Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012722.1 Kokia drynarioides strain JFW-HI SEQ_127733, 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: 95894
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1317 original size:32 final size:34
Alignment explanation
Indices: 1268--1330 Score: 112
Period size: 32 Copynumber: 1.9 Consensus size: 34
1258 CAAACGAAAA
1268 TTTGTGGAAAAAGGACACATAATAAAATATAATT
1 TTTGTGGAAAAAGGACACATAATAAAATATAATT
1302 TTTGTGG-AAAA-GACACATAATAAAATATA
1 TTTGTGGAAAAAGGACACATAATAAAATATA
1331 GTTTATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 18 0.62
33 4 0.14
34 7 0.24
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (34 bp):
TTTGTGGAAAAAGGACACATAATAAAATATAATT
Found at i:3907 original size:17 final size:17
Alignment explanation
Indices: 3887--3960 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
3877 TTAAAATCTT
* *
3887 AATTCATTTTAATTTTA
1 AATTTATTTTAAATTTA
*
3904 AATTTATTGTAAATTTA
1 AATTTATTTTAAATTTA
** ** *
3921 ACCTTATTTGGAGTTTA
1 AATTTATTTTAAATTTA
3938 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
3955 AATTTA
1 AATTTA
3961 AAAGTTTAAT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:4210 original size:17 final size:18
Alignment explanation
Indices: 4177--4212 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4167 ATGAAGATCT
4177 GCAAAAGATAAAACAGAG
1 GCAAAAGATAAAACAGAG
*
4195 GCAAAAGA-ACAACAGAG
1 GCAAAAGATAAAACAGAG
4212 G
1 G
4213 AGGAAAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.14, G:0.25, T:0.03
Consensus pattern (18 bp):
GCAAAAGATAAAACAGAG
Found at i:5393 original size:30 final size:28
Alignment explanation
Indices: 5317--5573 Score: 160
Period size: 30 Copynumber: 8.6 Consensus size: 28
5307 AAAAGGTCCT
* *
5317 TAAACTTTTTTAAAATTACATTTTAACCAC
1 TAAA-TTTTCTAAAATTATATTTTAACC-C
*
5347 -ATATTTTTCTAAAATTATATTTTAACCTC
1 TA-AATTTTCTAAAATTATATTTTAACC-C
*
5376 TAAATTTCTCAAAAATTATATTTTTAACCC
1 TAAATTT-TCTAAAATTATA-TTTTAACCC
* *
5406 TAAAACTTTTCCAAAATTATATTTTGACCC
1 T-AAA-TTTTCTAAAATTATATTTTAACCC
* * *
5436 TTAAAGTCTTCCAAAATTACATTTTAACCC
1 -TAAA-TTTTCTAAAATTATATTTTAACCC
* *
5466 TTGAACTTTTCTAAAATTATATTTTGACCCC
1 -T-AAATTTTCTAAAATTATATTTT-AACCC
* * *
5497 TAAATATTT-TCGAAATCACATTTTAACCC
1 TAAAT-TTTCT-AAAATTATATTTTAACCC
* * *
5526 TCAAACTTTTCTAAAATCATATCTTGACCC
1 T-AAA-TTTTCTAAAATTATATTTTAACCC
5556 TCAAACTTCTT-TAAAATT
1 T-AAA-TT-TTCTAAAATT
5574 TCATTTCCAT
Statistics
Matches: 185, Mismatches: 27, Indels: 30
0.76 0.11 0.12
Matches are distributed among these distances:
29 36 0.19
30 113 0.61
31 33 0.18
32 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAATTTTCTAAAATTATATTTTAACCC
Found at i:5532 original size:120 final size:120
Alignment explanation
Indices: 5328--5556 Score: 302
Period size: 120 Copynumber: 1.9 Consensus size: 120
5318 AAACTTTTTT
* * *
5328 AAAATTACATTTTAACCACATATTTTTCTAAAATTATATTTTAACCTCTAAATTTCTCAAAAATT
1 AAAATTACATTTTAACCACATACTTTTCTAAAATTATATTTTAACCCCTAAATTTCTCAAAAATC
* * *
5393 ATATTTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCTTAAAGTCTTCC
66 ACATTTTTAACCCTAAAACTTTTCCAAAATCATATCTTGACCCTTAAAGTCTTCC
* * * *
5448 AAAATTACATTTTAACC-CTTGAACTTTTCTAAAATTATATTTTGACCCCTAAATATTTTC-GAA
1 AAAATTACATTTTAACCACAT--ACTTTTCTAAAATTATATTTTAACCCCTAAAT-TTCTCAAAA
* *
5511 ATCACA-TTTTAACCCTCAAACTTTTCTAAAATCATATCTTGACCCT
63 ATCACATTTTTAACCCTAAAACTTTTCCAAAATCATATCTTGACCCT
5557 CAAACTTCTT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
119 2 0.02
120 53 0.56
121 35 0.37
122 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (120 bp):
AAAATTACATTTTAACCACATACTTTTCTAAAATTATATTTTAACCCCTAAATTTCTCAAAAATC
ACATTTTTAACCCTAAAACTTTTCCAAAATCATATCTTGACCCTTAAAGTCTTCC
Found at i:5579 original size:60 final size:60
Alignment explanation
Indices: 5325--5579 Score: 252
Period size: 60 Copynumber: 4.2 Consensus size: 60
5315 CTTAAACTTT
* * * *
5325 TTTAAAATTACATTTTAA-CCACATATTTTTCTAAAATTATATTTT-AACCTCTAAATTTC
