Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013230.1 Kokia drynarioides strain JFW-HI SEQ_128249, 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: 345372
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 111 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:179448 original size:22 final size:22
Alignment explanation
Indices: 179420--179471 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
179410 GCTTGAGAGC
*
179420 TTTTTTTTTAGAGAGAAAATGT
1 TTTTTTTTTAGAGAGAAAAGGT
179442 TTTTTTTTTAGAGAGAAAAGGT
1 TTTTTTTTTAGAGAGAAAAGGT
179464 TTTTTTTT
1 TTTTTTTT
179472 AAAGGGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (22 bp):
TTTTTTTTTAGAGAGAAAAGGT
Found at i:179905 original size:29 final size:29
Alignment explanation
Indices: 179800--180083 Score: 207
Period size: 30 Copynumber: 9.6 Consensus size: 29
179790 CCCAGAAGGT
* * *
179800 CCCTAAACTTTACAAAAATCATATTTTAA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
*** *
179829 CCCTCAAACTTTAATAAAATTACATTTTCAA
1 CCCT-AAACTTTTCCAAAATCACATTTT-AA
* * * *
179860 CCCTGAATTTTTCCAAAATTACATTTTCA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
* *
179889 CCCTAAACTTTTTCAAAATCACATTTTTAC
1 CCCTAAACTTTTCCAAAATCACA-TTTTAA
* * **
179919 CCCCAAACTTTCCCAAAATCGTATTTTAA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
* *
179948 CCCCTAAACTTTCCCAAAATCATATTTTAA
1 -CCCTAAACTTTTCCAAAATCACATTTTAA
* *
179978 CCCTAAAAAC-TTTCCTAAAATCATATTTTGAC
1 CCCT--AAACTTTTCC-AAAATCACATTTT-AA
* *
180010 CCCTAAAC-TTTCCTAAAATTACATTTCAA
1 CCCTAAACTTTTCC-AAAATCACATTTTAA
* ** *
180039 CCTTAATTTTTTCCAAAATTACA-TTTAA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
*
180067 CCCTAAA-TTCTCCAAAA
1 CCCTAAACTTTTCCAAAA
180084 CTTCATTTTT
Statistics
Matches: 209, Mismatches: 37, Indels: 20
0.79 0.14 0.08
Matches are distributed among these distances:
27 9 0.04
28 9 0.04
29 48 0.23
30 115 0.55
31 23 0.11
32 5 0.02
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATCACATTTTAA
Found at i:181694 original size:12 final size:12
Alignment explanation
Indices: 181679--181712 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
181669 CATGAACAAG
181679 CTCGTTTATTGA
1 CTCGTTTATTGA
181691 CTCGTTTATTGA
1 CTCGTTTATTGA
* *
181703 GTCATTTATT
1 CTCGTTTATT
181713 TATTAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.53
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:182190 original size:23 final size:24
Alignment explanation
Indices: 182134--182199 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
182124 AAAAAAAAAT
* *
182134 TGTTCGTGTACATATTCAATTATA
1 TGTTCGTGAACATATTCGATTATA
** *
182158 TGTTTATGAACATATTCGTTTA-A
1 TGTTCGTGAACATATTCGATTATA
*
182181 TGTTCGTGAACATGTTCGA
1 TGTTCGTGAACATATTCGA
182200 CTAAGTTAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (24 bp):
TGTTCGTGAACATATTCGATTATA
Found at i:182355 original size:40 final size:40
Alignment explanation
Indices: 182265--182394 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
182255 TTTAAATAAG
* * * *
182265 CGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCTGT-AAG
1 CGCCGCTATTGCTCT-ACCTTTTGCGGCGATTT-ATGTAAAA
*
182306 CGCCTCTATTGCTCTACCTTTTGCGGC-ATTTATGTAAAAA
1 CGCCGCTATTGCTCTACCTTTTGCGGCGATTTATGT-AAAA
* * *
182346 CGCCGCTATTGCTTTATCTTTTGCGGCGTTTTATGTCAAAA
1 CGCCGCTATTGCTCTACCTTTTGCGGCGATTTATGT-AAAA
182387 CGCCGCTA
1 CGCCGCTA
182395 AAAATGCCGC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 37 0.49
41 33 0.43
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (40 bp):
CGCCGCTATTGCTCTACCTTTTGCGGCGATTTATGTAAAA
Found at i:185309 original size:28 final size:26
Alignment explanation
Indices: 185234--185330 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 26
185224 TGCCAAAAAC
* * *
185234 ATTTTTAGAATTTAGTTCTTATATTTTC
1 ATTTTTAAAATTTAG-TCCTAT-TTTTA
*
185262 ATTTTTAGAAATTTATTCCTACTTTTTA
1 ATTTTTA-AAATTTAGTCCTA-TTTTTA
185290 ATTTTTAAAATTTAAGTCCTATTATTTA
1 ATTTTTAAAATTT-AGTCCTATT-TTTA
*
185318 TATTATTAAAATT
1 -ATTTTTAAAATT
185331 ATTTGTTTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
27 8 0.14
28 32 0.55
29 18 0.31
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (26 bp):
ATTTTTAAAATTTAGTCCTATTTTTA
Found at i:187868 original size:16 final size:16
Alignment explanation
Indices: 187847--187880 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
187837 AACATAAGCA
187847 CTACCAGTTCCATTTT
1 CTACCAGTTCCATTTT
*
187863 CTACCAGTTTCATTTT
1 CTACCAGTTCCATTTT
187879 CT
1 CT
187881 CACTTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (16 bp):
CTACCAGTTCCATTTT
Found at i:188748 original size:17 final size:17
Alignment explanation
Indices: 188695--188762 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
188685 TAAATTAAAA
188695 TAAGTTTGAATTTATTT
1 TAAGTTTGAATTTATTT
* ** *
188712 TAAATTCAAAATTCATTT
1 TAAGTT-TGAATTTATTT
*
188730 TAAGTTTGAATTTACTT
1 TAAGTTTGAATTTATTT
*
188747 TAAATTT-AAGTTTATT
1 TAAGTTTGAA-TTTATT
188763 CTAAATTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
16 2 0.05
17 23 0.61
18 13 0.34
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.53
Consensus pattern (17 bp):
TAAGTTTGAATTTATTT
Found at i:189912 original size:65 final size:65
Alignment explanation
Indices: 189836--189969 Score: 232
Period size: 65 Copynumber: 2.1 Consensus size: 65
189826 TGTACCAGCA
* * *
189836 GGTGATGGACGTCGAAGCATGGTGGTCACGCGCGTCGACCGACGAGGCGCGTGCAGCGGAGCCAC
1 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGCCGACCGACGAGGCGCGTGCAGCAGAGCCAC
*
189901 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGCCGACCGACGAGGCGCGTGCAGCAGAGCCAT
1 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGCCGACCGACGAGGCGCGTGCAGCAGAGCCAC
189966 GGTG
1 GGTG
189970 GCCGGACGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.19, C:0.28, G:0.42, T:0.12
Consensus pattern (65 bp):
GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGCCGACCGACGAGGCGCGTGCAGCAGAGCCAC
Found at i:190611 original size:29 final size:29
Alignment explanation
Indices: 190546--190944 Score: 359
Period size: 29 Copynumber: 13.6 Consensus size: 29
190536 GTCCCGAAGT
* *
190546 TTCCAAAAATTCCATTTTTGA-TCTCGAAAA
1 TTCCAAAAATTCCATTTTT-ACCCTCG-AAC
*
190576 TTCCAAAAATTCCATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* * *
