Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001861.1 Hibiscus syriacus cultivar Beakdansim tig00003764_pilon, 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: 120286
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3037 original size:28 final size:27
Alignment explanation
Indices: 2950--3042 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
2940 GTTGAGCTAT
* * * *
2950 TGTTTAAAATATTATGTCATCGAACCAG
1 TGTTTGAAACATTATGTCATCG-AGCAA
* * * *
2978 TGTTTGAAGCATTATATCATCAAGAAA
1 TGTTTGAAACATTATGTCATCGAGCAA
3005 GTGTTTGAAACATTATGTCATCGAGTCAA
1 -TGTTTGAAACATTATGTCATCGAG-CAA
3034 TGTTTGAAA
1 TGTTTGAAA
3043 TCAATAACGT
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 2 0.04
28 47 0.92
29 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (27 bp):
TGTTTGAAACATTATGTCATCGAGCAA
Found at i:22443 original size:21 final size:21
Alignment explanation
Indices: 22418--22458 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22408 TCTGGGCTAG
* *
22418 GGGAATCGGTACCCATTCAAA
1 GGGAACCGATACCCATTCAAA
*
22439 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
22459 GCGAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAA
Found at i:22531 original size:23 final size:22
Alignment explanation
Indices: 22487--22531 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22477 AATGTCATGG
*
22487 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
22509 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
22532 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:23768 original size:103 final size:103
Alignment explanation
Indices: 23543--23760 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
23533 GTCGAGGGTC
23543 TATGTGGTCCTTCGGGACATATAGGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATAGGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
23608 TTGATCCTTGGCATATGTATATGATTCTTAAGAAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
*
23646 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATAGGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
23711 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
23749 TATGTGGTCCTT
1 TATGTGGTCCTT
23761 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATAGGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
Found at i:23827 original size:23 final size:23
Alignment explanation
Indices: 23776--23836 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
23766 CATTATTATA
*
23776 TGGCACTACGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
** *
23799 CAGCACTATGGTGCAATTCTATG
1 TGGCACTATGGTGCAATTCTACG
23822 TGGCACT-TCGGTGCA
1 TGGCACTAT-GGTGCA
23837 TTTATATGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTCTACG
Found at i:28974 original size:16 final size:16
Alignment explanation
Indices: 28953--28989 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28943 AGCCTCTGAG
*
28953 TCATTCAGCATTTGAA
1 TCATTCAACATTTGAA
28969 TCATTCAACATTTGAA
1 TCATTCAACATTTGAA
28985 TCATT
1 TCATT
28990 TAGCGCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (16 bp):
TCATTCAACATTTGAA
Found at i:35132 original size:26 final size:26
Alignment explanation
Indices: 35084--35133 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
35074 ATATATTATT
*
35084 CTTCTCTTAAAATTTGATGAGTTTGA
1 CTTCTCTTAAAATTTGATAAGTTTGA
35110 CTTCTCTTAAAATATT-ATAAGTTT
1 CTTCTCTTAAAAT-TTGATAAGTTT
35134 TTTTTTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (26 bp):
CTTCTCTTAAAATTTGATAAGTTTGA
Found at i:40704 original size:3 final size:3
Alignment explanation
Indices: 40698--40727 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
40688 AAACAACAAC
40698 AAT AAT AAT AAT AAT AATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AA
40728 AACAACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44552 original size:16 final size:15
Alignment explanation
Indices: 44512--44552 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
44502 TTAAAGCATT
44512 TATTTAAGTTTTCGGA
1 TATTTAA-TTTTCGGA
44528 TATTATAATTTTCGGA
1 TATT-TAATTTTCGGA
44544 TACTTTAAT
1 TA-TTTAAT
44553 ACATGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (15 bp):
TATTTAATTTTCGGA
Found at i:45472 original size:20 final size:21
Alignment explanation
Indices: 45447--45539 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
45437 TTTTCCCAAT
*
45447 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
45467 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
45488 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
45508 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
45529 TCGCAATGCGA
1 TCGCAATGCGA
45540 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:45553 original size:20 final size:20
Alignment explanation
Indices: 45528--45662 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
45518 AATTGGGAAA
45528 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
45548 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
45569 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
45589 TTCGCAATGTGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
45609 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
45629 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
45649 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
45663 TTTCAAAGCG
