Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014159.1 Kokia drynarioides strain JFW-HI SEQ_129192, 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: 462093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 17 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1074 original size:158 final size:158
Alignment explanation
Indices: 786--1102 Score: 440
Period size: 158 Copynumber: 2.0 Consensus size: 158
776 CTCTGTATCA
* * * * * *
786 TGTAATGCTCACACGAGTTGTGTAATGGGCTTGCTCACATGAGCTGTGGGTCGAGATGTTAGGCT
1 TGTAATGCTCACACGAGTTGTGTAATGGGCCTACCCACACGAGCTATGAGTCGAGATGTTAGGCT
* * ** * *
851 ACACGATGCTGCTCATATGAGCTGTGGAGAATCCGTAACATATGCAGGATCTCAGCCATCGGTAG
66 ACACGATACTGCTCACACAAGCTGTGGAGAATCCGTAACACATGCAGGATCTCAGCCATAGGTAG
916 GACATCTAAAACCAGCACCCATATAACC
131 GACATCTAAAACCAGCACCCATATAACC
* *
944 TGTAATGCTCACACGAGTTGTG-AAGTGGGCCTACCCACACGTGCTATGAGTCGAGATGTTATGC
1 TGTAATGCTCACACGAGTTGTGTAA-TGGGCCTACCCACACGAGCTATGAGTCGAGATGTTAGGC
*
1008 TACACGATACTGCTTACACAAGCTGTGGAGAATCCGTAACACATGCTA-GATCTCAGCCATAGGT
65 TACACGATACTGCTCACACAAGCTGTGGAGAATCCGTAACACATGC-AGGATCTCAGCCATAGGT
* **
1072 AGGACATTTAAGTCCAGCACCCATATAACC
129 AGGACATCTAAAACCAGCACCCATATAACC
1102 T
1 T
1103 ATAAATCTCG
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
157 2 0.01
158 136 0.98
159 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (158 bp):
TGTAATGCTCACACGAGTTGTGTAATGGGCCTACCCACACGAGCTATGAGTCGAGATGTTAGGCT
ACACGATACTGCTCACACAAGCTGTGGAGAATCCGTAACACATGCAGGATCTCAGCCATAGGTAG
GACATCTAAAACCAGCACCCATATAACC
Found at i:10397 original size:20 final size:20
Alignment explanation
Indices: 10359--10448 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
10349 CATATAGTGA
* * *
10359 TTTACCAAAATTACAAAGGC
1 TTTACCAATATTTCTAAGGC
10379 TTTACCGAA-ATTTCTAAGG-
1 TTTACC-AATATTTCTAAGGC
* * *
10398 TTACACCAATATTTTTAAGGG
1 TT-TACCAATATTTCTAAGGC
*
10419 TTTACCAATATTTCTAAAGC
1 TTTACCAATATTTCTAAGGC
10439 TTTACCAATA
1 TTTACCAATA
10449 ATTTTAAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.07
20 50 0.86
21 4 0.07
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
TTTACCAATATTTCTAAGGC
Found at i:10456 original size:20 final size:20
Alignment explanation
Indices: 10402--10457 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
10392 CTAAGGTTAC
* * *
10402 ACCAATATTTTTAAGGGTTT
1 ACCAATAATTTTAAAGCTTT
10422 ACCAAT-ATTTCTAAAGCTTT
1 ACCAATAATTT-TAAAGCTTT
10442 ACCAATAATTTTAAAG
1 ACCAATAATTTTAAAG
10458 ATTTCCCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.77
21 4 0.13
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (20 bp):
ACCAATAATTTTAAAGCTTT
Found at i:10531 original size:20 final size:20
Alignment explanation
Indices: 10501--10679 Score: 141
Period size: 20 Copynumber: 9.1 Consensus size: 20
10491 CATTTTGGCA
*
10501 TACCAATATTTCTAAAGATT
1 TACCAAAATTTCTAAAGATT
* * * *
10521 AACCAAAATTTATAAGGTTT
1 TACCAAAATTTCTAAAGATT
*
10541 TACCAAAATTTCTAAAGCTT
1 TACCAAAATTTCTAAAGATT
*
10561 TA-CAAAATTTTCTAAGGATT
1 TACCAAAA-TTTCTAAAGATT
* * *
10581 TACGAAAGTTT-TTAAGATT
1 TACCAAAATTTCTAAAGATT
* *
10600 ATATCAAAATTTC-CAAGATT
1 -TACCAAAATTTCTAAAGATT
* *
10620 TACCAAAATTTTTAAGGATT
1 TACCAAAATTTCTAAAGATT
* * *
10640 TAAC-AATTTTCTAAAGGTT
1 TACCAAAATTTCTAAAGATT
* *
10659 TACCAATATTTCTAAATATT
1 TACCAAAATTTCTAAAGATT
10679 T
1 T
10680 CCCTAGTGTC
Statistics
Matches: 120, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
19 35 0.29
20 82 0.68
21 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (20 bp):
TACCAAAATTTCTAAAGATT
Found at i:10661 original size:39 final size:38
Alignment explanation
Indices: 10533--10669 Score: 116
Period size: 39 Copynumber: 3.5 Consensus size: 38
10523 CCAAAATTTA
* * * *
10533 TAAGGTTTTACCAAAATTTCTAAAGCTTTACAAAATTTTC
1 TAAGGATTTACCAAAATTT-TTAAGATTTA-ACAATTTTC
* * * *
10573 TAAGGATTTACGAAAGTTTTTAAGATTATATCAAAATTTC
1 TAAGGATTTACCAAAATTTTTAAGATT-TAAC-AATTTTC
*
10613 CAA-GATTTACCAAAATTTTTAAGGATTTAACAATTTTC
1 TAAGGATTTACCAAAATTTTTAA-GATTTAACAATTTTC
*
10651 TAAAGG-TTTACCAATATTT
1 T-AAGGATTTACCAAAATTT
10670 CTAAATATTT
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
38 6 0.08
39 40 0.52
40 31 0.40
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (38 bp):
TAAGGATTTACCAAAATTTTTAAGATTTAACAATTTTC
Found at i:10814 original size:20 final size:20
Alignment explanation
Indices: 10791--10848 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
10781 TATTTATGGT
10791 TTTATCAAAATTTCT-AAGG
1 TTTATCAAAATTTCTAAAGG
* *
10810 ATTTAACAATATTTCTAAAGG
1 -TTTATCAAAATTTCTAAAGG
* *
10831 TTTATCAATATCTCTAAA
1 TTTATCAAAATTTCTAAA
10849 TATTTCCCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTATCAAAATTTCTAAAGG
Found at i:13238 original size:17 final size:19
Alignment explanation
Indices: 13216--13258 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
13206 TCAAACTTAG
*
13216 AAAAATAATAAAT-AAA-T
1 AAAAATAAAAAATAAAATT
13233 AAAAATAAAAAATAAAATT
1 AAAAATAAAAAATAAAATT
13252 AAAAATA
1 AAAAATA
13259 CGTATGGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATAAAAAATAAAATT
Found at i:13247 original size:13 final size:13
Alignment explanation
Indices: 13222--13256 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
13212 TTAGAAAAAT
13222 AATAAATAAATAAA
1 AATAAA-AAATAAA
13236 AATAAAAAATAAA
1 AATAAAAAATAAA
*
13249 ATTAAAAA
1 AATAAAAA
13257 TACGTATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:14083 original size:39 final size:39
Alignment explanation
Indices: 14024--14165 Score: 212
Period size: 39 Copynumber: 3.6 Consensus size: 39
14014 AAACAGAACC
* * * * * *
14024 TTGGCTTTGCGGAGGAATGTATATGCCTAAATTTCGAAG
1 TTGGCTTTGCGGAGGGACGTATATGCTTTATTTTCGAAA
*
14063 TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
1 TTGGCTTTGCGGAGGGACGTATATGCTTTATTTTCGAAA
14102 TTGGCTTTGCGGAGGGACGTATATGCTTTATTTTCGAAA
1 TTGGCTTTGCGGAGGGACGTATATGCTTTATTTTCGAAA
*
14141 TTGGCTTTGCAGAGGGACGTATATG
1 TTGGCTTTGCGGAGGGACGTATATG
14166 TTGTGTTTTG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 96 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.37
Consensus pattern (39 bp):
TTGGCTTTGCGGAGGGACGTATATGCTTTATTTTCGAAA
Found at i:14312 original size:26 final size:26
Alignment explanation
Indices: 14233--14313 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
14223 GCGGAGGTAT
*
14233 GAGCTGTTATTACAATGCATTTGTGC
1 GAGCTGTTATTACAATGCATATGTGC
* * * *
14259 GAGCTATCATTGCAATGCATGTGTGC
1 GAGCTGTTATTACAATGCATATGTGC
* * *
14285 GAGCTGTTATTACCATACATATGCGC
1 GAGCTGTTATTACAATGCATATGTGC
14311 GAG
1 GAG
14314 TATTACAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (26 bp):
GAGCTGTTATTACAATGCATATGTGC
Found at i:15158 original size:21 final size:20
Alignment explanation
Indices: 15130--15168 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
15120 AAATCTAATT
15130 TCTGTTCATCTT-TTTTTATG
1 TCTGTTCAT-TTCTTTTTATG
15150 TCTGATTCATTTCTTTTTA
1 TCTG-TTCATTTCTTTTTA
15169 CTTTAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.15, G:0.08, T:0.64
Consensus pattern (20 bp):
TCTGTTCATTTCTTTTTATG
Found at i:19545 original size:32 final size:31
Alignment explanation
Indices: 19504--19568 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
19494 AATTTTGAAT
* *
19504 TAAATAATTTAAGTTATTTGTA-TCAACTCGAA
1 TAAAAAATTTAAATT-TTT-TATTCAACTCGAA
*
19536 TAAAAAATTTAAATTTTTTATTTAACTCGAA
1 TAAAAAATTTAAATTTTTTATTCAACTCGAA
19567 TA
1 TA
19569 TGAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 2 0.07
31 14 0.48
32 13 0.45
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (31 bp):
TAAAAAATTTAAATTTTTTATTCAACTCGAA
Found at i:22046 original size:19 final size:19
Alignment explanation
Indices: 22022--22063 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
22012 TGTGTGTATA
22022 TATGTA-TAATTATGTATGT
1 TATGTACTAA-TATGTATGT
*
22041 TATGTACTGATATGTATGT
1 TATGTACTAATATGTATGT
22060 TATG
1 TATG
22064 GTCCATACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (19 bp):
TATGTACTAATATGTATGT
Found at i:22150 original size:37 final size:37
Alignment explanation
Indices: 22102--22172 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
22092 TATAATTATA
* *
22102 TATGTTATGTTTACTGTTATGTTTGTATATTTGTATG
1 TATGTTATGTTTACTGCTATGCTTGTATATTTGTATG
*
22139 TATGTTATGTTTACTGCTATGCTTGTATGTTTGT
1 TATGTTATGTTTACTGCTATGCTTGTATATTTGT
22173 TAATTATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.58
Consensus pattern (37 bp):
TATGTTATGTTTACTGCTATGCTTGTATATTTGTATG
Found at i:27953 original size:42 final size:42
Alignment explanation
Indices: 27894--27992 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
27884 TGCGGATTCT
27894 CCACAGCTCGTGTGACCAACATTCTGTAGCTAACATCCCGAC
1 CCACAGCTCGTGTGACCAACATTCTGTAGCTAACATCCCGAC
* * *
27936 CCACAACTCATGTGACCAGCATTCTGTAGCTAACATCCCGAC
1 CCACAGCTCGTGTGACCAACATTCTGTAGCTAACATCCCGAC
27978 CCACAGCTCGTGTGA
1 CCACAGCTCGTGTGA
27993 GCAGGCCCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.21
Consensus pattern (42 bp):
CCACAGCTCGTGTGACCAACATTCTGTAGCTAACATCCCGAC
Found at i:29427 original size:74 final size:74
Alignment explanation
Indices: 29340--29492 Score: 209
Period size: 74 Copynumber: 2.1 Consensus size: 74
29330 AATGATAAAT
* * * * *
29340 GATGGTGAGGGAAAACGATGGTG-AAATCAAAAGAAAAAAAGGGTTTATATTTCTTTGAAGAAAA
1 GATGGTGAGGGAAAACAATAGTGAAAAT-AAAAGAAAAAAAGGGTTAAAATTTATTTGAAGAAAA
*
29404 AAGGGAAAAC
65 AAGAGAAAAC
*
29414 GATGGTGAGGGAAAACAATAGTGAAAATAAAAGAAAAAACGGGTTAAAATTTATTTGAAGAAAAA
1 GATGGTGAGGGAAAACAATAGTGAAAATAAAAGAAAAAAAGGGTTAAAATTTATTTGAAGAAAAA
* *
29479 TGAGAACAC
66 AGAGAAAAC
29488 GATGG
1 GATGG
29493 CATAAATGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 65 0.94
75 4 0.06
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.20
Consensus pattern (74 bp):
GATGGTGAGGGAAAACAATAGTGAAAATAAAAGAAAAAAAGGGTTAAAATTTATTTGAAGAAAAA
AGAGAAAAC
Found at i:32812 original size:46 final size:46
Alignment explanation
Indices: 32664--32792 Score: 177
Period size: 46 Copynumber: 2.8 Consensus size: 46
32654 TTACTTGCAG
*** * *
32664 AGGCAAAGAATATGCGTGCAGAAAAAATTATTTGCACCAATAATGT
