Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008358.1 Kokia drynarioides strain JFW-HI SEQ_123025, 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: 53424
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:4298 original size:2 final size:2
Alignment explanation
Indices: 4291--4322 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4281 GGTTGTGATG
4291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4323 ACTTGAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4897 original size:6 final size:6
Alignment explanation
Indices: 4886--4910 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4876 CTACCTTGTG
4886 TTTGGA TTTGGA TTTGGA TTTGGA T
1 TTTGGA TTTGGA TTTGGA TTTGGA T
4911 GGCTTGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTTGGA
Found at i:11653 original size:2 final size:2
Alignment explanation
Indices: 11646--11788 Score: 135
Period size: 2 Copynumber: 71.5 Consensus size: 2
11636 TAACGTTACT
* * * *
11646 TA TA TA TA TA TA TCA TA TA TA TT TG TA T- TA TG TA TA TA TG TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
11688 TG TA TA TA TG CA TA TG TA TA AA TA TA TA CA TA TA TA CA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
11730 TA TA TA TG TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11772 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
11789 TGTAAATGTT
Statistics
Matches: 110, Mismatches: 29, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
1 1 0.01
2 107 0.97
3 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11873 original size:4 final size:4
Alignment explanation
Indices: 11866--11926 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 4
11856 AGTAGGTATG
* * * * * *
11866 TATA TATA TACA TACA TGTA TATA TATA CATA CATA TATA TATA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
11914 TACA TACA TATA T
1 TATA TATA TATA T
11927 GTATTGTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (4 bp):
TATA
Found at i:11891 original size:22 final size:22
Alignment explanation
Indices: 11866--11930 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
11856 AGTAGGTATG
* *
11866 TATATATATACATACATGTATA
1 TATATACATACATATATGTATA
*
11888 TATATACATACATATATATATA
1 TATATACATACATATATGTATA
*
11910 TACATACATACATATATGTAT
1 TATATACATACATATATGTAT
11931 TGTAAATGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (22 bp):
TATATACATACATATATGTATA
Found at i:11919 original size:18 final size:18
Alignment explanation
Indices: 11866--11926 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
11856 AGTAGGTATG
*
11866 TATATATATACATACATG
1 TATATATATACATACATA
11884 TATATATATACATACATA
1 TATATATATACATACATA
11902 TATATATATACATACATA
1 TATATATATACATACATA
*
11920 CATATAT
1 TATATAT
11927 GTATTGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (18 bp):
TATATATATACATACATA
Found at i:11941 original size:142 final size:142
Alignment explanation
Indices: 11742--12003 Score: 452
Period size: 142 Copynumber: 1.8 Consensus size: 142
11732 TATATGTACA
* * * * *
11742 TATATACATATATATATATATATATATATATATATATATATATATATTGTAAATGTTCAGCAAAT
1 TATATACATACATACATATATATATATACATACATACATATATATATTGTAAATGTTCAGCAAAT
*
11807 TGGAAGCATTTGGAATTGAAGATGATCGAGAAAATGAAACGAAAGAGATAGTAGGTATGTATATA
66 TGGAAGCATTTGGAATTGAAGATGATCGAGAAAATGAAACAAAAGAGATAGTAGGTATGTATATA
11872 TATACATACATG
131 TATACATACATG
* *
11884 TATATATATACATACATATATATATATACATACATACATATATGTATTGTAAATGTTCAGCAAAT
1 TATATACATACATACATATATATATATACATACATACATATATATATTGTAAATGTTCAGCAAAT
11949 TGGAAGCATTTGGAATTGAAGATGATCGAGAAAATGAAACAAAAGAGATAGTAGG
66 TGGAAGCATTTGGAATTGAAGATGATCGAGAAAATGAAACAAAAGAGATAGTAGG
12004 CTTTATGCCG
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 112 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (142 bp):
