Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011013.1 Kokia drynarioides strain JFW-HI SEQ_125983, 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: 39094
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:234 original size:31 final size:32
Alignment explanation
Indices: 198--264 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
188 CAGTTTGATC
* *
198 ATTGAACTATTC-GAAAGTTTTTATTTAAGTT
1 ATTGAACTATTCAAAAAGTTGTTATTTAAGTT
229 ATTGAACTATTCAAAAAGTTGTTATTTAAGTT
1 ATTGAACTATTCAAAAAGTTGTTATTTAAGTT
261 ATTG
1 ATTG
265 GGTTGTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (32 bp):
ATTGAACTATTCAAAAAGTTGTTATTTAAGTT
Found at i:2086 original size:31 final size:31
Alignment explanation
Indices: 2051--2110 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2041 TAATTCGGTC
* *
2051 ATTGAAGTATTCAAAAGTTTTTATTTAAATT
1 ATTGAACTATTCAAAAGCTTTTATTTAAATT
2082 ATTGAACTATTCAAAAGCTTTTATTTAAA
1 ATTGAACTATTCAAAAGCTTTTATTTAAA
2111 CATTGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGCTTTTATTTAAATT
Found at i:2206 original size:17 final size:17
Alignment explanation
Indices: 2184--2223 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2174 AATAATAAAA
*
2184 AATTTAAATTAAATTTT
1 AATTTAAATTAAAATTT
*
2201 AATTTAATTTAAAATTT
1 AATTTAAATTAAAATTT
*
2218 CATTTA
1 AATTTA
2224 CACCCAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAAATTAAAATTT
Found at i:3727 original size:30 final size:29
Alignment explanation
Indices: 3648--3936 Score: 280
Period size: 30 Copynumber: 9.8 Consensus size: 29
3638 AGAGGTCCCT
* * * *
3648 AAACTTTTCTAAAATTATATTTTGACTCC
1 AAACTTTTCCAAAATTACATTTTAACCCC
* *
3677 AAACATTTCTC-AAATCACATTTTAACCCC
1 AAACTTTTC-CAAAATTACATTTTAACCCC
* *
3706 AAACTTTTTCTAAAATTACATTTTATCCCC
1 AAAC-TTTTCCAAAATTACATTTTAACCCC
*
3736 TAAACTTTTCCAAAATTACATTTTAACCCTT
1 -AAACTTTTCCAAAATTACATTTTAACCC-C
3767 AAACTTTTCCAAAATTACATTTTAACCCC
1 AAACTTTTCCAAAATTACATTTTAACCCC
*
3796 TAAACTTTTCC-AAATTACATTTTAACTCCT
1 -AAACTTTTCCAAAATTACATTTTAAC-CCC
* *
3826 AAAC-TTTCCAAGATTACATTTTGA-CCC
1 AAACTTTTCCAAAATTACATTTTAACCCC
** *
3853 ATAAAATTTCCAAAATTACATTTTGACCCCC
1 A-AACTTTTCCAAAATTACATTTT-AACCCC
* *
3884 AAACTTTTCCAAAATCACATTTTGACCCTC
1 AAACTTTTCCAAAATTACATTTTAACCC-C
* * * *
3914 GAGCTTTTCTAAAATTTCATTTT
1 AAACTTTTCCAAAATTACATTTT
3937 CATCTCGAGT
Statistics
Matches: 215, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
27 3 0.01
28 7 0.03
29 77 0.36
30 120 0.56
31 8 0.04
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
AAACTTTTCCAAAATTACATTTTAACCCC
Found at i:3911 original size:59 final size:59
Alignment explanation
Indices: 3648--3911 Score: 288
Period size: 59 Copynumber: 4.5 Consensus size: 59
3638 AGAGGTCCCT
* * *
3648 AAACTTTTCTAAAATTATATTTTGACTCC--AAACATTTCTCAAATCACATTTTAA-CCCC
1 AAACTTTTCCAAAATTACATTTTGAC-CCATAAACATTTC-CAAATTACATTTTAACCCCC
* * * **
3706 AAACTTTTTCTAAAATTACATTTT-ATCCCCTAAACTTTTCCAAAATTACATTTTAACCCTT
1 AAAC-TTTTCCAAAATTACATTTTGA-CCCATAAACATTTCC-AAATTACATTTTAACCCCC
* * * * *
3767 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAATTACATTTTAACTCCT
1 AAACTTTTCCAAAATTACATTTTGACCCATAAACATTTCCAAATTACATTTTAACCCCC
* *
3826 AAAC-TTTCCAAGATTACATTTTGACCCATAAA-ATTTCCAAAATTACATTTTGACCCCC
1 AAACTTTTCCAAAATTACATTTTGACCCATAAACATTTCC-AAATTACATTTTAACCCCC
*
3884 AAACTTTTCCAAAATCACATTTTGACCC
1 AAACTTTTCCAAAATTACATTTTGACCC
3912 TCGAGCTTTT
Statistics
Matches: 180, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
57 5 0.03
58 52 0.29
59 62 0.34
60 54 0.30
61 7 0.04
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (59 bp):
AAACTTTTCCAAAATTACATTTTGACCCATAAACATTTCCAAATTACATTTTAACCCCC
Found at i:4957 original size:29 final size:29
Alignment explanation
Indices: 4837--4950 Score: 219
Period size: 29 Copynumber: 3.9 Consensus size: 29
4827 TAAATTGATA
*
4837 TATGATCCTTCGCATTTTCTATGAAATAT
1 TATGATCCTTTGCATTTTCTATGAAATAT
4866 TATGATCCTTTGCATTTTCTATGAAATAT
1 TATGATCCTTTGCATTTTCTATGAAATAT
4895 TATGATCCTTTGCATTTTCTATGAAATAT
1 TATGATCCTTTGCATTTTCTATGAAATAT
4924 TATGATCCTTTGCATTTTCTATGAAAT
1 TATGATCCTTTGCATTTTCTATGAAAT
4951 GGCATGACAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (29 bp):
TATGATCCTTTGCATTTTCTATGAAATAT
Found at i:8263 original size:50 final size:51
Alignment explanation
Indices: 8161--8267 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 51
8151 AGAAGAAATG
*
8161 AAAGAAAGAAAAGGTCAAGATGAAAACATGCAAAGGGCATCTTTTTTAAAAAAA
1 AAAGAAAGAAAAGGTCAAGATGAAAACACGCAAAGGGCATC---TTTAAAAAAA
