Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008659.1 Hibiscus syriacus cultivar Beakdansim tig00111655_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: 244888
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:200592 original size:24 final size:23
Alignment explanation
Indices: 200540--200593 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
200530 ATTATATATC
* *
200540 TTAAATATTATTTTTAATATAAT
1 TTAAAAATTATTTTAAATATAAT
*
200563 TCTAAAAATTATTTTAAATTTAAT
1 T-TAAAAATTATTTTAAATATAAT
200587 GTTAAAA
1 -TTAAAA
200594 TAATCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAAAAATTATTTTAAATATAAT
Found at i:205898 original size:21 final size:21
Alignment explanation
Indices: 205872--205924 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
205862 GTTTCCAGAT
*
205872 TCGCAACGCGAACATCGACTA
1 TCGCAATGCGAACATCGACTA
*
205893 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACATCGACTA
205914 TCGCAATGCGA
1 TCGCAATGCGA
205925 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAACATCGACTA
Found at i:205962 original size:21 final size:21
Alignment explanation
Indices: 205936--206115 Score: 178
Period size: 21 Copynumber: 8.8 Consensus size: 21
205926 TTTCCAAATT
205936 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
205957 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
205976 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * * *
205997 CATTGCGGTTTATTCCAAATTCG
1 CGTTGC-G-ATAGTCCAAGTTCG
*
206020 C--TGTGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
206039 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
206058 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
206079 CGTTGTGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
206100 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
206116 AATCGCAACG
Statistics
Matches: 133, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
19 55 0.41
20 1 0.01
21 56 0.42
22 1 0.01
23 20 0.15
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:205964 original size:40 final size:40
Alignment explanation
Indices: 205920--206115 Score: 239
Period size: 40 Copynumber: 4.8 Consensus size: 40
205910 ACTATCGCAA
205920 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
** * *
205960 TGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* * *
206000 TGCGGTTTATTCCAAATTCGCTGTGATAGTCCAAGTTCGCGT
1 TGC-GATT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
** * * *
206042 TGCGATAGTCCAAGTTCGTTGTGATAGTCGAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
206082 TGTGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAA
206116 AATCGCAACG
Statistics
Matches: 129, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
40 72 0.56
41 5 0.04
42 52 0.40
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:206028 original size:82 final size:82
Alignment explanation
Indices: 205914--206115 Score: 318
Period size: 82 Copynumber: 2.5 Consensus size: 82
205904 ACTTCGACTA
*
205914 TCGCAATGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
205977 GTTGCGATAGTCCAAGT
66 GTTGCGATAGTCCAAGT
* * *
205994 TCGCATTGCGGTTTATTCCAAATTCGCTGTGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
* *
206059 GTTGTGATAGTCGAAGT
66 GTTGCGATAGTCCAAGT
* *
206076 TCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
206116 AATCGCAACG
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 9 0.08
81 2 0.02
82 98 0.90
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (82 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
GTTGCGATAGTCCAAGT
Found at i:206116 original size:19 final size:19
Alignment explanation
Indices: 205928--206115 Score: 169
Period size: 19 Copynumber: 9.3 Consensus size: 19
205918 AATGCGATTT
*
205928 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
205947 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
205968 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
205987 TCCAAGTTCGCATTGCGGTTTAT
1 TCCAAGTTCG--TTGC-G-ATAG
* * *
206010 TCCAAATTCGCTGTGATAG
1 TCCAAGTTCGTTGCGATAG
206029 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
206050 TCCAAGTTCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
206069 TCGAAGTTCGCGTTGTGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
206092 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
206111 TCCAA
1 TCCAA
206116 AATCGCAACG
Statistics
Matches: 139, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
19 61 0.44
20 1 0.01
21 57 0.41
22 1 0.01
23 19 0.14
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:206768 original size:20 final size:20
Alignment explanation
Indices: 206743--206835 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
206733 TTTTCCCAAT
206743 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
206763 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
206783 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
** *
206804 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
206825 TCGCAATGCGA
1 TCGCAATGCGA
206836 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:206785 original size:41 final size:41
Alignment explanation
Indices: 206740--206835 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
206730 CGATTTTCCC
206740 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
206781 AATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
206822 AAATCGCAATGCGA
1 AATTCGCAATGCGA
206836 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:206789 original size:21 final size:20
Alignment explanation
Indices: 206743--206835 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
206733 TTTTCCCAAT
*
206743 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
206763 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
206783 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
**
206804 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
206825 TCGCAATGCGA
1 TCGCAATGCGA
206836 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:206849 original size:20 final size:20
Alignment explanation
Indices: 206824--206917 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
206814 AATTGGGAAA
*
206824 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
206844 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
206865 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
206885 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
206905 TTCGCAACGCGAT
1 ATCGCAACGCGAT
206918 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:206898 original size:41 final size:41
Alignment explanation
Indices: 206821--206898 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
206811 GCGAATTGGG
* * **
206821 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
206862 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
206899 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:207481 original size:19 final size:19
Alignment explanation
Indices: 207432--207502 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
207422 TAGTTTCGAG
*
207432 AATGAGAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
207452 AATGACTATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
207471 AATAAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
207490 AACGAAAATCGCA
1 AATGAAAATCGCA
207503 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.66
20 15 0.34
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:207520 original size:19 final size:19
Alignment explanation
Indices: 207498--207682 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
207488 GAAACGAAAA
*
207498 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
207517 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
207536 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
207555 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
207575 TCGCGTTGTGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
207591 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
207608 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
