Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014996.1 Kokia drynarioides strain JFW-HI SEQ_130040, 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: 66596
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:178 original size:2 final size:2
Alignment explanation
Indices: 173--218 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
163 GTTAAATTCA
* *
173 AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
215 AT AT
1 AT AT
219 TATGATTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4035 original size:12 final size:12
Alignment explanation
Indices: 4020--4059 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
4010 TTGAAGAAAT
4020 CAAAGAAGATGG
1 CAAAGAAGATGG
*
4032 CAAAGAAAAT--
1 CAAAGAAGATGG
4042 CAAAGAAGATGG
1 CAAAGAAGATGG
4054 CAAAGA
1 CAAAGA
4060 CTACCCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.57, C:0.10, G:0.25, T:0.07
Consensus pattern (12 bp):
CAAAGAAGATGG
Found at i:4043 original size:22 final size:22
Alignment explanation
Indices: 4016--4059 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4006 AAGATTGAAG
4016 AAATCAAAGAAGATGGCAAAGA
1 AAATCAAAGAAGATGGCAAAGA
4038 AAATCAAAGAAGATGGCAAAGA
1 AAATCAAAGAAGATGGCAAAGA
4060 CTACCCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.23, T:0.09
Consensus pattern (22 bp):
AAATCAAAGAAGATGGCAAAGA
Found at i:4489 original size:22 final size:22
Alignment explanation
Indices: 4446--4489 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4436 GTATTACTTC
* *
4446 GATTGTATTACTATTTTATTTG
1 GATTGTATTAATATTCTATTTG
4468 GATTGTATTAGATATTCT-TTTG
1 GATTGTATTA-ATATTCTATTTG
4490 TAAGTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.57
Consensus pattern (22 bp):
GATTGTATTAATATTCTATTTG
Found at i:6681 original size:30 final size:30
Alignment explanation
Indices: 6333--6862 Score: 253
Period size: 29 Copynumber: 18.1 Consensus size: 30
6323 CCAATGAGGT
*
6333 CCCTAAACTTTCC-AAAATT-CTATTTTTAA
1 CCCTAAACTTTCCAAAAATTACCATTTTT-A
** * *
6362 CCCCGAATTTTCCAAAAAATA-C-TTGTTTA
1 CCCTAAACTTTCCAAAAATTACCATT-TTTA
* *
6391 CCCTCGAACTTTCC-AAAATT-CTATTTTTGAA
1 CCCT-AAACTTTCCAAAAATTACCATTTTT--A
* * *
6422 CCC-GAATTTTTCAAAAATTA-CATTTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
6450 TCCCTAAACTTTCC-AAAATT--CACTTTTTA
1 -CCCTAAACTTTCCAAAAATTACCA-TTTTTA
* * *
6479 ACCTCAAAATTTCCAAAAATTA-CAATTTTA
1 CCCT-AAACTTTCCAAAAATTACCATTTTTA
* *
6509 CCCCTGAACATTCC-AAAATT-CCATTTTTTA
1 -CCCTAAACTTTCCAAAAATTACCA-TTTTTA
* *
6539 CCCTAAATTTTACAAAAATTA-CATTTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
*
6568 CCCCTAAACTTTCC-AAAATT-TCATTTTTAA
1 -CCCTAAACTTTCCAAAAATTACCATTTTT-A
* *
6598 CCC-AAATTTTCCAAAACTTA-CATTTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
* *
6626 CCCTCGAACTTT--AAAAATT-CCATTTTGA
1 CCCT-AAACTTTCCAAAAATTACCATTTTTA
* *
6654 CTCTAAATTTTCCAAAAATTACCA-TTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
** * * *
6683 CCCCCGAAC-TCCCAAAAATT-TCATTATTGA
1 -CCCTAAACTTTCCAAAAATTACCATT-TTTA
* * *
6713 CCCCAAACATTCTAAAAATTACCA-TTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
** *
6742 TCCCCGAAC-TTCCAAAAATT-TCATTTTTGA
1 -CCCTAAACTTTCCAAAAATTACCATTTTT-A
** *
6772 -CCTTGATTTTCCAAAAATTACCA-TTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
** **
6800 CTCCCGAAC-TTCC-AAAATTTTCATTTTTA
1 C-CCTAAACTTTCCAAAAATTACCATTTTTA
* * *
6829 ACCTCGAACTTCCCAAAAATTACCA-TTTTA
1 CCCT-AAACTTTCCAAAAATTACCATTTTTA
6859 CCCT
1 CCCT
6863 CGAACTTCTA
Statistics
Matches: 382, Mismatches: 71, Indels: 95
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.01
28 52 0.14
29 179 0.47
30 127 0.33
31 19 0.05
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATTACCATTTTTA
Found at i:6870 original size:59 final size:57
Alignment explanation
Indices: 6342--6920 Score: 468
Period size: 59 Copynumber: 9.9 Consensus size: 57
6332 TCCCTAAACT
* * * *
6342 TTCCAAAA-TTCTATTTTTAACCCCGAATTTTCCAAAAAATA-CTTGTTTACCCTCGAAC
1 TTCCAAAATTTC-ATTTTTAACCTCAAATTTTCCAAAAATTACCAT-TTTACCC-CGAAC
* * **
6400 TTTCCAAAA-TTCTATTTTTGAACC-CGAATTTTTCAAAAATTA-CATTTTTATCCCTAAAC
1 -TTCCAAAATTTC-ATTTTT-AACCTCAAATTTTCCAAAAATTACCA-TTTTA-CCCCGAAC
* *
6459 TTTCCAAAA-TTCACTTTTTAACCTCAAAATTTCCAAAAATTACAATTTTACCCCTGAAC
1 -TTCCAAAATTTCA-TTTTTAACCTCAAATTTTCCAAAAATTACCATTTTACCCC-GAAC
* * * *
6518 ATTCCAAAATTCCATTTTTTACC-CTAAATTTTACAAAAATTA-CATTTTTACCCCTAAAC
1 -TTCCAAAATTTCATTTTTAACCTC-AAATTTTCCAAAAATTACCA-TTTTACCCC-GAAC
*
6577 TTTCCAAAATTTCATTTTTAACC-CAAATTTTCCAAAACTTA-CATTTTTACCCTCGAAC
1 -TTCCAAAATTTCATTTTTAACCTCAAATTTTCCAAAAATTACCA-TTTTACCC-CGAAC
** * *
6635 TTTAAAAATTCCA-TTTTGA-CTCTAAATTTTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAATTTCATTTTTAACCTC-AAATTTTCCAAAAATTACCATTTTA-CCCCGAAC
* * * * ** *
6692 TCCCAAAAATTTCATTATTGACCCCAAACATTCTAAAAATTACCATTTTATCCCCGAAC
1 TTCC-AAAATTTCATTTTTAACCTCAAATTTTCCAAAAATTACCATTTTA-CCCCGAAC
* **
6751 TTCCAAAAATTTCATTTTTGACCT-TGATTTTCCAAAAATTACCATTTTACTCCCGAAC
1 TTCC-AAAATTTCATTTTTAACCTCAAATTTTCCAAAAATTACCATTTTAC-CCCGAAC
* * *
6809 TTCCAAAATTTTCATTTTTAACCTCGAACTTCCCAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAA-TTTCATTTTTAACCTCAAATTTTCCAAAAATTACCATTTTACCC-CGAAC
* * * * *
6868 TTCTAAAGATTTCATTTTCT-ACCTCAAAGTGTCC-AAAATTACCGTTTTGCCCC
1 TTCCAAA-ATTTCATTTT-TAACCTCAAATTTTCCAAAAATTACCATTTTACCCC
6921 CGGGTATCCA
Statistics
Matches: 437, Mismatches: 59, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
55 1 0.00
56 6 0.01
57 43 0.10
58 115 0.26
59 256 0.59
60 16 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (57 bp):
TTCCAAAATTTCATTTTTAACCTCAAATTTTCCAAAAATTACCATTTTACCCCGAAC
Found at i:6906 original size:117 final size:118
Alignment explanation
Indices: 6332--6915 Score: 514
Period size: 117 Copynumber: 5.0 Consensus size: 118
6322 GCCAATGAGG
* * * * *
6332 TCCCTAAACTTTCCAAAA-TTCTATTTTTAACCCCGAATTTTCCAAAAAATA-CTTGTTTACCCT
1 TCCCTAAACTTTCCAAAATTTC-ATTTTTAACCTCAAACTTTCCAAAAATTACCAT-TTTACCC-
* * *
6395 CGAACTTTCC-AAAATTCTATTTTTGAACC-C-GAATTTTTCAAAAATTA-CATTTTTA-
63 CGAAC-TTCCAAAAATTCCATTTTT--ACCTCTAAATTTTCCAAAAATTACCA-TTTTAC
* *
6450 TCCCTAAACTTTCCAAAA-TTCACTTTTTAACCTCAAAATTTCCAAAAATTACAATTTTACCCCT
1 TCCCTAAACTTTCCAAAATTTCA-TTTTTAACCTCAAACTTTCCAAAAATTACCATTTTACCCC-
*
6514 GAACATTCC-AAAATTCCATTTTTTACC-CTAAATTTTACAAAAATTA-CATTTTTAC
