Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000691.1 Kokia drynarioides strain JFW-HI SEQ_111691, 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: 167807
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2759 original size:18 final size:17
Alignment explanation
Indices: 2717--2755 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2707 TCTCCCTCGA
*
2717 TCTTTAACCTTCCATCT
1 TCTTTAACCTTCCATAT
*
2734 TCTTTAACCTTTCATAT
1 TCTTTAACCTTCCATAT
2751 TCTTT
1 TCTTT
2756 TAACTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.28, G:0.00, T:0.54
Consensus pattern (17 bp):
TCTTTAACCTTCCATAT
Found at i:11933 original size:16 final size:15
Alignment explanation
Indices: 11896--11935 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
11886 AAATGACATG
*
11896 AAAATAAATAACAAC
1 AAAATAAATAACAAA
*
11911 AATATAAATAAACAAA
1 AAAATAAAT-AACAAA
11927 AAAATAAAT
1 AAAATAAAT
11936 GCTAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:11999 original size:19 final size:19
Alignment explanation
Indices: 11975--12022 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11965 TTAGGAATGA
11975 AAATAAATGAAAAATAAAT
1 AAATAAATGAAAAATAAAT
** *
11994 AAATAAACAAAAAATCAAT
1 AAATAAATGAAAAATAAAT
12013 AAATTAAATG
1 AAA-TAAATG
12023 TCAGAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (19 bp):
AAATAAATGAAAAATAAAT
Found at i:13102 original size:98 final size:99
Alignment explanation
Indices: 12918--13704 Score: 386
Period size: 98 Copynumber: 8.0 Consensus size: 99
12908 TTTTTTTCAA
* * * *
12918 AAGGTGTAAGATTCGTCATTAC-AGCTTCAATTTGTTCCCTCTTTG-GTTTTAA-GTAGTTAGGT
1 AAGGTGTAAGATTCGTCGTTGCGA-CTTCAATCT-TTCCCTCTTCGAGTTTTAAGGT-GTTAGGT
* * * * * *
12980 TCATCATCT-C-CCATTGAACGTATCCCTTTTTGGTTTT
63 CCACCAT-TGCGGC-TTCAACCTATCCCTTTTTGATTTT
* * *
13017 AAGGTGTAAGATTCGTCGTTGCGACTTTAATCTTTCCCTCTTCGA-TTTTAGGGTGTTAGGTCTA
1 AAGGTGTAAGATTCGTCGTTGCGACTTCAATCTTTCCCTCTTCGAGTTTTAAGGTGTTAGGTCCA
* * * * **
13081 TCGTTACGGCTTCAACCTATCCCTCTTCAATTTT
66 CCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
* * * * * * *
13115 AGGGTGTTAGGTCCGTCATTGTGACTTCAA-CTTATCCCTCTTC-AGTTTTAAGGTGTAAGGTCC
1 AAGGTGTAAGATTCGTCGTTGCGACTTCAATCTT-TCCCTCTTCGAGTTTTAAGGTGTTAGGTCC
* * * * *
13178 ACCTTTGCTGCTTCAATCTTTCCCTTTTTGGTTTT
65 ACCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
* * * * * * *
13213 AGGGTGTTAGATCCGCCGTT-CCAGCTTCAAT-TTATCCTTATTC-AGTTTTAAGGTGTTAGGTC
1 AAGGTGTAAGATTCGTCGTTGCGA-CTTCAATCTT-TCCCTCTTCGAGTTTTAAGGTGTTAGGTC
** * * *
13275 CGTCATTGCGACTTCAACCTATCCCTCTTCGATTTT
64 CACCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
* * * **
13311 AAGGTGTAAGA-TCAGTCATTGTGACTTCAATCTTTCCCTCTTCGATTTTTTGGGTGTTAGGTCC
1 AAGGTGTAAGATTC-GTCGTTGCGACTTCAATCTTTCCCTCTTCGAGTTTTAAGGTGTTAGGTCC
** * *
13375 ACCATTGCGGCTTCAATTTATCCC-TCTTCATTTT
65 ACCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
* * * * * * * * *
13409 AAGGTGTAAGGTTCATCGTTGCAACTTCAACCTATCCTTCTTCGA-TTTTAAGATGTAAGATCCA
1 AAGGTGTAAGATTCGTCGTTGCGACTTCAATCTTTCCCTCTTCGAGTTTTAAGGTGTTAGGTCCA
* * *** * * * *
13473 TCGTTGTAACTTTAACCTTTCCCTCTTCGATTTTT
66 CCATTGCGGCTTCAACCTATCCCTTTTTGA-TTTT
** * * * * ** * * * * * *
13508 TGGGTGTTAG-GTCTATCATTATGGCTTCAAGCTATCCCTCTTC-AGTTTTAAGGTGTAAGATCT
1 AAGGTGTAAGATTC-GTCGTTGCGACTTCAATCTTTCCCTCTTCGAGTTTTAAGGTGTTAGGTCC
** * * * * *
13571 GTCGTTGCGGCTTCAATCTTTCCCTCTTCGATTTT
65 ACCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
** * * * * * * * *
13606 AAATTGTTAG-GTCTGCCATTACGACTTCAACCTATCCCTCTTC-AGTTTTAAGGTGTAAGGTCC
1 AAGGTGTAAGATTC-GTCGTTGCGACTTCAATCTTTCCCTCTTCGAGTTTTAAGGTGTTAGGTCC
* * * * *
13669 GCTATTGCGGTTTCAACCTTTCCCTATTTGATTTT
65 ACCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
13704 A
1 A
13705 GGATGTTAGG
Statistics
Matches: 532, Mismatches: 138, Indels: 37
0.75 0.20 0.05
Matches are distributed among these distances:
97 35 0.07
98 351 0.66
99 145 0.27
100 1 0.00
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (99 bp):
AAGGTGTAAGATTCGTCGTTGCGACTTCAATCTTTCCCTCTTCGAGTTTTAAGGTGTTAGGTCCA
CCATTGCGGCTTCAACCTATCCCTTTTTGATTTT
