Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012048.1 Kokia drynarioides strain JFW-HI SEQ_127046, 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: 37350
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:1269 original size:13 final size:14
Alignment explanation
Indices: 1233--1282 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
1223 AAATGGTCTG
1233 AAAATAAATAACAGC
1 AAAATAAATAA-AGC
*
1248 AAGATAAATAAA-C
1 AAAATAAATAAAGC
**
1261 AAAATAAATAAATA
1 AAAATAAATAAAGC
1275 AAAATAAA
1 AAAATAAA
1283 AATTAAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.39
14 9 0.29
15 10 0.32
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.16
Consensus pattern (14 bp):
AAAATAAATAAAGC
Found at i:4887 original size:2 final size:2
Alignment explanation
Indices: 4880--4913 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4870 AAGATTTATA
4880 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4914 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4918 original size:2 final size:2
Alignment explanation
Indices: 4913--4939 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4903 TCTCTCTCTC
4913 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4940 TCATATAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5543 original size:158 final size:158
Alignment explanation
Indices: 5255--5577 Score: 398
Period size: 158 Copynumber: 2.0 Consensus size: 158
5245 GTAATCATAT
* * *
5255 ATGCTCACACGAGCTGTGAAATGGGTATGCTCACACAAGCTGTGGGTTGAGATGTGGGGCTACAC
1 ATGCTCACACAAGCTGTGAAATGGGTATGCTCACACAAGCTGTGGGTCGAGATGTGAGGCTACAC
* ** * *
5320 GATGTTGCTAACATGAGCTATGGAGAATCCGCAATAAATGTCGAACTTCAGCCATCGATAGGACA
66 GATGCTGCTAACACAAGCTATGGAGAATCCGCAACAAATGTCGAACCTCAGCCATCGATAGGACA
5385 TCTAAGACCAACACCCATATAACCTGTA
131 TCTAAGACCAACACCCATATAACCTGTA
* * * * *
5413 ATGCTCACACAAGCTGTGAAATGGGTTTGCTCACATGAGGC-GTGGGTCGAGATGTTAGGCTACG
1 ATGCTCACACAAGCTGTGAAATGGGTATGCTCACA-CAAGCTGTGGGTCGAGATGTGAGGCTACA
* * * * * * *
5477 CGATGCTGCTCACACAAGTTGTGGAGAATTCGTAACAAATG-CAGGACCTCAGCCATCGGTAGGA
65 CGATGCTGCTAACACAAGCTATGGAGAATCCGCAACAAATGTC-GAACCTCAGCCATCGATAGGA
* * * *
5541 CATTTAAGACTAGCACCCATATAACTTGTA
129 CATCTAAGACCAACACCCATATAACCTGTA
5571 ATGCTCA
1 ATGCTCA
5578 TACGAGTTGT
Statistics
Matches: 139, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
157 1 0.01
158 135 0.97
159 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (158 bp):
ATGCTCACACAAGCTGTGAAATGGGTATGCTCACACAAGCTGTGGGTCGAGATGTGAGGCTACAC
GATGCTGCTAACACAAGCTATGGAGAATCCGCAACAAATGTCGAACCTCAGCCATCGATAGGACA
TCTAAGACCAACACCCATATAACCTGTA
Found at i:8836 original size:13 final size:13
Alignment explanation
Indices: 8818--8843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8808 ATATATATTC
8818 AATAAAATGCAAA
1 AATAAAATGCAAA
8831 AATAAAATGCAAA
1 AATAAAATGCAAA
8844 GGATCACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AATAAAATGCAAA
Found at i:10054 original size:37 final size:36
Alignment explanation
Indices: 9945--10055 Score: 102
Period size: 40 Copynumber: 2.9 Consensus size: 36
9935 ATCAACATGT
* * *