1 AGGCAAAGAATACATGTGCAGAAAAAATAACTTGCACCAATAATGT
* * *
32710 AGGCAAAGAATACATGTGTAGAAAAACTAACTTGTACCAATAATGT
1 AGGCAAAGAATACATGTGCAGAAAAAATAACTTGCACCAATAATGT
*
32756 AGGCAAAGAATACATGTGCAGAAAAAATGACTTGCAC
1 AGGCAAAGAATACATGTGCAGAAAAAATAACTTGCAC
32793 AAAAAAAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (46 bp):
AGGCAAAGAATACATGTGCAGAAAAAATAACTTGCACCAATAATGT
Found at i:33776 original size:19 final size:21
Alignment explanation
Indices: 33737--33776 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33727 AGCTAACGAG
33737 GAAGGAGATGCAAGTGGGGAA
1 GAAGGAGATGCAAGTGGGGAA
*
33758 GAAGGAGGTGC-AG-GGGGAA
1 GAAGGAGATGCAAGTGGGGAA
33777 ATGATGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.35, C:0.05, G:0.53, T:0.07
Consensus pattern (21 bp):
GAAGGAGATGCAAGTGGGGAA
Found at i:42512 original size:21 final size:21
Alignment explanation
Indices: 42488--42532 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42478 CCTAAACCTT
* * *
42488 AAATCCTATATCCTAATATTA
1 AAATCCTAAACCCTAATATGA
42509 AAATCCTAAACCCTAATATGA
1 AAATCCTAAACCCTAATATGA
42530 AAA
1 AAA
42533 CACCAAACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATCCTAAACCCTAATATGA
Found at i:42540 original size:21 final size:21
Alignment explanation
Indices: 42499--42548 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
42489 AATCCTATAT
* *
42499 CCTAATATTAAAATCCTAAAC
1 CCTAATATGAAAATCCCAAAC
42520 CCTAATATGAAAA-CACCAAAC
1 CCTAATATGAAAATC-CCAAAC
42541 CCTTAATA
1 CC-TAATA
42549 CTAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (21 bp):
CCTAATATGAAAATCCCAAAC
Found at i:42913 original size:2 final size:2
Alignment explanation
Indices: 42906--42934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42896 TTAAAATTCA
42906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42935 AAATTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44988 original size:18 final size:18
Alignment explanation
Indices: 44961--44999 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
44951 CAAAAACAAA
44961 AAATAAAAGG-CTAAATT
1 AAATAAAAGGACTAAATT
44978 AAATAAAAAGGACTAAATT
1 AAAT-AAAAGGACTAAATT
44997 AAA
1 AAA
45000 ACCTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGACTAAATT
Found at i:55098 original size:25 final size:25
Alignment explanation
Indices: 55054--55201 Score: 218
Period size: 25 Copynumber: 6.1 Consensus size: 25
55044 GAGGTACATA
* *
55054 AGTGCTAGGGAAACAAAAGCACACAC
1 AGTGCT-GGGTAACAGAAGCACACAC
55080 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
55105 AGTGCT--G-AACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
55127 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
55152 AGTGCT--G-AACAGAAACACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
55174 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
55199 AGT
1 AGT
55202 ACTGAACAGA
Statistics
Matches: 112, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
22 41 0.37
23 2 0.02
24 2 0.02
25 61 0.54
26 6 0.05
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (25 bp):
AGTGCTGGGTAACAGAAGCACACAC
Found at i:55123 original size:47 final size:47
Alignment explanation
Indices: 55065--55214 Score: 273
Period size: 47 Copynumber: 3.2 Consensus size: 47
55055 GTGCTAGGGA
*
55065 AACAAAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
55112 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
* *
55159 AACAGAAACACACACAGTGCTGGGTAACAGAAGCACACACAGTACTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
55206 AACAGAAGC
1 AACAGAAGC
55215 GCGCTAGCGT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 99 1.00
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.10
Consensus pattern (47 bp):
AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
Found at i:55315 original size:24 final size:26
Alignment explanation
Indices: 55277--55324 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
55267 TCTACATGGA
55277 CATAATCTCTCATAT-TCATCATTTTT
1 CATAATCTCTCATATATCA-CATTTTT
55303 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
55325 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTTT
Found at i:61679 original size:18 final size:19
Alignment explanation
Indices: 61642--61679 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
61632 TTTATGATTT
*
61642 TAAATAATTTTTGGTAAAA
1 TAAATAATTTTGGGTAAAA
*
61661 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGTAAAA
61679 T
1 T
61680 TGGAACTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (19 bp):
TAAATAATTTTGGGTAAAA
Found at i:63313 original size:24 final size:24
Alignment explanation
Indices: 63286--63342 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
63276 AGTATTAAGC
63286 TTGAGTCTCCACTCATCGGGTTAT
1 TTGAGTCTCCACTCATCGGGTTAT
63310 TTGAGTCTCCACTCATCGGGTTAT
1 TTGAGTCTCCACTCATCGGGTTAT
63334 TTGAGTCTC
1 TTGAGTCTC
63343 TATAAGGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39
Consensus pattern (24 bp):
TTGAGTCTCCACTCATCGGGTTAT
Found at i:65081 original size:18 final size:17
Alignment explanation
Indices: 65038--65082 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
65028 AGTAGACAAC
65038 AAATAAAATAAAAAAGAA
1 AAAT-AAATAAAAAAGAA
*
65056 AAATAAATAAACAAATAA
1 AAATAAATAAA-AAAGAA
65074 AAATAAATA
1 AAATAAATA
65083 CATAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (17 bp):
AAATAAATAAAAAAGAA
Found at i:65109 original size:22 final size:21
Alignment explanation
Indices: 65038--65105 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
65028 AGTAGACAAC
*
65038 AAATAAAATAAAAAAGAAAAAT
1 AAATAAAA-AATAAAGAAAAAT
65060 AAATAAACAAATAAA-AATAAAT
1 AAATAAA-AAATAAAGAA-AAAT
* *
65082 ACATAAAAAATAAAGAAACAT
1 AAATAAAAAATAAAGAAAAAT
65103 AAA
1 AAA
65106 ATAAGGGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 14 0.36
22 24 0.62
23 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.15
Consensus pattern (21 bp):
AAATAAAAAATAAAGAAAAAT
Found at i:65220 original size:18 final size:18
Alignment explanation
Indices: 65193--65231 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
65183 GAAAAATAGA
65193 AAATAAAAGG-CTAAATT
1 AAATAAAAGGACTAAATT
65210 AAATAAAAAGGACTAAATT
1 AAAT-AAAAGGACTAAATT
65229 AAA
1 AAA
65232 ACCTAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGACTAAATT
Found at i:65423 original size:35 final size:35
Alignment explanation
Indices: 65384--65451 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
65374 ACTAAATCAC
*
65384 AAATAAAATAAAATAAAATGG-GAAATTAAAAAATA
1 AAATAAAAT-AAATAAAAAGGAGAAATTAAAAAATA
*
65419 AAATAAAATATATAAAAAGGACGAAATTAAAAA
1 AAATAAAATAAATAAAAAGGA-GAAATTAAAAA
65452 GACAATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 9 0.31
35 9 0.31
36 11 0.38
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.19
Consensus pattern (35 bp):
AAATAAAATAAATAAAAAGGAGAAATTAAAAAATA
Found at i:66974 original size:100 final size:100
Alignment explanation
Indices: 66870--67415 Score: 431
Period size: 100 Copynumber: 5.5 Consensus size: 100
66860 GACTTGCTAA
* * * * *
66870 TGTAGTTTCAATTTGATTCACTAC-AGTTTCAAGGATATAAGATTTGATGTCGTAACTTCATCTT
1 TGTAGCTTCAATCTGATCCACTACAACTTT-AAGGATATAGGATTTGATGTCGTAACTTCATCTT
* * * *
66934 GCTCCACTTCATCTTCAGGGAGAAAAGATTTACTTT
65 GCTCCACTGCAACTTCAGGGAGAAAAGATTTGCTTC
* * * * *
66970 TGTAGCTTCAAT-TCGACCCACTGCAACTTTAGGGGTATAGGATTTGATGTTGTAACTTCATCTT
1 TGTAGCTTCAATCT-GATCCACTACAACTTTAAGGATATAGGATTTGATGTCGTAACTTCATCTT
* * * *
67034 GCTCTACTGCAACTTCAGAGAGATAAAGCTTTGCTAC
65 GCTCCACTGCAACTTCAGGGAGA-AAAGATTTGCTTC
* * * * * *
67071 TCTAGTTTTAATCTGA-CCCCTGCAACTTTAAGGATATAGGATTTGATGTCGTAACTTCATCTTC
1 TGTAGCTTCAATCTGATCCACTACAACTTTAAGGATATAGGATTTGATGTCGTAACTTCATCTTG
* * * * *
67135 CTCCCCTGCATCTTCAGGAAGATAATATTTGCTTC
66 CTCCACTGCAACTTCAGGGAGAAAAGATTTGCTTC
* * * * *
67170 TGTAGCTTCAATCTAATCCACTACAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTG
1 TGTAGCTTCAATCTGATCCACTACAACTTTAAGGATATAGGATTTGATGTCGTAACTTCATCTTG
* * *
67235 CTCCACTGCAAC-TCTAGGGAGATAAGATTTGTTGTT
66 CTCCACTGCAACTTC-AGGGAGAAAAGATTTGCT-TC
** * ** * ** ** * ** * * * *
67271 TGTAATTTCATTCCAAACCGTTGTAACCTCTGCGGA-ACT-GGAATTGTTGTTGTAACCTCATCT
1 TGTAGCTTCAATCTGATCCACTACAA-CTTTAAGGATA-TAGGATTTGATGTCGTAACTTCATCT
* * *
67334 TGCTCCACTGCAACTTTAGGGAGATAAGATTTGTCAT-
64 TGCTCCACTGCAACTTCAGGGAGAAAAGATTTG-CTTC
* * *
67371 TATAGTTTCAATCTGATCCACTACAACTTCAAGGATATAGGATTT
1 TGTAGCTTCAATCTGATCCACTACAACTTTAAGGATATAGGATTT
67416 TACTGATCCA
Statistics
Matches: 347, Mismatches: 86, Indels: 26
0.76 0.19 0.06
Matches are distributed among these distances:
99 30 0.09
100 215 0.62
101 94 0.27
102 8 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (100 bp):
TGTAGCTTCAATCTGATCCACTACAACTTTAAGGATATAGGATTTGATGTCGTAACTTCATCTTG
CTCCACTGCAACTTCAGGGAGAAAAGATTTGCTTC
Found at i:67142 original size:50 final size:50
Alignment explanation
Indices: 66900--67265 Score: 169
Period size: 50 Copynumber: 7.3 Consensus size: 50
66890 CTACAGTTTC
* * * * * *
66900 AAGGATATAAGATTTGATGTCGTAACTTCATCTTGCTCCACTTCATCTTC
1 AAGGAGATAAGATTTGATGTCGTAGCTTCATCTTACTCCACTGCAACTTT
* * * * *
66950 AGGGAGAAAAGATTT-ACTTTTGTAGCTTCAAT-TCGAC-CCACTGCAACTTT
1 AAGGAGATAAGATTTGA-TGTCGTAGCTTC-ATCT-TACTCCACTGCAACTTT
* * * * * *
67000 -AGGGGTATAGGATTTGATGTTGTAACTTCATCTTGCTCTACTGCAAC-TT
1 AAGGAG-ATAAGATTTGATGTCGTAGCTTCATCTTACTCCACTGCAACTTT
* * * * * * *
67049 CAGAGAGATAAAGCTTTGCTACTC-TAGTTTTAATCTGAC-CC-CTGCAACTTT
1 AAG-GAGAT-AAGATTTGAT-GTCGTAG-CTTCATCTTACTCCACTGCAACTTT
* * * * * *
67100 AAGGATATAGGATTTGATGTCGTAACTTCATCTTCCTCCCCTGCATC-TT
1 AAGGAGATAAGATTTGATGTCGTAGCTTCATCTTACTCCACTGCAACTTT
* * * * * *
67149 CAGGAAGATAATATTTGCT-TCTGTAGCTTCAATC-TAATCCACTACAACTTC
1 AAGG-AGATAAGATTTGATGTC-GTAGCTTC-ATCTTACTCCACTGCAACTTT
* * * * * *
67200 AAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTGCAACTCT
1 AAGGAGATAAGATTTGATGTCGTAGCTTCATCTTACTCCACTGCAACTTT
*
67250 AGGGAGATAAGATTTG
1 AAGGAGATAAGATTTG
67266 TTGTTTGTAA
Statistics
Matches: 224, Mismatches: 70, Indels: 44
0.66 0.21 0.13
Matches are distributed among these distances:
48 9 0.04
49 30 0.13
50 149 0.67
51 28 0.12