Found at i:13220 original size:147 final size:147
Alignment explanation
Indices: 13013--13607 Score: 615
Period size: 147 Copynumber: 4.0 Consensus size: 147
13003 CCCTTTTTGG
* * * * *
13013 TTTTAAGGTGTAAGATTCGTCGTTGCGACTTTAATCTTTCCCTCTTCGA-TTTTAGGGTGTTAGG
1 TTTTAAGGTGTAAGATCCATCATTGTG-CTTCAATCTTTCCCTCTTCGATTTTTAGGGTGTTAGG
* * * * * * *
13077 TCTATCGTTACGGCTTCAACCTATCCCTCTTCAATTTTAGGGTGTTAGGTCCGTCATTGTGACTT
65 TCCACCATTACGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCGTCATTGCGACTT
*
13142 CAACTTATCCCTCTTC-A
130 CAACCTATCCCTCTTCGA
* * * * * *
13159 GTTTTAAGGTGTAAGGTCCACCTTTGCTGCTTCAATCTTTCCCTTTTTG-GTTTTAGGGTGTTAG
1 -TTTTAAGGTGTAAGATCCATCATTG-TGCTTCAATCTTTCCCTCTTCGATTTTTAGGGTGTTAG
* * * * * * * * * *
13223 ATCCGCCGTTCCAGCTTCAATTTATCCTTATTCAGTTTTAAGGTGTTAGGTCCGTCATTGCGACT
64 GTCCACCATTACGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCGTCATTGCGACT
13288 TCAACCTATCCCTCTTCGA
129 TCAACCTATCCCTCTTCGA
*
13307 TTTTAAGGTGTAAGAT-CAGTCATTGTGACTTCAATCTTTCCCTCTTCGATTTTTTGGGTGTTAG
1 TTTTAAGGTGTAAGATCCA-TCATTGTG-CTTCAATCTTTCCCTCTTCGATTTTTAGGGTGTTAG
* * * * * *
13371 GTCCACCATTGCGGCTTCAATTTATCCCTCTTC-ATTTTAAGGTGTAAGGTTCATCGTTGCAACT
64 GTCCACCATTACGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCGTCATTGCGACT
*
13435 TCAACCTATCCTTCTTCGA
129 TCAACCTATCCCTCTTCGA
* * * * * *
13454 TTTTAAGATGTAAGATCCATCGTTGTAACTTTAACCTTTCCCTCTTCGATTTTTTGGGTGTTAGG
1 TTTTAAGGTGTAAGATCCATCATTGT-GCTTCAATCTTTCCCTCTTCGATTTTTAGGGTGTTAGG
* * * * * * * * *
13519 TCTATCATTATGGCTTCAAGCTATCCCTCTTCAGTTTTAAGGTGTAAGATCTGTCGTTGCGGCTT
65 TCCACCATTACGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCGTCATTGCGACTT
* *
13584 CAATCTTTCCCTCTTCGA
130 CAACCTATCCCTCTTCGA
13602 TTTTAA
1 TTTTAA
13608 ATTGTTAGGT
Statistics
Matches: 374, Mismatches: 65, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
146 4 0.01
147 281 0.75
148 89 0.24
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.41
Consensus pattern (147 bp):
TTTTAAGGTGTAAGATCCATCATTGTGCTTCAATCTTTCCCTCTTCGATTTTTAGGGTGTTAGGT
CCACCATTACGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCGTCATTGCGACTTC
AACCTATCCCTCTTCGA
Found at i:13634 original size:49 final size:49
Alignment explanation
Indices: 13035--13734 Score: 414
Period size: 49 Copynumber: 14.3 Consensus size: 49
13025 AGATTCGTCG
* * * *** *
13035 TTGCGACTTTAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCTATCG
1 TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
* * * * * *
13084 TTACGGCTTCAACCTATCCCTCTTCAATTTTAGGGTGTTAGGTCCGTCA
1 TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
* * * *
13133 TTGTGACTTCAA-CTTATCCCTCTTC-AGTTTTAAGGTGTAAGGTCCACCT
1 TTGCGACTTCAACCTT-TCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGCCA
* * * * * * *
13182 TTGCTG-CTTCAATCTTTCCCTTTTTGGTTTTAGGGTGTTAGATCCGCCG
1 TTGC-GACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
* * * * *
13231 TT-CCAGCTTCAA-TTTATCCTTATTC-AGTTTTAAGGTGTTAGGTCCGTCA
1 TTGCGA-CTTCAACCTT-TCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGCCA
* * * * *
13280 TTGCGACTTCAACCTATCCCTCTTCGATTTTAAGGTGTAAGATCAGTCA
1 TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
* * ** *
13329 TTGTGACTTCAATCTTTCCCTCTTCGATTTTTTGGGTGTTAGGTCCACCA
1 TTGCGACTTCAACCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGCCA
* * * * ** *
13379 TTGCGGCTTCAA-TTTATCCCTCTTC-ATTTTAAGGTGTAAGGTTCATCG
1 TTGCGACTTCAACCTT-TCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
* * * * * * ** *
13427 TTGCAACTTCAACCTATCCTTCTTCGATTTTAAGATGTAAGATCCATCG
1 TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
** * ** ***
13476 TTGTAACTTTAACCTTTCCCTCTTCGATTTTTTGGGTGTTAGGTCTATCA
1 TTGCGACTTCAACCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGCCA
** * * * * * * * *
13526 TTATGGCTTCAAGCTATCCCTCTTC-AGTTTTAAGGTGTAAGATCTGTCG
1 TTGCGACTTCAACCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGCCA
* * ** *
13575 TTGCGGCTTCAATCTTTCCCTCTTCGATTTTAAATTGTTAGGTCTGCCA
1 TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
* * * *
13624 TTACGACTTCAACCTATCCCTCTTC-AGTTTTAAGGTGTAAGGTCCGCTA