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.04
20 62 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:45554 original size:41 final size:41
Alignment explanation
Indices: 45447--45539 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
45437 TTTTCCCAAT
45447 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
45488 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
45529 TCGCAATGCGA
1 TCGCAATGCGA
45540 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:45663 original size:41 final size:41
Alignment explanation
Indices: 45527--45662 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
45517 GAATTGGGAA
* * * *
45527 AATCGCAATGCGATACTGACTATCGCAATGCAATAATACAA
1 AATCGCAACGCGATACTGACTTTCGCAATGCGATAATACAT
* * * *
45568 AATCGCAACGAGATACTTACTTTCGCAATGTGATACTGAC-T
1 AATCGCAACGCGATACTGACTTTCGCAATGCGATAAT-ACAT
* * *
45609 -TTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACAT
1 AATCGCAACGCGATACTGACTTTCGCAATGCGATAATACAT
*
45649 AATCGCAATGCGAT
1 AATCGCAACGCGAT
45663 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.40
41 41 0.55
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (41 bp):
AATCGCAACGCGATACTGACTTTCGCAATGCGATAATACAT
Found at i:47493 original size:18 final size:18
Alignment explanation
Indices: 47472--47516 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
47462 TCCACTTCGG
*
47472 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
47490 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
47508 GAGCCATCA
1 GAGCCATCA
47517 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:48052 original size:19 final size:20
Alignment explanation
Indices: 47998--48064 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
47988 TAGTTTACTT
* *
47998 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
48018 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
48038 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
48057 TCGCAACG
1 TCGCAACG
48065 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:48072 original size:14 final size:14
Alignment explanation
Indices: 48053--48110 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
48043 ATGCGAAATG
48053 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
48067 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
48083 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
48099 AAAATCGCAACG
1 AAAATCGCAACG
48111 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:48095 original size:32 final size:33
Alignment explanation
Indices: 48037--48127 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
48027 GGAAATGGCT
48037 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
48070 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
48102 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
48128 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:48163 original size:14 final size:14
Alignment explanation
Indices: 48144--48201 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
48134 TTGTGTTTCG
48144 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
48158 CGTTGCGATTTTATTT
1 CGTTGCGA-TTT-TGT
48174 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
48190 CGTTGCGATTTT
1 CGTTGCGATTTT
48202 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
15 3 0.08
16 4 0.11
17 3 0.08
18 8 0.21
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:48178 original size:32 final size:33
Alignment explanation
Indices: 48139--48326 Score: 211
Period size: 32 Copynumber: 5.4 Consensus size: 33
48129 GCGATTTGTG
*
48139 TTTCGCGTTGCGATTTTGTCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
48171 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
48204 TTTCGCATTGCGATAGCCATTTCCG-CGTTGCGATACGATTTTCA
1 TTTCGCATTGCGAT-----TTT--GTCGTT--G---CGATTTTCA
* *
48248 TTTCACGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
48280 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
48313 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
48327 AGCCATTTCC
Statistics
Matches: 136, Mismatches: 5, Indels: 29
0.80 0.03 0.17
Matches are distributed among these distances:
32 61 0.45
33 36 0.26
36 1 0.01
37 1 0.01
38 7 0.05
39 7 0.05
40 1 0.01
41 1 0.01
44 21 0.15
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:48272 original size:14 final size:14
Alignment explanation
Indices: 48253--48310 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
48243 TTTCATTTCA
48253 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
48267 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
48283 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
48299 CGTTGCGATTTT
1 CGTTGCGATTTT
48311 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:48321 original size:109 final size:109
Alignment explanation
Indices: 48139--48347 Score: 382
Period size: 109 Copynumber: 1.9 Consensus size: 109
48129 GCGATTTGTG
* * *
48139 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCACGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
48204 TTTCGCATTGCGATAGCCATTTCCGCGTTGCGATACGATTTTCA
66 TTTCGCATTGCGATAGCCATTTCCGCATTGCGATACGATTTTCA
48248 TTTCACGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCACGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
48313 TTTCGCATTGCGATAGCCATTTCCGCATTGCGATA
