Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005835.1 Hibiscus syriacus cultivar Beakdansim tig00013679_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: 138766
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3557 original size:28 final size:29
Alignment explanation
Indices: 3517--3572 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
3507 AGTGTTGGTC
3517 GTAGGTCGCCATGCACTCC-GGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
3545 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
3573 ACCCTTGCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.14, C:0.36, G:0.30, T:0.20
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:3789 original size:14 final size:14
Alignment explanation
Indices: 3770--3797 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3760 TCGGATGCTC
3770 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
3784 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
3798 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:3800 original size:10 final size:10
Alignment explanation
Indices: 3750--3783 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3740 CATAGCTCGT
3750 TCGGATGGCC
1 TCGGATGGCC
3760 TCGGAT-GCTC
1 TCGGATGGC-C
3770 TCGGATGGCC
1 TCGGATGGCC
3780 TCGG
1 TCGG
3784 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:6273 original size:20 final size:20
Alignment explanation
Indices: 6250--6315 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
6240 ATTCTGTAAA
6250 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
6270 TCGCAACGC-GATAGTC-AAT
1 TCGCAACACAGA-AGTCAAAT
*
6289 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
6309 TCGCAAC
1 TCGCAAC
6316 TGAATTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:6325 original size:19 final size:19
Alignment explanation
Indices: 6303--6386 Score: 152
Period size: 19 Copynumber: 4.5 Consensus size: 19
6293 AACACAAAAG
6303 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
6322 TCAAATTCAC-ACTGAATT
1 TCAAATTCGCAACTGAATT
6340 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
6359 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
6378 TCAAATTCG
1 TCAAATTCG
6387 TAACACGAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
18 17 0.27
19 45 0.73
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:6329 original size:39 final size:39
Alignment explanation
Indices: 6250--6371 Score: 128
Period size: 39 Copynumber: 3.2 Consensus size: 39
6240 ATTCTGTAAA
* * *
6250 TCGCAACACAGAAGTCAAATTCGCAAC-GCGATAGTC-AAT
1 TCGCAACACAAAAGTCAAATTCGCAACTG-AAT-TTCAAAT
6289 TCGCAACACAAAAGTCAAATTCGCAACTGAATTTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACTGAATTTCAAAT
* **
6328 T--C-ACACTGAATTTCAAATTCGCAACTGAATTTCAAAT
1 TCGCAACAC-AAAAGTCAAATTCGCAACTGAATTTCAAAT
6365 TCGCAAC
1 TCGCAAC
6372 TGAATTTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
36 4 0.06
37 29 0.41
38 2 0.03
39 33 0.46
40 3 0.04
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (39 bp):
TCGCAACACAAAAGTCAAATTCGCAACTGAATTTCAAAT
Found at i:6353 original size:37 final size:38
Alignment explanation
Indices: 6303--6386 Score: 152
Period size: 37 Copynumber: 2.2 Consensus size: 38
6293 AACACAAAAG
6303 TCAAATTCGCAACTGAATTTCAAATTCAC-ACTGAATT
1 TCAAATTCGCAACTGAATTTCAAATTCACAACTGAATT
*
6340 TCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATTTCAAATTCACAACTGAATT
6378 TCAAATTCG
1 TCAAATTCG
6387 TAACACGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 28 0.62
38 17 0.38
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (38 bp):
TCAAATTCGCAACTGAATTTCAAATTCACAACTGAATT
Found at i:6409 original size:38 final size:38
Alignment explanation
Indices: 6303--6398 Score: 140
Period size: 37 Copynumber: 2.5 Consensus size: 38
6293 AACACAAAAG
* *
6303 TCAAATTCGCAACTGAATTTCAAATTCAC-ACTGAATT
1 TCAAATTCGCAACCGAATTTCAAATTCGCAACTGAATT
*
6340 TCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACCGAATTTCAAATTCGCAACTGAATT
*
6378 TCAAATTCGTAACACGAATTT
1 TCAAATTCGCAAC-CGAATTT
6399 AGTTTCGCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 28 0.52
38 20 0.37
39 6 0.11
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (38 bp):
TCAAATTCGCAACCGAATTTCAAATTCGCAACTGAATT
Found at i:7115 original size:12 final size:12
Alignment explanation
Indices: 7094--7127 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7084 ACCACATTTC