1 TTGCGACTTCAACCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGCCA
** * * **
13673 TTGCGGTTTCAACCTTTCCCTATTTGATTTT-AGGATGTTAGGTCTACCA
1 TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGG-TGTTAGGTCCGCCA
*
13722 TTGCGGCTTCAAC
1 TTGCGACTTCAAC
13735 ATATCCTTAT
Statistics
Matches: 504, Mismatches: 126, Indels: 42
0.75 0.19 0.06
Matches are distributed among these distances:
48 44 0.09
49 382 0.76
50 78 0.15
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (49 bp):
TTGCGACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGCCA
Found at i:13712 original size:98 final size:99
Alignment explanation
Indices: 13035--13740 Score: 504
Period size: 98 Copynumber: 7.2 Consensus size: 99
13025 AGATTCGTCG
* * * * * ** * *
13035 TTGCGACTTTAATCTTTCCCTCTTC-GATTTTAGGGTGTTAGGT-CTATCGTTACGGCTTCAACC
1 TTGCGACTTCAACCTATCCCTCTTCAG-TTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACC
* * * *
13098 TATCCCTCTTCAATTTTAGGGTGTTAGGTCCGTCA
65 TTTCCCTCTTCGATTTTAGGGTGTTAGGTCTGCCA
* * * * * *
13133 TTGTGACTTCAACTTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCAC-CTTTGCTGCTTCAATCT
1 TTGCGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACCT
* * * * * *
13197 TTCCCTTTTTGGTTTTAGGGTGTTAGATCCGCCG
66 TTCCCTCTTCGATTTTAGGGTGTTAGGTCTGCCA
* ** * * * *
13231 TT-CCAGCTTCAATTTATCCTTATTCAGTTTTAAGGTGTTAGGTCCG-TCATTGCGACTTCAACC
1 TTGCGA-CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACC
* * * * * *
13294 TATCCCTCTTCGATTTTAAGGTGTAAGATCAGTCA
65 TTTCCCTCTTCGATTTTAGGGTGTTAGGTCTGCCA
* * * * ** * * *
13329 TTGTGACTTCAATCTTTCCCTCTTCGATTTTTTGGGTGTTAGGTCCAC-CATTGCGGCTTCAA-T
1 TTGCGACTTCAACCTATCCCTCTTC-AGTTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACC
* * *
13392 TTATCCCTCTTC-ATTTTAAGGTGTAAGGT-T-CATCG
65 TT-TCCCTCTTCGATTTTAGGGTGTTAGGTCTGC--CA
* * * * * * *** *
13427 TTGCAACTTCAACCTATCCTTCTTC-GATTTTAAGATGTAAGATCC-ATCGTTGTAACTTTAACC
1 TTGCGACTTCAACCTATCCCTCTTCAG-TTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACC
* **
13490 TTTCCCTCTTCGATTTTTTGGGTGTTAGGTCTATCA
65 TTTCCCTCTTCGA-TTTTAGGGTGTTAGGTCTGCCA
** * * * * * *
13526 TTATGGCTTCAAGCTATCCCTCTTCAGTTTTAAGGTGTAAGATCTG-TCGTTGCGGCTTCAATCT
1 TTGCGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACCT
***
13590 TTCCCTCTTCGATTTTAAATTGTTAGGTCTGCCA
66 TTCCCTCTTCGATTTTAGGGTGTTAGGTCTGCCA
* *
13624 TTACGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGCT-ATTGCGGTTTCAACCT
1 TTGCGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACCT
* * * *
13688 TTCCCTATTTGATTTTAGGATGTTAGGTCTACCA
66 TTCCCTCTTCGATTTTAGGGTGTTAGGTCTGCCA
* *
13722 TTGCGGCTTCAACATATCC
1 TTGCGACTTCAACCTATCC
13741 TTATTCAAAC
Statistics
Matches: 471, Mismatches: 117, Indels: 40
0.75 0.19 0.06
Matches are distributed among these distances:
97 32 0.07
98 320 0.68
99 117 0.25
100 2 0.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (99 bp):
TTGCGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGCTCATTGCGGCTTCAACCT
TTCCCTCTTCGATTTTAGGGTGTTAGGTCTGCCA
Found at i:14880 original size:46 final size:46
Alignment explanation
Indices: 14823--14910 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
14813 CTTTTCCTTT
* *
14823 TTTTTTTTGCTAGTTTGAGCTGA-CCTTTTAGGTTTTCAACTCGAAC
1 TTTTTTTTGCTAGTTTGAGC-CACCCTTTCAGGTTTTCAACTCGAAC
14869 TTTTTTTTGCTAGTTTGAGCCACCCTTTCAGGTTTTCAACTC
1 TTTTTTTTGCTAGTTTGAGCCACCCTTTCAGGTTTTCAACTC
14911 AACCCCTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (46 bp):
TTTTTTTTGCTAGTTTGAGCCACCCTTTCAGGTTTTCAACTCGAAC
Found at i:16472 original size:33 final size:33
Alignment explanation
Indices: 16430--16497 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
16420 TGAGTTAATA
* * *
16430 AATTACTAATTCAGAATCTTTATATACTTTTTG
1 AATTACTAATGCAGAATCTTCATATAATTTTTG
16463 AATTACTAATGCAGAATCTTCATATAATTTTTG
1 AATTACTAATGCAGAATCTTCATATAATTTTTG
16496 AA
1 AA
16498 CCTGGATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (33 bp):
AATTACTAATGCAGAATCTTCATATAATTTTTG
Found at i:22423 original size:23 final size:22
Alignment explanation
Indices: 22388--22444 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