*
8215 AAAGAAAGAAAAGGTCAAGATGAAAACCCGCAAAGGGCATC-TTAAAAAAA
1 AAAGAAAGAAAAGGTCAAGATGAAAACACGCAAAGGGCATCTTTAAAAAAA
8265 AAA
1 AAA
8268 TTTGTTTCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 12 0.24
54 39 0.76
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.14
Consensus pattern (51 bp):
AAAGAAAGAAAAGGTCAAGATGAAAACACGCAAAGGGCATCTTTAAAAAAA
Found at i:10271 original size:49 final size:49
Alignment explanation
Indices: 10153--10579 Score: 300
Period size: 49 Copynumber: 8.7 Consensus size: 49
10143 ATTACCATGG
* * * * * *
10153 AGCATAAAGGGAAAGATTTAA-ACAGCAACGACGAATCTAGTACCAC-GA
1 AGCATGAAGGGAAAGATTTAAGTC-GCAACGGCGAACCTTGTACCTCAGA
* * * * * *
10201 GGACATGGA-GGAAAAAGTTTAAGTCGCAATGGTGAACCTTGTACCTTAGA
1 AG-CATGAAGGGAAAGA-TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * * * *
10251 AGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTAGCACA-A
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * *
10299 AGATATGAAGGGAAAGATTTAAGTCACAACAGCGAACCTTGTACCTTAGA
1 AG-CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * **
10349 AGCACGAAGGGAAAGATTTAAGCCGCAACGGGGAATCC-AATA-C-CAGGA
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GA
* * *
10397 AGATATTG-AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
1 AG-CA-TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * * *
10447 AG-ATGAGATGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCAC-GA
1 AGCATGA-A-GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * *
10496 AGATATGGAGGGAAATG-TTTAAGTCGCAACGGCGAACCTTGTACCTCAAA
1 AG-CATGAAGGGAAA-GATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * *
10546 AACATGAAGGGAAAGACTAAAGTCGCAACGGCGA
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGA
10580 GTTCGGTACC
Statistics
Matches: 289, Mismatches: 68, Indels: 43
0.72 0.17 0.11
Matches are distributed among these distances:
47 3 0.01
48 19 0.07
49 206 0.71
50 56 0.19
51 5 0.02
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (49 bp):
AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
Found at i:10322 original size:98 final size:98
Alignment explanation
Indices: 10153--10576 Score: 503
Period size: 98 Copynumber: 4.3 Consensus size: 98
10143 ATTACCATGG
* * * ** * * *
10153 AGCATAAAGGGAAAGATTTAAACAGCAACGACGAATCTAGTACCACGAGGACATGGA-GGAAAAA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGA
* * *
10217 GTTTAAGTCGCAATGGTGAACCTTGTACCTTAGA
66 -TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * *
10251 AGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTAGCACAAAGATATGAAGGGAAAGA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGA
* * *
10316 TTTAAGTCACAACAGCGAACCTTGTACCTTAGA
66 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * * * * *
10349 AGCACGAAGGGAAAGATTTAAGCCGCAACGGGGAATCCAATACCAGGAAGATATTGAGGGAAAGG
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGA
*
10414 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
66 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* *
10447 AG-ATGAGATGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAA
1 AGCATGA-A-GGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAA
*
10511 TG-TTTAAGTCGCAACGGCGAACCTTGTACCTCAAA
64 -GATTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * *
10546 AACATGAAGGGAAAGACTAAAGTCGCAACGG
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGG
10577 CGAGTTCGGT
Statistics
Matches: 278, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
97 3 0.01
98 183 0.66
99 87 0.31
100 5 0.02
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (98 bp):
AGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGA
TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
Found at i:10510 original size:197 final size:196
Alignment explanation
Indices: 10159--10612 Score: 563
Period size: 197 Copynumber: 2.3 Consensus size: 196
10149 ATGGAGCATA
* * * * * * * * *
10159 AAGGGAAAGATTTAAACAGCAACGACGAATCTAGTACCACGAGGACATGGAGGAAAAAGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGAGGGAAAGGTTTAAG
* *
10224 TCGCAATGGTGAACCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
66 TCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
* * * *
10289 AGTAGCACAAAGATATGAAGGGAAA-GATTTAAGTCACAACAGCGAACCTTGTACCTTAGAAGCA
131 AGTACCACAAAGATATGAAGGGAAATG-TTTAAGTCACAACAGCGAACCTTGTACCTCAAAAACA
10353 CG
195 CG
* * *
10355 AAGGGAAAGATTTAAGCCGCAACGGGGAATCCAATACCAGGAAGATATTGAGGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGAGGGAAAGGTTTAAG
* *
10420 TCGCAATGGCGAACCTTGTACCTCAGAAG-ATGAGATGGGAAAGATTTAAGTCGTAACGGTGAAT
66 TCGCAATGGCGAACCTTGTACCTCAGAAGCATGA-A-GGGAAAGATTTAAGCCGCAACGGTGAAT
* * * *
10484 CTAGTACCACGAAGATATGGAGGGAAATGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAC
129 CTAGTACCACAAAGATATGAAGGGAAATGTTTAAGTCACAACAGCGAACCTTGTACCTCAAAAAC
*
10549 ATG
194 ACG
* * * * * * *
10552 AAGGGAAAGACTAAAGTCGCAACGGCGAGTTCGGTACCATGAAGAT-TTGAAGGGAAAGGTT
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTG-AGGGAAAGGTT
10613 ACGACCGCGT
Statistics
Matches: 220, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
195 4 0.02
196 84 0.38
197 131 0.60
198 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.19
Consensus pattern (196 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGAGGGAAAGGTTTAAG
TCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
AGTACCACAAAGATATGAAGGGAAATGTTTAAGTCACAACAGCGAACCTTGTACCTCAAAAACAC
G
Found at i:10628 original size:49 final size:49
Alignment explanation
Indices: 10573--10736 Score: 175
Period size: 49 Copynumber: 3.3 Consensus size: 49
10563 TAAAGTCGCA
* *
10573 ACGGCGAGTTCGGTACCATGAAGATTTGAAGGGAAAGGTTACGACCGCG
1 ACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAAGGTTACGACCGCG
** * * * * *
10622 TTGGCGAACCCGATACCATGAAGATTTGAAGGGAAAGTTTATGACCACG
1 ACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAAGGTTACGACCGCG
* * ** *
10671 ACGACGAATCCGGTACCATGAAGATTTAAATAGAAAGGTTACGATCGCG
1 ACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAAGGTTACGACCGCG
* * *
10720 ACAGCGAACCCAGTACC
1 ACGGCGAATCCGGTACC
10737 TTAGAAACAT
Statistics
Matches: 90, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
49 90 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (49 bp):
ACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAAGGTTACGACCGCG
Found at i:10942 original size:102 final size:102
Alignment explanation
Indices: 10817--11024 Score: 326
Period size: 102 Copynumber: 2.0 Consensus size: 102
10807 TCAAAACTAC
*
10817 AATAAGAAGTCTTTATCTATCTGAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCT
1 AATAACAAGTCTTTATCTATCTGAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCT
* *
10882 ATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAAA
66 ATCCTCCTAAAGTTGCAGTAAAGTTGGATTAAAAAAA
* * *
10919 AATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTCT
1 AATAACAAGTCTTTATCTATCTGAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCT
* * * *
10984 ATCTTCCTAAAGTTGCAGTGAAGTTGGATTAGAAACA
66 ATCCTCCTAAAGTTGCAGTAAAGTTGGATTAAAAAAA
11021 AATA
1 AATA
11025 GCAAATCTCG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (102 bp):
AATAACAAGTCTTTATCTATCTGAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCT
ATCCTCCTAAAGTTGCAGTAAAGTTGGATTAAAAAAA
Found at i:10987 original size:51 final size:51
Alignment explanation
Indices: 10830--11002 Score: 136
Period size: 51 Copynumber: 3.4 Consensus size: 51
10820 AAGAAGTCTT
* * *
10830 TATCTATCTGAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGC
1 TATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
*** * ***** *** * *
10881 TATC-CTCTTGAAGTTGCAGTAA-AGTTGGATTAAAAAAAAATAACAAGTCTT
1 TATCTCTC-TGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT-TC
10932 TATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
1 TATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
*
10983 TATCT-TCCTAAAGTTGCAGT
1 TATCTCT-CTGAAGTTGCAGT
11003 GAAGTTGGAT
Statistics
Matches: 85, Mismatches: 32, Indels: 10
0.67 0.25 0.08
Matches are distributed among these distances:
50 16 0.19
51 53 0.62
52 16 0.19
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (51 bp):
TATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
Found at i:11047 original size:102 final size:102
Alignment explanation
Indices: 10839--11047 Score: 283
Period size: 102 Copynumber: 2.0 Consensus size: 102
10829 TTATCTATCT
* *
10839 GAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCTATCCTCTTGAAGTTGCAGTAAA
1 GAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCTATCCTCCTAAAGTTGCAGTAAA
* ** * *
10904 GTTGGATTAAAAAAAAATAACAAGTCTTTATCTCTCT
66 GTTGGATTAAAAAAAAATAACAAATCTCGATCTCCCC
* * * *
10941 GAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTCTATCTTCCTAAAGTTGCAGTGAA
1 GAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCTATCCTCCTAAAGTTGCAGTAAA
* * * *
11006 GTTGGATTAGAAACAAATAGCAAATCTCGATTTCCCC
66 GTTGGATTAAAAAAAAATAACAAATCTCGATCTCCCC
11043 GAAGT
1 GAAGT