190605 TTTCAAAAATTCCATTTTTACCCCCAAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
*
190634 TTCCAAAAATTCCATTTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTTACCCTCG-AAC
*
190664 TTCCAAAAATTCCATTTTTACCCTCAAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
*
190693 ATCCAAAAATTCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* *
190722 TTCTAAAAATTTCATTTTTGA--CTCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCG-AAC
* *
190751 TTCCAAAAATTCTATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
*
190780 TTCCAAAATTTCCATTTTTGA-CCTCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCG-AAC
* *
190810 TTCCAAAAATTACCA-TTTTGCCCCCGAAC
1 TTCCAAAAATT-CCATTTTTACCCTCGAAC
* * * * * *
190839 GTCCACAAACTCCATTTTCGACCTTAGAAC
1 TTCCAAAAATTCCATTTT-TACCCTCGAAC
*
190869 -TCTC-AAAATTACC-CTTTTACCCTCGAA-
1 TTC-CAAAAATT-CCATTTTTACCCTCGAAC
* *
190896 TATCTAAAAATTCCATTTTTAACCCT-GAATT
1 T-TCCAAAAATTCCATTTTT-ACCCTCGAA-C
*
190927 TTCCCAAAATTACCATTT
1 TTCCAAAAATT-CCATTT
190945 CACCCTGAGA
Statistics
Matches: 303, Mismatches: 44, Indels: 43
0.78 0.11 0.11
Matches are distributed among these distances:
28 17 0.06
29 179 0.59
30 97 0.32
31 10 0.03
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTCGAAC
Found at i:190665 original size:59 final size:59
Alignment explanation
Indices: 190546--190862 Score: 410
Period size: 59 Copynumber: 5.4 Consensus size: 59
190536 GTCCCGAAGT
* *
190546 TTCCAAAAATTCCATTTTTGATCTCGAAAATTCCAAAAATTCCATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAC
* * * * *
190605 TTTCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCG-AAC
* *
190664 TTCCAAAAATTCCATTTTT-ACCCTC-AAACATCCAAAAATTCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAC
* * *
190722 TTCTAAAAATTTCATTTTTGA-CTCGAAACTTCCAAAAATTCTATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAC
* *
190780 TTCCAAAATTTCCATTTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTGCCCCCGAAC
1 TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATT-CCATTTTTACCCCCGAAC
* * * *
190839 GTCCACAAACTCCATTTTCGACCT
1 TTCCAAAAATTCCATTTTTGACCT
190863 TAGAACTCTC
Statistics
Matches: 226, Mismatches: 26, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
57 3 0.01
58 98 0.43
59 120 0.53
60 5 0.02
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAC
Found at i:190700 original size:88 final size:87
Alignment explanation
Indices: 190546--190828 Score: 404
Period size: 88 Copynumber: 3.2 Consensus size: 87
190536 GTCCCGAAGT
* *
190546 TTCCAAAAATTCCATTTTTGATCTCGAAAATTCCAAAAATTCCATTTTTACCCCCGAACTTTCAA
1 TTCCAAAAATTCCATTTTTGA-CTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAA
190611 AAATTCCATTTTTACCCCCAAAC
65 AAATTCCATTTTTACCCCCAAAC
* * * *
190634 TTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACATCCAA
1 TTCCAAAAATTCCATTTTTGA-CTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAA
* *
190699 AAATTCCATTTTTACCCTCGAAC
65 AAATTCCATTTTTACCCCCAAAC
* * *
190722 TTCTAAAAATTTCATTTTTGACTCGAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAA
1 TTCCAAAAATTCCATTTTTGACTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAA
* * *
190787 ATTTCCATTTTTGACCTCGAAAC
66 AATTCCATTTTT-ACCCCCAAAC
190810 TTCCAAAAATTACCATTTT
1 TTCCAAAAATT-CCATTTT
190829 GCCCCCGAAC
Statistics
Matches: 170, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
87 51 0.30
88 113 0.66
89 6 0.04
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (87 bp):
TTCCAAAAATTCCATTTTTGACTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAA
AATTCCATTTTTACCCCCAAAC
Found at i:190877 original size:117 final size:115
Alignment explanation
Indices: 190546--190915 Score: 378
Period size: 117 Copynumber: 3.2 Consensus size: 115
190536 GTCCCGAAGT
* * *
190546 TTCCAAAAATTCCATTTTTGATCTCGAAAATTCCAAAAATTCCATTTTTACCCCCGAACTTTCAA
1 TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAA
* * *
190611 AAATTCCATTTTTACCCCCA-AACTTCCAAAAATTCCATTTTTAACCTCGAAAC
66 AAATTCCATTTTGA--CCTAGAACTTCCAAAAATT-CATTTTTACCCTCG-AAC
* * *
190664 TTCCAAAAATTCCATTTTT-ACCCTC-AAACATCCAAAAATTCCATTTTTACCCTCGAACTTCTA
1 TTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
* * *
190727 AAAATTTCATTTTTGA-CTCGAAACTTCCAAAAATTCTATTTTTACCCCCGAAC
65 AAAATTCCA-TTTTGACCTAG-AACTTCCAAAAATTC-ATTTTTACCCTCGAAC
* * *
190780 TTCCAAAATTTCCATTTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTGCCCCCGAACGTCCA
1 TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATT-CCATTTTTACCCCCGAACTTCCA
* * **
190844 CAAACTCCATTTTCGACCTTAGAAC-TCTC-AAAATTACCCTTTTACCCTCGAA-
65 AAAATTCCATTTT-GACC-TAGAACTTC-CAAAAATT-CATTTTTACCCTCGAAC
*
190896 TATCTAAAAATTCCATTTTT
1 T-TCCAAAAATTCCATTTTT
190916 AACCCTGAAT
Statistics
Matches: 211, Mismatches: 27, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
115 1 0.00
116 31 0.15
117 141 0.67
118 36 0.17
119 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (115 bp):
TTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAA
AAATTCCATTTTGACCTAGAACTTCCAAAAATTCATTTTTACCCTCGAAC
Found at i:190877 original size:146 final size:146
Alignment explanation
Indices: 190602--190878 Score: 387
Period size: 146 Copynumber: 1.9 Consensus size: 146
190592 TTTACCCCCG
*
190602 AACTTTCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* * * *
190667 CAAAAATTCCATTTTTACCCTCAAACATCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAAT
66 CAAAAATTCCATTTTTACCCCCAAACATCCAAAAACTCCATTTTGACCCTAGAACTTCTAAAAAT
190732 TTCATTTTTGACTCGA
131 TTCATTTTTGACTCGA
* * * *
190748 AACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAATTTCCATTTTTGACCTCGAAACTTC
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* * * * * *
190813 CAAAAATTACCA-TTTTGCCCCCGAACGTCCACAAACTCCATTTTCGACCTTAGAAC-TCTCAAA
66 CAAAAATT-CCATTTTTACCCCCAAACATCCAAAAACTCCATTTT-GACCCTAGAACTTCTAAAA
190876 ATT
129 ATT
190879 ACCCTTTTAC
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
146 103 0.90
147 11 0.10
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (146 bp):
AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
CAAAAATTCCATTTTTACCCCCAAACATCCAAAAACTCCATTTTGACCCTAGAACTTCTAAAAAT
TTCATTTTTGACTCGA
Found at i:193968 original size:11 final size:11
Alignment explanation
Indices: 193952--194045 Score: 72
Period size: 11 Copynumber: 8.7 Consensus size: 11