22378 TATAGTATTA
22388 AATAA-AATAACAATATAATAAT
1 AATAATAATAACAATA-AATAAT
* *
22410 AATAATAATGACAATAAATATT
1 AATAATAATAACAATAAATAAT
22432 AACTAATTAATAA
1 AA-TAA-TAATAA
22445 TATAAGCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.41
23 12 0.41
24 5 0.17
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAATAATAACAATAAATAAT
Found at i:22851 original size:13 final size:14
Alignment explanation
Indices: 22818--22851 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
22808 ATTAAATGCT
22818 AAAATAAACAAATA
1 AAAATAAACAAATA
*
22832 AATATAAAC-AATA
1 AAAATAAACAAATA
22845 AAAATAA
1 AAAATAA
22852 TTGAGATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAACAAATA
Found at i:22906 original size:15 final size:16
Alignment explanation
Indices: 22887--22928 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
22877 ACAAATAAAT
22887 AAATAAACAAAATATC
1 AAATAAACAAAATATC
**
22903 -AATAAATTAAATATC
1 AAATAAACAAAATATC
22918 AGAATAAACAA
1 A-AATAAACAA
22929 TTAAATATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
15 13 0.65
17 7 0.35
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAAACAAAATATC
Found at i:23878 original size:22 final size:21
Alignment explanation
Indices: 23840--23880 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
23830 AAAAAGAAAA
23840 AAAAAAACTTATATATTAATT
1 AAAAAAACTTATATATTAATT
* *
23861 AAAAATACTATATTTATTAA
1 AAAAAAACT-TATATATTAA
23881 ATATTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAAACTTATATATTAATT
Found at i:24197 original size:16 final size:16
Alignment explanation
Indices: 24176--24258 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 16
24166 TGAATTATTG
*
24176 ATTACAACTCTATTTT
1 ATTACAACTCTATTCT
* *
24192 ATTACAACTTTATTCA
1 ATTACAACTCTATTCT
* *
24208 ATTACAATTCTATTTT
1 ATTACAACTCTATTCT
**
24224 ATTACAGTTCTATTCT
1 ATTACAACTCTATTCT
* * *
24240 ATTATAGCCCTATTCT
1 ATTACAACTCTATTCT
24256 ATT
1 ATT
24259 CCAGTGAACC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 55 1.00
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:25748 original size:2 final size:2
Alignment explanation
Indices: 25741--25780 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
25731 TCTTTTCTTT
25741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25781 TACTTATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28378 original size:31 final size:31
Alignment explanation
Indices: 28340--28403 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
28330 AATTCAAATT
28340 ACTCAATTTTTTATCCATGCTTTGAACTCTA
1 ACTCAATTTTTTATCCATGCTTTGAACTCTA
28371 ACTCAATTTTTTATCCATGCTTTGAACTCTA
1 ACTCAATTTTTTATCCATGCTTTGAACTCTA
28402 AC
1 AC
28404 ACAACATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (31 bp):
ACTCAATTTTTTATCCATGCTTTGAACTCTA
Found at i:28548 original size:37 final size:31
Alignment explanation
Indices: 28473--28536 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
28463 TCAATTTCTC
28473 CATTTTTAAATTTAATCATTGTGACCACTCT
1 CATTTTTAAATTTAATCATTGTGACCACTCT
28504 CATTTTTAAATTTAATCATTGTGACCACTCT
1 CATTTTTAAATTTAATCATTGTGACCACTCT
28535 CA
1 CA
28537 CATTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (31 bp):
CATTTTTAAATTTAATCATTGTGACCACTCT
Found at i:30289 original size:15 final size:12
Alignment explanation
Indices: 30255--30296 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
30245 AATAAAGATG
30255 ATTCATAATAAT
1 ATTCATAATAAT
30267 ATTCATAATAAT
1 ATTCATAATAAT
*
30279 ATTCACAATAAAT
1 ATTCATAAT-AAT
30292 ATTCA
1 ATTCA
30297 AGAGGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTCATAATAAT
Found at i:32493 original size:40 final size:40
Alignment explanation
Indices: 32452--32588 Score: 161
Period size: 39 Copynumber: 3.4 Consensus size: 40
32442 TTTCTAAATC
32452 AATGAAAAGGTTGAAAATGATGTTATCCGAAAATGATATCA
1 AATGAAAAGGTTGAAAAT-ATGTTATCCGAAAATGATATCA
* *
32493 AATGAAAAAGGTTGAAAAAATGTTATCCGAAAGT-ATATCA
1 AATG-AAAAGGTTGAAAATATGTTATCCGAAAATGATATCA
* * * * * *
32533 AATAAAAAGGTTGAAAGTATGTTATTCAAAAAGGATAAC-
1 AATGAAAAGGTTGAAAATATGTTATCCGAAAATGATATCA
*
32572 AATGAAAAGGATGAAAA
