Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005481.1 Hibiscus syriacus cultivar Beakdansim tig00012567_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: 64573
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:376 original size:21 final size:20
Alignment explanation
Indices: 316--376 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
306 GACTCACCTG
316 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** * *
336 CCAATCGTTCAATAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
357 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
377 CCCACCGTTC
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.11, T:0.23
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:1819 original size:13 final size:14
Alignment explanation
Indices: 1784--1821 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1774 TTGATTGTTT
1784 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1798 AAATGATTTGT-AA
1 AATTGATTTGTAAA
*
1811 ATTTGATTTGT
1 AATTGATTTGT
1822 TTAATTGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1984 original size:19 final size:19
Alignment explanation
Indices: 1960--2024 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1950 GCAACGAGAG
1960 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1979 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1998 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
2012 AATCGCAATGCGA
1 AATCGCAATGCGA
2025 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2042 original size:19 final size:20
Alignment explanation
Indices: 2014--2085 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2004 AACGAGAAAA
* *
2014 TCGCAATGCGATTTTCA-TT
1 TCGCATTGCGATTGTCATTT
*
2033 TCGCATTGCGATTGCCATTT
1 TCGCATTGCGATTGTCATTT
* *
2053 TCGCGTTGCGATAGTCATTT
1 TCGCATTGCGATTGTCATTT
*
2073 TCGCGTTGCGATT
1 TCGCATTGCGATT
2086 TCCCCGTTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 14 0.31
20 31 0.69
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTGTCATTT
Found at i:2495 original size:21 final size:21
Alignment explanation
Indices: 2469--2523 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
2459 GAAAGTCAGA
2469 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
2490 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
2511 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
2524 AGTCAGTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:2535 original size:20 final size:19
Alignment explanation
Indices: 2453--2543 Score: 65
Period size: 21 Copynumber: 4.5 Consensus size: 19
2443 ATGTCGATCT
* *
2453 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGATAGT-AGTATCG
* *
2473 CGTTGCGATTTTGTATTATCG
1 CGTTGCGA--TAGTAGTATCG
* *
2494 CGTTGCGATTTTGTATTATCG
1 CGTTGCGA--TAGTAGTATCG
2515 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGT-AGTATCG
*
2535 CATTGCGAT
1 CGTTGCGAT
2544 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
19 3 0.05
20 22 0.36
21 34 0.56
22 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTAGTATCG
Found at i:2558 original size:21 final size:19
Alignment explanation
Indices: 2532--2582 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2522 ATAGTCAGTA
*
2532 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTAC-AAT
* *
2553 TCGCATTACGATTTACTAT
1 TCGCATTGCGATTTACAAT
2572 TCGCATTGCGA
1 TCGCATTGCGA
2583 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 12 0.46
20 4 0.15
21 10 0.38
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (19 bp):
TCGCATTGCGATTTACAAT
Found at i:2624 original size:21 final size:21
Alignment explanation
Indices: 2572--2624 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2562 GATTTACTAT
2572 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATT-GGAAAA
**
2593 TCGCAACGCGAAATT-GAATAA
1 TCGCATTGCGAAATTGGAA-AA
2614 TCGCATTGCGA
1 TCGCATTGCGA
2625 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCATTGCGAAATTGGAAAA
Found at i:3253 original size:16 final size:17
Alignment explanation
Indices: 3231--3269 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3221 GAAAGACTGA
*
3231 AAAAATG-TTACAAAAT
1 AAAAATGTTTAAAAAAT
*
3247 TAAAATGTTTAAAAAAT
1 AAAAATGTTTAAAAAAT
3264 AAAAAT
1 AAAAAT
3270 AATAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
AAAAATGTTTAAAAAAT
Found at i:3290 original size:12 final size:12
Alignment explanation
Indices: 3256--3302 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
3246 TTAAAATGTT
3256 TAAAAAATAAAAA
1 TAAAAAAT-AAAA
*
3269 TAATAAAATAACA
1 TAA-AAAATAAAA
3282 TAAAAAATAAAA
1 TAAAAAATAAAA
3294 TAAAAAATA
1 TAAAAAATA
3303 TAGATGATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
12 17 0.55
13 9 0.29
14 5 0.16
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:3715 original size:36 final size:37
Alignment explanation
Indices: 3634--3715 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 37
3624 TATAAATTGT
* * *
3634 TTAATATACTATATGAAATATTTACAATTTTTAGATA
1 TTAATATATTATATGAAACATTTACAATATTTAGATA
* *
3671 TTTA-ATATTATATGTACACATTTA-AATATTTA-ATA
1 TTAATATATTATATG-AAACATTTACAATATTTAGATA
3706 TTAATATATT
1 TTAATATATT
3716 TCCTAGAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
35 6 0.16
36 21 0.57
37 10 0.27
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.49
Consensus pattern (37 bp):
TTAATATATTATATGAAACATTTACAATATTTAGATA
Found at i:4994 original size:29 final size:30
Alignment explanation
Indices: 4962--5023 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4952 CCCACTAGAT