1 TTTAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAA-TTC
** * * * *
5384 TCAAAAATTATATTTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCT-TAAAGTC
1 TTTAAAATTACA-TTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAATTC
* **
5444 TTCCAAAATTACATTTTAACCCTTGAACTTTTCTAAAATTATATTTTGACCC-CTAAATAT-
1 TT-TAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAAT-TC
* * * *
5504 TTTCGAAATCACATTTTAACCCTCAAACTTTTCTAAAATCATATCTTGACCCTC-AAACTTC
1 TTT-AAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAA-TTC
*
5565 TTTAAAATTTCATTT
1 TTTAAAATTACATTT
5580 CCATCCCAAG
Statistics
Matches: 159, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
59 9 0.06
60 106 0.67
61 40 0.25
62 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (60 bp):
TTTAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAATTC
Found at i:6505 original size:29 final size:29
Alignment explanation
Indices: 6473--6528 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
6463 TAAATTTATA
* *
6473 TATGATCCTTTGCATTTTTTATGAAATAT
1 TATGATCCTTTACATTTTGTATGAAATAT
6502 TATGATCCTTTACATTTTGTATGAAAT
1 TATGATCCTTTACATTTTGTATGAAAT
6529 GGCATGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (29 bp):
TATGATCCTTTACATTTTGTATGAAATAT
Found at i:6535 original size:29 final size:29
Alignment explanation
Indices: 6474--6535 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
6464 AAATTTATAT
* * **
6474 ATGATCCTTTGCATTTTTTATGAAATATT
1 ATGATCCTTTACATTTTGTATGAAATAGC
*
6503 ATGATCCTTTACATTTTGTATGAAATGGC
1 ATGATCCTTTACATTTTGTATGAAATAGC
6532 ATGA
1 ATGA
6536 CAATATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
ATGATCCTTTACATTTTGTATGAAATAGC
Found at i:10628 original size:11 final size:10
Alignment explanation
Indices: 10612--10636 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10602 GATCTTACCT
10612 AAAAAAAATG
1 AAAAAAAATG
10622 AAAAAAAATG
1 AAAAAAAATG
10632 AAAAA
1 AAAAA
10637 GAAAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:11907 original size:98 final size:98
Alignment explanation
Indices: 11728--12409 Score: 778
Period size: 98 Copynumber: 6.9 Consensus size: 98
11718 GAAGATATGG
*
11728 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGT-CCTCAGAAGCATGAAGGGAGAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * *
11792 TGCAATGGCGAATCTAGTACCACGAAAACACAA
66 CGCAACGGCGAATCCAGTACCACGAAGACACAA
* *
11825 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAG-AGACATGAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAG
* * * *
11889 CCGTAACGACGAATCTAGTACCATGAAGACACAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACACAA
* *
11923 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAG-AGACATGAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAG
*
11987 CTGCAACGGCGAATCCAGTACCACGAAGACACAAA
65 CCGCAACGGCGAATCCAGTACCACGAAGACAC-AA
* * * * * * *
12022 AGAGAAAGGTTTAAGTCGTAACGACAAACCTTTTACCTCTGAAGCATAAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * * *****
12087 CACAACAGTGAATCCAGTACGACGAAGATTTGG
66 CGCAACGGCGAATCCAGTACCACGAAGACACAA
* * *
12120 AGAGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAGCATGAAGGGAGAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
*** * ***
12185 CGCAACGAAAAATCCAGTACCAC-AAGGATATGG
66 CGCAACGGCGAATCCAGTACCACGAA-GACACAA
* * * * * *
12218 AGAGAAAAGTTTAAGTCGTAATGGCGAACCTTGTACCTCGGAAGCATGAAAGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * * *
12283 CGCAACGGTGAATCCAGTACTACGAGGATATAAA
66 CGCAACGGCGAATCCAGTACCACGAAGACA-CAA
* * * * * *
12317 AAGGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCGGAAGCATGAAGGAAAAAATTTAACC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
12382 CGCAACGGCGAATCCAGTACCACGAAGA
66 CGCAACGGCGAATCCAGTACCACGAAGA
12410 TATGGAGGGA
Statistics
Matches: 506, Mismatches: 72, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
97 36 0.07
98 306 0.60
99 162 0.32
100 2 0.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCACGAAGACACAA
Found at i:12084 original size:49 final size:50
Alignment explanation
Indices: 11728--12393 Score: 303
Period size: 49 Copynumber: 13.6 Consensus size: 50
11718 GAAGATATGG
* * *
11728 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGT-CCTCAGAAG-CATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
* * * * * *
11776 AGGGAGAGATTTAAG-CTGCAATGGCGAATC-TAGTACCAC-GAAAACACAA
1 AGGGAAAGATTTAAGTC-GCAACGGCGAACCTTA-TACCTCAGAAGACATAA
* * *
11825 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAG-AGACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
* * * * *
11874 AGGGAAAGATTTAAGCCGTAACGACGAATC-TAGTA-C-CATGAAGACACAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTA-TACCTCA-GAAGACATAA
* * *
11923 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAG-AGACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
* *
11972 AGGGAAAGATTTAAG-CTGCAACGGCGAATCC--AGTACCAC-GAAGACACAAA
1 AGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTTA-TACCTCAGAAGACA-TAA
* * * * * * *
12022 AGAGAAAGGTTTAAGTCGTAACGACAAACCTTTTACCTCTGAAG-CATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
* * * * ** ** **
12071 AGGGAAAGATTTAAGCCACAACAGTGAATCC--AGTACGAC-GAAGATTTGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTA-TACCTCAGAAGACATAA
* * * * *
12120 AGAGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAG-CATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
* * *** * * * **
12169 AGGGAGAGATTTAAGCCGCAACGAAAAATCC--AGTACCACA-AGGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTA-TACCTCAGAAGACATAA
* * * * *
12218 AGAGAAA-AGTTTAAGTCGTAATGGCGAACCTTGTACCTCGGAAG-CATGAA
1 AGGGAAAGA-TTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACAT-AA
* * * *
12268 A-GGAAAGATTTAAGCCGCAACGGTGAATCC--AGTA-CT-ACGAGGATATAAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTA-TACCTCA-GAAGACAT-AA
* * * * * *
12317 AAGGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCGGAAG-CATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
* * **
12366 AGGAAAAAATTTAACCCGCAACGGCGAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA
12394 TCCAGTACCA
Statistics
Matches: 444, Mismatches: 128, Indels: 91
0.67 0.19 0.14
Matches are distributed among these distances:
47 4 0.01
48 51 0.11
49 298 0.67
50 79 0.18
51 12 0.03
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (50 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGACATAA
Found at i:12451 original size:295 final size:294
Alignment explanation
Indices: 11730--12422 Score: 872
Period size: 295 Copynumber: 2.4 Consensus size: 294
11720 AGATATGGAG
* * *
11730 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGT-CCTCAGAAGCATGAAGGGAGAGATTTAAGCTG
1 GGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
* * * * *** * *
11794 CAATGGCGAATCTAGTACCACGAAAACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTAT
66 CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAAGGCGAACCTTGT
* ** * *
11859 ACCTCAGAGACATGAAGGGAAAGATTTAAGCCGTAACGACGAATCTAGTACCATGAAGACACAAA
131 ACCTCAGAGACATGAAGGGAAAGATTTAAGCCGCAACGAAAAATCCAGTACCATCAAGACACAAA
* * * *
11924 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAGGGAAAGATTTAAGCT
196 GAGAAAAGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAAGGAAAGATTTAAGCC
*
11989 GCAACGGCGAATCCAGTACCACGAAGACACAAAA
261 GCAACGGCGAATCCAGTACCACGAAGACAAAAAA
* * * * *
12023 GAGAAAGGTTTAAGTCGTAACGACAAACCTTTTACCTCTGAAGCATAAAGGGAAAGATTTAAGCC
1 G-GAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCC
* * * * * *
12088 ACAACAGTGAATCCAGTACGACGAAGATTTGGAGAGAAAGGTTTAAGTCGCAAAGGCGAACCTTG
65 GCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAAGGCGAACCTTG
* * *
12153 TACCTCAGA-AGCATGAAGGGAGAGATTTAAGCCGCAACGAAAAATCCAGTACCA-CAAGGATAT
130 TACCTCAGAGA-CATGAAGGGAAAGATTTAAGCCGCAACGAAAAATCCAGTACCATCAA-GACAC
** * * *
12216 GGAGAGAAAAGTTTAAGTCGTAATGGCGAACCTTGTACCTCGGA-AGCATGAAAGGAAAGATTTA