*
7094 CAATACCAAACA
1 CAATATCAAACA
7106 CAATATCAAACA
1 CAATATCAAACA
*
7118 CAATCTCAAA
1 CAATATCAAA
7128 ACCCATAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:7304 original size:24 final size:24
Alignment explanation
Indices: 7253--7306 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
7243 GTATTTGAAA
*
7253 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
7277 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
7301 TTTGAT
1 TTTGAT
7307 GATGTGATGG
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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:9874 original size:20 final size:20
Alignment explanation
Indices: 9851--9889 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9841 AAGCGTTGCG
*
9851 ATAGTCAAATTCGCAACGCA
1 ATAGTCAAATTCACAACGCA
9871 ATAGTCAAATTCACAACGC
1 ATAGTCAAATTCACAACGC
9890 GAAATCGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21
Consensus pattern (20 bp):
ATAGTCAAATTCACAACGCA
Found at i:10032 original size:25 final size:25
Alignment explanation
Indices: 9992--10047 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
9982 AAATCAATTA
* *
9992 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATAGGTACATTATTTG
10017 AACATTGTTATAGGTACATTATTTG
1 AACATTGTTATAGGTACATTATTTG
10042 AACATT
1 AACATT
10048 ATTGAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (25 bp):
AACATTGTTATAGGTACATTATTTG
Found at i:10054 original size:10 final size:11
Alignment explanation
Indices: 10007--10057 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
9997 TGTTGTGGGT
10007 ACATTATTTGA
1 ACATTATTTGA
* *
10018 ACATTGTTATAGGT
1 ACATTATT-T--GA
10032 ACATTATTTGA
1 ACATTATTTGA
10043 ACATTA-TTGA
1 ACATTATTTGA
10053 ACATT
1 ACATT
10058 GTATGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 9 0.27
11 14 0.42
12 1 0.03
13 1 0.03
14 8 0.24
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (11 bp):
ACATTATTTGA
Found at i:12114 original size:20 final size:21
Alignment explanation
Indices: 12076--12130 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
12066 ATGAATCAGG
12076 CTCTTGAATGGCA-GAC-GGGAC
1 CTCTTGAAT-G-ATGACGGGGAC
*
12097 CTCTTGAATGATGACGGGGGC
1 CTCTTGAATGATGACGGGGAC
*
12118 CTCTTGAACGATG
1 CTCTTGAATGATG
12131 GGAGGGGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 4 0.13
21 25 0.83
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGATGACGGGGAC
Found at i:12120 original size:21 final size:21
Alignment explanation
Indices: 12096--12194 Score: 96
Period size: 21 Copynumber: 4.7 Consensus size: 21
12086 GCAGACGGGA
12096 CCTCTTGAATGATGACG-GGGG
1 CCTCTTGAATGATGA-GAGGGG
* *
12117 CCTCTTGAACGATGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
*
12138 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
12159 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAATGATGA-GAGGGG
*
12180 TCTCTTGAATGATGA
1 CCTCTTGAATGATGA
12195 TAGGTGTATC
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
20 3 0.05
21 58 0.92
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.25
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:12192 original size:42 final size:41
Alignment explanation
Indices: 12097--12194 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 41
12087 CAGACGGGAC
*
12097 CTCTTGAATGATGACGGGGGCCTCTTGAACGATGGGAGGGG
1 CTCTTGAATGATGACGGGGGCCTCTTGAACGATAGGAGGGG
*
12138 CTTCTTCG-ATGATGA-GAGGGGCCTCTTGAACGATAGGAGGCGT
1 C-TCTT-GAATGATGACG-GGGGCCTCTTGAACGATAGGAGG-GG
12181 CTCTTGAATGATGA
1 CTCTTGAATGATGA
12195 TAGGTGTATC
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
41 3 0.06
42 44 0.88
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (41 bp):
CTCTTGAATGATGACGGGGGCCTCTTGAACGATAGGAGGGG
Found at i:14393 original size:19 final size:20
Alignment explanation
Indices: 14371--14412 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
14361 AATCGCAACA
14371 CGATTTT-AGTTTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
*
14390 CGATTTTCATTTTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
14410 CGA
1 CGA
14413 ATTTGGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (20 bp):
CGATTTTCAGTTTCGCGTTG
Found at i:14459 original size:13 final size:13
Alignment explanation
Indices: 14441--14472 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
14431 AGGTTTCTTC
14441 AACAAAAAGACAA
1 AACAAAAAGACAA
14454 AACAAAAAGACAA
