Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005832.1 Hibiscus syriacus cultivar Beakdansim tig00013673_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: 84898
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2568 original size:24 final size:24
Alignment explanation
Indices: 2458--2570 Score: 105
Period size: 24 Copynumber: 4.8 Consensus size: 24
2448 TTTTATCTTT
2458 GTTTTAGGTATTTTAATTTAAATA
1 GTTTTAGGTATTTTAATTTAAATA
2482 G-TTTA-GTATTTTAA-TT--A-A
1 GTTTTAGGTATTTTAATTTAAATA
* *
2500 GTTTTAGGATATTTTTTATATTTATATTT
1 GTTTTAGG-TA--TTTTA-ATTTA-AATA
2529 GTTTTAGGTATTTTAATTTAAATA
1 GTTTTAGGTATTTTAATTTAAATA
2553 GGTTTTA-GTATTTTAATT
1 -GTTTTAGGTATTTTAATT
2571 AAGTTTTAGG
Statistics
Matches: 73, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
18 2 0.03
19 5 0.07
20 1 0.01
21 4 0.05
22 9 0.12
23 9 0.12
24 15 0.21
25 13 0.18
26 5 0.07
28 2 0.03
29 8 0.11
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.58
Consensus pattern (24 bp):
GTTTTAGGTATTTTAATTTAAATA
Found at i:2588 original size:24 final size:24
Alignment explanation
Indices: 2488--2591 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 24
2478 AATAGTTTAG
2488 TATTTTAATTAAGTTTTAGGATAT
1 TATTTTAATTAAGTTTTAGGATAT
*
2512 T-TTTTATATTTATATTTGTTTTAGGTATTT
1 TATTTTA-A-TTA-A---GTTTTAGG-ATAT
* * *
2542 TAATTTAAATAGGTTTTA-G----
1 TATTTTAATTAAGTTTTAGGATAT
2561 TATTTTAATTAAGTTTTAGGATAT
1 TATTTTAATTAAGTTTTAGGATAT
2585 TATTTTA
1 TATTTTA
2592 TATTTTATCT
Statistics
Matches: 60, Mismatches: 7, Indels: 26
0.65 0.08 0.28
Matches are distributed among these distances:
19 15 0.25
20 1 0.02
23 5 0.08
24 10 0.17
25 9 0.15
26 1 0.02
29 10 0.17
30 5 0.08
31 4 0.07
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.59
Consensus pattern (24 bp):
TATTTTAATTAAGTTTTAGGATAT
Found at i:2641 original size:74 final size:73
Alignment explanation
Indices: 2446--2661 Score: 332
Period size: 74 Copynumber: 3.0 Consensus size: 73
2436 TTTTAAATAT
2446 TATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAG-TTTAGTATTTTAATTAAGTTTTAGGAT
1 TATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGAT
2510 ATTTTTTA
66 ATTTTTTA
*
2518 TA-TTTATATTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGA
1 TATTTTATCTTTGTTTTAGGTATTTTAATTTAAATA-GTTTTAGTATTTTAATTAAGTTTTAGGA
2582 TATTATTTTA
65 TATT-TTTTA
* * *
2592 TATTTTATCTTTGTTTTA-GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTACA-TTTTAAG
1 TATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGTTTT-AGTATTTTAATTA-AGTTTTAGG
2655 ATATTTT
64 ATATTTT
2662 AGCTTGTTTT
Statistics
Matches: 133, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
71 32 0.24
72 3 0.02
73 37 0.28
74 46 0.35
75 15 0.11
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.59
Consensus pattern (73 bp):
TATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGAT
ATTTTTTA
Found at i:10759 original size:10 final size:10
Alignment explanation
Indices: 10746--10800 Score: 69
Period size: 10 Copynumber: 5.4 Consensus size: 10
10736 TTATTTTTAT
10746 TTTTTTTCTA
1 TTTTTTTCTA
10756 TTTTTTTCTA
1 TTTTTTTCTA
10766 -TTTTTTCTA
1 TTTTTTTCTA
10775 TTTATTTTCT-
1 TTT-TTTTCTA
10785 TCTTTTTCTCTA
1 T-TTTTT-TCTA
10797 TTTT
1 TTTT
10801 ATCAACTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.22
10 16 0.40
11 14 0.35
12 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTTCTA
Found at i:10759 original size:11 final size:11
Alignment explanation
Indices: 10739--10800 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 11
10729 TTCTTTCTTA
10739 TTTT-TATTTT
1 TTTTCTATTTT