193 AAAGAGAAAAGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGA-CATGAAAGGAAAGATTTA
* * * *
12280 AGCCGCAACGGTGAATCCAGTACTACGAGGATATAAAAA
257 AGCCGCAACGGCGAATCCAGTACCACGAAGACA-AAAAA
* * * *
12319 GGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCGGAAGCATGAAGGAAAAAATTTAACCCG
1 GGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
12384 CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAG
66 CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAG
12423 ATTACAACCA
Statistics
Matches: 335, Mismatches: 59, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
293 1 0.00
294 31 0.09
295 298 0.89
296 5 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (294 bp):
GGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAAGGCGAACCTTGT
ACCTCAGAGACATGAAGGGAAAGATTTAAGCCGCAACGAAAAATCCAGTACCATCAAGACACAAA
GAGAAAAGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAAGGAAAGATTTAAGCC
GCAACGGCGAATCCAGTACCACGAAGACAAAAAA
Found at i:12490 original size:197 final size:194
Alignment explanation
Indices: 11730--12491 Score: 690
Period size: 197 Copynumber: 3.9 Consensus size: 194
11720 AGATATGGAG
* * *
11730 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGT-CCTCAGAAGCATGAAGGGAGAGATTTAAGCTG
1 GGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
* * * * *** * * * *
11794 CAATGGCGAATCTAGTACCACGAAAACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTAT
66 CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAA-GTTTAAGTCGTAACGGCAAACCTTGT
* * ** ** * * * * *
11859 A-CCTCAGAGACATGAAGGGAAAGATTTAAGCCGTAACGACGAATCTAGTACCATGAAGACA-CA
130 ACCCTGA-AG-CATG-AGAGAAAGATTTAAGCCACAACGGTGAATCCAGTACGACGAAGATATAA
*
11922 AAG
192 AAA
* * *
11925 GGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAG-AGACATGAAGGGAAAGATTTAAGCT
1 GGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCC
* *** * *
11989 GCAACGGCGAATCCAGTACCACGAAGACACAAAAGAGAAAGGTTTAAGTCGTAACGACAAACCTT
65 GCAACGGCGAATCCAGTACCACGAAGATA-TGGAGGGAAA-GTTTAAGTCGTAACGGCAAACCTT
* * * * * *
12054 TTACCTCTGAAGCATAAAGGGAAAGATTTAAGCCACAACAGTGAATCCAGTACGACGAAGATTTG
128 GTACC-CTGAAGCAT-GAGAGAAAGATTTAAGCCACAACGGTGAATCCAGTACGACGAAGATATA
* *
12119 GAGA
191 AAAA
*
12123 -GAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAGCATGAAGGGAGAGATTTAAGCCG
1 GGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
*** * * *
12187 CAACGAAAAATCCAGTACCAC-AAGGATATGGAGAGAAAAGTTTAAGTCGTAATGGCGAACCTTG
66 CAACGGCGAATCCAGTACCACGAA-GATATGGAG-GGAAAGTTTAAGTCGTAACGGCAAACCTTG
* * * * *
12251 TACCTCGGAAGCATGAAAGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACTACGAGGATATAA
129 TACC-CTGAAGCATGAGA-GAAAGATTTAAGCCACAACGGTGAATCCAGTACGACGAAGATATAA
12316 AAA
192 AAA
* * * * * *
12319 GGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCGGAAGCATGAAGGAAAAAATTTAACCCG
1 GGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
* ** ** *
12384 CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGATTACAACCACAGCGGCAAACCTTGT
66 CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGTTTA-AGTCGTAACGGCAAACCTTGT
* * * * *
12449 ACCCTAGAAACATGACGAGAAAAATTGAACCCACGACGGTGAA
130 ACCCT-GAAGCATGA-GAGAAAGATTTAAGCCACAACGGTGAA
12492 ACTTCTACTT
Statistics
Matches: 466, Mismatches: 85, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
195 33 0.07
196 141 0.30
197 280 0.60
198 9 0.02
199 3 0.01
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (194 bp):
GGAAAGGTTTAAGTCGCAAAGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
CAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGTTTAAGTCGTAACGGCAAACCTTGTA
CCCTGAAGCATGAGAGAAAGATTTAAGCCACAACGGTGAATCCAGTACGACGAAGATATAAAAA
Found at i:12766 original size:39 final size:39
Alignment explanation
Indices: 12699--12922 Score: 161
Period size: 39 Copynumber: 5.7 Consensus size: 39
12689 CACCATAAAC
*
12699 CAATCTCTTACCCCGAGCCT-GAGACAGATTATAACCATT
1 CAATCTCTTACCCCGAGCCTAG-GGCAGATTATAACCATT
*
12738 CAATCTCTTACCCCGAGCCTAGGGCAG---ATCACCATT
1 CAATCTCTTACCCCGAGCCTAGGGCAGATTATAACCATT