1 AACAAAAAGACAA
14467 AACAAA
1 AACAAA
14473 GACAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:14475 original size:11 final size:12
Alignment explanation
Indices: 14445--14478 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
14435 TTCTTCAACA
14445 AAAAGACAAAAC
1 AAAAGACAAAAC
14457 AAAAAGACAAAAC
1 -AAAAGACAAAAC
14470 -AAAGACAAA
1 AAAAGACAAA
14479 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:14713 original size:22 final size:22
Alignment explanation
Indices: 14685--14735 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
14675 GATGGAGATA
14685 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
14707 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
14729 GACGGAT
1 GACGGAT
14736 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:14879 original size:20 final size:20
Alignment explanation
Indices: 14856--14947 Score: 82
Period size: 20 Copynumber: 4.6 Consensus size: 20
14846 GTGTTTCACA
14856 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
14876 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGCG
* *
14896 TTGCG-ATTT-ACAAATTCGCA
1 TTGCGAATTTGAC--TTTCGCG
**
14916 ACGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
14936 TTGCGAAATTGA
1 TTGCGAATTTGA
14948 AAACTGGGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
18 2 0.04
19 5 0.09
20 41 0.75
21 5 0.09
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:18258 original size:13 final size:13
Alignment explanation
Indices: 18240--18267 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18230 ATAAATCTTT
18240 TTAACATTTTCGG
1 TTAACATTTTCGG
18253 TTAACATTTTCGG
1 TTAACATTTTCGG
18266 TT
1 TT
18268 GAAATGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAACATTTTCGG
Found at i:19439 original size:2 final size:2
Alignment explanation
Indices: 19432--19462 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19422 CATGTCACAT
19432 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
19463 GTATGTATGG
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:21473 original size:43 final size:43
Alignment explanation
Indices: 21410--21497 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
21400 ACAAACATTG
*
21410 GCGGCGTTGTTTTTACAAACGATGCAATAGGTTCATACATTTA
1 GCGGCGTTGTTTTTACAAACGATGCAATAGGTTCAGACATTTA
* *
21453 GCGGCGTT-TTTCTTATAAACGCTGCAATAGGTTCAGACATTTA
1 GCGGCGTTGTTT-TTACAAACGATGCAATAGGTTCAGACATTTA
21496 GC
1 GC
21498 TTCATTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 3 0.07
43 38 0.93
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (43 bp):
GCGGCGTTGTTTTTACAAACGATGCAATAGGTTCAGACATTTA
Found at i:27606 original size:39 final size:38
Alignment explanation
Indices: 27537--27628 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 38
27527 TTAATAAAAT
27537 AATTTAGAATGTTAATGTGAAACAAGTTAAGAAATTAAG
1 AATTTAGAATGTT-ATGTGAAACAAGTTAAGAAATTAAG
* *
27576 AATTTAGAATGTTATGGTGACAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTAT-GTGA-AACAAGTTAAGAAATTAAG
*
27615 AATTTTGAATGTTA
1 AATTTAGAATGTTA
27629 GAGTAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
38 2 0.04
39 44 0.92
40 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (38 bp):
AATTTAGAATGTTATGTGAAACAAGTTAAGAAATTAAG
Found at i:27642 original size:39 final size:38
Alignment explanation
Indices: 27537--27650 Score: 108
Period size: 39 Copynumber: 2.9 Consensus size: 38
27527 TTAATAAAAT
* *
27537 AATTTAGAATGTTA-ATGTGAAACAAGTTAAGAAATTAAG
1 AATTTAGAATGTTAGA-GT-AAAAAATTTAAGAAATTAAG
* *
27576 AATTTAGAATGTTATG-GTGACAAAATTTAAGAAATTAGG
1 AATTTAGAATGTTA-GAGT-AAAAAATTTAAGAAATTAAG
* *
27615 AATTTTGAATGTTAGAGTAAAATAATTTGA-AAATTA
1 AATTTAGAATGTTAGAGTAAAA-AATTTAAGAAATTA
27651 TAAATAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
38 10 0.16
39 54 0.84
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (38 bp):
AATTTAGAATGTTAGAGTAAAAAATTTAAGAAATTAAG
Found at i:31040 original size:22 final size:22
Alignment explanation
Indices: 31015--31059 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
31005 TCTCTCAACG
31015 ACTATCCCTCTTTCTTGATCAA
1 ACTATCCCTCTTTCTTGATCAA
31037 ACTATCCCTCTTTCTTGATCAA
1 ACTATCCCTCTTTCTTGATCAA
31059 A
1 A
31060 GGCCGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.31, G:0.04, T:0.40
Consensus pattern (22 bp):
ACTATCCCTCTTTCTTGATCAA
Found at i:31309 original size:25 final size:25
Alignment explanation