10749 TTTTCTA-TTT
1 TTTTCTATTTT
10759 TTTTCTA--TT
1 TTTTCTATTTT
*
10768 TTTTCTATTTA
1 TTTTCTATTTT
10779 TTTTCT-TCTTT
1 TTTTCTAT-TTT
*
10790 TTCTCTATTTT
1 TTTTCTATTTT
10801 ATCAACTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.20
10 15 0.34
11 19 0.43
12 1 0.02
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTATTTT
Found at i:10769 original size:20 final size:19
Alignment explanation
Indices: 10739--10800 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 19
10729 TTCTTTCTTA
*
10739 TTTTTATTTTTTTTCTATT
1 TTTTTCTTTTTTTTCTATT
*
10758 TTTTTCTATTTTTTCTATT
1 TTTTTCTTTTTTTTCTATT
10777 TATTTTCTTCTTTTTCTCTATT
1 T-TTTTCTT-TTTTT-TCTATT
10799 TT
1 TT
10801 ATCAACTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.49
20 6 0.16
21 6 0.16
22 7 0.19
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTATT
Found at i:12663 original size:16 final size:16
Alignment explanation
Indices: 12642--12675 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12632 ACCCCTACAA
12642 CACATAAATTAGGCTC
1 CACATAAATTAGGCTC
12658 CACATAAATTAGGCTC
1 CACATAAATTAGGCTC
12674 CA
1 CA
12676 ATCCTCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (16 bp):
CACATAAATTAGGCTC
Found at i:13160 original size:18 final size:19
Alignment explanation
Indices: 13126--13167 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
13116 GAACACCGTA
13126 AAAACATGTTCATTTTAAT
1 AAAACATGTTCATTTTAAT
*
13145 AAAACAT-TTTATTTTAAT
1 AAAACATGTTCATTTTAAT
13163 AAAAC
1 AAAAC
13168 TATCGAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAACATGTTCATTTTAAT
Found at i:15246 original size:14 final size:14
Alignment explanation
Indices: 15223--15256 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
15213 GGGTTCAAAA
15223 ATAT-TAAATATAT
1 ATATATAAATATAT
15236 ATATATAAATATAT
1 ATATATAAATATAT
15250 ATATATA
1 ATATATA
15257 CTCGTATGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATAAATATAT
Found at i:16190 original size:97 final size:96
Alignment explanation
Indices: 15895--16266 Score: 506
Period size: 96 Copynumber: 3.9 Consensus size: 96
15885 AGTAAGGTAT
* * * * * *
15895 TGTTGATT-CAACTCCATATGCGAT-GAATTGAGCGAA-AATGACAATATTGATGATTCTGATCC
1 TGTTG-TTCCAACTCCGTATGTGATGGAATCGAGC-AAGAATAACAATGTTGATGATGCTGATCC
* **
15957 AACTCCGTATGTGATGGATGAGCCAAGTATCAG
64 AACTCCGTATGCGATGGATGAGCCAAGTATTGG
*
15990 TGTTGTTCCAACTCTGTATGTGATGGAATCGAGCAAGAATAACAATGTTGATGATGCTGATCCAA
1 TGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATAACAATGTTGATGATGCTGATCCAA
*
16055 CTCCGTATGCGATGGATGAGCCAAGCATTGG
66 CTCCGTATGCGATGGATGAGCCAAGTATTGG
* *
16086 TGCTGTTCCAACTCCGTATGTGATGGAATAGAGCAAGAATAACAATGTTTGATGATGCTGATCCA
1 TGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATAACAATG-TTGATGATGCTGATCCA
* * *
16151 ACTTCGTTTGTGATGGATGAGCCAAGTATTGG
65 ACTCCGTATGCGATGGATGAGCCAAGTATTGG
* *
16183 TGTTGTTCCAACTCCGTATGTGATGAAATCGAGCAAGAATGACAATG-TGATG-T--TGATCCAA
1 TGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATAACAATGTTGATGATGCTGATCCAA
16244 CTCCGTATGCGATGGATGAGCCA
66 CTCCGTATGCGATGGATGAGCCA
16267 GAATTAACAA
Statistics
Matches: 248, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
92 28 0.11
94 3 0.01
95 25 0.10
96 104 0.42
97 88 0.35
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (96 bp):
TGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATAACAATGTTGATGATGCTGATCCAA
CTCCGTATGCGATGGATGAGCCAAGTATTGG
Found at i:16433 original size:91 final size:91
Alignment explanation
Indices: 16272--16709 Score: 642
Period size: 91 Copynumber: 4.9 Consensus size: 91
16262 AGCCAGAATT
* *
