Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001516.1 Hibiscus syriacus cultivar Beakdansim tig00002963_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: 79200
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:2754 original size:31 final size:29
Alignment explanation
Indices: 2694--2761 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
2684 ACAAGCTTTA
*
2694 GAAAATTTAGGGACCATTCTATAAATTTT
1 GAAAAGTTAGGGACCATTCTATAAATTTT
*
2723 GAAAAGTTAGGGGACCCATTC-ATAATTTTTT
1 GAAAAGTTA-GGGA-CCATTCTATAA-ATTTT
2754 GAAAAGTT
1 GAAAAGTT
2762 GTAAATGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 8 0.24
30 8 0.24
31 18 0.53
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (29 bp):
GAAAAGTTAGGGACCATTCTATAAATTTT
Found at i:3604 original size:31 final size:31
Alignment explanation
Indices: 3566--3657 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
3556 TGTACATAAT
*
3566 TACCTATG-TCTTTCGGGACATATGGACAGTA
1 TACCTATGTTC-TTCGGGACATATGAACAGTA
** * *
3597 TACCTATGTTCTAAGGAACATATGAACAGTT
1 TACCTATGTTCTTCGGGACATATGAACAGTA
* *
3628 TACCTAGGTTCTTCGGGACCTATGAACAGT
1 TACCTATGTTCTTCGGGACATATGAACAGT
3658 TGCTGAGGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGAACAGTA
Found at i:3657 original size:62 final size:62
Alignment explanation
Indices: 3538--3657 Score: 154
Period size: 62 Copynumber: 1.9 Consensus size: 62
3528 AGGGTTTACA
* * * *
3538 TATGTTCTATGGAACATATGTACATAATTACCTATGTCTTTCGGGACATATGGACAGTATACC
1 TATGTTCTAAGGAACATATGAACAT-ATTACCTAGGTCTTTCGGGACATATGAACAGTATACC
*
3601 TATGTTCTAAGGAACATATGAACAGT-TTACCTAGGT-TCTTCGGGACCTATGAACAGT
1 TATGTTCTAAGGAACATATGAACA-TATTACCTAGGTCT-TTCGGGACATATGAACAGT
3658 TGCTGAGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
61 1 0.02
62 26 0.52
63 22 0.44
64 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (62 bp):
TATGTTCTAAGGAACATATGAACATATTACCTAGGTCTTTCGGGACATATGAACAGTATACC
Found at i:10087 original size:42 final size:41
Alignment explanation
Indices: 9942--10201 Score: 211
Period size: 43 Copynumber: 6.2 Consensus size: 41
9932 CCAAAGTTCA
*
9942 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCGATATCTATAG
1 CGGCGTTTTTGGAACAAACG-CGCAAAAGGTC-ATATCTATAG
* * * * ** * * *
9985 CGACATTTTTGGAACAAATGTCGTAAAACATCGAGATCTTTTG
1 CGGCGTTTTTGGAACAAACG-CGCAAAAGGTC-ATATCTATAG
10028 CGGCGTTTTTGGAACAAACGCAGCAAAAGGTCATATCTATAG
1 CGGCGTTTTTGGAACAAACGC-GCAAAAGGTCATATCTATAG
* * * * *
10070 CTGTGTTTTTGTAACAAACGTCGAAAAAAGTC--ATCTATAG
1 CGGCGTTTTTGGAACAAACG-CGCAAAAGGTCATATCTATAG
*
10110 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAG
1 CGGCGTTTTTGGAACAAACG-CGCAAAAGGTCATATCTATAG
** * * * ** *
10152 CAACATTTTTTGAACAAACTC-CGTAATGTCATATCTATAG
1 CGGCGTTTTTGGAACAAACGCGCAAAAGGTCATATCTATAG
*
10192 CGGCATTTTT
1 CGGCGTTTTT
10202 TTATACAAAC
Statistics
Matches: 173, Mismatches: 40, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
40 57 0.33
41 1 0.01
42 57 0.33
43 58 0.34
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
CGGCGTTTTTGGAACAAACGCGCAAAAGGTCATATCTATAG
Found at i:10119 original size:40 final size:41
Alignment explanation
Indices: 9942--10216 Score: 209
Period size: 40 Copynumber: 6.6 Consensus size: 41
9932 CCAAAGTTCA
* *
9942 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCGATATCTATAG
1 CGGCATTTTTGGAACAAACGTCGCAAAAAGTC-A-ATCTATAG
* * * * *
9985 CGACATTTTTGGAACAAATGTCGTAAAACA-TCGAGATCTTTTG
1 CGGCATTTTTGGAACAAACGTCGCAAAA-AGTC-A-ATCTATAG
* *
10028 CGGCGTTTTTGGAACAAACG-CAGCAAAAGGTCATATCTATAG