193942 AATTCTAAAA
*
193952 TTAAATTTACT
1 TTAAATTTAAT
193963 TTAAATTTAAAT
1 TTAAATTT-AAT
*
193975 TTAAA-TTCAT
1 TTAAATTTAAT
*
193985 TT---TTAAAT
1 TTAAATTTAAT
*
193993 TTAAATTTATT
1 TTAAATTTAAT
194004 TTAAATTTAAAT
1 TTAAATTT-AAT
*
194016 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
194027 TTAAATTTAGT
1 TTAAATTTAAT
194038 TTAAATTT
1 TTAAATTT
194046 GAAATAATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
8 5 0.08
10 4 0.06
11 42 0.64
12 15 0.23
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:193971 original size:6 final size:6
Alignment explanation
Indices: 193933--194071 Score: 112
Period size: 6 Copynumber: 24.0 Consensus size: 6
193923 TTAGATATGT
* * *
193933 TTTAGA TTT-AA TTCTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
193980 TTCATT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
194026 TTTAAA TTT-AG TTTAAA TTTGAAA --TAAT TTTAAA CTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
194072 ATCAATTACA
Statistics
Matches: 103, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
4 2 0.02
5 20 0.19
6 75 0.73
7 6 0.06
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:193972 original size:17 final size:17
Alignment explanation
Indices: 193968--194069 Score: 143
Period size: 17 Copynumber: 5.9 Consensus size: 17
193958 TTACTTTAAA
*
193968 TTTAAATTTAAATTCATT
1 TTTAAATTTAAATTTA-T
193986 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
194003 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
194020 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
194037 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
194054 TTTAAACTTAAATTTA
1 TTTAAATTTAAATTTA
194070 AAATCAATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
16 3 0.04
17 55 0.72
18 18 0.24
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:194752 original size:21 final size:20
Alignment explanation
Indices: 194718--194762 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
194708 GCATTAATAG
*
194718 TAAT-TAATAATATTATTTA
1 TAATATAATAATATTATTAA
194737 TAATATAATAAATATTATTAA
1 TAATATAAT-AATATTATTAA
194758 TAATA
1 TAATA
194763 ATATTAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATAATAATATTATTAA
Found at i:194768 original size:12 final size:12
Alignment explanation
Indices: 194712--194783 Score: 65
Period size: 12 Copynumber: 5.9 Consensus size: 12
194702 ATAAAGGCAT
*
194712 TAATAGTAATTAA
1 TAATATTAA-TAA
* *
194725 TAATATTATTTA
1 TAATATTAATAA
194737 TAATA-TAATAAA
1 TAATATTAAT-AA
*
194749 TATTATTAATAA
1 TAATATTAATAA
*
194761 TAATATTAGTAA
1 TAATATTAATAA
*
194773 TAATGTTAATA
1 TAATATTAATA
194784 GTAAATAGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
11 3 0.06
12 33 0.70
13 11 0.23
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:195899 original size:30 final size:30
Alignment explanation
Indices: 195863--196047 Score: 123
Period size: 30 Copynumber: 6.3 Consensus size: 30
195853 CTCAACTATC
*
195863 CAAAAATTCCAATTTTAACCTCGAAACTTT
1 CAAAAATTACAATTTTAACCTCGAAACTTT
* * **
195893 CAAAAATTAC-ATTTTTACCCCTTAAC-TT
1 CAAAAATTACAATTTTAACCTCGAAACTTT
* *
195921 CTAAAAATT-CAATTTTTGACCCCGAAACTTT
1 C-AAAAATTACAA-TTTTAACCTCGAAACTTT
* * *
195952 CAAAAATTAC-ATTTTTA-CTCCTAAACTTC
1 CAAAAATTACAATTTTAACCT-CGAAACTTT
* * *
195981 CAAAAATTCCACTTTTAACC-CTAAAACTTT
1 CAAAAATTACAATTTTAACCTC-GAAACTTT
** * * *
196011 TGAAAATTACATTTTTACCCTCG-AACTTC
1 CAAAAATTACAATTTTAACCTCGAAACTTT
196040 CAAAAATT
1 CAAAAATT
196048 CCATTCTTGA
Statistics
Matches: 119, Mismatches: 26, Indels: 21
0.72 0.16 0.13
Matches are distributed among these distances:
28 5 0.04
29 53 0.45
30 55 0.46
31 6 0.05
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
CAAAAATTACAATTTTAACCTCGAAACTTT
Found at i:195947 original size:59 final size:59
Alignment explanation
Indices: 195851--196113 Score: 314
Period size: 59 Copynumber: 4.4 Consensus size: 59
195841 CCCTAGAGGA
* * * *
195851 CCCTCAACTATCCAAAAATTCCAATTTTAACCTCGAAACTTTCAAAAATTACATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTAC
* * * * *
195911 CCCTTAACTTCTAAAAATTCAATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTAC
* * * **
195970 TCCTAAACTTCCAAAAATTCCACTTTTAACCCTAAAACTTTTGAAAATTACATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTAC
* * * * *
196028 CCCTCGAACTTCCAAAAATTCCATTCTTGACCCTAAAAC-TTCTAAAAATTACTTTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTC-AAAAATTACATTTTTAC
196088 CCCTAAACTTCCAAAAATTCCATTTT
1 CCCTAAACTTCCAAAAATTCCATTTT
196114 CACCCTAAAT
Statistics
Matches: 174, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
58 5 0.03
59 157 0.90
60 12 0.07
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTAC
Found at i:196075 original size:118 final size:117
Alignment explanation
Indices: 195851--196122 Score: 352
Period size: 118 Copynumber: 2.3 Consensus size: 117
195841 CCCTAGAGGA
* *
195851 CCCTCAACTATCCAAAAATTCCAATTTTAA-CCTCGAAACTTTCAAAAATTACATTTTTACCCCT
1 CCCTAAACT-TCCAAAAATTCC-ATTTTAACCCT-AAAACTTTCAAAAATTACATTTTTACCCCT
* * * *
195915 TAACTTCTAAAAATTCAATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTAC
63 GAACTTCCAAAAATTCAATTCTTGACCCCAAAACTTTCAAAAATTACATTTTTAC
* **
195970 TCCTAAACTTCCAAAAATTCCACTTTTAACCCTAAAACTTTTGAAAATTACATTTTTA-CCCTCG
1 CCCTAAACTTCCAAAAATTCCA-TTTTAACCCTAAAACTTTCAAAAATTACATTTTTACCCCT-G
* * *
196034 AACTTCCAAAAATTCCATTCTTGACCCTAAAAC-TTCTAAAAATTACTTTTTTAC
64 AACTTCCAAAAATTCAATTCTTGACCCCAAAACTTTC-AAAAATTACATTTTTAC
*
196088 CCCTAAACTTCCAAAAATTCCATTTTCACCCTAAA
1 CCCTAAACTTCCAAAAATTCCATTTTAACCCTAAA
196123 TTTTCCCAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
117 20 0.15
118 105 0.78
119 10 0.07
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (117 bp):
CCCTAAACTTCCAAAAATTCCATTTTAACCCTAAAACTTTCAAAAATTACATTTTTACCCCTGAA
CTTCCAAAAATTCAATTCTTGACCCCAAAACTTTCAAAAATTACATTTTTAC
Found at i:196128 original size:29 final size:28
Alignment explanation
Indices: 195850--196146 Score: 236
Period size: 29 Copynumber: 10.1 Consensus size: 28
195840 ACCCTAGAGG
* *
195850 ACCCTCAACTATCCAAAAATTCCAATTTTA
1 ACCCTAAACT-TCCAAAAATTCC-ATTTTT
* * *
195880 ACCTCGAAACTTTCAAAAATTACATTTTT
1 ACC-CTAAACTTCCAAAAATTCCATTTTT
* * *
195909 ACCCCTTAACTTCTAAAAATTCAATTTTT
1 A-CCCTAAACTTCCAAAAATTCCATTTTT
* * *
195938 GACCCCGAAACTTTCAAAAATTACATTTTT
