Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000244.1 Hibiscus syriacus cultivar Beakdansim tig00000429_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: 72086
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:8373 original size:36 final size:36
Alignment explanation
Indices: 8332--8435 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
8322 AGTTGAGTAT
*
8332 TATCAGCTTTGGTACATTCTTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
8368 TATCAGCTTTGGTATATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
8404 TATCAGCTTTGGTACATTCGTGTATCAATGTT
1 TATCAGCTTTGGTACATTCGTGTATCAATGTT
8436 CAGCACCGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:10251 original size:14 final size:14
Alignment explanation
Indices: 10214--10275 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
10204 TTGCTTGTTT
*
10214 AATTGATTTATAAA
1 AATTGATTTGTAAA
10228 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* * *
10242 AGTTGTTTTGTTTAA
1 AATTGATTTG-TAAA
* *
10257 TATTGATGTGTAAA
1 AATTGATTTGTAAA
10271 TAATT
1 -AATT
10276 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:10427 original size:20 final size:20
Alignment explanation
Indices: 10374--10427 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
10364 AGGTACACTT
* **
10374 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
**
10394 TCGCAATACGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
10414 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
10428 TCAATTCGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:10443 original size:19 final size:20
Alignment explanation
Indices: 10421--10463 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
10411 AAATCGCAAC
*
10421 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
10440 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
10460 GCGA
1 GCGA
10464 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:10654 original size:39 final size:39
Alignment explanation
Indices: 10580--10655 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
10570 TGTGTTATTT
* * * **
10580 ATTAAATGAACGAACATGAACAAGATTTTTTTTCGTTTA
1 ATTAAATGAACAAACATGAACAAGAGTCTCGTTCGTTTA
10619 ATTAAATGAACAAACATGAACATAG-GTCTCGTTCGTT
1 ATTAAATGAACAAACATGAACA-AGAGTCTCGTTCGTT
10656 CATTTACGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 29 0.94
40 2 0.06
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (39 bp):
ATTAAATGAACAAACATGAACAAGAGTCTCGTTCGTTTA
Found at i:10694 original size:14 final size:14
Alignment explanation
Indices: 10672--10717 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
10662 CGTTCGTGAA
10672 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
10686 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
*
10700 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
10714 CGTT
1 CGTT
10718 TATGTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.09, C:0.13, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:11489 original size:16 final size:16
Alignment explanation
Indices: 11462--11519 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
11452 GGGTCTTCAA
11462 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* *
11478 CATTTATATTCGTGTT
1 CGTTTATGTTCGTGTT
*
11494 CGTTTTTGTTCGTGTT
1 CGTTTATGTTCGTGTT
11510 CGTTTATGTT
1 CGTTTATGTT
11520 TGTTTATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.59
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:11613 original size:16 final size:16
Alignment explanation
Indices: 11592--11622 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11582 AAAAAAATTT
11592 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCA
11608 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
11623 GTTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCA
Found at i:11722 original size:20 final size:20
Alignment explanation
Indices: 11692--11906 Score: 196
Period size: 20 Copynumber: 11.7 Consensus size: 20
11682 TACAGGCCTA