1 CGGCATTTTTGGAACAAACGTC-GCAAAAAGTCA-ATCTATAG
* ** * *
10070 CTGTGTTTTTGTAACAAACGTCGAAAAAAGTC-ATCTATAG
1 CGGCATTTTTGGAACAAACGTCGCAAAAAGTCAATCTATAG
* *
10110 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAG
1 CGGCATTTTTGGAACAAACGTCGCAAAAAGTCA-ATCTATAG
** * ** *
10152 CAACATTTTTTGAACAAAC-TC-CGTAATGTCATATCTATAG
1 CGGCATTTTTGGAACAAACGTCGCAAAAAGTCA-ATCTATAG
**
10192 CGGCATTTTTTTATACAAACGTCGC
1 CGGCATTTTTGGA-ACAAACGTCGC
10217 TAATTACCTT
Statistics
Matches: 185, Mismatches: 38, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
40 59 0.32
41 7 0.04
42 59 0.32
43 59 0.32
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
CGGCATTTTTGGAACAAACGTCGCAAAAAGTCAATCTATAG
Found at i:10138 original size:82 final size:83
Alignment explanation
Indices: 9942--10170 Score: 284
Period size: 82 Copynumber: 2.7 Consensus size: 83
9932 CCAAAGTTCA
* *
9942 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCGATATCTATAGCGACATTTTTGGAACAAATGTC
1 CGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-ATATCTATAGCGACATTTTTGGAACAAACGTC
* * *
10007 GTAAAACATCGAGATCTTTTG
65 GTAAAAAATC--GATCTATAG
* ** *
10028 CGGCGTTTTTGGAACAAACGCAGCAAAAGGTCATATCTATAGCTG-TGTTTTTGTAACAAACGTC
1 CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGC-GACATTTTTGGAACAAACGTC
10092 G-AAAAAAGTC-ATCTATAG
65 GTAAAAAA-TCGATCTATAG
* * *
10110 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGCAACATTTTTTGAACAAAC
1 CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGCGACATTTTTGGAACAAAC
10171 TCCGTAATGT
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
82 59 0.48
84 5 0.04
85 29 0.23
86 31 0.25
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (83 bp):
CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGCGACATTTTTGGAACAAACGTCG
TAAAAAATCGATCTATAG
Found at i:10188 original size:82 final size:79
Alignment explanation
Indices: 9942--10201 Score: 254
Period size: 82 Copynumber: 3.1 Consensus size: 79
9932 CCAAAGTTCA
* * * *
9942 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCGATATCTATAGCGACATTTTTGGAACAAATGTC
1 CGGCATTTTTGGAACAAACGCCGCAAAAGGTC-ATATCTATAGC-ACATTTTTTGAACAAA-CTC
* * *
10007 GTAAAACATCGAGATCTTTTG
63 GT-AAA-GTC-A-ATCTATAG
* * **
10028 CGGCGTTTTTGGAACAAACGCAGCAAAAGGTCATATCTATAGC-TGTGTTTTTGTAACAAACGTC
1 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGCACAT-TTTTTG-AACAAAC-TC
*
10092 GAAAAAAGTC-ATCTATAG
63 G--TAAAGTCAATCTATAG
10110 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGCAACATTTTTTGAACAAACTCCG
1 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGC-ACATTTTTTGAACAAACT-CG
*
10175 TAATGTCATATCTATAG
64 TAAAGTCA-ATCTATAG
10192 CGGCATTTTT
1 CGGCATTTTT
10202 TTATACAAAC
Statistics
Matches: 148, Mismatches: 16, Indels: 24
0.79 0.09 0.13
Matches are distributed among these distances:
80 5 0.03
81 1 0.01
82 74 0.50
83 7 0.05
84 6 0.04
85 22 0.15
86 33 0.22
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (79 bp):
CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAGCACATTTTTTGAACAAACTCGTA
AAGTCAATCTATAG
Found at i:10203 original size:42 final size:41
Alignment explanation
Indices: 9942--10201 Score: 220
Period size: 42 Copynumber: 6.2 Consensus size: 41
9932 CCAAAGTTCA
* *
9942 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCGATATCTATAG
1 CGGCATTTTTGGAACAAACGCCG-AAAAGGTC-ATATCTATAG
* * * ** * * *
9985 CGACATTTTTGGAACAAATGTCGTAAAACATCGAGATCTTTTG
1 CGGCATTTTTGGAACAAACGCCG-AAAAGGTC-ATATCTATAG
* *
10028 CGGCGTTTTTGGAACAAACGCAGCAAAAGGTCATATCTATAG