4962 TTTATAAACGATAC-AATGTTGATTTATTA
1 TTTATAAACGATACAAATGTTGATTTATTA
4991 TTTATAAACGATACAAATGTTGATTTATTA
1 TTTATAAACGATACAAATGTTGATTTATTA
5021 TTT
1 TTT
5024 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (30 bp):
TTTATAAACGATACAAATGTTGATTTATTA
Found at i:5587 original size:5 final size:5
Alignment explanation
Indices: 5579--5633 Score: 92
Period size: 5 Copynumber: 11.0 Consensus size: 5
5569 TAACTTAGCT
* *
5579 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC GTTTC GTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
5629 TTTTC
1 TTTTC
5634 GTGCTTAGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:6817 original size:18 final size:18
Alignment explanation
Indices: 6785--6819 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6775 TTTATTATTA
*
6785 TTTTATTTTAGTATTTAT
1 TTTTATTTGAGTATTTAT
*
6803 TTTTATTTGATTATTTA
1 TTTTATTTGAGTATTTA
6820 ATTGTAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTATTTGAGTATTTAT
Found at i:7010 original size:14 final size:14
Alignment explanation
Indices: 6991--7021 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6981 ATTATTTAAA
6991 TTATTTGAATTTAT
1 TTATTTGAATTTAT
*
7005 TTATTTGAATTTGT
1 TTATTTGAATTTAT
7019 TTA
1 TTA
7022 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.65
Consensus pattern (14 bp):
TTATTTGAATTTAT
Found at i:8975 original size:20 final size:21
Alignment explanation
Indices: 8936--8977 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
8926 CACGCTGAAT
8936 GTTGAACGGTTCAACATTCAGC
1 GTTGAACGGTTC-ACATTCAGC
*
8958 GTTGAATGGTTC-CATTCAGC
1 GTTGAACGGTTCACATTCAGC
8978 AGTAAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
GTTGAACGGTTCACATTCAGC
Found at i:14056 original size:21 final size:21
Alignment explanation
Indices: 14030--14142 Score: 124
Period size: 21 Copynumber: 5.4 Consensus size: 21
14020 ATCGACCAAG
*
14030 GACGAGAAGAGCATTCATAAA
1 GACGAGAAGACCATTCATAAA
* *
14051 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATAAA
*
14072 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATAAA
* *
14093 GACAAGAAGACCCTTCATAAA
1 GACGAGAAGACCATTCATAAA
*
14114 GACGAGAAGACC-TTCGTAAA
1 GACGAGAAGACCATTCATAAA
14134 GACGAGAAG
1 GACGAGAAG
14143 TCCACATCGC
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
20 17 0.21
21 64 0.78
22 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:16481 original size:2 final size:2
Alignment explanation
Indices: 16474--16560 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
16464 CATTTATCCT
16474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16558 TA T
1 TA T
16561 CCCTTGTGGT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16802 original size:6 final size:6
Alignment explanation
Indices: 16787--16881 Score: 61
Period size: 6 Copynumber: 15.2 Consensus size: 6
16777 AGAGAAATAT
* * *
16787 AGAAAG AGAAAA AG-AAA AGATAAA A-AAAA AGGAAA TGAAAA AG-AAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
16833 AGAAAAA AGGAAA AGAAAG AGAAAA ATTGAAAA TGAGAAAA ATGAAAA
1 AG-AAAA AGAAAA AGAAAA AGAAAA A--GAAAA --AGAAAA A-GAAAA
16881 A
1 A
16882 AAGAATGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
5 14 0.20
6 30 0.43
7 15 0.21
8 10 0.14
10 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (6 bp):
AGAAAA
Found at i:16811 original size:12 final size:12
Alignment explanation
Indices: 16789--16857 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 12
16779 AGAAATATAG
16789 AAAGAGAAAAAGA
1 AAAGAG-AAAAGA
* *
16802 AAAGATAAAAAA
1 AAAGAGAAAAGA
*
16814 AAAG-GAAATGA
1 AAAGAGAAAAGA
16825 AAA-AGAAAAGA
1 AAAGAGAAAAGA
*
16836 AAAAAGGAAAAG-
1 AAAGA-GAAAAGA
16848 AAAGAGAAAA
1 AAAGAGAAAA
16858 ATTGAAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
11 21 0.46
12 14 0.30
13 11 0.24
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (12 bp):
AAAGAGAAAAGA
Found at i:16817 original size:17 final size:16
Alignment explanation
Indices: 16795--16838 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
16785 ATAGAAAGAG
16795 AAAAAGAAAAGATAAAA
1 AAAAAGAAAAGA-AAAA
*
16812 AAAAAGGAAATGAAAAA
1 AAAAA-GAAAAGAAAAA
*
16829 GAAAAGAAAA
1 AAAAAGAAAA
16839 AAGGAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 13 0.57
18 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:16827 original size:11 final size:11
Alignment explanation
Indices: 16766--16858 Score: 60
Period size: 12 Copynumber: 7.8 Consensus size: 11
16756 TTGACATCAT
*
16766 AAAGAGAAAGA
1 AAAGAAAAAGA
*
16777 AGAGAAATATAGA
1 AAAGAAA-A-AGA
16790 AAGAGAAAAAGA
1 AA-AGAAAAAGA
*
16802 AAAGATAAAAAA
1 AAAGA-AAAAGA
* *
16814 AAAGGAAATGAA
1 AAAGAAAAAG-A
*
16826 AAAGAAAAGAAA
1 AAAGAAAA-AGA
*
16838 AAAGGAAAAGA
1 AAAGAAAAAGA
16849 AAGAGAAAAA
1 AA-AGAAAAA
16859 TTGAAAATGA
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
11 15 0.24
12 37 0.60
13 5 0.08
14 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:16828 original size:24 final size:23
Alignment explanation
Indices: 16796--16858 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
16786 TAGAAAGAGA
16796 AAAAG-AAAAGATAAAAAAAAAGG
1 AAAAGAAAAAGA-AAAAAAAAAGG
*
16819 AAATGAAAAAGAAAAGAAAAAAGG
1 AAAAGAAAAAGAAAA-AAAAAAGG
*
16843 AAAAGAAAGAGAAAAA
1 AAAAGAAAAAGAAAAA
16859 TTGAAAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.23
24 27 0.77
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAAAAAAAGG
Found at i:16857 original size:29 final size:28
Alignment explanation
Indices: 16787--16857 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 28