66 TTTCGCATTGCGATAGCCATTTCCGCATTGCGATA
48348 GTCATTTTCG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 96 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44
Consensus pattern (109 bp):
TTTCACGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
TTTCGCATTGCGATAGCCATTTCCGCATTGCGATACGATTTTCA
Found at i:48341 original size:20 final size:19
Alignment explanation
Indices: 48311--48366 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
48301 TTGCGATTTT
48311 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
48330 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
48350 CATTTTCGCGTTGCGAT
1 CA-TTTCGCATTGCGAT
48367 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:50253 original size:14 final size:14
Alignment explanation
Indices: 50234--50269 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
50224 ATTGTTTAAT
50234 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
50248 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
50262 TGATTTGT
1 TGATTTGT
50270 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:50408 original size:19 final size:19
Alignment explanation
Indices: 50386--50472 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
50376 ATCGCAACGA
*
50386 GAAAATAGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
50405 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
50424 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
50443 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
50457 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
50473 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 48 0.75
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:50437 original size:38 final size:33
Alignment explanation
Indices: 50357--50472 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
50347 AAAACAGATT
* ***
50357 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
50390 ATAGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
50428 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
50461 ATCGCAATGCGA
1 ATCGCAATGCGA
50473 TTTTCATTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
33 37 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 29 0.40
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:50523 original size:20 final size:20
Alignment explanation
Indices: 50491--50568 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
50481 TCGCATTGCG
*
50491 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
50511 ATCTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
50531 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
50551 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
50569 TCAAATGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:51652 original size:24 final size:24
Alignment explanation
Indices: 51625--51678 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
51615 GTATTCGAAA
* *
51625 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
51649 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
51673 TTTGAT
1 TTTGAT
51679 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:51870 original size:12 final size:12
Alignment explanation
Indices: 51853--51877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51843 ATATAATCCT
51853 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51865 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51877 G
1 G
51878 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:54216 original size:33 final size:33
Alignment explanation
Indices: 54169--54295 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
54159 GGAAATTACT
54169 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
54202 ATCGCAATGTGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
54234 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
54268 ATCGCAATGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
54296 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:54255 original size:66 final size:66
Alignment explanation
Indices: 54173--54302 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
54163 ATTACTATCG
*
54173 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAACGCGAATTTC
54238 A
66 A
*
54239 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGTGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAACGCGAATTT
54303 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAACGCGAATTTC
A
Found at i:54346 original size:33 final size:33
Alignment explanation
Indices: 54295--54384 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
54285 AAATCGCAAC
* *
54295 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
54328 GCGATTTTCATTTCGCGTTGTGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
* * *
54361 GCTATTTTCATTTTGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
54385 AGTACTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:54510 original size:14 final size:14
Alignment explanation
Indices: 54491--54527 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54481 CATCAATTAA
54491 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
54505 ACAAATCACCTTTT
1 ACAAATCAACTTTT
54519 ACAAATCAA
1 ACAAATCAA
54528 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:55948 original size:21 final size:21
Alignment explanation