1 CGGCATTTTTGGAACAAACGCCG-AAAAGGTCATATCTATAG
* ** * * *
10070 CTGTGTTTTTGTAACAAACGTCGAAAAAAGTC--ATCTATAG
1 CGGCATTTTTGGAACAAACGCCG-AAAAGGTCATATCTATAG
10110 CGGCATTTTTGGAACAAACGCCGCAAAAGGTCATATCTATAG
1 CGGCATTTTTGGAACAAACGCCG-AAAAGGTCATATCTATAG
** * * * *
10152 CAACATTTTTTGAACAAACTCCG-TAATGTCATATCTATAG
1 CGGCATTTTTGGAACAAACGCCGAAAAGGTCATATCTATAG
10192 CGGCATTTTT
1 CGGCATTTTT
10202 TTATACAAAC
Statistics
Matches: 172, Mismatches: 43, Indels: 7
0.77 0.19 0.03
Matches are distributed among these distances:
40 56 0.33
42 59 0.34
43 57 0.33
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
CGGCATTTTTGGAACAAACGCCGAAAAGGTCATATCTATAG
Found at i:12137 original size:20 final size:20
Alignment explanation
Indices: 12101--12138 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12091 ATCCTATTCC
**
12101 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
12121 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
12139 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:13896 original size:15 final size:15
Alignment explanation
Indices: 13876--13919 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
13866 CGATAAATAT
13876 TATTAATTTATAAAA
1 TATTAATTTATAAAA
*
13891 TATTAAATTATAAAA
1 TATTAATTTATAAAA
13906 TATTAAATTTATAA
1 TATT-AATTTATAA
13920 TTATAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTAATTTATAAAA
Found at i:13951 original size:21 final size:21
Alignment explanation
Indices: 13920--14039 Score: 77
Period size: 22 Copynumber: 5.5 Consensus size: 21
13910 AAATTTATAA
13920 TTATAAATTAATTTAATAATAT
1 TTAT-AATTAATTTAATAATAT
13942 TTATAATTAACGATTTAAT-AT-T
1 TTATAATT-A--ATTTAATAATAT
*
13964 TTATACATTAATTTAATGATAT
1 TTATA-ATTAATTTAATAATAT
*
13986 TCATAATTAA--TAATTTAATATT
1 TTATAATTAATTTAA--TAATA-T
* * *
14008 TTATAAACTAGTTTAATGATAT
1 TTAT-AATTAATTTAATAATAT
*
14030 TCATAATTAA
1 TTATAATTAA
14040 CAATGTTCAT
Statistics
Matches: 77, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
19 3 0.04
20 7 0.09
21 19 0.25
22 25 0.32
23 13 0.17
24 7 0.09
25 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (21 bp):
TTATAATTAATTTAATAATAT
Found at i:13968 original size:44 final size:44
Alignment explanation
Indices: 13920--14043 Score: 185
Period size: 44 Copynumber: 2.8 Consensus size: 44
13910 AAATTTATAA
* * *
13920 TTATAAATTAATTTAATAATATTTATAATTAACGATTTAATATT
1 TTATAAATTAATTTAATGATATTCATAATTAACAATTTAATATT
* *
13964 TTATACATTAATTTAATGATATTCATAATTAATAATTTAATATT
1 TTATAAATTAATTTAATGATATTCATAATTAACAATTTAATATT
* *
14008 TTATAAACTAGTTTAATGATATTCATAATTAACAAT
1 TTATAAATTAATTTAATGATATTCATAATTAACAAT
14044 GTTCATCTGT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (44 bp):
TTATAAATTAATTTAATGATATTCATAATTAACAATTTAATATT
Found at i:14659 original size:21 final size:20
Alignment explanation
Indices: 14610--14660 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
14600 CAGCAGAAGC
14610 AGAAGAAGAGGAAGGTACAA
1 AGAAGAAGAGGAAGGTACAA
* *
14630 ATGATGAAG-GGAAAGGTGATAA
1 A-GAAGAAGAGG-AAGGT-ACAA
14652 AGAAGAAGA
1 AGAAGAAGA
14661 TAACAATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.35, T:0.10
Consensus pattern (20 bp):
AGAAGAAGAGGAAGGTACAA
Found at i:20300 original size:56 final size:56
Alignment explanation
Indices: 20232--20343 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
20222 ATCCGGTCAC
*
20232 CTAACTATTTAAATTTTGTCAATCAAGCCACCTGCCGTTAAATATTAATGGAGGAG
1 CTAACTATTTAAATCTTGTCAATCAAGCCACCTGCCGTTAAATATTAATGGAGGAG