16777 AGAGAAATAT
16787 AGAAAGAGAAAAAGAAAAGATAAAAAAAA
1 AGAAAGAG-AAAAGAAAAGATAAAAAAAA
16816 AGGAAATGA-AAAAGAAAAGA-AAAAAGGAAA
1 A-GAAA-GAGAAAAGAAAAGATAAAAA--AAA
16846 AGAAAGAGAAAA
1 AGAAAGAGAAAA
16858 ATTGAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
28 7 0.19
29 20 0.54
30 8 0.22
31 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (28 bp):
AGAAAGAGAAAAGAAAAGATAAAAAAAA
Found at i:16881 original size:16 final size:16
Alignment explanation
Indices: 16851--16880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16841 GGAAAAGAAA
16851 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
16867 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
16881 AAAGAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:18436 original size:125 final size:124
Alignment explanation
Indices: 18141--18444 Score: 484
Period size: 124 Copynumber: 2.4 Consensus size: 124
18131 AAGTTGTGAT
* * * *
18141 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGAAGACAAGATTCAGACCAAGGAGGTATTAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
* *
18206 GAATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGATGCCCGTACCAGTATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAGGCCCGTACCAGTATAAGATA
*
18265 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
*
18330 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTGTAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTG-AGGCCCGTACCAGTATAAGATA
** *
18390 ATGTTGGGGCGA-GACCAAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAG
1 ATGTTGGGGC-ACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAG
18445 AAATTATTGA
Statistics
Matches: 167, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
124 96 0.57
125 70 0.42
126 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (124 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAGGCCCGTACCAGTATAAGATA
Found at i:19361 original size:36 final size:36
Alignment explanation
Indices: 19165--19394 Score: 291
Period size: 36 Copynumber: 6.4 Consensus size: 36
19155 AGCAAAGTCA
*
19165 ATCTTAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
19201 ATCCTAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * *
19237 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
19273 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
19309 ATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
19345 ATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTTAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACC
*
19382 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
19395 TCAGAAGAGT
Statistics
Matches: 172, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 2 0.01
36 156 0.91
37 14 0.08
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
Found at i:19371 original size:108 final size:109
Alignment explanation
Indices: 19162--19394 Score: 326
Period size: 108 Copynumber: 2.1 Consensus size: 109
19152 TGGAGCAAAG
* * **
19162 TCAATCTTAAGCCTTCACTGGAGAATAGTGAAGCAAACCATCCTAAGCCTTCACTGGAGAATAGT
1 TCAATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATAGT
* *
19227 GAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCA-A
66 GAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGAAGCAGA
* * *
19270 TCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCATAAGTCTTCACCAGAGAGTAGT
1 TCAATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATAGT
* *
19335 GAAGCAAACCATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGA
66 GAAGCAAACCATCTGAAGCCTTCACCGAAAAA-TAGTGAAGCAGA
* *
19379 TCCATTTTAAGCCTTC
1 TCAATCTTAAGCCTTC
19395 TCAGAAGAGT
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 3 0.03
108 92 0.84
109 14 0.13
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (109 bp):
TCAATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATAGT
GAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGAAGCAGA
Found at i:19656 original size:51 final size:51
Alignment explanation
Indices: 19591--20768 Score: 1004
Period size: 51 Copynumber: 22.5 Consensus size: 51
19581 AAGATTATTT
* *
19591 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
19642 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
19693 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
19744 GAGTTCCATACTCCTTAAAAAAAGAAGGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-TC
* * * *
19796 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
1 -GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
19848 GAGTTCCATACTCCTTA-ATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGA-GAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* ** * * * ** * *
19899 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCATAAGAAGAAGATTTTT
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGT---TTGAAGATGTTC
* *
19953 GAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCCATACTCCCTAG-AGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* * *
20004 GAGTTCCATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-TC
* * * *
20056 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
1 -GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
20108 GAGTTCCATACTCCTTA-ATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGA-GAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* ** * * ** * *
20159 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTT
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGT---TTGAAGATGTTC
*