16272 AACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCA-CGGATGAG---TTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
* *
16333 CCACTGGAAATGATGAGCCAATGTTG
66 CCACTGGAAATGTTGAGCCAAGGTTG
*
16359 AACAGGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
*
16424 CCACTGGAAATGTTAAGCCAAGGTTG
66 CCACTGGAAATGTTGAGCCAAGGTTG
* *
16450 AACAAATTCTTCTCATTATGAACTTCTTCTCTCTCATTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
* **
16515 CCACTAGG-AATGCTGAGAAAAGGTTG
66 CCACT-GGAAATGTTGAGCCAAGGTTG
* *
16541 AACAAATTTTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
*
16606 CCACTAGAAATGTTGAGCCAAGGTTG
66 CCACTGGAAATGTTGAGCCAAGGTTG
*
16632 AACAAGTTCTTCTC---ATGAACTTCTTCTCCCTCATAT-GATGAGTTTTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCAT-TGGATGAGTTCTTCTCATTATGAACTC
* *
16693 CCCACTGGCAATGTTGA
65 TCCACTGGAAATGTTGA
16710 TCGATTTATC
Statistics
Matches: 319, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
87 34 0.11
88 65 0.20
89 1 0.00
90 1 0.00
91 216 0.68
92 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (91 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCT
CCACTGGAAATGTTGAGCCAAGGTTG
Found at i:17276 original size:36 final size:36
Alignment explanation
Indices: 17226--17455 Score: 182
Period size: 36 Copynumber: 6.4 Consensus size: 36
17216 TAAATGATTT
* *
17226 TTTGTTTCAAGAGAAACTGCCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * ******
17262 TTAGTTTCAAGAGAAA-TATATTCAA-AGA-TTTTTT
1 TTTGTTTCAAGAGAAACTGT-CTCAAGAGAGACAAAA
* * *
17296 TTTGTTTCAAAATAAACTGTCTCAAGCGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
17332 TTTGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
17368 CTCGTTTCAAG-GAAAACTATCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA
* * * * *
17404 TTTTTTTCAAGGGAAATTGTCTTAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
17440 CTTTGTTTCAAG-GAAA
1 -TTTGTTTCAAGAGAAA
17456 ACAATCTCAA
Statistics
Matches: 147, Mismatches: 40, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
34 17 0.12
35 8 0.05
36 111 0.76
37 11 0.07
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:17393 original size:72 final size:73
Alignment explanation
Indices: 17309--17465 Score: 226
Period size: 72 Copynumber: 2.2 Consensus size: 73
17299 GTTTCAAAAT
* *
17309 AAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAAC-TCGT
1 AAACTATCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTCGT
17373 TTCAAGGA
66 TTCAAGGA
* * * * * *
17381 AAACTATCTCAAGGGAGACAAAATTTTTTTCAAGGGAAATTGTCTTAAGAGAGATAAAACTTTGT
1 AAACTATCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTCGT
17446 TTCAAGGA
66 TTCAAGGA
*
17454 AAACAATCTCAA
1 AAACTATCTCAA
17466 AGGTTGGCGT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 53 0.71
73 22 0.29
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (73 bp):
AAACTATCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTCGT
TTCAAGGA
Found at i:17646 original size:102 final size:102
Alignment explanation
Indices: 17372--17659 Score: 236
Period size: 101 Copynumber: 2.8 Consensus size: 102
17362 ACAAAACTCG
* * * * ** *
17372 TTTCAAG-GAAAACTATCTCAAGGGAGACAAAATTT-TTTTCAAGGGAAATTGTCTTAAGAGAGA
1 TTTCAAGAGAAAA-TGTCTCAAGAGAGACAGAATTTGTTTT-GAGAAAAATTGTCTCAAGAGAGA
* * *
17435 TAAAACTTTGTTTCAAGGAAAACAATCTCAAAGGTTGGCG
64 CAAAACTTTGTTTCAAGGAAAACAAACTCAAA-GTTGGCA
* *** * *
17475 TTTCAAGAGAAACTGTCTCAAGAGAGACAGAATTTGTTTTGAGAAAAACAATCCCAAGTGAGATC
1 TTTCAAGAGAAAATGTCTCAAGAGAGACAGAATTTGTTTTGAGAAAAATTGTCTCAAGAGAGA-C
* *
17540 --AACTTTGTTTCAAGTG-AAACAAACTCGAAA-TTTGTA
65 AAAACTTTGTTTCAAG-GAAAACAAACTC-AAAGTTGGCA