64 GAAC-TTCCAAAAATTCCA-TTTTTACCTCTAAATTTTCCAAAAATTACCA-TTTTAC
* *
6569 -CCCTAAACTTTCCAAAATTTCATTTTTAACC-CAAATTTTCCAAAACTTA-CATTTTTACCCTC
1 TCCCTAAACTTTCCAAAATTTCATTTTTAACCTCAAACTTTCCAAAAATTACCA-TTTTACCC-C
* *
6631 GAACTT-TAAAAATTCCATTTTGA-CTCTAAATTTTCCAAAAATTACCATTTTAC
64 GAACTTCCAAAAATTCCATTTTTACCTCTAAATTTTCCAAAAATTACCATTTTAC
** * * * * * *
6684 -CCCCGAAC-TCCCAAAAATTTCATTATTGACCCCAAACATTCTAAAAATTACCATTTTATCCCC
1 TCCCTAAACTTTCC-AAAATTTCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTA-CCCC
* *
6747 GAACTTCCAAAAATTTCATTTTTGACCT-T-GATTTTCCAAAAATTACCATTTTAC
64 GAACTTCCAAAAATTCCATTTTT-ACCTCTAAATTTTCCAAAAATTACCATTTTAC
* * *
6801 TCCC-GAAC-TTCCAAAATTTTCATTTTTAACCTCGAACTTCCCAAAAATTACCATTTTACCCTC
1 TCCCTAAACTTTCCAAAA-TTTCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTACCC-C
* * * * * *
6864 GAACTTCTAAAGATTTCATTTTCTACCTC-AAAGTGTCC-AAAATTACCGTTTT
64 GAACTTCCAAAAATTCCATTTT-TACCTCTAAATTTTCCAAAAATTACCATTTT
6916 GCCCCCGGGT
Statistics
Matches: 398, Mismatches: 43, Indels: 51
0.81 0.09 0.10
Matches are distributed among these distances:
114 4 0.01
115 51 0.13
116 47 0.12
117 155 0.39
118 129 0.32
119 12 0.03
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (118 bp):
TCCCTAAACTTTCCAAAATTTCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTACCCCGA
ACTTCCAAAAATTCCATTTTTACCTCTAAATTTTCCAAAAATTACCATTTTAC
Found at i:11303 original size:17 final size:17
Alignment explanation
Indices: 11281--11323 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
11271 AAAACCCAAT
11281 AAAAAAAAGAGAAAAAG
1 AAAAAAAAGAGAAAAAG
*
11298 AAAAAAGAA-AGAAAAGG
1 AAAAAA-AAGAGAAAAAG
*
11315 AAGAAAAAG
1 AAAAAAAAG
11324 TTAAGATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAAG
Found at i:12186 original size:12 final size:12
Alignment explanation
Indices: 12149--12225 Score: 57
Period size: 13 Copynumber: 5.9 Consensus size: 12
12139 ATAAATAAAG
12149 AAAAAAGAAAAA
1 AAAAAAGAAAAA
12161 AGAAAAAGAAAAA
1 A-AAAAAGAAAAA
12174 AAAAAGAGGAAAAA
1 AAAAA-A-GAAAAA
* *
12188 CAAGAAGAAAATA
1 AAAAAAGAAAA-A
*
12201 AAATAAA-ATAAATG
1 AAA-AAAGA-AAA-A
12215 AAAAAAGAAAA
1 AAAAAAGAAAA
12226 GGAGAGGTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
12 10 0.19
13 24 0.45
14 19 0.36
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:12186 original size:26 final size:24
Alignment explanation
Indices: 12149--12203 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
12139 ATAAATAAAG
*
12149 AAAAAAGAAAAAAGAAAAAGAAAA
1 AAAAAAGAAAAAACAAAAAGAAAA
*
12173 AAAAAAGAGGAAAAACAAGAAGAAAA
1 AAAAAAGA--AAAAACAAAAAGAAAA
*
12199 TAAAA
1 AAAAA
12204 TAAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 8 0.31
26 18 0.69
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAAAACAAAAAGAAAA
Found at i:13277 original size:49 final size:48
Alignment explanation
Indices: 13156--14743 Score: 799
Period size: 49 Copynumber: 32.3 Consensus size: 48
13146 GAAAAAAATT
* * * * * *
13156 AAGATTTGAAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * * *
13206 AAGA-TGAGATGCGAAAGATTTAAGCCGTAATGGCGAATCTAGTACCACG
1 AAGATTGA-A-GGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * * * *
13255 AAGATTTGAAAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAA
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * *
13305 AAGCA-TAAAGAGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACG
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * *
13353 AAGATTTGAAGGGAAAGGTTTAAGTCACAACGACAAACCTTGTACCTCAG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
** * * *
13403 AAGCATACAA-GGAAAGATTTAAGCCGCAACGGCGAGTCCAGTACCACG
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * **
13451 AAGACATGAAGGGAAAGCTTTAAGTCGCAACGGCGAA-CTTGTACCTTG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * *
13499 AAAGA-TGAGATGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACG
1 -AAGATTGA-A-GGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * *
13549 AAGATTTGAAGGGAAAGATTTAAGTCGCAACGACGAACCTTA-TACCTCAG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATC-TAGTACCAC-G
** *
13599 AAGCA-CAAAGGGAAAGATTTAAGCCGCAAC-AGCGAATCCAGTACCACG
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGA-CGAATCTAGTACCACG
* * * * * * *
13647 AAGACATGAAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* *
13697 AAGCA-TGAAGGGAAAGATTTAAGCTGCAACGACGAATCCAGTACCACG
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * ** *
13745 AAGATTTAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTTTACCTCAG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* *
13795 AAGCA-TAAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACG
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * ** * * * * *
13843 AAGACATGAAGGAAAAGGCTTAAGTCGTAACGACGAACCTTGTACCTCAG
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
13893 AAGA-TGAGATGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
1 AAGATTGA-A-GGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * * *
13942 AAGATATGGAGGGAAAGGTTTGAGTCGCAACGGCGAACCTTGTGTCTCA-G
1 AAGAT-TGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGT-AC-CACG
* ** * ** *
13992 AAGCA-TGAAGGGAACGATTTAAATCGCAATGGTGAATCCAGTACCAC-
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * *
14039 AAGGATATAAAGGGAAATG-TTTAAGTCACAACGATGAACCTTA-TACCTCAG
1 AA-GAT-TGAAGGGAAA-GATTTAAGCCGCAACGACGAATC-TAGTACCAC-G
* * * * * *
14090 AAGCA-TAAAGGGAAAGAGTTAAGCCGCAATGGCGAATCCAGTACCACA
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * * * *
14138 AAGACATGAAGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAA
1 AAGA-TTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * *
14188 AAGA-TGAGATGGGAAATATTTAAGCCGCAATGACGAATCTAGTACCACA
1 AAGATTGA-A-GGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * *
14237 AAGATATGGAGGGAAGGACTTAAGTCGCAACGACGAACCTTGTACCTCAG
1 AAGAT-TGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * * * * *
14287 AAGCA-TGAAGGGAAGGACTTAAGTCGCAACGACGAACCTTGTACCTCAG
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * *
14336 AAGCA-TGAAGGGAAAGATTTAAGTCGCAACGACAAATCCAGTACCAC-
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * *
14383 AAGGATATAAAGGGAAATG-TTTAAGTCGTAACGGCAAACTTTA-TACCTCAG
1 AA-GAT-TGAAGGGAAA-GATTTAAGCCGCAACGACGAA-TCTAGTACCAC-G
* *
14434 AAGCA-TGAAGGGAAAGATTTAAGTCGTAACTG-CGAATCTAGTACCAC-
