Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020008.1 Corchorus olitorius cultivar O-4 contig20041, 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: 122034
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:603 original size:9 final size:9
Alignment explanation
Indices: 583--620 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
573 TTAATTCATT
583 TAATTTCC-
1 TAATTTCCA
591 TAATTTCCA
1 TAATTTCCA
*
600 TAATTTCCC
1 TAATTTCCA
609 TAATTTCCA
1 TAATTTCCA
618 TAA
1 TAA
621 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:612 original size:18 final size:17
Alignment explanation
Indices: 583--620 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
573 TTAATTCATT
583 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
600 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
618 TAA
1 TAA
621 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Found at i:8621 original size:33 final size:33
Alignment explanation
Indices: 8579--8645 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
8569 AAAGGGGGGA
8579 CCTGATGTTATTGAGATCCATGAAACAAAGAAG
1 CCTGATGTTATTGAGATCCATGAAACAAAGAAG
*
8612 CCTGATGTTATTGAGATCCATGAAACAGAGAAG
1 CCTGATGTTATTGAGATCCATGAAACAAAGAAG
8645 C
1 C
8646 TTCTTCAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (33 bp):
CCTGATGTTATTGAGATCCATGAAACAAAGAAG
Found at i:11272 original size:32 final size:32
Alignment explanation
Indices: 11236--11300 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
11226 TCTGAATCTG
11236 AATTTCAAAAAATTAGAAA-ACCATGTTCATAC
1 AATTTCAAAAAATTA-AAATACCATGTTCATAC
* * **
11268 AATTTCAGAAATTTAAAATGGCATGTTCATAC
1 AATTTCAAAAAATTAAAATACCATGTTCATAC
11300 A
1 A
11301 CTTTTGAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (32 bp):
AATTTCAAAAAATTAAAATACCATGTTCATAC
Found at i:18671 original size:14 final size:14
Alignment explanation
Indices: 18652--18679 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18642 CTCCTAATTC
18652 GATCCAGTTTCCTA
1 GATCCAGTTTCCTA
18666 GATCCAGTTTCCTA
1 GATCCAGTTTCCTA
18680 CTAGGTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (14 bp):
GATCCAGTTTCCTA
Found at i:20372 original size:32 final size:30
Alignment explanation
Indices: 20319--20377 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
20309 TTTTTTAATG
*
20319 AATTTTTTAATGTAGATTATAAGGTATTCAT
1 AATTTTTTAATGTAAATTATAA-GTATTCAT
20350 AATTTTTTAATG-AAATAATATAAGTATT
1 AATTTTTTAATGTAAAT--TATAAGTATT
20378 TAATTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 17 0.68
32 5 0.20
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
AATTTTTTAATGTAAATTATAAGTATTCAT
Found at i:29589 original size:15 final size:15
Alignment explanation
Indices: 29569--29598 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29559 CAAATCTCAC
29569 AAGTAGATGTTCAAA
1 AAGTAGATGTTCAAA
29584 AAGTAGATGTTCAAA
1 AAGTAGATGTTCAAA
29599 GTCTTGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (15 bp):
AAGTAGATGTTCAAA
Found at i:35276 original size:24 final size:25
Alignment explanation
Indices: 35228--35280 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
35218 GGGATTGGAG
*
35228 TATTATTTATCTTGTTGCTTAATTT
1 TATTATTTATCTTGTTGATTAATTT
* *
35253 TATTATTT-TCTTGTTTATTTATTT
1 TATTATTTATCTTGTTGATTAATTT
35277 TATT
1 TATT
35281 GTTCACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70
Consensus pattern (25 bp):
TATTATTTATCTTGTTGATTAATTT
Found at i:36183 original size:12 final size:12
Alignment explanation
Indices: 36166--36191 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36156 GGGGAAAGGG
