * *
435881 GCAACCATCTGATCTTTTACCTTGAG-CTTGGGACAGATC
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGG-CAGATT
** * *
435920 ATTATCAGCCAATCTCTTACCCCGAGCCTGGGGTAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
* * * * * * * *
435959 A-CAGCCATCCGATCTTTTACCTCGAGCCTAAGGTAGATC
1 ACCA-TCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
* *
435998 ACCATCAGCCAATCTCTTACCTCGAG-CTTGAGGCAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATT
* ** *
436037 A-CAGTAAGCCAATCTCTTACCTTGAGCCTAGTGCAGATT
1 ACCA-TCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
* * ** * * *
436076 -GCAGCCATTCGATCTTTTACCTCGAGCCT-GAGGCAGATT
1 ACCA-TCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATT
436115 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
** * ** * * * * *
436154 ATAACCATTCGATCTTTTACCCCGAGCTTGGGGCAGATC
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
* *
436193 ACCATCAACCAATCTCTTACCCTGAGCC-AGGGACAGATT
1 ACCATCAGCCAATCTCTTACCCCGAGCCTAGGG-CAGATT
436232 GCAACCATCC
Statistics
Matches: 371, Mismatches: 111, Indels: 48
0.70 0.21 0.09
Matches are distributed among these distances:
37 7 0.02
38 43 0.12
39 294 0.79
40 27 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (39 bp):
ACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATT
Found at i:436943 original size:17 final size:17
Alignment explanation
Indices: 436898--436946 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
436888 ACCCACATAA
* *
436898 ATTTAAAATTTAAAATT
1 ATTTTAAATTTAAATTT
*
436915 ATTTT-TATTTAAATTT
1 ATTTTAAATTTAAATTT
436931 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
436947 AAAAAATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:438741 original size:17 final size:18
Alignment explanation
Indices: 438719--438754 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
438709 TAAATGAGTT
438719 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
438736 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
438754 A
1 A
438755 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:439066 original size:18 final size:18
Alignment explanation
Indices: 439043--439079 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
439033 TTTATGATCA
439043 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
439061 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
439079 A
1 A
439080 TATGAATTGT
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:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:446152 original size:17 final size:18
Alignment explanation
Indices: 446130--446165 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
446120 TAAATGAGTT
446130 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
446147 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
446165 A
1 A
446166 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:446485 original size:18 final size:18
Alignment explanation
Indices: 446462--446498 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
446452 TTAGTGATCA
446462 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
446480 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
446498 A
1 A
446499 TATGAATTGT
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:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:447295 original size:8 final size:8
Alignment explanation
Indices: 447284--447319 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
447274 CATATATACA
447284 TATATATG
1 TATATATG
447292 TATATATG
1 TATATATG
447300 --TATATG
1 TATATATG
447306 TATATATG
1 TATATATG
447314 TATATA
1 TATATA
447320 CAACCAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:447310 original size:14 final size:14
Alignment explanation
Indices: 447286--447318 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
447276 TATATACATA
447286 TATATGTATATATG
1 TATATGTATATATG
447300 TATATGTATATATG
1 TATATGTATATATG
447314 TATAT
1 TATAT
447319 ACAACCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
TATATGTATATATG
Found at i:448405 original size:29 final size:29
Alignment explanation
Indices: 448373--448633 Score: 249
Period size: 30 Copynumber: 8.8 Consensus size: 29
448363 GAATTTCTTA
448373 AAAATCACATTTTAACCCCAAACTTTCTC
1 AAAATCACATTTTAACCCCAAACTTTCTC
448402 AAAATCACATTTTAACTCCCAAACCTTTCT-
1 AAAATCACATTTTAAC-CCCAAA-CTTTCTC
* * *
448432 AAAATCACATTTTAACCCTAAAACTTTTTT
1 AAAATCACATTTTAACCC-CAAACTTTCTC
* **
448462 ACAATCACATTTTAACACTTAAAC-TTCTC
1 AAAATCACATTTTAAC-CCCAAACTTTCTC
* * *
448491 TAAAATAACATTTTAACCACTAAACCTTCTC
1 -AAAATCACATTTTAACC-CCAAACTTTCTC
** *
448522 AAAATCACATTTTAACCCCAAACTACCCC
1 AAAATCACATTTTAACCCCAAACTTTCTC
* *
448551 AAAATCACCTTTTAACCCCAAAACTTCCT-
1 AAAATCACATTTTAACCCC-AAACTTTCTC
* * * * *
448580 AAAATTACATTTTTACTCCTAAACTTTTTA
1 AAAATCACATTTTAAC-CCCAAACTTTCTC
*
448610 AAAATCACATTTTAACCCCGAACT
1 AAAATCACATTTTAACCCCAAACT
448634 CTCCGAAACT
Statistics
Matches: 192, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
29 78 0.41
30 102 0.53
31 12 0.06
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATCACATTTTAACCCCAAACTTTCTC
Found at i:452674 original size:39 final size:39
Alignment explanation
Indices: 452626--452716 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
452616 CGTGAAAGTA
* * * ** *
452626 TTTATAGTGTCACAACCAATTTAGTGTAGTATCGCAGTG
1 TTTACAGTGTCACAACCAATTGAGTATAACATCGCAATG
** *
452665 TTTACAGTGTCACTGCCAATTGAGTATAACATTGCAATG
1 TTTACAGTGTCACAACCAATTGAGTATAACATCGCAATG
452704 TTTACAGTGTCAC
1 TTTACAGTGTCAC
452717 TGCCAGTACT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (39 bp):
TTTACAGTGTCACAACCAATTGAGTATAACATCGCAATG
Found at i:453010 original size:29 final size:29
Alignment explanation
Indices: 452961--453016 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
452951 CACAGCCTGA
* * *
452961 CACACGACCATGTACTAGCCCGTGTATGT
1 CACACGACCAGGCACTAGCCCATGTATGT