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAAC-GACGAATCTAGTACCACG
* * * * * * * * *
14481 AAGCATATAAAGGGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCAA
1 AAG-AT-TGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * * *
14532 AAGCA-TGAAGGGAAAGATTTAAGTCACAAC-AGTGAATCCAGTACCAC-
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGA-CGAATCTAGTACCACG
* * * * *
14579 AAGGATATGGAGGGAAAGATTTAAGCCGTAACGAGGAATCAAGTAGCACG
1 AA-GAT-TGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
* * * * * * * *
14629 AAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAG
1 AAGAT-TGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-G
* * * *
14679 AAGCA-TGAAGGGAAAGATTCAAGCCGTAAC-AGCGAATTTAGTACCACA
1 AAG-ATTGAAGGGAAAGATTTAAGCCGCAACGA-CGAATCTAGTACCACG
*
14727 AAGATATGGAGGGAAAG
1 AAGAT-TGAAGGGAAAG
14744 GTTACGACCG
Statistics
Matches: 1183, Mismatches: 266, Indels: 179
0.73 0.16 0.11
Matches are distributed among these distances:
47 26 0.02
48 57 0.05
49 910 0.77
50 159 0.13
51 31 0.03
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (48 bp):
AAGATTGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
Found at i:14765 original size:98 final size:98
Alignment explanation
Indices: 13156--14746 Score: 1576
Period size: 98 Copynumber: 16.2 Consensus size: 98
13146 GAAAAAAATT
* * *
13156 AAGATTTGAAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAG-ATGAGATGCGA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA-A-GGGA
* * *
13220 AAGATTTAAGCCGTAATGGCGAATCTAGTACCACG
64 AAGATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * * * * *
13255 AAGATTTGAAAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAGCATAAAGAGAAA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
*
13320 GATTTAAGCCGCAACGACGAATCCAGTACCACG
66 GATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * *
13353 AAGATTTGAAGGGAAAGGTTTAAGTCACAACGACAAACCTTGTACCTCAGAAGCAT-ACAAGGAA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA-AGGGAA
*
13417 AGATTTAAGCCGCAACGGCGAGTCCAGTACCACG
65 AGATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * *
13451 AAGACATGAAGGGAAAGCTTTAAGTCGCAACGGCGAA-CTTGTACCT-TGAAAG-ATGAGATGGG
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAG-AAGCATGA-A-GGG
*
13513 AAAGATTTAAGCTGCAACGGCGAATCCAGTACCACG
63 AAAGATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * **
13549 AAGATTTGAAGGGAAAGATTTAAGTCGCAACGACGAACCTTATACCTCAGAAGCACAAAGGGAAA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
*
13614 GATTTAAGCCGCAACAGCGAATCCAGTACCACG
66 GATTTAAGCCGCAACGGCGAATCCAGTACCACG
* *
13647 AAGACATGAAGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCTCAGAAGCATGAAGGGAAA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
* *
13712 GATTTAAGCTGCAACGACGAATCCAGTACCACG
66 GATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * * *
13745 AAGATTTAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTTTACCTCAGAAGCATAAAGGGAAA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
*
13810 GATTTAAGCCGCAACGACGAATCCAGTACCACG
66 GATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * *
13843 AAGACATGAAGGAAAAGGCTTAAGTCGTAACGACGAACCTTGTACCTCAGAAG-ATGAGATGGGA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA-A-GGGA
* *
13907 AAGATTTAAGCCGCAACGACGAATCTAGTACCACG
64 AAGATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * ** *
13942 AAGATATGGAGGGAAAGGTTTGAGTCGCAACGGCGAACCTTGTGTCTCAGAAGCATGAAGGGAAC
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
** * *
14007 GATTTAAATCGCAATGGTGAATCCAGTACCAC-
66 GATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * * * *
14039 AAGGATATAAAGGGAAATGTTTAAGTCACAACGATGAACCTTATACCTCAGAAGCATAAAGGGAA
1 AA-GATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAA
* * *
14104 AGAGTTAAGCCGCAATGGCGAATCCAGTACCACA
65 AGATTTAAGCCGCAACGGCGAATCCAGTACCACG
* * * *
14138 AAGACATGAAGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAG-ATGAGATGGGA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA-A-GGGA
* * * * *
14202 AATATTTAAGCCGCAATGACGAATCTAGTACCACA
64 AAGATTTAAGCCGCAACGGCGAATCCAGTACCACG
* *
14237 AAGATATGGAGGG-AAGGACTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAA
1 AAGATATGAAGGGAAAGG-TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAA
* * * * * *
14301 GGACTTAAGTCGCAACGACGAA-CCTTGTACCTCAG
65 AGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-G
* * * * * * * *
14336 AAG-CATGAAGGGAAAGATTTAAGTCGCAACGACAAATCC-AGTACCACA-AGGATATAAAGGGA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAA-CCTTGTACCTCAGAAG-CATGAAGGGA
* * * ** *
14398 AATG-TTTAAGTCGTAACGGCAAACTTTA-TACCTCAG
64 AA-GATTTAAGCCGCAACGGCGAA-TCCAGTACCAC-G
* * * * * * *
14434 AAG-CATGAAGGGAAAGATTTAAGTCGTAACTG-CGAATCTAGTA-C-CACAAGCATATAAAGGG
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAAC-GACGAACCTTGTACCTCAGAAGC--ATGAAGGG
* * * * *
14495 AAAGGTTTAAGTCGTAACGGCGAA-CCTTGTACCTC-
63 AAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACG
* * * * * * * * * *
14530 AAAAGCATGAAGGGAAAGATTTAAGTCACAAC-AGTGAATCC-AGTACCACA-AGGATATGGAGG
1 AAGA-TATGAAGGGAAAGGTTTAAGTCGCAACGA-CGAA-CCTTGTACCTCAGAAG-CATGAAGG
* * *
14592 GAAAGATTTAAGCCGTAACGAG-GAATCAAGTAGCACG
62 GAAAGATTTAAGCCGCAACG-GCGAATCCAGTACCACG
* * *
14629 AAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAA
1 AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
* * * ** *
14694 GATTCAAGCCGTAACAGCGAATTTAGTACCACA
66 GATTTAAGCCGCAACGGCGAATCCAGTACCACG
*
14727 AAGATATGGAGGGAAAGGTT
1 AAGATATGAAGGGAAAGGTT
14747 ACGACCGTAA
Statistics
Matches: 1254, Mismatches: 190, Indels: 97
0.81 0.12 0.06
Matches are distributed among these distances:
96 7 0.01
97 34 0.03
98 952 0.76
99 245 0.20
100 16 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
AAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAA
GATTTAAGCCGCAACGGCGAATCCAGTACCACG
Found at i:15034 original size:101 final size:101
Alignment explanation
Indices: 14859--15052 Score: 307
Period size: 101 Copynumber: 1.9 Consensus size: 101
14849 ATACAATGAC
* *
14859 AAGTCTTTATCTCTCTGATGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTC
1 AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCCTC
*
14924 TTAAAGTTGCAGTAAAGTTGGATTAAAAAAAATTAA
66 CTAAAGTTGCAGTAAAGTTGGATTAAAAAAAATTAA
* * * *
14960 AAGTCTTTGTCTCTTTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCGACATCAAATCCTATCTTC
1 AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCCTC
* *
15025 CTGAAGTTGCAGTGAAGTTGGATTAAAA
66 CTAAAGTTGCAGTAAAGTTGGATTAAAA
15053 TTCCAGCAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (101 bp):
AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCCTC
CTAAAGTTGCAGTAAAGTTGGATTAAAAAAAATTAA
Found at i:15309 original size:78 final size:78
Alignment explanation
Indices: 15119--15516 Score: 392
Period size: 78 Copynumber: 5.1 Consensus size: 78
15109 TTATCAATTG
* * * *
15119 ATCTCTTACCCCGAGCTTGGGGCA-AAT-CAGCCATTTGATCTTTTACCCCGAGCTTGGGGC-AA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAAA
15181 TCATCATCAACCA
66 TCATCATCAACCA
* * * *
15194 ATCTCTTACACCAAGCCTGGGGCAAATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAAA
*
15259 TCATCATCAATCA
66 TCATCATCAACCA
* * * * * *
15272 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGTCATTCGATCTCTTACCCCGAACCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAAA
***
15337 TCATCATCAGTAA
66 TCATCATCAACCA
* * * * *
15350 ATCTCTTACCCCCGAGCCTGGGGCAGATTGCAACCATTC-AGTCTCTTACCTCAAGCCTGAGGCA
1 ATCTCTTA-CCCCGAGCCTGGGGCAGATTGCAGCCATTCGA-TCTCTTACCCCGAGCTTGGGGCA
* * *
15414 GAT-AACTATCAGCCA
64 AATCATC-ATCAACCA
* * * * * * * * *
15429 ATCTCCTACCCTGAGCCTGGGGTAGATTGCAGTCATTCAATCTCTTACCTCGAGCTTGAGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAAA
* *
15494 TCATTATCAGCCA
66 TCATCATCAACCA
*
15507 AACTCTTACC
1 ATCTCTTACC
15517 TGATCATGGG
Statistics
Matches: 274, Mismatches: 41, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
75 21 0.08
76 2 0.01
77 32 0.12
78 156 0.57
79 63 0.23
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAAA
TCATCATCAACCA
Found at i:15494 original size:39 final size:38
Alignment explanation
Indices: 15119--15483 Score: 250
Period size: 39 Copynumber: 9.4 Consensus size: 38
15109 TTATCAATTG
* * * **
15119 ATCTCTTACCCCGAGCTTGGGGCA-AAT-CAGCCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACA-TCATTCA
* * * **
15156 ATCTTTTACCCCGAGCTTGGGGCA-ATCATCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTA-CATCATTCA
* * * * * *
15194 ATCTCTTACACCAAGCCTGGGGCAAATTGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACA-TCATTCA
* * * * *
15233 ATCTTTTACCCCGAGCTTGGGGCAAATCATCATCAATCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTA-CATCATTCA
* *
15272 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACA-TCATTCA
* * * *
15311 ATCTCTTACCCCGAACCTGGGGCAGATCATCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTA-CATCATTCA
* *
15350 ATCTCTTACCCCCGAGCCTGGGGCAGATTGCAACCATTCA
1 ATCTCTTA-CCCCGAGCCTGGGGCAGATTAC-ATCATTCA
* * * * * **
15390 GTCTCTTACCTCAAGCCTGAGGCAGATAACTATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTAC-ATCATTCA
* * * *
15429 ATCTCCTACCCTGAGCCTGGGGTAGATTGCAGTCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACA-TCATTCA
*
15468 ATCTCTTACCTCGAGC
1 ATCTCTTACCCCGAGC
15484 TTGAGGTAGA
Statistics
Matches: 250, Mismatches: 68, Indels: 18
0.74 0.20 0.05
Matches are distributed among these distances:
37 24 0.10
38 27 0.11
39 165 0.66
40 34 0.14
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTACATCATTCA
Found at i:15495 original size:157 final size:157
Alignment explanation
Indices: 15119--15516 Score: 405
Period size: 157 Copynumber: 2.6 Consensus size: 157
15109 TTATCAATTG
* * * * ** *
15119 ATCTCTTACCCCGAGCTTGGGGCA-AAT-CAGCCATTTGATCTTTTACCCCGAGCTTGGGGCA-A
1 ATCTCCTACCCCGAGCCTGGGGCAGATTACAGTCATTCAATCTCTTACCCCGAGCTTGGGGCAGA
* * * *
15181 TCATCATCAACCAATCTCTTA-CACCAAGCCTGGGGCAAATTGCAGCCATTCGATCTTTTACCCC
66 TCATCATCAGCAAATCTCTTACCACCAAGCCTGGGGCAAATTGCAACCATTCGATCTCTTACCCC
* * * * *
15245 GAGCTTGGGGCAAATCATCATCAATCA
131 AAGCCTGAGGCAAATAATCATCAACCA
* * * * *
15272 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGTCATTCGATCTCTTACCCCGAACCTGGGGCAGA
1 ATCTCCTACCCCGAGCCTGGGGCAGATTACAGTCATTCAATCTCTTACCCCGAGCTTGGGGCAGA
* * * * *
15337 TCATCATCAGTAAATCTCTTACCCCCGAGCCTGGGGCAGATTGCAACCATTC-AGTCTCTTACCT
66 TCATCATCAGCAAATCTCTTACCACCAAGCCTGGGGCAAATTGCAACCATTCGA-TCTCTTACCC
* *
15401 CAAGCCTGAGGCAGATAA-CTATCAGCCA
130 CAAGCCTGAGGCAAATAATC-ATCAACCA
* * * * * *
15429 ATCTCCTACCCTGAGCCTGGGGTAGATTGCAGTCATTCAATCTCTTACCTCGAGCTTGAGGTAGA
1 ATCTCCTACCCCGAGCCTGGGGCAGATTACAGTCATTCAATCTCTTACCCCGAGCTTGGGGCAGA
*
15494 TCATTATCAGCCAAA-CTCTTACC
66 TCATCATCAG-CAAATCTCTTACC
15517 TGATCATGGG
Statistics
Matches: 203, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
153 24 0.12
154 2 0.01
155 29 0.14
156 21 0.10
157 124 0.61
158 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (157 bp):
ATCTCCTACCCCGAGCCTGGGGCAGATTACAGTCATTCAATCTCTTACCCCGAGCTTGGGGCAGA
TCATCATCAGCAAATCTCTTACCACCAAGCCTGGGGCAAATTGCAACCATTCGATCTCTTACCCC
AAGCCTGAGGCAAATAATCATCAACCA
Found at i:16006 original size:12 final size:13
Alignment explanation
Indices: 15975--16009 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
15965 TTCAAAACCC
15975 AAATTTTAATTTTA
1 AAATTTT-ATTTTA
15989 AAATTTTATTTT-
1 AAATTTTATTTTA
16001 AAATTTTAT
1 AAATTTTAT
16010 GCCCATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 5 0.24
14 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATTTTATTTTA
Found at i:17956 original size:30 final size:29
Alignment explanation
Indices: 17542--18032 Score: 310
Period size: 29 Copynumber: 16.8 Consensus size: 29
17532 GAGGTCTCCG
* *
17542 AACTTTTC-AAAATTCCATTTTTAACCC-CG
1 AACTTTCCAAAAATTCCA-TTTT-ACCCTCA
* * **
17571 AATTTTCCAAAAATTACATTTTTACCCTTG
1 AACTTTCCAAAAATTCCA-TTTTACCCTCA
* **
17601 AACTTTCC-AAAATTCCATTTTTAACCTTG
1 AACTTTCCAAAAATTCCA-TTTTACCCTCA
* * * *
17630 AATTTTCCAAAAATTACATTTTTACCTTCG
1 AACTTTCCAAAAATTCCA-TTTTACCCTCA
* *
17660 AACTTTCC-AAAATTCAATTTTTGAACC-CA
1 AACTTTCCAAAAATTCCA-TTTT-ACCCTCA
* ** * *
17689 AATTTTCCAAAAATTACGTTTTTACCCCCG
1 AACTTTCCAAAAATT-CCATTTTACCCTCA
*
17719 AACTTTCC-AAAATTCCATTTCTTA-CCTCG
1 AACTTTCCAAAAATTCCA-TT-TTACCCTCA
* * * *
17748 AATTTTCCAAAAATTACATTTTTACCATCT
1 AACTTTCCAAAAATTCCA-TTTTACCCTCA
*
17778 GACTTTCC-AAAATTCCATTTTGACCC-CA
1 AACTTTCCAAAAATTCCATTTT-ACCCTCA
* * *
17806 AATTTTCCAAAAATTACATTTTACCCCCA
1 AACTTTCCAAAAATTCCATTTTACCCTCA
* * *
17835 AACTTT-CAAAAATTCTATTTTTAACATCA
1 AACTTTCCAAAAATTCCA-TTTTACCCTCA
*
17864 AATTTTCCAAAAATTACCATTTTACCCTCA