* * * * **
12774 AGCCAATCTCCTACCCCGAGCCTGGGGTAAATTGCAACCATT
1 ---CAATCTCTTACCCCGAGCCTAGGGCAGATTATAACCATT
* * * * * * * **
12816 CGATCTCTTACCTCAAGTCTAAGGCAGATCACT-ATCAAC
1 CAATCTCTTACCCCGAGCCTAGGGCAGATTA-TAACCATT
* * *
12855 CAATCTCTTACCCCGAGCCTAGGGGAGATTACAATCATT
1 CAATCTCTTACCCCGAGCCTAGGGCAGATTATAACCATT
* * *
12894 CGATCTCTTACCTCGAGCCTAAGGCAGAT
1 CAATCTCTTACCCCGAGCCTAGGGCAGAT
12923 CATCATCAAC
Statistics
Matches: 138, Mismatches: 38, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
36 8 0.06
39 123 0.89
40 1 0.01
42 6 0.04
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.24
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCCTAGGGCAGATTATAACCATT
Found at i:12816 original size:78 final size:78
Alignment explanation
Indices: 12687--12962 Score: 338
Period size: 78 Copynumber: 3.5 Consensus size: 78
12677 GTGAAGTTAC
* * * * * * *
12687 ATCACCATAAACCAATCTCTTACCCCGAGCCTGAGACAGATTATAACCATTCAATCTCTTACCCC
1 ATCACCATCAACCAATCTCCTACCCCGAGCCTGGGGCAGATTACAACCATTCGATCTCTTACCTC
*
12752 GAGCCTAGGGCAG
66 GAGCCTAAGGCAG
* * * * *
12765 ATCACCATTAGCCAATCTCCTACCCCGAGCCTGGGGTAAATTGCAACCATTCGATCTCTTACCTC
1 ATCACCATCAACCAATCTCCTACCCCGAGCCTGGGGCAGATTACAACCATTCGATCTCTTACCTC
* *
12830 AAGTCTAAGGCAG
66 GAGCCTAAGGCAG
* * *
12843 ATCACTATCAACCAATCTCTTACCCCGAGCCTAGGGG-AGATTACAATCATTCGATCTCTTACCT
1 ATCACCATCAACCAATCTCCTACCCCGAGCCT-GGGGCAGATTACAACCATTCGATCTCTTACCT
12907 CGAGCCTAAGGCAG
65 CGAGCCTAAGGCAG
* * * *
12921 ATCATCATCAACCAATTTCCTACCCCAAGTCTGGGGCAGATT
1 ATCACCATCAACCAATCTCCTACCCCGAGCCTGGGGCAGATT
12963 GCAGTTATCC
Statistics
Matches: 167, Mismatches: 29, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
77 4 0.02
78 159 0.95
79 4 0.02
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (78 bp):
ATCACCATCAACCAATCTCCTACCCCGAGCCTGGGGCAGATTACAACCATTCGATCTCTTACCTC
GAGCCTAAGGCAG
Found at i:13488 original size:23 final size:23
Alignment explanation
Indices: 13452--13495 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
13442 AAAAATTAAA
13452 ATTTTAGATTTTAAATCTTAATTC
1 ATTTTAGATTTTAAAT-TTAATTC
13476 ATTTTA-ATTTTAAATTTAAT
1 ATTTTAGATTTTAAATTTAAT
13496 ATAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTTAGATTTTAAATTTAATTC
Found at i:13503 original size:24 final size:25
Alignment explanation
Indices: 13445--13503 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
13435 TTGGATCAAA
13445 AATTAAAATTTTAGATTTTAAATCTT
1 AATT-AAATTTTAGATTTTAAATCTT
*
13471 AATT-CATTTTA-ATTTTAAAT-TT
1 AATTAAATTTTAGATTTTAAATCTT
13493 AATATAAATTT
1 AAT-TAAATTT
13504 AAGCTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 5 0.17
23 10 0.34
24 10 0.34
26 4 0.14
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTAAATTTTAGATTTTAAATCTT
Found at i:15006 original size:60 final size:61
Alignment explanation
Indices: 14926--15092 Score: 169
Period size: 60 Copynumber: 2.8 Consensus size: 61
14916 AAAAGGTCCT
* * * *
14926 TAAACTTTTCTAAAACTACATTTTAACCCCTAAAGTTTTCCAAAATTACATTTTGA-CCCC
1 TAAATTTTTCAAAAATTACATTTTAACCCCTAAAGTTTTCCAAAATCACATTTTGACCCCC
* * * * *
14986 TAAATTTTTCCAAAATTACATTTTGACCTCT-AAGCTTTTCCAAAATCATATTTTTACCCCC
1 TAAATTTTTCAAAAATTACATTTTAACCCCTAAAG-TTTTCCAAAATCACATTTTGACCCCC
* * * * *
15047 TAAATGTTTCAAAAATCATATTTTAA-CCCTCAAACTTTTCTAAAAT
1 TAAATTTTTCAAAAATTACATTTTAACCCCT-AAAGTTTTCCAAAAT
15093 AATATCTTGA
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 3 0.03
60 47 0.54
61 35 0.40
62 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (61 bp):
TAAATTTTTCAAAAATTACATTTTAACCCCTAAAGTTTTCCAAAATCACATTTTGACCCCC
Found at i:15085 original size:61 final size:61
Alignment explanation
Indices: 14943--15105 Score: 179
Period size: 61 Copynumber: 2.7 Consensus size: 61
14933 TTCTAAAACT
* * * * * *
14943 ACATTTTAACCC-CTAAAGTTTTCCAAAATTACATTTTGACCCCTAAATTTTTCCAAAATT
1 ACATTTTAACCCTCTAAACTTTTCCAAAATAATATTTTGACCCCTAAATGTTTCAAAAATC
* * * *
15003 ACATTTTGA-CCTCTAAGCTTTTCCAAAATCATATTTTTACCCCCTAAATGTTTCAAAAATC