*
11692 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
11712 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
11732 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
11746 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
11766 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
11786 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
11806 GCGAT--T----TTTGCGTT
1 GCGATAGTCAAATTCGCGTT
11820 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
11840 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
11854 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
11874 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
11894 GCGATATTCAAAT
1 GCGATAGTCAAAT
11907 GAATGTGTAG
Statistics
Matches: 157, Mismatches: 20, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
14 35 0.22
16 3 0.02
18 3 0.02
20 116 0.74
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:11756 original size:34 final size:34
Alignment explanation
Indices: 11707--11878 Score: 211
Period size: 34 Copynumber: 4.9 Consensus size: 34
11697 AATCAAATTC
*
11707 GCGTTACGATAGTCAAATTCGCGTTGCGATTTTCT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
* * *
11742 -CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTC
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTT
11781 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
11815 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * *
11849 GAGTTGCGATAATCAAATTCGCGTTACGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
11879 AGTCAAATTC
Statistics
Matches: 120, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
34 89 0.74
36 1 0.01
38 1 0.01
40 29 0.24
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (34 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:11777 original size:54 final size:54
Alignment explanation
Indices: 11692--11898 Score: 224
Period size: 54 Copynumber: 3.8 Consensus size: 54
11682 TACAGGCCTA
*
11692 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTCTCGTT
1 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTCTAGTT
* * * * * ** * *
11746 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATT
1 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTCTAGTT
** * *
11800 CGCG-T--TGCGATTTTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTT
1 -GCGATAAT-C-AAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTCT-AGTT
11854 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGAT
1 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGAT
11899 ATTCAAATGA
Statistics
Matches: 122, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
52 1 0.01
53 4 0.03
54 112 0.92
55 4 0.03
56 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (54 bp):
GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTCTAGTT
Found at i:11813 original size:74 final size:74
Alignment explanation
Indices: 11692--11844 Score: 263
Period size: 74 Copynumber: 2.1 Consensus size: 74
11682 TACAGGCCTA
11692 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATAGTCA
1 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTGCGATAGTCA
11756 AATACCCGTT
65 AATACCCGTT
*
11766 GCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAA
1 GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAA
* *
11831 ATTCGCGTT
66 ATACCCGTT
11840 GCGAT
1 GCGAT
11845 TTTTGAGTTG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
73 1 0.01
74 74 0.99
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (74 bp):
GCGATAATCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAA
ATACCCGTT
Found at i:12129 original size:140 final size:140
Alignment explanation
Indices: 11877--12146 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
11867 TCGCGTTACG
* * * *
11877 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAGTAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCA
11942 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
12007 AATACACATA