20288 CTAACTATTTAAATCTTGTCAATCAAGCCACCTGCCGTTAAATATTAATGGAGGAG
1 CTAACTATTTAAATCTTGTCAATCAAGCCACCTGCCGTTAAATATTAATGGAGGAG
20344 ATGATGTGGC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (56 bp):
CTAACTATTTAAATCTTGTCAATCAAGCCACCTGCCGTTAAATATTAATGGAGGAG
Found at i:24667 original size:2 final size:2
Alignment explanation
Indices: 24660--24718 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
24650 ATCCCCTATT
24660 TA TA TA TA 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 TA TA TA TA
24702 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
24719 TCTTGGGTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24767 original size:2 final size:2
Alignment explanation
Indices: 24760--24790 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24750 TTAGTTTTAT
24760 TA TA 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 TA TA T
24791 CATTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24923 original size:23 final size:24
Alignment explanation
Indices: 24886--24942 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
24876 TATTTTATTA
24886 ATATTATTATTTTTAT-ATATATCT
1 ATATTATT-TTTTTATCATATATCT
*
24910 -TATTATTTTGTTTATCTTATATCT
1 ATATTATTTT-TTTATCATATATCT
*
24934 ATTTTATTT
1 ATATTATTT
24943 ATCTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 12 0.43
24 7 0.25
25 7 0.25
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATTATTTTTTTATCATATATCT
Found at i:24934 original size:57 final size:58
Alignment explanation
Indices: 24823--24941 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 58
24813 CTATTTTAGA
* *
24823 TATTATATCTTATTATTTTGTATATATATATATATATATTCTTTCCCTTTATCTATTT
1 TATTATATATTATTATTTTGTATATATATATATATATATTCTTTACCTTTATCTATTT
* * * *
24881 TATTA-ATATTATTATTTT-TATATATATCT-TATTATTTTGTTTATCTTATATCTATTT
1 TATTATATATTATTATTTTGTATATATATATATA-TATATTCTTTACCTT-TATCTATTT
24938 TATT
1 TATT
24942 TATCTAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
55 2 0.04
56 21 0.40
57 25 0.47
58 5 0.09
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.63
Consensus pattern (58 bp):
TATTATATATTATTATTTTGTATATATATATATATATATTCTTTACCTTTATCTATTT
Found at i:25059 original size:23 final size:23
Alignment explanation
Indices: 25020--25065 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
25010 TTTTCCAGTA
* *
25020 TTTTATTTATTTCATTTGTTTTT
1 TTTTATTCATTTCATTTATTTTT
25043 TTTTACTTCATTT-ATTTATTTTT
1 TTTTA-TTCATTTCATTTATTTTT
25066 ATGTCGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTATTCATTTCATTTATTTTT
Found at i:25064 original size:19 final size:18
Alignment explanation
Indices: 25021--25117 Score: 64
Period size: 19 Copynumber: 5.7 Consensus size: 18
25011 TTTCCAGTAT
* *
25021 TTTATTTAT-TTCATTTG
1 TTTATTTTTATTCATTTA
*
25038 TTTTTTTTTACTTCATTTA
1 TTTATTTTTA-TTCATTTA
*
25057 TTTATTTTTATGTCGTTTA
1 TTTATTTTTAT-TCATTTA
*
25076 -TT-TTATT-TT-ATTTA
1 TTTATTTTTATTCATTTA
* *
25090 TTT-TTCTT-TTCGTTTA
1 TTTATTTTTATTCATTTA
25106 TTTATTTTTATT
1 TTTATTTTTATT
25118 TTGTTTTATT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.06
15 9 0.14
16 8 0.13
17 15 0.24
18 5 0.08
19 22 0.35
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTATTTTTATTCATTTA
Found at i:25082 original size:5 final size:5
Alignment explanation
Indices: 25072--25191 Score: 68
Period size: 5 Copynumber: 23.0 Consensus size: 5
25062 TTTTATGTCG
* ** *
25072 TTTAT TTTAT TTTA- TTTATT TTTCT TTTCG TTTA- TTTATT TTTAT TTTGT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT
* * *