Indices: 31275--31324 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
31265 TTGCCCCGTC
31275 CTCAAACCCG-ACCCGAAATATTATA
1 CTCAAACCCGAACCC-AAATATTATA
*
31300 CTCAGACCCGAACCCAAATATTATA
1 CTCAAACCCGAACCCAAATATTATA
31325 TATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.20
Consensus pattern (25 bp):
CTCAAACCCGAACCCAAATATTATA
Found at i:34083 original size:3 final size:3
Alignment explanation
Indices: 34075--34198 Score: 221
Period size: 3 Copynumber: 41.3 Consensus size: 3
34065 TACCCATATC
*
34075 ATT ATT ATT ATT ATT ATT ATT ATC 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
* *
34123 ATT ATC ATT ATC 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
34171 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
34199 AATATATTAA
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:34812 original size:19 final size:19
Alignment explanation
Indices: 34772--34811 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
34762 ACCACTCAGC
*
34772 AAAGAAACAGAAAGAAAGA
1 AAAGAAAAAGAAAGAAAGA
34791 AAAGAAAAAGAAAG-AAGA
1 AAAGAAAAAGAAAGAAAGA
34809 AAA
1 AAA
34812 ACTTACTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAGAAAGAAAGA
Found at i:35679 original size:13 final size:13
Alignment explanation
Indices: 35663--35709 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
35653 ATATAATAAA
35663 TAAATATTTATTT
1 TAAATATTTATTT
*
35676 TAAATAAATTATTT
1 TAAAT-ATTTATTT
35690 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
35703 TCAATAT
1 TAAATAT
35710 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:44462 original size:36 final size:38
Alignment explanation
Indices: 44415--44500 Score: 131
Period size: 37 Copynumber: 2.3 Consensus size: 38
44405 TATTTTAGGG
* *
44415 ACCAAATATGAAATTCCCAT-TGCAAAGTTGTCCACCA
1 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCA
*
44452 ACC-AAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
1 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCA
44489 ACCAAAGATGAA
1 ACCAAAGATGAA
44501 TTTTCTAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 15 0.34
37 21 0.48
38 8 0.18
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (38 bp):
ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCA
Found at i:47868 original size:23 final size:23
Alignment explanation
Indices: 47808--47874 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
47798 CACCACAGCT
* **
47808 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
47831 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
47854 CGTAGAATTGCACCGGAGTGC
1 CGTAGAATTGCACCGGAGTGC
47875 TATATAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:48063 original size:103 final size:103
Alignment explanation
Indices: 47892--48104 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
47882 TAATGTCCAT
*
47892 AAGGACCACATATCATTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
47957 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
47995 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-GTCAATGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACT-AAGGATCAAGTATGTGTCTCACC
48059 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
48098 AAGGACC
1 AAGGACC
48105 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 104 0.99
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCATTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:53044 original size:23 final size:23
Alignment explanation
Indices: 53026--53109 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
53016 CTCGTATAAC
*
53026 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGGAGTGCCACGTAGAAT
*
53049 TGCACCGGAGTGCCGCGTAGAAT
1 TGCACCGGAGTGCCACGTAGAAT
*
53072 TGCACCGGAGTGCCGCGTAGAAT
1 TGCACCGGAGTGCCACGTAGAAT
*
53095 TGCACCGTAGTGCCA
1 TGCACCGGAGTGCCA
53110 TATAATAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.24, C:0.27, G:0.31, T:0.18
Consensus pattern (23 bp):
TGCACCGGAGTGCCACGTAGAAT
Found at i:53246 original size:103 final size:103
Alignment explanation
Indices: 53125--53337 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
53115 TAATGTCCAT
* **
53125 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
53190 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
* *
53228 AAGGACCATATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
*
53293 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