131 AATACACATA
12017 ATAGTCAAATTCACGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
12082 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAGAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
12147 TAAAACGTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:12221 original size:12 final size:12
Alignment explanation
Indices: 12206--12236 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12196 AAGCCGGTTG
*
12206 TGATTGGGATTT
1 TGATTGCGATTT
12218 TGATTGCGATTT
1 TGATTGCGATTT
12230 TGATTGC
1 TGATTGC
12237 CTTTTTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.48
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:14293 original size:14 final size:14
Alignment explanation
Indices: 14274--14310 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14264 TCCCGTGGCA
14274 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
14288 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
14302 TTCTTCTTC
1 TT-TTCTTC
14311 TTCTTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:15396 original size:20 final size:20
Alignment explanation
Indices: 15371--15460 Score: 99
Period size: 20 Copynumber: 4.3 Consensus size: 20
15361 GAAATTCAGT
*
15371 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
15391 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
15411 GTTGCGATAGTCAAAAAAATCGC
1 GTTGCGATAGTC---AGAATCGC
* *
15434 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
15454 ATTGCGA
1 GTTGCGA
15461 ATTACATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 44 0.72
23 17 0.28
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:15468 original size:20 final size:20
Alignment explanation
Indices: 15430--15523 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
15420 GTCAAAAAAA
* *
15430 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGA-ATTACATAT
15450 TCGCATTGCGAATTACATAT
1 TCGCATTGCGAATTACATAT
*
15470 TCGCATTGCGATTTACATAT
1 TCGCATTGCGAATTACATAT
*
15490 TCGCATTGCGATTTACATAT
1 TCGCATTGCGAATTACATAT
15510 TCGCATTGCGAATT
1 TCGCATTGCGAATT
15524 CGGAAAATCG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 2 0.03
20 67 0.97
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGAATTACATAT
Found at i:17557 original size:16 final size:16
Alignment explanation
Indices: 17536--17568 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17526 TAATAAATAA
*
17536 ACGAACATAAGCGAAC
1 ACGAACATAAACGAAC
17552 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
17568 A
1 A
17569 AAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.15, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:17659 original size:10 final size:10
Alignment explanation
Indices: 17644--17711 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 10
17634 CATTTAAATG
17644 ATAAACGAAC
1 ATAAACGAAC
17654 ATAAACGAACAC
1 ATAAACG-A-AC
*
17666 AAACGAACGAAC
1 ATA--AACGAAC
*
17678 ATAAACAAAC
1 ATAAACGAAC
17688 ATAATAAACGAAC
1 ---ATAAACGAAC
17701 ATAAACGAAC
1 ATAAACGAAC
17711 A
1 A
17712 ACACAACACA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 24 0.51
11 1 0.02
12 8 0.17
13 10 0.21
14 4 0.09
ACGTcount: A:0.62, C:0.21, G:0.09, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:23865 original size:24 final size:25
Alignment explanation
Indices: 23838--23885 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
23828 TTATTTAATC
* *
23838 ATTTTAGATTATT-AAAAAATAAAT
1 ATTTCAGACTATTAAAAAAATAAAT
*
23862 ATTTCGGACTATTAAAAAAATAAA
1 ATTTCAGACTATTAAAAAAATAAA
23886 CCTACGATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
ATTTCAGACTATTAAAAAAATAAAT
Found at i:24913 original size:30 final size:30
Alignment explanation
Indices: 24867--25012 Score: 136
Period size: 30 Copynumber: 4.8 Consensus size: 30
24857 TATTTTAAGA
* *
24867 ATTTTATACAATTTTAAGAATTATAAACAT
1 ATTTTGTATAATTTTAAGAATTATAAACAT
* *
24897 ATTTTGTATAACTTTAAGAATTATATATATAT
1 ATTTTGTATAATTTTAAGAATTATA-A-ACAT
* * * * *