52 8 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (50 bp):
AAGGAGATAAGATTTGATGTCGTAGCTTCATCTTACTCCACTGCAACTTT
Found at i:68355 original size:129 final size:129
Alignment explanation
Indices: 68079--68325 Score: 327
Period size: 129 Copynumber: 1.9 Consensus size: 129
68069 TGAGAGATAA
* * * * * *
68079 GACCATTTCATGCCCATCCTTTGATCCAAATTTGAGCCGCCCTTTCGAGTTTTCAACTCAAATCT
1 GACCATTACATACCAATTCTTTGATCCAAATTTGAGCCACCATTTCGAGTTTTCAACTCAAATCT
* * * * *
68144 CCTTTGGTTTCGAGATGTCGTTTACGGGTTTTCATCTCGACCTCTCCCTTTTCTAGGGTGAAGC
66 CCTTTGGTTTCAAAATGCCCTTTACGAGTTTTCATCTCGACCTCTCCCTTTTCTAGGGTGAAGC
* * *
68208 GACCATTACATACCAATTCTTTGGTCCAAATTTGAGCCACCATTTCGGGTTTTCTACTCAAA-CT
1 GACCATTACATACCAATTCTTTGATCCAAATTTGAGCCACCATTTCGAGTTTTCAACTCAAATCT
68272 -CTTTAGGTTTCAAAATGCCCTTTACGAGTTTTCATCTCGACCTCTTCCCCTTTT
66 CCTTT-GGTTTCAAAATGCCCTTTACGAGTTTTCATCTCGACCTC-T-CCCTTTT
68326 TTTTAGGTGA
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
127 4 0.04
128 36 0.36
129 54 0.53
130 7 0.07
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (129 bp):
GACCATTACATACCAATTCTTTGATCCAAATTTGAGCCACCATTTCGAGTTTTCAACTCAAATCT
CCTTTGGTTTCAAAATGCCCTTTACGAGTTTTCATCTCGACCTCTCCCTTTTCTAGGGTGAAGC
Found at i:69334 original size:22 final size:22
Alignment explanation
Indices: 69309--69354 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
69299 GATAACAAAT
* *
69309 AAAAA-AAAGATAGATAAATAA
1 AAAAATAAAAATAAATAAATAA
*
69330 AAAAATAAAAATAAATACATAA
1 AAAAATAAAAATAAATAAATAA
69352 AAA
1 AAA
69355 TAAAGAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAATAAATAAATAA
Found at i:69343 original size:14 final size:14
Alignment explanation
Indices: 69324--69369 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
69314 AAAGATAGAT
69324 AAATAAAAAAATAA
1 AAATAAAAAAATAA
* *
69338 AAATAAATACATAA
1 AAATAAAAAAATAA
69352 AAATAAAGAAACATAA
1 AAATAAA-AAA-ATAA
69368 AA
1 AA
69370 TAAGGGATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 19 0.73
15 1 0.04
16 6 0.23
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:69343 original size:18 final size:20
Alignment explanation
Indices: 69322--69358 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
69312 AAAAAGATAG
69322 ATAAATA-A-AAAAATAAAA
1 ATAAATACATAAAAATAAAA
69340 ATAAATACATAAAAATAAA
1 ATAAATACATAAAAATAAA
69359 GAAACATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (20 bp):
ATAAATACATAAAAATAAAA
Found at i:69488 original size:19 final size:17
Alignment explanation
Indices: 69456--69494 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
69446 CAAAAACAGA
69456 AAATAAAAGGCTAAATT
1 AAATAAAAGGCTAAATT
69473 AAATAAAAATGGCTAAATT
1 AAAT-AAAA-GGCTAAATT
69492 AAA
1 AAA
69495 ACCTAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 12 0.60
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (17 bp):
AAATAAAAGGCTAAATT
Found at i:75270 original size:40 final size:40
Alignment explanation
Indices: 75215--75395 Score: 227
Period size: 40 Copynumber: 4.4 Consensus size: 40
75205 AACCTACTAT
* *
75215 GTCGTAGCTTAAGTTTTGACACCGGCTCATAGCCTGCTAA
1 GTCGTAGCTTGAGTTTTTACACCGGCTCATAGCCTGCTAA
*
75255 GTCGTAACTTGAGTTTTTTTTTACACCGGCTCATAGCCTGCTAA
1 GTCGTAGCTTGAG----TTTTTACACCGGCTCATAGCCTGCTAA
* *
75299 GTCGTAGCTTGAGTTTTCTTACACTGGCTCATAGCCTACTAA
1 GTCGTAGCTTGAG-TTT-TTACACCGGCTCATAGCCTGCTAA
* * * *
75341 GCCGTAGCTTAAGTTTTTACACTGGCTCATAACCTGCTAA
1 GTCGTAGCTTGAGTTTTTACACCGGCTCATAGCCTGCTAA
75381 GTCGTAGCTTGAGTT
1 GTCGTAGCTTGAGTT
75396 GATTCAAACA
Statistics
Matches: 124, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
40 46 0.37
41 7 0.06
42 33 0.27
44 38 0.31
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (40 bp):
GTCGTAGCTTGAGTTTTTACACCGGCTCATAGCCTGCTAA
Found at i:85055 original size:41 final size:41
Alignment explanation
Indices: 84998--85076 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
84988 CCGTATCAGC
* * *
84998 CTTGGTTTAGCGTCCTTCTTTGCAAAAAGATATTTCAAAGA
1 CTTGGTTTAACATCCTTCTTTGCAAAAAGATATCTCAAAGA
85039 CTTGGTTTAACATCCTTCTTTGCAAAAAGATATCTCAA
1 CTTGGTTTAACATCCTTCTTTGCAAAAAGATATCTCAA
85077 TACTGAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (41 bp):
CTTGGTTTAACATCCTTCTTTGCAAAAAGATATCTCAAAGA
Found at i:94310 original size:52 final size:52
Alignment explanation
Indices: 94231--94471 Score: 369
Period size: 52 Copynumber: 4.6 Consensus size: 52
94221 TAAATGAAAA
* **
94231 AGGTCTGATTACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTGTG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
* * *
94283 AGGTCTGATGACTATGTGTTATTGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
*
94335 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
94387 AGGT-TCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
1 AGGTCT-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
*
94439 AGGT-TCGATGACTATGTGTCATTGATGAGTATA
1 AGGTCT-GATGACTATGTGTCATCG-TGAGTATA
94472 AAATGAAATG
Statistics
Matches: 177, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
52 169 0.95
53 8 0.05
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (52 bp):
AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
Found at i:94511 original size:61 final size:61
Alignment explanation
Indices: 94418--94541 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
94408 TCGTGAGTAT
* * * *
94418 ATGAATCCTTTACGGATTAAGAGGTTCGATGACTATGTGTCATTGATGAGTATAAAATG-AA
1 ATGAATCCATTACGAATTAAGAGGTCCGATGACTATGTGTCATCG-TGAGTATAAAATGCAA
* *
94479 ATGAATCCCATTACGAATTAA-AGGTCCGATGACTCTGTGTCATCGTGAGTATCAAATGCAA
1 ATGAAT-CCATTACGAATTAAGAGGTCCGATGACTATGTGTCATCGTGAGTATAAAATGCAA
94540 AT
1 AT
94542 TGAAACCAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 12 0.22
61 31 0.56
62 12 0.22
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (61 bp):
ATGAATCCATTACGAATTAAGAGGTCCGATGACTATGTGTCATCGTGAGTATAAAATGCAA
Found at i:101623 original size:52 final size:52
Alignment explanation
Indices: 101544--101730 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 52
101534 TGAATGAAAA
* * * * *
101544 AGGTCTGATAACTATGTGTCATCATGAGTATATGAATCCTTTACGGATCATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTACAGATTATG
* *
101596 AGGTCCGATGACTATGTGTCATTATGAGTATATGAATCTTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTACAGATTATG
* * * *
101648 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACATATTAAG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTACAGATTATG
* *
101700 AGGTTCGATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCATGAGTAT
101731 TAAATGAAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTACAGATTATG
Found at i:106408 original size:35 final size:36
Alignment explanation
Indices: 106347--106430 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
106337 TGCTCTTTCA
* *
106347 AGCCAGTAGTGCCCAAACGAGCCAGTACGCCCAAATG
1 AGCCAGTA-TGCTCAAACGAGCCAGTACGCCCAAACG
* * *
106384 AGCCAGTATGCTC-AACGAGTCAGTATGCTCAAACG
1 AGCCAGTATGCTCAAACGAGCCAGTACGCCCAAACG
*
106419 AGTCAGTATGCT
1 AGCCAGTATGCT
106431 ATTCCTTCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 29 0.71
36 4 0.10
37 8 0.20
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (36 bp):
AGCCAGTATGCTCAAACGAGCCAGTACGCCCAAACG
Found at i:106430 original size:18 final size:18
Alignment explanation
Indices: 106347--106430 Score: 98
Period size: 18 Copynumber: 4.7 Consensus size: 18
106337 TGCTCTTTCA
*
106347 AGCCAGTAGTGCCCAAACG
1 AGCCAGTA-TGCTCAAACG
* * *
106366 AGCCAGTACGCCCAAATG
1 AGCCAGTATGCTCAAACG
106384 AGCCAGTATGCTC-AACG
1 AGCCAGTATGCTCAAACG
*
106401 AGTCAGTATGCTCAAACG
1 AGCCAGTATGCTCAAACG
*
106419 AGTCAGTATGCT
1 AGCCAGTATGCT
106431 ATTCCTTCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.26
18 35 0.60
19 8 0.14
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (18 bp):
AGCCAGTATGCTCAAACG
Found at i:108008 original size:23 final size:24
Alignment explanation
Indices: 107961--108009 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
107951 ACAAATTACA
*
107961 TTTTTGTACATTTTTCTTTTGTGT
1 TTTTTGTACATTTTTCTTTTCTGT
* *
107985 TTTTTGTCCTTTTTTC-TTTCTGT
1 TTTTTGTACATTTTTCTTTTCTGT
108008 TT
1 TT
108010 GTAGGTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.04, C:0.12, G:0.10, T:0.73
Consensus pattern (24 bp):
TTTTTGTACATTTTTCTTTTCTGT
Found at i:112411 original size:21 final size:22
Alignment explanation
Indices: 112369--112413 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
112359 AGAGTCATGC
*
112369 CTCAAGACATACTGAACTTTGT
1 CTCAAGACATACAGAACTTTGT
*
112391 CTCAAGACATA-AGATCTTTGT
1 CTCAAGACATACAGAACTTTGT
112412 CT
1 CT
112414 TGATATAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (22 bp):
CTCAAGACATACAGAACTTTGT
Found at i:117801 original size:15 final size:14
Alignment explanation
Indices: 117776--117809 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
117766 CAGGAACTTC
117776 CTCTTTCTCTTCTT
1 CTCTTTCTCTTCTT
117790 CTCTTTCATCTTCTT
1 CTCTTTC-TCTTCTT
*
117805 TTCTT
1 CTCTT
117810 CTTCCTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (14 bp):
CTCTTTCTCTTCTT
Found at i:127422 original size:21 final size:21
Alignment explanation
Indices: 127398--127459 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
127388 CTACCCTGTA
127398 CTTCTACCGATACATGTATGG
1 CTTCTACCGATACATGTATGG
127419 CTTCTACCGATACATGTATGG
1 CTTCTACCGATACATGTATGG
* *
127440 CTTCTACCGAAACAAGTATG
1 CTTCTACCGATACATGTATG
127460 CAGAATCACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (21 bp):
CTTCTACCGATACATGTATGG
Found at i:130874 original size:2 final size:2
Alignment explanation
Indices: 130867--130903 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
130857 ATTTAATGCA
* *
130867 AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
130904 AATTAACTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:132445 original size:14 final size:13
Alignment explanation
Indices: 132414--132459 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
132404 TACATATATT
132414 TTTA-TTTTTTTA
1 TTTATTTTTTTTA
132426 TATTATTTTTTGTTA
1 T-TTATTTTTT-TTA
132441 TTTATTTTTATTTA
1 TTTATTTTT-TTTA
132455 TTTAT