9945 AATTAAATAAAAAT-ATAAAAACATAAAATTTAATG
1 AATTAAATAAAAATAATAAAAAGATAAAAATAAATG
9980 -A-TAAATAAATAAATAAATAAACAAGATAATAACAATAAATG
1 AATTAAAT-AA-AAAT-AATAAA-AAGAT-A-AA-AATAAATG
10021 AATTAAATAAAAATAATAAAAGAGATAAAAATAAA
1 AATTAAATAAAAATAATAAAA-AGATAAAAATAAA
10056 ATGGTCTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
33 5 0.08
34 3 0.05
35 4 0.06
37 11 0.18
38 6 0.10
39 3 0.05
40 12 0.19
41 10 0.16
42 3 0.05
43 5 0.08
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (36 bp):
AATTAAATAAAAATAATAAAAAGATAAAAATAAATG
Found at i:10098 original size:13 final size:13
Alignment explanation
Indices: 10064--10108 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
10054 AAATGGTCTA
10064 AAAATAAATAACAAC
1 AAAATAAAT-A-AAC
*
10079 AAGATAAATAAAC
1 AAAATAAATAAAC
*
10092 AAAATAAATAAAT
1 AAAATAAATAAAC
10105 AAAA
1 AAAA
10109 ATTAAATGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 18 0.67
14 1 0.04
15 8 0.30
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAATAAATAAAC
Found at i:11786 original size:32 final size:32
Alignment explanation
Indices: 11750--11814 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
11740 TTTTATATGG
11750 TAATGTAAGTTATTTATAACCTTATTTCTAAA
1 TAATGTAAGTTATTTATAACCTTATTTCTAAA
11782 TAATGTAAGTTATTTATAACCTTATTTCTAAA
1 TAATGTAAGTTATTTATAACCTTATTTCTAAA
11814 T
1 T
11815 TTTTATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (32 bp):
TAATGTAAGTTATTTATAACCTTATTTCTAAA
Found at i:13333 original size:49 final size:49
Alignment explanation
Indices: 13223--13561 Score: 244
Period size: 49 Copynumber: 6.9 Consensus size: 49
13213 GTAAGATTCG
* * * * * *
13223 CCGTTGCGGA-TTCAATCTATTCCCTCTTTGGTTTCAAGGTGTTAGATCCA
1 CCGTTGC-GACTTCAACCTA-TCCCTCTTCGATTTTATGGTGTTAGGTCCA
* * * *
13273 CCGTCGTGACTTCAATCTATCCCTCTTC-AGTTTTATGGTATTAGGT-CA
1 CCGTTGCGACTTCAACCTATCCCTCTTCGA-TTTTATGGTGTTAGGTCCA
* * * * *
13321 GCCGTTCCGACTTCAACCTATCCCTTTTCGATTTTAAGGTGTAAGATCCA
1 -CCGTTGCGACTTCAACCTATCCCTCTTCGATTTTATGGTGTTAGGTCCA
** * * * *
13371 TTGTTGTGACTTTAATCTTTCCCTCTTCGATTTT-TGGGTGTTAGGTCCA
1 CCGTTGCGACTTCAACCTATCCCTCTTCGATTTTAT-GGTGTTAGGTCCA
* * *
13420 CCGTTGCGACTTCAACCTATCCCTCTTC-AGTTTTAAGGTGTAAGATCCA
1 CCGTTGCGACTTCAACCTATCCCTCTTCGA-TTTTATGGTGTTAGGTCCA
* * * * * *
13469 TCGTTGTGACTTCAATCTTTCCCTCTTCGATTTTAGGGTG-TAAGTCCA
1 CCGTTGCGACTTCAACCTATCCCTCTTCGATTTTATGGTGTTAGGTCCA
* * * *
13517 TCATTACAACTTCAACCTATCCCTCTTCTG-TTTTA-GGATGTTAGG
1 CCGTTGCGACTTCAACCTATCCCTCTTC-GATTTTATGG-TGTTAGG
13562 CCAACCTATC
Statistics
Matches: 225, Mismatches: 52, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
47 2 0.01
48 37 0.16
49 168 0.75
50 18 0.08
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.39
Consensus pattern (49 bp):
CCGTTGCGACTTCAACCTATCCCTCTTCGATTTTATGGTGTTAGGTCCA
Found at i:13415 original size:98 final size:98
Alignment explanation
Indices: 13233--13551 Score: 378
Period size: 98 Copynumber: 3.3 Consensus size: 98
13223 CCGTTGCGGA
* ** * * * * *
13233 TTCAATCTATTCCCTCTTTGGTTTCAAGGTGTTAGATCCACCGTCGTGACTTCAATCTATCCCTC
1 TTCAACCTA-TCCCTCTTCAGTTTTAAGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTC
*
13298 TTC-AGTTTTAT-GGTATTAGGT-CAGCCGTTCCGAC
65 TTCGA-TTTT-TGGGTGTTAGGTCCA-CCGTTCCGAC
* * *
13332 TTCAACCTATCCCTTTTC-GATTTTAAGGTGTAAGATCCATTGTTGTGACTTTAATCTTTCCCTC
1 TTCAACCTATCCCTCTTCAG-TTTTAAGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTC
*
13396 TTCGATTTTTGGGTGTTAGGTCCACCGTTGCGAC
65 TTCGATTTTTGGGTGTTAGGTCCACCGTTCCGAC
13430 TTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTCT
1 TTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTCT
* * * * * *
13495 TCGATTTTAGGGTG-TAAGTCCATCATTACAAC
66 TCGATTTTTGGGTGTTAGGTCCACCGTTCCGAC
*
13527 TTCAACCTATCCCTCTTCTGTTTTA
1 TTCAACCTATCCCTCTTCAGTTTTA
13552 GGATGTTAGG
Statistics
Matches: 193, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
97 39 0.20
98 142 0.74
99 12 0.06
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (98 bp):
TTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCATCGTTGTGACTTCAATCTTTCCCTCT
TCGATTTTTGGGTGTTAGGTCCACCGTTCCGAC
Found at i:13723 original size:49 final size:49
Alignment explanation
Indices: 13570--14028 Score: 168
Period size: 49 Copynumber: 9.4 Consensus size: 49
13560 GGCCAACCTA
* * * *
13570 TCCCTCTTCGATTTTATGGTGTAAGATTCGTCGTAGT--GACTTCAATCTT
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCG-C-TATTACGACTTCAATCTT
*** * * * * * * * *
13619 TCCCTCTTTGGTTTT-TGGTGTTAGGT-CGCCATTGCGGCTTCAACCTA
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGACTTCAATCTT
* * *
13666 TCCTTCTTCAATTTTAAGGTGTAAGATCTGCTGTTACGACTTCAATCTT
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGACTTCAATCTT
* * * * * *
13715 TCTCTCTTCAATTTTAAGATGTTAGATCCGCCATTACAACTTCAATCTA
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGACTTCAATCTT
** * * * * ** ** *
13764 TCCCTCTTTGATTCTAGGGTGTTAGGT-CTATCATTGTGACTTC-ATCCT
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCGCT-ATTACGACTTCAATCTT
* * *
13812 TCCCTCTTCAGTTTTAAAGTGTAAGATCCG-TCATTACGACTTAAATCTT
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCGCT-ATTACGACTTCAATCTT
* ** * * ** ** * * *
13861 TCCCT-TCTCGATTTTTGGGTGTTAGGTCTACCGTTACGGCTTCAACCTA
1 TCCCTCT-TCAATTTTAAGGTGTAAGATCCGCTATTACGACTTCAATCTT
* * * *
13910 T-CCTTTTCAGTTTTAAGGTGTAAGATCCACTGTTAC-AGCTTCAATCTT
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGA-CTTCAATCTT
* * ** * * * * * *
13958 TTCCTTTTCGGTTTT-AGAGTGTTAGATTCG-TCGTTACGGCTTTAATCTA
1 TCCCTCTTCAATTTTAAG-GTGTAAGATCCGCT-ATTACGACTTCAATCTT
* *
14007 TCCTTATTCAATTTTAAGGTGT
1 TCCCTCTTCAATTTTAAGGTGT
14029 TAGGTTCGTC
Statistics
Matches: 296, Mismatches: 98, Indels: 32
0.69 0.23 0.08
Matches are distributed among these distances:
45 2 0.01
46 1 0.00
47 22 0.07
48 88 0.30
49 181 0.61
50 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.42
Consensus pattern (49 bp):
TCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGACTTCAATCTT
Found at i:13847 original size:97 final size:97
Alignment explanation
Indices: 13699--13937 Score: 250
Period size: 97 Copynumber: 2.5 Consensus size: 97
13689 AGATCTGCTG
* * * * *
13699 TTACGACTTCAATCTTTCTCTCTTCAATTTT-AAGATGTTAGATCCGCCATTACAACTTCAATCT