452990 CACACGACCAGGCAC-ATGCCCATGTAT
1 CACACGACCAGGCACTA-GCCCATGTAT
453017 CCAGCCCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.20
Consensus pattern (29 bp):
CACACGACCAGGCACTAGCCCATGTATGT
Found at i:454466 original size:18 final size:18
Alignment explanation
Indices: 454443--454477 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
454433 AGCTTACTCA
*
454443 TGTTGAAATTTTTGGAAT
1 TGTTGAAATTTATGGAAT
*
454461 TGTTGAAGTTTATGGAA
1 TGTTGAAATTTATGGAA
454478 GTTGCCATTG
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:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (18 bp):
TGTTGAAATTTATGGAAT
Found at i:457974 original size:30 final size:30
Alignment explanation
Indices: 457882--457974 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
457872 AACTGTTTAG
457882 AAATCATATTTTGACCTCC-AAACTTTTTC-A
1 AAATCATATTTTGACC-CCTAAA-TTTTTCAA
* * * * * *
457912 AAATTACATTTTAACCCATAAACTTTCCAA
1 AAATCATATTTTGACCCCTAAATTTTTCAA
457942 AAATCATATTTTGACCCCTAAATTTTTCAA
1 AAATCATATTTTGACCCCTAAATTTTTCAA
457972 AAA
1 AAA
457975 AATACATTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
29 5 0.10
30 44 0.90
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATCATATTTTGACCCCTAAATTTTTCAA
Found at i:457984 original size:31 final size:29
Alignment explanation
Indices: 457889--457984 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
457879 TAGAAATCAT
*
457889 ATTTTGACCTCC-AAACTTTTTCAAAATTAC
1 ATTTTGACC-CCTAAA-TTTTTCAAAAATAC
* * * * *
457919 ATTTTAACCCATAAACTTTCCAAAAATCAT
1 ATTTTGACCCCTAAATTTTTCAAAAAT-AC
457949 ATTTTGACCCCTAAATTTTTCAAAAAAATAC
1 ATTTTGACCCCTAAATTTTTC--AAAAATAC
457980 ATTTT
1 ATTTT
457985 CCCCCCAAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
29 10 0.20
30 29 0.57
31 6 0.12
32 6 0.12
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.39
Consensus pattern (29 bp):
ATTTTGACCCCTAAATTTTTCAAAAATAC
Found at i:458013 original size:29 final size:28
Alignment explanation
Indices: 457972--458042 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
457962 AATTTTTCAA
*
457972 AAAAATACA-TTTTCCCCCCAAACATCC
1 AAAAATACATTTTTACCCCCAAACATCC
* * * *
457999 AAAAATCACATTTTTACCCTCGAACTTCT
1 AAAAAT-ACATTTTTACCCCCAAACATCC
458028 AAAAATTACATTTTT
1 AAAAA-TACATTTTT
458043 GCCCTTGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.17
28 3 0.08
29 26 0.72
30 1 0.03
ACGTcount: A:0.39, C:0.27, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAATACATTTTTACCCCCAAACATCC
Found at i:458047 original size:29 final size:30
Alignment explanation
Indices: 457996--458063 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
457986 CCCCCAAACA
457996 TCCAAAAATCACATTTTTACCCTCGAAC-T
1 TCCAAAAATCACATTTTTACCCTCGAACTT
* * * *
458025 TCTAAAAATTACATTTTTGCCCTTGAACTT
1 TCCAAAAATCACATTTTTACCCTCGAACTT
458055 TCCAAAAAT
1 TCCAAAAAT
458064 GTGTTTTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 24 0.73
30 9 0.27
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAAATCACATTTTTACCCTCGAACTT
Found at i:458518 original size:96 final size:96
Alignment explanation
Indices: 458348--458529 Score: 267
Period size: 96 Copynumber: 1.9 Consensus size: 96
458338 AATCAAGGTT
458348 ATATTCCTTTATTTCCAGTTTTGAAAATTCGTGCCTTAACTTATGAGGCACGATTTTTCTTCAAA
1 ATATTCCTTTATTTCCAGTTTTGAAAATTCGTGCCTTAACTTATGAGGCACGATTTTTCTTCAAA
* * *
458413 TCGGGATAATCGAATACCCTTAATCGAGACA
66 CCGGAATAATCAAATACCCTTAATCGAGACA
** * * * *
458444 ATATTCCTTTATTTCGGGTTTTGAGAATTTGTGCCTTAACTTACT-AGGCGCGATTTTTCTTTAA
1 ATATTCCTTTATTTCCAGTTTTGAAAATTCGTGCCTTAACTTA-TGAGGCACGATTTTTCTTCAA
458508 ACCGGAATAATCAAATACCCTT
65 ACCGGAATAATCAAATACCCTT
458530 TTTCAAGGTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
96 75 0.99
97 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (96 bp):
ATATTCCTTTATTTCCAGTTTTGAAAATTCGTGCCTTAACTTATGAGGCACGATTTTTCTTCAAA
CCGGAATAATCAAATACCCTTAATCGAGACA
Found at i:464863 original size:34 final size:34
Alignment explanation
Indices: 464820--464889 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
464810 CATATCCGAT
*
464820 AATGCCTTAAATTTGAACAATAGCACAATAACGA
1 AATGCCTTAAATTTGAACAATAGCAAAATAACGA
464854 AATGCCTTAAATTTGAACAATAGCAAAATAACGA
1 AATGCCTTAAATTTGAACAATAGCAAAATAACGA
464888 AA
1 AA
464890 GTTTGCGAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (34 bp):
AATGCCTTAAATTTGAACAATAGCAAAATAACGA
Found at i:465599 original size:39 final size:38
Alignment explanation
Indices: 465542--465617 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
465532 GTCGTCTCCT
* * *
465542 AAAAAAAAGAGATTAAGATGAAAACCCGTAAAGGGCATG
1 AAAAAAAAAAGATCAAGAT-AAAACCCGCAAAGGGCATG
*
465581 AAAAAAAAAAGATCAAGATAAAACCTGCAAAGGGCAT
1 AAAAAAAAAAGATCAAGATAAAACCCGCAAAGGGCAT
465618 CTTGAAACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 16 0.48
39 17 0.52
ACGTcount: A:0.57, C:0.12, G:0.20, T:0.12
Consensus pattern (38 bp):
AAAAAAAAAAGATCAAGATAAAACCCGCAAAGGGCATG
Found at i:466515 original size:50 final size:49
Alignment explanation
Indices: 466314--466683 Score: 232
Period size: 50 Copynumber: 7.6 Consensus size: 49
466304 CAGATTTGAC
* * * * * *
466314 AGGG-AAGGATTGAGGCCGCAACGGTGAATCTGGTATC-TTAAGAGATGTTA
1 AGGGAAAGG-TTGAGGCCGCAATGGCGAACCTGGTACCATGAAGAGACG--A
* *
466364 AGGAAAAGGTTGAGGCTGCAATGGCGAA-CTCGGTACCATGAAGAGACGA
1 AGGGAAAGGTTGAGGCCGCAATGGCGAACCT-GGTACCATGAAGAGACGA
* * *
466413 A-GGAAAGGATTGAAGTCGCAATGGCGAATACCT--TA--A--AAGATG-TGA
1 AGGGAAAGG-TTGAGGCCGCAATGGCG-A-ACCTGGTACCATGAAGA-GACGA
* *
466458 AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACC-T-AAGAAGAGGTA
1 AGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCATGAAG-AGACG-A
* * * *
466507 ATGGGAAAGGTTAAAGCCGTAATGGCGAACCTAGTACCATGAAGAGACGA
1 A-GGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCATGAAGAGACGA
* ** * * * *
466557 AGGG-AAGAATTGAGGCCGCAACAGCGAATCTGGTACC-TTAAAAGATGTGA
1 AGGGAAAG-GTTGAGGCCGCAATGGCGAACCTGGTACCATGAAGAGA--CGA