TATATACATACATACATATATATATATACATACATACATATATATATTGTAAATGTTCAGCAAAT
TGGAAGCATTTGGAATTGAAGATGATCGAGAAAATGAAACAAAAGAGATAGTAGGTATGTATATA
TATACATACATG
Found at i:12752 original size:34 final size:34
Alignment explanation
Indices: 12714--12782 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
12704 ATGCATACTT
12714 TAAGTTATGTACAATTGTGTTATTAAACTTGTGA
1 TAAGTTATGTACAATTGTGTTATTAAACTTGTGA
12748 TAAGTTATGTACAATTGTGTTATTAAACTTGTGA
1 TAAGTTATGTACAATTGTGTTATTAAACTTGTGA
12782 T
1 T
12783 TTGGCATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (34 bp):
TAAGTTATGTACAATTGTGTTATTAAACTTGTGA
Found at i:22724 original size:34 final size:34
Alignment explanation
Indices: 22686--22758 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
22676 AGTAAACAAC
* * *
22686 ATTTGGTTAAGGTAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
22720 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
22754 ATTTG
1 ATTTG
22759 AGTTTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
Found at i:23317 original size:15 final size:16
Alignment explanation
Indices: 23283--23317 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
23273 TTTTGTTATT
*
23283 TTATTTCTTAATATAA
1 TTATTTCTTAATAAAA
23299 TTATTTCTTAA-AAAA
1 TTATTTCTTAATAAAA
23314 TTAT
1 TTAT
23318 AATTATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTTCTTAATAAAA
Found at i:23797 original size:12 final size:12
Alignment explanation
Indices: 23780--23814 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
23770 TCAAAAACCT
23780 TAAACCCTAAAA
1 TAAACCCTAAAA
23792 TAAACCCTAAAA
1 TAAACCCTAAAA
23804 TAAACCCTAAA
1 TAAACCCTAAA
23815 TCTTAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAACCCTAAAA
Found at i:24470 original size:15 final size:16
Alignment explanation
Indices: 24437--24472 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
24427 TTGTCAATTT
*
24437 TTTTAAAAAAGAATCA
1 TTTTAAAAAAAAATCA
24453 TTTTAAAAAAAAAT-A
1 TTTTAAAAAAAAATCA
24468 TTTTA
1 TTTTA
24473 TATAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTTAAAAAAAAATCA
Found at i:25956 original size:6 final size:6
Alignment explanation
Indices: 25936--26028 Score: 74
Period size: 6 Copynumber: 16.2 Consensus size: 6
25926 CCAAACTCAT
* *
25936 TTTAAA TTT-AT TTTAAA TTTAAA TCT--A TCTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
* *
25981 TTTAAG TTTAAA TTT-AT TTTAAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
26028 T
1 T
26029 AAATAAAAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
4 5 0.07
5 15 0.22
6 40 0.58
7 9 0.13
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:25958 original size:17 final size:17
Alignment explanation
Indices: 25936--26028 Score: 132
Period size: 17 Copynumber: 5.4 Consensus size: 17
25926 CCAAACTCAT
25936 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
25953 TTTAAATCTATCTTAAA
1 TTTAAATTTATTTTAAA
* *
25970 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
25987 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
*
26005 TTTAAATTTATTATAAA
1 TTTAAATTTATTTTAAA
26022 TTTAAAT
1 TTTAAAT
26029 AAATAAAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
17 51 0.77
18 15 0.23
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:25994 original size:12 final size:12
Alignment explanation
Indices: 25936--26028 Score: 74
Period size: 11 Copynumber: 8.1 Consensus size: 12
25926 CCAAACTCAT
*
25936 TTTAAATTT-AT
1 TTTAAATTTAAA
25947 TTTAAATTTAAA
1 TTTAAATTTAAA
*
25959 TCT--ATCTTAAA
1 TTTAAAT-TTAAA
25970 TTTAAATTT-AA
1 TTTAAATTTAAA
*
25981 TTTAAGTTTAAA
1 TTTAAATTTAAA
*
25993 TTT-ATTTTAAAA
1 TTTAAATTT-AAA
26005 TTTAAATTT--A
1 TTTAAATTTAAA
26015 TTATAAATTTAAA
1 TT-TAAATTTAAA
26028 T
1 T
26029 AAATAAAAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
10 5 0.08
11 37 0.56
12 16 0.24