1 TTACGACTTC-ATCCTTCCCTCTTCAGTTTTAAAG-TGTAAGATCCGCCATTACAACTTAAATCT
* *
13763 ATCCC-TCTTTGATTCTAGGGTGTTAGGTCTATCA
64 ATCCCTTC-TCGATTCTAGGGTGTTAGGTCTACCA
** * * *
13797 TTGTGACTTCATCCTTCCCTCTTCAGTTTTAAAGTGTAAGATCCGTCATTACGACTTAAATCTTT
1 TTACGACTTCATCCTTCCCTCTTCAGTTTTAAAGTGTAAGATCCGCCATTACAACTTAAATCTAT
* * *
13862 CCCTTCTCGATTTTTGGGTGTTAGGTCTACCG
66 CCCTTCTCGATTCTAGGGTGTTAGGTCTACCA
* * * *
13894 TTACGGCTTCAACCTAT-CCTTTTCAGTTTTAAGGTGTAAGATCC
1 TTACGACTTCATCCT-TCCCTCTTCAGTTTTAAAGTGTAAGATCC
13938 ACTGTTACAG
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
97 103 0.88
98 14 0.12
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (97 bp):
TTACGACTTCATCCTTCCCTCTTCAGTTTTAAAGTGTAAGATCCGCCATTACAACTTAAATCTAT
CCCTTCTCGATTCTAGGGTGTTAGGTCTACCA
Found at i:13886 original size:325 final size:327
Alignment explanation
Indices: 13278--13865 Score: 738
Period size: 325 Copynumber: 1.8 Consensus size: 327
13268 ATCCACCGTC
*
13278 GTGACTTCAATCTATCCCTCTTCAGTTTTATGGTATTAGGTCAGCCGTTCCGACTTCAACCTATC
1 GTGACTTCAATCTATCCCTCTTCAGTTTTATGGTATTAGGTCAGCCATTCCGACTTCAACCTATC
* * ** * * **
13343 CCTTTTCGATTTTAAGGTGTAAGATCCATTGTTGTGACTTTAATCTTTCCCTCTTCGATTTTTGG
66 CCTTTTCAATTTTAAGGTGTAAGATCCACTGTTACGACTTCAATCTTTCCCTCTTCAATTTTAAG
* * * * * * *
13408 GTGTTAGGTCCACCGTTGCGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCATCGT
131 ATGTTAGATCCACCATTACAACTTCAACCTATCCCTCTTCAGTTCTAAGGTGTAAGATCCATCAT
* ** *
13473 TGTGACTTCAATCTTTCCCTCTTCGATTTTAGGGTGTAAGTCCATCATTACAACTTCAACCTATC
196 TGTGACTTCAATCCTTCCCTCTTCGATTTTAAAGTGTAAGTCCATCATTACAACTTAAACCTATC
13538 CCTCTTCTGTTTTAGGATGTTAGGCCAACCTATCCCTCTTCGATTTTATGGTGTAAGATTCGTCG
261 CCTCTTCTGTTTTAGGATGTTAGGCCAACCTATCCCTCTTCGATTTTATGGTGTAAGATTCGTCG
13603 TA
326 TA
* ** * * *
13605 GTGACTTCAATCTTTCCCTCTTTGGTTTT-TGGTGTTAGGTC-GCCATTGCGGCTTCAACCTAT-
1 GTGACTTCAATCTATCCCTCTTCAGTTTTATGGTATTAGGTCAGCCATTCCGACTTCAACCTATC
** *
13667 CCTTCTTCAATTTTAAGGTGTAAGATCTGCTGTTACGACTTCAATCTTTCTCTCTTCAATTTTAA
66 CCTT-TTCAATTTTAAGGTGTAAGATCCACTGTTACGACTTCAATCTTTCCCTCTTCAATTTTAA
* * * * * * *
13732 GATGTTAGATCCGCCATTACAACTTCAATCTATCCCTCTT-TGATTCTAGGGTGTTAGGTCTATC
130 GATGTTAGATCCACCATTACAACTTCAACCTATCCCTCTTCAG-TTCTAAGGTGTAAGATCCATC
* * *
13796 ATTGTGACTTC-ATCCTTCCCTCTTC-AGTTTTAAAGTGTAAGATCCGTCATTACGACTTAAATC
194 ATTGTGACTTCAATCCTTCCCTCTTCGA-TTTTAAAGTGTAAG-TCCATCATTACAACTTAAACC
*
13859 TTTCCCT
257 TATCCCT
13866 TCTCGATTTT
Statistics
Matches: 217, Mismatches: 40, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
323 1 0.00
324 30 0.14
325 149 0.69
326 11 0.05
327 26 0.12
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (327 bp):
GTGACTTCAATCTATCCCTCTTCAGTTTTATGGTATTAGGTCAGCCATTCCGACTTCAACCTATC
CCTTTTCAATTTTAAGGTGTAAGATCCACTGTTACGACTTCAATCTTTCCCTCTTCAATTTTAAG
ATGTTAGATCCACCATTACAACTTCAACCTATCCCTCTTCAGTTCTAAGGTGTAAGATCCATCAT
TGTGACTTCAATCCTTCCCTCTTCGATTTTAAAGTGTAAGTCCATCATTACAACTTAAACCTATC
CCTCTTCTGTTTTAGGATGTTAGGCCAACCTATCCCTCTTCGATTTTATGGTGTAAGATTCGTCG
TA
Found at i:13956 original size:97 final size:96
Alignment explanation
Indices: 13698--14028 Score: 249