1 TTTAT
132460 ATTGAAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 3 0.10
14 21 0.70
15 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTTTA
Found at i:137834 original size:678 final size:674
Alignment explanation
Indices: 136512--137853 Score: 1956
Period size: 678 Copynumber: 2.0 Consensus size: 674
136502 ACCACCCTTC
* * * *
136512 CCGATCATACTAAAAATAGACTGATTAGTAAATTCTCATTTATTAGGATTTAAATACAATTTATC
1 CCGATCATACTAAAAATAAACTAATTAGTAAATCCTCATTTATTAGGATTTAAATACAATTTACC
*
136577 AAAATCTGAAGAGTTTCACATCATTTCTATTATTAGACCATTTAAAGAGGGTTCAATTTCATAAA
66 AAAATCTAAAGAGTTTCACATCATTTCTATTATTAGACCATTTAAAGAGGGTTCAATTTCATAAA
* * **
136642 TGGTCCTTCAATTATATTAAATTCCAACTAAATAAACTTTATTTCAATTTAACCTTAAACTGCTT
131 TAGTCCTTCAATTATATTAAATTCCAACTAAACAAACTTTATTTCAATTTAACCTTAAACTAATT
* * * ** * * *
136707 AGGACTATAGGAATAAATATTCCAAAAGTTAGTGGAAGGTAATCATATCCTCCACCTCTTGGACT
196 AGAACTAAAGAAATAAATAACCCAAAAGTTAGTAGAAGGTAATCATATCCACCACCGCTTGGACT
136772 TTTTGACCATGGTGTAATTACCACTTTGGTCCCTTTTATTTTTAATCAATAGCAATTAACTTTTA
261 TTTTGACCATGGTGTAATTACCACTTTGGTCCCTTTTATTTTTAATCAATAGCAATTAACTTTTA
* * * *
136837 TCCCTTTTACAATTTACTCCTTTTTCCTTAATTAAGCAATTAATCATCAAAATTATCCAACCGAA
326 GCCCTTTTACAATTTACTCCTTTTTCCTTAATTAAACAATTAATCATCAAAATTAACCAACCAAA
* * *
136902 CTTCAATTCACATATAATAAGACTCTGTAAATATTTAATAAAAATATTTACGGCTCTTAATTTCA
391 CTTCAATTCACATAAAATAAGAATCTGTAAATATTTAATAAAAATATTTACGGCTCTAAATTTCA
* * *
136967 GAAACAAGGTCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACTAAATCACTTATACTA
456 GAAACAAGGTCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACCAAACCACTTATACCA
*
137032 ACTTTTAATTCAATAATTAAAATTCTTCAATTCAAAATTTCATATAAAATTATTATTGACTTATT
521 ACTTTTAATTCAATAATTAAAATAC-TCAATTCAAAATTTCATATAAAATTATTATTGACTTATT
* * * * *
137097 TAATTTAAACACTCATTATAAAAATTTTCTCGTCGGGTTTATGGTCCCGAAATCATTGTTTCCGA
585 TAATTTAAAAACTCATCAGAAAAATTTTCTCGTCGGGTTTATGGTCCCAAAACCATTGTTTCCGA
137162 CACCACTGAAAAACAAGTTGTTGCA
650 CACCACTGAAAAACAAGTTGTTGCA
* * *
137187 CCGATCATACTAAAAATAAATTAATTAGTAAATCCTCATTTTATTAGGATTTAATTGCAATTTAC
1 CCGATCATACTAAAAATAAACTAATTAGTAAATCCTCA-TTTATTAGGATTTAAATACAATTTAC
* *
137252 CAAAATCTAAAGAGTTTCACATCATTTTTATTATTAGGA-CATTTAAAGAGGG-TCTATTTCATA
65 CAAAATCTAAAGAGTTTCACATCATTTCTATTATTA-GACCATTTAAAGAGGGTTCAATTTCATA
* * * ** *
137315 ATTAGTCCTTCAATTATATTAAATTTCAATTAAACAAACTTGT-TTTCAATTTAGTCTTAAATTA
129 AATAGTCCTTCAATTATATTAAATTCCAACTAAACAAACTT-TATTTCAATTTAACCTTAAACTA
* * *
137379 ATTAGAACTAAATAAATAAATAACCCAAAAGTTAGTAGATGGTATTCATATCCACCACCGCTTGG
193 ATTAGAACTAAAGAAATAAATAACCCAAAAGTTAGTAGAAGGTAATCATATCCACCACCGCTTGG
* * * * *
137444 ACTTTTTGACCATGGTTTAATTATCATTTTGGTCTCTTTACTATTTTTTAATCCATAGCAATTAA
258 ACTTTTTGACCATGGTGTAATTACCACTTTGGTCCCTTT--TA-TTTTTAATCAATAGCAATTAA
* * *
137509 CTTTTAGCTCTTTTACAATTTACTTCTTTTTCCTTAATTAAACAATTAATTATCAAAATTAACCA
320 CTTTTAGCCCTTTTACAATTTACTCCTTTTTCCTTAATTAAACAATTAATCATCAAAATTAACCA
*
137574 ACCAAACTTCAATTCACATAAAATAAGAATCTGTAAATATTTAATAAAAATATTTAC-GATCCTA
385 ACCAAACTTCAATTCACATAAAATAAGAATCTGTAAATATTTAATAAAAATATTTACGGCT-CTA
* * * *
137638 AATTTCATAAACGAGGTCCCGATACCTCATTTTCTAAAACCACTTGACTTTTGAACCGAACCACT
449 AATTTCAGAAACAAGGTCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACCAAACCACT
* *
137703 TATACCAACTTTTAATTCAATAATTAAACTAC-CCATTCAAAATTTCATATAAAAATTATTATTG
514 TATACCAACTTTTAATTCAATAATTAAAATACTCAATTCAAAATTTCATAT-AAAATTATTATTG
* * * *
137767 ACTTATTTAATTTAAAAACTTATCAGAAGAATTTTCTCGTCGGGTTTTTTGGTCCTAAAACCATT
578 ACTTATTTAATTTAAAAACTCATCAGAAAAATTTTCTCGTCGGG-TTTATGGTCCCAAAACCATT
*
137832 GTTTGCGACACCACTGAAAAAC
642 GTTTCCGACACCACTGAAAAAC
137854 GGATTGTTAC
Statistics
Matches: 591, Mismatches: 67, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
675 185 0.31
676 88 0.15
677 58 0.10
678 260 0.44
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (674 bp):
CCGATCATACTAAAAATAAACTAATTAGTAAATCCTCATTTATTAGGATTTAAATACAATTTACC
AAAATCTAAAGAGTTTCACATCATTTCTATTATTAGACCATTTAAAGAGGGTTCAATTTCATAAA
TAGTCCTTCAATTATATTAAATTCCAACTAAACAAACTTTATTTCAATTTAACCTTAAACTAATT
AGAACTAAAGAAATAAATAACCCAAAAGTTAGTAGAAGGTAATCATATCCACCACCGCTTGGACT
TTTTGACCATGGTGTAATTACCACTTTGGTCCCTTTTATTTTTAATCAATAGCAATTAACTTTTA
GCCCTTTTACAATTTACTCCTTTTTCCTTAATTAAACAATTAATCATCAAAATTAACCAACCAAA
CTTCAATTCACATAAAATAAGAATCTGTAAATATTTAATAAAAATATTTACGGCTCTAAATTTCA
GAAACAAGGTCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACCAAACCACTTATACCA
ACTTTTAATTCAATAATTAAAATACTCAATTCAAAATTTCATATAAAATTATTATTGACTTATTT
AATTTAAAAACTCATCAGAAAAATTTTCTCGTCGGGTTTATGGTCCCAAAACCATTGTTTCCGAC
ACCACTGAAAAACAAGTTGTTGCA
Found at i:141349 original size:109 final size:108
Alignment explanation
Indices: 141199--141411 Score: 329
Period size: 109 Copynumber: 2.0 Consensus size: 108
141189 ACAGATAATA
* * * *
141199 TTTATCGATTCTAAATAGGATATTCAATTATTTAGGTTCAAAGAAAAACCATACCCAGTGCGTTA
1 TTTATCGATTCTAAACAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATA-CCAGTACATTA
* *
141264 GGGCACAATTTCTTGAGTTCAATAAAAATAAAAGAACATTGAATT
65 GAGCACAATTTCTCGAGTTCAAT-AAAATAAAAGAACATTGAATT
*
141309 TTTATCGATT-TAAACAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCAGTACATTAG
1 TTTATCGATTCTAAACAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATACCAGTACATTAG
*
141373 AGCACAATTTCTCGAGTTCCATAAAATAAAAGAACATTG
66 AGCACAATTTCTCGAGTTCAATAAAATAAAAGAACATTG
141412 CCTTAATTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
107 17 0.18
108 29 0.31
109 39 0.41
110 10 0.11
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (108 bp):
TTTATCGATTCTAAACAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATACCAGTACATTAG
AGCACAATTTCTCGAGTTCAATAAAATAAAAGAACATTGAATT
Found at i:149691 original size:48 final size:48
Alignment explanation
Indices: 149632--149772 Score: 158
Period size: 50 Copynumber: 2.9 Consensus size: 48
149622 GTAGATGGAA
* *
149632 GATTGAGATGATAAAACCAGTCACTGCATGAGTTGATGGAAGCTTGAT
1 GATTGAAATGATAAAACAAGTCACTGCATGAGTTGATGGAAGCTTGAT
* *
149680 GATTGAAATGATAAAACAAATCTATCTGCATGAGTTGATGGAAGTTTGAT
1 GATTGAAATGATAAAACAAGTC-A-CTGCATGAGTTGATGGAAGCTTGAT
* * * ** *
149730 -TTCTAAAATGATAAAACAAGTCTCTGCACAAATTGATGGAAGC
1 GAT-TGAAATGATAAAACAAGTCACTGCATGAGTTGATGGAAGC
149773 CTATTGTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
48 35 0.45
49 2 0.03
50 41 0.53
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (48 bp):
GATTGAAATGATAAAACAAGTCACTGCATGAGTTGATGGAAGCTTGAT
Found at i:154514 original size:24 final size:24
Alignment explanation
Indices: 154487--154569 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
154477 AGAAAGTATA
* *
154487 TTTATGCTCATCAGTCGCTATATG
1 TTTATGCTCATCAGCCACTATATG
*
154511 TTTATGCTCGTCAGCCACTATATG
1 TTTATGCTCATCAGCCACTATATG
* *
154535 TTTATACTCATCAACCACTATATG
1 TTTATGCTCATCAGCCACTATATG
154559 TTTATGCTCAT
1 TTTATGCTCAT
154570 TTATTTAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (24 bp):
TTTATGCTCATCAGCCACTATATG
Found at i:156705 original size:52 final size:52
Alignment explanation
Indices: 156632--156766 Score: 198
Period size: 52 Copynumber: 2.6 Consensus size: 52
156622 ATTTCATTTA
* *
156632 ATACTCATGATGACATATAGTCATCGGACCTCAAAATCCATAAAGTATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCAAAATCCATAAAGGATTCAT
* * * * *
156684 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAATGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCAAAATCCATAAAGGATTCAT
*
156736 ATACTCATGATGACACATAGTCATCGAACCT
1 ATACTCATGATGACACATAGTCATCGGACCT
156767 TTTCTTTTAC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (52 bp):
ATACTCATGATGACACATAGTCATCGGACCTCAAAATCCATAAAGGATTCAT
Found at i:157695 original size:21 final size:22
Alignment explanation
Indices: 157664--157712 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
157654 TGACAGTCCA
*
157664 TTAT-ATCCCTTTAGGGTATAT
1 TTATGATCCTTTTAGGGTATAT
157685 TTATGATCCTTTTAGGGTATAT
1 TTATGATCCTTTTAGGGTATAT
157707 TTATGA
1 TTATGA
157713 ATTAAGGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (22 bp):
TTATGATCCTTTTAGGGTATAT
Found at i:171713 original size:52 final size:52
Alignment explanation
Indices: 171652--171889 Score: 287
Period size: 52 Copynumber: 4.6 Consensus size: 52
171642 GGGATTTGTT
* * * *
171652 TACTAACGATGAAACAGAGTCATCGGACCTTTTAATCCGTAAAGGATCCCTA
1 TACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATCCATA
* * * * * * * *
171704 TACTCACGATGACGCATAGCCACCGAACCTTATAATCCGCAAGGGATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATCCATA
* * * * * *
171756 TACTCACGATGACATAGAGTCATCAGACCTCTCAATCCGTAAAGGATCCTTA
1 TACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATCCATA
* * *
171808 TACTCATGATGACACATAGTCATCGGACCTTTTAATCTGTAAAGGATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATCCATA
171860 TACTCACGATGACACATAGTCATCGGACCT
1 TACTCACGATGACACATAGTCATCGGACCT
171890 CTTCGTTTAT
Statistics
Matches: 150, Mismatches: 36, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 150 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (52 bp):
TACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATCCATA
Found at i:171778 original size:104 final size:104
Alignment explanation
Indices: 171598--171891 Score: 365
Period size: 104 Copynumber: 2.8 Consensus size: 104
171588 ACTTCATTCA
* * * * ** * *
171598 TATACTGACAATGACACATAGCCACTGGACCTTATAATCCAAAAGGGATTTGTTTACTAACGATG
1 TATACTCACGATGACACATAGCCACCGGACCTTATAATCCGAAAGGGATTCATATACTCACGATG
* * *
171663 AAACAGAGTCATCGGACCTTTTAATCCGTAAAGGATCCC
66 ACACAGAGTCATCGGACCTCTCAATCCGTAAAGGATCCC
* * *
171702 TATACTCACGATGACGCATAGCCACCGAACCTTATAATCCGCAAGGGATTCATATACTCACGATG
1 TATACTCACGATGACACATAGCCACCGGACCTTATAATCCGAAAGGGATTCATATACTCACGATG
* * *
171767 ACATAGAGTCATCAGACCTCTCAATCCGTAAAGGATCCT
66 ACACAGAGTCATCGGACCTCTCAATCCGTAAAGGATCCC
* * * * *
171806 TATACTCATGATGACACATAGTCATCGGACCTTTTAATCTGTAAA-GGATTCATATACTCACGAT
1 TATACTCACGATGACACATAGCCACCGGACCTTATAATCCG-AAAGGGATTCATATACTCACGAT
*
171870 GACACATAGTCATCGGACCTCT
65 GACACAGAGTCATCGGACCTCT
171892 TCGTTTATGG
Statistics
Matches: 161, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
104 159 0.99