13 8 0.12
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:26689 original size:3 final size:3
Alignment explanation
Indices: 26683--26797 Score: 104
Period size: 3 Copynumber: 37.3 Consensus size: 3
26673 TAATCTGCAT
* * * * * *
26683 TAA TAA TACT TAA TAA TAC TAC TGA TAT TAA TAA TAA TCA TAA TTAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* **
26730 TAA TAA TAA TAA TAA TAA CTAT TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
26776 TAA TAA TAA TAT TAG TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
26798 GAAATAAAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
3 85 0.92
4 7 0.08
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:27898 original size:29 final size:29
Alignment explanation
Indices: 27855--28199 Score: 151
Period size: 29 Copynumber: 11.8 Consensus size: 29
27845 AAGGTCCCTA
*
27855 AACTATCCAGAAATTACATTTTTACCCTCG
1 AACTTTCCA-AAATTACATTTTTACCCTCG
*
27885 AACTTTCCAAAATT-CTATTTTTGA-CCT-T
1 AACTTTCCAAAATTAC-ATTTTT-ACCCTCG
*
27913 AATTTTTCCAAAAATTACATTTTTACCCCTCG
1 AA-CTTTCC-AAAATTACATTTTTA-CCCTCG
*
27945 AA-TATTCCAAAATT-CATTCTTGA-CCTCG
1 AACT-TTCCAAAATTACATT-TTTACCCTCG
*** ** *
27973 GTTTTTCCAAAATTACATTTTTAAGCTCA
1 AACTTTCCAAAATTACATTTTTACCCTCG
*
28002 AACTTTCCAAAATTCCATTTTTAACCC-CG
1 AACTTTCCAAAATTACATTTTT-ACCCTCG
** * * *
28031 ATTTTTCTAAAAATTGCCA-TTTTACCCTCA
1 AACTTTC-CAAAATT-ACATTTTTACCCTCG
* * * *
28061 AAC-TTCCAAAAACTCCATTTTGA-CCTTG
1 AACTTTCC-AAAATTACATTTTTACCCTCG
** *
28089 ATTTTTCCAAAAATTACCA-TTTTACCCCCG
1 AACTTTCC-AAAATTA-CATTTTTACCCTCG
*
28119 AAC-TTCCAAAAATTTCATTTTTGA-CCTCG
1 AACTTTCC-AAAATTACATTTTT-ACCCTCG
** * * *
28148 ATTTTTCCAAAAAGTACCA-TTTTACCCCCA
1 AACTTTCC-AAAATTA-CATTTTTACCCTCG
* *
28178 AACTTTCAAAAATTATATTTTT
1 AACTTTCCAAAATTACATTTTT
28200 GACCTTTTTT
Statistics
Matches: 237, Mismatches: 50, Indels: 57
0.69 0.15 0.17
Matches are distributed among these distances:
28 31 0.13
29 117 0.49
30 74 0.31
31 13 0.05
32 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTTACCCTCG
Found at i:27968 original size:59 final size:56
Alignment explanation
Indices: 27860--28204 Score: 307
Period size: 59 Copynumber: 5.9 Consensus size: 56
27850 CCCTAAACTA
* **
27860 TCCAGAAATTACATTTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCTTAATTTT
1 TCCAAAAATTACA-TTTTACCCTCGAA-TTTCCAAAATTC-ATTTTTGACCTCGATTTT
* *
27919 TCCAAAAATTACATTTTTACCCCTCGAATATTCCAAAATTCATTCTTGACCTCGGTTTT
1 TCCAAAAATTACA-TTTTA-CCCTCGAAT-TTCCAAAATTCATTTTTGACCTCGATTTT
** * * *
27978 TCC-AAAATTACATTTTTAAGCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTT
1 TCCAAAAATTACA-TTTTACCCTCGAA-TTTCCAAAATT-CATTTTTGACCTCGATTTT
* * * * * *
28036 TCTAAAAATTGCCATTTTACCCTCAAACTTCCAAAAACTCCA-TTTTGACCTTGATTTT
1 TCCAAAAATT-ACATTTTACCCTCGAATTTCC-AAAA-TTCATTTTTGACCTCGATTTT
* *
28094 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCTCGATTTT
1 TCCAAAAATTA-CATTTTACCCTCGAATTTCC-AAAA-TTCATTTTTGACCTCGATTTT
* * * * *
28153 TCCAAAAAGTACCATTTTACCCCCAAACTTTCAAAAATTATATTTTTGACCT
1 TCCAAAAATTA-CATTTTACCCTCGAA-TTTCCAAAATT-CATTTTTGACCT
28205 TTTTTTAAAT
Statistics
Matches: 241, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
57 15 0.06
58 87 0.36
59 114 0.47
60 25 0.10
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (56 bp):
TCCAAAAATTACATTTTACCCTCGAATTTCCAAAATTCATTTTTGACCTCGATTTT
Found at i:28102 original size:117 final size:116
Alignment explanation
Indices: 27860--28190 Score: 368
Period size: 117 Copynumber: 2.8 Consensus size: 116
27850 CCCTAAACTA
* * **
27860 TCCAGAAATTACATTTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCTTAATTTTTCCAAA
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAAA
* * *
27925 AATTACATTTTTACCCCTCGAATA-TTCC-AAAATTCATTCTTGACCTCGGTTTT
66 AATTCCA-TTTTA-CCCTC-AA-ACTTCCAAAAATCCATTCTTGACCTCGATTTT