20213 GAGTTCTATACTCCCT-GAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCCATACTCCCTAG-AGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* *
20264 GAGTTCCATACTCCCGAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* *
20315 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* **
20366 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAG---ATGTTC
*
20420 GAGTTCCATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGTTC
1 GAGTTCCATACTCCCTAG-AGAAAGAAGGAGCGAACCCG-TTT--GAAGA-TGTTC
* * * ** *
20475 GAGTTCTATACTTCCTGGAGAAAG-AGCGAAGCGAACCCGTAAGAAGAAGATCTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAG-G-AGCGAACCCGT---TTGAAGATGTTC
* * * * *
20530 GAGTTCTATACTCCCT-GAAGAAAGAGGGAGTGAGCCCGTTTTCAGAAGATCATTC
1 GAGTTCCATACTCCCTAG-AGAAAGAAGGAGCGAACCCG-TTT--GAAGAT-GTTC
* * * * * * *
20585 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTC
1 GAGTTCCATACTCCCT-AGAGAAAGAAGGAGCGAACCCGTTT---GAAGA-TGTTC
* * * ** * *
20641 GAGTTCTATACTCCTTAAAGAAA-AA-G-G-GAATTCGCTTACAGAAGATTATTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCG-TT--TGAAGA-TGTTC
* * * * **
20692 AAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGT---TTGAAGATGTTC
* *
20746 GAGTTCTATAATCCCTAGAGAAA
1 GAGTTCCATACTCCCTAGAGAAA
20769 TAGGGAGTAG
Statistics
Matches: 940, Mismatches: 124, Indels: 123
0.79 0.10 0.10
Matches are distributed among these distances:
49 2 0.00
50 7 0.01
51 505 0.54
52 14 0.01
53 89 0.09
54 164 0.17
55 96 0.10
56 58 0.06
57 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
Found at i:20049 original size:260 final size:260
Alignment explanation
Indices: 19591--20761 Score: 1312
Period size: 260 Copynumber: 4.5 Consensus size: 260
19581 AAGATTATTT
* *
19591 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCC
* * * * * *
19656 CTAGAGAAAGAAGGAGCGAACCCGT--G-TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGA
66 CTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGA
* *
19718 AGGAGCGAACCC-GTTTGAAGATGTTCGAGTTCCATACTCCTTAAAAAAAGAAGGAGCGAACCCG
131 AGGAGCGAACCCAG-TTGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCG
*
19782 TTTGAAGAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATC
195 TTTGAAGAGATGTCTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTGTGAAGATATC
19847 C
260 C
* *
19848 GAGTTCCATACTCCTTA-ATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
1 GAGTTCCATACTCCCTAGA-GAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTC
** * * *
19912 TTTAAAGAGAGAAGGAGCGAACCCATAAGAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAAG
65 CCTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAG
* * *
19977 AGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGCGAACCCG
130 AAGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCG
*
20042 TTTGAAGAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATC
195 TTTGAAGAGATGTCTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTGTGAAGATATC
20107 C
260 C
* *
20108 GAGTTCCATACTCCTTA-ATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
1 GAGTTCCATACTCCCTAGA-GAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTC
** * *
20172 TTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAAG
65 CCTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAG
* * *
20237 AAGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCGAGAGAAAGAGGGAGCGAACCCG
130 AAGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCG
* * * *
20302 --TGAAGAGATGT-TCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGT
195 TTTGAAGAGATGTCT-GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTGTGAAGATAT
*
20364 TC
259 CC
* **
20366 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTTCGAGTTCCATAC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAG---ATGTTCGAGTTCCATAC
* * **** * *
20431 TCCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTATACTTCCTGGAGA
63 TCCCTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATT-TTCGAGTTCTATACTCCCTGAAGA
** * * * *
20496 AAG-AGCGAAGCGAACCCGTAAGAAGAAGATCTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAG
127 AAGAAG-G-AGCGAACCC---AGTTGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAAGGAG
* * * * * *
20560 TGAGCCCGTTTTCAGAAGATCAT-TC-GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCC
187 CGAACCCG-TTT--GAAGA-GATGTCTGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCC
* * *
20623 GTTTCCAAAAGATTATTC
247 GTGT---GAAGA-TATCC
* * * ** * * * *
20641 GAGTTCTATACTCCTTAAAGAAA-AA-G-G-GAATTCGCTTACAGAAGATTATTCAAGTTCTATA
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCG-TT--TGAAGA-TGTTCGAGTTCCATA
* * * * *
20702 CTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTCGAGTTCTATAATCCCT
62 CTCCCTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTCCCT
20762 AGAGAAATAG
Statistics
Matches: 799, Mismatches: 83, Indels: 50
0.86 0.09 0.05
Matches are distributed among these distances:
256 1 0.00
257 80 0.10
258 95 0.12
259 2 0.00
260 342 0.43
261 50 0.06
262 25 0.03
263 9 0.01
266 43 0.05
269 1 0.00
270 15 0.02
271 52 0.07
272 50 0.06
273 1 0.00
274 8 0.01
275 25 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (260 bp):
GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCC
CTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGA
AGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGT
TTGAAGAGATGTCTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
Found at i:20457 original size:156 final size:156
Alignment explanation
Indices: 19591--20775 Score: 1161
Period size: 156 Copynumber: 7.5 Consensus size: 156