25122 TTTA- TTTACT TGTTAT CTTTAT TTTAT TATTAT TCTTTT CTTTGT CTTTCT
1 TTTAT TTTA-T T-TTAT -TTTAT TTTAT T-TTAT T-TTAT -TTTAT -TTTAT
25173 TTTA- TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT
25192 CTTCTATATT
Statistics
Matches: 94, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
4 16 0.17
5 44 0.47
6 29 0.31
7 5 0.05
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:25099 original size:20 final size:20
Alignment explanation
Indices: 25076--25160 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
25066 ATGTCGTTTA
25076 TTTTATTTTATTTATTTTTC
1 TTTTATTTTATTTATTTTTC
** *
25096 TTTTCGTTTATTTATTTTTA
1 TTTTATTTTATTTATTTTTC
*
25116 TTTTGTTTTATTTACTTGTTATC
1 TTTTATTTTATTTA-TT-TT-TC
*
25139 -TTTATTTTA-TTATTATTC
1 TTTTATTTTATTTATTTTTC
25157 TTTT
1 TTTT
25161 CTTTGTCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.04
19 4 0.08
20 31 0.58
21 5 0.09
22 10 0.19
23 1 0.02
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTATTTTATTTATTTTTC
Found at i:25176 original size:61 final size:60
Alignment explanation
Indices: 25073--25188 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 60
25063 TTTATGTCGT
* *
25073 TTATTTTATTTTATTTATTTTTCTTTTCGTTTATTTATTTTTATTTTGTTTTATTTACTTG
1 TTATTTTATTTTATTTATTATTCTTTTCGTTTATTTATTTTTA-TTTATTTTATTTACTTG
*
25134 TTATCTTTATTTTA-TTATTATTCTTTTC-TTTGTCTT-TCTTTTATTTATTTTATTT
1 TTAT-TTTATTTTATTTATTATTCTTTTCGTTTAT-TTAT-TTTTATTTATTTTATTT
25189 TATCTTCTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
60 16 0.33
61 24 0.49
62 9 0.18
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (60 bp):
TTATTTTATTTTATTTATTATTCTTTTCGTTTATTTATTTTTATTTATTTTATTTACTTG
Found at i:34703 original size:3 final size:3
Alignment explanation
Indices: 34697--34860 Score: 247
Period size: 3 Copynumber: 54.0 Consensus size: 3
34687 TTTATCCATC
* *
34697 ATT ATT ATT ATT ATT ATT ATC ATT ATT AAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* **
34745 ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
34793 ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
34839 ATAT ATT ATT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT ATT ATT
34861 TAATAAATAA
Statistics
Matches: 145, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
3 140 0.97
4 5 0.03
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:47655 original size:26 final size:27
Alignment explanation
Indices: 47614--47686 Score: 93
Period size: 25 Copynumber: 2.9 Consensus size: 27
47604 ATTATGCTTG
47614 AAGAAA-AAAAAA-AAAAAAAAA-GAA
1 AAGAAAGAAAAAAGAAAAAAAAAGGAA
*
47638 GAGAAAGAAAAAAGAAAAAAAAAGGAA
1 AAGAAAGAAAAAAGAAAAAAAAAGGAA
47665 AAG-AAG-AAAAAGAAAAAGAAAA
1 AAGAAAGAAAAAAGAAAAA-AAAA
47687 AAGGGGTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.12
25 17 0.40
26 16 0.37
27 5 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAAAAGAAAAAAAAAGGAA
Found at i:47656 original size:27 final size:26
Alignment explanation
Indices: 47614--47687 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 26
47604 ATTATGCTTG
47614 AAGAA-AAAAAA-AAAAAAAAAAGAA
1 AAGAAGAAAAAAGAAAAAAAAAAGAA
* *
47638 GAGAAAGAAAAAAGAAAAAAAAAGGAA
1 AAG-AAGAAAAAAGAAAAAAAAAAGAA
47665 AAGAAG-AAAAAGAAAAAGAAAAA
1 AAGAAGAAAAAAGAAAAA-AAAAA
47688 AGGGGTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 2 0.05
25 13 0.31
26 13 0.31
27 14 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (26 bp):
AAGAAGAAAAAAGAAAAAAAAAAGAA
Found at i:47667 original size:32 final size:29
Alignment explanation