1 AATGAAAAGGTTGAAAA
32589 GGCTACTAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.46
40 13 0.16
41 18 0.22
42 13 0.16
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (40 bp):
AATGAAAAGGTTGAAAATATGTTATCCGAAAATGATATCA
Found at i:32632 original size:24 final size:24
Alignment explanation
Indices: 32561--32632 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
32551 ATGTTATTCA
* *
32561 AAAAGGATAACAATGAAAAGGATG
1 AAAAGGATACCAATGAAAAGGTTG
* * *
32585 AAAAGGCTACTAATGAAAAAGTTG
1 AAAAGGATACCAATGAAAAGGTTG
* *
32609 AAAATGATACCAATGAAAGGGTTG
1 AAAAGGATACCAATGAAAAGGTTG
32633 GAAACTGGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (24 bp):
AAAAGGATACCAATGAAAAGGTTG
Found at i:38702 original size:17 final size:17
Alignment explanation
Indices: 38680--38717 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
38670 CAAGAACACC
38680 ATCCTCGTGGGATCGAT
1 ATCCTCGTGGGATCGAT
*
38697 ATCCTCGTGGGATTGAT
1 ATCCTCGTGGGATCGAT
38714 ATCC
1 ATCC
38718 AATAGATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (17 bp):
ATCCTCGTGGGATCGAT
Found at i:40620 original size:41 final size:39
Alignment explanation
Indices: 40565--40669 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 39
40555 ATTTTCGGAT
40565 AAATGAAAAGGTTGAAAATGATGTTACTCGAAAAGGATATC
1 AAATGAAAA-GTTGAAAATGATGTT-CTCGAAAAGGATATC
* * * *
40606 AAATAAAAATGTTGAAAAAGATGTTTTCTAAAAGGATATC
1 AAATGAAAA-GTTGAAAATGATGTTCTCGAAAAGGATATC
40646 AAATGAAAAGTTTGAAAAATGATG
1 AAATGAAAAG-TTG-AAAATGATG
40670 AAAAGGGCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.02
40 24 0.44
41 30 0.55
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.27
Consensus pattern (39 bp):
AAATGAAAAGTTGAAAATGATGTTCTCGAAAAGGATATC
Found at i:40648 original size:40 final size:40
Alignment explanation
Indices: 40565--40669 Score: 131
Period size: 40 Copynumber: 2.5 Consensus size: 40
40555 ATTTTCGGAT
*
40565 AAATGAAAAGGTTGAAAATGATGTTACTCGAAAAGGATATC
1 AAATGAAAA-GTTGAAAAAGATGTTACTCGAAAAGGATATC
* * *
40606 AAATAAAAATGTTGAAAAAGATGTT-TTCTAAAAGGATATC
1 AAATGAAAA-GTTGAAAAAGATGTTACTCGAAAAGGATATC
40646 AAATGAAAAGTTTGAAAAATGATG
1 AAATGAAAAG-TTGAAAAA-GATG
40670 AAAAGGGCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.02
40 29 0.52
41 26 0.46
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.27
Consensus pattern (40 bp):
AAATGAAAAGTTGAAAAAGATGTTACTCGAAAAGGATATC
Found at i:42883 original size:16 final size:16
Alignment explanation
Indices: 42862--42892 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42852 TTATGTATCC
42862 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
42878 CATTTTATCTTTATT
1 CATTTTACCTTTATT
42893 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:47607 original size:3 final size:3
Alignment explanation
Indices: 47599--47655 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
47589 TAGGCAATTC
* *
47599 CTT CTT CTT CTT CTT ATT CCTT C-T CTT CTT GTT CTT CTT CTT -TT
1 CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT
47643 CTTT CTT CTT CTT
1 C-TT CTT CTT CTT
47656 TTGCCTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 37 0.80
4 5 0.11
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:64508 original size:253 final size:253
Alignment explanation
Indices: 64060--64566 Score: 996
Period size: 253 Copynumber: 2.0 Consensus size: 253
64050 GGATCCAAAA
*
64060 AAAAAATAAAAGAAATTGTTCAATGGAAAGCACCCAAGAATGTATCGGAAATTCGTAGTTTCATT
1 AAAAAATAAAAGAAATTGTTCAATGGAAAGCACCCAAGAATGTATCGAAAATTCGTAGTTTCATT
*
64125 GACCTAGCTGGATATTATCGTCGTTTCGTGAAAGGATTTTCAAAAATAGCTATGCCGATGACGAA
66 GACCTAGCTGGATATTATCGTCGTTTCGTGAAAGAATTTTCAAAAATAGCTATGCCGATGACGAA
64190 GCTTCTTCAGAAGAATGCACAGTTTGTTTGGAGCAAGAAATGCCAAGAGAGTTTCGAAGAGTTGA
131 GCTTCTTCAGAAGAATGCACAGTTTGTTTGGAGCAAGAAATGCCAAGAGAGTTTCGAAGAGTTGA
64255 AGTGGTTTTTCACAAAGGCACCAGTTTTAGCCTTATCGGAATCAGGAAAAGAATTTGT
196 AGTGGTTTTTCACAAAGGCACCAGTTTTAGCCTTATCGGAATCAGGAAAAGAATTTGT
64313 AAAAAATAAAAGAAATTGTTCAATGGAAAGCACCCAAGAATGTATCGAAAATTCGTAGTTTCATT
1 AAAAAATAAAAGAAATTGTTCAATGGAAAGCACCCAAGAATGTATCGAAAATTCGTAGTTTCATT