Period size: 97 Copynumber: 3.4 Consensus size: 96
13688 AAGATCTGCT
* * * * * *
13698 GTTACGACTTCAATCTTTCTCTCTTCAATTTTAAGATGTTAGATCCGCCATTACAACTTCAATCT
1 GTTACGACTTCAACCTATC-CTCTTCAATTTTAAGGTGTAAGATCC-CTATTACAGCTTCAATCT
* * * *
13763 ATCCC-TCTTTGATTCTAGGGTGTTAGGTCTATC
64 TTCCCTTC-TCGATTTTAGGGTGTTAGGTCTACC
* ** * * * * *
13796 ATTGTGACTTCATCCT-TCCCTCTTCAGTTTTAAAGTGTAAGATCCGTCATTAC-GACTTAAATC
1 GTTACGACTTCAACCTAT-CCTCTTCAATTTTAAGGTGTAAGATCCCT-ATTACAG-CTTCAATC
*
13859 TTTCCCTTCTCGATTTTTGGGTGTTAGGTCTACC
63 TTTCCCTTCTCGATTTTAGGGTGTTAGGTCTACC
* * * *
13893 GTTACGGCTTCAACCTATCCTTTTCAGTTTTAAGGTGTAAGATCCACTGTTACAGCTTCAATCTT
1 GTTACGACTTCAACCTATCCTCTTCAATTTTAAGGTGTAAGATCC-CTATTACAGCTTCAATCTT
* * * * *
13958 TTCCTTTTCGGTTTTAGAGTGTTAGAT-T-CGTC
65 TCCCTTCTCGATTTTAGGGTGTTAGGTCTAC--C
* * * *
13990 GTTACGGCTTTAATCTATCCTTATTCAATTTTAAGGTGT
1 GTTACGACTTCAACCTATCC-TCTTCAATTTTAAGGTGT
14029 TAGGTTCGTC
Statistics
Matches: 185, Mismatches: 38, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
95 1 0.01
96 1 0.01
97 150 0.81
98 33 0.18
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (96 bp):
GTTACGACTTCAACCTATCCTCTTCAATTTTAAGGTGTAAGATCCCTATTACAGCTTCAATCTTT
CCCTTCTCGATTTTAGGGTGTTAGGTCTACC
Found at i:21374 original size:15 final size:15
Alignment explanation
Indices: 21354--21396 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
21344 AACATATATT
21354 CAATAAAATGCAAAG
1 CAATAAAATGCAAAG
21369 CAATAAAATGCAAA-
1 CAATAAAATGCAAAG
21383 -AATAAAATGCAAAG
1 CAATAAAATGCAAAG
21397 GATCACAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.48
15 14 0.52
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.14
Consensus pattern (15 bp):
CAATAAAATGCAAAG
Found at i:22664 original size:16 final size:16
Alignment explanation
Indices: 22627--22767 Score: 56
Period size: 16 Copynumber: 8.8 Consensus size: 16
22617 AAATGCTCTG
*
22627 AAAATAAAT-AACAAT
1 AAAATAAATAAACAAA
*
22642 AAGATAAATAAACAAA
1 AAAATAAATAAACAAA
* **
22658 AAAATAAAAAAATTAA
1 AAAATAAATAAACAAA
***
22674 ATGCTAAAATAAACAAA
1 AAAAT-AAATAAACAAA
* *
22691 CAAAT--ATAAATAATA
1 AAAATAAATAAACAA-A
* * **
22706 AAAATAATTGAGAGGCATG
1 AAAATAAAT-A-A-ACAAA
*
22725 AAAATAAAT-GACAAA
1 AAAATAAATAAACAAA
*
22740 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
*
22756 AAAATCAATAAA
1 AAAATAAATAAA
22768 TTAAATGTCA
Statistics
Matches: 85, Mismatches: 32, Indels: 17
0.63 0.24 0.13
Matches are distributed among these distances:
14 7 0.08
15 23 0.27
16 34 0.40
17 10 0.12
18 1 0.01
19 9 0.11
20 1 0.01
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:22752 original size:98 final size:98
Alignment explanation
Indices: 22625--22801 Score: 279
Period size: 98 Copynumber: 1.8 Consensus size: 98
22615 TAAAATGCTC
22625 TGAAAATAAATAACAATAAGATAAATAAACAAAAAAATAAAAAAATTAAATG-CTAAAATAAACA
1 TGAAAATAAATAACAATAAGATAAATAAACAAAAAAATAAAAAAATTAAATGTC-AAAATAAAC-
22689 AAC-AAATATAAATAATAAAAATAATTGAGAGGCA
64 AACTAAATATAAATAATAAAAATAATTGAGAGGCA
* * *
22723 TGAAAATAAATGACAAATAA-ATAAATAAACAAAAAAATCAATAAATTAAATGTCAAAATAAACA
1 TGAAAATAAATAAC-AATAAGATAAATAAACAAAAAAATAAAAAAATTAAATGTCAAAATAAACA