1 -A-CCCTAAACTTCCAAAAATTCCATTTTT
*
195968 ACTCCTAAACTTCCAAAAATTCCACTTTTA
1 AC-CCTAAACTTCCAAAAATTCCA-TTTTT
*** *
195998 ACCCTAAAACTTTTGAAAATTACATTTTT
1 ACCCT-AAACTTCCAAAAATTCCATTTTT
* *
196027 ACCCTCGAACTTCCAAAAATTCCATTCTTG
1 ACCCT-AAACTTCCAAAAATTCCATT-TTT
* * *
196057 ACCCTAAAACTTCTAAAAATTACTTTTTT
1 ACCCT-AAACTTCCAAAAATTCCATTTTT
*
196086 ACCCCTAAACTTCCAAAAATTCCATTTTC
1 A-CCCTAAACTTCCAAAAATTCCATTTTT
* * *
196115 ACCCTAAATTTTCCCAAAATACCA-TTTT
1 ACCCTAAA-CTTCCAAAAATTCCATTTTT
196143 ACCC
1 ACCC
196147 CTTGAGAGTC
Statistics
Matches: 211, Mismatches: 47, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
28 15 0.07
29 106 0.50
30 85 0.40
31 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (28 bp):
ACCCTAAACTTCCAAAAATTCCATTTTT
Found at i:196160 original size:28 final size:29
Alignment explanation
Indices: 196128--196190 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
196118 CTAAATTTTC
*
196128 CCAAAA-TACCATTTTACCCCTTGAG-AGT
1 CCAAAATTACCATTTTACCCCTCGAGTA-T
*
196156 CCAAAATTACCATTTTGCCCCTCGAGTAT
1 CCAAAATTACCATTTTACCCCTCGAGTAT
196185 CCAAAA
1 CCAAAA
196191 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.19
29 24 0.77
30 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCCTCGAGTAT
Found at i:200868 original size:38 final size:39
Alignment explanation
Indices: 200826--200905 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
200816 GTTAGCAAAT
* **
200826 AAAAA-GATGGGTCAAAATCCGCAAAGGACATTTAAAAA
1 AAAAAGGATAGGTCAAAATCCAAAAAGGACATTTAAAAA
*
200864 AAAAAGGATAGGTCAAAATCCAAAAAGGGCATTTAAAAA
1 AAAAAGGATAGGTCAAAATCCAAAAAGGACATTTAAAAA
200903 AAA
1 AAA
200906 GTCAAGATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 5 0.14
39 32 0.86
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.15
Consensus pattern (39 bp):
AAAAAGGATAGGTCAAAATCCAAAAAGGACATTTAAAAA
Found at i:201715 original size:15 final size:14
Alignment explanation
Indices: 201697--201759 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 14
201687 GATGCAATGA
201697 AGAAAAAAATAAAAG
1 AGAAAAAAA-AAAAG
*
201712 AGAAAAAAAAGAAAAA
1 AG-AAAAAAA-AAAAG
* *
201728 AGAAATAGAAAAAG
1 AGAAAAAAAAAAAG
*
201742 CAGAAAAAGAAAAAG
1 -AGAAAAAAAAAAAG
201757 AGA
1 AGA
201760 GGTAGAGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 7 0.17
15 20 0.50
16 13 0.32
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (14 bp):
AGAAAAAAAAAAAG
Found at i:201720 original size:16 final size:16
Alignment explanation
Indices: 201699--201755 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
201689 TGCAATGAAG
* *
201699 AAAAAAATAAAAGAGA
1 AAAAAAAGAAAAAAGA
201715 AAAAAAAGAAAAAAGAA
1 AAAAAAAGAAAAAAG-A
201732 ATAGAAAAAGCAGAAAAAGA
1 A-A-AAAAAG-A-AAAAAGA
201752 AAAA
1 AAAA
201756 GAGAGGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 13 0.38
17 2 0.06
18 3 0.09
19 7 0.21
20 3 0.09
21 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Found at i:201737 original size:22 final size:21
Alignment explanation
Indices: 201712--201753 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
201702 AAAATAAAAG
201712 AGAAAAAAAAGAAAAAAGAAAT
1 AGAAAAAAAAG-AAAAAGAAAT
**
201734 AGAAAAAGCAGAAAAAGAAA
1 AGAAAAAAAAGAAAAAGAAA
201754 AAGAGAGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (21 bp):
AGAAAAAAAAGAAAAAGAAAT
Found at i:204201 original size:250 final size:249
Alignment explanation
Indices: 203761--204219 Score: 670
Period size: 250 Copynumber: 1.8 Consensus size: 249
203751 ATGCGATCAT
* * * *
203761 CTTCCTGATTAGATACTAAGAAGAAGACCAAATCAAACCATGCTCGATATGAGCAAATCTTCGAA
1 CTTCCTGATAAGATACTAAGAAGAAGACCAAATCAAACCACGCTCAATACGAGCAAATCTTCGAA
* * * *
203826 CCCCAGCTTCCTGATGAGATATTGAGAAGTAGGTCGAAACAATAAAATGGTTAGCTTCCTGATGA
66 CCCCACCTTCCTGATGAGATATTGAGAAGCAGGGCGAAACAATAAAAAGGTTAGCTTCCTGATGA
* * *
203891 GATACTGACAAGTGAATCAAATTCGTCTTCCTGATGAGATATAGAGAAGCAGATTGAAACAGGCG
131 GATACTGACAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCG
*
203956 ATGCGGTCACCTTCTCAAACCCACGCTCAATGCGAGCAAATCTTCGAACCCCAC
196 AGGCGGTCACCTTCTCAAACCCACGCTCAATGCGAGCAAATCTTCGAACCCCAC
* * *
204010 CTTCCTGATAAGATGCTAAGATGAAGACCAAATCAAACCCACGCTCAATGCGAGCAAATCTTCGA
1 CTTCCTGATAAGATACTAAGAAGAAGACCAAATCAAA-CCACGCTCAATACGAGCAAATCTTCGA
*
204075 ACCCCACCTTCCTGATGAGATCTTGAGAAGCAGGGC-AAAGCAATAAAAAGGTTAGCTTCCTGAT
65 ACCCCACCTTCCTGATGAGATATTGAGAAGCAGGGCGAAA-CAATAAAAAGGTTAGCTTCCTGAT
* * * * *
204139 GAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGGT-AGGATACAGAGAAGCGGATTGAAACAA
129 GAGATACTGACAAGTGAACCAAATTCGTCTTCCTGATGA-GATACAGAGAAGCAGATTGAAACAA
* *
204203 GTGAGGCGGTCATCTTC
193 GCGAGGCGGTCACCTTC
204220 CTAATGAGAT
Statistics
Matches: 184, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
249 38 0.21
250 146 0.79
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (249 bp):
CTTCCTGATAAGATACTAAGAAGAAGACCAAATCAAACCACGCTCAATACGAGCAAATCTTCGAA
CCCCACCTTCCTGATGAGATATTGAGAAGCAGGGCGAAACAATAAAAAGGTTAGCTTCCTGATGA
GATACTGACAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCG
AGGCGGTCACCTTCTCAAACCCACGCTCAATGCGAGCAAATCTTCGAACCCCAC
Found at i:204382 original size:194 final size:194
Alignment explanation
Indices: 204053--204432 Score: 548
Period size: 194 Copynumber: 2.0 Consensus size: 194
204043 CAAACCCACG
* *
204053 CTCAATGCGAGCAAATCTTCGAACCCCACCTTCCTGATGAGATCTTGAGAAGCAGGGCAAAGCAA
1 CTCAATGCGAACAAATCTTCGAACCCCACCTTCCTGATGAGATATTGAGAAGCAGGGCAAAGCAA
* * * * * *
204118 TAAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGGTAGGATAC
66 TAAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATAGAACAC
** *
204183 AGAGAAGCGGATTGAAACAAGTGAGGCGGTCATCTTCCTAATGAGATACA-GAGAAGTATATCAA
131 AGAGAAGCGGATCAAAACAAGTGAGACGGTCATCTTCCTAATGAGATA-ATGAGAAGTATATCAA
* * * *
204247 CTCAATGCGAACAAATCTTCGACCCCCAGCTTCCTGATGAGATATTGAGAAGCAGGGCGATGCAA
1 CTCAATGCGAACAAATCTTCGAACCCCACCTTCCTGATGAGATATTGAGAAGCAGGGCAAAGCAA
*
204312 TAAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCTTGAT-GAAACA
66 TAAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATAG-AACA
* * * *
204376 CAGAGAAGTGGATCAAAACAAGTGATACGGTCGTCTTCCTGATGAGATAATGAGAAG
130 CAGAGAAGCGGATCAAAACAAGTGAGACGGTCATCTTCCTAATGAGATAATGAGAAG
204433 AAAGCCAAGT
Statistics
Matches: 164, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
193 2 0.01
194 162 0.99