64378 GACCTAGCTGGATATTATCGTCGTTTCGTGAAAGAATTTTCAAAAATAGCTATGCCGATGACGAA
66 GACCTAGCTGGATATTATCGTCGTTTCGTGAAAGAATTTTCAAAAATAGCTATGCCGATGACGAA
64443 GCTTCTTCAGAAGAATGCACAGTTTGTTTGGAGCAAGAAATGCCAAGAGAGTTTCGAAGAGTTGA
131 GCTTCTTCAGAAGAATGCACAGTTTGTTTGGAGCAAGAAATGCCAAGAGAGTTTCGAAGAGTTGA
64508 AGTGGTTTTTCACAAAGGCACCAGTTTTAGCCTTATCGGAATCAGGAAAAGAATTTGT
196 AGTGGTTTTTCACAAAGGCACCAGTTTTAGCCTTATCGGAATCAGGAAAAGAATTTGT
64566 A
1 A
64567 GTTTTTAGCG
Statistics
Matches: 252, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
253 252 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (253 bp):
AAAAAATAAAAGAAATTGTTCAATGGAAAGCACCCAAGAATGTATCGAAAATTCGTAGTTTCATT
GACCTAGCTGGATATTATCGTCGTTTCGTGAAAGAATTTTCAAAAATAGCTATGCCGATGACGAA
GCTTCTTCAGAAGAATGCACAGTTTGTTTGGAGCAAGAAATGCCAAGAGAGTTTCGAAGAGTTGA
AGTGGTTTTTCACAAAGGCACCAGTTTTAGCCTTATCGGAATCAGGAAAAGAATTTGT
Found at i:67922 original size:47 final size:46
Alignment explanation
Indices: 67833--67940 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 46
67823 CTCACATTTA
** * *
67833 CGGTTTATCCGCTAAGCACTGGTGCTAAGATTTGATAGATATTTTT
1 CGGTTTATCAACTAAGCACTGGTGCTAAGATTTCAGAGATATTTTT
67879 CGGTTTATCAACTAAGCACTGGGTGCTAAGATTTCACGA-ATATTTTT
1 CGGTTTATCAACTAAGCACT-GGTGCTAAGATTTCA-GAGATATTTTT
* *
67926 TGGTTAATCCAACTA
1 CGGTTTAT-CAACTA
67941 GAGCTGGGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 18 0.34
47 28 0.53
48 7 0.13
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (46 bp):
CGGTTTATCAACTAAGCACTGGTGCTAAGATTTCAGAGATATTTTT
Found at i:69035 original size:119 final size:119
Alignment explanation
Indices: 68819--69056 Score: 458
Period size: 119 Copynumber: 2.0 Consensus size: 119
68809 ATGGGTGTTA
68819 CAGTATTTGTTTTTTCCTTTCTTTTATTCTGTTTACTGGAGTTATATTGGATTATTGTGCGCTTT
1 CAGTATTTGTTTTTTCCTTTCTTTTATTCTGTTTACTGGAGTTATATTGGATTATTGTGCGCTTT
68884 CTTGTTGTTCTGTTTCCTTTGGATTTATTTGTGGTGGGAGATAGCTGGGGCGTG
66 CTTGTTGTTCTGTTTCCTTTGGATTTATTTGTGGTGGGAGATAGCTGGGGCGTG
* *
68938 CAGTGTTTGTTTTTTCCTTTCTTTTATTCTGTTTACTGGAGTTATTTTGGATTATTGTGCGCTTT
1 CAGTATTTGTTTTTTCCTTTCTTTTATTCTGTTTACTGGAGTTATATTGGATTATTGTGCGCTTT
69003 CTTGTTGTTCTGTTTCCTTTGGATTTATTTGTGGTGGGAGATAGCTGGGGCGTG
66 CTTGTTGTTCTGTTTCCTTTGGATTTATTTGTGGTGGGAGATAGCTGGGGCGTG
69057 GTTTCTTGTG
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.11, C:0.12, G:0.26, T:0.52
Consensus pattern (119 bp):
CAGTATTTGTTTTTTCCTTTCTTTTATTCTGTTTACTGGAGTTATATTGGATTATTGTGCGCTTT
CTTGTTGTTCTGTTTCCTTTGGATTTATTTGTGGTGGGAGATAGCTGGGGCGTG
Found at i:76089 original size:30 final size:30
Alignment explanation
Indices: 76053--76129 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
76043 CAAAATAAAA
* *
76053 TTTTGGAAAGTTTGATGGCCAAGTTCAAAT
1 TTTTGGAAAGTTTGAGGGCCAAATTCAAAT
* ** **
76083 TTTTGGAAAGTTCGAGGGTTAAATTTGAAT
1 TTTTGGAAAGTTTGAGGGCCAAATTCAAAT
76113 TTTTGGAAAGTTTGAGG
1 TTTTGGAAAGTTTGAGG
76130 TCAAAACATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (30 bp):
TTTTGGAAAGTTTGAGGGCCAAATTCAAAT
Found at i:76143 original size:29 final size:29
Alignment explanation
Indices: 76039--76153 Score: 88
Period size: 30 Copynumber: 3.9 Consensus size: 29
76029 GGGAAAAAAG
* *
76039 GGGTCAAAATAAAATTTTGGAAAGTTTGA
1 GGGTCAAAACAAATTTTTGGAAAGTTTGA
* * ** *
76068 TGGCCAAGTTCAAATTTTTGGAAAGTTCGA
1 GGGTCAA-AACAAATTTTTGGAAAGTTTGA
* ***
76098 GGGTTAAATTTGAATTTTTGGAAAGTTTGA
1 GGGTCAAA-ACAAATTTTTGGAAAGTTTGA
*
76128 -GGTCAAAACATAATTTTTTGAAAGTT
1 GGGTCAAAACA-AATTTTTGGAAAGTT
76154 CAAGGGTTAA
Statistics
Matches: 64, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
29 25 0.39
30 39 0.61
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.37
Consensus pattern (29 bp):
GGGTCAAAACAAATTTTTGGAAAGTTTGA
Found at i:76176 original size:59 final size:59
Alignment explanation
Indices: 76039--76176 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 59
76029 GGGAAAAAAG
* * ** *
76039 GGGTCAAAATAAAATTTTGGAAAGTTTGATGGCCAAGTTCAAATTTTTGGAAAGTTCGA
1 GGGTTAAAATAGAATTTTGGAAAGTTTGATGGCCAAGAACAAATTTTTGGAAAGTTCAA
* * * *
76098 GGGTTAAATTTGAATTTTTGGAAAGTTTGA-GGTCAA-AACATAATTTTTTGAAAGTTCAA