24929 ATATATGTATTAGTTTTAA-TATT-TTAAGAT
1 AT-TTTGTA-TAATTTTAAGAATTATAAACAT
* *
24959 -TTTTATACAATTTTAAGAATTATAAACAT
1 ATTTTGTATAATTTTAAGAATTATAAACAT
24988 ATTTTGTATAATTTTAAGAATTATA
1 ATTTTGTATAATTTTAAGAATTATA
25013 TATATATATA
Statistics
Matches: 90, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
27 7 0.08
28 7 0.08
29 6 0.07
30 47 0.52
31 2 0.02
32 6 0.07
33 8 0.09
34 7 0.08
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (30 bp):
ATTTTGTATAATTTTAAGAATTATAAACAT
Found at i:24954 original size:91 final size:91
Alignment explanation
Indices: 24842--25025 Score: 341
Period size: 91 Copynumber: 2.0 Consensus size: 91
24832 GGCCAAAAAA
24842 ATGTATTAATTTTAATATTTTAAGAATTTTATACAATTTTAAGAATTATAAACATATTTTGTATA
1 ATGTATTAATTTTAATATTTTAAGAATTTTATACAATTTTAAGAATTATAAACATATTTTGTATA
24907 ACTTTAAGAATTATATATATATATAT
66 ACTTTAAGAATTATATATATATATAT
* *
24933 ATGTATTAGTTTTAATATTTTAAGATTTTTATACAATTTTAAGAATTATAAACATATTTTGTATA
1 ATGTATTAATTTTAATATTTTAAGAATTTTATACAATTTTAAGAATTATAAACATATTTTGTATA
*
24998 ATTTTAAGAATTATATATATATATAT
66 ACTTTAAGAATTATATATATATATAT
25024 AT
1 AT
25026 ATATATATAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (91 bp):
ATGTATTAATTTTAATATTTTAAGAATTTTATACAATTTTAAGAATTATAAACATATTTTGTATA
ACTTTAAGAATTATATATATATATAT
Found at i:25016 original size:2 final size:2
Alignment explanation
Indices: 25009--25037 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24999 TTTTAAGAAT
25009 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 T
25038 TTTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27934 original size:63 final size:64
Alignment explanation
Indices: 27815--27936 Score: 176
Period size: 63 Copynumber: 1.9 Consensus size: 64
27805 ATTTATTATT
* * *
27815 TATTTAACTTTGAATATTAAAAGATAATTGTATACTTTTAAATATTTCAAATTAAAATAATTTC
1 TATTTAACTTTGAATAGTAAAAGAGAATTGTATACTTTTAAATATTTCAAAGTAAAATAATTTC
* *
27879 TATTTAAGTTTGAATAGTAAAAG-GAATT-TATATCTTTTGAATATTTCAAAGTAAAATA
1 TATTTAACTTTGAATAGTAAAAGAGAATTGTATA-CTTTTAAATATTTCAAAGTAAAATA
27937 TATTATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 4 0.08
63 27 0.52
64 21 0.40
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (64 bp):
TATTTAACTTTGAATAGTAAAAGAGAATTGTATACTTTTAAATATTTCAAAGTAAAATAATTTC
Found at i:27947 original size:64 final size:65
Alignment explanation
Indices: 27808--27947 Score: 180
Period size: 64 Copynumber: 2.2 Consensus size: 65
27798 AAAAGATATT
* * *
27808 TATTATTTATTTAACTTTGAATATTAAAAGATAATTGTATACTTTTAAATATTTCAAATTAAAAT
1 TATTA-TTATTTAACTTTGAATAGTAAAAGAGAATTGTATACTTTTAAATATTTCAAAGTAAAAT
27873 A
65 A
* *
27874 -ATT-TCTATTTAAGTTTGAATAGTAAAAG-GAATT-TATATCTTTTGAATATTTCAAAGTAAAA
1 TATTAT-TATTTAACTTTGAATAGTAAAAGAGAATTGTATA-CTTTTAAATATTTCAAAGTAAAA
27935 TA
64 TA
27937 TATTATTATTT
1 TATTATTATTT
27948 GTTTATATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
62 4 0.06
63 28 0.43
64 29 0.45
65 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (65 bp):
TATTATTATTTAACTTTGAATAGTAAAAGAGAATTGTATACTTTTAAATATTTCAAAGTAAAATA
Found at i:30692 original size:65 final size:63
Alignment explanation
Indices: 30623--30805 Score: 226
Period size: 65 Copynumber: 2.8 Consensus size: 63
30613 AATTAAATTG
* *
30623 AACATCGAATGCATTTCATGCATCGATTCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACAT-CCATGCACCGATGCACTGAGGATATTT-TG-
30687 A
63 A
* ** *
30688 AACATCGAATGCATTTGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATCCATGCACCGATGCACTGAGGATATTTTGA
* *
30752 AACATCGAATGCACTTGATGCATCGATGCAC-TCTTAGTGCACCGATGCACTGAG
1 AACATCGAATGCATTTGATGCATCGATGCACATC-CA-TGCACCGATGCACTGAG
30806 AGTCCAACGG
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 44 0.43
65 49 0.48
66 6 0.06
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACATCCATGCACCGATGCACTGAGGATATTTTGA
Found at i:30779 original size:64 final size:64
Alignment explanation
Indices: 30573--30782 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
30563 TTTTTCAAAG
* * * **