11048 CACAGTGGAA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (102 bp):
GAAGTTGCAATAAGAGCAAGATGAAGCTTCAACGTCAAATGCTATCCTCCTAAAGTTGCAGTAAA
GTTGGATTAAAAAAAAATAACAAATCTCGATCTCCCC
Found at i:12771 original size:30 final size:30
Alignment explanation
Indices: 12728--13055 Score: 364
Period size: 30 Copynumber: 11.0 Consensus size: 30
12718 CAAGAGGTCT
* * *
12728 CTAAACTTCTCTAAAATTATATTTTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
* * * * *
12758 CTAAACCTTTCTAAAATCATATATTAA-CC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
* *
12787 CTCAAACTTTTCTAAAATTACATTTTAACAC
1 CT-AAACTTTTCCAAAATTACATTTTAACCC
* *
12818 TTAAACTTTTCTAAAATTACATTTTAA-CC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
12847 CTAAACTTTTCCAAAATTACATTTTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
* *
12877 TTAAAC-TTTCCAAAATTACAATTTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
* * *
12906 CTAAAATTTTCCAAGATTATATTTTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
*
12936 CTAAACTTTTCCAAAATTACATATTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCC
* *
12966 CTAAACTTTT-CAAAATTACATTTTGACCTA
1 CTAAACTTTTCCAAAATTACATTTTAACC-C
*
12996 C-AAACTTTTCCAAAATTACATTTTGACTCC
1 CTAAACTTTTCCAAAATTACATTTTAAC-CC
* *
13026 C-AAAATTTTCC-AAATTCACATTTTGACCC
1 CTAAACTTTTCCAAAATT-ACATTTTAACCC
13055 C
1 C
13056 CGAGCTCTTC
Statistics
Matches: 261, Mismatches: 29, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
29 88 0.34
30 170 0.65
31 3 0.01
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.38
Consensus pattern (30 bp):
CTAAACTTTTCCAAAATTACATTTTAACCC
Found at i:12880 original size:59 final size:59
Alignment explanation
Indices: 12728--13054 Score: 356
Period size: 59 Copynumber: 5.5 Consensus size: 59
12718 CAAGAGGTCT
* * * * * * * * *
12728 CTAAACTTCTCTAAAATTATATTTTAACCCCTAAACCTTTCTAAAATCATATATTAACC
1 CTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACC
* * *
12787 CTCAAACTTTTCTAAAATTACATTTTAACACTTAAACTTTTCTAAAATTACATTTTAACC
1 CT-AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACC
*
12847 CTAAACTTTTCCAAAATTACATTTTAACCCTTAAAC-TTTCCAAAATTACAATTTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAA-CC
* * * * *
12906 CTAAAATTTTCCAAGATTATATTTTAACCCCTAAACTTTTCCAAAATTACATATTAACCC
1 CTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAA-CC
* * *
12966 CTAAACTTTT-CAAAATTACATTTTGA-CCTACAAACTTTTCCAAAATTACATTTTGACTC
1 CTAAACTTTTCCAAAATTACATTTTAACCCT-TAAACTTTTCCAAAATTACATTTTAAC-C
* * *
13025 CCAAAATTTTCC-AAATTCACATTTTGACCC
1 CTAAACTTTTCCAAAATT-ACATTTTAACCC
13055 CCGAGCTCTT
Statistics
Matches: 232, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
58 21 0.09
59 118 0.51
60 91 0.39
61 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.38
Consensus pattern (59 bp):
CTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACC
Found at i:12884 original size:89 final size:88
Alignment explanation
Indices: 12729--13039 Score: 374
Period size: 89 Copynumber: 3.5 Consensus size: 88
12719 AAGAGGTCTC
* * * * * * * *
12729 TAAACTTCTCTAAAATTATATTTTAACCCCTAAACCTTTCTAAAATCATATATTAACCCTCAAAC
1 TAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATATTAACCCTTAAAC
12794 TTTTCTAAAATTACATTTTAACACT
66 TTTTC-AAAATTACATTTTAAC-CT
* *
12819 TAAACTTTTCTAAAATTACATTTTAA-CCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAAC
1 TAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATATTAACCCTTAAAC
* * *
12883 TTTCCAAAATTACAATTTAACCCC
66 TTTTCAAAATTACATTTTAA-CCT
* * * *
12907 TAAAATTTTCCAAGATTATATTTTAACCCCTAAACTTTTCCAAAATTACATATTAACCCCTAAAC
1 TAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATATTAACCCTTAAAC
*
12972 TTTTCAAAATTACATTTTGACCT
66 TTTTCAAAATTACATTTTAACCT
* * *
12995 ACAAACTTTTCCAAAATTACATTTTGACTCCC-AAAATTTTCCAAA
1 -TAAACTTTTCCAAAATTACATTTTAAC-CCCTAAACTTTTCCAAA
13040 TTCACATTTT
Statistics
Matches: 190, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
88 39 0.21
89 124 0.65
90 27 0.14
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.38
Consensus pattern (88 bp):
TAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATATTAACCCTTAAAC
TTTTCAAAATTACATTTTAACCT
Found at i:15297 original size:23 final size:25
Alignment explanation
Indices: 15261--15307 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
15251 TAGTTGAATC
*
15261 AAATCTAAACTCTAAAAGATAATTA
1 AAATCTAAACTCTAAAAAATAATTA
15286 AAAT-TAAA-TCTAAAAAATAATT
1 AAATCTAAACTCTAAAAAATAATT
15308 CCCTAGTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (25 bp):