** * * * *
27978 TCC-AAAATTACATTTTTAAGCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTTCTAAA
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAAA
*
28042 AATTGCCATTTTACCCTCAAACTTCCAAAAACTCCATT-TTGACCTTGATTTT
66 AATT-CCATTTTACCCTCAAACTTCCAAAAA-TCCATTCTTGACCTCGATTTT
* *
28094 TCCAAAAATTACCA-TTTTACCCCCGAAC-TTCCAAAAATTTCATTTTTGACCTCGATTTTTCCA
1 TCCAAAAATTA-CATTTTTACCCTCGAACTTTCC-AAAATTCCATTTTTGACCTCGATTTTTCCA
* * *
28157 AAAAGTACCATTTTACCCCCAAACTTTCAAAAAT
64 AAAA-TTCCATTTTACCCTCAAACTTCCAAAAAT
28191 TATATTTTTG
Statistics
Matches: 180, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
114 1 0.01
115 6 0.03
116 29 0.16
117 136 0.76
118 8 0.04
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (116 bp):
TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAAA
AATTCCATTTTACCCTCAAACTTCCAAAAATCCATTCTTGACCTCGATTTT
Found at i:39992 original size:49 final size:49
Alignment explanation
Indices: 39934--40311 Score: 282
Period size: 49 Copynumber: 7.7 Consensus size: 49
39924 CTACAGGTTT
* *
39934 CAGTAACCACGAAGACATGAAGGGAAAGATCT-AGACCGCAACGGTGGATC
1 CAGT-ACCACGAAGACATGAAGGGAAAGATTTAAG-CCGCAACGGCGGATC
* ** * * * *
39984 CAGTACCACAAAGACAAAAAGGGAAAGGTTTAAGTCGCAACGGCGAACC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
* * * * * *
40033 CAGAACCTCGGAGACATGAAGAGAAAGATTTAAGCCGGAACGGCGAATC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
* * * * *
40082 CAGTACCACCAAGACATGAAGGGAAAGATCTAAGCCACAACGACAGATC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
** * * * * *
40131 CAGTACCACGAAGACACAAAGGGAAAGGTTTTAGTCGCAACGGC-TAAC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
* * * *
40179 CTAGTACCTTA-GAAG-CATTAAGGGAAAGATTTAAGCTGCAACAGTGGATC
1 C-AGTACC--ACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
** * * * * * *
40229 CAGTACCACGAAGACACCAAGGGAAAGGTTTAAGTCACAATGGC-AAAC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
* *
40277 CTAGTACCTC-AGGGACATGAAGGGAAAGATTTAAG
1 C-AGTACCACGA-AGACATGAAGGGAAAGATTTAAG
40312 TCGTAATGGA
Statistics
Matches: 251, Mismatches: 68, Indels: 19
0.74 0.20 0.06
Matches are distributed among these distances:
47 1 0.00
48 11 0.04
49 225 0.90
50 13 0.05
51 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (49 bp):
CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATC
Found at i:40206 original size:147 final size:147
Alignment explanation
Indices: 39934--40255 Score: 405
Period size: 147 Copynumber: 2.2 Consensus size: 147
39924 CTACAGGTTT
* ***
39934 CAGTAACCACGAAGACATGAAGGGAAAGATCTAGACCGCAACGGTGGATCCAGTACCACAAAGAC
1 CAGT-ACCACGAAGACATGAAGGGAAAGATCTAGACCACAACGACAGATCCAGTACCACAAAGAC
* *
39999 AAAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACCTCGGAGACATGAAGAGAAAGATTT
65 AAAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACCTAGAAGACATGAAGAGAAAGATTT
* *
40064 AAGCCGGAACGGCGAATC
130 AAGCCGCAACAGCGAATC
* *
40082 CAGTACCACCAAGACATGAAGGGAAAGATCTA-AGCCACAACGACAGATCCAGTACCACGAAGAC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAGA-CCACAACGACAGATCCAGTACCACAAAGAC
* * * * * * *
40146 ACAAAGGGAAAGGTTTTAGTCGCAACGGCTAACCTAGTACCTTAGAAG-CATTAAGGGAAAGATT
65 AAAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACC-TAGAAGACATGAAGAGAAAGATT
* * *
40210 TAAGCTGCAACAGTGGATC
129 TAAGCCGCAACAGCGAATC
**
40229 CAGTACCACGAAGACACCAAGGGAAAG
1 CAGTACCACGAAGACATGAAGGGAAAG
40256 GTTTAAGTCA
Statistics
Matches: 149, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
146 1 0.01
147 140 0.94
148 8 0.05
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (147 bp):
CAGTACCACGAAGACATGAAGGGAAAGATCTAGACCACAACGACAGATCCAGTACCACAAAGACA
AAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACCTAGAAGACATGAAGAGAAAGATTTA
AGCCGCAACAGCGAATC
Found at i:40283 original size:147 final size:147