105 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (104 bp):
TATACTCACGATGACACATAGCCACCGGACCTTATAATCCGAAAGGGATTCATATACTCACGATG
ACACAGAGTCATCGGACCTCTCAATCCGTAAAGGATCCC
Found at i:178877 original size:52 final size:52
Alignment explanation
Indices: 178729--178997 Score: 380
Period size: 52 Copynumber: 5.2 Consensus size: 52
178719 ATTTCACTTC
* * * * * * *
178729 ATTCATATACTCATGATGACACATAGTCACCGGACCATATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
* * *
178781 ATTCATATACTCACGATGACA--TAGTCATCAGACCTCTCAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
* * * *
178831 ATCCTTATACTCATGATGACACTTAGTCATCGGAGCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
*
178883 ATTCATATACTCACGATGACACTTAGTCATCGGAGCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
178935 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
*
178987 ATTCCTATACT
1 ATTCATATACT
178998 ACCTTTTAAT
Statistics
Matches: 194, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
50 39 0.20
52 155 0.80
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
Found at i:179004 original size:30 final size:30
Alignment explanation
Indices: 178968--179027 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
178958 TAGTCATCGG
*
178968 ACCTTTTAATCCGTAAAGGATTCCTATACT
1 ACCTTTTAATCCGTAAAGGATTCATATACT
*
178998 ACCTTTTAATTCGTAAAGGATTCATATACT
1 ACCTTTTAATCCGTAAAGGATTCATATACT
179028 CACGATGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (30 bp):
ACCTTTTAATCCGTAAAGGATTCATATACT
Found at i:179055 original size:82 final size:82
Alignment explanation
Indices: 178918--179080 Score: 265
Period size: 82 Copynumber: 2.0 Consensus size: 82
178908 GTCATCGGAG
*
178918 CTTTTAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTA
1 CTTTTAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCAGACCTTTTAATCCGTA
* *
178983 AAGGATTCCTATACTAC
66 AAGCATTCATATACTAC
* *
179000 CTTTTAATTCGTAAAGGATTCATATACTCACGATGACA-TATAGTCATCAGACCTTTTAGTCCGT
1 CTTTTAATCCGTAAAGGATTCATATACTCACGATGACACT-TAGTCATCAGACCTTTTAATCCGT
179064 AAAGCATTCATATACTA
65 AAAGCATTCATATACTA
179081 ACGATGACAC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
81 1 0.01
82 74 0.99
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (82 bp):
CTTTTAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCAGACCTTTTAATCCGTA
AAGCATTCATATACTAC
Found at i:179076 original size:52 final size:52
Alignment explanation
Indices: 178998--179105 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 52
178988 TTCCTATACT
* * * *
178998 ACCTTTTAATTCGTAAAGGATTCATATACTCACGATGACATATAGTCATCAG
1 ACCTTTTAATCCGTAAAGCATTCATATACTAACGATGACACATAGTCATCAG
* *
179050 ACCTTTTAGTCCGTAAAGCATTCATATACTAACGATGACACATAGTCATCGG
1 ACCTTTTAATCCGTAAAGCATTCATATACTAACGATGACACATAGTCATCAG
179102 ACCT
1 ACCT
179106 CTTCGTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (52 bp):
ACCTTTTAATCCGTAAAGCATTCATATACTAACGATGACACATAGTCATCAG
Found at i:183231 original size:21 final size:24
Alignment explanation
Indices: 183187--183231 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
183177 ACAACTGTTA
183187 GTAGTTGTGTGTATTGATGTATCG
1 GTAGTTGTGTGTATTGATGTATCG
*
183211 GTAGTT-TGTTTATT-A-GTATCG
1 GTAGTTGTGTGTATTGATGTATCG
183232 ATAGAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 1 0.05
23 7 0.35
24 6 0.30
ACGTcount: A:0.18, C:0.04, G:0.29, T:0.49
Consensus pattern (24 bp):
GTAGTTGTGTGTATTGATGTATCG
Found at i:183316 original size:21 final size:21
Alignment explanation
Indices: 183275--183350 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
183265 GGAGTTTTTG
**
183275 GTATCGGTAGATGCATG-ACTT
1 GTATCGGTAGAAAC-TGCACTT
183296 GTATCGGTAGAAACTGCACTT
1 GTATCGGTAGAAACTGCACTT
***
183317 GTA-CTGGTAG-AACTAGCAGAA
1 GTATC-GGTAGAAACT-GCACTT
183338 GTATCGGTAGAAA
1 GTATCGGTAGAAA
183351 TCTGTACAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
20 7 0.16
21 35 0.78
22 3 0.07
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (21 bp):
GTATCGGTAGAAACTGCACTT
Found at i:209769 original size:52 final size:51
Alignment explanation
Indices: 209713--209835 Score: 169
Period size: 52 Copynumber: 2.4 Consensus size: 51
209703 GCTGGCAAGT
*
209713 GTAAACGAAAATGAATAAGCTGACGAGCGTAAACATGTACAAGCTAGTG-AGC
1 GTAAACGAAAATGAATAAACTGACGAGCGTAAACATGTACAAGC-AG-GAAGC
*
209765 GTAAACGTAAAA-GAATAAACTGACGAGCGTAAACGTGTACAAGCAGGCAAGC
1 GTAAACG-AAAATGAATAAACTGACGAGCGTAAACATGTACAAGCAGG-AAGC
*
209817 GTAAACGTAAATGAATAAA
1 GTAAACGAAAATGAATAAA
209836 ATAGTGAGTA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
50 1 0.02
51 5 0.08
52 54 0.84
53 4 0.06
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.16
Consensus pattern (51 bp):
GTAAACGAAAATGAATAAACTGACGAGCGTAAACATGTACAAGCAGGAAGC
Found at i:209969 original size:52 final size:52
Alignment explanation
Indices: 209913--210063 Score: 187
Period size: 52 Copynumber: 2.9 Consensus size: 52
209903 ACTAATGAAT
* *
209913 AAGCTGGTGAGCATAAATGCAAAAGAATAAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTGC
* * * *
209965 AAGCTGGCGAG-AGTAAACGCAAATGAATAAGCTGATGAGCGTGAACATGTGC
1 AAGCTGGCGAGCA-TAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTGC
* * * * *
210017 AAGCTGGCGAGCGTAAACGCATAAGTATAAGCTGGCAAGCGTAAACG
1 AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACG
210064 CATAAGTATA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
51 1 0.01
52 81 0.99
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.17
Consensus pattern (52 bp):
AAGCTGGCGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTGC
Found at i:209975 original size:24 final size:24
Alignment explanation
Indices: 209941--210035 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
209931 GCAAAAGAAT
209941 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * ***
209965 AAGCTGGCGAGAGTAAACGCAAATGAAT
1 AAGCTGACGAGCGTAAACG----TGTGC
* * *
209993 AAGCTGATGAGCGTGAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
210017 AAGCTGGCGAGCGTAAACG
1 AAGCTGACGAGCGTAAACG
210036 CATAAGTATA
Statistics
Matches: 50, Mismatches: 17, Indels: 8
0.67 0.23 0.11
Matches are distributed among these distances:
24 34 0.68
28 16 0.32
ACGTcount: A:0.34, C:0.18, G:0.33, T:0.16
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:209998 original size:80 final size:80
Alignment explanation
Indices: 209753--209997 Score: 319
Period size: 80 Copynumber: 3.1 Consensus size: 80
209743 AAACATGTAC
* * * * *
209753 AAGCTAGTGAGCGTAAACGTAAAAGAATAAACTGACGAGCGTAAACGTGTACAAGCAGGCAAGCG
1 AAGCTAGTGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTACAAGCTGGCAAGAG
*
209818 TAAACGTAAATGAAT
66 TAAACGCAAATGAAT
** * * * * *
209833 AAAATAGTGAGTATAAACGCAAATGAATAAGCTGACAAGCGTAAACTTGTACAAGCTGGCAAGTG
1 AAGCTAGTGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTACAAGCTGGCAAGAG
* *
209898 TAAACACTAATGAAT
66 TAAACGCAAATGAAT
* * * *
209913 AAGCTGGTGAGCATAAATGCAAAAGAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGAG
1 AAGCTAGTGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTACAAGCTGGCAAGAG
209978 TAAACGCAAATGAAT
66 TAAACGCAAATGAAT
209993 AAGCT
1 AAGCT
209998 GATGAGCGTG
Statistics
Matches: 138, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 138 1.00
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (80 bp):
AAGCTAGTGAGCATAAACGCAAAAGAATAAGCTGACGAGCGTAAACGTGTACAAGCTGGCAAGAG
TAAACGCAAATGAAT
Found at i:210057 original size:28 final size:28
Alignment explanation
Indices: 209885--210124 Score: 149
Period size: 28 Copynumber: 8.8 Consensus size: 28
209875 AAACTTGTAC
* * * *
209885 AAGCTGGCAAGTGTAAACAC-TAATGAAT
1 AAGCTGGCGAGCGTAAACGCATAA-GTAT
* * * * *
209913 AAGCTGGTGAGCATAAATGCAAAAGAAT
1 AAGCTGGCGAGCGTAAACGCATAAGTAT
* **
209941 AAGCTGACGAGCGTAAACG--T--GTGC
1 AAGCTGGCGAGCGTAAACGCATAAGTAT
* *
209965 AAGCTGGCGAGAGTAAACGCA-AATGAAT
1 AAGCTGGCGAGCGTAAACGCATAA-GTAT
** * **
209993 AAGCTGATGAGCGTGAA--CAT--GTGC
1 AAGCTGGCGAGCGTAAACGCATAAGTAT
210017 AAGCTGGCGAGCGTAAACGCATAAGTAT
1 AAGCTGGCGAGCGTAAACGCATAAGTAT
*
210045 AAGCTGGCAAGCGTAAACGCATAAGTAT
1 AAGCTGGCGAGCGTAAACGCATAAGTAT
* * * *
210073 AAGCTAGCGAGCGGAAACACATATGAATAT
1 AAGCTGGCGAGCGTAAACGCATA--AGTAT
*
210103 AAGCTGGCGAGCATAAACGCAT
1 AAGCTGGCGAGCGTAAACGCAT
210125 TTTCAATTAG
Statistics
Matches: 157, Mismatches: 42, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
24 33 0.21
26 5 0.03
28 95 0.61
29 2 0.01
30 22 0.14
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (28 bp):
AAGCTGGCGAGCGTAAACGCATAAGTAT
Found at i:210084 original size:132 final size:132
Alignment explanation
Indices: 209846--210090 Score: 314
Period size: 132 Copynumber: 1.9 Consensus size: 132
209836 ATAGTGAGTA
* *
209846 TAAACGCAAATGAATAAGCTGACAAGCGTAAACTTGTACAAGCTGGCAAGTGTAAACACTAATGA
1 TAAACGCAAATGAATAAGCTGACAAGCGTAAACATGTACAAGCTGGCAAGCGTAAACACTAATGA
** * *
209911 ATAAGCTGGTGAGCATAAATGCAAAAGAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAG
66 ATAAGCTGGCAAGCATAAACGCAAAAGAATAAGCTGACGAGCGGAAACGTGTGCAAGCTGGCGAG
209976 AG
131 AG
** * * * *
209978 TAAACGCAAATGAATAAGCTGATGAGCGTGAACATGTGCAAGCTGGCGAGCGTAAACGCATAA-G
1 TAAACGCAAATGAATAAGCTGACAAGCGTAAACATGTACAAGCTGGCAAGCGTAAACAC-TAATG
* * * *
210042 TATAAGCTGGCAAGCGTAAACGCATAAGTATAAGCT-AGCGAGCGGAAAC
65 AATAAGCTGGCAAGCATAAACGCAAAAGAATAAGCTGA-CGAGCGGAAAC
210091 ACATATGAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
131 1 0.01
132 91 0.96
133 3 0.03
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.18
Consensus pattern (132 bp):
TAAACGCAAATGAATAAGCTGACAAGCGTAAACATGTACAAGCTGGCAAGCGTAAACACTAATGA
ATAAGCTGGCAAGCATAAACGCAAAAGAATAAGCTGACGAGCGGAAACGTGTGCAAGCTGGCGAG
AG
Found at i:210120 original size:58 final size:56
Alignment explanation
Indices: 210017--210124 Score: 144
Period size: 58 Copynumber: 1.9 Consensus size: 56
210007 GAACATGTGC
* * * * *
210017 AAGCTGGCGAGCGTAAACGCATAAGTATAAGCTGGCAAGCGTAAACGCATAAGTAT
1 AAGCTAGCGAGCGGAAACACATAAATATAAGCTGGCAAGCATAAACGCATAAGTAT
*
210073 AAGCTAGCGAGCGGAAACACATATGAATATAAGCTGGCGAGCATAAACGCAT
1 AAGCTAGCGAGCGGAAACACATA--AATATAAGCTGGCAAGCATAAACGCAT
210125 TTTCAATTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 20 0.45