53331 AAGGACC
1 AAGGACC
53338 GCGTAGACCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:60442 original size:20 final size:20
Alignment explanation
Indices: 60417--60470 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
60407 TGGAAGCTCG
*
60417 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
60437 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
60457 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
60471 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:60497 original size:19 final size:20
Alignment explanation
Indices: 60457--60507 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
60447 TTCTTTTTAA
*
60457 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
60477 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
60496 CGTTGCGATTTT
1 CGTTGCGATTTT
60508 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:60629 original size:17 final size:17
Alignment explanation
Indices: 60609--60790 Score: 113
Period size: 17 Copynumber: 10.2 Consensus size: 17
60599 TTATATCATA
*
60609 TTATATTGTATATTATT
1 TTATATTATATATTATT
* *
60626 TTATATAGTATATATGATA
1 TTATAT--TATATATTATT
*
60645 TGATATTATATA-TATT
1 TTATATTATATATTATT
*
60661 ATAGTATTATATATTATT
1 TTA-TATTATATATTATT
* *
60679 ATATAGTATATATTATT
1 TTATATTATATATTATT
60696 TATATAATTATATAGTATATT
1 T-TAT-ATTATATA-T-TATT
*
60717 ATTATATTATATATTATA
1 -TTATATTATATATTATT
*
60735 GTATA-TATAT-TT-TT
1 TTATATTATATATTATT
*
60749 ACTATTATTAT-TATTATT
1 -TTA-TATTATATATTATT
60767 ATTATTATTATATTTATTATT
1 -TTA-TATTATA--TATTATT
60788 TTA
1 TTA
60791 GGTCTAAATT
Statistics
Matches: 132, Mismatches: 16, Indels: 31
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.01
15 4 0.03
16 11 0.08
17 43 0.33
18 25 0.19
19 21 0.16
20 12 0.09
21 14 0.11
22 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (17 bp):
TTATATTATATATTATT
Found at i:60677 original size:53 final size:50
Alignment explanation
Indices: 60597--60779 Score: 145
Period size: 51 Copynumber: 3.7 Consensus size: 50
60587 CTCTTCTTTT
*
60597 TATTATATCATAT-TA-TATTGTATATTATTTTATATAGTATATATGATATGA
1 TATTATAT-ATATATAGTATTAT-TATTATTTTATATAGTATATATGATAT-A
* *
60648 TATTATATATATTATAGTATTA-TA-TATTATTATATAGTATATATTATTTA
1 TATTATATATA-TATAGTATTATTATTATT-TTATATAGTATATATGATATA
* *
60698 TA-TA-AT-TATATAGTA-TATTATTATATTATATATTATAGTAT-ATATA
1 TATTATATATATATAGTATTATTATTATTTTATATAGTATA-TATGATATA
* *
60744 T-TTTTACTAT-TATTATTATTATTATTATTATTATAT
1 TATTATA-TATATA-TAGTATTATTATTATT-TTATAT
60780 TTATTATTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
45 2 0.02
46 26 0.24
47 9 0.08
48 5 0.05
49 7 0.06
50 19 0.17
51 35 0.32
52 2 0.02
53 4 0.04
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (50 bp):
TATTATATATATATAGTATTATTATTATTTTATATAGTATATATGATATA
Found at i:60731 original size:12 final size:12
Alignment explanation
Indices: 60606--60786 Score: 123
Period size: 12 Copynumber: 15.0 Consensus size: 12
60596 TTATTATATC
*
60606 ATATTATATTGT
1 ATATTATATTAT
*
60618 ATATTATTTTAT
1 ATATTATATTAT
*
60630 ATAGTATA-TAT
1 ATATTATATTAT
*
60641 GATATGATA-T-T
1 -ATATTATATTAT
60652 ATA-TATATTAT
1 ATATTATATTAT
60663 AGTATTATA-TAT
1 A-TATTATATTAT
60675 -TATTATATAGTAT
1 ATATTATAT--TAT
60688 ATATTAT-TTAT
1 ATATTATATTAT
60699 ATAATTATATAGTAT
1 AT-ATTATAT--TAT
60714 ATTATTATATTAT
1 A-TATTATATTAT
*
60727 ATATTATAGTAT
1 ATATTATATTAT
*
60739 ATA-TAT-TTTT
1 ATATTATATTAT
60749 ACTATTATTATTAT
1 A-TATTA-TATTAT
60763 -TATTATTATTATT
1 ATATTA-TATTA-T
60776 ATATT-TATTAT
1 ATATTATATTAT
60787 TTTAGGTCTA
Statistics
Matches: 138, Mismatches: 11, Indels: 41
0.73 0.06 0.22
Matches are distributed among these distances:
9 3 0.02
10 14 0.10
11 17 0.12
12 64 0.46
13 15 0.11
14 13 0.09
15 11 0.08
16 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:60769 original size:15 final size:15
Alignment explanation
Indices: 60648--60787 Score: 80
Period size: 15 Copynumber: 9.3 Consensus size: 15
60638 TATGATATGA
60648 TATTA-TATATATTA-
1 TATTATTAT-TATTAT
*
60662 TAGTATTATATATTAT
1 TATTATTAT-TATTAT
*
60678 TATATAGTATATATTAT
1 TAT-TATTAT-TATTAT
* *
60695 T-TATATAATTATATAG
1 TAT-TATTATTAT-TAT
60711 TA-TATTATTA-TAT
1 TATTATTATTATTAT
*
60724 TATATATTA-TAGTA-
1 TAT-TATTATTATTAT
* *
60738 TATATATTTTTACTAT
1 TAT-TATTATTATTAT
60754 TATTATTATTATTAT
1 TATTATTATTATTAT
60769 TATTATTA-TATTTAT
1 TATTATTATTA-TTAT
60784 TATT
1 TATT