* * * *
466607 AGGGAAAGGTTGAGGCCGTAATAGTGAACCTAGTACCATGAAGAGACGA
1 AGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCATGAAGAGACGA
*
466656 AGGG-AAGGATTGAAGCCGCAATGGCGAA
1 AGGGAAAGG-TTGAGGCCGCAATGGCGAA
466684 TCCGATAGGT
Statistics
Matches: 248, Mismatches: 46, Indels: 53
0.71 0.13 0.15
Matches are distributed among these distances:
43 3 0.01
44 1 0.00
45 24 0.10
46 8 0.03
47 5 0.02
48 21 0.08
49 67 0.27
50 87 0.35
51 27 0.11
52 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.33, T:0.17
Consensus pattern (49 bp):
AGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCATGAAGAGACGA
Found at i:466684 original size:99 final size:99
Alignment explanation
Indices: 466456--466687 Score: 317
Period size: 99 Copynumber: 2.3 Consensus size: 99
466446 TAAAAGATGT
*
466456 GAAGGGAAAGG-TTGAGGCCGCAATGGCGAACCCGGTACCTAAGAAGAGGTAATGGGAAAGGTTA
1 GAAGGG-AAGGATTGAGGCCGCAATGGCGAATCCGGTACCTAAGAAGAGGTAATGGGAAAGGTTA
*
466520 AAGCCGTAATGGCGAACCTAGTACCATGAAGAGAC
65 AAGCCGTAATAGCGAACCTAGTACCATGAAGAGAC
* ** * *
466555 GAAGGGAAGAATTGAGGCCGCAACAGCGAATCTGGTACCTTAA-AAGATGTGAA-GGGAAAGGTT
1 GAAGGGAAGGATTGAGGCCGCAATGGCGAATCCGGTACC-TAAGAAGAGGT-AATGGGAAAGGTT
* * *
466618 GAGGCCGTAATAGTGAACCTAGTACCATGAAGAGAC
64 AAAGCCGTAATAGCGAACCTAGTACCATGAAGAGAC
*
466654 GAAGGGAAGGATTGAAGCCGCAATGGCGAATCCG
1 GAAGGGAAGGATTGAGGCCGCAATGGCGAATCCG
466688 ATAGGTTGAG
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
98 3 0.03
99 107 0.93
100 5 0.04
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.15
Consensus pattern (99 bp):
GAAGGGAAGGATTGAGGCCGCAATGGCGAATCCGGTACCTAAGAAGAGGTAATGGGAAAGGTTAA
AGCCGTAATAGCGAACCTAGTACCATGAAGAGAC
Found at i:466718 original size:28 final size:28
Alignment explanation
Indices: 466665--466718 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
466655 AAGGGAAGGA
* *
466665 TTGAAGCCGCAATGGCGAATCCGATAGG
1 TTGAAGCCGCAACGGCGAAGCCGATAGG
*
466693 TTGAGGCCGCAACGGCG-AGCCTGATA
1 TTGAAGCCGCAACGGCGAAGCC-GATA
466719 CCTTAGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (28 bp):
TTGAAGCCGCAACGGCGAAGCCGATAGG
Found at i:466801 original size:127 final size:127
Alignment explanation
Indices: 466566--466807 Score: 317
Period size: 127 Copynumber: 1.9 Consensus size: 127
466556 AAGGGAAGAA
* * *
466566 TTGAGGCCGCAACAGCGAATCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGTAATAG
1 TTGAGGCCGCAACAGCGAACCTGATACCTTAAAAGATGCGAAGGGAAAGGTTGAGGCCGTAATAG
**
466631 TGAACCTAGTACCATGAAGAGACGAAGGGAAGGATTGAAGCCGCAATGGCGAATCCGATAGG
66 CAAACCTAGTACCATGAAGAGACGAAGGGAAGGATTGAAGCCGCAATGGCGAATCCGATAGG
* * * * * *
466693 TTGAGGCCGCAACGGCGAGCCTGATACCTTAGAAGATGCGATGGGAAAGGTTGAGGTCGTAATGG
1 TTGAGGCCGCAACAGCGAACCTGATACCTTAAAAGATGCGAAGGGAAAGGTTGAGGCCGTAATAG
* * * *
466758 CAAACTTGGTACCATGAAGATAC-AATGGGAAAGG-TTGAGGCCGCAATGGC
66 CAAACCTAGTACCATGAAGAGACGAA-GGG-AAGGATTGAAGCCGCAATGGC
466808 AAACCCGGTA
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
126 2 0.02
127 92 0.94
128 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.33, T:0.18
Consensus pattern (127 bp):
TTGAGGCCGCAACAGCGAACCTGATACCTTAAAAGATGCGAAGGGAAAGGTTGAGGCCGTAATAG
CAAACCTAGTACCATGAAGAGACGAAGGGAAGGATTGAAGCCGCAATGGCGAATCCGATAGG
Found at i:466889 original size:49 final size:49
Alignment explanation
Indices: 466690--467008 Score: 246
Period size: 49 Copynumber: 6.5 Consensus size: 49
466680 CGAATCCGAT
* * * * *
466690 AGGTTGAGGCCGCAACGGCGAGCCTGATACCTTAGAAGATGCGATGGGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCAT-GAAGATACGAAGGGAA
* * * * ** *
466740 AGGTTGAGGTCGTAATGGCAAACTTGGTACCATGAAGATAC-AATGGGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGATACGAA-GGGAA
* * * * *
466789 AGGTTGAGGCCGCAATGGCAAACCCGGTACCACGAAGATACAAAGGGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGATACGAAGGGAA
**
466838 AGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGATACGAAGAAAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGATACGAAGGGAA
* * * * * * * ** *
466887 AGGTTGAGACTGCAACGACAAATCCAATACCTTAGAAGATGTGATGGGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCAT-GAAGATACGAAGGGAA
** * * * * * **
466937 ATATTGAGGTCGCAACGGCGAATCCGATACCCTGAAGACA-AAAGCAAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGATACGAAGGGAA
*
466985 AGGTTGAGGCCGCAACGGAGAACC
1 AGGTTGAGGCCGCAACGGCGAACC
467009 TAGCACCTTA
Statistics
Matches: 212, Mismatches: 54, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
48 24 0.11
49 126 0.59
50 62 0.29
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15
Consensus pattern (49 bp):
AGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGATACGAAGGGAA
Found at i:469566 original size:97 final size:97
Alignment explanation
Indices: 469394--469577 Score: 287
Period size: 97 Copynumber: 1.9 Consensus size: 97
469384 AAATCGAGAT
* *
469394 AATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGGTGCGATTTTTCTTCAA
1 AATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCCTAACTTACTAGGCGCGATTTTTCTTCAA
* * *
469459 ATCTGGATAATCGAATACCCTTAAATTGAGGC
66 ACCAGAATAATCGAATACCCTTAAATTGAGGC
* ** *
469491 AATATTCTTTTATTTCGGGTTTTGAAAATTTGTGCCCTAACTTACTAGGCGCGATTTTTCTTTAA
1 AATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCCTAACTTACTAGGCGCGATTTTTCTTCAA
469556 ACCAGAATAATCGAATACCCTT
66 ACCAGAATAATCGAATACCCTT
469578 TTTCAAGGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (97 bp):
AATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCCTAACTTACTAGGCGCGATTTTTCTTCAA
ACCAGAATAATCGAATACCCTTAAATTGAGGC
Found at i:477751 original size:22 final size:25
Alignment explanation
Indices: 477712--477761 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
477702 TTGAATATAA
* *
477712 ATAATTAAATGAAGACAAT-CAAAT
1 ATAATTAAATGAACACAATAAAAAT
477736 ATAATT-AAT-AACACAATAAAAAT
1 ATAATTAAATGAACACAATAAAAAT
477759 ATA
1 ATA
477762 GTTATAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 10 0.43