Indices: 47614--47688 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 29
47604 ATTATGCTTG
*
47614 AAGAAAAA-AAAAAAAAAAAAAGAAGAGA
1 AAGAAAAAGAAAAAAAAAAAAAGAAGAAA
47642 AAGAAAAAAGAAAAAAAAAGGAAAAGAAGAAA
1 AAG-AAAAAGAAAAAAAAA--AAAAGAAGAAA
47674 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAA
47689 GGGGTCAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 9 0.21
31 12 0.29
32 13 0.31
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (29 bp):
AAGAAAAAGAAAAAAAAAAAAAGAAGAAA
Found at i:49817 original size:52 final size:52
Alignment explanation
Indices: 48617--49798 Score: 2246
Period size: 52 Copynumber: 22.8 Consensus size: 52
48607 TATGTGATCA
* *
48617 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-AGCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
48668 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
48720 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
48772 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
48824 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
48876 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
48928 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
*
48980 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAAC
* *
49032 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-AGCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49083 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49135 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49187 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49239 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49291 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49343 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49395 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49447 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
*
49499 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAAC
49551 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49603 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
* *
49655 ATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49707 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
49759 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
49799 ATTGGACAGA
Statistics
Matches: 1114, Mismatches: 11, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
50 1 0.00
51 94 0.08
52 1015 0.91
53 4 0.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
Found at i:50748 original size:113 final size:113
Alignment explanation
Indices: 50435--51210 Score: 1214
Period size: 114 Copynumber: 6.8 Consensus size: 113
50425 ATTCAAATCT
*
50435 ATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATTCGTCATCTGAAGA
1 ATCATTTGATGGATCATCTTTTCCAG-AGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* *
50500 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTC
61 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
*
50553 ATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
50618 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
*
50667 ATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
50732 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *
50780 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
50845 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTGTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* * * * *
50894 ATCAGTTGATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
50959 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *
51007 ATCAAATTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
51072 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* * *
51121 ATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
51185 AG-AGAAAGTTCATAATGAGAAGAACT
65 AGAAG-AAGTTCATAATGAGAAGAACT
51211 CATCAAGAGC
Statistics
Matches: 611, Mismatches: 42, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
112 3 0.00
113 276 0.45
114 285 0.47
115 1 0.00
117 18 0.03
118 19 0.03
119 9 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
Found at i:50835 original size:227 final size:227
Alignment explanation
Indices: 50430--51210 Score: 1298
Period size: 227 Copynumber: 3.4 Consensus size: 227
50420 CAAAGATTCA
* *
50430 AATCTATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATTCGTCATCT
1 AATCCATCATTTGATGGATCAACATTTCCAG-AGAA-AGTTCATAATGAGAAGAA--C-TCATCT
50495 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTT
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTT
50560 GATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
126 GATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
50625 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
191 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * *
50662 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
50727 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
*
50792 ATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 ATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
50857 TAATGAGAAGAATTTGTTCAACCTGTTGCTTG
196 TAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * *
50889 AATTCATCAGTTGATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
50954 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAATTGGTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATC-ACTTGATG
51019 GATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
130 GATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
51083 ATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
195 ATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* *
51116 AATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
51180 AAGGAAG-AGAAAGTTCATAATGAGAAGAACT
65 AAGGAAGAAG-AAGTTCATAATGAGAAGAACT
51211 CATCAAGAGC
Statistics
Matches: 523, Mismatches: 23, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
226 3 0.01
227 458 0.88
228 12 0.02
230 18 0.03
231 4 0.01
232 28 0.05
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (227 bp):
AATCCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
ATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTGCTTG
Found at i:51469 original size:3 final size:3
Alignment explanation
Indices: 51463--51625 Score: 254
Period size: 3 Copynumber: 54.0 Consensus size: 3
51453 TTTATCCATC
* *
51463 ATT ATT ATT ATT ATT ATT ATC ATT ATT AAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* **
51511 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
51559 ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
51605 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
51626 TAATAAATAA
Statistics
Matches: 145, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
3 143 0.99
4 2 0.01
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:57930 original size:5 final size:5
Alignment explanation
Indices: 57920--58057 Score: 56
Period size: 5 Copynumber: 27.0 Consensus size: 5
57910 TTTTATGCCG
* ** *
57920 TTTAT TTTA- TTTA- TTTA- TTTA- TTTATT TTTCT TTTCG TTT-C TTTATT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTA-T
*