AAATCTAAACTCTAAAAAATAATTA
Found at i:15781 original size:32 final size:32
Alignment explanation
Indices: 15732--15796 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
15722 CCGTTCGAGT
*
15732 ACAAAACTCAAAACATCCCCGCCCCACGACCC
1 ACAAAACTCAAAACATCCCCGCCCCACCACCC
*
15764 ACAAGACT-AAAACCATCCCCGCCCCACCACCC
1 ACAAAACTCAAAA-CATCCCCGCCCCACCACCC
15796 A
1 A
15797 TGTGGGTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.37, C:0.51, G:0.06, T:0.06
Consensus pattern (32 bp):
ACAAAACTCAAAACATCCCCGCCCCACCACCC
Found at i:20556 original size:19 final size:19
Alignment explanation
Indices: 20532--20577 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
20522 TTTTATCAAC
*
20532 TTTTTTGAAATTTTTTGAT
1 TTTTTTAAAATTTTTTGAT
20551 TTTTTTAAAATTTTTTGAT
1 TTTTTTAAAATTTTTTGAT
20570 TTTTTTAA
1 TTTTTTAA
20578 TTTTTATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTTTAAAATTTTTTGAT
Found at i:20575 original size:10 final size:10
Alignment explanation
Indices: 20507--20568 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
20497 ACATATGGAT
*
20507 AAATTTTTTA
1 AAATTTTTTG
*
20517 AAAGTTTTTATC
1 AAA-TTTTT-TG
*
20529 AACTTTTTTG
1 AAATTTTTTG
20539 AAATTTTTTG
1 AAATTTTTTG
* *
20549 -ATTTTTTTA
1 AAATTTTTTG
20558 AAATTTTTTG
1 AAATTTTTTG
20568 A
1 A
20569 TTTTTTTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
9 7 0.17
10 21 0.51
11 10 0.24
12 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (10 bp):
AAATTTTTTG
Found at i:20589 original size:10 final size:9
Alignment explanation
Indices: 20532--20589 Score: 55
Period size: 10 Copynumber: 6.2 Consensus size: 9
20522 TTTTATCAAC
20532 TTTTTTGAAA
1 TTTTTTG-AA
*
20542 TTTTTTGAT
1 TTTTTTGAA
*
20551 TTTTTTAAAA
1 TTTTTT-GAA
20561 TTTTTTG-A
1 TTTTTTGAA
*
20569 TTTTTTTAA
1 TTTTTTGAA
20578 TTTTTATGAA
1 TTTTT-TGAA
20588 TT
1 TT
20590 ACACATGGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.18
9 13 0.33
10 19 0.49
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:21078 original size:13 final size:13
Alignment explanation
Indices: 21060--21084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21050 ATTAACCCAT
21060 AATATGTTTTAAA
1 AATATGTTTTAAA
21073 AATATGTTTTAA
1 AATATGTTTTAA
21085 TAGTGGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATATGTTTTAAA
Found at i:21173 original size:10 final size:11
Alignment explanation
Indices: 21148--21176 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
21138 AGCTTTTAAT
21148 TTTAAATTAGG
1 TTTAAATTAGG
21159 TTTAAATTA-G
1 TTTAAATTAGG
21169 TTTAAATT
1 TTTAAATT
21177 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (11 bp):
TTTAAATTAGG
Found at i:21219 original size:23 final size:22
Alignment explanation
Indices: 21159--21228 Score: 95
Period size: 23 Copynumber: 3.1 Consensus size: 22
21149 TTAAATTAGG
*
21159 TTTAAATTAGTTTAAATTTAAA
1 TTTAAATTTGTTTAAATTTAAA
*
21181 TTTAAATTTATCTTAAATTTAAA
1 TTTAAATTTGT-TTAAATTTAAA
*
21204 TTTAAATTTGCTTTAAATTTGAA
1 TTTAAATTTG-TTTAAATTTAAA
21227 TT
1 TT
21229 GATTTAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 9 0.21
23 32 0.76
24 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTAAATTTGTTTAAATTTAAA
Found at i:21228 original size:6 final size:6
Alignment explanation
Indices: 21169--21212 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
21159 TTTAAATTAG
21169 TTTAAA TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTT
21213 GCTTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
6 29 0.83
7 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:23115 original size:29 final size:30
Alignment explanation
Indices: 23077--23177 Score: 120
Period size: 30 Copynumber: 3.4 Consensus size: 30
23067 TAAGGTCCCT
* *
23077 AAACTATCCAAAAATTACATTTAT-CCCCC
1 AAACTTTCCAAAAATTACATTTTTACCCCC
23106 AAACTTTCC-AAAATT-CAATTTTTGA-CCCC
1 AAACTTTCCAAAAATTAC-ATTTTT-ACCCCC
* *
23135 AAACTTTTCAAAAATTACATTTTTACCCCT
1 AAACTTTCCAAAAATTACATTTTTACCCCC
23165 AAACTTTCCAAAA
1 AAACTTTCCAAAA
23178 TTCTATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
27 1 0.02
28 11 0.18
29 21 0.34
30 27 0.44
31 1 0.02
ACGTcount: A:0.40, C:0.27, G:0.01, T:0.33
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTTACCCCC
Found at i:23157 original size:30 final size:29
Alignment explanation
Indices: 23085--23421 Score: 121
Period size: 29 Copynumber: 11.6 Consensus size: 29
23075 CTAAACTATC
* *
23085 CAAAAATTACATTTATCCCCCAAAC-TTT
1 CAAAAATTACATTTTTACCCCAAACTTTT
*