36166 GATCACCTTGAC
1 GATCACCTTGAC
36178 GATCACCTTGAC
1 GATCACCTTGAC
36190 GA
1 GA
36192 ATTCCTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (12 bp):
GATCACCTTGAC
Found at i:39192 original size:30 final size:31
Alignment explanation
Indices: 39140--39199 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
39130 TGGAAGTTTC
39140 TATAGAAAGTAAGGAGATAGAAAGT-CTTTT
1 TATAGAAAGTAAGGAGATAGAAAGTACTTTT
* *
39170 TATAGAAAGTTTAGGATA-AGAAAGTACTTT
1 TATAGAAAG-TAAGGAGATAGAAAGTACTTT
39200 AACATGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (31 bp):
TATAGAAAGTAAGGAGATAGAAAGTACTTTT
Found at i:39465 original size:19 final size:19
Alignment explanation
Indices: 39441--39483 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
39431 TAAACTTTCT
39441 ACAAAAAAAAAAAAAAAAA
1 ACAAAAAAAAAAAAAAAAA
* * *
39460 ACAAAAAACAAACAAACAA
1 ACAAAAAAAAAAAAAAAAA
39479 ACAAA
1 ACAAA
39484 CAAACATGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (19 bp):
ACAAAAAAAAAAAAAAAAA
Found at i:39472 original size:4 final size:4
Alignment explanation
Indices: 39458--39489 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
39448 AAAAAAAAAA
39458 AAAC AAA- AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC A
39490 TGCTAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:41983 original size:41 final size:41
Alignment explanation
Indices: 41926--42244 Score: 399
Period size: 41 Copynumber: 7.7 Consensus size: 41
41916 TTTTCGTTTG
* *
41926 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATTAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
41967 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
42008 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTGTCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
42049 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
42090 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
** * * * *
42131 TTCAAGAACAAGTCATCGAGACCCTTAAATCGAATTATTTTTAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
** * * * * *
42175 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTTAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
42216 TTCAAGACCAAGTCATTC--GACCCTTGAAT
1 TTCAAGATTAAGTCA-TCGAGACCCTTGAAT
42245 CAAAACAAAT
Statistics
Matches: 252, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
40 11 0.04
41 204 0.81
42 4 0.02
43 1 0.00
44 32 0.13
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (41 bp):
TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:44824 original size:16 final size:16
Alignment explanation
Indices: 44803--44834 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44793 CATAGTTCAG
*
44803 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAACTCT
44819 AAAGCAGAAAAACTCT
1 AAAGCAGAAAAACTCT
44835 GAAGTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.16, T:0.12
Consensus pattern (16 bp):
AAAGCAGAAAAACTCT
Found at i:44991 original size:41 final size:41
Alignment explanation
Indices: 44934--45257 Score: 418
Period size: 41 Copynumber: 7.9 Consensus size: 41
44924 TTTTCGTTTG
*
44934 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
44975 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
45016 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
45057 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
45098 TTCAAGATTGAGTCATCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
** * *
45139 TTCAAGAACAAGTCATCAAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