1 ACATTTTAACCCTCTAAACTTTTCCAAAATAATATTTTGA-CCCCTAAATGTTTCAAAAATC
* * *
15064 ATATTTTAACCCTC-AAACTTTTCTAAAATAATATCTTGACCC
1 ACATTTTAACCCTCTAAACTTTTCCAAAATAATATTTTGACCC
15106 TCGAACTTCT
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 33 0.39
61 45 0.54
62 4 0.05
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (61 bp):
ACATTTTAACCCTCTAAACTTTTCCAAAATAATATTTTGACCCCTAAATGTTTCAAAAATC
Found at i:15092 original size:30 final size:31
Alignment explanation
Indices: 14926--15107 Score: 151
Period size: 30 Copynumber: 6.0 Consensus size: 31
14916 AAAAGGTCCT
* *
14926 TAAACTTTTCTAAAA-CTACATTTTAACCC-C
1 TAAACTTTTCCAAAATC-ACATTTTGACCCTC
* *
14956 TAAAGTTTTCCAAAATTACATTTTGACCC-C
1 TAAACTTTTCCAAAATCACATTTTGACCCTC
* *
14986 TAAATTTTTCCAAAATTACATTTTGA-CCTC
1 TAAACTTTTCCAAAATCACATTTTGACCCTC
* * * *
15016 TAAGCTTTTCCAAAATCATATTTTTACCCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCTC
* * *
15047 TAAA-TGTTTCAAAAATCATATTTTAACCCTC
1 TAAACT-TTTCCAAAATCACATTTTGACCCTC
* * * *
15078 -AAACTTTTCTAAAATAATATCTTGACCCTC
1 TAAACTTTTCCAAAATCACATTTTGACCCTC
15108 GAACTTCTTT
Statistics
Matches: 128, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.02
30 97 0.76
31 29 0.23
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (31 bp):
TAAACTTTTCCAAAATCACATTTTGACCCTC
Found at i:15113 original size:30 final size:30
Alignment explanation
Indices: 15053--15122 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
15043 CCCCTAAATG
* * *
15053 TTTCAAAAATCATATTTTAACCCTCAAACT
1 TTTCTAAAATAATATCTTAACCCTCAAACT
* *
15083 TTTCTAAAATAATATCTTGACCCTCGAACT
1 TTTCTAAAATAATATCTTAACCCTCAAACT
15113 TCTT-TAAAAT
1 T-TTCTAAAAT
15123 TTCATTTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (30 bp):
TTTCTAAAATAATATCTTAACCCTCAAACT
Found at i:17692 original size:32 final size:33
Alignment explanation
Indices: 17622--17693 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
17612 AGCTAAAAAT
* *
17622 AAGTAACATTGAAAAAAAAAAAAAGTAAACAGT
1 AAGTAAAATTGAAAAAAAAAAAAAGTAAACAGA
*
17655 AAGTAAAATTGAAAAAAAAGAAAAG-AAA-AGA
1 AAGTAAAATTGAAAAAAAAAAAAAGTAAACAGA
17686 AGAGTAAA
1 A-AGTAAA
17694 TAATAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 3 0.09
32 9 0.26
33 23 0.66
ACGTcount: A:0.69, C:0.03, G:0.15, T:0.12
Consensus pattern (33 bp):
AAGTAAAATTGAAAAAAAAAAAAAGTAAACAGA
Found at i:25927 original size:34 final size:34
Alignment explanation
Indices: 25881--25960 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
25871 ATGACTTTAA
* *
25881 TTTTTATATTTTT-ATTTTAAAAAATTTAGTGTTTT
1 TTTTTATATTTTTGAATTT-AAAAATTTAG-GTTAT
25916 TTTTTAT-TTTTTGAATTTAAAAATTTAGGTTAT
1 TTTTTATATTTTTGAATTTAAAAATTTAGGTTAT
25949 TTTATTAGTATT
1 TTT-TTA-TATT
25961 ATCGGAATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 7 0.18
34 18 0.46
35 12 0.31
36 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (34 bp):
TTTTTATATTTTTGAATTTAAAAATTTAGGTTAT
Found at i:27057 original size:24 final size:25
Alignment explanation
Indices: 27030--27085 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
27020 TTATTGAAAT
* *
27030 ATAATTAAAT-AATTGAAAAAACCC
1 ATAATTAAATAAAATAAAAAAACCC
* *
27054 ATAAAT-AATAAAATAAAAAAACGC
1 ATAATTAAATAAAATAAAAAAACCC
27078 ATAATTAA
1 ATAATTAA
27086 TTTCGAGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.12
24 21 0.84
25 1 0.04
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (25 bp):
ATAATTAAATAAAATAAAAAAACCC
Found at i:28666 original size:14 final size:15
Alignment explanation
Indices: 28637--28667 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28627 TATGGGAAAC
28637 AGTAGAAGAGAACCA
1 AGTAGAAGAGAACCA
28652 AGTAGAAGA-AACCA
1 AGTAGAAGAGAACCA
28666 AG
1 AG
28668 AATCTATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.55, C:0.13, G:0.26, T:0.06
Consensus pattern (15 bp):
AGTAGAAGAGAACCA
Found at i:29684 original size:15 final size:16
Alignment explanation
Indices: 29664--29697 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29654 AATCTTTTAA