58 24 0.55
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (56 bp):
AAGCTAGCGAGCGGAAACACATAAATATAAGCTGGCAAGCATAAACGCATAAGTAT
Found at i:212239 original size:52 final size:52
Alignment explanation
Indices: 212099--212255 Score: 197
Period size: 52 Copynumber: 3.0 Consensus size: 52
212089 ATTCCAAAAA
* * * * * * *
212099 TTTAACTCATGCGAGCCTAAACAGAAGTTAGCTTATATGAGCCCAAATAGAG
1 TTTAGCTCATTCGAGCCTAGACAGAATTTAGCTCATTTGAGCCCAGATAGAG
* *
212151 TTTAGCTCATTCGAGCCCAGACAGAGTTTAGCTCATTTGAGCCCAGATAGAG
1 TTTAGCTCATTCGAGCCTAGACAGAATTTAGCTCATTTGAGCCCAGATAGAG
* * * *
212203 TTTAGCTCATTCGAGCCTAGACATAATTTAGCTCATTCGAGCCTAGACAGAG
1 TTTAGCTCATTCGAGCCTAGACAGAATTTAGCTCATTTGAGCCCAGATAGAG
212255 T
1 T
212256 AACGCTCTTA
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 90 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (52 bp):
TTTAGCTCATTCGAGCCTAGACAGAATTTAGCTCATTTGAGCCCAGATAGAG
Found at i:212262 original size:26 final size:26
Alignment explanation
Indices: 212137--212255 Score: 166
Period size: 26 Copynumber: 4.6 Consensus size: 26
212127 TAGCTTATAT
* *
212137 GAGCCCAAATAGAGTTTAGCTCATTC
1 GAGCCCAGACAGAGTTTAGCTCATTC
*
212163 GAGCCCAGACAGAGTTTAGCTCATTT
1 GAGCCCAGACAGAGTTTAGCTCATTC
*
212189 GAGCCCAGATAGAGTTTAGCTCATTC
1 GAGCCCAGACAGAGTTTAGCTCATTC
* * *
212215 GAGCCTAGACATAATTTAGCTCATTC
1 GAGCCCAGACAGAGTTTAGCTCATTC
*
212241 GAGCCTAGACAGAGT
1 GAGCCCAGACAGAGT
212256 AACGCTCTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (26 bp):
GAGCCCAGACAGAGTTTAGCTCATTC
Found at i:214881 original size:17 final size:17
Alignment explanation
Indices: 214838--214872 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
214828 TAACCCGCCA
*
214838 ACCCCAGAAAATTGCGT
1 ACCCCAGAAAATTACGT
214855 ACCCCAGAAAATTACGT
1 ACCCCAGAAAATTACGT
214872 A
1 A
214873 TCTCAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (17 bp):
ACCCCAGAAAATTACGT
Found at i:219265 original size:33 final size:32
Alignment explanation
Indices: 219201--219265 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
219191 TCAAATCATG
* * * *
219201 AAAAATAATAATCAAATTAATATAATTAAAAT
1 AAAAATAAAAATAAAATTAATAGAATAAAAAT
*
219233 AAAAGATAAAAATAAAATTAATAGCATAAAAAT
1 AAAA-ATAAAAATAAAATTAATAGAATAAAAAT
219266 GCCACATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (32 bp):
AAAAATAAAAATAAAATTAATAGAATAAAAAT
Found at i:219404 original size:37 final size:36
Alignment explanation
Indices: 219353--219428 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
219343 AATAAATAAT
*
219353 AAATAAAATAAATAACTAAAATCATGCAAATTATAC
1 AAATAAAATAAATAACTAAAATCATGCAAATTAAAC
* * *
219389 AAATAGAAATGAATAATTAAGATCATGCAAATTAAAC
1 AAATA-AAATAAATAACTAAAATCATGCAAATTAAAC
219426 AAA
1 AAA
219429 AAATAATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
36 5 0.14
37 30 0.86
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.24
Consensus pattern (36 bp):
AAATAAAATAAATAACTAAAATCATGCAAATTAAAC
Found at i:221291 original size:98 final size:98
Alignment explanation
Indices: 221149--221403 Score: 269
Period size: 98 Copynumber: 2.6 Consensus size: 98
221139 TTTATCTCTT
* * * * * * *
221149 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCATCAACCTATCCCTCTTCAATTTTAAGGTGT
1 TTCAATTTTAGAGTGTTAGGTCCGTCATCACAGCTTCAACCTATCCCTCTTCAATTTTAAGGTGT
* ** *
221214 AAGAT-TCATCGTCGTGGCTTCAATCTTTCCCTT
66 AAGATCT-ACCGTCGTAACTTCAATCTTTCCCTC
** * * ** * * *
221247 TTCGGTTTTAGAGTGTTAGGTCTGTCGTCAGGGCTTCAACCTATCCCTTTTCGATTTTATGGTGT
1 TTCAATTTTAGAGTGTTAGGTCCGTCATCACAGCTTCAACCTATCCCTCTTCAATTTTAAGGTGT
*
221312 AAGATCTACCGTTGTAACTTCAATCTTTCCCTC
66 AAGATCTACCGTCGTAACTTCAATCTTTCCCTC
* * * *
221345 TTCAATTTTAGGGTGTTAGGTCCGTCATTACAGCTTCAACATATCCCTCTTCAACTTTA
1 TTCAATTTTAGAGTGTTAGGTCCGTCATCACAGCTTCAACCTATCCCTCTTCAATTTTA
221404 GGATTTGGTG
Statistics
Matches: 127, Mismatches: 29, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
98 126 0.99
99 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (98 bp):
TTCAATTTTAGAGTGTTAGGTCCGTCATCACAGCTTCAACCTATCCCTCTTCAATTTTAAGGTGT
AAGATCTACCGTCGTAACTTCAATCTTTCCCTC
Found at i:221382 original size:49 final size:49
Alignment explanation
Indices: 221149--221405 Score: 190
Period size: 49 Copynumber: 5.2 Consensus size: 49
221139 TTTATCTCTT
*
221149 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCATCAACCTATCCCTC
1 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCTTCAACCTATCCCTC
* * * *** * * *
221198 TTCAATTTTAAGGTGTAAGATTCATCGTCGTGGCTTCAATCTTTCCCTT
1 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCTTCAACCTATCCCTC
** * * ** * * *
221247 TTCGGTTTTAGAGTGTTAGGTCTGTCGTCAGGGCTTCAACCTATCCCTT
1 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCTTCAACCTATCCCTC
* * * * * **** * *
221296 TTCGATTTTATGGTGTAAGATCTACCGTTGTAACTTCAATCTTTCCCTC
1 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCTTCAACCTATCCCTC
* * * * *
221345 TTCAATTTTAGGGTGTTAGGTCCGTCATTACAGCTTCAACATATCCCTC
1 TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCTTCAACCTATCCCTC
*
221394 TTCAACTTTAGG
1 TTCAATTTTAGG
221406 ATTTGGTGTG
Statistics
Matches: 155, Mismatches: 53, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
49 155 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (49 bp):
TTCAATTTTAGGGTGTTAGATCCATCGTTACGGCTTCAACCTATCCCTC
Found at i:232913 original size:18 final size:19
Alignment explanation
Indices: 232890--232927 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
232880 TTAATATAAT
232890 TAAAATAAAAG-ATAAAAA
1 TAAAATAAAAGCATAAAAA
*
232908 TAAAATAATAGCATAAAAA
1 TAAAATAAAAGCATAAAAA
232927 T
1 T
232928 GCCACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (19 bp):
TAAAATAAAAGCATAAAAA
Found at i:233024 original size:16 final size:17
Alignment explanation
Indices: 233002--233033 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
232992 ATATGAATAG
233002 AAAATAAATAA-TAAAT
1 AAAATAAATAACTAAAT
233018 AAAATAAATAACTAAA
1 AAAATAAATAACTAAA
233034 ATCATGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATAAATAACTAAAT
Found at i:233065 original size:37 final size:37
Alignment explanation
Indices: 233014--233122 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 37
233004 AATAAATAAT
*
233014 AAAT-AAAATAAATAACTAAAATCATGCAAATTATAC
1 AAATAAAAATAAATAACTAAAATCATGCAAATTAAAC
* *
233050 AAATAAAAATAAATAATTAAGATCATGCAAATTAAAC
1 AAATAAAAATAAATAACTAAAATCATGCAAATTAAAC
* *
233087 ----AAAAATAAATAA-TGAAAATAATGAAAATTAAAC
1 AAATAAAAATAAATAACT-AAAATCATGCAAATTAAAC
233120 AAA
1 AAA
233123 AAATAATGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
32 1 0.02
33 28 0.45
36 4 0.06
37 29 0.47
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (37 bp):
AAATAAAAATAAATAACTAAAATCATGCAAATTAAAC
Found at i:233091 original size:33 final size:33
Alignment explanation
Indices: 233018--233124 Score: 124
Period size: 33 Copynumber: 3.1 Consensus size: 33
233008 AATAATAAAT
* *
233018 AAAATAAATAACTAAAATCATGCAAATTATACAAATA
1 AAAATAAATAATTAAAATCATGCAAA-T-T--AAACA
*
233055 AAAATAAATAATTAAGATCATGCAAATTAAACA
1 AAAATAAATAATTAAAATCATGCAAATTAAACA
* * *
233088 AAAATAAATAATGAAAATAATGAAAATTAAACA
1 AAAATAAATAATTAAAATCATGCAAATTAAACA
233121 AAAA
1 AAAA
233125 ATAATGTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 37 0.59
35 1 0.02
36 1 0.02
37 24 0.38
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.22
Consensus pattern (33 bp):
AAAATAAATAATTAAAATCATGCAAATTAAACA
Found at i:234024 original size:24 final size:24
Alignment explanation
Indices: 233993--234050 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
233983 ACCTTTGATT
233993 CAAAATTTTGTATGTTC-TTACAAA
1 CAAAATTTT-TATGTTCATTACAAA
234017 -AATAA-TTTTATGTTCATTTACAAA
1 CAA-AATTTTTATGTTCA-TTACAAA
234041 CAAAATTTTT
1 CAAAATTTTT
234051 GTTTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
22 7 0.24
23 5 0.17
24 11 0.38
25 6 0.21
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (24 bp):
CAAAATTTTTATGTTCATTACAAA
Found at i:234847 original size:26 final size:26
Alignment explanation
Indices: 234807--234986 Score: 200
Period size: 26 Copynumber: 7.0 Consensus size: 26
234797 TCCAAAAATC
* * * *
234807 TAGCTCATGCAAGCCTAGACAAAATT
1 TAGCTCATACGAGCCCAGACAAAGTT
* *
234833 TAGCTCATACGAGCCCAAACAGAGTT
1 TAGCTCATACGAGCCCAGACAAAGTT
* *
234859 TAGCTCTTACGAGCCCAGATAAAGTT
1 TAGCTCATACGAGCCCAGACAAAGTT
* * *
234885 TAGCTCTTACGAGCCCAAACAGAGTT
1 TAGCTCATACGAGCCCAGACAAAGTT
* *
234911 TAGCTCTTACGAGCCCAGACAGAGTT
1 TAGCTCATACGAGCCCAGACAAAGTT
* * *
234937 TAGCTCATTCGAGCCCA-AAAAAATT
1 TAGCTCATACGAGCCCAGACAAAGTT
*
234962 TAGCTCATTCGAGCCCAGACAAAGT
1 TAGCTCATACGAGCCCAGACAAAGT
234987 AATGTTCTTA
Statistics
Matches: 132, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
25 22 0.17
26 110 0.83
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (26 bp):
TAGCTCATACGAGCCCAGACAAAGTT
Found at i:234887 original size:52 final size:52
Alignment explanation
Indices: 234818--234986 Score: 243
Period size: 52 Copynumber: 3.3 Consensus size: 52
234808 AGCTCATGCA
* *
234818 AGCCTAGACAAAATTTAGCTCATACGAGCCCAAACAGAGTTTAGCTCTTACG
1 AGCCCAGACAAAGTTTAGCTCATACGAGCCCAAACAGAGTTTAGCTCTTACG
* *
234870 AGCCCAGATAAAGTTTAGCTCTTACGAGCCCAAACAGAGTTTAGCTCTTACG
1 AGCCCAGACAAAGTTTAGCTCATACGAGCCCAAACAGAGTTTAGCTCTTACG
* * * *
234922 AGCCCAGACAGAGTTTAGCTCATTCGAGCCCAAA-AAAATTTAGCTCATT-CG
1 AGCCCAGACAAAGTTTAGCTCATACGAGCCCAAACAGAGTTTAGCTC-TTACG
234973 AGCCCAGACAAAGT
1 AGCCCAGACAAAGT
234987 AATGTTCTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
51 25 0.24
52 80 0.76
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (52 bp):
AGCCCAGACAAAGTTTAGCTCATACGAGCCCAAACAGAGTTTAGCTCTTACG
Found at i:237055 original size:97 final size:97
Alignment explanation
Indices: 236889--237078 Score: 328
Period size: 97 Copynumber: 2.0 Consensus size: 97
236879 TTGAAAAACA
* * *
236889 GTATTCGATTATCCCGGTTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGTACAAATTTTCAAAAC
1 GTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
236954 CCGAAATAAAGGAATATTGCCTCGATTTAAGG
66 CCGAAATAAAGGAATATTGCCTCGATTTAAGG