1 AACTTTCCAAAAATT-CCATTTTACCCTCA
*
17894 AAC-TCCCAAAAATTCCATTATTGACCCT-A
1 AACTTTCCAAAAATTCCATT-TT-ACCCTCA
* *
17923 AACTTTCTAAAAATTACCATTTTACCCTAA
1 AACTTTCCAAAAATT-CCATTTTACCCTCA
* * *
17953 AAC-TCCCAAAAATTCTATTTTTGACCC-CG
1 AACTTTCCAAAAATTCCA-TTTT-ACCCTCA
* *
17982 AACTTCCCAAAAATTACCATTTTACCCTCG
1 AACTTTCCAAAAATT-CCATTTTACCCTCA
* *
18012 AAC-TTCCAAAGATTCAATTTT
1 AACTTTCCAAAAATTCCATTTT
18033 TGACCTAGAA
Statistics
Matches: 373, Mismatches: 62, Indels: 55
0.76 0.13 0.11
Matches are distributed among these distances:
28 38 0.10
29 174 0.47
30 151 0.40
31 10 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTTCCAAAAATTCCATTTTACCCTCA
Found at i:18034 original size:59 final size:58
Alignment explanation
Indices: 17540--18037 Score: 513
Period size: 59 Copynumber: 8.5 Consensus size: 58
17530 ATGAGGTCTC
* * *
17540 CGAACTTTTCAAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACATTTTTACCCT
1 CGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTACA-TTTTACCCT
* * *** *
17599 TGAACTTTCCAAAATTCCATTTTTAACCTTGAATTTTCCAAAAATTACATTTTTACCTT
1 CGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTACA-TTTTACCCT
* * * *
17658 CGAACTTTCCAAAATTCAATTTTTGAACCCAAATTTTCCAAAAATTACGTTTTTACCCC
1 CGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTAC-ATTTTACCCT
* * *
17717 CGAACTTTCCAAAATTCCATTTCTT-ACCTCGAATTTTCCAAAAATTACATTTTTACCAT
1 CGAACTTTCCAAAATTCCATTT-TTGACCCCAAATTTTCCAAAAATTACA-TTTTACCCT
*
17776 CTG-ACTTTCCAAAATTCCA-TTTTGACCCCAAATTTTCCAAAAATTACATTTTACCCC
1 C-GAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTACATTTTACCCT
* * * * **
17833 CAAACTTTCAAAAATTCTATTTTTAACATCAAATTTTCCAAAAATTACCATTTTACCCT
1 CGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTA-CATTTTACCCT
* * * * * *
17892 CAAAC-TCCCAAAAATTCCATTATTGACCCTAAACTTTCTAAAAATTACCATTTTACCCT
1 CGAACTTTCC-AAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTA-CATTTTACCCT
** * * * * *
17951 AAAAC-TCCCAAAAATTCTATTTTTGACCCCGAACTTCCCAAAAATTACCATTTTACCCT
1 CGAACTTTCC-AAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTA-CATTTTACCCT
*
18010 CGAAC-TTCCAAAGATTCAATTTTTGACC
1 CGAACTTTCCAAA-ATTCCATTTTTGACC
18038 TAGAAGTGTC
Statistics
Matches: 375, Mismatches: 54, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
57 24 0.06
58 53 0.14
59 295 0.79
60 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
CGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTACATTTTACCCT
Found at i:28090 original size:23 final size:23
Alignment explanation
Indices: 28052--28109 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
28042 TCGTCATCCT
* * * *
28052 TGCTGACTAGACCTTCTGGAAGT
1 TGCTGACTGGATCTTCTAGAAGC
*
28075 TGTTGACTGGATCTTCTAGAAGC
1 TGCTGACTGGATCTTCTAGAAGC
28098 TGCTGACTGGAT
1 TGCTGACTGGAT
28110 GCCACGTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (23 bp):
TGCTGACTGGATCTTCTAGAAGC
Found at i:29921 original size:13 final size:12
Alignment explanation
Indices: 29900--29935 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
29890 ATTAATGATG
29900 AAAAATAAAATA
1 AAAAATAAAATA
29912 AAATAATAAAAATA
1 AAA-AAT-AAAATA
29926 AAAAATAAAA
1 AAAAATAAAA
29936 ACAATGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:29936 original size:13 final size:13
Alignment explanation
Indices: 29900--29936 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
29890 ATTAATGATG
29900 AAAAAT-AAAATA
1 AAAAATAAAAATA
29912 AAATAATAAAAATA
1 AAA-AATAAAAATA
29926 AAAAATAAAAA
1 AAAAATAAAAA
29937 CAATGGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:31175 original size:23 final size:23
Alignment explanation
Indices: 31147--31200 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
31137 CGTCCATCCT
* *
31147 TGCTGACTAGACCTTTTGGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
*
31170 TGCTGACTAGATCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
*
31193 TACTGACT
1 TGCTGACT
31201 GGATGTCACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:36976 original size:23 final size:23
Alignment explanation
Indices: 36931--36976 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
36921 CTGACTAGAC
* * **
36931 CTTCTGGAAGCTGTTGATTGGAT
1 CTTCTAGAAGCTGCTGACAGGAT
36954 CTTCTAGAAGCTGCTGACAGGAT
1 CTTCTAGAAGCTGCTGACAGGAT
36977 GCCACGTCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (23 bp):
CTTCTAGAAGCTGCTGACAGGAT
Found at i:38778 original size:5 final size:5
Alignment explanation
Indices: 38768--38815 Score: 71
Period size: 5 Copynumber: 9.4 Consensus size: 5
38758 TTAATGATGA
38768 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AATAA- AATAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAAT AA
38816 TAAAAACAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:38803 original size:8 final size:8
Alignment explanation
Indices: 38775--38820 Score: 69
Period size: 8 Copynumber: 5.9 Consensus size: 8
38765 TGAAAAATAA
38775 AATAAAAT
1 AATAAAAT
38783 AA-AATAA-
1 AATAA-AAT
38790 AATAAAAT
1 AATAAAAT
38798 AATAAAAT
1 AATAAAAT
38806 AATAAAAT
1 AATAAAAT
38814 AATAAAA
1 AATAAAA
38821 ACAATGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.17
8 29 0.83
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AATAAAAT
Found at i:43141 original size:96 final size:97
Alignment explanation
Indices: 42967--43142 Score: 232
Period size: 96 Copynumber: 1.8 Consensus size: 97
42957 TGGCACCTAT
* * * * * *
42967 TTGGATATTTGAACTTTTAAAATATATAAAAAATACCTTCAATCCTTTTAAAAAAAGCAATTAAG
1 TTGGATACTTGAACTTTTAAAATATATAAAAAAAACCTTCAAACCTTTAAAAAAAAACAAATAAG
*
43032 CCCTTATTATTATTATTATTTTTTGCACTCAA
66 CCCTGATTATTATTATTATTTTTTGCACTCAA
43064 TTGGATACTTGAAC-TTTAAAATGA-ATAAAAAAAACCTTCAAACC-TTAAAAAAAAACAAATAA
1 TTGGATACTTGAACTTTTAAAAT-ATATAAAAAAAACCTTCAAACCTTTAAAAAAAAACAAATAA
* *
43126 GCTCCTGCTTTTTATTA
65 GC-CCTGATTATTATTA
43143 AAAATTATAA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
95 17 0.25
96 37 0.54
97 14 0.21
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (97 bp):
TTGGATACTTGAACTTTTAAAATATATAAAAAAAACCTTCAAACCTTTAAAAAAAAACAAATAAG
CCCTGATTATTATTATTATTTTTTGCACTCAA
Found at i:43222 original size:21 final size:20
Alignment explanation
Indices: 43175--43222 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
43165 AATAAAAGCT
* **
43175 ATAAATATTATTAAATTTTA
1 ATAAAAATTATTAAAAATTA
43195 ATAAAAAATTATTAAAAATTA