24 6 0.26
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (25 bp):
ATAATTAAATGAACACAATAAAAAT
Found at i:478133 original size:15 final size:16
Alignment explanation
Indices: 478115--478152 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
478105 AATGCAAATT
*
478115 AAATAAAA-GAGATAA
1 AAATAAAATGACATAA
*
478130 AAATAAAATGACATGA
1 AAATAAAATGACATAA
478146 AAATAAA
1 AAATAAA
478153 TAACAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.16
Consensus pattern (16 bp):
AAATAAAATGACATAA
Found at i:478182 original size:14 final size:14
Alignment explanation
Indices: 478146--478198 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
478136 AATGACATGA
*
478146 AAATAAATAACAAT
1 AAATAAATAAAAAT
478160 AAGATAAATAAAAAT
1 AA-ATAAATAAAAAT
478175 AAATAAATAAAAAT
1 AAATAAATAAAAAT
478189 AAA-AAATAAA
1 AAATAAATAAA
478199 TGCTAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
13 7 0.19
14 17 0.46
15 13 0.35
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:478287 original size:16 final size:16
Alignment explanation
Indices: 478251--478294 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
478241 GATTAGGCAT
*
478251 AAAAATAAAT-GACAA
1 AAAAATAAATAAACAA
*
478266 ATAAATAAATAAACAA
1 AAAAATAAATAAACAA
*
478282 AAAAATCAATAAA
1 AAAAATAAATAAA
478295 TTAAATGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAAATAAATAAACAA
Found at i:478570 original size:24 final size:25
Alignment explanation
Indices: 478526--478579 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
478516 ATATTTTCTT
*
478526 TGAATGTATGTCTAAAAAAAATCTC
1 TGAATGTATGTATAAAAAAAATCTC
*
478551 TGAATGT-TGTATAAAAAAAATCTT
1 TGAATGTATGTATAAAAAAAATCTC
478575 TGAAT
1 TGAAT
478580 CTTATTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (25 bp):
TGAATGTATGTATAAAAAAAATCTC
Found at i:479343 original size:49 final size:49
Alignment explanation
Indices: 479284--480038 Score: 543
Period size: 49 Copynumber: 15.5 Consensus size: 49
479274 ATATTTGTCG
* *
479284 TTACGACTTTAATCTGTCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
** * * * **
479333 TTGTGGCTTTAATCTTTCCCTTTTC-GATTTTAGGGTGTTAA-ATCTGTTG
1 TTACGGCTTTAATCTATCCCTCTTCAG-TTTTAGGGTG-TAAGATCTATCA
* * * * * * **
479382 TTATGACTTTAATTTATCCTTATTTAGTTTTAGGGTGTAAGAT-TCGCCA
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCT-ATCA
* * * * *
479431 TTACAGCTTTAATATTTCCCTCTTC-GATTTTAAGGTGTTAGATCTATCA
1 TTACGGCTTTAATCTATCCCTCTTCAG-TTTTAGGGTGTAAGATCTATCA
* * * *
479480 TTACGACTTTAATCTATCCCTCTTCAGTTTTAGAGTCTAAG---T-T-G
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
** * * * * *
479524 TTACAACTTTAATCTTTCCCTCTTCTA-TTTTAAGGTGTTAGATCCATCG
1 TTACGGCTTTAATCTATCCCTCTTC-AGTTTTAGGGTGTAAGATCTATCA
* * * * *
479573 TTGCGGCTTTAATCTATCTCTCTTTAATTTTAGGGTGTAAGATCCATCA
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
* * * ** * *
479622 TTACGACTTTAATCTTTCCCTTTTTGGTTTTAGGGTGTTAA-ATGTGTCA
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTG-TAAGATCTATCA
* * * * *
479671 TTACGGCTTTAATTTATCCCTCTTTAATTTTAGGGTGTAAGATTTATCT
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
* * * * * * *
479720 TTATGGCTTTAATCTTTCCTTCTTC-GATTTTAGGGTGTTAGATATGTCG
1 TTACGGCTTTAATCTATCCCTCTTCAG-TTTTAGGGTGTAAGATCTATCA
* * * * * * *
479769 TTACGACTTTAATTTATCCCTCTTTAATTTTAAGGTGTAAGATCCATCG
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
* * * *
479818 TTA-GGCTTTAATCTTTCCCTTTTC-GATTTTAGGGTGTTAGATCTGTCA
1 TTACGGCTTTAATCTATCCCTCTTCAG-TTTTAGGGTGTAAGATCTATCA
* * * * *
479866 TTACGGCTTTAATCTATCTCTCTTCATTTTTAGGATGTAAGAT-TCACCG
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCT-ATCA
* * * * * *
479915 TTGCGGCTTTAATCTTTCCCTCTTCAATTTTAGGGTGTATGAT-TCACCG
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCT-ATCA
* * * *
479964 TTACGGCTTTAATCTATTCGTCTTCAGTTTTAAGGTGTAAGATCCATCA
1 TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
* *
480013 TTGCGGCTTTAATTTATCCCTCTTCA
1 TTACGGCTTTAATCTATCCCTCTTCA
480039 ACTCTAGGAT
Statistics
Matches: 546, Mismatches: 136, Indels: 48
0.75 0.19 0.07
Matches are distributed among these distances:
44 33 0.06
45 2 0.00
46 1 0.00
48 48 0.09
49 453 0.83
50 9 0.02
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (49 bp):
TTACGGCTTTAATCTATCCCTCTTCAGTTTTAGGGTGTAAGATCTATCA
Found at i:479418 original size:98 final size:98
Alignment explanation
Indices: 479279--480033 Score: 697
Period size: 98 Copynumber: 7.8 Consensus size: 98
479269 GTGTAATATT
* * * * **
479279 TGTCGTTACGACTTTAATCTGTCCCTCTTCAGTTTTAGGGTGTAAGATCTATCATTGTGGCTTTA
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTTA
*
479344 ATCTTTCCCTTTTCGATTTTAGGGTGTTAAATC
66 ATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
** * * * * * ** *
479377 TGTTGTTATGACTTTAATTTATCCTTATTTAGTTTTAGGGTGTAAGAT-TCGCCATTACAGCTTT
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCT-ATCATTACGGCTTT
* * *
479441 AATATTTCCCTCTTCGATTTTAAGGTGTTAGATC
65 AATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
* * * * * * **
479475 TATCATTACGACTTTAATCTATCCCTCTTCAGTTTTAGAGTCTAAG---T-T-GTTACAACTTTA
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTTA
* * *
479535 ATCTTTCCCTCTTCTATTTTAAGGTGTTAGATC
66 ATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
** * * * * * *
479568 CATCGTTGCGGCTTTAATCTATCTCTCTTTAATTTTAGGGTGTAAGATCCATCATTACGACTTTA
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTTA
* * * *
479633 ATCTTTCCCTTTTTGGTTTTAGGGTGTTAAATG
66 ATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
* * * * *
479666 TGTCATTACGGCTTTAATTTATCCCTCTTTAATTTTAGGGTGTAAGATTTATCTTTATGGCTTTA
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTTA
*
479731 ATCTTT-CCTTCTTCGATTTTAGGGTGTTAGATA
66 ATCTTTCCCTT-TTCGATTTTAGGGTGTTAGATC
* * * * *
479764 TGTCGTTACGACTTTAATTTATCCCTCTTTAATTTTAAGGTGTAAGATCCATCGTTA-GGCTTTA
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTTA
479828 ATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
66 ATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
* * * * * * * *
479861 TGTCATTACGGCTTTAATCTATCTCTCTTCATTTTTAGGATGTAAGAT-TCACCGTTGCGGCTTT
1 TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCT-ATCATTACGGCTTT
* *
479925 AATCTTTCCCTCTTCAATTTTAGGGTG-TATGAT-
65 AATCTTTCCCTTTTCGATTTTAGGGTGTTA-GATC
** * * * * * * * * *
479958 TCACCGTTACGGCTTTAATCTATTCGTCTTCAGTTTTAAGGTGTAAGATCCATCATTGCGGCTTT
1 T-GTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTT
480023 AAT-TTATCCCT
65 AATCTT-TCCCT
480034 CTTCAACTCT
Statistics
Matches: 546, Mismatches: 97, Indels: 28
0.81 0.14 0.04
Matches are distributed among these distances:
93 78 0.14
96 1 0.00
97 90 0.16
98 377 0.69
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (98 bp):
TGTCATTACGACTTTAATCTATCCCTCTTTAATTTTAGGGTGTAAGATCTATCATTACGGCTTTA
ATCTTTCCCTTTTCGATTTTAGGGTGTTAGATC
Found at i:479781 original size:289 final size:291
Alignment explanation
Indices: 479281--479952 Score: 821
Period size: 289 Copynumber: 2.3 Consensus size: 291
479271 GTAATATTTG
* * * * * *
479281 TCGTTACGACTTTAATCTGTCCCTCTTCAGTTTTAGGGTGTAAGATCTATCATTGTGGCTTTAAT
1 TCGTTACGGCTTTAATCTATCTCTCTTCAATTTTAGGGTGTAAGATCCATCATTGCGGCTTTAAT
** * * *
479346 CTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTTGTTATGACTTTAATTTATCCTTATTTAGTT
66 CTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTCATTACGACTTTAATTTATCCCTATTTAATT
* *
479411 TTAGGGTGTAAGATTCGCCATTACAGCTTTAATATTTCCCTCTTCGATTTTAAGGTGTTAGATCT
131 TTAGGGTGTAAGATTCACCATTACAGCTTTAATATTTCCCTCTTCGATTTTAAGGTGTTAGATAT
*
479476 ATCATTACGACTTTAATCTATCCCTCTTCAGTTTT-AGAGTCTAAG-T-T-GTTACAACTTTAAT
196 ATCATTACGACTTTAATCTATCCCTCTTCAATTTTAAG-GTCTAAGATCTCGTTA-AACTTTAAT
*
479537 CTTTCCCTCTTCTATTTTAAGGTGTTAGATCCA
259 CTTTCCCTCTTCGATTTTAAGGTGTTAGATCCA
* * * *
479570 TCGTTGCGGCTTTAATCTATCTCTCTTTAATTTTAGGGTGTAAGATCCATCATTACGACTTTAAT
1 TCGTTACGGCTTTAATCTATCTCTCTTCAATTTTAGGGTGTAAGATCCATCATTGCGGCTTTAAT
* * * * *
479635 CTTTCCCTTTTTGGTTTTAGGGTGTTAAATGTGTCATTACGGCTTTAATTTATCCCTCTTTAATT
66 CTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTCATTACGACTTTAATTTATCCCTATTTAATT
* * * ** * * *
479700 TTAGGGTGTAAGATTTATCTTTATGGCTTTAATCTTTCCTTCTTCGATTTTAGGGTGTTAGATAT
131 TTAGGGTGTAAGATTCACCATTACAGCTTTAATATTTCCCTCTTCGATTTTAAGGTGTTAGATAT
* * * * * **
479765 GTCGTTACGACTTTAATTTATCCCTCTTTAATTTTAAGGTGTAAGATCCATCGTTAGGCTTTAAT
196 ATCATTACGACTTTAATCTATCCCTCTTCAATTTTAAGGTCTAAGAT-C-TCGTTAAACTTTAAT
* * **
479830 CTTTCCCTTTTCGATTTTAGGGTGTTAGATCTG
259 CTTTCCCTCTTCGATTTTAAGGTGTTAGATCCA
* * * * * *
479863 TCATTACGGCTTTAATCTATCTCTCTTCATTTTTAGGATGTAAGATTCACCGTTGCGGCTTTAAT
1 TCGTTACGGCTTTAATCTATCTCTCTTCAATTTTAGGGTGTAAGATCCATCATTGCGGCTTTAAT
* *
479928 CTTTCCCTCTTCAATTTTAGGGTGT
66 CTTTCCCTTTTCGATTTTAGGGTGT
479953 ATGATTCACC
Statistics
Matches: 320, Mismatches: 57, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
289 201 0.63
290 3 0.01
293 112 0.35
294 4 0.01
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (291 bp):
TCGTTACGGCTTTAATCTATCTCTCTTCAATTTTAGGGTGTAAGATCCATCATTGCGGCTTTAAT
CTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTCATTACGACTTTAATTTATCCCTATTTAATT
TTAGGGTGTAAGATTCACCATTACAGCTTTAATATTTCCCTCTTCGATTTTAAGGTGTTAGATAT
ATCATTACGACTTTAATCTATCCCTCTTCAATTTTAAGGTCTAAGATCTCGTTAAACTTTAATCT
TTCCCTCTTCGATTTTAAGGTGTTAGATCCA
Found at i:486758 original size:21 final size:21
Alignment explanation
Indices: 486732--486776 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
486722 TTAGTATCGA
* *
486732 TAGTTGTATGACTTATATTGG
1 TAGTTGCATCACTTATATTGG
* *
486753 TAGTTGCCTCACTTGTATTGG
1 TAGTTGCATCACTTATATTGG
486774 TAG
1 TAG
486777 AATTTTCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.44
Consensus pattern (21 bp):
TAGTTGCATCACTTATATTGG
Found at i:490238 original size:37 final size:35
Alignment explanation
Indices: 490194--490275 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 35
490184 CAAATTTAAT
** *
490194 TAAATTTAAATTTAAGGCAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTTAACACAAATTTAAATCT-AAAA-A
*
490231 TAAATTTAAATTTAACATAAATTTAAATCTAAAAA
1 TAAATTTAAATTTAACACAAATTTAAATCTAAAAA
490266 TAAATTTAAA
1 TAAATTTAAA
490276 CGAATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 11 0.27
36 4 0.10
37 26 0.63
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (35 bp):
TAAATTTAAATTTAACACAAATTTAAATCTAAAAA
Found at i:490252 original size:17 final size:17
Alignment explanation
Indices: 490185--490275 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
490175 AAATCCATTC
*
490185 AAATTTAA-TTAAATTT
1 AAATTTAAGATAAATTT
**
490201 AAATTTAAGGCAAATTT
1 AAATTTAAGATAAATTT
490218 AAATTTAAAAAGATAAATTT
1 AAATTT---AAGATAAATTT
*
490238 AAATTTAACATAAATTT
1 AAATTTAAGATAAATTT
* *
490255 AAATCTAAAAATAAATTT
1 AAAT-TTAAGATAAATTT
490273 AAA
1 AAA
490276 CGAATTTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
16 8 0.13
17 26 0.41
18 14 0.22
20 15 0.24
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AAATTTAAGATAAATTT
Found at i:499053 original size:36 final size:39
Alignment explanation
Indices: 499008--499086 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 39
498998 ATCATTAAAT
499008 ATTTGTAATT-A-GATATTAACACAGTTGTATTA-TTTA
1 ATTTGTAATTAATGATATTAACACAGTTGTATTATTTTA
* * *
499044 ATTTTTAATTAATGATTTTAACACATTTGTATTATTTTA
1 ATTTGTAATTAATGATATTAACACAGTTGTATTATTTTA
499083 ATTT
1 ATTT
499087 AAAATATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 9 0.24
37 1 0.03
38 19 0.51
39 8 0.22
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (39 bp):
ATTTGTAATTAATGATATTAACACAGTTGTATTATTTTA
Found at i:516629 original size:2 final size:2
Alignment explanation
Indices: 516622--516646 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
516612 GGAGTAAATT