1 GGGTTAAAATAGAA-TTTTGGAAAGTTTGATGGCCAAGAACA-AATTTTTGGAAAGTTCAA
76157 GGGTTAAAAATAGAATTTTG
1 GGGTT-AAAATAGAATTTTG
76177 AAGAGTTCAA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
58 2 0.03
59 41 0.63
60 22 0.34
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (59 bp):
GGGTTAAAATAGAATTTTGGAAAGTTTGATGGCCAAGAACAAATTTTTGGAAAGTTCAA
Found at i:77149 original size:37 final size:37
Alignment explanation
Indices: 77094--77197 Score: 181
Period size: 37 Copynumber: 2.8 Consensus size: 37
77084 TGCAACAATG
* *
77094 GTGGTAGCTTTCGATGGTGCTGGTGGTGGTGGATGAC
1 GTGGCAGCTTTCGGTGGTGCTGGTGGTGGTGGATGAC
77131 GTGGCAGCTTTCGGTGGTGCTGGTGGTGGTGGATGAC
1 GTGGCAGCTTTCGGTGGTGCTGGTGGTGGTGGATGAC
*
77168 GTGGCAGCTTTCGGTGATGCTGGTGGTGGT
1 GTGGCAGCTTTCGGTGGTGCTGGTGGTGGT
77198 AGGTGCAACT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.09, C:0.12, G:0.47, T:0.32
Consensus pattern (37 bp):
GTGGCAGCTTTCGGTGGTGCTGGTGGTGGTGGATGAC
Found at i:77783 original size:22 final size:22
Alignment explanation
Indices: 77722--77783 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
77712 TTAAGGTTTA
*
77722 GGTTTAGG-GTTATGGGTT-ATG
1 GGTTT-GGAGTTATGGGTTCAAG
* *
77743 AGTTTGGAGTT-TAGTGTTCAAG
1 GGTTTGGAGTTAT-GGGTTCAAG
77765 GGTTTGGAGTTATGGGTTC
1 GGTTTGGAGTTATGGGTTC
77784 GATGTTTGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 17 0.53
23 1 0.03
ACGTcount: A:0.16, C:0.03, G:0.39, T:0.42
Consensus pattern (22 bp):
GGTTTGGAGTTATGGGTTCAAG
Found at i:78576 original size:94 final size:89
Alignment explanation
Indices: 78419--78608 Score: 290
Period size: 94 Copynumber: 2.1 Consensus size: 89
78409 TAATATAAAG
* *
78419 TATTGTAAACTTAAAATGAGTCGGGTCGAGCCAGGTTTGGGCTTGAACATTTAAGCTCTAGCACA
1 TATTGTAAACTTAAAATGAGTCGGGTCGAGCCAAGTTTGGGCTTGAACATTTAAGCTCAAGCACA
* *
78484 ATCCATATTTTAAAGGAGTCTAAT
66 ATACATATTTTAAAGGAGCCTAAT
78508 TATTGTAAACTTAAAATGAGTCGAGTCGAGTCGAGCCAAGTTTGGGCTTGAACATTTAAGCTCAA
1 TATTGTAAACTTAAAATGAGTC--G--G-GTCGAGCCAAGTTTGGGCTTGAACATTTAAGCTCAA
78573 GCACAATACATATTTTAAAGGAGCCTAAT
61 GCACAATACATATTTTAAAGGAGCCTAAT
*
78602 TTTTGTA
1 TATTGTA
78609 CTTAAGTCCA
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
89 22 0.24
91 1 0.01
93 1 0.01
94 67 0.74
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (89 bp):
TATTGTAAACTTAAAATGAGTCGGGTCGAGCCAAGTTTGGGCTTGAACATTTAAGCTCAAGCACA
ATACATATTTTAAAGGAGCCTAAT
Found at i:89057 original size:24 final size:24
Alignment explanation
Indices: 89030--89075 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
89020 ACAATCAATT
89030 CATTTTATATTACATTTGCACTAA
1 CATTTTATATTACATTTGCACTAA
**
89054 CATTTTATATTAGTTTTGCACT
1 CATTTTATATTACATTTGCACT
89076 GACAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (24 bp):
CATTTTATATTACATTTGCACTAA
Found at i:90709 original size:18 final size:18
Alignment explanation
Indices: 90686--90728 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
90676 CAATCTGACT
*
90686 AGATGCGATCACAGAATC
1 AGATGCAATCACAGAATC
* *
90704 AGATGCAATCACATACTC
1 AGATGCAATCACAGAATC
90722 AGATGCA
1 AGATGCA
90729 GCCACAGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (18 bp):
AGATGCAATCACAGAATC
Found at i:99877 original size:24 final size:24
Alignment explanation
Indices: 99850--99904 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
99840 ACAATCAATT
99850 CATTTTATATTACATTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
* *
99874 CATTTTATATTACTTTTGCATTGA
1 CATTTTATATTACATTTGCACTGA
99898 CAATTTT
1 C-ATTTT
99905 TAATCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (24 bp):
CATTTTATATTACATTTGCACTGA
Found at i:110313 original size:25 final size:24
Alignment explanation
Indices: 110211--110387 Score: 173
Period size: 24 Copynumber: 7.4 Consensus size: 24
110201 AAACTTTGTT
* *
110211 TGGGCTCATAAGAGCTAA-ATATC
1 TGGGCTCGTAAGAGCTAACCTATC
* * *
110234 TAGGCTCGTATGAGCTAACCTATT
1 TGGGCTCGTAAGAGCTAACCTATC
*
110258 TGGGCTCATATA-AGCTAACCTAT-
1 TGGGCTCGTA-AGAGCTAACCTATC
* * *
110281 TTGGCTCGTAAGAGCTAATTCTGTC
1 TGGGCTCGTAAGAGCTAA-CCTATC
*
110306 TGGGCTCGTATGAGCTAACCTATC
1 TGGGCTCGTAAGAGCTAACCTATC