*
17576 TTTCAA-AGGAAAAATGTCTCAA-ATGAGAC-GAATTTGTTTTGAGAAAAATTGTCTCAAAAGAG
1 TTTCAAGA-G-AAAATGTCTCAAGA-GAGACAGAATTTGTTTTGAGAAAAATTGTCTCAAGAGAG
* *
17638 ACAAAAC-TTGTTTTAAGAAAAA
63 ACAAAACTTTGTTTCAAGGAAAA
17660 ATTGTCTCAA
Statistics
Matches: 147, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
100 2 0.01
101 51 0.35
102 42 0.29
103 44 0.30
104 8 0.05
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (102 bp):
TTTCAAGAGAAAATGTCTCAAGAGAGACAGAATTTGTTTTGAGAAAAATTGTCTCAAGAGAGACA
AAACTTTGTTTCAAGGAAAACAAACTCAAAGTTGGCA
Found at i:17669 original size:37 final size:36
Alignment explanation
Indices: 17584--17680 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 36
17574 TATTTCAAAG
* * *
17584 GAAAAA-TGTCTCAAATGAGAC-GAATTTGTTTTGA
1 GAAAAATTGTCTCAAATGAGACAAAACTTGTTTTAA
*
17618 GAAAAATTGTCTCAAAAGAGACAAAACTTGTTTTAA
1 GAAAAATTGTCTCAAATGAGACAAAACTTGTTTTAA
*
17654 GAAAAAATTGTCTCAAGTGAGACAAAA
1 G-AAAAATTGTCTCAAATGAGACAAAA
17681 TTCTCTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
34 6 0.11
35 14 0.26
36 11 0.20
37 23 0.43
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (36 bp):
GAAAAATTGTCTCAAATGAGACAAAACTTGTTTTAA
Found at i:19874 original size:41 final size:43
Alignment explanation
Indices: 19829--19908 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 43
19819 ATCTGTCTAT
*
19829 TTTCTTCTTTCTTATTT-TTATCTT-TTT-TTTCTATTTTTCTC
1 TTTCTTCTTTC-TATTTATTATCTTCTTTCTCTCTATTTTTCTC
* *
19870 TTTCTTTTTTCTATTTATTTTCTTCTTTCTCTCTATTTT
1 TTTCTTCTTTCTATTTATTATCTTCTTTCTCTCTATTTT
19909 ATCAACTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.15
41 16 0.48
42 3 0.09
43 9 0.27
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (43 bp):
TTTCTTCTTTCTATTTATTATCTTCTTTCTCTCTATTTTTCTC
Found at i:19906 original size:18 final size:18
Alignment explanation
Indices: 19870--19908 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19860 TATTTTTCTC
* *
19870 TTTCTTTTTTCTATTTAT
1 TTTCTTCTTTCTATCTAT
*
19888 TTTCTTCTTTCTCTCTAT
1 TTTCTTCTTTCTATCTAT
19906 TTT
1 TTT
19909 ATCAACTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTCTTTCTATCTAT
Found at i:28304 original size:3 final size:3
Alignment explanation
Indices: 28296--28399 Score: 199
Period size: 3 Copynumber: 34.7 Consensus size: 3
28286 TTTTTACCCA
28296 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
28344 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28392 TAT TAT TA
1 TAT TAT TA
28400 AATATATACA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28945 original size:15 final size:15
Alignment explanation
Indices: 28925--28966 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
28915 ACCACTCAGC
28925 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
28940 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
28955 AAAGAAGAGAAA
1 AAAGAAAAGAAA
28967 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:28950 original size:20 final size:20
Alignment explanation
Indices: 28925--28966 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28915 ACCACTCAGC
*
28925 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
28945 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
28965 AA
1 AA
28967 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:37658 original size:9 final size:8
Alignment explanation
Indices: 37635--37664 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
37625 ATATGGCAAT
37635 CATTCTTTA
1 CATT-TTTA
37644 CATTTTTA
1 CATTTTTA
37652 CATTTTTA
1 CATTTTTA
37660 CATTT
1 CATTT
37665 ATTTATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (8 bp):