** * * * * * *
45183 TTCAAGACCAAGTCGTCAAGATCCTTGAATTAGATTGTTAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
45224 TTCAAGACCAAGTCAATC--GACCCTTGAATCAAAT
1 TTCAAGATTAAGTC-ATCGAGACCCTTGAATTAAAT
45258 CAAATCAAAC
Statistics
Matches: 259, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
40 13 0.05
41 206 0.80
42 4 0.02
43 1 0.00
44 35 0.14
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (41 bp):
TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:56063 original size:27 final size:28
Alignment explanation
Indices: 56028--56094 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
56018 AAATAATTAC
*
56028 TTTGAATATTGT-T-ATATGCTAAACTTA
1 TTTGGATATTGTATCATATGCTAAAC-TA
* * *
56055 TTTGGATATTGTATCATTTGTTACACTA
1 TTTGGATATTGTATCATATGCTAAACTA
56083 TTTGGATATTGT
1 TTTGGATATTGT
56095 CTGATTTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.32
28 15 0.44
29 8 0.24
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (28 bp):
TTTGGATATTGTATCATATGCTAAACTA
Found at i:56887 original size:18 final size:18
Alignment explanation
Indices: 56866--56901 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56856 CGAGGACATT
*
56866 GATGGTGATGAAAATGAA
1 GATGATGATGAAAATGAA
*
56884 GATGATGATGAAGATGAA
1 GATGATGATGAAAATGAA
56902 CAATTTGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (18 bp):
GATGATGATGAAAATGAA
Found at i:64031 original size:20 final size:21
Alignment explanation
Indices: 64003--64058 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
63993 GGCCAAATTA
* * *
64003 AAATAAAAAATTATAGGGAC-
1 AAATTAAAAATAAAAGGGACT
64023 AAATTAAAAA-AAAAGGGACT
1 AAATTAAAAATAAAAGGGACT
64043 AAATTAGAAAATAAAA
1 AAATTA-AAAATAAAA
64059 ATTATGAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
20 15 0.50
21 4 0.13
22 4 0.13
ACGTcount: A:0.66, C:0.04, G:0.12, T:0.18
Consensus pattern (21 bp):
AAATTAAAAATAAAAGGGACT
Found at i:64039 original size:19 final size:22
Alignment explanation
Indices: 64017--64058 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
64007 AAAAAATTAT
64017 AGGGAC-AAATTA-AAAA-AAA
1 AGGGACTAAATTAGAAAATAAA
64036 AGGGACTAAATTAGAAAATAAA
1 AGGGACTAAATTAGAAAATAAA
64058 A
1 A
64059 ATTATGAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 4 0.20
22 4 0.20
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (22 bp):
AGGGACTAAATTAGAAAATAAA
Found at i:69406 original size:76 final size:76
Alignment explanation
Indices: 69232--69393 Score: 254
Period size: 76 Copynumber: 2.1 Consensus size: 76
69222 CTATGCTTCA
* * *
69232 GACGATCGTGATTTTAGCTTGTTGATAAGTGACCTTATTTAAGGCTCTCGTTAGAGTTAGCGATC
1 GACGATCGTGACTTCAGCTTGTTGACAAGTGACCTTATTTAAGGCTCTCGTTAGAGTTAGCGATC
69297 CTGTTAGTGTT
66 CTGTTAGTGTT
* *
69308 GACGATCGTGATTTCAGCTTGTTGACAAGTGACCTT-TTTAAAGGCTCTTGTTAAGAGTTAGCGA
1 GACGATCGTGACTTCAGCTTGTTGACAAGTGACCTTATTT-AAGGCTCTCGTT-AGAGTTAGCGA
69372 TCCTGTTAGTGTT
64 TCCTGTTAGTGTT
69385 GACGATCGT
1 GACGATCGT
69394 CCTTCGCTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
75 3 0.04
76 45 0.56
77 33 0.41
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (76 bp):
GACGATCGTGACTTCAGCTTGTTGACAAGTGACCTTATTTAAGGCTCTCGTTAGAGTTAGCGATC
CTGTTAGTGTT
Found at i:69520 original size:15 final size:15
Alignment explanation
Indices: 69502--69536 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
69492 CCTTTGAAAT
69502 CTAAAATGCTGAATA
1 CTAAAATGCTGAATA
69517 CTAAAATGCTGAATA
1 CTAAAATGCTGAATA
69532 CTAAA
1 CTAAA
69537 TAAATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (15 bp):
CTAAAATGCTGAATA
Found at i:77261 original size:2 final size:2
Alignment explanation