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (194 bp):
CTCAATGCGAACAAATCTTCGAACCCCACCTTCCTGATGAGATATTGAGAAGCAGGGCAAAGCAA
TAAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATAGAACAC
AGAGAAGCGGATCAAAACAAGTGAGACGGTCATCTTCCTAATGAGATAATGAGAAGTATATCAA
Found at i:204839 original size:6 final size:6
Alignment explanation
Indices: 204830--204922 Score: 86
Period size: 6 Copynumber: 16.0 Consensus size: 6
204820 TTAAAATTAC
* ** *
204830 TTTAAA TTTAAA TTTAAA TTCATT TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
204877 TTTAAA TTT-AG TTTAAA TTTGAAA --TAAT TTTAAA CTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
204923 ATCAATTACA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 54 0.79
7 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:204859 original size:18 final size:17
Alignment explanation
Indices: 204836--204920 Score: 109
Period size: 17 Copynumber: 4.9 Consensus size: 17
204826 TTACTTTAAA
*
204836 TTTAAATTTAAATTCATT
1 TTTAAATTTAAATTTA-T
204854 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
204871 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
204888 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
204905 TTTAAACTTAAATTTA
1 TTTAAATTTAAATTTA
204921 AAATCAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 3 0.05
17 38 0.64
18 18 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:205604 original size:21 final size:20
Alignment explanation
Indices: 205570--205614 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
205560 GCATTAATAG
*
205570 TAAT-TAATAATATTATTTA
1 TAATATAATAATATTATTAA
205589 TAATATAATAAATATTATTAA
1 TAATATAAT-AATATTATTAA
205610 TAATA
1 TAATA
205615 ATATTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATAATAATATTATTAA
Found at i:205627 original size:12 final size:12
Alignment explanation
Indices: 205564--205635 Score: 74
Period size: 12 Copynumber: 5.9 Consensus size: 12
205554 ATAAAGGCAT
*
205564 TAATAGTAATTAA
1 TAATATTAA-TAA
* *
205577 TAATATTATTTA
1 TAATATTAATAA
205589 TAATA-TAATAAA
1 TAATATTAAT-AA
*
205601 TATTATTAATAA
1 TAATATTAATAA
205613 TAATATTAATAA
1 TAATATTAATAA
*
205625 TAATGTTAATA
1 TAATATTAATA
205636 GTAAATAGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
11 3 0.06
12 35 0.71
13 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:206806 original size:29 final size:29
Alignment explanation
Indices: 206742--206954 Score: 155
Period size: 29 Copynumber: 7.3 Consensus size: 29
206732 AAAGGTACCG
* * *
206742 AAACTTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTT-TAAAAATTCCATTTTT-ACCCCT
* *
206773 AAACTTTTGAAAATTACATTTTTACCCCT
1 AAACTTTTAAAAATTCCATTTTTACCCCT
** * * *
206802 AAACTTCAAAAAATTCCACTTTTAACCTT
1 AAACTTTTAAAAATTCCATTTTTACCCCT
*
206831 AAAACTTTTAAAAATTACATTTTTA-CCCT
1 -AAACTTTTAAAAATTCCATTTTTACCCCT
* * *
206860 CGAACTTAT-AAAATTCCATTCTTGA-CCCT
1 -AAACTTTTAAAAATTCCATT-TTTACCCCT
* * * *
206889 AAAATTTCTAAGAATTACATTTTTACCCAT
1 AAACTTT-TAAAAATTCCATTTTTACCCCT
** *
206919 AAACTTCCAAAAATTCCATTTTTAACCCT
1 AAACTTTTAAAAATTCCATTTTTACCCCT
206948 AAA-TTTT
1 AAACTTTT
206955 CCCAAAATTA
Statistics
Matches: 139, Mismatches: 38, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
28 16 0.12
29 66 0.47
30 50 0.36
31 7 0.05
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
AAACTTTTAAAAATTCCATTTTTACCCCT
Found at i:206965 original size:59 final size:57
Alignment explanation
Indices: 206742--206954 Score: 234
Period size: 59 Copynumber: 3.6 Consensus size: 57
206732 AAAGGTACCG
* * *
206742 AAACTTTCCAAAAATTCCATTTTTGACCTCGAAACTTTTGAAAATTACATTTTTACCCCT
1 AAAC-TTCCAAAAATTCCATTTTTAACC-CTAAACTTTTAAAAATTACATTTTTA-CCCT
* * *
206802 AAACTTCAAAAAATTCCACTTTTAACCTTAAAACTTTTAAAAATTACATTTTTACCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCT-AAACTTTTAAAAATTACATTTTTACCCT
* * * * *
206860 CGAACTT--ATAAAATTCCATTCTTGACCCTAAAATTTCTAAGAATTACATTTTTACCCAT
1 -AAACTTCCA-AAAATTCCATTTTTAACCCTAAACTTT-TAAAAATTACATTTTTACCC-T
206919 AAACTTCCAAAAATTCCATTTTTAACCCTAAA-TTTT
1 AAACTTCCAAAAATTCCATTTTTAACCCTAAACTTTT
206955 CCCAAAATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
57 8 0.06
58 47 0.36
59 70 0.54
60 5 0.04
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTAACCCTAAACTTTTAAAAATTACATTTTTACCCT
Found at i:210631 original size:12 final size:12
Alignment explanation
Indices: 210614--210646 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
210604 AAAACTCTTC
210614 TAAAAGAAAACT
1 TAAAAGAAAACT
210626 TAAAAGAAAACT
1 TAAAAGAAAACT
*
210638 CAAAAGAAA
1 TAAAAGAAA
210647 TTCTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (12 bp):
TAAAAGAAAACT
Found at i:210738 original size:44 final size:44
Alignment explanation
Indices: 210675--210764 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
210665 CAAAGAGAGA
*
210675 AGTTGCTGAATGAATTATGAATTTTGTAGAACGAAAAGGCATTT
1 AGTTGCTGAATGAATTATGAATTTTGTACAACGAAAAGGCATTT
*
210719 AGTTGCTGAATGAATTATGAATTTTGTACAACGAAGAGGCATTT
1 AGTTGCTGAATGAATTATGAATTTTGTACAACGAAAAGGCATTT
210763 AG
1 AG
210765 ATAGGTTAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (44 bp):
AGTTGCTGAATGAATTATGAATTTTGTACAACGAAAAGGCATTT
Found at i:213568 original size:3 final size:3
Alignment explanation
Indices: 213560--213596 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
213550 TTATATGCAA
213560 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
213597 ACAATACTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:215878 original size:30 final size:29
Alignment explanation
Indices: 215813--215870 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
215803 GTTTAATATA
* * *
215813 TAATGTTATATATAAATTTTAATTTTATG
1 TAATTTTATAAATAAATTTTAATTTGATG
215842 TAATTTTATAAATAAAATTTTAATTTGAT
1 TAATTTTATAAAT-AAATTTTAATTTGAT
215871 TCGATTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TAATTTTATAAATAAATTTTAATTTGATG
Found at i:218690 original size:15 final size:15
Alignment explanation
Indices: 218647--218690 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
218637 TGATAAACCG
*
218647 AAAAA-TTAAGTGTT
1 AAAAATTTAAGTATT
218661 AAAAATTTGAA-TATT
1 AAAAATTT-AAGTATT
218676 AAAAATTTAAGTATT
1 AAAAATTTAAGTATT
218691 GAATTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.27
15 17 0.65