CATTTTTA
Found at i:41210 original size:18 final size:17
Alignment explanation
Indices: 41186--41240 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 17
41176 ATTATGCTTG
41186 AAGAAAAAG-AAAAAAA
1 AAGAAAAAGAAAAAAAA
41202 AAGAGAAAAGAAAAAAAA
1 AAGA-AAAAGAAAAAAAA
*
41220 AAGAAAAAAAAAAGAAAA
1 AAGAAAAAGAAAA-AAAA
41238 AAG
1 AAG
41241 GGGGGTCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 4 0.11
17 13 0.37
18 18 0.51
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAA
Found at i:41215 original size:16 final size:16
Alignment explanation
Indices: 41186--41232 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
41176 ATTATGCTTG
41186 AAGA-AAAAGAAAAAAA
1 AAGAGAAAAG-AAAAAA
41202 AAGAGAAAAGAAAAAA
1 AAGAGAAAAGAAAAAA
*
41218 AAAAGAAAA-AAAAAA
1 AAGAGAAAAGAAAAAA
41233 GAAAAAAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 6 0.21
16 18 0.62
17 5 0.17
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAGAAAAGAAAAAA
Found at i:42507 original size:83 final size:83
Alignment explanation
Indices: 42368--43255 Score: 1479
Period size: 83 Copynumber: 10.7 Consensus size: 83
42358 AATTAAATGA
*
42368 AAGATGAATTGGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
*
42432 AACCAATCATTGAATTTGG
65 AACCAATCATTGAATTTAG
* *
42451 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
1 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
*
42514 GAACCAATCATTGAATTTGG
64 GAACCAATCATTGAATTTAG
* * * *
42534 AAGATGAATGTGTTC-ATAGCATATTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTTTGG-CA
1 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
*
42597 GAACCAATCATTGAATTTGG
64 GAACCAATCATTGAATTTAG
* *
42617 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
42681 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
42700 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
42765 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
42783 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
42848 ACCAAAT-ATTGAATTTAG
66 ACC-AATCATTGAATTTAG
42866 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
42931 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
42949 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
* *
43013 AACCGATCATTGAATTTGG
65 AACCAATCATTGAATTTAG
* *
43032 AAGATGAATATGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
43096 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
43115 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
43180 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
43198 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTCATCTGGTT
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
43256 TGGTAGGAAC
Statistics
Matches: 777, Mismatches: 19, Indels: 18
0.95 0.02 0.02
Matches are distributed among these distances:
82 13 0.02
83 755 0.97
84 9 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACCAATCATTGAATTTAG
Found at i:44195 original size:113 final size:113
Alignment explanation
Indices: 43992--44786 Score: 1466
Period size: 113 Copynumber: 7.0 Consensus size: 113
43982 ATTCAAATCT
* ** * *
43992 ATCATTTGATGGATTTACATTT-CCAGAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 ATCACTTGATGGA-TTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
**
44056 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
44105 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
44170 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
44218 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
44283 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