Indices: 55882--55948 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
55872 GTGAATCGGG
*
55882 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
55902 TCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
55924 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
55945 CTCT
1 CTCT
55949 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:55967 original size:42 final size:41
Alignment explanation
Indices: 55882--56004 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
55872 GTGAATCGGG
* * * *
55882 CTCTTGAATGGTGGGA-GGGATCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
55924 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
55966 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
56005 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:58044 original size:20 final size:19
Alignment explanation
Indices: 57999--58130 Score: 112
Period size: 19 Copynumber: 7.1 Consensus size: 19
57989 TCTTTTGGTT
* *
57999 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
58018 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
58038 GGAAATGACTATCGCGA--C
1 -GAAATGAAAATCGCAACGC
* *
58056 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
58072 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
58091 GGAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
58110 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
58129 GA
1 GA
58131 TTTTTGTTTC
Statistics
Matches: 90, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
14 8 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 49 0.54
20 25 0.28
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:58162 original size:19 final size:19
Alignment explanation
Indices: 58126--58170 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
58116 AAAATCGCAA
*
58126 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
58145 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
58164 TGCGATT
1 TGCGATT
58171 CTCTCATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:58746 original size:20 final size:20
Alignment explanation
Indices: 58722--58855 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
58712 CGCTATGTAA
* * *
58722 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
58742 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
58762 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
58783 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
58803 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
58823 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
58843 ATCGCATTGCGAT
1 ATCGCATTGCGAT
58856 TTTTCCAATT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 84 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:58966 original size:21 final size:21
Alignment explanation
Indices: 58926--58966 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58916 ACTGTAGACC
**
58926 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
58947 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
58967 ACGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:68165 original size:2 final size:2
Alignment explanation
Indices: 68158--68182 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68148 TAAATAATTT
68158 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 T
68183 TAAAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68268 original size:21 final size:21
Alignment explanation
Indices: 68225--68266 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
68215 TATTTAGATT
*
68225 TAAAATTACTATAAAAATAAA
1 TAAAATTAATATAAAAATAAA
*
68246 TAAAATTAAATATCAAAATAA
1 TAAAATT-AATATAAAAATAA
68267 TATTTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAATTAATATAAAAATAAA
Found at i:75029 original size:36 final size:34
Alignment explanation
Indices: 74989--75072 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 34
74979 GAAGTTAAAA
* *
74989 TAAATATTTTAAAAAATAATTTTGGAATGTTATGAT
1 TAAATAATTTAAAAAATAA--TTAGAATGTTATGAT
*
75025 TAAATAATTT--AAGA-AATTAGAATGTTATGAT
1 TAAATAATTTAAAAAATAATTAGAATGTTATGAT
*
75056 GAAATAATTTAAAAAAT
1 TAAATAATTTAAAAAAT
75073 TATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
31 23 0.57
33 5 0.12
34 3 0.08
36 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (34 bp):
TAAATAATTTAAAAAATAATTAGAATGTTATGAT
Found at i:75048 original size:31 final size:32
Alignment explanation
Indices: 75013--75079 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
75003 AATAATTTTG
* *
75013 GAATGTTATGATTAAATAATTTAAGAAATTA-
1 GAATGTTATGATGAAATAATTTAAAAAATTAT
75044 GAATGTTATGATGAAATAATTTAAAAAATTAT
1 GAATGTTATGATGAAATAATTTAAAAAATTAT
75076 GAAT
1 GAAT
75080 TTAAAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (32 bp):
GAATGTTATGATGAAATAATTTAAAAAATTAT
Found at i:80341 original size:17 final size:17
Alignment explanation
Indices: 80321--80353 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
80311 TTTAGGGAAG
80321 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
80338 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
80354 TTAACTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:81347 original size:15 final size:16
Alignment explanation
Indices: 81327--81364 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
81317 CTTTAACCTT
81327 ACAACAC-TTACCACG
1 ACAACACTTTACCACG
81342 ACAACACTATTTACCACG