30573 TGATGCACCGATTCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACC-ATCCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
30636 TT
63 TT
* * * **
30638 TCATGCATCGATTCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCAT-CCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCA
30701 TT
63 TT
* *
30703 TGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
30767 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
30783 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 49 0.40
65 62 0.50
66 6 0.05
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:30782 original size:17 final size:19
Alignment explanation
Indices: 30754--30802 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
30744 TATTTTGAAA
30754 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
30772 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
30791 CACCGATGCACT
1 CATCGATGCACT
30803 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:36598 original size:22 final size:22
Alignment explanation
Indices: 36570--36645 Score: 152
Period size: 22 Copynumber: 3.5 Consensus size: 22
36560 ACACCTAACA
36570 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
36592 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
36614 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
36636 GTGCATCGAT
1 GTGCATCGAT
36646 ACACCATGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:36665 original size:13 final size:13
Alignment explanation
Indices: 36647--36676 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36637 TGCATCGATA
36647 CACCATGAAGGTG
1 CACCATGAAGGTG
36660 CACCATGAAGGTG
1 CACCATGAAGGTG
36673 CACC
1 CACC
36677 GATGCACGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (13 bp):
CACCATGAAGGTG
Found at i:38817 original size:2 final size:2
Alignment explanation
Indices: 38810--38837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38800 CAGCTTAAGC
38810 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
38838 ATCAATTGGC
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):
TA
Found at i:39397 original size:65 final size:64
Alignment explanation
Indices: 39320--39460 Score: 169
Period size: 65 Copynumber: 2.2 Consensus size: 64
39310 AATTAAATTG
*
39320 AACATCGAATGCATTTCAAGCATCGATCCA-CATACCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTCAAGCATCGATCCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG
39383 AA
64 -A
* * * * * * *
39385 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCAAGCATCGATCCACCAACCATGCACCGATGCACTCAGGATATTTTGA
39449 AACATCGAATGC
1 AACATCGAATGC
39461 GCTTGATGCA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 13 0.20
65 48 0.73
66 5 0.08
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
AACATCGAATGCATTTCAAGCATCGATCCACCAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:39495 original size:64 final size:63
Alignment explanation
Indices: 39320--39499 Score: 159
Period size: 65 Copynumber: 2.8 Consensus size: 63
39310 AATTAAATTG
* * * * * * *
39320 AACATCGAATGCATTTCAAGCATCGATCCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAA
* * * *
39385 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-
1 AACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGA
39448 A
63 A
*
39449 AACATCGAATGCGCTTGATGCATCGATGCACTCTTAG-TGCACCGATGCACT
1 AACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
39500 GAGAGTCCAA
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
64 44 0.45
65 49 0.50
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAA
Found at i:44789 original size:98 final size:98
Alignment explanation
Indices: 44620--44814 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
44610 ATAAATAAAC
* *
44620 AATGAAAAATAATTATCAACAAAATATGTGCAAATTAAAACACTCATCATTATTCTATTCTTGTA
1 AATGAAAAATAATTATCAACAAAATATGTGCAAATTAAAACACTCATCATTATTATATGCTTGTA
*
44685 TGTTGATTAAATGGTAAAACGTACCAAAGACAA
66 TATTGATTAAATGGTAAAACGTACCAAAGACAA
*