207622 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
207641 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
207661 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
207681 TC
1 TC
207683 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:207575 original size:39 final size:38
Alignment explanation
Indices: 207498--207587 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
207488 GAAACGAAAA
* *
207498 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
207536 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
*
207575 TCGCGTTGTGATT
1 TCGCGTTGCGATT
207588 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:207607 original size:33 final size:33
Alignment explanation
Indices: 207570--207657 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
207560 GTTGCGATTT
* * *
207570 TCATTTCGCGTTGTGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
207603 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
207636 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
207658 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:207659 original size:20 final size:20
Alignment explanation
Indices: 207625--207682 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
207615 GCGATTCTCT
**
207625 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
207645 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
207665 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
207683 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:208595 original size:21 final size:21
Alignment explanation
Indices: 208569--208621 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
208559 GTTTCCAGAT
208569 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
208590 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
208611 TCGCAATGCGA
1 TCGCAACGCGA
208622 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:208659 original size:21 final size:21
Alignment explanation
Indices: 208633--208812 Score: 178
Period size: 21 Copynumber: 8.8 Consensus size: 21
208623 TTTCCAAATT
208633 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
208654 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
208673 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * * *
208694 CATTGCGGTTTATTCCAAATTCG
1 CGTTGC-G-ATAGTCCAAGTTCG
*
208717 C--TGTGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
208736 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
208755 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
208776 CGTTGTGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
208797 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
208813 AATCGCAACG
Statistics
Matches: 133, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
19 55 0.41
20 1 0.01
21 56 0.42
22 1 0.01
23 20 0.15
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:208675 original size:40 final size:40
Alignment explanation
Indices: 208625--208812 Score: 241
Period size: 40 Copynumber: 4.6 Consensus size: 40
208615 AATGCGATTT
208625 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * * *
208665 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCATTGCGGTTTAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGC-G-ATAG
* *
208707 TCCAAATTCGCTGTGATAGTCCAAGTTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * * * *
208747 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGTGATTTAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAG
208789 TCCAAATTCGTTGCGATAGTCCAA
1 TCCAAATTCGTTGCGATAGTCCAA
208813 AATCGCAACG
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 68 0.54
41 2 0.02
42 56 0.44
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (40 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
Found at i:208729 original size:82 final size:82
Alignment explanation
Indices: 208611--208812 Score: 318
Period size: 82 Copynumber: 2.5 Consensus size: 82
208601 ACTTCGACTA
*
208611 TCGCAATGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
208674 GTTGCGATAGTCCAAGT
66 GTTGCGATAGTCCAAGT
* * *
208691 TCGCATTGCGGTTTATTCCAAATTCGCTGTGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
* *
208756 GTTGTGATAGTCGAAGT
66 GTTGCGATAGTCCAAGT
* *
208773 TCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
208813 AATCGCAACG
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 9 0.08
81 2 0.02
82 98 0.90
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (82 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC
GTTGCGATAGTCCAAGT
Found at i:208813 original size:19 final size:19
Alignment explanation
Indices: 208625--208812 Score: 169
Period size: 19 Copynumber: 9.3 Consensus size: 19
208615 AATGCGATTT
*
208625 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
208644 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
208665 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
208684 TCCAAGTTCGCATTGCGGTTTAT
1 TCCAAGTTCG--TTGC-G-ATAG
* * *
208707 TCCAAATTCGCTGTGATAG
1 TCCAAGTTCGTTGCGATAG
208726 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
208747 TCCAAGTTCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
208766 TCGAAGTTCGCGTTGTGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
208789 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
208808 TCCAA
1 TCCAA
208813 AATCGCAACG
Statistics
Matches: 139, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
19 61 0.44
20 1 0.01
21 57 0.41
22 1 0.01
23 19 0.14
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:208932 original size:5 final size:6
Alignment explanation
Indices: 208902--208938 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
208892 GACACGTATT
208902 ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
208939 CGAGACGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:209470 original size:20 final size:20
Alignment explanation
Indices: 209445--209537 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
209435 TTTTCCCAAT
209445 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
209465 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
209485 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
** *
209506 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
209527 TCGCAATGCGA
1 TCGCAATGCGA
209538 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:209487 original size:41 final size:41
Alignment explanation
Indices: 209442--209537 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
209432 CGATTTTCCC
209442 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
209483 AATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
209524 AAATCGCAATGCGA
1 AATTCGCAATGCGA
209538 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:209491 original size:21 final size:20
Alignment explanation
Indices: 209445--209537 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
209435 TTTTCCCAAT
*
209445 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
209465 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
209485 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
**
209506 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
209527 TCGCAATGCGA
1 TCGCAATGCGA
209538 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:209551 original size:20 final size:20
Alignment explanation
Indices: 209526--209618 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
209516 AATTGGGAAA
*
209526 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
209546 ATCGCAATGCGATAATAAAA
1 ATCGCAACGCGATACTGACT
* *
209566 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
209586 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
209606 TTCGCAACGCGAT
1 ATCGCAACGCGAT
209619 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:209599 original size:40 final size:40
Alignment explanation
Indices: 209523--209599 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
209513 GCGAATTGGG
* * **
209523 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATA
* *
209563 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