1 ACAACAC--TTTACCACG
81360 ACAAC
1 ACAAC
81365 GCCATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
18 13 0.65
ACGTcount: A:0.42, C:0.37, G:0.05, T:0.16
Consensus pattern (16 bp):
ACAACACTTTACCACG
Found at i:88914 original size:178 final size:182
Alignment explanation
Indices: 88610--88984 Score: 521
Period size: 178 Copynumber: 2.1 Consensus size: 182
88600 ATATTTATCG
* * *
88610 AATATTAAAGTAAGATTTTTTTTCATTAAACTAATGTGAATTACAAAATAGTATCAATTCTAAGT
1 AATATTAAAGTAAGATTTTTTTTCATGAAACTAATGTGAATTACAAAATAATATCAATTCTAAAT
* * *
88675 AATCTAAACCATTTAACAATAAATGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGAC
66 AATCTAAACCATTTAACAATAAATGTGTAATCATCTATGCTGTTGATGGTATCTAAACTCATGAC
* **
88740 CTCTAGAAACAATAACAA-TATTTTTAACCGC-TGAAATAAGTTGATTTGTGA
131 CTCTAGAAACAATAACAACT-TTTTTAACCACAAAAAATAAGTTGATTTGTGA
* *
88791 AATATTAAAGTAA-A-TTTTTTTCATGAAACTAATGTG-ATTACAAAGTAATATCAGTTCTAAAT
1 AATATTAAAGTAAGATTTTTTTTCATGAAACTAATGTGAATTACAAAATAATATCAATTCTAAAT
* * * *
88853 ACTCTAAACCATTTGACAATGAATGTGTAATCATCTTTG-TAGTT-ATTGGTATCTAAACTCATG
66 AATCTAAACCATTTAACAATAAATGTGTAATCATCTATGCT-GTTGA-TGGTATCTAAACTCATG
* *
88916 ACCTCTATAAATAATAACAACTTTTTTAACCACAAAAAATAAGTTGATTTGTGA
129 ACCTCTAGAAACAATAACAACTTTTTTAACCACAAAAAATAAGTTGATTTGTGA
88970 AATATTAAAGTAAGA
1 AATATTAAAGTAAGA
88985 ACTAAATTTG
Statistics
Matches: 172, Mismatches: 17, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
177 2 0.01
178 102 0.59
179 53 0.31
180 2 0.01
181 13 0.08
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (182 bp):
AATATTAAAGTAAGATTTTTTTTCATGAAACTAATGTGAATTACAAAATAATATCAATTCTAAAT
AATCTAAACCATTTAACAATAAATGTGTAATCATCTATGCTGTTGATGGTATCTAAACTCATGAC
CTCTAGAAACAATAACAACTTTTTTAACCACAAAAAATAAGTTGATTTGTGA
Found at i:96478 original size:3 final size:3
Alignment explanation
Indices: 96470--96517 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
96460 GTCAAAATGC
96470 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
96518 GTATTAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:98700 original size:18 final size:18
Alignment explanation
Indices: 98677--98730 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
98667 CCACTAGGAA
98677 ATGTCCCGAAAGACCACT
1 ATGTCCCGAAAGACCACT
*
98695 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAAGACCACT
*
98713 ATGTCCCGAATGACCACT
1 ATGTCCCGAAAGACCACT
98731 GATAATCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACT
Found at i:100137 original size:22 final size:22
Alignment explanation
Indices: 100107--100151 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
100097 ATGTAAAATT
100107 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
*
100129 TGTCTCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
100151 T
1 T
100152 CCCTCGACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:100157 original size:22 final size:22
Alignment explanation
Indices: 100112--100158 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
100102 AAATTTGTCC
**
100112 CGAAGGACCACTGTATATGTCT
1 CGAAGGACCACTGTATATCCCT
100134 CGAAGGACCACTGTATATCCCT
1 CGAAGGACCACTGTATATCCCT
100156 CGA
1 CGA
100159 CTCTTGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
CGAAGGACCACTGTATATCCCT
Found at i:101929 original size:15 final size:16
Alignment explanation
Indices: 101906--101938 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
101896 TAATTTATAC
101906 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
101921 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
101937 AT
1 AT
101939 TTTGTAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Found at i:102660 original size:2 final size:2
Alignment explanation
Indices: 102653--102686 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
102643 AACAGTGGAT
102653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102687 ATTTTATAGG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:103196 original size:29 final size:29
Alignment explanation
Indices: 103158--103220 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
103148 ATATATTTAA
* * *
103158 ATATTTTATTCTTATCTTCACGTAAAAAT
1 ATATTCTATTCTTATCTTAAAGTAAAAAT
* * *
103187 ATATTCTATTTTTATTTTAAATTAAAAAT
1 ATATTCTATTCTTATCTTAAAGTAAAAAT
103216 ATATT
1 ATATT
103221 TTATCATTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (29 bp):
ATATTCTATTCTTATCTTAAAGTAAAAAT
Found at i:103356 original size:24 final size:23
Alignment explanation
Indices: 103315--103370 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 23
103305 TACACTAAAA
*
103315 TAAAAATAAGTATATTTAATAAGT
1 TAAAAA-AAATATATTTAATAAGT
103339 TAAGAAAAAATATATTTAATAAGT
1 TAA-AAAAAATATATTTAATAAGT
103363 TAAAAAAA
1 TAAAAAAA
103371 TAAATGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.17
24 22 0.73
25 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TAAAAAAAATATATTTAATAAGT
Found at i:106876 original size:15 final size:16
Alignment explanation
Indices: 106856--106895 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
106846 GATTATTAGA
106856 AAAATATATCAAA-TT
1 AAAATATATCAAATTT
106871 AAAATATA--AAATTT
1 AAAATATATCAAATTT
106885 ACAAATATATC
1 A-AAATATATC
106896 CCATTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.14
14 3 0.14
15 15 0.71
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATATCAAATTT
Done.