*
236986 GTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTCAA-GCACAAATTTTCAACA
1 GTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTT-AAGGCACAAATTTTCAAAA
237050 CCCGAAATAAAGGAATATTGCCTCGATTT
65 CCCGAAATAAAGGAATATTGCCTCGATTT
237079 TAAATATTCG
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 86 0.98
98 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (97 bp):
GTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
CCGAAATAAAGGAATATTGCCTCGATTTAAGG
Found at i:237227 original size:15 final size:15
Alignment explanation
Indices: 237207--237252 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
237197 CAAATATATG
237207 AAAATAAAAATGAGA
1 AAAATAAAAATGAGA
237222 AAAAT-AAAAT-ACGA
1 AAAATAAAAATGA-GA
*
237236 AAAA-ATAAATGAGA
1 AAAATAAAAATGAGA
237250 AAA
1 AAA
237253 TACAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 1 0.04
14 20 0.74
15 6 0.22
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (15 bp):
AAAATAAAAATGAGA
Found at i:237409 original size:28 final size:28
Alignment explanation
Indices: 237378--237577 Score: 186
Period size: 29 Copynumber: 7.0 Consensus size: 28
237368 AAATTTTTAA
* * *
237378 GGGTAAAAATGTCATTTTGGGAAATTCG
1 GGGTAAAAATGTAATTTTTGGAAGTTCG
** *
237406 GGGTAAAAACATGATTTTTGGAAGTTCG
1 GGGTAAAAATGTAATTTTTGGAAGTTCG
*
237434 AGGGTAAAAATGTGATTTTTGGAAGTTCG
1 -GGGTAAAAATGTAATTTTTGGAAGTTCG
* *
237463 AGGGCAAAATTGTAATTTTTGGAAGTTCGG
1 -GGGTAAAAATGTAATTTTTGGAAGTTC-G
**
237493 GGGT-AAAATGTAATTTTTGGAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAG-TTCG
* *
237521 GGGTAAAAATGTAATTTTTAAGAAGTTTG
1 GGGTAAAAATGTAATTTTT-GGAAGTTCG
* * **
237550 GGGCAAAAATATGGTTTTTGGATAGTTC
1 GGGTAAAAATGTAATTTTTGGA-AGTTC
237578 AGGGACCTTT
Statistics
Matches: 143, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
28 47 0.33
29 91 0.64
30 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCG
Found at i:237480 original size:29 final size:29
Alignment explanation
Indices: 237377--237539 Score: 204
Period size: 29 Copynumber: 5.7 Consensus size: 29
237367 GAAATTTTTA
* * *
237377 AGGGTAAAAATGTCATTTTGGGAAATTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
** *
237406 -GGGTAAAAACATGATTTTTGGAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
*
237434 AGGGTAAAAATGTGATTTTTGGAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
* *
237463 AGGGCAAAATTGTAATTTTTGGAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
* **
237492 GGGGT-AAAATGTAATTTTTGGAAGTTTA
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
237520 AGGGTAAAAATGTAATTTTT
1 AGGGTAAAAATGTAATTTTT
237540 AAGAAGTTTG
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
28 47 0.41
29 69 0.59
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTCG
Found at i:237534 original size:57 final size:58
Alignment explanation
Indices: 237377--237539 Score: 186
Period size: 57 Copynumber: 2.8 Consensus size: 58
237367 GAAATTTTTA
* * * * * ** *
237377 AGGGTAAAAATGTCATTTTGGGAAATTC-GGGGTAAAAACATGATTTTTGGAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTCAAGGGCAAAAATGTAATTTTTGGAAGTTCG
* * *
237434 AGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAATTGTAATTTTTGGAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTTCAAGGGCAAAAATGTAATTTTTGGAAGTTCG
* * *
237492 GGGGT-AAAATGTAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTT
1 AGGGTAAAAATGTAATTTTTGGAAGTTCAAGGGCAAAAATGTAATTTTT
237540 AAGAAGTTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
57 63 0.70
58 27 0.30
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (58 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTCAAGGGCAAAAATGTAATTTTTGGAAGTTCG
Found at i:238657 original size:3 final size:3
Alignment explanation
Indices: 238649--238677 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
238639 ACCTTTCGGT
238649 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
238678 TATTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:238750 original size:18 final size:19
Alignment explanation
Indices: 238720--238768 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
238710 ACGTTTAGAA
238720 ATAATAAATAATAATGGTAAT
1 ATAATAAATAAT-A-GGTAAT
238741 ATAATAAATAAATAGGT-AT
1 ATAATAAAT-AATAGGTAAT
238760 -TAATAAATA
1 ATAATAAATA
238769 TATGCAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 2 0.07
20 3 0.11
21 10 0.37
22 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
ATAATAAATAATAGGTAAT
Found at i:239418 original size:18 final size:18
Alignment explanation
Indices: 239373--239426 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
239363 GTTTAAATTT
*
239373 AATTTAAAATAAATT-GA
1 AATTTAAAATAAATTCAA
* * *
239390 AACTCAAAATAAGTTCAA
1 AATTTAAAATAAATTCAA
239408 AATTTAAAATAAATTCAA
1 AATTTAAAATAAATTCAA
239426 A
1 A
239427 CTTAAATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (18 bp):
AATTTAAAATAAATTCAA
Found at i:239448 original size:34 final size:35
Alignment explanation
Indices: 239373--239450 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
239363 GTTTAAATTT
*
239373 AATTTAAAATAAATTGAAACTCAAAATAAGTTCAA
1 AATTTAAAATAAATTCAAACTCAAAATAAGTTCAA
* *
239408 AATTTAAAATAAATTCAAACT-TAAATAA-TTTAA
1 AATTTAAAATAAATTCAAACTCAAAATAAGTTCAA
*
239441 AATTTTAAAT
1 AATTTAAAAT
239451 TTAAAATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 13 0.33
34 6 0.15
35 20 0.51
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (35 bp):
AATTTAAAATAAATTCAAACTCAAAATAAGTTCAA
Found at i:239937 original size:39 final size:39
Alignment explanation
Indices: 239894--240631 Score: 333
Period size: 39 Copynumber: 19.3 Consensus size: 39
239884 CCATGATCAA
*
239894 GGTAAGAGATTGGCTGATGATGATATGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* *
239933 GGTAAAGGATCGAATGGCTG--CA--ATCTGCCCCAGGCTCGG
1 GGT-AA-GA--GATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * * *
239972 TGTAAGAAATTGGCTAATGATGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * * ** **
240011 GGTAAGAGATCGAATGGTTACAATCTGCCTTAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * * * *
240050 GGTAAGAGATTTGCTGATGCTAATCTACCCCAGGCTCGA
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * ** * ** * *
240089 GATAAGAGATAGAATGGCT-ACAATCTGCCCTAGGCTCGA
1 GGTAAGAGATTGGCT-GATGATGATCTGCCCCAGGCTCGG
* * * *
240128 GGTAAGGGATTCGCTGATAATGATCTGCCCTAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * ** *
240167 GGTAAGAGATCGAATGGCT-ACAATCTGCCCCAGGCTCGA
1 GGTAAGAGATTGGCT-GATGATGATCTGCCCCAGGCTCGG
* * * **
240206 GGTAAGAGATTTGCTGATAATGATCTACCTAAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * ** * *
240245 GGTAAGAGATCGAATGGCT-ACAATCTTCCTCAGGCTCGG
1 GGTAAGAGATTGGCT-GATGATGATCTGCCCCAGGCTCGG
* *
240284 GGTAAGAGATTGGCTAATGATGATCTGCCCTAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * *
240323 GGTAAGAGATCGAATG--GTTGCAATCTG-CCCAGGCTTGG
1 GGTAAGAGATTGGCTGATGATG--ATCTGCCCCAGGCTCGG
* * * *
240361 GATAAGAGATTTGCTGATGATGATCTGTCTCAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* *
240400 GGTAAGAGATTTGTTGATGATGATCT---------T-GG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * *
240429 GGTAAGAGATCGAAT-A-GTTGCAATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGATG--ATCTGCCCCAGGCTCGG
* * * * *
240468 GGTAAGAGATTGGCTGATGGTGATTTTCCCAAGGCTCGA
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* **
240507 GGTAAGAGA-T--CAGATCCTCGATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGAT-GATCTGCCCCAGGCTCGG
* ** * *
240544 GGTAAGAGATCGAATG--GTTGCAATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGATG--ATCTGCCCCAGGCTCGG
* * ** * **
240583 CGTAAGAGATTGGCTGATGGTTTTCTACCTAAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
240622 GGTAAGAGAT
1 GGTAAGAGAT
240632 CGAATTTTCG
Statistics
Matches: 508, Mismatches: 150, Indels: 82
0.69 0.20 0.11
Matches are distributed among these distances:
27 3 0.01
28 1 0.00
29 17 0.03
30 1 0.00
35 6 0.01
36 5 0.01
37 30 0.06
38 35 0.07
39 381 0.75
40 13 0.03
41 8 0.02
43 8 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (39 bp):
GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
Found at i:239985 original size:78 final size:77
Alignment explanation
Indices: 239894--240409 Score: 640
Period size: 78 Copynumber: 6.6 Consensus size: 77
239884 CCATGATCAA
* *
239894 GGTAAGAGATTGGCTGATGATGATATGCCCCAGGCTCGGGGTAA-AGGATCGAATGGCTGCAATC
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGA-GATCGAATGGCTACAATC
239958 TGCCCCAGGCTCG
65 TGCCCCAGGCTCG
* * * *
239971 GTGTAAGAAATTGGCTAATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGTTACAATC
1 G-GTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATC
**
240036 TGCCTTAGGCTCGG
65 TGCCCCAGGCTC-G
* * * * * * *
240050 GGTAAGAGATTTGCTGATGCTAATCTACCCCAGGCTCGAGATAAGAGATAGAATGGCTACAATCT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATCT
*
240115 GCCCTAGGCTCG
66 GCCCCAGGCTCG
* * * *
240127 AGGTAAGGGATTCGCTGATAATGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTACAATC
1 -GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATC
240192 TGCCCCAGGCTCG
65 TGCCCCAGGCTCG
* * * **
240205 AGGTAAGAGATTTGCTGATAATGATCTACCTAAGGCTCGGGGTAAGAGATCGAATGGCTACAATC
1 -GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATC
* *
240270 TTCCTCAGGCTCGG
65 TGCCCCAGGCTC-G
* * * *
240284 GGTAAGAGATTGGCTAATGATGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGTTGCAATCT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATCT
*
240349 G-CCCAGGCTTG
66 GCCCCAGGCTCG
* * *
240360 GGATAAGAGATTTGCTGATGATGATCTGTCTCAGGCTCGGGGTAAGAGAT
1 GG-TAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGAT
240410 TTGTTGATGA
Statistics
Matches: 379, Mismatches: 54, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
76 3 0.01
77 51 0.13
78 321 0.85
79 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (77 bp):
GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATCT
GCCCCAGGCTCG
Found at i:254074 original size:22 final size:24
Alignment explanation
Indices: 254034--254078 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
254024 AAATTTTAAT