44718 AATGAGAAATAATTATCAACAAAATATGTGCAAATTAAAACACTCATCATTATTATATGCTTGTA
1 AATGAAAAATAATTATCAACAAAATATGTGCAAATTAAAACACTCATCATTATTATATGCTTGTA
44783 TATTGATTAAATGGTAAAACGTACCAAAGACA
66 TATTGATTAAATGGTAAAACGTACCAAAGACA
44815 TGTTAAATTC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (98 bp):
AATGAAAAATAATTATCAACAAAATATGTGCAAATTAAAACACTCATCATTATTATATGCTTGTA
TATTGATTAAATGGTAAAACGTACCAAAGACAA
Found at i:48609 original size:39 final size:39
Alignment explanation
Indices: 48331--48958 Score: 566
Period size: 39 Copynumber: 16.6 Consensus size: 39
48321 CTTAAAACAA
* *
48331 ATTTTATCTCGCTTGAGATGGTTTCACTCGAAACATAA-
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * ** * *
48369 A-GTTATCTCACTTGAGATTA-TTTTTCT-TAAA-ACAA-
1 ATTTTATCTCGCTTGAGA-TAGTTTCACTCGAAACAGAAG
* *
48404 ATTTTATCTCGCTTGAGATGGTTTCACTCGAAACATAA-
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * * * **
48442 ACTTTATCTCACTTGAGATTGTTT--TTC-TTAC---AG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * * * *
48475 ACTTTATCTCGCTTGAGATAATTTTTACTCGAAATA-AGAC
1 ATTTTATCTCGCTTGAGAT-AGTTTCACTCGAAACAGA-AG
* * * ** * ** * **
48515 ATTTCATTTCACTCAAGATTGTTTTTCT-TAAA-ACTAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
*
48552 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
48591 ATATTATCTCGCTTGAGATAATTTCACTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
*
48630 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
*
48669 A-TTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
48707 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
48746 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
48785 A-TTCATCTCGCTTGAGATAGTTTCACTCGAAACATAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
48823 ATTTTATCTCACTTGAGATAGTTTCACTTGAAACA-AA-
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * * ** * *
48860 ATATTTAGCTCACTTGAGATTGTTTTTCT-TAAA-ACAAG
1 AT-TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
** * *
48898 A-TTCGTCTCGCTTGAGATAGTTTCACTTGAAACATAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
48936 A-TTTATCTCACTTGAGATTGTTT
1 ATTTTATCTCGCTTGAGATAGTTT
48959 TATTTTAAAA
Statistics
Matches: 484, Mismatches: 83, Indels: 46
0.79 0.14 0.08
Matches are distributed among these distances:
32 1 0.00
33 18 0.04
34 3 0.01
35 7 0.01
36 46 0.10
37 55 0.11
38 152 0.31
39 188 0.39
40 14 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
Found at i:48685 original size:116 final size:115
Alignment explanation
Indices: 48557--48958 Score: 587
Period size: 116 Copynumber: 3.5 Consensus size: 115
48547 ACTAGATTTT
* * * *
48557 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATATTATCTCGCTTGAGATAATTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
48622 AACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTC
66 AACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAA-AGAAGATTC
*
48673 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
48738 AACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
66 AACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAA-AGAAGATTC
* *
48789 ATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTTTATCTCACTTGAGATAGTTTCACTTGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
* * * ** * *
48854 AACA-AA-ATATTTAGCTCACTTGAGATTGTTTTTCT-TAAAACAAGATTC
66 AACAGAAGAT-TTTATCTCGCTTGAGATAGTTTCACTCGAAAAGAAGATTC
* * * *
48902 GTCTCGCTTGAGATAGTTTCACTTGAAACATAAGA-TTTATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTT
48959 TATTTTAAAA
Statistics
Matches: 268, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
112 21 0.08
113 41 0.15
114 5 0.02
115 23 0.09
116 178 0.66
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (115 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
AACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAAGAAGATTC
Found at i:48716 original size:77 final size:77
Alignment explanation
Indices: 48331--48958 Score: 569
Period size: 77 Copynumber: 8.3 Consensus size: 77