1 AT-AAAAATTATTAAAAATTA
43216 GATAAAA
1 -ATAAAA
43223 TATAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAAATTATTAAAAATTA
Found at i:43265 original size:19 final size:18
Alignment explanation
Indices: 43243--43365 Score: 101
Period size: 19 Copynumber: 6.5 Consensus size: 18
43233 TGTAAGATTT
43243 TATAAAAAGTGTAAAAAAA
1 TATAAAAA-TGTAAAAAAA
43262 TAT-AAAA--TAAATAGAAA
1 TATAAAAATGTAAA-A-AAA
*
43279 TATAAAAATTATAAAAAAA
1 TATAAAAA-TGTAAAAAAA
43298 TAT-AAAATCGTAAAAAAA
1 TATAAAAAT-GTAAAAAAA
43316 TTATACAAAATGTAAAAAAA
1 -TATA-AAAATGTAAAAAAA
**
43336 TATAAATTTCGTAAAAAAA
1 TATAAAAAT-GTAAAAAAA
43355 TTTATAAAAAT
1 --TATAAAAAT
43366 TATTGCACCA
Statistics
Matches: 86, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
15 4 0.05
16 1 0.01
17 7 0.08
18 23 0.27
19 25 0.29
20 10 0.12
21 16 0.19
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (18 bp):
TATAAAAATGTAAAAAAA
Found at i:43267 original size:10 final size:10
Alignment explanation
Indices: 43254--43341 Score: 53
Period size: 10 Copynumber: 9.4 Consensus size: 10
43244 ATAAAAAGTG
43254 TAAAAAAATA
1 TAAAAAAATA
*
43264 TAAAATAA-A
1 TAAAAAAATA
*
43273 T--AGAAATA
1 TAAAAAAATA
*
43281 T-AAAAATTA
1 TAAAAAAATA
43290 TAAAAAAATA
1 TAAAAAAATA
***
43300 TAAAATCGTA
1 TAAAAAAATA
*
43310 -AAAAAATTA
1 TAAAAAAATA
* *
43319 T-ACAAAATG
1 TAAAAAAATA
43328 TAAAAAAATA
1 TAAAAAAATA
43338 TAAA
1 TAAA
43342 TTTCGTAAAA
Statistics
Matches: 56, Mismatches: 17, Indels: 10
0.67 0.20 0.12
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 20 0.36
10 31 0.55
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:43332 original size:38 final size:38
Alignment explanation
Indices: 43242--43364 Score: 139
Period size: 36 Copynumber: 3.2 Consensus size: 38
43232 TTGTAAGATT
43242 TTATAAAAAGTGTAAAAAAATATAAAA---TAAATAGAAA
1 TTATAAAAAGTGTAAAAAAATATAAAATCGTAAA-A-AAA
* *
43279 -TATAAAAATTATAAAAAAATATAAAATCGTAAAAAAA
1 TTATAAAAAGTGTAAAAAAATATAAAATCGTAAAAAAA
*
43316 TTATACAAAA-TGTAAAAAAATATAAATTTCGTAAAAAAA
1 TTATA-AAAAGTGTAAAAAAATATAAA-ATCGTAAAAAAA
43355 TTTATAAAAA
1 -TTATAAAAA
43365 TTATTGCACC
Statistics
Matches: 75, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
36 24 0.32
37 3 0.04
38 20 0.27
39 23 0.31
40 5 0.07
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (38 bp):
TTATAAAAAGTGTAAAAAAATATAAAATCGTAAAAAAA
Found at i:43577 original size:20 final size:20
Alignment explanation
Indices: 43540--43577 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43530 TAAAGGGATA
43540 TTTTTGATGCATTTTATAGT
1 TTTTTGATGCATTTTATAGT
*
43560 TTTTTTATG-ATTTCTATA
1 TTTTTGATGCATTT-TATA
43578 AAAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (20 bp):
TTTTTGATGCATTTTATAGT
Found at i:43630 original size:35 final size:36
Alignment explanation
Indices: 43560--43629 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 36
43550 ATTTTATAGT
43560 TTTTTTATGATTTCTATAAAAATTTACAATTTTTTA
1 TTTTTTATGATTTCTATAAAAATTTACAATTTTTTA
43596 TTTTTTATGATTT-TATAAAAAATTT-CGAATTTTT
1 TTTTTTATGATTTCTAT-AAAAATTTAC-AATTTTT
43630 AATAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (36 bp):
TTTTTTATGATTTCTATAAAAATTTACAATTTTTTA
Found at i:43661 original size:19 final size:19
Alignment explanation
Indices: 43639--43675 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43629 TAATAAATTT
43639 TAAAAATTTTAA-ATTTTTA
1 TAAAAA-TTTAATATTTTTA
43658 TAAAAATTTAATATTTTT
1 TAAAAATTTAATATTTTT
43676 TTTTCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAAAATTTAATATTTTTA
Found at i:43675 original size:27 final size:27
Alignment explanation
Indices: 43613--43668 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
43603 TGATTTTATA
** *
43613 AAAAATTTCGAATTTTTAATAAATTTT
1 AAAAATTTTAAATTTTTAATAAAATTT
43640 AAAAATTTTAAATTTTT-ATAAAAATTT
1 AAAAATTTTAAATTTTTAAT-AAAATTT
43667 AA
1 AA
43669 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAAATTTTAAATTTTTAATAAAATTT
Found at i:46871 original size:41 final size:41
Alignment explanation
Indices: 46801--46925 Score: 135
Period size: 41 Copynumber: 3.0 Consensus size: 41
46791 TACTTTTCCC
* * * *
46801 ACAAACGCCACTAAAAAATATGGTCTTTAGCGGCGCTTTTT
1 ACAAACGCCACTAAAGAACATGATATTTAGCGGCGCTTTTT
* * * *
46842 TCAAACGTCATTAAAGAACATGATATTTAGCGGCGCTTTTACC
1 ACAAACGCCACTAAAGAACATGATATTTAGCGGCGCTTTT--T
* *
46885 ACAAACGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTT
1 ACAAACGCCACTAAAGAACATGATATTTAGCGGCGCTTTTT
46925 A
1 A
46926 TTTTTTTCCC
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
40 1 0.01
41 33 0.49
42 4 0.06
43 30 0.44
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (41 bp):
ACAAACGCCACTAAAGAACATGATATTTAGCGGCGCTTTTT
Found at i:46925 original size:43 final size:43
Alignment explanation
Indices: 46760--46925 Score: 167
Period size: 43 Copynumber: 3.9 Consensus size: 43
46750 TTATGAGGAA
* * ** *
46760 AAACGCCGCTATAGAACAT-AGTCTTTAGCGGTACTTTTCCCAC
1 AAACGCCACTAAAGAACATGA-TCTTTAGCGGCGCTTTTACCAC
* * * **
46803 AAACGCCACTAAAAAATATGGTCTTTAGCGGCGCTTTT--TTC
1 AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTACCAC
* * *
46844 AAACGTCATTAAAGAACATGATATTTAGCGGCGCTTTTACCAC
1 AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTACCAC
* *
46887 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTA
1 AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTA
46926 TTTTTTTCCC
Statistics
Matches: 98, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 33 0.34
43 65 0.66
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (43 bp):
AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTACCAC
Found at i:47351 original size:66 final size:66
Alignment explanation
Indices: 47221--47352 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
47211 TTTGAAGCTA
* * * **
47221 TAGCTGCAGTTCGTCATACTTTTTTTGAGACCTTGCTTCCCTCGCTGCTGCCTTGGCTTCAAGTT
1 TAGCTGAAGTTCATCATACTTTTTTTAAGACCTTGCTTCCCTCGCTGCTGCCTCCGCTTCAAGTT
47286 G
66 G
* *
47287 TAGCTGAAGTTCATCATA-TTTTCTTTAAG-CCTTTGCTTCCCTCGCTGCTGTCTCCGCTTTAAG
1 TAGCTGAAGTTCATCATACTTTT-TTTAAGACC-TTGCTTCCCTCGCTGCTGCCTCCGCTTCAAG
47350 TTG
64 TTG
47353 AGAAATTTGC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 6 0.11
66 51 0.89
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.41
Consensus pattern (66 bp):
TAGCTGAAGTTCATCATACTTTTTTTAAGACCTTGCTTCCCTCGCTGCTGCCTCCGCTTCAAGTT