Indices: 77254--77281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
77244 ATAAAGGAAG
77254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77282 TCTTCAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80033 original size:17 final size:17
Alignment explanation
Indices: 80011--80045 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
80001 ACAGTGAATA
*
80011 TAAAATTTCATCTATAT
1 TAAAATTTCATCCATAT
80028 TAAAATTTCATCCATAT
1 TAAAATTTCATCCATAT
80045 T
1 T
80046 GTATAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTTCATCCATAT
Found at i:90996 original size:52 final size:51
Alignment explanation
Indices: 90939--91107 Score: 137
Period size: 52 Copynumber: 3.3 Consensus size: 51
90929 CAGAAATAGA
* *
90939 AAAAAGCCATAAAT-CAACCTAAGCCATTCAC-ACATCCAACCAAATATTAAGC
1 AAAAAGCCATAAATCCAACCT--GCCATTCACTA-ATCAAACCAAATATTAACC
* **
90991 AAAAAGGCATAAATCCATGCTGCCATTCACTAATCAAACCAAATATTAACC
1 AAAAAGCCATAAATCCAACCTGCCATTCACTAATCAAACCAAATATTAACC
* ** ** ** * *
91042 AAAATTG-CATATTTGTATTGCTGCCATTCACAAATCAAACCAAAGATTAACC
1 AAAA-AGCCATAAATCCA-ACCTGCCATTCACTAATCAAACCAAATATTAACC
*
91094 AAATAGCCATAAAT
1 AAAAAGCCATAAAT
91108 TAGTTGCTTC
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
51 37 0.39
52 55 0.57
53 4 0.04
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (51 bp):
AAAAAGCCATAAATCCAACCTGCCATTCACTAATCAAACCAAATATTAACC
Found at i:91115 original size:52 final size:51
Alignment explanation
Indices: 90961--91121 Score: 164
Period size: 52 Copynumber: 3.1 Consensus size: 51
90951 ATCAACCTAA
* * * * *
90961 GCCATTCACACATCCAACCAAATATTAAGCAAAAAGGCATAAATCCA-TGCT
1 GCCATTCACAAATCAAACCAAATATTAACCAAATA-GCATAAATCTATTGCT
* * ** *
91012 GCCATTCACTAATCAAACCAAATATTAACCAAAATTGCATATTTGTATTGCT
1 GCCATTCACAAATCAAACCAAATATTAACC-AAATAGCATAAATCTATTGCT
*
91064 GCCATTCACAAATCAAACCAAAGATTAACCAAATAGCCATAAAT-TAGTTGCT
1 GCCATTCACAAATCAAACCAAATATTAACCAAATAG-CATAAATCTA-TTGCT
*
91116 TCCATT
1 GCCATT
91122 AGTAGATCCA
Statistics
Matches: 90, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
51 40 0.44
52 50 0.56
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (51 bp):
GCCATTCACAAATCAAACCAAATATTAACCAAATAGCATAAATCTATTGCT
Found at i:92735 original size:1 final size:1
Alignment explanation
Indices: 92729--92757 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
92719 GTGATCGAGG
92729 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
92758 ATCTTAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:94051 original size:740 final size:739
Alignment explanation
Indices: 91885--96075 Score: 4510
Period size: 740 Copynumber: 5.7 Consensus size: 739
91875 ACCAAACGGC
* * *
91885 CCCTAAGAACTTGTAGATA-TGGTCAATAAAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
1 CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
* * * * *
91949 TTAAGACACACCATACTGTTGGTCATGCTACGGTGCTTGAAGTATGTTTTTAGCTTAGTAATAAT
66 TTAAGACACACCATACTGTCGGTCATGCTGCGGTGCTTAAAGTGTTTTTTTAGCTTAGTAATAAT
* ** * * *
92014 TCATTCTTATTCCAATAATTTGTTTTCTAATTGGTT-AGCAATTTGGGGATTGACAATTTCTGGG
131 TCGTTCCCATTCCAATAATTTGTTTTCTGATTGATTGA-CCATTTGGGGATTGACAATTTCTGGG
* * *
92078 AAGGTTTTAC-AAATAAGTTATACGAGAGTGTATTAGTTTTTCCATGTAGTATAGTATCAGATCC
195 AAGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGTAGTATAGTATCAGAGCC
* * * *
92142 AAGTTAC-GTATAAAACTGGCGCAATCTGCGAGATATTATGCAATTTGCAACAAAAGCCTCATGA
260 AAGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCATGA
** * * *
92206 ATTTGCCCATCCCAAAAGTCGCCTTAATTTTGTGTGAAATAAACCTATATCTTCAACTAGGTATT