22787 ACTAAATATAAATAA
65 ACTAAATATAAATAA
22802 AAATAAAAAG
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
97 3 0.04
98 64 0.88
99 6 0.08
ACGTcount: A:0.67, C:0.07, G:0.06, T:0.20
Consensus pattern (98 bp):
TGAAAATAAATAACAATAAGATAAATAAACAAAAAAATAAAAAAATTAAATGTCAAAATAAACAA
CTAAATATAAATAATAAAAATAATTGAGAGGCA
Found at i:22792 original size:25 final size:25
Alignment explanation
Indices: 22752--22799 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
22742 AATAAATAAA
22752 CAAAAAAATCAATAAAT-TAAATGT
1 CAAAAAAATCAATAAATATAAATGT
22776 CAAAATAAA-CAACTAAATATAAAT
1 CAAAA-AAATCAA-TAAATATAAAT
22800 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (25 bp):
CAAAAAAATCAATAAATATAAATGT
Found at i:24019 original size:16 final size:15
Alignment explanation
Indices: 23993--24034 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
23983 TAAAAATTTT
23993 ATTTTTATAATTTCAA
1 ATTTTT-TAATTTCAA
*
24009 CATTTTTTAATTTTAA
1 -ATTTTTTAATTTCAA
24025 A-TTTTTAATT
1 ATTTTTTAATT
24035 AAATTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 1 0.04
16 8 0.33
17 6 0.25
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTAATTTCAA
Found at i:32065 original size:10 final size:10
Alignment explanation
Indices: 32050--32092 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
32040 AAATTTCACC
*
32050 AAAAAGAGAA
1 AAAAAGAAAA
32060 AAAAAGAAAA
1 AAAAAGAAAA
32070 AAAAAGAAATA
1 AAAAAGAAA-A
32081 GAAAAAGAAAA
1 -AAAAAGAAAA
32092 A
1 A
32093 GTAGAGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:32093 original size:18 final size:17
Alignment explanation
Indices: 32050--32091 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
32040 AAATTTCACC
*
32050 AAAAAGAGAA-AAAAAG
1 AAAAAGAAAAGAAAAAG
*
32066 AAAAA-AAAAGAAATAG
1 AAAAAGAAAAGAAAAAG
32082 AAAAAGAAAA
1 AAAAAGAAAA
32092 AGTAGAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:33372 original size:49 final size:48
Alignment explanation
Indices: 32954--33645 Score: 488
Period size: 49 Copynumber: 14.1 Consensus size: 48
32944 ACATTGAATC
* * * * * ** *
32954 TATACCCTAAAGATGTGAAGGGAGAGATTGAAGTCGCAATGATAAATCT
1 TATACCTTAGAGATGTG-AGGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * * * * *
33003 CATGCCCTAGAGATGTGAAGGGAAAGATTAAAGCTGCAAAGGCGAATCT
1 TATACCTTAGAGATGTG-AGGGAAAGATTGAAGCCGCAACGACGAACCT
* * *
33052 TATACATT-GAGGATGTGGAGGGAAAGGTTGAAACCGCAACTG-CGAACCT
1 TATACCTTAGA-GATGT-GAGGGAAAGATTGAAGCCGCAAC-GACGAACCT
* * * * *
33101 TGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGAAATGACGAATCT
1 TATACCTTAGAGATGTGA-GGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * * * * * *
33150 TGTACCCTAAAGATATGGAGGGAAAGGTTAAAACCGAAATGACGAACCT
1 TATACCTTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAACCT
* * *
33199 TATACCCTAGAGATATGGAGGGAAAGATTGAACCCGCAACGACGAACCT
1 TATACCTTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * * * *
33248 TATACCTTAAAGATGTGATGAGAAAGATTGAAGCTGTAATGACAAAACT
1 TATACCTTAGAGATGTGA-GGGAAAGATTGAAGCCGCAACGACGAACCT
* * *
33297 TATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCACAACGACGAACCT
1 TATACCTTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAACCT
* * * **
33346 TATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCTGCAACGGGGAACCT
1 TATACCTTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * * *** *
33395 TTTACGTTAGAAATGTGATGGGAATGATTGAAGCCGTAACGGTAAATCT
1 TATACCTTAGAGATGTGA-GGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * *
33444 TATACGTTAGAGATGTAGAGGGAAAGGTTGAAGTCACAACGATGAACCT
1 TATACCTTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAACCT
** * * ** *
33493 TATACCTTAGAGATGTGATTAGAAAGATTGAAGTCGCAATGGTGAATCT
1 TATACCTTAGAGATGTGA-GGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * *
33542 TATACCTTAGAGATGTAGAGGAAAAGGTTGAAGCCGCAATGATGAATCT
1 TATACCTTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAACCT
* * * * *
33591 TATACCTTAGAGATGTGAAAGGAAAGATTGAAGCTGTAACGACAAATCT
1 TATACCTTAGAGATGTG-AGGGAAAGATTGAAGCCGCAACGACGAACCT
33640 TATACC
1 TATACC
33646 CTGAAGATGA
Statistics
Matches: 520, Mismatches: 109, Indels: 28
0.79 0.17 0.04
Matches are distributed among these distances:
48 12 0.02
49 496 0.95
50 12 0.02
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (48 bp):
TATACCTTAGAGATGTGAGGGAAAGATTGAAGCCGCAACGACGAACCT
Found at i:33654 original size:98 final size:98
Alignment explanation
Indices: 32949--33654 Score: 585
Period size: 98 Copynumber: 7.2 Consensus size: 98
32939 AAAAAACATT
* * * ** * * * *
32949 GAATC-TATACCCTAAAGATGT-GAAGGGAGAGATTGAAGTCGCAATGATAAATCTCATGCCCTA
1 GAATCTTATACCCTAAAGATGTAG-AGGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTA
* * * *
33012 GAGATGTGAAGGGAAAGATTAAAGCTGCAAAGGC
65 GAGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
** * * * * *
33046 GAATCTTATACATTGAGGATGTGGAGGGAAAGGTTGAAACCGCAACTG-CGAACCTTGTACCTTA
1 GAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTGAAGCCGCAA-TGACGAACCTTATACCTTA
* * * *
33110 GAGATATGATGGGAAAGATTGAAGCCGAAATGAC
65 GAGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
* * * * * * *
33144 GAATCTTGTACCCTAAAGATATGGAGGGAAAGGTTAAAACCGAAATGACGAACCTTATACCCTAG
1 GAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTAG
* * *
33209 AGATATGGAGGGAAAGATTGAACCCGCAACGAC
66 AGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
* * * * * * * * *
33242 GAACCTTATACCTTAAAGATGT-GATGAGAAAGATTGAAGCTGTAATGACAAAACTTATACCCTA
1 GAATCTTATACCCTAAAGATGTAGA-GGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTA
* *
33306 GAGATGT-AGAGGGAAAGGTTGAAGCCACAACGAC
65 GAGATGTGA-AGGGAAAGATTGAAGCCGCAACGAC
* * * * ** * *
33340 GAACCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCTGCAACGGGGAACCTTTTACGTTAG
1 GAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTAG
* * * * **
33405 AAATGTGATGGGAATGATTGAAGCCGTAACGGT
66 AGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
* ** * * * * *
33438 AAATCTTATACGTTAGAGATGTAGAGGGAAAGGTTGAAGTCACAACGATGAACCTTATACCTTAG
1 GAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTAG
*** * * **
33503 AGATGTGATTAGAAAGATTGAAGTCGCAATGGT
66 AGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
* * * * *