29664 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
29679 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
29695 AAA
1 AAA
29698 ATCTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:33903 original size:10 final size:10
Alignment explanation
Indices: 33890--33923 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
33880 TTTTTGCTAT
33890 TTTTTTGTTG
1 TTTTTTGTTG
*
33900 TTTTTTATTG
1 TTTTTTGTTG
*
33910 TTTTATGTTG
1 TTTTTTGTTG
33920 TTTT
1 TTTT
33924 CTTATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (10 bp):
TTTTTTGTTG
Found at i:33913 original size:20 final size:21
Alignment explanation
Indices: 33887--33934 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
33877 TTTTTTTTGC
33887 TATT-TTTT-TGTTGTTTT-T
1 TATTATTTTATGTTGTTTTCT
*
33905 TATTGTTTTATGTTGTTTTCT
1 TATTATTTTATGTTGTTTTCT
33926 TATTATTTT
1 TATTATTTT
33935 GCTATCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 9 0.35
21 9 0.35
ACGTcount: A:0.10, C:0.02, G:0.10, T:0.77
Consensus pattern (21 bp):
TATTATTTTATGTTGTTTTCT
Found at i:41326 original size:14 final size:14
Alignment explanation
Indices: 41281--41328 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
41271 CACCTAATTA
41281 TTAATGTATTTTATT
1 TTAAT-TATTTTATT
* *
41296 TTAATTATTTAAGT
1 TTAATTATTTTATT
*
41310 TTAATTTTTTTATT
1 TTAATTATTTTATT
41324 TTAAT
1 TTAAT
41329 CATTAATCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 23 0.82
15 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TTAATTATTTTATT
Found at i:52836 original size:24 final size:24
Alignment explanation
Indices: 52804--52865 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
52794 GTTAGCATTG
52804 ACGAAAAAACCGACGAGAAGCCCA
1 ACGAAAAAACCGACGAGAAGCCCA
52828 ACGAAAAAACCGACGAGAAGCCCA
1 ACGAAAAAACCGACGAGAAGCCCA
52852 ACGAAAAAACCGAC
1 ACGAAAAAACCGAC
52866 ACAGATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.29, G:0.19, T:0.00
Consensus pattern (24 bp):
ACGAAAAAACCGACGAGAAGCCCA
Found at i:53176 original size:9 final size:9
Alignment explanation
Indices: 53164--53188 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53154 GCATTCAACA
53164 AATTCGATC
1 AATTCGATC
53173 AATTCGATC
1 AATTCGATC
53182 AATTCGA
1 AATTCGA
53189 ATTAACGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (9 bp):
AATTCGATC
Found at i:55931 original size:6 final size:6
Alignment explanation
Indices: 55920--55950 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
55910 GATTGAAAGG
55920 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
55951 ATGATGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:55973 original size:14 final size:14
Alignment explanation
Indices: 55922--55974 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
55912 TTGAAAGGGG
55922 GAGAGGGAGAG-G-
1 GAGAGGGAGAGTGA
*
55934 GAGAGGGAGAGGGA
1 GAGAGGGAGAGTGA
*
55948 GAGA-TGATGAGTGA
1 GAGAGGGA-GAGTGA
55962 GAGAGGGAGAGTG
1 GAGAGGGAGAGTG
55975 GTACAAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.32
13 3 0.09
14 18 0.53
15 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.58, T:0.08
Consensus pattern (14 bp):
GAGAGGGAGAGTGA
Found at i:60147 original size:36 final size:34
Alignment explanation
Indices: 60082--60150 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 34
60072 GAAATAGTCA
*
60082 TAAAATTAATAATAAAATAAATATTATATAATATT
1 TAAAATTAACAATAAAATAAATA-TATATAATATT
60117 TAAACATTAACAATAAAATAGTAATA-ATATAATA
1 TAAA-ATTAACAATAAAATA--AATATATATAATA
60151 GTAAAATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 4 0.13
36 22 0.73
38 4 0.13
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (34 bp):
TAAAATTAACAATAAAATAAATATATATAATATT
Found at i:62252 original size:23 final size:24
Alignment explanation
Indices: 62209--62257 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
62199 AAGTAATCCT
62209 TTTTCAAATATTTTGATGAGT-AA
1 TTTTCAAATATTTTGATGAGTGAA
62232 TTTTC-AATATTTTTG-TGGAGTGAA