Alignment explanation
Indices: 39934--40314 Score: 363
Period size: 147 Copynumber: 2.6 Consensus size: 147
39924 CTACAGGTTT
* ** * *** *
39934 CAGTAACCACGAAGACATGAAGGGAAAGATCT-AGACCGCAACGGTGGATCCAGTACCACAAAGA
1 CAGT-ACCACCAAGACACCAAGGGAAAGATCTAAG-CCACAACGACAGAACCAGTACCACAAAGA
* *
39998 CAAAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACCTCGGAGACATGAAGAGAAAGATT
64 CAAAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACCTAGAAGACATGAAGAGAAAGATT
* *
40063 TAAGCCGGAACGGCGAATC
129 TAAGCCGCAACAGCGAATC
** * *
40082 CAGTACCACCAAGACATGAAGGGAAAGATCTAAGCCACAACGACAGATCCAGTACCACGAAGACA
1 CAGTACCACCAAGACACCAAGGGAAAGATCTAAGCCACAACGACAGAACCAGTACCACAAAGACA
* * * * * * *
40147 CAAAGGGAAAGGTTTTAGTCGCAACGGCTAACCTAGTACCTTAGAAG-CATTAAGGGAAAGATTT
66 AAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACC-TAGAAGACATGAAGAGAAAGATTT
* * *
40211 AAGCTGCAACAGTGGATC
130 AAGCCGCAACAGCGAATC
* * * * * * * **
40229 CAGTACCACGAAGACACCAAGGGAAAGGTTTAAGTCACAATGGCA-AACCTAGTACCTCAGGGAC
1 CAGTACCACCAAGACACCAAGGGAAAGATCTAAGCCACAACGACAGAACC-AGTACCACAAAGAC
** *
40293 ATGAAGGGAAAGATTTAAGTCG
65 AAAAAGGGAAAGGTTTAAGTCG
40315 TAATGGAAAA
Statistics
Matches: 193, Mismatches: 37, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
146 3 0.02
147 180 0.93
148 10 0.05
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (147 bp):
CAGTACCACCAAGACACCAAGGGAAAGATCTAAGCCACAACGACAGAACCAGTACCACAAAGACA
AAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGAACCTAGAAGACATGAAGAGAAAGATTTA
AGCCGCAACAGCGAATC
Found at i:40758 original size:17 final size:17
Alignment explanation
Indices: 40735--40795 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
40725 CCAAACCCAT
40735 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
40753 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
40769 TTTAAATCTATCTTAAA
1 TTTAAATTTATTTTAAA
40786 TTTAAATTTA
1 TTTAAATTTA
40796 GGCATAAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
16 1 0.03
17 38 0.97
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41079 original size:16 final size:15
Alignment explanation
Indices: 41053--41096 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
41043 AAAATTAATT
41053 ATTTTTTAAAATATA
1 ATTTTTTAAAATATA
41068 ATTTTTTAAAA-AT-
1 ATTTTTTAAAATATA
41081 A--TTTTAAAAT-TA
1 ATTTTTTAAAATATA
41093 ATTT
1 ATTT
41097 AAAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 1 0.04
14 3 0.12
15 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTTAAAATATA
Found at i:41087 original size:11 final size:11
Alignment explanation
Indices: 41067--41107 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
41057 TTTAAAATAT
41067 AATT-TTTTAA
1 AATTATTTTAA
*
41077 AAATATTTTAA
1 AATTATTTTAA
*
41088 AATTAATTTAA
1 AATTATTTTAA
41099 AATTATTTT
1 AATTATTTT
41108 TTAAATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 3 0.12
11 23 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:41977 original size:11 final size:10
Alignment explanation
Indices: 41947--41989 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
41937 TAATAATTTT
*
41947 ATATTTAAAA
1 ATATTTTAAA
41957 ATATTTTTAAA
1 ATA-TTTTAAA
*
41968 TTAATTTTAAA
1 AT-ATTTTAAA
41979 ATATTTTAAA
1 ATATTTTAAA
41989 A
1 A
41990 AATAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.43
11 15 0.54
12 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATTTTAAA
Found at i:42974 original size:28 final size:28
Alignment explanation
Indices: 42943--43027 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 28
42933 CTACTGATAT
* * *
42943 TAATAATAACCGTAATTAATATTATTAA
1 TAATAATAACCATAATTAATAATAATAA
* **
42971 TAATAATAACTATTTTTAATAATAATAA
1 TAATAATAACCATAATTAATAATAATAA
**
42999 TAATAATAATAATAA-TAATAATAATAA
1 TAATAATAACCATAATTAATAATAATAA
43026 TA