325 ATTTGCCTTTCCCAAAAGTCGCCTCAATTTTGTTTGAAATAAACCGATATCTTCAACTAGGTATT
* * *
92271 CATGATAGATTAACTCTATTACAT-AGTTAGTTTTGTATA-GGTCCCATATAAAAATATATATTA
390 CATGATTGCTTAACTCTATTACATAAGTTAGTTTTGTATATGG-CCCATATAAAAACATATATTA
* * * * *
92334 GTGATTCACTGGCAATCGTTATAAATTCTACACAACCGATGTCTATAATTACCCATACAGCGCCT
454 GTGATTCACTGGCAATCGTTAT-AAGTCTAAACAACCGATGTCGATAATTACCCCT-GAGCGCCT
* * * * *
92399 AGCACCCAACTTATTATGCCGTTACAGATTACGCTCGTACAAAATACTGCATCTAATGCGAATAT
517 AGCACCCAACTTATTATGCCGTTATAGATTACGCTCGTACAAAATACTCCAGCTAACGCGAATAA
* * * * *
92464 CGAAACCAACATTTCGT-TCAAGAGGAACTTGTGTTGCTTAAAGATGAAACCCTTCCTTGGATCC
582 CGAAACCAACATTCCGTCT-AGGAGGAACTTGTGTTGCTTCAAGATGAACCCCTTCCTCGG-TCC
*
92528 AACAGTCTAATGAGGTTCAGAAATACAAACAGTCCGCTCAATATTATTTTTAAGGGAAGCAACTC
645 AACAGTCTAATGAGGTTCAGATATACAAACAGTCCGCTCAATATTATTTTTAAGGGAAGCAACTC
92593 TGTTATGATAACCTTAAGCCGATCCGATAA
710 TGTTATGATAACCTTAAGCCGATCCGATAA
* * ** * * * * *
92623 TCTTAAGATTTTAGAGAT-TTGGTCAACATATTTCT-TCCATAAAGAATGGTTAGCAATGAAAAC
1 CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCT-CATATAGAATGGGTAGCAGTGAAAAC
* * * ** **** *
92686 GTTGAGACACATCATACTGTCGGTTATGTTGCAGTGATCGAGGTTTTTTTTTTTTTTTTTTTTTT
65 GTTAAGACACACCATACTGTCGGTCA---TGC--TG--C--GG------TGCTTAAAGTGTTTTT
*** * * * * * * * *
92751 TTTTTTTATCTTAGTTATTCGTTCGCATTCTAATATTTTGTTTTCAGATTGGTTGACCATTTGGG
115 TTAGCTTA--GTAATAATTCGTTCCCATTCCAATAATTTGTTTTCTGATTGATTGACCATTTGGG
*
92816 GATTGACAATTTTTGGGAAGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGT
178 GATTGACAATTTCTGGGAAGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGT
* * * *
92881 AGTATAGTATCAGATCCAAGTTACTGTATAGAACTGGCCCAA-CT-TGTG--ATCATGCAATTTG
243 AGTATAGTATCAGAGCCAAGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTG
*
92942 CCACAAAAGCCTCATGAATTTGCCTTTCCCGAAAGTCGCCTCAATTTTGTTTGAAATAAACCGAT
308 CCACAAAAGCCTCATGAATTTGCCTTTCCCAAAAGTCGCCTCAATTTTGTTTGAAATAAACCGAT
* *
93007 ATCTTTAACTAGGTATTCATGATTGCTTAACTCTATTACATAGAGTTAGTTTTGTATATGTCCCA
373 ATCTTCAACTAGGTATTCATGATTGCTTAACTCTATTACATA-AGTTAGTTTTGTATATGGCCCA
* * ** *
93072 TATAAAAACATACATTAGTGATTCACTGGAAATCGTTATAAGTCTAAACAATTGATGTCTATAAT
437 TATAAAAACATATATTAGTGATTCACTGGCAATCGTTATAAGTCTAAACAACCGATGTCGATAAT
* * * * * * ** * * ** **** *
93137 TACCCCTGCAGCGCCGATCACCTAGCTCACTATATCATCATAGACAATAAACGTACAAAATGCTC
502 TACCCCTG-AGCGCCTAGCACCCAACTTATTATGCCGTTATAGATTACGCTCGTACAAAATACTC
* * * * * * * * * * * * * *
93202 CAGCTATCACGACTGACAAAACCAAAATTCTGTCGAGGATGAACTT-TAATTGGTCCACGATGGA
566 CAGCTAACGCGAATAACGAAACCAACATTCCGTCTAGGAGGAACTTGT-GTTGCTTCAAGATGAA
* *
93266 CCCCTTCCTCGGTTCC-ACAAGTCTAATGAGGTTAAAATATACAAACAGTCCGCTTC-AT-TTAT
630 CCCCTTCCTCGG-TCCAAC-AGTCTAATGAGGTTCAGATATACAAACAGTCCGC-TCAATATTAT
* * * * *
93328 TTTTAAGGGAATCAATTCTGATATGATAACCTTAAACCCATCCGATAA
692 TTTTAAGGGAAGCAACTCTGTTATGATAACCTTAAGCCGATCCGATAA
* * *
93376 CCCTAAGAATTTGTAGATATT-GTCAACATAGTTCTCTCGTATAGAATGGGTAGCAGTGAAAACG
1 CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
* * * *
93440 TTAAGACAGACCATACTGTCGGTCATGCTGCTGTTCTTAAAGTGTTTTTTTAGCTTAGTAATAAA
66 TTAAGACACACCATACTGTCGGTCATGCTGCGGTGCTTAAAGTGTTTTTTTAGCTTAGTAATAAT
*
93505 TCGTTCCCATTCCAATAATTTGTTTTCCT-ATTGATT-AGCCATTTGGGGATTGACAATTTCTAG
131 TCGTTCCCATTCCAATAATTTGTTTT-CTGATTGATTGA-CCATTTGGGGATTGACAATTTCTGG
* * * *
93568 GAAGGTTATACAAAATAAGTTATACGACA-TGGTTTTAGTTTTTCCACGTAGTATGGTATCGGAG
194 GAAGGTTATACAAAATAAGTTATACGAGAGT-GTATTAGTTTTTCCACGTAGTATAGTATCAGAG
* * * ** * *
93632 CCAATTTACTGTA-ATGAACTGTCCCAACCTGCGGGATATTATGCGCTTTGCCCCAAAAGGCTCA
258 CCAAGTTACTGTATA-GAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCA
* **
93696 T-AGATTTGTCTTTCCCAAAAGTCGCCTCAATTTTTGTTTGAAATAAACATATATCTTCAACTAG
322 TGA-ATTTGCCTTTCCCAAAAGTCGCCTCAA-TTTTGTTTGAAATAAACCGATATCTTCAACTAG
* * *
93760 GTATTCATGATTGCTTGACTCTATTACAT-ATTTGGTTTTGTAT-TGGCCCTATATAAAAACATA
385 GTATTCATGATTGCTTAACTCTATTACATAAGTTAGTTTTGTATATGGCCC-ATATAAAAACATA
* ** * * *
93823 TATTAGAGATTCGTTGGCAATTGCTATAAGTTCTACACAACCGATGTCGATAATTACCCCTGAGC
449 TATTAGTGATTCACTGGCAATCGTTATAAG-TCTAAACAACCGATGTCGATAATTACCCCTGAG-
* *
93888 CGCCTAGCACCAAACTTATTATGCCGTTATAGATTACGCTCGTACAAAATACTACAGCTAACGCG
512 CGCCTAGCACCCAACTTATTATGCCGTTATAGATTACGCTCGTACAAAATACTCCAGCTAACGCG
93953 AATAACGAAACCAACATTCCGTCTAGGAGGAACTTGTGTTGCTTCAAGATGAACCCCTTCCTCGA
577 AATAACGAAACCAACATTCCGTCTAGGAGGAACTTGTGTTGCTTCAAGATGAACCCCTTCCTCG-
* *
94018 GTCTAACAGTCTAATGATGTTCAGATATACAAACAGTCCGCTCAATATTATTTTTAA-GGAAGCA
641 GTCCAACAGTCTAATGAGGTTCAGATATACAAACAGTCCGCTCAATATTATTTTTAAGGGAAGCA
* *
94082 ACTCCGTTATGATAACCTTAAGCCGATCCGACAA
706 ACTCTGTTATGATAACCTTAAGCCGATCCGATAA
* * * *
94116 TCTTAAGGACTTATAGAT-TTGGTCAACATAGTTCTCTCATATAGAATGGTTAGCAGTGAAAACG
1 CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
* * * * * * *
94180 TTGAGACACATCC-TACTGTCAGTTAT-CTTGCGGTGATTAAGGTGTTTTTTTATCTTACT--T-
66 TTAAGACACA-CCATACTGTCGGTCATGC-TGCGGTGCTTAAAGTGTTTTTTTAGCTTAGTAATA
* * * * * * * ** * *
94240 ATTCGTTCGCGTTCAAATATTTTGTTTACCGATTGGTTGACCATTTATGAATTGACAATTTTTGG
129 ATTCGTTCCCATTCCAATAATTTGTTTTCTGATTGATTGACCATTTGGGGATTGACAATTTCTGG
* * * * * *
94305 GACGGTTATACAAAATAAGTTATACGATAGTGTATTAATTTTTCCATGTAGTATAGTCTCAGATC
194 GAAGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGTAGTATAGTATCAGAGC
*
94370 CAAGTTAC----T----CT-----AACCTGCGAGATATTATGCAATTTGCCACAAAAACCTCATG
259 CAAGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCATG
* *
94422 AATTTGCCTTTCCCGAAAGTCGCCTCAATTTTGTTTGAAATAAACCGATATCTTTAACTAGGTAT
324 AATTTGCCTTTCCCAAAAGTCGCCTCAATTTTGTTTGAAATAAACCGATATCTTCAACTAGGTAT
*
94487 TCATGATTGCTTAACTCTATTACATAGAGTTAGTTTTGTATATGTCCCATATAAAAACATATATT
389 TCATGATTGCTTAACTCTATTACATA-AGTTAGTTTTGTATATGGCCCATATAAAAACATATATT
* * *
94552 AGTGATTCACTGGCAATCGTTATAAGTCTAAACAACTGATGTCGATAATTAACCCTGCAGCG-GT
453 AGTGATTCACTGGCAATCGTTATAAGTCTAAACAACCGATGTCGATAATTACCCCTG-AGCGCCT
* * * * ** * * * *
94616 GATCACCCAACTCACTATGTCGTCT-TAGAAAATGC-CTGTACAAAATGCTCCAGCTATCACGAA
517 -AGCACCCAACTTATTATGCCGT-TATAGATTACGCTC-GTACAAAATACTCCAGCTAACGCGAA
* * * * * * * * * * * *
94679 TTACGAAACTAAAATTCTGTCGATGATGAACTT-TAATTGGTTCACGATGGACCCCTTCCTTGGT
579 TAACGAAACCAACATTCCGTCTAGGAGGAACTTGT-GTTGCTTCAAGATGAACCCCTTCCTCGG-
* * * * **
94743 TCCACCAGTCTGATGAGGTTCAGATATACAAACAGTCTGCTTC-AT-TTATTTTTAAGAGACTCA
642 TCCAACAGTCTAATGAGGTTCAGATATACAAACAGTCCGC-TCAATATTATTTTTAAGGGAAGCA
* * * * *
94806 ATTCTGATATGATACCCTTAAACCCATCCGATAA
706 ACTCTGTTATGATAACCTTAAGCCGATCCGATAA
** * * *
94840 CCCTAAGAACTTATAGATA-ACGTCAACATATTTCTCTCGTATAGAATAGGTAGCAGTGAAAACG
1 CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
* *
94904 TTAAGACACACCATACTGTCGGTCATGCTGCAGTGCTTAAAGTGTTTTTTTAGCTTAGTAATAAA
66 TTAAGACACACCATACTGTCGGTCATGCTGCGGTGCTTAAAGTGTTTTTTTAGCTTAGTAATAAT
** * **
94969 TCGTTCTTATTCCAATAATTTGTTTTCTGATTGATTGGCCATTTGGGGATTGACAATTTCTAAGA
131 TCGTTCCCATTCCAATAATTTGTTTTCTGATTGATTGACCATTTGGGGATTGACAATTTCTGGGA
* * * * **
95034 AGGTTACACAAAATAAGTTATACGAGAGT-TTTTAGTTTTTCCATGTAGTATGGTATTGGAGCCA
196 AGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGTAGTATAGTATCAGAGCCA
* * * * * *
95098 ATTTACTGTAAATAACTGTCCCAACCTGCGAGATATTATGCACTTTGCCACAAAAGGCTCAT-AG