57967 TTTAT TTTGT TTTAT TTTA- TTTACT TGTTAT CTTTAT TTTAT TATTAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T T-TTAT -TTTAT TTTAT T-TTAT
* * * *
58015 TATTAT TCTTTT CTTTTT CTTTCT TTTA- TTTGT TTTAT TTTAT
1 T-TTAT T-TTAT -TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT
58058 CTTCTATATT
Statistics
Matches: 110, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
4 26 0.24
5 43 0.39
6 36 0.33
7 5 0.05
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:57932 original size:9 final size:9
Alignment explanation
Indices: 57920--58078 Score: 58
Period size: 9 Copynumber: 16.9 Consensus size: 9
57910 TTTTATGCCG
57920 TTTATTTTA
1 TTTATTTTA
57929 TTTA-TTTA
1 TTTATTTTA
*
57937 TTTATTTATT
1 TTTATTT-TA
* *
57947 TTTCTTTTCG
1 TTTATTTT-A
* *
57957 TTTCTTTATT
1 TTTATTT-TA
*
57967 TTTATTTTGT
1 TTTATTTT-A
57977 TTTATTTTA
1 TTTATTTTA
57986 TTTACTTGTTA
1 TTTA-TT-TTA
57997 TCTTTATTTTA
1 --TTTATTTTA
58008 -TTATTATTA
1 TTTATT-TTA
58017 -TTATTCTT-
1 TTTATT-TTA
*
58025 TTCT-TTTTC
1 TT-TATTTTA
*
58034 TTTCTTTTA
1 TTTATTTTA
*
58043 TTTGTTTTA
1 TTTATTTTA
* *
58052 TTTTATCTTC
1 -TTTATTTTA
* *
58062 TATATTTCA
1 TTTATTTTA
58071 TTTATTTT
1 TTTATTTT
58079 CTATTTTGTT
Statistics
Matches: 117, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
8 16 0.14
9 50 0.43
10 38 0.32
11 7 0.06
12 2 0.02
13 4 0.03
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTATTTTA
Found at i:63526 original size:30 final size:30
Alignment explanation
Indices: 63468--63526 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
63458 CCAAAATTTG
* * * *
63468 TTTAGTGACTAAAATGCAAGTTTTGAAAAA
1 TTTAATGACTAAAATGAAAATTTAGAAAAA
63498 TTTAATGACTAAAATGAAAATTTAGAAAA
1 TTTAATGACTAAAATGAAAATTTAGAAAA
63527 GTGAAGGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (30 bp):
TTTAATGACTAAAATGAAAATTTAGAAAAA
Found at i:68909 original size:29 final size:29
Alignment explanation
Indices: 68877--68936 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
68867 TTGACCCTTC
*
68877 AATTTTTCAAAA-TTTCATTTTAGTTACTA
1 AATTTTTCAAAACTTACATTTT-GTTACTA
*
68906 AATTTTTCAAAACTTACATTTTTTTACTA
1 AATTTTTCAAAACTTACATTTTGTTACTA
68935 AA
1 AA
68937 CAAAATTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (29 bp):
AATTTTTCAAAACTTACATTTTGTTACTA
Found at i:73886 original size:14 final size:14
Alignment explanation
Indices: 73864--73909 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
73854 TTTAATATTA
73864 TTAATAAATTAATT
1 TTAATAAATTAATT
*
73878 TTAAAAAATTAAAATT
1 TTAATAAATT--AATT
*
73894 TTAATATATTAATT
1 TTAATAAATTAATT
73908 TT
1 TT
73910 TCGAGTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 15 0.56
16 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATAAATTAATT
Found at i:73899 original size:30 final size:31
Alignment explanation
Indices: 73850--73909 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
73840 AACAAAATAC
* *
73850 AAAATTTAATATTATTAATAAATTAATTTTA
1 AAAAATTAAAATTATTAATAAATTAATTTTA
*
73881 AAAAATTAAAATT-TTAATATATTAATTTT
1 AAAAATTAAAATTATTAATAAATTAATTTT
73910 TCGAGTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AAAAATTAAAATTATTAATAAATTAATTTTA
Found at i:76560 original size:20 final size:21
Alignment explanation
Indices: 76527--76565 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
76517 TTCTAAAATC
76527 TAAAAGTCAATTAACCAATTT
1 TAAAAGTCAATTAACCAATTT
76548 TAAAAGT-AATTAACCAAT
1 TAAAAGTCAATTAACCAAT
76566 ATTCACGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAAAGTCAATTAACCAATTT
Done.