254034 AAATAAAAAAATTATTAAATATTA
1 AAATAAAAAAATTATTAAATATTA
*
254058 AAATAAAATAA-TA-TAAATATT
1 AAATAAAAAAATTATTAAATATT
254079 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAAAAAATTATTAAATATTA
Found at i:254082 original size:24 final size:24
Alignment explanation
Indices: 254018--254084 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
254008 TTAAATGATT
*
254018 ATATAAAAATTTTAATAAATAAAAAA
1 ATATAAATATTTT-A-AAATAAAAAA
*
254044 ATTATTAAATA--TTAAAATAAAATA
1 A-TA-TAAATATTTTAAAATAAAAAA
254068 ATATAAATATTTTAAAA
1 ATATAAATATTTTAAAA
254085 AATTAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
22 6 0.17
23 2 0.06
24 16 0.46
25 1 0.03
26 3 0.09
27 2 0.06
28 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAAATATTTTAAAATAAAAAA
Found at i:258538 original size:15 final size:15
Alignment explanation
Indices: 258518--258568 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
258508 GCACATCAAA
258518 CAAGAATTAATATAC
1 CAAGAATTAATATAC
* *
258533 CAAGAA-TAATAAAT
1 CAAGAATTAATATAC
258547 CAAGAATTAATATAC
1 CAAGAATTAATATAC
258562 CAAGAAT
1 CAAGAAT
258569 ACTAAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.24
Consensus pattern (15 bp):
CAAGAATTAATATAC
Found at i:258550 original size:14 final size:14
Alignment explanation
Indices: 258518--258582 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
258508 GCACATCAAA
*
258518 CAAGAATTAATATAC
1 CAAGAA-TAATAAAC
*
258533 CAAGAATAATAAAT
1 CAAGAATAATAAAC
*
258547 CAAGAATTAATATAC
1 CAAGAA-TAATAAAC
* *
258562 CAAGAATACTAAAT
1 CAAGAATAATAAAC
258576 CAAGAAT
1 CAAGAAT
258583 TAAGCACAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 24 0.57
15 18 0.43
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.23
Consensus pattern (14 bp):
CAAGAATAATAAAC
Found at i:258560 original size:29 final size:29
Alignment explanation
Indices: 258518--258585 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
258508 GCACATCAAA
258518 CAAGAATTAATATACCAAGAATAATAAAT
1 CAAGAATTAATATACCAAGAATAATAAAT
*
258547 CAAGAATTAATATACCAAGAATACTAAAT
1 CAAGAATTAATATACCAAGAATAATAAAT
258576 CAAGAATTAA
1 CAAGAATTAA
258586 GCACAATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (29 bp):
CAAGAATTAATATACCAAGAATAATAAAT
Found at i:260704 original size:15 final size:15
Alignment explanation
Indices: 260684--260712 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
260674 TATATTTCTT
260684 TTCTTTTCTCTTTTC
1 TTCTTTTCTCTTTTC
260699 TTCTTTTCTCTTTT
1 TTCTTTTCTCTTTT
260713 TTTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTCTCTTTTC
Found at i:263691 original size:20 final size:20
Alignment explanation
Indices: 263668--263710 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
263658 TATAAAATTT
263668 AAAGGA-AACAAGTAAAAGTA
1 AAAGGATAA-AAGTAAAAGTA
*
263688 AAAGGATAAAAGTAAATGTA
1 AAAGGATAAAAGTAAAAGTA
263708 AAA
1 AAA
263711 ATGTGTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.65, C:0.02, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAGGATAAAAGTAAAAGTA
Found at i:270890 original size:25 final size:23
Alignment explanation
Indices: 270858--270903 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
270848 GTTAGATCCA
270858 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
270883 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
270904 TCCTCATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:271972 original size:17 final size:15
Alignment explanation
Indices: 271943--271996 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
271933 CACACTTGTC
*
271943 TTTTTTTTCTCAATT
1 TTTTTTTTTTCAATT
271958 TTCTCTTTTTTTCAATT
1 TT-T-TTTTTTTCAATT
* *
271975 TTTTTTTTTTGACTT
1 TTTTTTTTTTCAATT
271990 TTTTTTT
1 TTTTTTT
271997 CTTTTTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 19 0.56
16 2 0.06
17 13 0.38
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTTCAATT
Found at i:272971 original size:6 final size:6
Alignment explanation
Indices: 272930--272973 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
272920 AGTGCATAAT
* * * *
272930 AAAATA AACATA AAACTA AAAATG AAAATG AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
272974 TGTACTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:287007 original size:13 final size:13
Alignment explanation
Indices: 286968--287009 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
286958 AAAAGAACCT
286968 ATAAA-TAAAAAA
1 ATAAATTAAAAAA
286980 ATTAAATGT-AAAAA
1 A-TAAAT-TAAAAAA
286994 ATAAATTAAAAAA
1 ATAAATTAAAAAA
287007 ATA
1 ATA
287010 TGAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.08
13 17 0.65
14 6 0.23
15 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
ATAAATTAAAAAA
Found at i:294552 original size:25 final size:24
Alignment explanation
Indices: 294514--294561 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
294504 ATTAATATAA
294514 AATTATTTTATTTAATACTAATAC
1 AATTATTTTATTTAATACTAATAC
*
294538 AATTATTTTTATTTAATATTAATA
1 AATTA-TTTTATTTAATACTAATA
294562 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATTTTATTTAATACTAATAC
Found at i:295333 original size:21 final size:20
Alignment explanation
Indices: 295290--295334 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
295280 ATAATAGCAT
* *
295290 AATCCAAATATAAGTTTAGA
1 AATCCAAACATAAATTTAGA
*
295310 AATCCAAACATAAAATTTATA
1 AATCCAAACAT-AAATTTAGA
295331 AATC
1 AATC
295335 TAAATTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
AATCCAAACATAAATTTAGA
Found at i:296172 original size:19 final size:19
Alignment explanation
Indices: 296126--296172 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
296116 TAATTGAGGT
*
296126 AATAAATATATAATATTAA
1 AATAAAAATATAATATTAA
** *
296145 AATGCAAATATTATATTAA
1 AATAAAAATATAATATTAA
296164 AATAAAAAT
1 AATAAAAAT
296173 TTGATTTAGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AATAAAAATATAATATTAA
Found at i:303436 original size:56 final size:56
Alignment explanation
Indices: 303359--303506 Score: 230
Period size: 56 Copynumber: 2.7 Consensus size: 56
303349 TGGGAAAAAA
*
303359 GAAAAAA-AATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGT-TCGAGAAAATCT
1 GAAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAATCT-GAGAAAATCT
*
303414 GAAAAAATAATGAGAGAAAATGGATGTTTGGAAAGAGAGAAAATCTGAGAAAATCT
1 GAAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAATCTGAGAAAATCT
*
303470 -AGAAAAATAATGAGAGAAAATGGGAGTTTGGAAAGAG
1 GA-AAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAG
303507 TCTAAGAAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
55 8 0.09
56 77 0.90
57 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.28, T:0.18
Consensus pattern (56 bp):
GAAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAATCTGAGAAAATCT
Found at i:322286 original size:26 final size:26
Alignment explanation
Indices: 322248--322328 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
322238 TTACTACTAA
*
322248 TGTCACTGTATGAGCATGTCCAAAAT
1 TGTCGCTGTATGAGCATGTCCAAAAT
* * * *
322274 TGTCGCTGCATGAACTTGTCCAGAAT
1 TGTCGCTGTATGAGCATGTCCAAAAT
* *
322300 TGTCGCTGTATGAGCACGTCCATAAT
1 TGTCGCTGTATGAGCATGTCCAAAAT
322326 TGT
1 TGT
322329 GTCCAGAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (26 bp):
TGTCGCTGTATGAGCATGTCCAAAAT
Found at i:331086 original size:17 final size:17
Alignment explanation
Indices: 331032--331108 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
331022 GTTAGTAAGT
** *
331032 ATTGTCATCACATTCCC
1 ATTGTCATTGCATTTCC
* **
331049 ATTGTCATTACATTTTA
1 ATTGTCATTGCATTTCC
*
331066 ATTGTCATTGCATTTGC
1 ATTGTCATTGCATTTCC
331083 ATTGTTC-TTGCATTTCC
1 ATTG-TCATTGCATTTCC
331100 ATTTGTCAT
1 A-TTGTCAT
331109 GGTATTTTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
17 43 0.88
18 6 0.12
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (17 bp):
ATTGTCATTGCATTTCC
Found at i:337926 original size:24 final size:24
Alignment explanation
Indices: 337894--337939 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
337884 AAAGATGCGA
337894 GGAAACAAATATGGATCTAAATTG
1 GGAAACAAATATGGATCTAAATTG
*
337918 GGAAACAAATATGGTTCTAAAT
1 GGAAACAAATATGGATCTAAAT
337940 ATGGCAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (24 bp):
GGAAACAAATATGGATCTAAATTG
Found at i:350129 original size:5 final size:5
Alignment explanation
Indices: 350119--350148 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
350109 TATTTTTCAA
*
350119 TTCTT TTCTT TACTT TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
350149 CCAAATAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:351151 original size:2 final size:2
Alignment explanation
Indices: 351144--351168 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
351134 CACGCCTAAG
351144 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
351169 CAAACATGTA
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:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:352868 original size:21 final size:21
Alignment explanation
Indices: 352829--352868 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
352819 TTTTATATGA
*
352829 AATTTTGAATTAAGGAGTTTT
1 AATTTTGAATTAAGAAGTTTT
352850 AATTATTGAATTAA-AAGTT
1 AATT-TTGAATTAAGAAGTT
352869 ATTATAAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
AATTTTGAATTAAGAAGTTTT
Found at i:364018 original size:21 final size:21
Alignment explanation
Indices: 363985--364036 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
363975 TGGAGTTTTA
*
363985 GTATCGGTGGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
364006 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
364027 GTATCGGTAG
1 GTATCGGTAG
364037 TATTATCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:364936 original size:27 final size:27
Alignment explanation
Indices: 364892--364944 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
364882 ACACATGTGT
*
364892 GGTGCCATGTTAAATGGCGGCACCAAA
1 GGTGCCATGTTAAATGGCGACACCAAA
*
364919 GGTGCCAT-TCTAAGTGGCGACACCAA
1 GGTGCCATGT-TAAATGGCGACACCAA
364945 GGGGTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (27 bp):
GGTGCCATGTTAAATGGCGACACCAAA
Done.