23113 CCAAAATT-CAATTTTTGACCCCAAACTTTT
1 CAAAAATTAC-ATTTTT-ACCCCAAACTTTT
23143 CAAAAATTACATTTTTACCCCTAAAC-TTT
1 CAAAAATTACATTTTTACCCC-AAACTTTT
* * * *
23172 CCAAAATT-CTATTTTTAACCTC-GATTTTT
1 CAAAAATTAC-ATTTTT-ACCCCAAACTTTT
23201 CCAAAAA-TACCA-TTTTACCGCCAAA-TTTT
1 -CAAAAATTA-CATTTTTACC-CCAAACTTTT
* * * ** *
23230 CTATAATTCCATTTTTGA-CCCTGATTTTT
1 CAAAAATTACATTTTT-ACCCCAAACTTTT
* * *
23259 CCAAAAATCACCA-TTTTACCGTCAAAC-TTC
1 -CAAAAATTA-CATTTTTACC-CCAAACTTTT
* * * * **
23289 CTAAAATTCCATTTTTTACCTCGATTTTTT
1 CAAAAATTACA-TTTTTACCCCAAACTTTT
* *
23319 CAAAAAATATCA-TTTTACTCCCGAAC-TTT
1 CAAAAATTA-CATTTTTAC-CCCAAACTTTT
* * ** * * *
23348 CAAATATTCCATTTTTACGTCGATCTTAT
1 CAAAAATTACATTTTTACCCCAAACTTTT
23377 CAAAAATTACCA-TTTTACCCTCAAA-TTTT
1 CAAAAATTA-CATTTTTACCC-CAAACTTTT
23406 CAAAAATT-CTATTTTT
1 CAAAAATTAC-ATTTTT
23422 GACCTAGATT
Statistics
Matches: 225, Mismatches: 52, Indels: 63
0.66 0.15 0.19
Matches are distributed among these distances:
27 2 0.01
28 35 0.16
29 113 0.50
30 67 0.30
31 8 0.04
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCCAAACTTTT
Found at i:23178 original size:29 final size:29
Alignment explanation
Indices: 23073--23188 Score: 114
Period size: 29 Copynumber: 4.0 Consensus size: 29
23063 TCCCTAAGGT
* *
23073 CCCTAAACTATCCAAAAATT-ACATTTAT-C
1 CCCTAAACTTTCC-AAAATTCA-ATTTTTAC
*
23102 CCCCAAACTTTCCAAAATTCAATTTTTGAC
1 CCCTAAACTTTCCAAAATTCAATTTTT-AC
*
23132 CCC-AAACTTTTCAAAAATT-ACATTTTTAC
1 CCCTAAAC-TTTCCAAAATTCA-ATTTTTAC
*
23161 CCCTAAACTTTCCAAAATTCTATTTTTA
1 CCCTAAACTTTCCAAAATTCAATTTTTA
23189 ACCTCGATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
28 11 0.15
29 39 0.53
30 24 0.32
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTCAATTTTTAC
Found at i:23201 original size:58 final size:59
Alignment explanation
Indices: 23083--23514 Score: 365
Period size: 58 Copynumber: 7.4 Consensus size: 59
23073 CCCTAAACTA
* * * * *
23083 TCCAAAAATTA-CA-TTTATCCCCCAAACTTTCCAAAATTCAATTTTTGACCCCAAACTTT
1 TCCAAAAATTACCATTTTA-CCCCTAAACTTTCCAAAATTCCATTTTTGACCTC-GATTTT
* *
23142 T-CAAAAATTA-CATTTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCTCGATTTT
1 TCCAAAAATTACCA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTT
* * *
23200 TCCAAAAA-TACCATTTTACCGCC-AAATTTTCTATAATTCCATTTTTGACC-CTGATTTT
1 TCCAAAAATTACCATTTTACC-CCTAAACTTTCCAAAATTCCATTTTTGACCTC-GATTTT
* * *
23258 TCCAAAAATCACCATTTTA-CCGTCAAAC-TTCCTAAAATTCCATTTTTTACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCCT-AAACTTTCC-AAAATTCCATTTTTGACCTCGATTTT
* * * * * *
23317 TTCAAAAAATATCATTTTACTCCC-GAACTTT-CAAATATTCCATTTTT-ACGTCGATCTTA
1 TCCAAAAATTACCATTTTAC-CCCTAAACTTTCCAAA-ATTCCATTTTTGACCTCGAT-TTT
* * * *
23376 T-CAAAAATTACCATTTTA-CCCTCAAATTTTCAAAAATTCTATTTTTGACCTAGATTTT
1 TCCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTGACCTCGATTTT
* * * * **
23434 TCCAAAAATTACCATTTTACTCCC-GAA-TGTCTAAAATTCCATTTTTGATCTCGAACTT
1 TCCAAAAATTACCATTTTAC-CCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTT
* *
23492 TCCCAAAATTACCATTTTTCCCC
1 TCCAAAAATTACCATTTTACCCC
23515 CCGAGCGAAC
Statistics
Matches: 306, Mismatches: 44, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
56 3 0.01
57 5 0.02
58 150 0.49
59 136 0.44
60 7 0.02
61 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTT
Found at i:23530 original size:117 final size:116
Alignment explanation
Indices: 23107--23509 Score: 406
Period size: 117 Copynumber: 3.4 Consensus size: 116
23097 TTATCCCCCA
* * * * * *
23107 AACTTTCCAAAATTCAATTTTTGACCCCAAACTTTTCAAAAATTA-CATTTTTACCC-CTAAACT
1 AACTTTCTAAAATTCCATTTTTGA-CTCGATCTTTCCAAAAATTACCA-TTTTACCCTC-AAACT
* * *
23170 TTCCAAAATTCTATTTTTAACCTCGATTTTTCCAAAAATACCATTTTAC-CGCCA
63 TACAAAAATTCTATTTTTAACCTCGATTTTTCCAAAAATACCATTTTACTC-CCG
* * * * * * *
23224 AATTTTCTATAATTCCATTTTTGACCCTGATTTTTCCAAAAATCACCATTTTACCGTCAAACTTC
1 AACTTTCTAAAATTCCATTTTTGACTC-GATCTTTCCAAAAATTACCATTTTACCCTCAAACTTA
* * * * *
23289 CTAAAATTCCATTTTTTACCTCGATTTTTTCAAAAAATATCATTTTACTCCCG
65 CAAAAATTCTATTTTTAACCTCGA-TTTTTCCAAAAATACCATTTTACTCCCG
*
23342 AACTTTC-AAATATTCCATTTTT-ACGTCGATCTTAT-CAAAAATTACCATTTTACCCTCAAATT
1 AACTTTCTAAA-ATTCCATTTTTGAC-TCGATCTT-TCCAAAAATTACCATTTTACCCTCAAACT
* * *
23404 TTCAAAAATTCTATTTTTGACCTAGATTTTTCCAAAAATTACCATTTTACTCCCG
63 TACAAAAATTCTATTTTTAACCTCGATTTTTCCAAAAA-TACCATTTTACTCCCG
* * *
23459 AA-TGTCTAAAATTCCATTTTTGATCTCGAACTTTCCCAAAATTACCATTTT
1 AACTTTCTAAAATTCCATTTTTGA-CTCGATCTTTCCAAAAATTACCATTTT
23510 TCCCCCCGAG
Statistics