G
Found at i:49850 original size:86 final size:85
Alignment explanation
Indices: 49734--49920 Score: 241
Period size: 85 Copynumber: 2.2 Consensus size: 85
49724 ACTCGCTTTT
* *
49734 CCACAAACGCCACTAAAGAACATGTTCTTTAGCGGTGCTTATACCACAAACGCC-TCTAAAAAAC
1 CCACAAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTT-TACCACAAACGCCGT-TAAAAAAC
49798 ATGGTCTTTAGCAACACTTATC
64 ATGGTCTTTAGCAACACTTATC
* * * * * *
49820 CCACAAATGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCACAAGCGCCGTTAAAGAGCAT
1 CCACAAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTTACCACAAACGCCGTTAAAAAACAT
** * *
49885 GGTCTTTAGCGGCGCTTTTC
66 GGTCTTTAGCAACACTTATC
49905 CCACAAACGCCACTAA
1 CCACAAACGCCACTAA
49921 CATTAACAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 49 0.57
86 37 0.43
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (85 bp):
CCACAAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTTACCACAAACGCCGTTAAAAAACAT
GGTCTTTAGCAACACTTATC
Found at i:49879 original size:42 final size:42
Alignment explanation
Indices: 49692--49920 Score: 233
Period size: 43 Copynumber: 5.3 Consensus size: 42
49682 TTATGAGGAA
* **
49692 AAACGCCGCTATAGAACATGGTCTTTAACGACACTCGCTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTT-A-G-C-GGCGCTTTTCCAC
* * * *
49738 AAACGCCACTAAAGAACATGTTCTTTAGCGGTGCTTATACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TTCCAC
* * ** * *
49781 AAACGCCTCTAAAAAACATGGTCTTTAGCAACACTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TTCCAC
*
49824 AAATGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
* * *
49866 AAGCGCCGTTAAAGAGCATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTT-CCAC
*
49909 AAACGCCACTAA
1 AAACGCCGCTAA
49921 CATTAACAAA
Statistics
Matches: 152, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
42 43 0.28
43 84 0.55
44 1 0.01
45 1 0.01
46 23 0.15
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
Found at i:55327 original size:21 final size:21
Alignment explanation
Indices: 55301--55342 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55291 GCTTTTGGGA
55301 AAGCGTCGCTATTACTCTGAC
1 AAGCGTCGCTATTACTCTGAC
* *
55322 AAGCGTCGCTGTTGCTCTGAC
1 AAGCGTCGCTATTACTCTGAC
55343 CTCTAGCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (21 bp):
AAGCGTCGCTATTACTCTGAC
Found at i:55469 original size:41 final size:41
Alignment explanation
Indices: 55411--55685 Score: 248
Period size: 41 Copynumber: 6.7 Consensus size: 41
55401 GCAAACGCCA
* * * ** *
55411 CTATAGCTCTAATCTTTAGCGGTACTTGACCATAAGCACCG
1 CTATTGCTCTAACCTTTAGCAGCGCTTGCCCATAAGCACCG
* **
55452 CTATTGCTCTGACCTTTAGC-GACGCTTGCCCATAAGCGTCG
1 CTATTGCTCTAACCTTTAGCAG-CGCTTGCCCATAAGCACCG
* * ** * * *
55493 CTATTGCTTTGACCTTTAGC-GTCGCTTTTCAAAAAGCGCCG
1 CTATTGCTCTAACCTTTAGCAG-CGCTTGCCCATAAGCACCG
* * **
55534 CTATTGCTCTAACCTTTAGCAGCGCTTTCCTATAAGCATTG
1 CTATTGCTCTAACCTTTAGCAGCGCTTGCCCATAAGCACCG
* * * *
55575 CTATTGCTCCAACCTTTAGCAGCACTTTCCCATAAGCGCCG
1 CTATTGCTCTAACCTTTAGCAGCGCTTGCCCATAAGCACCG
* *
55616 CTACTGCTCTAACCTTTAGCAACGCTTGCCCATAAGCACCG
1 CTATTGCTCTAACCTTTAGCAGCGCTTGCCCATAAGCACCG
* * * *
55657 CTATTGCTCTGATCTTTAGCGGCGATTGC
1 CTATTGCTCTAACCTTTAGCAGCGCTTGC
55686 TTTGATCTTT
Statistics
Matches: 191, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 189 0.99
42 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (41 bp):
CTATTGCTCTAACCTTTAGCAGCGCTTGCCCATAAGCACCG
Found at i:55542 original size:82 final size:80
Alignment explanation
Indices: 55444--55677 Score: 279
Period size: 82 Copynumber: 2.9 Consensus size: 80
55434 ACTTGACCAT
* * * *
55444 AAGCACCGCTATTGCTCTGACCTTTAGCGACGCTTGCCCATAAGCGTCGCTATTGCTTTGACCTT
1 AAGCGCCGCTATTGCTCTAACCTTTAGC-ACGCTTGCCCATAAGCATCGCTATTGCTCTGACCTT
* *
55509 TAGCGTCGCTTTTCAAA
65 TAGCG-CACTTTCCAAA
* * * **
55526 AAGCGCCGCTATTGCTCTAACCTTTAGCAGCGCTTTCCTATAAGCATTGCTATTGCTCCAACCTT
1 AAGCGCCGCTATTGCTCTAACCTTTAGCA-CGCTTGCCCATAAGCATCGCTATTGCTCTGACCTT
* *
55591 TAGCAGCACTTTCCCAT
65 TAGC-GCACTTTCCAAA
* * *
55608 AAGCGCCGCTACTGCTCTAACCTTTAGCAACGCTTGCCCATAAGCACCGCTATTGCTCTGATCTT
1 AAGCGCCGCTATTGCTCTAACCTTTAGC-ACGCTTGCCCATAAGCATCGCTATTGCTCTGACCTT
55673 TAGCG
65 TAGCG
55678 GCGATTGCTT
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
81 2 0.02
82 124 0.97
83 2 0.02
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.30
Consensus pattern (80 bp):
AAGCGCCGCTATTGCTCTAACCTTTAGCACGCTTGCCCATAAGCATCGCTATTGCTCTGACCTTT
AGCGCACTTTCCAAA
Found at i:55590 original size:123 final size:123
Alignment explanation
Indices: 55442--55676 Score: 283
Period size: 123 Copynumber: 1.9 Consensus size: 123
55432 GTACTTGACC
** * * * * *
55442 ATAAGCACCGCTATTGCTCTGACCTTTAGC-GACGCTTGCCCATAAGCGTCGCTATTGCTTTGAC
1 ATAAGCACCGCTATTGCTCCAACCTTTAGCAG-CACTTGCCCATAAGCGCCGCTACTGCTCTAAC
** ** *
55506 CTTTAGCGTCGCTTTTCAAAAAGCGCCGCTATTGCTCTAACCTTTAGCAGCGCTTTCCT
65 CTTTAGCAACGCTTGCCAAAAAGCACCGCTATTGCTCTAACCTTTAGCAGCGCTTTCCT
** *
55565 ATAAGCATTGCTATTGCTCCAACCTTTAGCAGCACTTTCCCATAAGCGCCGCTACTGCTCTAACC
1 ATAAGCACCGCTATTGCTCCAACCTTTAGCAGCACTTGCCCATAAGCGCCGCTACTGCTCTAACC
* * * *
55630 TTTAGCAACGCTTGCCCATAAGCACCGCTATTGCTCTGATCTTTAGC
66 TTTAGCAACGCTTGCCAAAAAGCACCGCTATTGCTCTAACCTTTAGC
55677 GGCGATTGCT
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
123 91 0.99
124 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (123 bp):
ATAAGCACCGCTATTGCTCCAACCTTTAGCAGCACTTGCCCATAAGCGCCGCTACTGCTCTAACC
TTTAGCAACGCTTGCCAAAAAGCACCGCTATTGCTCTAACCTTTAGCAGCGCTTTCCT
Found at i:55691 original size:22 final size:22
Alignment explanation
Indices: 55659--55707 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
55649 AAGCACCGCT
55659 ATTGCTCTGATCTTTAGCGGCG
1 ATTGCTCTGATCTTTAGCGGCG
*
55681 ATTGCTTTGATCTTTAGCGGCG
1 ATTGCTCTGATCTTTAGCGGCG
*
55703 CTTGC
1 ATTGC
55708 CCATAAGCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (22 bp):
ATTGCTCTGATCTTTAGCGGCG
Found at i:55738 original size:41 final size:41
Alignment explanation
Indices: 55681--55783 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
55671 TTTAGCGGCG
* *
55681 ATTGCTTTGATCTTTAGCGGCGCTTGCCCATAAGCGCCACT
1 ATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCACT
* * *
55722 ATTGCTCTGACCTTTAGTGGCGCTTTCCCATAAGCGCCGCT
1 ATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCACT
*
55763 ATTGCTCT-ACCTTTTGCGGCG