19581 AAGATTATTT
* *
19591 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-A-AGATGTCCGAGTTCCATACT
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAGATGTTCGAGTTCCATACT
* * *
19654 CCCT-AGAGAAAGAAGGAGCGAACCCGTGTGA-AGATATGCGAGTTCTATACTCCTTAAAGAAAG
66 CCCTGAGAGAAAGAGGGAGCGAACCCGT-TGAGAGATGTTCGAGTTCTATACTCCTTAAAGAAAG
19717 AAGGAGCGAACCCGTTTGAAGATGTTC
130 AAGGAGCGAACCCGTTTGAAGATGTTC
* * * * *
19744 GAGTTCCATACTCCTTAAAAAAAGAAGGAGCGAACCCGTTTGAAGAGATG-TCTGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAGATGTTC-GAGTTCCATAC
* * * *
19808 TCCCT-AGAGAAAGAGGGAGCGAACCCGTGTGA-AGATATCCGAGTTCCATACTCCTTAATGAAA
65 TCCCTGAGAGAAAGAGGGAGCGAACCCGT-TGAGAGATGTTCGAGTTCTATACTCCTTAAAGAAA
19871 GAAGGAGCGAACCCGTTTGAAGATGTTC
129 GAAGGAGCGAACCCGTTTGAAGATGTTC
** * * * * ** * * *
19899 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCATAAGAAGAAGATTTTTGAGTTCTATAC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-AGATGTTCGAGTTCCATAC
*
19964 TCCCTGA-AGAAAGAGGGAGCGAACCCAGTTGA-AGATGTTCGAGTTCCATACTCCTTAAAGAAA
65 TCCCTGAGAGAAAGAGGGAGCGAACCC-GTTGAGAGATGTTCGAGTTCTATACTCCTTAAAGAAA
*
20027 GAATGAGCGAACCCGTTTGAAGA-GATGTC
129 GAAGGAGCGAACCCGTTTGAAGATG-T-TC
* * * *
20056 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTG-A-AGATATCCGAGTTCCATAC
1 -GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAGATGTTCGAGTTCCATAC
* * * *
20119 T-CCTTA-ATGAAAGAAGGAGCGAACCCGTTTGA-AGATGTTCGAGTTCTATACTCTTTAAAGAG
65 TCCCTGAGA-GAAAGAGGGAGCGAACCCG-TTGAGAGATGTTCGAGTTCTATACTCCTTAAAGAA
** * *
20181 AGAAGGAGCGAACCCGTAAGAAGAAGATTTTT
128 AGAAGGAGCGAACCCGT---TTGAAGATGTTC
*
20213 GAGTTCTATACTCCCT-GAAGAAAGAAGGAGCGAACCCAG-TTG-A-AGATGTTCGAGTTCCATA
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCC-GTTTGAAGAGATGTTCGAGTTCCATA
*
20274 CTCCC-GAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTTCGAGTTCTATACTCCCTAAAGAA
64 CTCCCTGAGAGAAAGAGGGAGCGAACCCGTTG-AGAGATGTTCGAGTTCTATACTCCTTAAAGAA
20337 AGAAGGAGCGAACCCGTTTGAAGATGTTC
128 AGAAGGAGCGAACCCGTTTGAAGATGTTC
* *
20366 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTTCGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-AGATGTTCGAGTTCCATAC
* **
20431 TCCCTGA-AGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTATACTTCC-TGGA
65 TCCCTGAGAGAAAGAGGGAGCGAACCCG--TTGAG-AGA-TGTTCGAGTTCTATAC-TCCTTAAA
** *
20494 GAAAG-AGCGAAGCGAACCCGTAAGAAGAAGATCTTC
125 GAAAGAAG-G-AGCGAACCCGT---TTGAAGATGTTC
* * ** * *
20530 GAGTTCTATACTCCCT-GAAGAAAGAGGGAGTGAGCCCGTTTTCAGAAGATCATTCGAGTTCTAT
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAG-AGAT-GTTCGAGTTCCAT
* * * * * *
20594 ACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTCGAGTTCTATACTCCTTAA
63 ACTCCCTGAGAGAAAGAGGGAGCGAACCCG-TT--GAGAGA-TGTTCGAGTTCTATACTCCTTAA
** * *
20659 AGAAA-AA-G-G-GAATTCGCTTACAGAAGATTATTC
124 AGAAAGAAGGAGCGAACCCG-TT--TGAAGA-TGTTC
* * ** * *
20692 AAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTCGAGTTCTATAA
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-AGATGTTCGAGTTCCATAC
*
20757 TCCCT-AGAGAAATAGGGAG
65 TCCCTGAGAGAAAGAGGGAG
20776 TAGACCCGAT
Statistics
Matches: 880, Mismatches: 101, Indels: 95
0.82 0.09 0.09
Matches are distributed among these distances:
152 1 0.00
153 82 0.09
154 12 0.01
155 224 0.25
156 251 0.29
157 14 0.02
158 41 0.05
159 6 0.01
160 36 0.04
161 42 0.05
162 46 0.05
163 2 0.00
164 52 0.06
165 25 0.03
166 45 0.05
167 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (156 bp):
GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAGATGTTCGAGTTCCATACT
CCCTGAGAGAAAGAGGGAGCGAACCCGTTGAGAGATGTTCGAGTTCTATACTCCTTAAAGAAAGA
AGGAGCGAACCCGTTTGAAGATGTTC
Found at i:20801 original size:326 final size:316
Alignment explanation
Indices: 19591--20812 Score: 997
Period size: 311 Copynumber: 3.9 Consensus size: 316
19581 AAGATTATTT
* * * *
19591 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCC-GTTTGAAGATGTCCGAGTTCCATACT
1 GAGTTCTATACTCCCTGA-AGAAAGAAGGAGCGAACCCAG-TTGAAGATATTCGAGTTCCATACT
* * * * *** * *
19654 CCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAA
64 CCCGAAAGAAAGAGGGAGCAAACCCGTCAAAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAA
* * * * * * * * *
19719 GGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAAAAAAGAAGGAGCGAACCCGTT
129 GGAGCGAACCCGTTAGAAGATATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * *
19784 TGAAG-AGATG-TCTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG-TGT-GAAGA-
194 AGAAGAAGATGTTC-GAGTTCCATAATCCCTGA-AGAAAGAGGGAGAGAACCCGTTTTAGAAGAT
* * * ** ** *
19843 TATCCGAGT-TCCATAC-TCCTTAATGAAAGAAG-G-AGCGAACCCGT---TTGAAGATGTTC
257 TGTTCGAGTCT-TATACTTCCTGGA-GAAAG-AGCGAAGCGAACCCGTAAGAAGAAGATCTTC
** * * ** * * *
19899 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCATAAGAAGAAGATTTTTGAGTTCTATAC
1 GAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCC---AGTTGAAGATATTCGAGTTCCATAC
* ** * * *
19964 TCCCTG-AAGAAAGAGGGAGCGAACCCAGT-TGAAGATGTTCGAGTTCCATACTCCTTAAAGAAA
63 TCCC-GAAAGAAAGAGGGAGCAAACCC-GTCAAAAGATATTCGAGTTCTATACTCCCTAAAGAAA
* * * * *
20027 GAATGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAAC
126 GAAGGAGCGAACCCGTTAGAAGATAT-TC-AAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAAC
* * * * * * *
20092 CCGT--G-TGAAGATATCCGAGTTCCATACT-CCTTAATGAAAGAAGGAGCGAACCCG-TTT-GA
189 CCGTAAGAAGAAGATGTTCGAGTTCCATAATCCCTGAA-GAAAGAGGGAGAGAACCCGTTTTAGA
** * * *
20151 AGA-TGTTCGAGT-TCTATAC-T-CTTTA-AAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTT
253 AGATTGTTCGAGTCT-TATACTTCCTGGAGAA-AGAG-CGAAGCGAACCCGTAAGAAGAAGATCT
*
20211 TT
315 TC
*
20213 GAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCC
1 GAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCAGTTGAAGATATTCGAGTTCCATACTCC
* * * * *
20278 CGAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAAGG
66 CGAAAGAAAGAGGGAGCAAACCCGTCAAAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAAGG
* * * * **
20343 AGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTG
131 AGCGAACCCGTTAGAAGATATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * *
20408 AAGAATATGTTCGAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGT
196 AAGAAGATGTTCGAGTTCCATAATCCCTGAAGAAAGAGGGAGAGAACCCGTTTT-AGAAGATTGT
20473 TCGAGT-TCTATACTTCCTGGAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATCTTC
260 TCGAGTCT-TATACTTCCTGGAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATCTTC
* * * *
20530 GAGTTCTATACTCCCTGAAGAAAGAGGGAGTGAGCCC-GTTTTCAGAAGATCATTCGAGTTCTAT
1 GAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCAG--TT--GAAGAT-ATTCGAGTTCCAT
* *
20594 ACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTCGAGTTCTATACTCCTTAA
61 AC-TCCCGAAAGAAAGAGGGAGCAAACCCG--T-CAAAAGA-TATTCGAGTTCTATACTCCCTAA
**
20659 AGAAA-AA-G-G-GAATTCGCTTACAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGG
121 AGAAAGAAGGAGCGAACCCG-TT--AGAAGA-TATTCAAGTTCTATACTCCCTAGAGAAAGAGGG
* * *
20720 AGCGAACCTGTAAGAAGAAGATGTTCGAGTTCTATAATCCCT-AGAGAAATAGGGAGTAG-ACCC
182 AGCGAACCCGTAAGAAGAAGATGTTCGAGTTCCATAATCCCTGA-AGAAAGAGGGAG-AGAACCC
*
20783 GATTGTT-GAAGTTTGTTCGAGTCTTATACT
245 G-TT-TTAGAAGATTGTTCGAGTCTTATACT
20813 CTCTGAAAGA
Statistics
Matches: 766, Mismatches: 96, Indels: 86
0.81 0.10 0.09
Matches are distributed among these distances:
308 34 0.04
309 40 0.05
310 15 0.02
311 257 0.34
312 43 0.06
313 43 0.06
314 41 0.05
315 5 0.01
316 17 0.02
317 60 0.08
318 9 0.01
319 2 0.00
320 6 0.01
321 13 0.02
322 29 0.04
323 3 0.00
324 2 0.00
325 13 0.02
326 128 0.17
327 4 0.01
328 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (316 bp):
GAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCAGTTGAAGATATTCGAGTTCCATACTCC
CGAAAGAAAGAGGGAGCAAACCCGTCAAAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAAGG
AGCGAACCCGTTAGAAGATATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
AAGAAGATGTTCGAGTTCCATAATCCCTGAAGAAAGAGGGAGAGAACCCGTTTTAGAAGATTGTT
CGAGTCTTATACTTCCTGGAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATCTTC
Found at i:20829 original size:55 final size:55
Alignment explanation
Indices: 20764--21479 Score: 773
Period size: 55 Copynumber: 13.2 Consensus size: 55
20754 TAATCCCTAG
* * * *
20764 AGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
20819 A-AGAATAGGGAGCAGACACGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGA
1 AGA-AATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
20874 A-AGAATAGGGAGTAGACACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA
1 AGA-AATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * * * * *
20929 AGGAATAGGGAGCATACACG-TT-TTCAAAAGATT-TTCGAGT-TCTATAGTCCCTGG
1 AGAAATAGGGGGCAGACACGATTGTT--GAAGATTGTTCGAGTCT-TATACTCTCTGA
* ** * *
20983 AGAAAGAGGGAAC-GAACCCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAG-ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
** * * *
21036 AGAAATAGGGGGCAGATGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
21091 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
21146 AGAAATAGGGGGCAGACACAATTGATGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* *
21199 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
21254 AGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * **
21307 AGAAAAAGGGGGCAGACGCAATCATTGAAGATTGTTCG-GATCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAG-TCTTATACTCTCTGA
* * * * *
21362 AGAAATAGGGGGCAGATACGATTGATAAAGATT-AT-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * *
21415 AGAAATAGGGGGCAGACAAGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTG-TTCGAGTCTTATACTCTCTGA
21470 AGAAATAGGG
1 AGAAATAGGG
21480 AGCGAACCCA
Statistics
Matches: 569, Mismatches: 70, Indels: 44
0.83 0.10 0.06
Matches are distributed among these distances:
52 1 0.00
53 177 0.31
54 50 0.09
55 339 0.60
56 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:21210 original size:108 final size:109
Alignment explanation
Indices: 20764--21479 Score: 792
Period size: 108 Copynumber: 6.6 Consensus size: 109
20754 TAATCCCTAG
* * * * *
20764 AGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAA-AGAATAGG
1 AGAAATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGG
* * * * *
20828 GAGCAGACACGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGA
65 GGGCAGACACGATTGATGAAGATT-GTCGGGTCTTATACTCTCTGA
* * * * *
20874 A-AGAATAGGGAGTAGACACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGG
1 AGA-AATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * * * * * * * *
20938 GAGCATACACGTTTTCA-AAAGATTTTCGAGT-TCTATAGTCCCTGG
65 GGGCAGACACG-ATTGATGAAGATTGTCGGGTCT-TATACTCTCTGA
* ** * * *
20983 AGAAAGAGGGAAC-GAACCCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGG
1 AGAAATAGGGGGCAG-ACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
** * * *
21045 GGGCAGATGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCTGA
65 GGGCAGACACGATTGATGAAGATTG-TCGGGTCTTATACTCTCTGA
* *
21091 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
*
21156 GGCAGACACAATTGATGAAGATTGT-GGGTCTTATACTCTCTGA