33536 GAATCTTATACCTTAGAGATGTAGAGGAAAAGGTTGAAGCCGCAATGATGAATCTTATACCTTAG
1 GAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTAG
* * *
33601 AGATGTGAAAGGAAAGATTGAAGCTGTAACGAC
66 AGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
* *
33634 AAATCTTATACCCTGAAGATG
1 GAATCTTATACCCTAAAGATG
33655 AGGAGAAGCA
Statistics
Matches: 488, Mismatches: 113, Indels: 15
0.79 0.18 0.02
Matches are distributed among these distances:
97 9 0.02
98 473 0.97
99 6 0.01
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (98 bp):
GAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTGAAGCCGCAATGACGAACCTTATACCTTAG
AGATGTGAAGGGAAAGATTGAAGCCGCAACGAC
Found at i:33654 original size:147 final size:147
Alignment explanation
Indices: 32954--33647 Score: 610
Period size: 147 Copynumber: 4.7 Consensus size: 147
32944 ACATTGAATC
* * * * * * * *
32954 TATACCCTAAAGATGTGAAGGGAGAGATTGAAGTCGCAATGATAAATCTCATGCCCTAGAGATGT
1 TATACCTTAGAGATGTGATGGAAAAGATTGAAGCCGCAATGATAAATCTTATACCCTAGAGATGT
* * * * * * * *
33019 GAAGGGAAAGATTAAAGCTGCAAAGGCGAATCTTATA-CATTGAGGATGTGGAGGGAAAGGTTGA
66 GAAGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCCTAGA-GATGTGGAGGGAAAGATTGA
* *
33083 AACCGCAACTGCGAACCT
130 AGCCGCAACGGCGAACCT
* * * * ** * * *
33101 TGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGAAATGACGAATCTTGTACCCTAAAGATAT
1 TATACCTTAGAGATGTGATGGAAAAGATTGAAGCCGCAATGATAAATCTTATACCCTAGAGATGT
* * * * * * *
33166 GGAGGGAAAGGTTAAAACCGAAATGACGAACCTTATACCCTAGAGATATGGAGGGAAAGATTGAA
66 GAAGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCCTAGAGATGTGGAGGGAAAGATTGAA
* *
33231 CCCGCAACGACGAACCT
131 GCCGCAACGGCGAACCT
* * * * *
33248 TATACCTTAAAGATGTGAT-GAGAAAGATTGAAGCTGTAATGACAAAACTTATACCCTAGAGATG
1 TATACCTTAGAGATGTGATGGA-AAAGATTGAAGCCGCAATGATAAATCTTATACCCTAGAGATG
** * *
33312 T-AGAGGGAAAGGTTGAAGCCACAACGACGAACCTTATACCCTAGAGATGTAGAGGGAAAGGTTG
65 TGA-AGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCCTAGAGATGTGGAGGGAAAGATTG
* *
33376 AAGCTGCAACGGGGAACCT
129 AAGCCGCAACGGCGAACCT
* * * * * * * * **
33395 TTTACGTTAGAAATGTGATGGGAATGATTGAAGCCGTAACGGTAAATCTTATACGTTAGAGATGT
1 TATACCTTAGAGATGTGATGGAAAAGATTGAAGCCGCAATGATAAATCTTATACCCTAGAGATGT
* * * **
33460 -AGAGGGAAAGGTTGAAG-TCACAACGATGAACCTTATACCTTAGAGATGT-GATTAGAAAGATT
66 GA-AGGGAAAGGTTGAAGCT-GCAACGACGAACCTTATACCCTAGAGATGTGGA-GGGAAAGATT
* * * *
33522 GAAGTCGCAATGGTGAATCT
128 GAAGCCGCAACGGCGAACCT
* * *
33542 TATACCTTAGAGATGTAGA-GGAAAAGGTTGAAGCCGCAATGATGAATCTTATACCTTAGAGATG
1 TATACCTTAGAGATGT-GATGGAAAAGATTGAAGCCGCAATGATAAATCTTATACCCTAGAGATG
* * * * *
33606 TGAAAGGAAAGATTGAAGCTGTAACGACAAATCTTATACCCT
65 TGAAGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCCT
33648 GAAGATGAGG
Statistics
Matches: 441, Mismatches: 97, Indels: 18
0.79 0.17 0.03
Matches are distributed among these distances:
146 3 0.01
147 429 0.97
148 9 0.02
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (147 bp):
TATACCTTAGAGATGTGATGGAAAAGATTGAAGCCGCAATGATAAATCTTATACCCTAGAGATGT
GAAGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCCTAGAGATGTGGAGGGAAAGATTGAA
GCCGCAACGGCGAACCT
Done.