44331 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
44396 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
44444 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
44509 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
44557 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
**
44622 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
44670 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
**
44735 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
44783 ATCA
1 ATCA
44787 TCTAAAGAAA
Statistics
Matches: 671, Mismatches: 10, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
112 6 0.01
113 665 0.99
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (113 bp):
ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:45081 original size:3 final size:3
Alignment explanation
Indices: 45073--45143 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
45063 TTTTTACCCA
45073 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
45121 TAT CAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
45144 AATATATACA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:45684 original size:15 final size:15
Alignment explanation
Indices: 45664--45705 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
45654 ACCACTCAGC
45664 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
45679 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
45694 AAAGAAGAGAAA
1 AAAGAAAAGAAA
45706 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:45689 original size:20 final size:20
Alignment explanation
Indices: 45664--45705 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
45654 ACCACTCAGC
*
45664 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
45684 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
45704 AA
1 AA
45706 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:52832 original size:146 final size:146
Alignment explanation
Indices: 52568--52855 Score: 495
Period size: 146 Copynumber: 2.0 Consensus size: 146
52558 GACAACAATA
* *
52568 ATGAGTTTTACCATCTAATATTTTTGTCATTTGGTCTATAAATCGAAGAGGAAAATGGTCTTTCT
1 ATGAGTTTTACCAGCTAATATTTTTGTCACTTGGTCTATAAATCGAAGAGGAAAATGGTCTTTCT
* *
52633 GTGTTCAAGAATTCAACTTCTTGTAATCGATGTAGACTCACCATCCATTCTGAACTCTAGTCGTA
66 GTGTTCAAGAATTCAACTTCCTGTAATCGATGCAGACTCACCATCCATTCTGAACTCTAGTCGTA
*
52698 ACTATCTCACCTTTCG
131 ACTAACTCACCTTTCG
* *
52714 ATGAGTTTTAGCAGCTAATATTTTTGTCACTTGGTCTATAAATCGAAGAGGAAAATGGTCTTTTT
1 ATGAGTTTTACCAGCTAATATTTTTGTCACTTGGTCTATAAATCGAAGAGGAAAATGGTCTTTCT
* *
52779 GTGTTCAAGAATTCAACTTCCTGTAATTGATGCAGACTCACCATCCATTCTGAACTCTAGTTGTA
66 GTGTTCAAGAATTCAACTTCCTGTAATCGATGCAGACTCACCATCCATTCTGAACTCTAGTCGTA
52844 ACTAACTCACCT
131 ACTAACTCACCT
52856 GTTGAGTTCT
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
146 133 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (146 bp):
ATGAGTTTTACCAGCTAATATTTTTGTCACTTGGTCTATAAATCGAAGAGGAAAATGGTCTTTCT
GTGTTCAAGAATTCAACTTCCTGTAATCGATGCAGACTCACCATCCATTCTGAACTCTAGTCGTA
ACTAACTCACCTTTCG
Found at i:53226 original size:19 final size:18
Alignment explanation
Indices: 53186--53224 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53176 GAATTTGAGG
53186 AAATTAATCGTGAATCAA
1 AAATTAATCGTGAATCAA
53204 AAATTAAAT-GTGAATCAA
1 AAATT-AATCGTGAATCAA
53222 AAA
1 AAA
53225 ATAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (18 bp):
AAATTAATCGTGAATCAA
Found at i:57125 original size:124 final size:124
Alignment explanation
Indices: 56904--57154 Score: 484
Period size: 124 Copynumber: 2.0 Consensus size: 124
56894 ACAAGTCGAT
*