66 GGCAGACACGATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
*
21199 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
*
21264 GGCAGACGCGATTGATGAAGATTGT-GGGTCTTATACTCTCTGA
66 GGCAGACACGATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
* * **
21307 AGAAAAAGGGGGCAGACGCAATCATTGAAGATTGTTCG-GATCTTATACTCTCTGAAGAAATAGG
1 AGAAATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGG
* * *
21371 GGGCAGATACGATTGATAAAGATTAT-GGGTCTTATACTCTCTGA
65 GGGCAGACACGATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
* * *
21415 AGAAATAGGGGGCAGACA-AGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAG
1 AGAAATAGGGGGCAGACACA-ATTGTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAG
21478 GG
64 GG
21480 AGCGAACCCA
Statistics
Matches: 527, Mismatches: 63, Indels: 34
0.84 0.10 0.05
Matches are distributed among these distances:
106 1 0.00
107 40 0.08
108 316 0.60
109 47 0.09
110 121 0.23
111 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (109 bp):
AGAAATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
GGCAGACACGATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
Found at i:26417 original size:16 final size:16
Alignment explanation
Indices: 26393--26424 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26383 AAGGGAAATT
26393 CATCATGTCGATATGA
1 CATCATGTCGATATGA
*
26409 CATCGTGTCGATATGA
1 CATCATGTCGATATGA
26425 TGAGTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (16 bp):
CATCATGTCGATATGA
Found at i:26960 original size:18 final size:18
Alignment explanation
Indices: 26933--26972 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
26923 AAAAATCTTA
26933 TTTA-TTTATAAATATAT
1 TTTATTTTATAAATATAT
26950 TTTATTTTATAAATATAT
1 TTTATTTTATAAATATAT
*
26968 ATTAT
1 TTTAT
26973 GAGGTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATTTTATAAATATAT
Found at i:27926 original size:53 final size:53
Alignment explanation
Indices: 27850--28073 Score: 425
Period size: 53 Copynumber: 4.3 Consensus size: 53
27840 CATTCCAAAG
27850 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
27903 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
*
27956 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGATGTTTTTGTAGGATATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
28009 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGG--ATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
28060 CCTACTGATAAATT
1 CCTACTGATAAATT
28074 CTTTTCAACC
Statistics
Matches: 169, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
51 18 0.11
53 151 0.89
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (53 bp):
CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
Found at i:34352 original size:115 final size:113
Alignment explanation
Indices: 34126--34361 Score: 391
Period size: 115 Copynumber: 2.0 Consensus size: 113
34116 TTTGGTTGCC
*
34126 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGCTATAGAGTAAGACAAAGC
1 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAGC
34191 AAAATTTTCCAAATCTTACATCACATTTACTGGCAATAAATGAATGAGCA
66 AAAATTTTCCAAATCTTACATCACATTTACTGGCAAT-AA-GAATGAGCA
34241 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAGC
1 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAG-
34306 AACAAAACTTTTCCAAATCTTACATCACATTTACTGGCAATAAATGAATGAGCA
65 --CAAAA-TTTTCCAAATCTTACATCACATTTACTGGCAAT-AA-GAATGAGCA
34360 TG
1 TG
34362 ATCTTCCATG
Statistics
Matches: 116, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
115 63 0.54
118 5 0.04
119 48 0.41
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (113 bp):
TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAGC
AAAATTTTCCAAATCTTACATCACATTTACTGGCAATAAGAATGAGCA
Found at i:44391 original size:17 final size:17
Alignment explanation
Indices: 44369--44405 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
44359 ATTTGATTTG
*
44369 AAAATTTTGGGTATCTA
1 AAAATTTTGGATATCTA
*
44386 AAAATTTTGGATATTTA
1 AAAATTTTGGATATCTA
44403 AAA
1 AAA
44406 TAGTGATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.41
Consensus pattern (17 bp):
AAAATTTTGGATATCTA
Found at i:44405 original size:16 final size:16
Alignment explanation
Indices: 44364--44406 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
44354 TCCGAATTTG
*
44364 ATTTGAAAATTTTGGGT
1 ATTT-AAAATTTTGGAT
*
44381 ATCTAAAAATTTTGGAT
1 AT-TTAAAATTTTGGAT
44398 ATTTAAAAT
1 ATTTAAAAT
44407 AGTGATCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.27
17 15 0.68
18 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (16 bp):
ATTTAAAATTTTGGAT
Found at i:44533 original size:85 final size:85
Alignment explanation
Indices: 44274--44533 Score: 394
Period size: 85 Copynumber: 3.1 Consensus size: 85
44264 ACCCGATATG
* * * * *
44274 ATTTCATTTGAAATTTTTGGCCATCTAAAAGTTTTAGATATTTAAAATAGTGATCCATATACCAT
1 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCATATACGAT
44339 TGAAAATATTACATATCCGA
66 TGAAAATATTACATATCCGA
* * *
44359 ATTTGATTTGAAAATTTTGGGTATCTAAAAATTTTGGATATTTAAAATAGTGATCCATATACGAT
1 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCATATACGAT
44424 TGAAAATATTACATATCCGA
66 TGAAAATATTACATATCCGA
* * *
44444 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCCTGTAAGAT
1 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCATATACGAT
* * *
44509 TAAAAATATTATATATTCGA
66 TGAAAATATTACATATCCGA
44529 ATTTT
1 ATTTT
44534 TAGATTGGGT
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 159 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (85 bp):
ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCATATACGAT
TGAAAATATTACATATCCGA
Found at i:45276 original size:31 final size:31
Alignment explanation
Indices: 45214--45277 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
45204 TTCATATATC
*
45214 AAATGGATATTTTATCTAAAATTTACGGTCA
1 AAATGGATATTTTATCTAAAATTTAAGGTCA
*
45245 AAAT-GATATTTTATAC-AAAGTTTAAGAGTCA
1 AAATGGATATTTTAT-CTAAAATTTAAG-GTCA
45276 AA
1 AA
45278 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
AAATGGATATTTTATCTAAAATTTAAGGTCA
Found at i:45642 original size:21 final size:22
Alignment explanation
Indices: 45618--45658 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
45608 AAAAATTAAT
*
45618 TAAAACATT-ATTTTTTTTACC
1 TAAAACATTAATGTTTTTTACC
45639 TAAAACATTAATGTTTTTTA
1 TAAAACATTAATGTTTTTTA
45659 ATATTTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAAACATTAATGTTTTTTACC
Found at i:49582 original size:3 final size:3
Alignment explanation
Indices: 49574--49604 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
49564 TAATGGGAAT
49574 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
49605 GTTTCTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:54912 original size:21 final size:21
Alignment explanation
Indices: 54888--54930 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
54878 TTCAAGCTAC
54888 ATAATTATTTCACATTGGTTT
1 ATAATTATTTCACATTGGTTT
*
54909 ATAATTATTTCGCATTGGTTT
1 ATAATTATTTCACATTGGTTT
54930 A
1 A
54931 AGAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (21 bp):
ATAATTATTTCACATTGGTTT
Found at i:55287 original size:21 final size:21
Alignment explanation
Indices: 55261--55303 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55251 TTAGAAACTC
*
55261 TAATGTCTTCCCCTGATCTGA
1 TAATGTCTTCCCCTGACCTGA
55282 TAATGTCTTCCCCTGACCTGA
1 TAATGTCTTCCCCTGACCTGA
55303 T
1 T
55304 CGAAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (21 bp):
TAATGTCTTCCCCTGACCTGA
Found at i:59084 original size:10 final size:9
Alignment explanation
Indices: 59069--59102 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
59059 TATTATTTTT
59069 TTTTTTGTAA
1 TTTTTTG-AA
*
59079 TTTTTTGGA
1 TTTTTTGAA
59088 TTTTTTGAA
1 TTTTTTGAA
59097 TTTTTT
1 TTTTTT
59103 CTGATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:59093 original size:19 final size:19
Alignment explanation
Indices: 59069--59112 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
59059 TATTATTTTT
59069 TTTTTTGTAATTTTTT-GGA
1 TTTTTTG-AATTTTTTCGGA
*
59088 TTTTTTGAATTTTTTCTGA
1 TTTTTTGAATTTTTTCGGA
59107 TTTTTT
1 TTTTTT
59113 TATATTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.14, C:0.02, G:0.11, T:0.73
Consensus pattern (19 bp):
TTTTTTGAATTTTTTCGGA
Found at i:59495 original size:17 final size:17
Alignment explanation
Indices: 59475--59509 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
59465 AAAAGTAAAA
*
59475 TTTATCGGATATATTTT
1 TTTATCAGATATATTTT
59492 TTTATCAGATATATTTT
1 TTTATCAGATATATTTT
59509 T
1 T
59510 ATTTATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTATCAGATATATTTT
Found at i:59514 original size:19 final size:18
Alignment explanation
Indices: 59474--59515 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
59464 AAAAAGTAAA
*
59474 ATTTATCGGATATATTTT
1 ATTTATCAGATATATTTT
59492 -TTTATCAGATATATTTTT
1 ATTTATCAGATATA-TTTT
59510 ATTTAT
1 ATTTAT
59516 GTCACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTATCAGATATATTTT
Found at i:59657 original size:82 final size:83
Alignment explanation
Indices: 59511--59667 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 83
59501 TATATTTTTA
* *
59511 TTTATGTCACATGTTTCATTTATCGAACAAAAATTGTTTGTCTTTTTCGTCTCTGTCATATCCTT
1 TTTATGT-ACATGTTTCATTTATCGAACAAAAATTGGTTATCTTTTTCGTCTCTGTCATATCCTT
59576 ATTAACACAAAAATGTTTG
65 ATTAACACAAAAATGTTTG
* * * * *
59595 TTTATGT-CATGTTTCATTTATCGGACAAAAATTGGTTATCTTTTTCTTCTTTGTCTTATCCTTG
1 TTTATGTACATGTTTCATTTATCGAACAAAAATTGGTTATCTTTTTCGTCTCTGTCATATCCTTA
59659 TTAACACAA
66 TTAACACAA
59668 GAATATGCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
82 59 0.89
84 7 0.11
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (83 bp):
TTTATGTACATGTTTCATTTATCGAACAAAAATTGGTTATCTTTTTCGTCTCTGTCATATCCTTA
TTAACACAAAAATGTTTG
Found at i:59748 original size:21 final size:21
Alignment explanation
Indices: 59721--59768 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
59711 GGTCGAAAAA
*
59721 AATATTTTAAATATTATTATT
1 AATATTTTAAATATTAATATT
* * *
59742 AGTATTTTTATTATTAATATT
1 AATATTTTAAATATTAATATT
59763 AATATT
1 AATATT
59769 AATATTTCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AATATTTTAAATATTAATATT
Found at i:59866 original size:33 final size:33
Alignment explanation
Indices: 59797--59866 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
59787 ATTACCTAAC
* ** * *
59797 CTAAAAACTCATTACCTATTAAATAATCATCTA
1 CTAAAAACTCACTACCTATTAAATAAAAACCCA
* *
59830 CTAAAAATTCACTATCTATTAAATAAAAACCCA
1 CTAAAAACTCACTACCTATTAAATAAAAACCCA
59863 CTAA
1 CTAA
59867 CTATTAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (33 bp):
CTAAAAACTCACTACCTATTAAATAAAAACCCA
Found at i:61546 original size:23 final size:23
Alignment explanation
Indices: 61511--61558 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
61501 ATCAAGTACA
* *
61511 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCACTTAT
* *
61534 ATAATGTAATAGGTATCACTTAT
1 ATAATATAATAGGTAGCACTTAT
61557 AT
1 AT
61559 TGACTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCACTTAT
Done.