1 TTTTCAAATA-TTTTGAT-GAGTGAA
62256 TT
1 TT
62258 CAGCCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (24 bp):
TTTTCAAATATTTTGATGAGTGAA
Found at i:62304 original size:5 final size:5
Alignment explanation
Indices: 62294--62318 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62284 AAAGGACAAG
62294 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
62319 ATCCCCTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:73531 original size:31 final size:31
Alignment explanation
Indices: 73496--73561 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
73486 TATACAAAAT
73496 AGTCACTGAACTATTCAAAAG-TTTTCATTTA
1 AGTCACTGAACTATTCAAAAGCTTTT-ATTTA
**
73527 AGTCACTGAACTATTTGAAAGCTTTTATTTA
1 AGTCACTGAACTATTCAAAAGCTTTTATTTA
73558 AGTC
1 AGTC
73562 TTTGGGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (31 bp):
AGTCACTGAACTATTCAAAAGCTTTTATTTA
Found at i:75079 original size:16 final size:16
Alignment explanation
Indices: 75026--75072 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
75016 AAGAGTGGAA
*
75026 AGAAAATTGGAA-GACT
1 AGAAAATT-GAAGGAGT
75042 AGAAAATTGAAGGAGT
1 AGAAAATTGAAGGAGT
75058 AGAAAATTAGAAGGA
1 AGAAAATT-GAAGGA
75073 TGGAAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 3 0.11
16 19 0.68
17 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.28, T:0.17
Consensus pattern (16 bp):
AGAAAATTGAAGGAGT
Found at i:77954 original size:31 final size:31
Alignment explanation
Indices: 77912--78017 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
77902 GTACTAACCT
* *
77912 AAAAAAGTGTCAAGTTTAGGTACCAGATTAG
1 AAAAAAATGTCAAGTTTAGGTACCAAATTAG
*
77943 AAAAAAATGTCAAGTTT-GAGTACCAAATTGG
1 AAAAAAATGTCAAGTTTAG-GTACCAAATTAG
77974 ACCAAAAAA----AAGTTTAGGTACCAAATTAG
1 A--AAAAAATGTCAAGTTTAGGTACCAAATTAG
* *
78003 -GAAAAGTGTCAAGTT
1 AAAAAAATGTCAAGTT
78018 CAGATATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
26 4 0.07
29 17 0.28
30 7 0.11
31 27 0.44
33 6 0.10
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (31 bp):
AAAAAAATGTCAAGTTTAGGTACCAAATTAG
Found at i:85225 original size:31 final size:32
Alignment explanation
Indices: 85190--85257 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
85180 TAAGTTTCTG
* * *
85190 ATCAATCCTAATTT-TTTAAGGGTTTGTATTA
1 ATCAATCCTAATTTCTTGAAGGATTTGTATGA
* *
85221 ATCAATCTTAATTTCTTGAATGATTTGTATGA
1 ATCAATCCTAATTTCTTGAAGGATTTGTATGA
85253 ATCAA
1 ATCAA
85258 CCTCTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (32 bp):
ATCAATCCTAATTTCTTGAAGGATTTGTATGA
Found at i:86850 original size:20 final size:21
Alignment explanation
Indices: 86817--86859 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
86807 ATATCAAGAA
86817 AATCGTTAAAATTTAATAGTC
1 AATCGTTAAAATTTAATAGTC
*
86838 AATCGTT-AAATTTAATTGTC
1 AATCGTTAAAATTTAATAGTC
86858 AA
1 AA
86860 AAATTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
AATCGTTAAAATTTAATAGTC
Found at i:89702 original size:7 final size:8
Alignment explanation
Indices: 89630--89706 Score: 61
Period size: 8 Copynumber: 9.4 Consensus size: 8
89620 TTATTTTAGA
89630 AAATTTTT
1 AAATTTTT
89638 AAATTTTT
1 AAATTTTT
89646 AAATATCTTT
1 AAAT-T-TTT
89656 ATATATTCTTT
1 A-A-ATT-TTT
*
89667 AGATTTTT
1 AAATTTTT
**
89675 ---TTTAA
1 AAATTTTT
89680 AAATTTTT
1 AAATTTTT
89688 AAATTTTT
1 AAATTTTT
89696 AAATTTTT
1 AAATTTTT
89704 AAA
1 AAA
89707 AATTATTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
5 3 0.05
8 37 0.65
9 4 0.07
10 4 0.07
11 7 0.12
12 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (8 bp):
AAATTTTT
Found at i:90256 original size:23 final size:24
Alignment explanation
Indices: 90230--90288 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
90220 CGAAAGGATC
**
90230 AAAATTTAAAATTATTCTATTTAA
1 AAAATTTAAAATTATTAAATTTAA
* * *
90254 AAACTTT-AATTTTTTAAATTTAA
1 AAAATTTAAAATTATTAAATTTAA
90277 AAAATTTAAAAT
1 AAAATTTAAAAT
90289 GAATTTGAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATTTAAAATTATTAAATTTAA
Done.