16 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (15 bp):
AAAAATTTAAGTATT
Found at i:219922 original size:10 final size:10
Alignment explanation
Indices: 219907--219945 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
219897 AAAATATTAA
219907 ATAATTTTTT
1 ATAATTTTTT
219917 ATAA-TTTTT
1 ATAATTTTTT
*
219926 ATACTTTTTT
1 ATAATTTTTT
219936 -TAATTTTTT
1 ATAATTTTTT
219945 A
1 A
219946 AAATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:219961 original size:28 final size:26
Alignment explanation
Indices: 219880--219980 Score: 71
Period size: 26 Copynumber: 3.8 Consensus size: 26
219870 TAGCAGTTAA
* *
219880 TTAATTTTTTATAATTTAAAATA-TTAA
1 TTAATTTTTTAAAATTT-AAATACTT-T
* * **
219907 ATAATTTTTTATAATTTTTATACTTTTT
1 TTAATTTTTTAAAATTTAAATAC--TTT
219935 TTAATTTTTTAAAATATTAAATA-TTT
1 TTAATTTTTTAAAAT-TTAAATACTTT
* *
219961 TGAATTTTTTAAATTTTAAA
1 TTAATTTTTTAAAATTTAAA
219981 AATAATTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
25 5 0.08
26 19 0.32
27 16 0.27
28 13 0.22
29 7 0.12
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
TTAATTTTTTAAAATTTAAATACTTT
Found at i:219975 original size:9 final size:9
Alignment explanation
Indices: 219909--219977 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
219899 AATATTAAAT
219909 AATTTTTTA
1 AATTTTTTA
219918 TAA-TTTTTA
1 -AATTTTTTA
* *
219927 TACTTTTTTT
1 -AATTTTTTA
219937 AATTTTTTA
1 AATTTTTTA
* *
219946 AA-ATATTA
1 AATTTTTTA
* *
219954 AATATTTTG
1 AATTTTTTA
219963 AATTTTTTA
1 AATTTTTTA
219972 AATTTT
1 AATTTT
219978 AAAAATAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
8 6 0.13
9 34 0.72
10 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
AATTTTTTA
Found at i:225689 original size:28 final size:27
Alignment explanation
Indices: 225635--225698 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
225625 GGGGTCACCC
* *
225635 CTTTTTGAATTAATTTTTTAATTTATTA
1 CTTTTT-ATTTAATTTTTTAATATATTA
*
225663 TTATTTTATTTAATTTTATTAA-ATATTA
1 CT-TTTTATTTAATTTT-TTAATATATTA
225691 CTTTTTAT
1 CTTTTTAT
225699 AAGTGATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 6 0.20
28 16 0.53
29 8 0.27
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
CTTTTTATTTAATTTTTTAATATATTA
Found at i:227798 original size:29 final size:27
Alignment explanation
Indices: 227765--227840 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 27
227755 ACTAATGGAT
227765 GTATCAATTTGAAAAAAAAAATAGTTTAA
1 GTATCAATTTGAAAAAAAAAATA--TTAA
* *
227794 GTATCACTTATGATAAAAAAAAATATTAG
1 GTATCAATT-TGA-AAAAAAAAATATTAA
* *
227823 GTATCAATATGAGAAAAA
1 GTATCAATTTGAAAAAAA
227841 CGACATAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.12
28 3 0.08
29 18 0.45
30 3 0.08
31 11 0.28
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.29
Consensus pattern (27 bp):
GTATCAATTTGAAAAAAAAAATATTAA
Found at i:233049 original size:33 final size:35
Alignment explanation
Indices: 233012--233083 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 35
233002 CAATATAAAT
* * *
233012 ATAAGTAGTCCTTTAAC-AAACTTTCAAGCA-AAC
1 ATAAGTAATCCCTTAACAAAACTTGCAAGCATAAC
233045 ATAAGTAATCCCTTAACAAAACTTGCAAGCATAAC
1 ATAAGTAATCCCTTAACAAAACTTGCAAGCATAAC
233080 ATAA
1 ATAA
233084 TAGAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 15 0.44
34 12 0.35
35 7 0.21
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (35 bp):
ATAAGTAATCCCTTAACAAAACTTGCAAGCATAAC
Found at i:240124 original size:30 final size:31
Alignment explanation
Indices: 240090--240147 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
240080 ATTTGAATTG
240090 TTTAA-TTTATATTCGAGTTAAATCGAAAAA
1 TTTAATTTTATATTCGAGTTAAATCGAAAAA
* *
240120 TTTAATTTTTTATTCGAGTTAATTCGAA
1 TTTAATTTTATATTCGAGTTAAATCGAA
240148 TAACTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTAATTTTATATTCGAGTTAAATCGAAAAA
Found at i:248610 original size:142 final size:139
Alignment explanation
Indices: 248320--248630 Score: 324
Period size: 142 Copynumber: 2.2 Consensus size: 139
248310 AGTAAAATCG
* * * * * * *
248320 AAGAGTTTGGATAACATAG-GTATTTTTACTATTTAGTTTTAAATCTGAAAGCTTAAAGTGAAAA
1 AAGAGATTGGATAATATAGATTATTTTTACTACTTAGTTTTAAATATGAAAGCATAAAGTAAAAA
* * * * *
248384 TTGCTTTGAGATGAATAAAATATCTGAATTATGTCGAACACAGGTCTCAGACACATAGGTTATAG
66 CTGCTTTGAGATAAATAAAATATATAAATTATGTCAAACACAGGTCTCAGACACATAGGTTATAG
* ***
248449 GAGAAAGTG
131 GAAAAAACA
* *
248458 AAGAGATTGGATAATATAGATTAATTTTACTACTTAGTTTTAAATATGGAAGCATAAAGTAAAAA
1 AAGAGATTGGATAATATAGATTATTTTTACTACTTAGTTTTAAATATGAAAGCATAAAGTAAAAA
* * * * *
248523 CTGCATTTGAGATCAAATCAAATGTATAAATCTATGTCAAACATAGGTCTCA-AGCGCATATGTC
66 CTGC-TTTGAGAT-AAATAAAATATATAAAT-TATGTCAAACACAGGTCTCAGA-CACATAGGT-
248587 T-TAGGAAAAAACA
126 TATAGGAAAAAACA
*
248600 AAGAGGTTGGATAATATA-AGTTATTTTTACT
1 AAGAGATTGGATAATATAGA-TTATTTTTACT
248631 TTGCTTAAAC
Statistics
Matches: 141, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
138 17 0.12
139 41 0.29
140 8 0.06
141 14 0.10
142 60 0.43
143 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (139 bp):
AAGAGATTGGATAATATAGATTATTTTTACTACTTAGTTTTAAATATGAAAGCATAAAGTAAAAA
CTGCTTTGAGATAAATAAAATATATAAATTATGTCAAACACAGGTCTCAGACACATAGGTTATAG
GAAAAAACA
Found at i:249876 original size:176 final size:176
Alignment explanation
Indices: 249666--250005 Score: 644
Period size: 176 Copynumber: 1.9 Consensus size: 176
249656 AGGCAAGAAA
* *
249666 TTGTTGAGCAGACGTATGATCTGCTTCTTCAATTTTCTTTTTTTATGTACATAAATGCTTTTCAA
1 TTGTTGAGCAGACATATGATCTGCTTCTTCAATTTTCTTTTTTCATGTACATAAATGCTTTTCAA
* *
249731 AGCTCTTTCTAGAATTTAGTTCAGTTGATTTTTGCAATCTCTCTTAAGTGGTGATATTTGGTAGG
66 AGCTCTTTCTAGAATTTAGTTAAGTTGATTTATGCAATCTCTCTTAAGTGGTGATATTTGGTAGG
249796 TTTGAGATTTGAATCCTAGCTAAATTTCTAGATTAATAGAGGCTGT
131 TTTGAGATTTGAATCCTAGCTAAATTTCTAGATTAATAGAGGCTGT
249842 TTGTTGAGCAGACATATGATCTGCTTCTTCAATTTTCTTTTTTCATGTACATAAATGCTTTTCAA
1 TTGTTGAGCAGACATATGATCTGCTTCTTCAATTTTCTTTTTTCATGTACATAAATGCTTTTCAA
249907 AGCTCTTTCTAGAATTTAGTTAAGTTGATTTATGCAATCTCTCTTAAGTGGTGATATTTGGTAGG
66 AGCTCTTTCTAGAATTTAGTTAAGTTGATTTATGCAATCTCTCTTAAGTGGTGATATTTGGTAGG
249972 TTTGAGATTTGAATCCTAGCTAAATTTCTAGATT
131 TTTGAGATTTGAATCCTAGCTAAATTTCTAGATT
250006 CTGGAAGAAT
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 160 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (176 bp):
TTGTTGAGCAGACATATGATCTGCTTCTTCAATTTTCTTTTTTCATGTACATAAATGCTTTTCAA