60788 TTAGGTCTAA
Statistics
Matches: 103, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
13 4 0.04
14 16 0.16
15 56 0.54
16 14 0.14
17 13 0.13
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:60785 original size:53 final size:53
Alignment explanation
Indices: 60596--60786 Score: 170
Period size: 53 Copynumber: 3.6 Consensus size: 53
60586 TCTCTTCTTT
* *
60596 TTATTATATCA-TATTATATTGTATATTATTTTATATAGTATATATGA--TATGA-TA
1 TTATTATAT-ATTATTATA-T-TATATT-TATTATATAGTATATATTATTTAT-ATTA
*
60650 TTA-TATATATTA-TAGTATTATATATTATTATATAGTATATATTATTTATATAA
1 TTATTATATATTATTA-TATTATAT-TTATTATATAGTATATATTATTTATATTA
60703 TTATATAGTATATTATTATATTATA--TATTATAGTA-TATATATT-TTTACTATTA
1 TTAT-TA-TATATTATTATATTATATTTATTATA-TAGTATATATTATTTA-TATTA
60756 TTATTAT-TATTATTATTATTATATTTATTAT
1 TTATTATATATTATTA-TATTATATTTATTAT
60787 TTTAGGTCTA
Statistics
Matches: 118, Mismatches: 4, Indels: 31
0.77 0.03 0.20
Matches are distributed among these distances:
50 8 0.07
51 30 0.25
52 12 0.10
53 45 0.38
54 5 0.04
55 2 0.02
56 14 0.12
57 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (53 bp):
TTATTATATATTATTATATTATATTTATTATATAGTATATATTATTTATATTA
Found at i:60790 original size:41 final size:43
Alignment explanation
Indices: 60597--60787 Score: 173
Period size: 44 Copynumber: 4.4 Consensus size: 43
60587 CTCTTCTTTT
* * *
60597 TATTATATCATATTATATTGTATATTATT-TTATATAGTATATATGA
1 TATTATATTATA-TATATTATATATTATTATTAT-TATTAT-TAT-A
* *
60643 TATGATATTATATATATTATAGTATTATATATTATTATATAGTATA
1 TATTATATTATATATATTATA-TATTAT-TATTATTAT-TATTATA
*
60689 TATTAT-TTATATA-ATTATATAGTA-TATTATTA-TATTATA
1 TATTATATTATATATATTATATATTATTATTATTATTATTATA
* *
60728 TATTATAGTATATATATTTTTACTATTATTATTATTATTATTAT-
1 TATTATATTATATATA-TTATA-TATTATTATTATTATTATTATA
60772 TATTATATT-TAT-TATT
1 TATTATATTATATATATT
60788 TTAGGTCTAA
Statistics
Matches: 123, Mismatches: 12, Indels: 25
0.77 0.08 0.16
Matches are distributed among these distances:
39 12 0.10
40 6 0.05
41 11 0.09
42 6 0.05
43 11 0.09
44 22 0.18
45 21 0.17
46 22 0.18
47 6 0.05
48 6 0.05
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (43 bp):
TATTATATTATATATATTATATATTATTATTATTATTATTATA
Found at i:66782 original size:11 final size:11
Alignment explanation
Indices: 66768--66797 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
66758 CTAATCCCTC
66768 TTTAATTTTTA
1 TTTAATTTTTA
66779 TTTAATTTTTA
1 TTTAATTTTTA
66790 TTTAATTT
1 TTTAATTT
66798 AGTTTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTAATTTTTA
Found at i:67911 original size:13 final size:13
Alignment explanation
Indices: 67893--67921 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
67883 TAATCAATAT
67893 AATAAATTACTGA
1 AATAAATTACTGA
67906 AATAAATTACTGA
1 AATAAATTACTGA
67919 AAT
1 AAT
67922 TTTAGGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (13 bp):
AATAAATTACTGA
Found at i:68243 original size:107 final size:107
Alignment explanation
Indices: 68068--68286 Score: 311
Period size: 115 Copynumber: 2.0 Consensus size: 107
68058 TAATAAACTG
*
68068 TATTTTATTTTTAGTATATAAAAAATCAAAGAATAAAACAAAGTGAATTAGATTTAACTTTATCA
1 TATTTTATTTTTAGTAAATAAAAAATCAAAGAATAAAACAAAGTGAATTAG---T-ACTTTA-CA
68133 TAGACCCTTAAAATATTATAATAGTAATTTA-TTATTTATTAATTAATA
61 TAGACCCTTAAAATATTATAATAGTAATTTATTTA-TTATT-ATTAATA
68181 TATTTTATTTTTAAAGTAAATAAAAAATCAAAGAATAAAACAAAGTGAATTAG-A-TTTA-ATAG
1 TATTTTATTTTT--AGTAAATAAAAAATCAAAGAATAAAACAAAGTGAATTAGTACTTTACATAG
*
68243 ACCGTTAAAATATTATAATAGTAATTTATTTATTATTATTAATA
64 ACCCTTAAAATATTATAATAGTAATTTATTTATTATTATTAATA
68287 AATAATTATC
Statistics
Matches: 101, Mismatches: 2, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
106 7 0.07
107 36 0.36
108 3 0.03
109 4 0.04
110 1 0.01
113 12 0.12
115 38 0.38
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (107 bp):
TATTTTATTTTTAGTAAATAAAAAATCAAAGAATAAAACAAAGTGAATTAGTACTTTACATAGAC
CCTTAAAATATTATAATAGTAATTTATTTATTATTATTAATA
Found at i:68560 original size:20 final size:20
Alignment explanation
Indices: 68516--68564 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
68506 AATTCTACAT
*
68516 TTTTTTAT-ATTTTTTGTTT
1 TTTTTTATGATTTTTTGTTA
68535 TGTTTTTATGATTTTTAT-TTA
1 T-TTTTTATGATTTTT-TGTTA
68556 -TTTTTATGA
1 TTTTTTATGA
68565 AACATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.38
20 7 0.27
21 8 0.31
22 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTTTATGATTTTTTGTTA
Found at i:72081 original size:16 final size:16
Alignment explanation
Indices: 72060--72095 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
72050 TGTTATATCA
72060 CTTTTCAAGCATAATC
1 CTTTTCAAGCATAATC
*
72076 CTTTTCAAGTATAATC
1 CTTTTCAAGCATAATC
72092 CTTT
1 CTTT
72096 ATTGAATCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (16 bp):
CTTTTCAAGCATAATC
Found at i:76006 original size:158 final size:158
Alignment explanation
Indices: 75818--76155 Score: 450
Period size: 158 Copynumber: 2.1 Consensus size: 158
75808 TTTATTTTAA
* *
75818 GTACTTTCAATTTCT-CTTTTTGATAACAAATTTTCTA-TTTTCTATTTAGGCCCTCAATTTTTT
1 GTACTTTCAATTCCTACTTTTTGATAACAAATTTTCTATTTTTCAATTTAGGCCCTCAA-TTTTT
* *
75881 TATAACTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATATTTTTA-CTAAATTTGAATCA
65 TATAACTTCCTTATTTCGTCAATTCATCATTTATTTTAAGTATATTTTTATC-AAATTTGAACCA
* * **
75945 TATGCTCCTAAACCATCGTAGAATACATAT
129 CATGCTCATAAACCATAATAGAATACATAT
* *
75975 GTACTTTCAATTCCTACTTTTTGATAACAAATTTTCTATTTTTCAATTTTGTCCCTCAATTTTTT
1 GTACTTTCAATTCCTACTTTTTGATAACAAATTTTCTATTTTTCAATTTAGGCCCTCAATTTTTT
* * * *
76040 ATAATTTTCTTATTTCGTCAATTCATCTTTTATTTTAAGTATGTTTTTATCAAATTTGAACCACA
66 ATAACTTCCTTATTTCGTCAATTCATCATTTATTTTAAGTATATTTTTATCAAATTTGAACCACA
* * *
76105 TGCTCATATATCATAATAGAATACCTAT
131 TGCTCATAAACCATAATAGAATACATAT
*
76133 GTAAC-TTCAATTCTTACCTTTTT
1 GT-ACTTTCAATTCCTA-CTTTTT
76156 TTTTACTAAA
Statistics
Matches: 158, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
157 14 0.09
158 118 0.75
159 26 0.16
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (158 bp):
GTACTTTCAATTCCTACTTTTTGATAACAAATTTTCTATTTTTCAATTTAGGCCCTCAATTTTTT
ATAACTTCCTTATTTCGTCAATTCATCATTTATTTTAAGTATATTTTTATCAAATTTGAACCACA
TGCTCATAAACCATAATAGAATACATAT
Found at i:81270 original size:3 final size:3
Alignment explanation
Indices: 81264--81315 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
81254 CAATAGGATG
81264 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
81312 ATA A
1 ATA A
81316 AGCTTTGGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:85378 original size:23 final size:25
Alignment explanation
Indices: 85329--85378 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
85319 CATCTTATCT
*
85329 ATAATTAGATTGATTCTTTTTTACATA
1 ATAATTAGATTGA-T-TTTATTACATA
85356 ATAATTAGATTGA-TTTATT-CATA
1 ATAATTAGATTGATTTTATTACATA
85379 TTCATTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
27 13 0.59
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (25 bp):
ATAATTAGATTGATTTTATTACATA
Found at i:86379 original size:17 final size:18
Alignment explanation
Indices: 86338--86384 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
86328 TGTTTACGAG
*
86338 GGAATTGAAATATGTGAA
1 GGAATTGAAATCTGTGAA
* *
86356 TGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
*
86373 GGAATTGGAATC
1 GGAATTGAAATC
86385 CAATTCCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:90494 original size:23 final size:23
Alignment explanation
Indices: 90468--90511 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
90458 AGTATAATGC
*
90468 TACAGTGCAGACATCAAAACAGT
1 TACAGAGCAGACATCAAAACAGT
**
90491 TACAGAGCATTCATCAAAACA
1 TACAGAGCAGACATCAAAACA
90512 ACCAGTGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (23 bp):
TACAGAGCAGACATCAAAACAGT
Found at i:94860 original size:22 final size:22
Alignment explanation
Indices: 94835--94885 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
94825 TCTAATTAGG
* *
94835 TTAATTCGGTC-AGTTAATTCAT
1 TTAATTCGATCGA-TTAATTCAA
*
94857 TTAATTTGATCGATTAATTCAA
1 TTAATTCGATCGATTAATTCAA
94879 TTAATTC
1 TTAATTC
94886 CGAAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (22 bp):
TTAATTCGATCGATTAATTCAA
Found at i:95530 original size:2 final size:2
Alignment explanation
Indices: 95523--95584 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
95513 GGAGCAAAAC
95523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
95565 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
95585 GTGTCATCGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99504 original size:4 final size:4
Alignment explanation
Indices: 99495--99526 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
99485 AATTTCTAGA
99495 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
99527 GTGATAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:101105 original size:37 final size:36