1 TA
43028 GTTGTAGTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 14 0.30
28 33 0.70
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (28 bp):
TAATAATAACCATAATTAATAATAATAA
Found at i:43047 original size:3 final size:3
Alignment explanation
Indices: 42968--43027 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
42958 TTAATATTAT
* **
42968 TAA TAA TAA TAA CTAT TTT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43014 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
43028 GTTGTAGTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:44251 original size:27 final size:27
Alignment explanation
Indices: 44219--44308 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
44209 AATTTTATTC
44219 TTTACCTCAAATTTTTAAAAATTACAT
1 TTTACCTCAAATTTTTAAAAATTACAT
* * * ** *
44246 TTTACCCCGAACTTTCCAAAATTCCATT
1 TTTACCTCAAATTTTTAAAAATTACA-T
*
44274 TTTAACCTCAATTTTTTCAAAAATTACCAT
1 TTT-ACCTCAAATTTTT-AAAAATTA-CAT
44304 TTTAC
1 TTTAC
44309 TCCCAAACTT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
27 20 0.43
28 4 0.09
29 10 0.22
30 10 0.22
31 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.01, T:0.42
Consensus pattern (27 bp):
TTTACCTCAAATTTTTAAAAATTACAT
Found at i:44337 original size:59 final size:58
Alignment explanation
Indices: 44118--44484 Score: 376
Period size: 59 Copynumber: 6.3 Consensus size: 58
44108 CTAAACTATC
* * * **
44118 CAAAAATTA-CATTTTTACCCCTGAACTTTCTAAAATTCCATTTTTGACCTTTA-TTTTT
1 CAAAAATTACCA-TTTTACCCC-GAACTTCCAAAAATTCCATTTTTAACCTCAATTTTTT
** *
44176 CAAAAATTA-CATTTTTACCCCTGAACTTTCC-AAAATTTTATTCTTT-ACCTCAAATTTTT
1 CAAAAATTACCA-TTTTACCCC-GAAC-TTCCAAAAATTCCATT-TTTAACCTCAATTTTTT
44235 -AAAAATTA-CATTTTACCCCGAACTTTCC-AAAATTCCATTTTTAACCTCAATTTTTT
1 CAAAAATTACCATTTTACCCCGAAC-TTCCAAAAATTCCATTTTTAACCTCAATTTTTT
* * *
44291 CAAAAATTACCATTTTACTCCCAAACTTCCAAAAACTCCATTTTTAACCTCGATTTTTTT
1 CAAAAATTACCATTTTAC-CCCGAACTTCCAAAAATTCCATTTTTAACCTC-AATTTTTT
* * *
44351 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATTCCATTTTCAACCTCGA-TTTTT
1 -CAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATTCCATTTTTAACCTCAATTTTTT
* * * *
44410 CTAAAAAGTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTT
1 C-AAAAATTACCATTTTACCC-CGAACTTCCAAAAATTCCATTTTTAACCTCAATTTTTT
*
44470 -TAAAATTACCATTTT
1 CAAAAATTACCATTTT
44485 TCCCTCATAT
Statistics
Matches: 271, Mismatches: 24, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
55 3 0.01
56 30 0.11
57 17 0.06
58 79 0.29
59 84 0.31
60 12 0.04
61 45 0.17
62 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCTCAATTTTTT
Found at i:44455 original size:29 final size:29
Alignment explanation
Indices: 44111--44578 Score: 166
Period size: 29 Copynumber: 15.9 Consensus size: 29
44101 AAGGTCCCTA
*
44111 AACTATCCAAAAATTACATTTTTACCC-CTG
1 AACT-TCCAAAAATTCCATTTTTACCCTC-G
* * **
44141 AACTTTCTAAAATTCCATTTTTGA-CCTTT
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
** * *
44170 ATTTTTCAAAAATTACATTTTTACCC-CTG
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
** *
44199 AACTTTCC-AAAATTTTATTCTTTA-CCTCA
1 AAC-TTCCAAAAATTCCATT-TTTACCCTCG
* ** *
44228 AATTTTTAAAAATTACA-TTTTACCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
44255 AACTTTCC-AAAATTCCATTTTTAACCTC-
1 AAC-TTCCAAAAATTCCATTTTTACCCTCG
* * *
44283 AATTTTTTCAAAAATTACCA-TTTTACTCC-CA
1 AA--CTTCCAAAAATT-CCATTTTTAC-CCTCG
* *
44314 AACTTCCAAAAACTCCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
** * *
44343 ATTTTTTTCCAAAAATTAC-TATTTTACCCCCG
1 A---ACTTCCAAAAATTCCAT-TTTTACCCTCG
* *
44375 AACTTCCAAAAATTCCATTTTCAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
** * *
44404 ATTTTTCTAAAAAGTACCA-TTTTACCCTCG
1 A-ACTTCCAAAAA-TTCCATTTTTACCCTCG
44434 AACTTCCAAAAATTCCATTTTTGACCC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