516622 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
516647 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:517084 original size:7 final size:7
Alignment explanation
Indices: 517072--517101 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
517062 GATTGAAATG
517072 ATTTAAA
1 ATTTAAA
517079 ATTTAAA
1 ATTTAAA
*
517086 ATTTAGA
1 ATTTAAA
517093 ATTTAAA
1 ATTTAAA
517100 AT
1 AT
517102 GTCTGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (7 bp):
ATTTAAA
Found at i:519015 original size:85 final size:86
Alignment explanation
Indices: 518857--519017 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 86
518847 GTGGTGGTCT
* *
518857 TCCACAAAACCCAGTGGTAGTTTGTTTAGTCCATGAATATGTGGCGAACTCACAACAAGTGGCAA
1 TCCACAAAACCCAGTGGTAGTTTGTTTAATCCATGAACATGTGGCGAACTCACAACAAGTGGCAA
*
518922 TAATTGCAAATATATGGCTTG
66 TAAATGCAAATATATGGCTTG
* * * *
518943 TCCAC-AAACCCAGTGGTAGTTTGTTTAAT-C-TGCAACCATGTTGTGCACTCACAATAAGTGGC
1 TCCACAAAACCCAGTGGTAGTTTGTTTAATCCATG-AA-CATGTGGCGAACTCACAACAAGTGGC
*
519005 AGTAAATGCAAAT
64 AATAAATGCAAAT
519018 GTTTTTATCT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
83 2 0.03
84 3 0.05
85 55 0.85
86 5 0.08
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (86 bp):
TCCACAAAACCCAGTGGTAGTTTGTTTAATCCATGAACATGTGGCGAACTCACAACAAGTGGCAA
TAAATGCAAATATATGGCTTG
Found at i:521474 original size:108 final size:107
Alignment explanation
Indices: 520973--521487 Score: 568
Period size: 108 Copynumber: 4.8 Consensus size: 107
520963 CTGCAATTTA
** * * * *
520973 TCGG-TTATCCGACTAGCATTGGGCGCAACATTGTTGGTTTATCCAACTAGAGCTGGGTTCATTA
1 TCGGTTTATCCGACTAGCGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCATT-
* * * *
521037 ATAATATCGTCAGTTTATCTGATTAGTGCTAGGCACACTTTTG
65 ATAATATCGTCAGTTTATCTAACTAGTGCTGGGCACACTTTCG
* *
521080 TCGATTTATCCGACTAGAGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCTAGGG-TCATT
1 TCGGTTTATCCGACTAGCGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCT-GGGCTCATT
* * * * *
521144 GAGAATATCATCAGTTTATCTTACTAGTGTTGGGCACACTTTCT
65 -ATAATATCGTCAGTTTATCTAACTAGTGCTGGGCACACTTTCG
* * * * * *
521188 TCGGTTTATCTGATTAGCGCTGGGCGCAATATCGTTAGTTTTTCCAACTAGAGCTGGGCTTATTG
1 TCGGTTTATCCGACTAGCGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCATT-
* *
521253 ATAATACCGTCAGTTTACCTAACTAGTGCTGGGCACACTTTCG
65 ATAATATCGTCAGTTTATCTAACTAGTGCTGGGCACACTTTCG
** * * * *
521296 TAAGTTTATCCGACTAGCACTGTGCGCAATATCGTTGATTTATCCAACTAGAGATGGGCTCATTA
1 TCGGTTTATCCGACTAGCGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCATT-
*
521361 ATAATATCGTCAGTTTATCTAACTAGTACTGGGCACACTTTCG
65 ATAATATCGTCAGTTTATCTAACTAGTGCTGGGCACACTTTCG
** * * * * * *
521404 TCGGTTTATCCGGTTAGCGTTAAGTGCAATATTGTTGGTTTATCCAACTAGAACTTGGCTCACAT
1 TCGGTTTATCCGACTAGCGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCTGGGCT--CAT
**
521469 T-TAATATCGTTGGTTTATC
64 TATAATATCGTCAGTTTATC
521488 CGACTACCAC
Statistics
Matches: 341, Mismatches: 62, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
107 6 0.02
108 328 0.96
109 3 0.01
110 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (107 bp):
TCGGTTTATCCGACTAGCGCTGAGCGCAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCATTA
TAATATCGTCAGTTTATCTAACTAGTGCTGGGCACACTTTCG
Found at i:526767 original size:152 final size:149
Alignment explanation
Indices: 526607--527011 Score: 588
Period size: 153 Copynumber: 2.7 Consensus size: 149
526597 TGATTAAAAC
* * *
526607 AAAATCACTACTTTACTTCAAAA-TCAAAATTTTTATTTCGAAATAGTTAAAAAAATTAAAATTT
1 AAAATCACTATTTTACTTAAAAATTC-AAACTTTTATTTCGAAATAGTTAAAAAAATTAAAATTT
526671 TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAAAAACATATTTTTATTTTT-AAAAA
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAAAAA-ATA--TTTATTTTTAAAAAA
*
526735 TATAAACTTTCTCTTTTTTTTAAA-
127 TATAAACTTTATC--TTTTTTAAAG
* *
526759 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAAAATTAAAATTT
** * *
526824 CATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATATTTATTTTTAAAAAATAT
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAAAAAATATTTATTTTTAAAAAATAT
526889 AAACTTTATCTTTTTTAAAG
130 AAACTTTATCTTTTTTAAAG
*
526909 AAAATCACTATTTTACTTAAAAATTC-AACTTTTATTTCGAAATAGTTAAAAAAA-TCAAATCTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATTAAAAT-TT
526972 TGTTTAAAAATTTAAAC-TTTTCTTTTAAAATCACTAAAAA
65 TGTTTAAAAATTTAAACTTTTTC-TTTAAAATCACTAAAAA
527012 CAGATTATTA
Statistics
Matches: 231, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
147 8 0.03
148 40 0.17
149 30 0.13
150 35 0.15
151 17 0.07
152 45 0.19
153 56 0.24
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (149 bp):
AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATTAAAATTTT
GTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAAAAAATATTTATTTTTAAAAAATATA
AACTTTATCTTTTTTAAAG
Found at i:526855 original size:52 final size:52
Alignment explanation
Indices: 526647--527002 Score: 189
Period size: 52 Copynumber: 7.1 Consensus size: 52
526637 TTTTATTTCG
* *
526647 AAATAGTT-AAAAAAATTAAAATTTTGTTTAAAAATTTAAACTTTTTCTTTA
1 AAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
* * * * * *
526698 AAATCA-CTAAAAAAAAACATATTTTTATTTTTAAAAATATAAACTTTCTCTTT-
1 AAAT-AGTTAAAAAAAATCAAAATTTTA--TTTAAAAATTTAAACTTTTTCTTTA
* * ** * * **
526751 ---T-TTTTAAAAAAATCACTATTTTACTTAAAAATTCAAACTTTTAT-TTCG
1 AAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTT-TCTTTA
* *
526799 AAATAGTTAAAAAAAATCAAAACTTCATTTAAAAATTTAAACTTTTTCTTTA
1 AAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
** * * *
526851 AAATAACT--AAAAAAT-AAATATTTATTTTTAAAAAATATAAACTTTATCTTT-
1 AAATAGTTAAAAAAAATCAAA-ATTT-TATTT-AAAAATTTAAACTTTTTCTTTA
* ** * * **
526902 ---T--TTAAAGAAAATCACTATTTTACTTAAAAA-TTCAACTTTTAT-TTCG
1 AAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTT-TCTTTA
*
526948 AAATAGTT-AAAAAAATC-AAATCTTTGTTTAAAAATTTAAAC-TTTTCTTTTA
1 AAATAGTTAAAAAAAATCAAAAT-TTTATTTAAAAATTTAAACTTTTTC-TTTA