Alignment explanation
Indices: 101058--101131 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
101048 TCATTAACAT
*
101058 TTTTATAATTTCAATTTTATAAAAAAAATATATAAA
1 TTTTATAATTTAAATTTTATAAAAAAAATATATAAA
* *
101094 TTTTATGAATTTAAATTTTTTAAATAAAATATATAAA
1 TTTTAT-AATTTAAATTTTATAAAAAAAATATATAAA
101131 T
1 T
101132 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (36 bp):
TTTTATAATTTAAATTTTATAAAAAAAATATATAAA
Found at i:101783 original size:29 final size:29
Alignment explanation
Indices: 101751--101815 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
101741 AGAAAAAAAA
* * *
101751 TTATTTCGTTCCAATTTGGTGCTTAACGT
1 TTATTTCATTCCAATTTGGCGCTTAACAT
* *
101780 TTATTTCATTCCAGTTTTGCGCTTAACAT
1 TTATTTCATTCCAATTTGGCGCTTAACAT
*
101809 TTCTTTC
1 TTATTTC
101816 CCTCTCTTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (29 bp):
TTATTTCATTCCAATTTGGCGCTTAACAT
Found at i:102456 original size:28 final size:30
Alignment explanation
Indices: 102412--102471 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
102402 CATTTTGAGT
*
102412 AACGAAATGAAACGTTAGACAC-CAACTAG
1 AACGAAATGAAACGTTAGACACTAAACTAG
102441 AACGAAAT-AAACGTTAGACACTAAACTAG
1 AACGAAATGAAACGTTAGACACTAAACTAG
102470 AA
1 AA
102472 AAAATAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (30 bp):
AACGAAATGAAACGTTAGACACTAAACTAG
Found at i:102476 original size:28 final size:28
Alignment explanation
Indices: 102416--102478 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
102406 TTGAGTAACG
* *
102416 AAATGAAACGTTAGACACCAACTAGAACG
1 AAAT-AAACGTTAGACACAAACTAGAACA
102445 AAATAAACGTTAGACACTAAACTAGAA-A
1 AAATAAACGTTAGACAC-AAACTAGAACA
102473 AAATAA
1 AAATAA
102479 GCATAGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.16
Consensus pattern (28 bp):
AAATAAACGTTAGACACAAACTAGAACA
Found at i:102545 original size:46 final size:47
Alignment explanation
Indices: 102470--102559 Score: 121
Period size: 46 Copynumber: 1.9 Consensus size: 47
102460 ACTAAACTAG
* *
102470 AAAAAATAAGCATAGATTGGACACCTTTTGTA-AGCTTAAGCCTTACT
1 AAAAAATAAGCATAAATTGGACACATTTTGTATA-CTTAAGCCTTACT
* *
102517 AAAAAATTA-CATAAATTGTACACATTTTGTATACTTAAGCCTT
1 AAAAAATAAGCATAAATTGGACACATTTTGTATACTTAAGCCTT
102560 TGAAAAATCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 29 0.76
47 9 0.24
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (47 bp):
AAAAAATAAGCATAAATTGGACACATTTTGTATACTTAAGCCTTACT
Found at i:107050 original size:19 final size:19
Alignment explanation
Indices: 107026--107062 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
107016 ATGCATTGGG
*
107026 CTATGAATTTGAAAATAAA
1 CTATGAATCTGAAAATAAA
*
107045 CTATGAATCTGGAAATAA
1 CTATGAATCTGAAAATAA
107063 GTTCTGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.30
Consensus pattern (19 bp):
CTATGAATCTGAAAATAAA
Found at i:107133 original size:12 final size:12
Alignment explanation
Indices: 107116--107149 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
107106 TTTGAACATG
107116 GAATATGAAAAT
1 GAATATGAAAAT
**
107128 GAATATGTGAAT
1 GAATATGAAAAT
107140 GAATATGAAA
1 GAATATGAAA
107150 GTGGAAAATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (12 bp):
GAATATGAAAAT
Found at i:135389 original size:56 final size:56
Alignment explanation
Indices: 135303--135409 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 56
135293 TAACTGTTTC
* *
135303 TCGTCATTACAGAGAAAATATAAATCAACAACCCAGTGGAGGGTTGAATTTCATTG
1 TCGTCATAACAAAGAAAATATAAATCAACAACCCAGTGGAGGGTTGAATTTCATTG
*
135359 TCGTCATAACAAAGAAAATGTAAATCAACAACCCAGTGGAGGGTTGAATTT
1 TCGTCATAACAAAGAAAATATAAATCAACAACCCAGTGGAGGGTTGAATTT
135410 GGGCCAGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (56 bp):
TCGTCATAACAAAGAAAATATAAATCAACAACCCAGTGGAGGGTTGAATTTCATTG
Found at i:136009 original size:46 final size:44
Alignment explanation
Indices: 135930--136018 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
135920 ATCAACATCA
* *
135930 GCCTGGGAAGTAGCAACGGGTTATACAATAATATACCTAAGTTC
1 GCCTGGGAAGTAACAACAGGTTATACAATAATATACCTAAGTTC
* *
135974 GCCTGGGGAAGTAACAAACAGGTTGTATAATAATATACCTAAGTT
1 GCCT-GGGAAGTAAC-AACAGGTTATACAATAATATACCTAAGTT
136019 ATAAAGGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 4 0.10
45 9 0.23
46 26 0.67
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (44 bp):
GCCTGGGAAGTAACAACAGGTTATACAATAATATACCTAAGTTC
Done.