** ***
44463 ATTTTTTTAAAATTACCATTTTT-CCCTC-
1 AACTTCCAAAAATT-CCATTTTTACCCTCG
* *
44491 ATA-TGTCTAAAAATTCCATTTTTTTAGCCTCG
1 A-ACT-TCCAAAAATTCCA--TTTTTACCCTCG
* **
44523 AACTTTCCTAAAATTACCATTTTGCCCCTCG
1 AAC-TTCCAAAAATT-CCATTTTTACCCTCG
*
44554 -AGTGTCC-AAAATTACCA-TTTTACCC
1 AACT-TCCAAAAATT-CCATTTTTACCC
44579 CCGGGCATCC
Statistics
Matches: 322, Mismatches: 75, Indels: 84
0.67 0.16 0.17
Matches are distributed among these distances:
27 15 0.05
28 40 0.12
29 142 0.44
30 65 0.20
31 26 0.08
32 30 0.09
33 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:44534 original size:120 final size:118
Alignment explanation
Indices: 44230--44554 Score: 317
Period size: 120 Copynumber: 2.7 Consensus size: 118
44220 TTACCTCAAA
* * * **
44230 TTTTTAAAAATTA-CATTTTA-CCCCGAACTTTCC-AAAATTCCATTTTTAACCTC-AATTTTTT
1 TTTTTCAAAATTACCATTTTACCCCCGAAC-TTCCAAAAATTCCATTTTCAACCTCGACTTTCCT
* *
44291 CAAAAATTACCATTTTACTCC-CAAACTTCCAAAAACTCCATTTTTAACCTCGATT
65 -AAAAATTACCATTTTAC-CCTCGAACTTCCAAAAACTCCATTTTTAACCCCGATT
* * *
44346 TTTTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATTCCATTTTCAACCTCGATTTTTC
1 TTTTT-C-AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTCAACCTCGACTTTCC
* * *
44411 TAAAAAGTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGATT
64 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAACTCCATTTTTAACCCCGATT
* * * * *
44466 TTTTT-AAAATTACCATTTTTCCCTC-ATA-TGTCTAAAAATTCCATTTTTTTAGCCTCGAACTT
1 TTTTTCAAAATTACCATTTTACCCCCGA-ACT-TCCAAAAATTCCA--TTTTCAACCTCG-ACTT
*
44528 TCCT-AAAATTACCATTTTGCCCCTCGA
61 TCCTAAAAATTACCATTTT-ACCCTCGA
44555 GTGTCCAAAA
Statistics
Matches: 176, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
116 7 0.04
117 30 0.17
118 7 0.04
119 35 0.20
120 91 0.52
121 6 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (118 bp):
TTTTTCAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTCAACCTCGACTTTCCTA
AAAATTACCATTTTACCCTCGAACTTCCAAAAACTCCATTTTTAACCCCGATT
Found at i:44594 original size:29 final size:29
Alignment explanation
Indices: 44532--44592 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
44522 GAACTTTCCT
* **
44532 AAAATTACCATTTTGCCCCTCGAGTGTCC
1 AAAATTACCATTTTACCCCTCGAGCATCC
*
44561 AAAATTACCATTTTACCCC-CGGGCATCC
1 AAAATTACCATTTTACCCCTCGAGCATCC
44589 AAAA
1 AAAA
44593 ATCTCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.26
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTCGAGCATCC
Found at i:46611 original size:23 final size:23
Alignment explanation
Indices: 46568--46611 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
46558 TTCTTTTAGG
* *
46568 AATTATAGGAAAATTATTAAATA
1 AATTATAGCAAAACTATTAAATA
46591 AATTATA-CAAAACTATATAAA
1 AATTATAGCAAAACTAT-TAAA
46612 ATTCATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
AATTATAGCAAAACTATTAAATA
Found at i:47261 original size:18 final size:18
Alignment explanation
Indices: 47228--47262 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47218 TTATTAAAAT
* *
47228 ATTATAAAATTTGAGAAA
1 ATTATAAAAATAGAGAAA
47246 ATTATAAAAATAGAGAA
1 ATTATAAAAATAGAGAA
47263 TTGCAGACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
ATTATAAAAATAGAGAAA
Found at i:47827 original size:170 final size:170
Alignment explanation
Indices: 47641--47964 Score: 567
Period size: 170 Copynumber: 1.9 Consensus size: 170
47631 TTGTTACCAA
* * *
47641 AAAAAAAATTGTGCATATTAAAATAGAAATGTATAAAATACATCAAAATAAAGCTTTTGGTTAAG
1 AAAAAAAATTGTGCATATTAAAACAAAAATGTATAAAATACATCAAAATAAAACTTTTGGTTAAG
* *
47706 TGGTAAATTTAAAATTTTACGAATATAATTAGCAATGGTTGAAATATCATCGTATGTATTTTTTA
66 TAGTAAATTTAAAATTTTACGAATATAATTAGCAAGGGTTGAAATATCATCGTATGTATTTTTTA
*
47771 AATTTTTATTAGTTTAGGGTTTAGATAGTAATATAAGTAT
131 AATTTTTATTAGTTTAAGGTTTAGATAGTAATATAAGTAT
*