261 AGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCATGA-
* * * *
95162 ATTTGCGTTTCCCAAAAGTCGCCTCAATTTTTGTATGAAATAAACCTATATCATCAACTAGGTAT
325 ATTTGCCTTTCCCAAAAGTCGCCTCAA-TTTTGTTTGAAATAAACCGATATCTTCAACTAGGTAT
* * * **
95227 TCATGATTACTTAACTCTATTACAT-ATTTAGTTTTGTAT-TGTTCATATATAAAAACATATATT
389 TCATGATTGCTTAACTCTATTACATAAGTTAGTTTTGTATATG-GCCCATATAAAAACATATATT
* * * * *
95290 AGAGATTCACTGGCGATCGTTATAAAATCTACACAACCAATGTCGATAATTA-CCCTGAGCCGCC
453 AGTGATTCACTGGCAATCGTTAT-AAGTCTAAACAACCGATGTCGATAATTACCCCTGAG-CGCC
* * * * * *
95354 TAGCACCCAACTTATTATGCCGTCATAGATTACGCTCGTACAAAA-AGTTGCAGTTAATGCCAAT
516 TAGCACCCAACTTATTATGCCGTTATAGATTACGCTCGTACAAAATA-CTCCAGCTAACGCGAAT
* * *
95418 AACGAAACCAACATTCCATTTAGGAGGAACTTGTGTTGCTTCAAGATGAACCCCTTCATCGAGTC
580 AACGAAACCAACATTCCGTCTAGGAGGAACTTGTGTTGCTTCAAGATGAACCCCTTCCTCG-GTC
* * *
95483 CAACAGTCTAATGAGATTCAAATATACAAACAGTCCGCTCAATATTATTTTTAAGGGAAGGAACT
644 CAACAGTCTAATGAGGTTCAGATATACAAACAGTCCGCTCAATATTATTTTTAAGGGAAGCAACT
*
95548 CTGTTATGATAACCTTAAGCCGATCCGACAA
709 CTGTTATGATAACCTTAAGCCGATCCGATAA
* * * * *
95579 TCTTAAGAACTTATAGAT-TTGGTCAACATAGTTCTCCCACATAGAATGGTTAGCAGTGAAAACG
1 CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
** * * * * * * **
95643 TTAAGACACGTCATACTGCCAGTTATGCTGCGGTGATTGAGGTGTTTTTTTTATATTAGT--T-A
66 TTAAGACACACCATACTGTCGGTCATGCTGCGGTGCTTAAAGTG-TTTTTTTAGCTTAGTAATAA
* * * * * * *
95705 TTCGTT-CGATTCTAATATTTTGTTTTCTGATTGATTGACCAATTGTGGAATGACAATTTTTGGG
130 TTCGTTCCCATTCCAATAATTTGTTTTCTGATTGATTGACCATTTGGGGATTGACAATTTCTGGG
* * *
95769 AAGGTTATACAAAATAAGTTATCCGAGAGTATATTAATTTTTCCACGTAGTATAGTATCAGATG-
195 AAGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGTAGTATAGTATCAGA-GC
*
95833 CAAGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCATA
259 CAAGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCATG
* *
95898 AATTTGCCTTTCCC-----TCGCCTCAATTTTATTTGAAATAAACCGATATCTTCAACTAGATAT
324 AATTTGCCTTTCCCAAAAGTCGCCTCAATTTTGTTTGAAATAAACCGATATCTTCAACTAGGTAT
*
95958 TCATGATTGCTTAACTCTATTACATAGAGTTAGTTTTTGTATAT-G-TCATATAAAAACATATAT
389 TCATGATTGCTTAACTCTATTACATA-AGTTAG-TTTTGTATATGGCCCATATAAAAACATATAT
* * *
96021 TAGTGATTCACTGGCAATCGTTATAAGTCTAAACAACTGATGCCGATAAATACCC
452 TAGTGATTCACTGGCAATCGTTATAAGTCTAAACAACCGATGTCGATAATTACCC
96076 TTGCAGCGAC
Statistics
Matches: 2833, Mismatches: 509, Indels: 228
0.79 0.14 0.06
Matches are distributed among these distances:
723 74 0.03
724 351 0.12
725 57 0.02
726 39 0.01
727 77 0.03
729 2 0.00
731 78 0.03
732 49 0.02
733 5 0.00
734 10 0.00
735 4 0.00
736 212 0.07
737 220 0.08
738 283 0.10
739 276 0.10
740 407 0.14
741 77 0.03
743 1 0.00
744 1 0.00
745 1 0.00
746 1 0.00
747 2 0.00
748 2 0.00
750 3 0.00
753 241 0.09
754 155 0.05
755 126 0.04
756 64 0.02
757 15 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (739 bp):
CCCTAAGAACTTATAGATATTGGTCAACATAGTTCTCTCATATAGAATGGGTAGCAGTGAAAACG
TTAAGACACACCATACTGTCGGTCATGCTGCGGTGCTTAAAGTGTTTTTTTAGCTTAGTAATAAT
TCGTTCCCATTCCAATAATTTGTTTTCTGATTGATTGACCATTTGGGGATTGACAATTTCTGGGA
AGGTTATACAAAATAAGTTATACGAGAGTGTATTAGTTTTTCCACGTAGTATAGTATCAGAGCCA
AGTTACTGTATAGAACTGGCCCAACCTGCGAGATATTATGCAATTTGCCACAAAAGCCTCATGAA
TTTGCCTTTCCCAAAAGTCGCCTCAATTTTGTTTGAAATAAACCGATATCTTCAACTAGGTATTC
ATGATTGCTTAACTCTATTACATAAGTTAGTTTTGTATATGGCCCATATAAAAACATATATTAGT
GATTCACTGGCAATCGTTATAAGTCTAAACAACCGATGTCGATAATTACCCCTGAGCGCCTAGCA
CCCAACTTATTATGCCGTTATAGATTACGCTCGTACAAAATACTCCAGCTAACGCGAATAACGAA
ACCAACATTCCGTCTAGGAGGAACTTGTGTTGCTTCAAGATGAACCCCTTCCTCGGTCCAACAGT
CTAATGAGGTTCAGATATACAAACAGTCCGCTCAATATTATTTTTAAGGGAAGCAACTCTGTTAT