1 ATTGCTCTGACCTTTAGCGGCG
55784 TTTATGTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 11 0.20
41 44 0.80
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (41 bp):
ATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCACT
Found at i:55762 original size:104 final size:103
Alignment explanation
Indices: 55588--55783 Score: 266
Period size: 104 Copynumber: 1.9 Consensus size: 103
55578 TTGCTCCAAC
* *
55588 CTTTAGCAGCACTTTCCCATAAGCGCCGCTACTGCTCTAACCTTTAGCAACGCTTGCCCATAAGC
1 CTTTAGCAGCACTTGCCCATAAGCGCCACTACTGCTCTAACCTTTAGCAACGCTTGCCCATAAGC
*
55653 ACCGCTATTGCTCTGATCTTTAGCGGCGATTGCTTTGAT
66 ACCGCTATTGCTCT-ACCTTTAGCGGCGATTGCTTTGAT
* * * * *** *
55692 CTTTAGCGGCGCTTGCCCATAAGCGCCACTATTGCTCTGACCTTTAGTGGCGCTTTCCCATAAGC
1 CTTTAGCAGCACTTGCCCATAAGCGCCACTACTGCTCTAACCTTTAGCAACGCTTGCCCATAAGC
* *
55757 GCCGCTATTGCTCTACCTTTTGCGGCG
66 ACCGCTATTGCTCTACCTTTAGCGGCG
55784 TTTATGTAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
103 11 0.14
104 68 0.86
ACGTcount: A:0.17, C:0.32, G:0.20, T:0.31
Consensus pattern (103 bp):
CTTTAGCAGCACTTGCCCATAAGCGCCACTACTGCTCTAACCTTTAGCAACGCTTGCCCATAAGC
ACCGCTATTGCTCTACCTTTAGCGGCGATTGCTTTGAT
Found at i:55800 original size:40 final size:40
Alignment explanation
Indices: 55756--55866 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
55746 TTCCCATAAG
55756 CGCCGCTATTGCTCTACCTTTTGCGGCGTTTATGTAAAAA
1 CGCCGCTATTGCTCTACCTTTTGCGGCGTTTATGTAAAAA
*
55796 CGCCGCTATTGCTCTACCCTTTT-CGACGTTTATGTAAAAA
1 CGCCGCTATTGCTCTA-CCTTTTGCGGCGTTTATGTAAAAA
* * * * *
55836 CGCCGCTACTGATTTATCTTTTGCGGTGTTT
1 CGCCGCTATTGCTCTACCTTTTGCGGCGTTT
55867 TCTATCCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.08
40 51 0.82
41 6 0.10
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (40 bp):
CGCCGCTATTGCTCTACCTTTTGCGGCGTTTATGTAAAAA
Found at i:59112 original size:16 final size:17
Alignment explanation
Indices: 59091--59136 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
59081 ATGAGGTTCG
*
59091 GGCGTGAAGAA-ATTCC
1 GGCGTGAAGAAGATTCA
59107 GGCGTGAAGAAGATTCA
1 GGCGTGAAGAAGATTCA
*
59124 AGCGTGAAGAAGA
1 GGCGTGAAGAAGA
59137 GAAGGGTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.37, C:0.13, G:0.35, T:0.15
Consensus pattern (17 bp):
GGCGTGAAGAAGATTCA
Found at i:60975 original size:42 final size:42
Alignment explanation
Indices: 60884--61123 Score: 213
Period size: 42 Copynumber: 5.8 Consensus size: 42
60874 GTTTATGGAA
* * * **
60884 AAACGCCGCTATTGCT-TAACCTTTAGCGTTGTTTTTCCCAT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTTCCCAT
* * * *
60925 AAATGCTGCTAATGCTCTTACGTTTTGCGGCGTTTTTCTCAT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTTCCCAT
* * *
60967 AAACGCTGCTAATGCTCTTACCTTTTACGGCGTTTTGT--CAA
1 AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTTT-TCCCAT
* * *
61008 AAAAGCCGCTAATGCTCTTACCTTTTGCGGTGTTTATCCCAT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTTCCCAT
* * * ***
61050 AAACGCCGCTATTGCT-TTACCTTTTGCAGCGTTTATGGGA-
1 AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTTCCCAT
* * *
61090 AAACGCGGCTATTGCT-TTACCTTTTACGGCGTTT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTT
61124 ATGAAAAACA
Statistics
Matches: 166, Mismatches: 29, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
40 32 0.19
41 65 0.39
42 68 0.41
43 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (42 bp):
AAACGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTTCCCAT
Found at i:61023 original size:83 final size:82
Alignment explanation
Indices: 60932--61125 Score: 230
Period size: 83 Copynumber: 2.4 Consensus size: 82
60922 CATAAATGCT
* * * * *
60932 GCTAATGCTCTTACGTTTTGCGGCGTTTTTCTCATAAACGCTGCTAATGCTCTTACCTTTTACGG
1 GCTAATGCTCTTACCTTTTGCGGCGTTTATCCCATAAACGCCGCTAATGCT-TTACCTTTTACAG
60997 CGTTTTGTCAAAAAAGCC
65 CGTTTTGTCAAAAAAGCC
* * *
61015 GCTAATGCTCTTACCTTTTGCGGTGTTTATCCCATAAACGCCGCTATTGCTTTACCTTTTGCAGC
1 GCTAATGCTCTTACCTTTTGCGGCGTTTATCCCATAAACGCCGCTAATGCTTTACCTTTTACAGC
** * *
61080 GTTTATG-GGAAAACGCG
66 GTTT-TGTCAAAAAAGCC
* *
61097 GCTATTGCT-TTACCTTTTACGGCGTTTAT
1 GCTAATGCTCTTACCTTTTGCGGCGTTTAT
61126 GAAAAACACT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.19
82 30 0.32
83 47 0.49
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (82 bp):
GCTAATGCTCTTACCTTTTGCGGCGTTTATCCCATAAACGCCGCTAATGCTTTACCTTTTACAGC
GTTTTGTCAAAAAAGCC
Found at i:61143 original size:39 final size:40
Alignment explanation
Indices: 60869--61162 Score: 205
Period size: 41 Copynumber: 7.2 Consensus size: 40
60859 AAATAAATTC
* * * *
60869 GCGGTGTTTATGGAAAAACGCCGCTATTGCTTAACCTTTA
1 GCGGCGTTTATCGAAAAACGCCGCTATTGCTTTACCTTTT
** * * * * * * *
60909 GCGTTGTTTTTCCCATAAATGCTGCTAATGCTCTTACGTTTT
1 GCGGCGTTTAT-CGAAAAACGCCGCTATTGCT-TTACCTTTT
* * * * *
60951 GCGGCGTTTTTCTCATAAACGCTGCTAATGCTCTTACCTTTT
1 GCGGCGTTTATC-GAAAAACGCCGCTATTGCT-TTACCTTTT
* * * *
60993 ACGGCGTTTTGTC-AAAAAAGCCGCTAATGCTCTTACCTTTT
1 GCGGCG-TTTATCGAAAAACGCCGCTATTGCT-TTACCTTTT
* * *
61034 GCGGTGTTTATCCCATAAACGCCGCTATTGCTTTACCTTTT
1 GCGGCGTTTAT-CGAAAAACGCCGCTATTGCTTTACCTTTT
* * * *
61075 GCAGCGTTTATGGGAAAACGCGGCTATTGCTTTACCTTTT
1 GCGGCGTTTATCGAAAAACGCCGCTATTGCTTTACCTTTT
* * * *
61115 ACGGCGTTTAT-GAAAAACACTGCTATTGCTTTACTTTTT
1 GCGGCGTTTATCGAAAAACGCCGCTATTGCTTTACCTTTT
*
61154 GCGACGTTT
1 GCGGCGTTT
61163 TCGGTCCAAA
Statistics
Matches: 207, Mismatches: 41, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
39 31 0.15
40 46 0.22
41 63 0.30
42 62 0.30
43 5 0.02
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (40 bp):
GCGGCGTTTATCGAAAAACGCCGCTATTGCTTTACCTTTT
Found at i:62473 original size:13 final size:14
Alignment explanation
Indices: 62446--62475 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
62436 AATTATGTAA
62446 AAAAATTAAAGTAT
1 AAAAATTAAAGTAT
62460 AAAAATTAAA-TAT
1 AAAAATTAAAGTAT
62473 AAA
1 AAA
62476 TTAAAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AAAAATTAAAGTAT
Found at i:64046 original size:12 final size:12
Alignment explanation
Indices: 64029--64066 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
64019 AATGTGATAA
64029 AATTTAATCTAT
1 AATTTAATCTAT
*
64041 AATTTAATATA-
1 AATTTAATCTAT
*
64052 AATTTAAGCTAT
1 AATTTAATCTAT
64064 AAT
1 AAT
64067 AGTATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (12 bp):
AATTTAATCTAT
Done.