**
110330 TGGGCTCGTATTAGCTAACCTAT-
1 TGGGCTCGTAAGAGCTAACCTATC
* *
110353 TTGGCTCGTAAGAGGTAACCCTATC
1 TGGGCTCGTAAGAGCTAA-CCTATC
110378 TGGGCTCGTA
1 TGGGCTCGTA
110388 TGGAAAAATT
Statistics
Matches: 125, Mismatches: 22, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
22 1 0.01
23 43 0.34
24 56 0.45
25 25 0.20
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (24 bp):
TGGGCTCGTAAGAGCTAACCTATC
Found at i:110328 original size:72 final size:72
Alignment explanation
Indices: 110213--110389 Score: 250
Period size: 72 Copynumber: 2.5 Consensus size: 72
110203 ACTTTGTTTG
* * * *
110213 GGCTCATAAGAGCTAA--ATATCTAGGCTCGTATGAGCTAACCTATTTGGGCTCATATAAGCTAA
1 GGCTCGTAAGAGCTAACCCTATCTGGGCTCGTATGAGCTAACCTATCTGGGCTCATATAAGCTAA
110276 CCTATTT
66 CCTATTT
** * * *
110283 GGCTCGTAAGAGCTAATTCTGTCTGGGCTCGTATGAGCTAACCTATCTGGGCTCGTATTAGCTAA
1 GGCTCGTAAGAGCTAACCCTATCTGGGCTCGTATGAGCTAACCTATCTGGGCTCATATAAGCTAA
110348 CCTATTT
66 CCTATTT
*
110355 GGCTCGTAAGAGGTAACCCTATCTGGGCTCGTATG
1 GGCTCGTAAGAGCTAACCCTATCTGGGCTCGTATG
110390 GAAAAATTCT
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 15 0.16
72 79 0.84
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (72 bp):
GGCTCGTAAGAGCTAACCCTATCTGGGCTCGTATGAGCTAACCTATCTGGGCTCATATAAGCTAA
CCTATTT
Found at i:110388 original size:48 final size:47
Alignment explanation
Indices: 110213--110389 Score: 180
Period size: 47 Copynumber: 3.7 Consensus size: 47
110203 ACTTTGTTTG
* * *
110213 GGCTCATAAGAGCTAA-ATATCTAGGCTCGTATGAGCTAACCTATTT
1 GGCTCGTAAGAGCTAACCTATCTGGGCTCGTATGAGCTAACCTATTT
* * * * * *
110259 GGGCTCATATA-AGCTAACCTAT-TTGGCTCGTAAGAGCTAATTCTGTCTG
1 -GGCTCGTA-AGAGCTAACCTATCTGGGCTCGTATGAGCTAA-CCTAT-TT
* *
110308 GGCTCGTATGAGCTAACCTATCTGGGCTCGTATTAGCTAACCTATTT
1 GGCTCGTAAGAGCTAACCTATCTGGGCTCGTATGAGCTAACCTATTT
*
110355 GGCTCGTAAGAGGTAACCCTATCTGGGCTCGTATG
1 GGCTCGTAAGAGCTAA-CCTATCTGGGCTCGTATG
110390 GAAAAATTCT
Statistics
Matches: 106, Mismatches: 17, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
47 45 0.42
48 45 0.42
49 16 0.15
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (47 bp):
GGCTCGTAAGAGCTAACCTATCTGGGCTCGTATGAGCTAACCTATTT
Found at i:119396 original size:17 final size:17
Alignment explanation
Indices: 119374--119420 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
119364 ATATAAAATC
119374 TAAATAAAATAAATAAA
1 TAAATAAAATAAATAAA
*
119391 TAAAT-AAATCAATAAA
1 TAAATAAAATAAATAAA
* *
119407 AATAATAAACTAAA
1 TA-AATAAAATAAA
119421 AGAAATCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 11 0.46
17 8 0.33
18 5 0.21
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAATAAAATAAATAAA
Found at i:125773 original size:54 final size:54
Alignment explanation
Indices: 125671--125776 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 54
125661 GTTTAGACTA
* * * *
125671 TGACATCTAGCAATAAGTAGTCTCTATCGACTTGCTATGCCGGCGGAAGATCTG
1 TGACATCTAGCAATAAGTAGACTCTATCAACTTGCTATGACGACGGAAGATCTG
** * *
125725 TGACATCTAGTGATAAGTAGACTCTATTAACTTGCTATGACGATGGAAGATC
1 TGACATCTAGCAATAAGTAGACTCTATCAACTTGCTATGACGACGGAAGATC
125777 GGAAGATCCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (54 bp):
TGACATCTAGCAATAAGTAGACTCTATCAACTTGCTATGACGACGGAAGATCTG
Found at i:125953 original size:24 final size:25
Alignment explanation
Indices: 125909--125958 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
125899 CAATCTTTTA
125909 CTTTTATGTTTTTCACAACTA-AAC
1 CTTTTATGTTTTTCACAACTATAAC
* *
125933 CTTTTATTTTGTTTCA-TACTATAAC
1 CTTTTATGTT-TTTCACAACTATAAC
125958 C
1 C
125959 CCTAAAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (25 bp):
CTTTTATGTTTTTCACAACTATAAC
Found at i:153427 original size:21 final size:23
Alignment explanation
Indices: 153382--153428 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
153372 AAAATATTAG
153382 AAATAAGTAGGATTAATTAAAGCT
1 AAATAAGTA-GATTAATTAAAGCT
153406 AAATAAGT-GATTAATT-AAGCT
1 AAATAAGTAGATTAATTAAAGCT
153427 AA
1 AA
153429 TTATGAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
24 8 0.35
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
AAATAAGTAGATTAATTAAAGCT
Done.