48321 CTTAAAACAA
* * * * **
48331 ATTTTATCTCGCTTGAGATGGTTTCACTCGAAACATAA-AGTTATCTCACTTGAGATTA-TTTTT
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCGCTTGAGA-TAGTTTCA
* *
48394 CT-TAAA-ACAA-
65 CTCGAAACAGAAG
* * * *
48404 ATTTTATCTCGCTTGAGATGGTTTCACTCGAAACATAA-ACTTTATCTCACTTGAGATTGTTT--
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCA
* **
48466 TTC-TTAC---AG
65 CTCGAAACAGAAG
* * * * * * * ** *
48475 ACTTTATCTCGCTTGAGATAATTTTTACTCGAAATA-AGACATTTCATTTCACTCAAGATTGTTT
1 ATTTTATCTCGCTTGAGAT-AGTTTCACTCGAAACAGA-AGATTT-ATCTCGCTTGAGATAGTTT
** * **
48539 TTCT-TAAA-ACTAG
63 CACTCGAAACAGAAG
* *
48552 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATATTATCTCGCTTGAGATAATTTCA
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT-TTATCTCGCTTGAGATAGTTTCA
48617 CTCGAAACAGAAG
65 CTCGAAACAGAAG
* *
48630 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTCATCTCGCTTGAGATAGTTTCAC
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
48695 TCGAAACAGAAG
66 TCGAAACAGAAG
48707 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCA
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCA
48772 CTCGAAACAGAAG
65 CTCGAAACAGAAG
* * *
48785 A-TTCATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTTTATCTCACTTGAGATAGTTTCA
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCA
*
48849 CTTGAAACA-AA-
65 CTCGAAACAGAAG
* * * ** * * **
48860 ATATTTAGCTCACTTGAGATTGTTTTTCT-TAAA-ACAAGATTCGTCTCGCTTGAGATAGTTTCA
1 AT-TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCA
* *
48923 CTTGAAACATAAG
65 CTCGAAACAGAAG
* *
48936 A-TTTATCTCACTTGAGATTGTTT
1 ATTTTATCTCGCTTGAGATAGTTT
48959 TATTTTAAAA
Statistics
Matches: 480, Mismatches: 51, Indels: 47
0.83 0.09 0.08
Matches are distributed among these distances:
70 1 0.00
71 19 0.04
72 18 0.04
73 57 0.12
74 69 0.14
75 10 0.02
76 38 0.08
77 187 0.39
78 81 0.17
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (77 bp):
ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
TCGAAACAGAAG
Found at i:49073 original size:59 final size:59
Alignment explanation
Indices: 48977--49090 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
48967 AACAAACTAC
* *
48977 GCCTCACTTGAGGGATTAACATTTCCTTTGCTCGATTCACAACACTTT-GAATCAGTAAT
1 GCCTCACTTAAGGGATCAACATTTCCTTTGCTCGATTCACAACA-TTTCGAATCAGTAAT
* * * *
49036 GCCTCACTTAAGGGATCAACATTTTCTTTTCTTGATTCACGACATTTCGAATCAG
1 GCCTCACTTAAGGGATCAACATTTCCTTTGCTCGATTCACAACATTTCGAATCAG
49091 CGGCGCCTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 3 0.06
59 45 0.94
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (59 bp):
GCCTCACTTAAGGGATCAACATTTCCTTTGCTCGATTCACAACATTTCGAATCAGTAAT
Found at i:49099 original size:59 final size:59
Alignment explanation
Indices: 48975--49120 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 59
48965 AAAACAAACT
* * *
48975 ACGCCTCACTTGAGGGATTAACATTTCCTTTGCTCGATTCACAACACTTTGAATCAGTA
1 ACGCCTCACTTAAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTTGAATCAGCA
* * * * * *
49034 ATGCCTCACTTAAGGGATCAACATTTTCTTTTCTTGATTCACGACA-TTTCGAATCAGCG
1 ACGCCTCACTTAAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTT-GAATCAGCA
* **
49093 GCGCCTCACTCGAGGGA-CGAACATTTCC
1 ACGCCTCACTTAAGGGATC-AACATTTCC
49121 AGTAGAAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
58 4 0.06
59 67 0.94
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (59 bp):
ACGCCTCACTTAAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTTGAATCAGCA
Found at i:62981 original size:30 final size:30
Alignment explanation
Indices: 62945--63013 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
62935 TTAGTCCTTA
*
62945 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAAATATAAATACCCTAGCTCATTT
62975 AGCTTCAAATATAAATACCCTAGCTCATTT
1 AGCTTCAAATATAAATACCCTAGCTCATTT
63005 AGCTTCAAA
1 AGCTTCAAA
63014 ACATCCCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (30 bp):
AGCTTCAAATATAAATACCCTAGCTCATTT
Done.