Matches: 239, Mismatches: 34, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
116 29 0.12
117 163 0.68
118 46 0.19
119 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (116 bp):
AACTTTCTAAAATTCCATTTTTGACTCGATCTTTCCAAAAATTACCATTTTACCCTCAAACTTAC
AAAAATTCTATTTTTAACCTCGATTTTTCCAAAAATACCATTTTACTCCCG
Found at i:33498 original size:48 final size:48
Alignment explanation
Indices: 33309--33674 Score: 246
Period size: 49 Copynumber: 7.5 Consensus size: 48
33299 CAAGTCTCAA
* * **
33309 TACCAC-GAAACATGAAGGGAAAGATTTAAGTCGCAACGATGAATCCAG
1 TACCACAGAGACATGAAGGG-AAGATTTAAGCCGCAACGGCGAATCCAG
* * * *
33357 TACCA-AGAAGATATGGAGGGAA-ATGTTTAAAGTCGCAACGGCGAA-CCGTG
1 TACCACAG-AGACATGAAGGGAAGA--TTT-AAGCCGCAACGGCGAATCC-AG
* * *
33407 TACCTCAGA-AGCATGAAGAGAAAGATTTAGGCCGCAACGGCGAATCCAG
1 TACCACAGAGA-CATGAAG-GGAAGATTTAAGCCGCAACGGCGAATCCAG
* **
33456 TAGCACAGAGACATGAAGGGAAGATTTAAGCCGCAATAGCGAATCCAG
1 TACCACAGAGACATGAAGGGAAGATTTAAGCCGCAACGGCGAATCCAG
* * * * * *
33504 TACCACAAAGACACGAAAGGAAGGGTTTAAGTCGCAACGGCGAA-CCTTG
1 TACCACAGAGACATGAAGGGAA-GATTTAAGCCGCAACGGCGAATCC-AG
* * *
33553 TACCTCAGAGACATGAAGGGAAAGATTTAAGCCGCAACGGTGGATCCAG
1 TACCACAGAGACATGAAGGG-AAGATTTAAGCCGCAACGGCGAATCCAG
* * * * * * *
33602 TACCGCAAAGATACA-AAAGGGAAAGGTTTAAGTCTCAACGACGAA-CCTAG
1 TA-C-CACAGAGACATGAAGGG-AAGATTTAAGCCGCAACGGCGAATCC-AG
*
33652 TA-CATCAAAGACATGAAGGGAAG
1 TACCA-CAGAGACATGAAGGGAAG
33675 GATATCCAGT
Statistics
Matches: 246, Mismatches: 51, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
47 3 0.01
48 62 0.25
49 105 0.43
50 63 0.26
51 12 0.05
52 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (48 bp):
TACCACAGAGACATGAAGGGAAGATTTAAGCCGCAACGGCGAATCCAG
Found at i:33600 original size:146 final size:148
Alignment explanation
Indices: 33318--33603 Score: 384
Period size: 146 Copynumber: 1.9 Consensus size: 148
33308 ATACCACGAA
* * * * * * * *
33318 ACATGAAGGGAAAGATTTAAGTCGCAACGATGAATCCAGTACCAAGAAGATATGGAGGGAAATGT
1 ACATGAAGGGAAAGATTTAAGCCGCAAAGACGAATCCAGTACCAAGAAGACACGAAAGGAAAGGT
*
33383 TTAAAGTCGCAACGGCGAACCGTGTACCTCAGAAGCATGAAGAGAAAGATTTAGGCCGCAACGGC
66 TTAAAGTCGCAACGGCGAACCGTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGCCGCAACGGC
33448 GAATCCAGTAGCACAGAG
131 GAATCCAGTAGCACAGAG
*
33466 ACATGAAGGG-AAGATTTAAGCCGCAATAG-CGAATCCAGTACCACA-AAGACACGAAAGGAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAA-AGACGAATCCAGTACCA-AGAAGACACGAAAGGAAAG
* *
33528 GTTT-AAGTCGCAACGGCGAACCTTGTACCTCAG-AGACATGAAGGGAAAGATTTAAGCCGCAAC
64 GTTTAAAGTCGCAACGGCGAACCGTGTACCTCAGAAG-CATGAAGAGAAAGATTTAAGCCGCAAC
* *
33591 GGTGGATCCAGTA
128 GGCGAATCCAGTA
33604 CCGCAAAGAT
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
145 2 0.02
146 64 0.53
147 43 0.36
148 12 0.10
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.16
Consensus pattern (148 bp):
ACATGAAGGGAAAGATTTAAGCCGCAAAGACGAATCCAGTACCAAGAAGACACGAAAGGAAAGGT
TTAAAGTCGCAACGGCGAACCGTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGCCGCAACGGC
GAATCCAGTAGCACAGAG
Found at i:34285 original size:16 final size:16
Alignment explanation
Indices: 34249--34286 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
34239 ATTTTATCTT
*
34249 TTTAAATTTGAATTTA
1 TTTAAATTTGAATTGA
*
34265 ATTAAATTTGAATTGA
1 TTTAAATTTGAATTGA
34281 TTTAAA
1 TTTAAA
34287 ACTTAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
TTTAAATTTGAATTGA
Found at i:35054 original size:25 final size:25
Alignment explanation
Indices: 35026--35073 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
35016 TTGAAAAGTC
35026 TTAATAAATAAATAAATAATAATTA
1 TTAATAAATAAATAAATAATAATTA
*
35051 TTAATTAATAAATAAATAATAAT
1 TTAATAAATAAATAAATAATAAT
35074 AATCGAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAATAAATAAATAAATAATAATTA
Found at i:36437 original size:30 final size:28
Alignment explanation
Indices: 36072--36556 Score: 162
Period size: 29 Copynumber: 16.5 Consensus size: 28
36062 CTAAACTATC
* *
36072 CAAAAATTACA-TTTTATCCACCAAACTTT
1 CAAAAATTCCATTTTTA-CC-CCGAACTTT
* *
36101 CCAAAATTCCATTTTTGACCCCAAACTTTT
1 CAAAAATTCCATTTTT-ACCCCGAAC-TTT
* *
36131 TAAAAATTACATTTTTACCCCCGAACTTT
1 CAAAAATTCCATTTTTA-CCCCGAACTTT
* * * *
36160 CCAAAATTCCATTTTGA-CCCTAATTTT
1 CAAAAATTCCATTTTTACCCCGAACTTT
* * *
36187 CCAAAAATTAC-TATTTTACCCCCAAACTTC
1 -CAAAAATTCCAT-TTTTA-CCCCGAACTTT
*** **
36217 CAAAAATTCCATTTTTCACCTTTATTTTTT
1 CAAAAATTCCATTTTT-ACCCCGA-ACTTT
*
36247 CAAAAA-T-CATCATTTTACCCCCGAACTTC
1 CAAAAATTCCAT--TTTTA-CCCCGAACTTT
* * **
36276 CTAAAATTCCATTTTTGACCCTGATTTTT