526999 AAAT
1 AAAT
527003 CACTAAAAAC
Statistics
Matches: 222, Mismatches: 54, Indels: 58
0.66 0.16 0.17
Matches are distributed among these distances:
45 9 0.04
46 7 0.03
47 20 0.09
48 12 0.05
49 23 0.10
50 32 0.14
51 23 0.10
52 74 0.33
54 22 0.10
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.42
Consensus pattern (52 bp):
AAATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCTTTA
Found at i:526896 original size:22 final size:22
Alignment explanation
Indices: 526858--526902 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
526848 TTAAAATAAC
526858 TAAAAAATAAATATTTAT-TTT
1 TAAAAAATAAATATTTATCTTT
526879 TAAAAAATATAA-ACTTTATCTTT
1 TAAAAAATA-AATA-TTTATCTTT
526902 T
1 T
526903 TTAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAAAATAAATATTTATCTTT
Found at i:527081 original size:3 final size:3
Alignment explanation
Indices: 527073--527167 Score: 127
Period size: 3 Copynumber: 31.7 Consensus size: 3
527063 ATGAAACCCT
* *
527073 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAT AAT AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * * *
527121 AAC AAC AAC AAC AAC AAC AAC AAT AAT AAT AAT AAC AGC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
527168 TAATTTGGGC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.66, C:0.26, G:0.01, T:0.06
Consensus pattern (3 bp):
AAC
Found at i:529010 original size:21 final size:21
Alignment explanation
Indices: 528983--529059 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
528973 AGAGTTTTTA
528983 GTATCGGTAGAAGTTACACTT
1 GTATCGGTAGAAGTTACACTT
*
529004 GTTTCGGTAGAAGTTACACTT
1 GTATCGGTAGAAGTTACACTT
* * * **
529025 GTATCGGTAGAATTTTCCCAA
1 GTATCGGTAGAAGTTACACTT
529046 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
529060 ATGCATTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (21 bp):
GTATCGGTAGAAGTTACACTT
Found at i:530835 original size:12 final size:12
Alignment explanation
Indices: 530820--530862 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
530810 CATCATCCTC
530820 ACCAGCATCGGA
1 ACCAGCATCGGA
530832 ACCAGCATCGGA
1 ACCAGCATCGGA
**
530844 ACCAGCATCAAA
1 ACCAGCATCGGA
530856 ACCAGCA
1 ACCAGCA
530863 AGCACATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.40, C:0.35, G:0.19, T:0.07
Consensus pattern (12 bp):
ACCAGCATCGGA
Found at i:531665 original size:21 final size:21
Alignment explanation
Indices: 531641--531684 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
531631 TAACGGGACC
531641 GCTGATGTGGCAAGTTAACTT
1 GCTGATGTGGCAAGTTAACTT
*
531662 GCTGATGTGGCTAGTTAACTT
1 GCTGATGTGGCAAGTTAACTT
531683 GC
1 GC
531685 CACGTTGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACTT
Found at i:531928 original size:20 final size:20
Alignment explanation
Indices: 531903--531954 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
531893 CCGAGAAATC
* * *
531903 AAGAAATGAAGAAGAAGAAG
1 AAGAAAAGAAAAAAAAGAAG
*
531923 AAGAAAAGAAAAAAAAGGAG
1 AAGAAAAGAAAAAAAAGAAG
*
531943 AAGAAAGGAAAA
1 AAGAAAAGAAAA
531955 TGGAAGGAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (20 bp):
AAGAAAAGAAAAAAAAGAAG
Found at i:532653 original size:3 final size:3
Alignment explanation
Indices: 532645--532674 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
532635 CCATTTTTTC
532645 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
532675 ATAGCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:533338 original size:13 final size:13
Alignment explanation
Indices: 533322--533346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
533312 ACAATAATTA
533322 TTAAAAAAACTTT
1 TTAAAAAAACTTT
533335 TTAAAAAAACTT
1 TTAAAAAAACTT
533347 AAAATGAAAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAAAACTTT
Found at i:536741 original size:3 final size:3
Alignment explanation
Indices: 536735--536770 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
536725 AGATGATGGC
536735 GAT GAT GAT GAT GAT -AT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
536771 CAAGAAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:543359 original size:87 final size:87
Alignment explanation
Indices: 543259--543429 Score: 315
Period size: 87 Copynumber: 2.0 Consensus size: 87
543249 AATCTAATAT
* *
543259 CAAATGATAGAACGAGGCATGTAAAAGTCTTAAAGAGCCTTGGAAACAAGAAGAATCCACAACCC
1 CAAATGATAGAACGAGGCATGTAAAAGTCCTAAAGAGCCTTGAAAACAAGAAGAATCCACAACCC
543324 CTTCAAGCAACTCTAATTTTAC
66 CTTCAAGCAACTCTAATTTTAC
*
543346 CAAATGATAGAACGTGGCATGTAAAAGTCCTAAAGAGCCTTGAAAACAAGAAGAATCCACAACCC
1 CAAATGATAGAACGAGGCATGTAAAAGTCCTAAAGAGCCTTGAAAACAAGAAGAATCCACAACCC
543411 CTTCAAGCAACTCTAATTT
66 CTTCAAGCAACTCTAATTT
543430 CCCCTCCAAG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (87 bp):
CAAATGATAGAACGAGGCATGTAAAAGTCCTAAAGAGCCTTGAAAACAAGAAGAATCCACAACCC
CTTCAAGCAACTCTAATTTTAC
Found at i:547405 original size:31 final size:31
Alignment explanation
Indices: 547358--547518 Score: 115
Period size: 31 Copynumber: 5.4 Consensus size: 31
547348 TTAATATAAT
*
547358 ATTTGGTACCTGAACTTGACATTTTTTCCTA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTA
* ** *
547389 ATTTAGTACCTAAACTT----TTTTGACCCA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTA
* *
547416 ATTTGGTATCTAAACTTGACA-CTTTTCCTA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTA
* *
547446 ATTTGGTACCTAAA-TT---TTTTTTTGACCCA
1 ATTTGGTACCTAAACTTGACATTTTTT--CCTA
* * * *
547475 ATTTGGTACATGAACTTGGCACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTA
*
547506 ATTTGGCACCTAA
1 ATTTGGTACCTAA
547519 TCTTTTTTTT
Statistics
Matches: 96, Mismatches: 23, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
27 26 0.27
29 17 0.18
30 20 0.21
31 28 0.29
33 5 0.05
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACATTTTTTCCTA
Found at i:547511 original size:60 final size:59
Alignment explanation
Indices: 547358--547529 Score: 224