AGCTCTTTCTAGAATTTAGTTAAGTTGATTTATGCAATCTCTCTTAAGTGGTGATATTTGGTAGG
TTTGAGATTTGAATCCTAGCTAAATTTCTAGATTAATAGAGGCTGT
Found at i:252743 original size:6 final size:7
Alignment explanation
Indices: 252726--252751 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
252716 AATACAACTT
252726 AAAAAGG
1 AAAAAGG
252733 AAAAAGG
1 AAAAAGG
252740 AAAAAGG
1 AAAAAGG
252747 AAAAA
1 AAAAA
252752 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:261415 original size:6 final size:7
Alignment explanation
Indices: 261393--261417 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
261383 AATAAAAAAG
261393 AAATGAA
1 AAATGAA
261400 AAATGAA
1 AAATGAA
261407 AAATGAA
1 AAATGAA
261414 AAAT
1 AAAT
261418 AAATGACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (7 bp):
AAATGAA
Found at i:263061 original size:31 final size:30
Alignment explanation
Indices: 262993--263080 Score: 142
Period size: 29 Copynumber: 2.9 Consensus size: 30
262983 GTTATTGAAC
262993 TATTTGAAAGTTTTTATTTAAGTCACTATA
1 TATTTGAAAGTTTTTATTTAAGTCACTATA
*
263023 -ATTTGAAAGTTTCTATTTAAGTCACTATA
1 TATTTGAAAGTTTTTATTTAAGTCACTATA
*
263052 TTATTTGAAAGTTTTTATTTAAGTTACTA
1 -TATTTGAAAGTTTTTATTTAAGTCACTA
263081 GTTGTTAAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
29 28 0.53
31 25 0.47
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (30 bp):
TATTTGAAAGTTTTTATTTAAGTCACTATA
Found at i:263564 original size:112 final size:112
Alignment explanation
Indices: 263364--263574 Score: 260
Period size: 112 Copynumber: 1.9 Consensus size: 112
263354 CATATAGTAG
* * * * *
263364 CGATGAATTAAATTTTGTTCAAGACCGACAAAATTGTGTCTTACAAATTGAAAATGATCTTGTTT
1 CGATGAATTAAATTTCGTTCAAGACCAACAAAATTGTGTCTTACAAATTGAAAAAGACCATGTTT
* *
263429 AACAACAATACGAGCAAATTTCTCAATACTAATAAAACATAAATAAA
66 AACAACAACACGAGCAAACTTCTCAATACTAATAAAACATAAATAAA
* * ** * *
263476 CGATGGATTTAATTTCGTTCAAGATTAACAACATTGTGTCTTACAAATTGAAAAAGCCCATGTTT
1 CGATGAATTAAATTTCGTTCAAGACCAACAAAATTGTGTCTTACAAATTGAAAAAGACCATGTTT
** * * *
263541 AACGGCAACATGAGCAAGCTTCTCAGTACTAATA
66 AACAACAACACGAGCAAACTTCTCAATACTAATA
263575 TTTGCAGCTC
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
112 81 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (112 bp):
CGATGAATTAAATTTCGTTCAAGACCAACAAAATTGTGTCTTACAAATTGAAAAAGACCATGTTT
AACAACAACACGAGCAAACTTCTCAATACTAATAAAACATAAATAAA
Found at i:272458 original size:23 final size:23
Alignment explanation
Indices: 272432--272533 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
272422 AGTGCTGGGC
272432 AACAGAGAGCACACACAA-TGCTA
1 AACAGAGAGCACACA-AAGTGCTA
*
272455 AACAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
272478 ATCAGAAAGCACACAAAGTGTTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
272501 ATCAGAGAGCACGA-GACGTGCTA
1 AACAGAGAGCAC-ACAAAGTGCTA
272524 AACAGAGAGC
1 AACAGAGAGC
272534 GCGCTAGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 2 0.03
23 64 0.96
24 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:280514 original size:30 final size:31
Alignment explanation
Indices: 280464--280523 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
280454 ATTTTTTATT
*
280464 ATAAATTTTCTTATTATTTT-ATTATTTAAA
1 ATAAATTTTCTTATTATTTTAATAATTTAAA
280494 ATAAATTTT-TT-TCTATTTTTAATAATTTAA
1 ATAAATTTTCTTAT-TA-TTTTAATAATTTAA
280524 TCACACATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 1 0.04
29 4 0.15
30 13 0.50
31 8 0.31
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (31 bp):
ATAAATTTTCTTATTATTTTAATAATTTAAA
Found at i:282668 original size:5 final size:5
Alignment explanation
Indices: 282658--282685 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
282648 GACTTATTGC
282658 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
282686 GGAGTCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:282860 original size:19 final size:21
Alignment explanation
Indices: 282827--282876 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
282817 AAATTATAAA
*
282827 ATAATATAATATT-AA-AATT
1 ATAATTTAATATTAAATAATT
* *
282846 ATATTTTAATCTTAAATAATT
1 ATAATTTAATATTAAATAATT
282867 ATAATTTAAT
1 ATAATTTAAT
282877 TTTGACACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTTAATATTAAATAATT
Found at i:284768 original size:16 final size:18
Alignment explanation
Indices: 284729--284762 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
284719 TAAGTTTATA
284729 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
284746 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
284763 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:288652 original size:30 final size:30
Alignment explanation
Indices: 288577--288656 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
288567 AATAATAATT
* * *
288577 TATATTTTTATAATTTTT-AAAAATTGAAG
1 TATAATTTTATAATTTTTAAAAAATTAAAA
* *
288606 T-TAAATTTTTTTATTTTTAAAAAATTAAAA
1 TAT-AATTTTATAATTTTTAAAAAATTAAAA
*
288636 TATAATTTTATCA-TTTTAAAA
1 TATAATTTTATAATTTTTAAAA
288657 TTTAAGGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 1 0.02
29 21 0.51
30 18 0.44
31 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TATAATTTTATAATTTTTAAAAAATTAAAA
Found at i:288787 original size:3 final size:3
Alignment explanation
Indices: 288781--288805 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
288771 AAAGAAGACA
288781 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
288806 TTTACATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:289632 original size:40 final size:40
Alignment explanation
Indices: 289588--289667 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
289578 ATACTTTTAT
* * *
289588 TATTCCTTTTTAAACTAAACGGTCTATTTAATTTAGGAAA
1 TATTCCTTCTTAAACTAAACCGTCCATTTAATTTAGGAAA
* **
289628 TATTCCTTCTTAAATTAAACCGTCCATTTGTTTTAGGAAA
1 TATTCCTTCTTAAACTAAACCGTCCATTTAATTTAGGAAA
289668 ATGTTGATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (40 bp):
TATTCCTTCTTAAACTAAACCGTCCATTTAATTTAGGAAA
Found at i:289742 original size:6 final size:6
Alignment explanation
Indices: 289731--289757 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
289721 TATGGTATGT
289731 TCAAAA TCAAAA TCAAAA TCAAAA TCA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCA
289758 GTATCTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (6 bp):
TCAAAA