47811 AAAAAAATTTGTGCATATTAAAACAAAAATGTATAAAATACATCAAAATAAAACTTTTGGTTAAG
1 AAAAAAAATTGTGCATATTAAAACAAAAATGTATAAAATACATCAAAATAAAACTTTTGGTTAAG
* *
47876 TAGTAAATTTAAAATTTTACTAATATAATTAGCAAGGGTTGAAATATCATTGTATGTATTTTTTA
66 TAGTAAATTTAAAATTTTACGAATATAATTAGCAAGGGTTGAAATATCATCGTATGTATTTTTTA
47941 AATTTTTATTAGTTTAAGGTTTAG
131 AATTTTTATTAGTTTAAGGTTTAG
47965 GGTGTAAATA
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
170 145 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (170 bp):
AAAAAAAATTGTGCATATTAAAACAAAAATGTATAAAATACATCAAAATAAAACTTTTGGTTAAG
TAGTAAATTTAAAATTTTACGAATATAATTAGCAAGGGTTGAAATATCATCGTATGTATTTTTTA
AATTTTTATTAGTTTAAGGTTTAGATAGTAATATAAGTAT
Found at i:48408 original size:32 final size:32
Alignment explanation
Indices: 48338--48408 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
48328 AATAATCTAT
*
48338 TTTTTAA-TCAATTCTTTAATAATTTTTATAG
1 TTTTTAATTCAATTCTTTAATAATTTTTATAA
*
48369 TTATTAATTC-ATT-TTTATATAATTTTTTATAA
1 TTTTTAATTCAATTCTTTA-ATAA-TTTTTATAA
48401 TTTTTAAT
1 TTTTTAAT
48409 AGTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.12
31 13 0.38
32 17 0.50
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (32 bp):
TTTTTAATTCAATTCTTTAATAATTTTTATAA
Found at i:48414 original size:20 final size:20
Alignment explanation
Indices: 48356--48416 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
48346 CAATTCTTTA
* *
48356 ATAATTTTT-ATAGTTATTA
1 ATAATTTTTAATAGTTTTTT
* *
48375 ATTCATTTTTATATAATTTTTT
1 A-TAATTTTTA-ATAGTTTTTT
48397 ATAATTTTTAATAGTTTTTT
1 ATAATTTTTAATAGTTTTTT
48417 TTTTATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 8 0.24
22 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (20 bp):
ATAATTTTTAATAGTTTTTT
Found at i:48480 original size:30 final size:31
Alignment explanation
Indices: 48440--48506 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
48430 CTATAATTTC
*
48440 TAAAATTCAATTAAA-CATT-ATTAAAATAAT-
1 TAAAAATCAATTAAATC-TTCA-TAAAATAATT
48470 TAAAAATCAATTAAATCTTCATAAAATAATT
1 TAAAAATCAATTAAATCTTCATAAAATAATT
48501 TAAAAA
1 TAAAAA
48507 ATTAAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 25 0.76
31 8 0.24
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.34
Consensus pattern (31 bp):
TAAAAATCAATTAAATCTTCATAAAATAATT
Found at i:48524 original size:24 final size:25
Alignment explanation
Indices: 48500--48545 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
48490 ATAAAATAAT
*
48500 TTAAA-AAATTAAATCA-AATCAAA
1 TTAAATAAATTAAACCACAATCAAA
48523 TTAAATAAATTAAACCACAATCA
1 TTAAATAAATTAAACCACAATCA
48546 TCAATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (25 bp):
TTAAATAAATTAAACCACAATCAAA
Found at i:48582 original size:24 final size:23
Alignment explanation
Indices: 48554--48601 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
48544 CATCAATTTT
*
48554 TCATATTAA-CTACCACGTCAGTCA
1 TCATA-TAAGCTACCACATCA-TCA
48578 TCATATAAGCTACCACATCATCA
1 TCATATAAGCTACCACATCATCA
48601 T
1 T
48602 TCAACCGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (23 bp):
TCATATAAGCTACCACATCATCA
Found at i:50268 original size:16 final size:16
Alignment explanation
Indices: 50247--50280 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50237 TCAATCAAAG
50247 TATCATTTGCTTTTTA
1 TATCATTTGCTTTTTA
**
50263 TATCATTTTTTTTTTA
1 TATCATTTGCTTTTTA
50279 TA
1 TA
50281 AAATTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (16 bp):
TATCATTTGCTTTTTA
Found at i:50286 original size:16 final size:16
Alignment explanation
Indices: 50257--50300 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
50247 TATCATTTGC
** *
50257 TTTTTATATCATTTTT
1 TTTTTATAAAATTTTA
50273 TTTTTATAAAATTTTA
1 TTTTTATAAAATTTTA
*
50289 TTTTTAAAAAAT
1 TTTTTATAAAAT
50301 AAATTATCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTATAAAATTTTA
Done.