56904 CCTTCCTCCCAACTATTAATAAAAAACACCAAAAATCCAATGTGCACTTTTGAAAAGAAAATGTT
1 CCTTCCTCCCAACTATTAATAAAAAAAACCAAAAATCCAATGTGCACTTTTGAAAAGAAAATGTT
56969 TTTAATCATAAAAGGATGGTCGATTACCGATCCTTGATTCCAGAGAACTGAGAATGTAA
66 TTTAATCATAAAAGGATGGTCGATTACCGATCCTTGATTCCAGAGAACTGAGAATGTAA
57028 CCTTCCTCCCAACTATTAATAAAAAAAACCAAAAATCCAATGTGCACTTTTGAAAAGAAAATGTT
1 CCTTCCTCCCAACTATTAATAAAAAAAACCAAAAATCCAATGTGCACTTTTGAAAAGAAAATGTT
*
57093 TTTAATCATAAAAGGATGGTCGATTACTGATCCTTGATTCCAGAGAACTGAGAATGTAA
66 TTTAATCATAAAAGGATGGTCGATTACCGATCCTTGATTCCAGAGAACTGAGAATGTAA
57152 CCT
1 CCT
57155 GAAAGGTATG
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (124 bp):
CCTTCCTCCCAACTATTAATAAAAAAAACCAAAAATCCAATGTGCACTTTTGAAAAGAAAATGTT
TTTAATCATAAAAGGATGGTCGATTACCGATCCTTGATTCCAGAGAACTGAGAATGTAA
Found at i:57436 original size:23 final size:24
Alignment explanation
Indices: 57410--57474 Score: 93
Period size: 23 Copynumber: 2.8 Consensus size: 24
57400 AAAATGCTTG
57410 AAGATAATTCCTACT-AAA-TACAA
1 AAGATAATTCCT-CTAAAATTACAA
57433 AAGATAATTCC-CTAAAATTACAA
1 AAGATAATTCCTCTAAAATTACAA
57456 AAGATAATTCCT-TAAAATT
1 AAGATAATTCCTCTAAAATT
57475 GTTTGAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.05
22 3 0.08
23 34 0.87
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (24 bp):
AAGATAATTCCTCTAAAATTACAA
Found at i:62354 original size:22 final size:22
Alignment explanation
Indices: 62326--62367 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
62316 TCCAGGGGTA
62326 TGAAAGTTCATTGT-CAAATAGT
1 TGAAAG-TCATTGTACAAATAGT
*
62348 TGAAAGTCTTTGTACAAATA
1 TGAAAGTCATTGTACAAATA
62368 TTACCTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TGAAAGTCATTGTACAAATAGT
Found at i:68347 original size:12 final size:12
Alignment explanation
Indices: 68330--68354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68320 CTTGAGAGTC
68330 GAGCCACAAGTT
1 GAGCCACAAGTT
68342 GAGCCACAAGTT
1 GAGCCACAAGTT
68354 G
1 G
68355 GTTACCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (12 bp):
GAGCCACAAGTT
Found at i:72413 original size:2 final size:2
Alignment explanation
Indices: 72406--72430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72396 TCTTCCAATC
72406 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
72431 AGTAAATAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78046 original size:24 final size:24
Alignment explanation
Indices: 78018--78113 Score: 110
Period size: 23 Copynumber: 4.1 Consensus size: 24
78008 CTGCTAATAT
78018 AATTT-TCACCGAAGTG-CCACATAG
1 AATTTGTC-CCGAAG-GACCACATAG
78042 AATTTGTCCCGAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
* * *
78066 -GTTTTTCTCGAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
*
78089 -ATTTGACCCGAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
78112 AA
1 AA
78114 CCCTCGAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
23 40 0.65
24 20 0.32
25 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACATAG
Found at i:78475 original size:2 final size:2
Alignment explanation
Indices: 78468--78498 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
78458 TTCACATAGA
78468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78499 GAAATAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82743 original size:22 final size:22
Alignment explanation
Indices: 82702--82743 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
82692 GTAAATATAC
*
82702 TTTTAAAATTAATTTATTAAAT
1 TTTTAAAAATAATTTATTAAAT
82724 TTTTAAAAATATATTT-TTAA
1 TTTTAAAAATA-ATTTATTAA
82744 TTTAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAAAAATAATTTATTAAAT
Done.