GATAACCTTAAGCCGATCCGATAA
Found at i:99342 original size:19 final size:19
Alignment explanation
Indices: 99318--99356 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
99308 GGTTCTAACT
99318 CGATGAAGACTCGAGGTGG
1 CGATGAAGACTCGAGGTGG
99337 CGATGAAGACTCGAGGTGG
1 CGATGAAGACTCGAGGTGG
99356 C
1 C
99357 TTGGTTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.41, T:0.15
Consensus pattern (19 bp):
CGATGAAGACTCGAGGTGG
Found at i:104379 original size:15 final size:15
Alignment explanation
Indices: 104359--104389 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
104349 CTCTCTAACT
104359 CTCTGTAATGGTTAC
1 CTCTGTAATGGTTAC
*
104374 CTCTGTAATGTTTAC
1 CTCTGTAATGGTTAC
104389 C
1 C
104390 GAATTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (15 bp):
CTCTGTAATGGTTAC
Found at i:116444 original size:18 final size:17
Alignment explanation
Indices: 116418--116451 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
116408 TAGTACCTCC
116418 AGCAACCTCATCGAATAT
1 AGCAACCTCATC-AATAT
*
116436 AGCATCCTCATCAATA
1 AGCAACCTCATCAATA
116452 GCTCGTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (17 bp):
AGCAACCTCATCAATAT
Found at i:117120 original size:60 final size:60
Alignment explanation
Indices: 117022--117221 Score: 355
Period size: 60 Copynumber: 3.3 Consensus size: 60
117012 AAACAGTCTT
*
117022 ACCTTTCACTAAACAGAAACTAAACACCCATTTTATCCAACACTCAAAGACAGAAGATAA
1 ACCTTTCACTAAACAGAAACTAAACACCCATTTTATCCAACACTCAAAGACAGAACATAA
* * *
117082 ACCTATCACTAAACAGAAACTAAACACCCATTTTATCCAACACTCTAAGACAGAACAGAA
1 ACCTTTCACTAAACAGAAACTAAACACCCATTTTATCCAACACTCAAAGACAGAACATAA
*
117142 ACCTTTCACTAAATAGAAACTAAACACCCATTTTATCCAACACTCAAAGACAGAACATAA
1 ACCTTTCACTAAACAGAAACTAAACACCCATTTTATCCAACACTCAAAGACAGAACATAA
117202 ACCTTTCACTAAACAGAAAC
1 ACCTTTCACTAAACAGAAAC
117222 CTTTCACTCA
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 131 1.00
ACGTcount: A:0.47, C:0.28, G:0.06, T:0.20
Consensus pattern (60 bp):
ACCTTTCACTAAACAGAAACTAAACACCCATTTTATCCAACACTCAAAGACAGAACATAA
Found at i:117221 original size:18 final size:18
Alignment explanation
Indices: 117195--117229 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
117185 TCAAAGACAG
*
117195 AACATAAACCTTTCACTA
1 AACAGAAACCTTTCACTA
117213 AACAGAAACCTTTCACT
1 AACAGAAACCTTTCACT
117230 CAAAATCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.29, G:0.03, T:0.26
Consensus pattern (18 bp):
AACAGAAACCTTTCACTA
Found at i:117566 original size:22 final size:22
Alignment explanation
Indices: 117541--117593 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
117531 AAATCAAACT
**
117541 AACAATTAAGACTATCT-AAGAA
1 AACAATTAAGAAAAT-TAAAGAA
*
117563 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAATTAAAGAA
117585 AACAATTAA
1 AACAATTAA
117594 TCAGAAAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAATTAAAGAA
Found at i:119198 original size:15 final size:16
Alignment explanation
Indices: 119178--119207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
119168 TGTAAGTTTA
119178 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
119193 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
119208 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:120142 original size:11 final size:11
Alignment explanation
Indices: 120126--120150 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
120116 GGGGAATAAT
120126 CAATCCAAAAA
1 CAATCCAAAAA
120137 CAATCCAAAAA
1 CAATCCAAAAA
120148 CAA
1 CAA
120151 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Done.