1 CAAAAATTCCATTTTT-ACCCCGAACTTT
* ** *
36305 CCAAAAATCACCA-TTTTACCCTTTAACTTC
1 -CAAAAAT-TCCATTTTTACCC-CGAACTTT
* * **
36335 CTAAAATTCCATTTTTGACCTCGATTTTT
1 CAAAAATTCCATTTTT-ACCCCGAACTTT
* * *
36364 CCAAAAAAT-CACTATTTTACCACTGAACTTC
1 -CAAAAATTCCA-T-TTTTACC-CCGAACTTT
** *
36395 CAAAAGGTCCATTTTTGACCCCGATCTTT
1 CAAAAATTCCATTTTT-ACCCCGAACTTT
* ** *
36424 CTAAAATTACCA-TTTTACCCTTAAACTTC
1 CAAAAATT-CCATTTTTACCC-CGAACTTT
**
36453 CAAAAATTCCATTTTTTACCCCGATTTTT
1 CAAAAATTCCA-TTTTTACCCCGAACTTT
* *
36482 CCAAAAATTACCA-TTTTACCCTCGGA-TGT
1 -CAAAAATT-CCATTTTTACCC-CGAACTTT
* * * *
36511 CTAAAATTCTATTTTTGATCCCAAACTTT
1 CAAAAATTCCATTTTT-ACCCCGAACTTT
*
36540 CCCAAAATTACCATTTT
1 -CAAAAATT-CCATTTT
36557 GCCCCCCAAG
Statistics
Matches: 330, Mismatches: 86, Indels: 78
0.67 0.17 0.16
Matches are distributed among these distances:
27 11 0.03
28 38 0.12
29 135 0.41
30 120 0.36
31 26 0.08
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.38
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCCGAACTTT
Found at i:36517 original size:58 final size:59
Alignment explanation
Indices: 36070--36556 Score: 435
Period size: 59 Copynumber: 8.3 Consensus size: 59
36060 CCCTAAACTA
* *
36070 TCCAAAAATTA-CATTTTATCCAC-CAAACTTTCC-AAAATTCCATTTTTGACCCCAAACTTTT
1 TCCAAAAATTACCATTTTA-CC-CTCGAAC-TTCCTAAAATTCCATTTTTGACCCC-GA-TTTT
* * *
36131 T--AAAAATTA-CATTTTTACCCCCGAACTTTCC-AAAATTCCA-TTTTGA-CCCTAATTT
1 TCCAAAAATTACCA-TTTTACCCTCGAAC-TTCCTAAAATTCCATTTTTGACCCCGATTTT
* * * * * ***
36186 TCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATTCCATTTTTCACCTTTATTTT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTT
* * * * *
36245 TTCAAAAATCATCATTTTACCCCCGAACTTCCTAAAATTCCATTTTTGACCCTGATTTT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTT
* ** *
36304 TCCAAAAATCACCATTTTACCCTTTAACTTCCTAAAATTCCATTTTTGACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTT
* * * *
36363 TCCAAAAAATCACTATTTTACCACT-GAACTTCC-AAAAGGTCCATTTTTGACCCCGATCTT
1 TCC-AAAAATTACCATTTTACC-CTCGAACTTCCTAAAA-TTCCATTTTTGACCCCGATTTT
* ** * *
36423 T-CTAAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTTACCCCGATTTT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTT
* * * * **
36481 TCCAAAAATTACCATTTTACCCTCGGA-TGT-CTAAAATTCTATTTTTGATCCCAAACTT
1 TCCAAAAATTACCATTTTACCCTCGAACT-TCCTAAAATTCCATTTTTGACCCCGATTTT
*
36539 TCCCAAAATTACCATTTT
1 TCCAAAAATTACCATTTT
36557 GCCCCCCAAG
Statistics
Matches: 362, Mismatches: 49, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
55 4 0.01
56 5 0.01
57 35 0.10
58 94 0.26
59 172 0.48
60 49 0.14
61 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTT
Found at i:36575 original size:118 final size:116
Alignment explanation
Indices: 36065--36562 Score: 481
Period size: 118 Copynumber: 4.2 Consensus size: 116
36055 AAGGTCCCTA
* * *
36065 AACTATCCAAAAATTA-CATTTTATCCACCAAACTTTCC-AAAATTCCATTTTTGACCCCAAACT
1 AACTTTCCAAAAATTACCATTTTA-CCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCC-GA-T
* *
36128 TTTT--AAAAATTA-CATTTTTACCCCCGAACTTTCCAAAATTCCA-TTTTGACCCT
62 TTTTCCAAAAATCACCA-TTTTACCCCCGAAC-TTCCAAAATTCCATTTTTGACCCG
* * * ***
36181 AATTTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATTCCATTTTTCACCTTTATTTTT
1 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTT
* *
36246 TCAAAAATCATCATTTTACCCCCGAACTTCCTAAAATTCCATTTTTGACCCTG
66 CCAAAAATCACCATTTTACCCCCGAACTTCC-AAAATTCCATTTTTGACCC-G
** * *** * *
36299 ATTTTTCCAAAAATCACCATTTTACCCTTTAACTTCCTAAAATTCCATTTTTGACCTCGATTTTT
1 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTT
* * * *
36364 CCAAAAAATCACTATTTTACCACTGAACTTCCAAAAGGTCCATTTTTGACCCCG
66 CC-AAAAATCACCATTTTACCCCCGAACTTCCAAAA-TTCCATTTTTGA-CCCG
* * ** *
36418 ATCTTT-CTAAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTTACCCCGATTTTT
1 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTT
* * * * * *
36482 CCAAAAATTACCATTTTACCCTCGGA-TGTCTAAAATTCTATTTTTGATCCCA
66 CCAAAAATCACCATTTTACCCCCGAACT-TCCAAAATTCCATTTTTGA-CCCG
* *
36534 AACTTTCCCAAAATTACCATTTTGCCCCC
1 AACTTTCCAAAAATTACCATTTTACCCCC
36563 CAAGCGACCA
Statistics
Matches: 320, Mismatches: 49, Indels: 25
0.81 0.12 0.06
Matches are distributed among these distances:
114 5 0.02
115 9 0.03
116 88 0.28
117 59 0.18
118 114 0.36
119 42 0.13
120 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (116 bp):
AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTT
CCAAAAATCACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTGACCCG
Done.