Period size: 59 Copynumber: 2.9 Consensus size: 59
547348 TTAATATAAT
* * *
547358 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTAGTACCTAAA--CTTTTTTGACCCA
1 ATTTGGTA-CTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTTTGACCCA
*
547416 ATTTGGTATCTAAACTTGACAC-TTTTCCTAATTTGGTACCTAAATTTTTTTTTGACCCA
1 ATTTGGTA-CTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTTTGACCCA
* * *
547475 ATTTGGTACATGAACTTGGCACTTTTTCCTAATTTGGCACCTAATCTTTTTTTTT
1 ATTTGGTAC-TGAACTTGACACTTTTTCCTAATTTGGTACCTAA-ATTTTTTTTT
547530 TTAGATTCAA
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
57 21 0.21
58 20 0.20
59 30 0.30
60 20 0.20
61 9 0.09
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (59 bp):
ATTTGGTACTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTTTGACCCA
Found at i:548938 original size:24 final size:24
Alignment explanation
Indices: 548906--548953 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
548896 ACTGCTGAAC
548906 CTCTAATACCCGATGTACCAACTT
1 CTCTAATACCCGATGTACCAACTT
548930 CTCTAATACCCGATGTACCAACTT
1 CTCTAATACCCGATGTACCAACTT
548954 TCAACTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.29
Consensus pattern (24 bp):
CTCTAATACCCGATGTACCAACTT
Found at i:551812 original size:22 final size:20
Alignment explanation
Indices: 551787--551834 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
551777 AAATTTATTT
551787 TTTATATTTTTATTTCTAAAA
1 TTTA-ATTTTTATTTCTAAAA
*
551808 GTTTAATTTTTTATTTTTAAAA
1 -TTTAA-TTTTTATTTCTAAAA
551830 TTTAA
1 TTTAA
551835 ATTTAGGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTAATTTTTATTTCTAAAA
Found at i:551838 original size:22 final size:22
Alignment explanation
Indices: 551793--551834 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
551783 ATTTTTTATA
551793 TTTTTATTTCTAAAAGTTTAAT
1 TTTTTATTTCTAAAAGTTTAAT
*
551815 TTTTTATTTTTAAAA-TTTAA
1 TTTTTATTTCTAAAAGTTTAA
551835 ATTTAGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTATTTCTAAAAGTTTAAT
Found at i:565781 original size:44 final size:44
Alignment explanation
Indices: 565727--565834 Score: 180
Period size: 44 Copynumber: 2.5 Consensus size: 44
565717 AATAAATTTA
* * *
565727 ATTTAGATTGCCATGTAAGACATCCAAGTTGGAATTTAAAATTC
1 ATTTGGATTGCCACGTAAGACATCCAAGTTGGAATTTAAAACTC
565771 ATTTGGATTGCCACGTAAGACATCCAAGTTGGAATTTAAAACTC
1 ATTTGGATTGCCACGTAAGACATCCAAGTTGGAATTTAAAACTC
*
565815 ATTTGAATTGCCACGTAAGA
1 ATTTGGATTGCCACGTAAGA
565835 TTGCCGTTAG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (44 bp):
ATTTGGATTGCCACGTAAGACATCCAAGTTGGAATTTAAAACTC
Found at i:585483 original size:52 final size:52
Alignment explanation
Indices: 585405--585539 Score: 243
Period size: 52 Copynumber: 2.6 Consensus size: 52
585395 TTCTCATTTA
585405 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
*
585457 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* *
585509 ATACTCATGATGACACATAGTCATTGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
585540 TTTGCATTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 80 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
Found at i:586536 original size:16 final size:16
Alignment explanation
Indices: 586512--586544 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
586502 GTCCTACAAA
*
586512 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
586528 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
586544 T
1 T
586545 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:595139 original size:17 final size:18
Alignment explanation
Indices: 595117--595150 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
595107 ATAATTGTAA
*
595117 TTTAAAT-TTTAATTATT
1 TTTAAATGTGTAATTATT
595134 TTTAAATGTGTAATTAT
1 TTTAAATGTGTAATTAT
595151 CAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTAAATGTGTAATTATT
Found at i:596900 original size:19 final size:19
Alignment explanation
Indices: 596876--596913 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
596866 TTGATTTGAG
596876 ATTGTTAGTTATAGTCACT
1 ATTGTTAGTTATAGTCACT
596895 ATTGTTAGTTATAGTCACT
1 ATTGTTAGTTATAGTCACT
596914 GATCAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
ATTGTTAGTTATAGTCACT
Found at i:601981 original size:35 final size:36
Alignment explanation
Indices: 601916--602013 Score: 144
Period size: 35 Copynumber: 2.8 Consensus size: 36
601906 GTAAAAATTT
* * *
601916 GTAAATCAATGAACCGTAAAAATGATAATCGTGATA
1 GTAAATCAATGAACTGTAAAAATGACAATCGCGATA
*
601952 GTAAATCAATGAAATGT-AAAATGACAATCGCGATA
1 GTAAATCAATGAACTGTAAAAATGACAATCGCGATA
*
601987 GTAAATCAACGAACTGTAAAAATGACA
1 GTAAATCAATGAACTGTAAAAATGACA
602014 GACACAATAG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 31 0.56
36 24 0.44
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.22
Consensus pattern (36 bp):
GTAAATCAATGAACTGTAAAAATGACAATCGCGATA
Found at i:602024 original size:36 final size:35
Alignment explanation
Indices: 601949--602025 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
601939 GATAATCGTG
* * *
601949 ATAGTAAATCAATGAAATGTAAAATGACAATCGCG
1 ATAGTAAATCAACGAAATGTAAAATGACAATCACA
*
601984 ATAGTAAATCAACGAACTGTAAAAATGACAGA-CACA
1 ATAGTAAATCAACGAAATGT-AAAATGACA-ATCACA
602020 ATAGTA
1 ATAGTA
602026 GATTAGTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 18 0.50
36 17 0.47
37 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.21
Consensus pattern (35 bp):
ATAGTAAATCAACGAAATGTAAAATGACAATCACA
Found at i:602163 original size:36 final size:36
Alignment explanation
Indices: 602099--602168 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
602089 AAACTGAAGG
* ** *
602099 TCGCAATAGTAAATCAGCGGACTGTAAAAATGACGA
1 TCGCAATAGTAAATAAGCAAACTATAAAAATGACGA
*
602135 TCGCAATAGTAAATAATCAAACTATAAAAATGAC
1 TCGCAATAGTAAATAAGCAAACTATAAAAATGAC
602169 AGTCATGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (36 bp):
TCGCAATAGTAAATAAGCAAACTATAAAAATGACGA
Done.