Found at i:293201 original size:3 final size:3
Alignment explanation
Indices: 293195--293220 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
293185 GGGGGGGGGT
293195 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
293221 CCCTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:293984 original size:17 final size:19
Alignment explanation
Indices: 293952--293986 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
293942 TTTTACTATT
293952 TTCTTTCTTAATGAATAAC
1 TTCTTTCTTAATGAATAAC
293971 TTCTTT-TT-ATGAATAA
1 TTCTTTCTTAATGAATAA
293987 TAGATACTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (19 bp):
TTCTTTCTTAATGAATAAC
Found at i:310081 original size:30 final size:30
Alignment explanation
Indices: 310039--310109 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
310029 AATAATCTAT
*
310039 ATTTTATAATTTTTAAAAGATT-AAAT-CAA
1 ATTTTATTATTTTTAAAAGATTAAAATAC-A
* *
310068 ATTTTTATTATTTTTAAGAGGTTAAAATACA
1 A-TTTTATTATTTTTAAAAGATTAAAATACA
310099 ATTTTATTATT
1 ATTTTATTATT
310110 ACTAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.78
31 6 0.17
32 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (30 bp):
ATTTTATTATTTTTAAAAGATTAAAATACA
Found at i:311578 original size:14 final size:14
Alignment explanation
Indices: 311559--311613 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
311549 TAGTTACAGA
311559 TTTATTTAAAAATT
1 TTTATTTAAAAATT
*
311573 TTTATTTAAATCATT
1 TTTATTTAAA-AATT
* *
311588 AAATTATTTGAAAATT
1 --TTTATTTAAAAATT
311604 TTTATTTAAA
1 TTTATTTAAA
311614 TCATTGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 18 0.56
15 3 0.09
16 3 0.09
17 8 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTATTTAAAAATT
Found at i:311602 original size:31 final size:31
Alignment explanation
Indices: 311560--311623 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
311550 AGTTACAGAT
311560 TTATTTAAAAATTTTTATTTAAATCATTAAA
1 TTATTTAAAAATTTTTATTTAAATCATTAAA
* *
311591 TTATTTGAAAATTTTTATTTAAATCATTGAA
1 TTATTTAAAAATTTTTATTTAAATCATTAAA
311622 TT
1 TT
311624 GTTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TTATTTAAAAATTTTTATTTAAATCATTAAA
Found at i:315660 original size:3 final size:3
Alignment explanation
Indices: 315652--315685 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
315642 GATTGAGGTT
315652 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
315686 AGACATCCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:317737 original size:65 final size:65
Alignment explanation
Indices: 317659--317789 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
317649 TTAATATTTA
317659 CTGAATATGAAATCGTTGAAATGCACCTCATTATAGTGTCCACCCATTCCTTATCAAAACCCATT
1 CTGAATATGAAATCGTTGAAATGCACCTCATTATAGTGTCCACCCATTCCTTATCAAAACCCATT
317724 CTGAATATGAAATCGTTGAAATGCACCTCATTATAGTGTCCACCCATTCCTTATCAAAACCCATT
1 CTGAATATGAAATCGTTGAAATGCACCTCATTATAGTGTCCACCCATTCCTTATCAAAACCCATT
317789 C
1 C
317790 GTTCCATTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.31
Consensus pattern (65 bp):
CTGAATATGAAATCGTTGAAATGCACCTCATTATAGTGTCCACCCATTCCTTATCAAAACCCATT
Found at i:322334 original size:11 final size:11
Alignment explanation
Indices: 322312--322368 Score: 78
Period size: 11 Copynumber: 5.2 Consensus size: 11
322302 GAGATAAGTT
*
322312 AGAAAAGAGAA
1 AGAAATGAGAA
*
322323 AGAAATGGGAA
1 AGAAATGAGAA
*
322334 ATAAATGAGAA
1 AGAAATGAGAA
*
322345 AGAAATGGGAA
1 AGAAATGAGAA
322356 AGAAATGAGAA
1 AGAAATGAGAA
322367 AG
1 AG
322369 GCTTTCGGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (11 bp):
AGAAATGAGAA
Found at i:322346 original size:22 final size:22
Alignment explanation
Indices: 322312--322368 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
322302 GAGATAAGTT
*
322312 AGAAAAGAGAAAGAAATGGGAA
1 AGAAATGAGAAAGAAATGGGAA
*
322334 ATAAATGAGAAAGAAATGGGAA
1 AGAAATGAGAAAGAAATGGGAA
322356 AGAAATGAGAAAG
1 AGAAATGAGAAAG
322369 GCTTTCGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (22 bp):
AGAAATGAGAAAGAAATGGGAA
Found at i:326424 original size:31 final size:32
Alignment explanation
Indices: 326348--326426 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 32
326338 CTTGGAATTA
** * *
326348 AAATTTTAAATGATTTTTAATAATTGTATTTG
1 AAATTTTAAAAAAATTTTAATAATTGTATTTC
** * *
326380 AAATTTTTTAAAAATTTTAATTA-TGTTTTTC
1 AAATTTTAAAAAAATTTTAATAATTGTATTTC
326411 AAATTTTAAAAAAATT
1 AAATTTTAAAAAAATT
326427 AAGTCCGAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 20 0.54
32 17 0.46
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (32 bp):
AAATTTTAAAAAAATTTTAATAATTGTATTTC
Found at i:326881 original size:22 final size:22
Alignment explanation
Indices: 326856--326900 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
326846 ATGCGGTTTT
*
326856 TAAATTTATTAAAAAAAATATA
1 TAAATATATTAAAAAAAATATA
* * *
326878 TAAATATCTTGAAAATAATATA
1 TAAATATATTAAAAAAAATATA
326900 T
1 T
326901 TATTTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATATATTAAAAAAAATATA
Found at i:336787 original size:11 final size:11
Alignment explanation
Indices: 336767--336800 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
336757 TTACATGAGG
336767 TACC-TCTTGC
1 TACCATCTTGC
336777 TACCATCTTGC
1 TACCATCTTGC
*
336788 TATCATCTTGC
1 TACCATCTTGC
336799 TA
1 TA
336801 TCAATAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (11 bp):
TACCATCTTGC
Found at i:336801 original size:11 final size:11
Alignment explanation
Indices: 336771--336803 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
336761 ATGAGGTACC
*
336771 TCTTGCTACCA
1 TCTTGCTATCA
336782 TCTTGCTATCA
1 TCTTGCTATCA
336793 TCTTGCTATCA
1 TCTTGCTATCA
336804 ATAACTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (11 bp):
TCTTGCTATCA
Found at i:339358 original size:33 final size:36
Alignment explanation
Indices: 339299--339368 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 36
339289 AACAGGCATT
*
339299 ACCTTCAGGTCAATATGGAGAAAAATGAGCAACATG
1 ACCTTCAGGTCAATATGGAGAAAAATGAACAACATG
*
339335 ACCTTC-GGTTAATAT-G-GAAAAATGAACAACATG
1 ACCTTCAGGTCAATATGGAGAAAAATGAACAACATG
339368 A
1 A
339369 TCTATGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 17 0.53
34 1 0.03
35 8 0.25
36 6 0.19
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (36 bp):
ACCTTCAGGTCAATATGGAGAAAAATGAACAACATG
Done.