209600 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATA
Found at i:210202 original size:19 final size:19
Alignment explanation
Indices: 210180--210364 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
210170 GAAACGAAAA
*
210180 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
210199 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
210218 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
210237 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
210257 TCGCGTTGTGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
210273 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
210290 TCGCGTTTCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
210304 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
210323 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
210343 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
210363 TC
1 TC
210365 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 18 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 58 0.43
20 49 0.37
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:210257 original size:39 final size:38
Alignment explanation
Indices: 210180--210269 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
210170 GAAACGAAAA
* *
210180 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
210218 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
*
210257 TCGCGTTGTGATT
1 TCGCGTTGCGATT
210270 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:210289 original size:33 final size:33
Alignment explanation
Indices: 210252--210339 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 33
210242 GTTGCGATTT
* *
210252 TCATTTCGCGTTGTGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGTGATTCTCTCGTCGCGATAG
*
210285 TCATTTCGCGTT-TCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGT-GATTCTCTCGTCGCGATAG
*
210318 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGTGATTCTC
210340 ATTATCTCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 1 0.02
33 34 0.71
34 13 0.27
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGTGATTCTCTCGTCGCGATAG
Found at i:210341 original size:20 final size:20
Alignment explanation
Indices: 210307--210364 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
210297 TCGATTCTCT
**
210307 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
210327 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
210347 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
210365 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:212426 original size:42 final size:42
Alignment explanation
Indices: 212366--212458 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
212356 GCTCGACTCG
* *
212366 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTAAAGAGGCC
* * * *
212408 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTAAAGAGGCC
* *
212450 ACTGTCATC
1 CCTATCATC
212459 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTAAAGAGGCC
Found at i:212446 original size:21 final size:21
Alignment explanation
Indices: 212422--212488 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
212412 TCATTCCTCG
212422 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
212443 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
212464 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
212485 AGAG
1 AGAG
212489 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:213866 original size:14 final size:14
Alignment explanation
Indices: 213847--213882 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
213837 ATTGTTTAAT
213847 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
213861 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
213875 TGATTTGT
1 TGATTTGT
213883 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:214081 original size:19 final size:19
Alignment explanation
Indices: 214059--214158 Score: 94
Period size: 19 Copynumber: 5.8 Consensus size: 19
214049 CGCAAAATTA
*
214059 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
214078 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
**
214095 -CCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
214111 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
214128 ---TCTCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
214144 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
214159 AGTAATTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 16 0.25
16 9 0.14
17 9 0.14
19 30 0.47
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:214107 original size:33 final size:33
Alignment explanation
Indices: 214065--214158 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
214055 ATTAATTTCG
214065 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
214098 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
214131 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
214159 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:218352 original size:20 final size:20
Alignment explanation
Indices: 218327--218377 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
218317 ATTCATTTGA
*
218327 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
218347 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
218367 TTATCGCAACG
1 CTATCGCAACG
218378 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:218427 original size:14 final size:15
Alignment explanation
Indices: 218407--218479 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
218397 TGAAAATCGC
218407 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
218422 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
218439 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
218457 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
218473 -TTGCGAT
1 ATTGCGAT
218480 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:218444 original size:19 final size:19
Alignment explanation
Indices: 218403--218469 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
218393 GAAATGAAAA
218403 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
218419 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
218436 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
218454 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
218470 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:218605 original size:14 final size:14
Alignment explanation
Indices: 218586--218622 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
218576 CATCAATTAA
218586 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
218600 ACAAATCATCTTTT
1 ACAAATCAACATTT
218614 ACAAATCAA
1 ACAAATCAA
218623 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:220536 original size:14 final size:14
Alignment explanation
Indices: 220517--220574 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
220507 ATGCGAAATG
220517 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
220531 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
220547 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
220563 AAAATCGCAACG
1 AAAATCGCAACG
220575 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:220559 original size:32 final size:33
Alignment explanation
Indices: 220501--220579 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
220491 GGAAATGGCT
*
220501 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
220534 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
220566 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
220580 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:220608 original size:19 final size:18
Alignment explanation
Indices: 220586--220650 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
220576 GAAACACAAA
*
220586 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
220605 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
220621 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
220637 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
220651 TGTCGTTGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 11 0.28
16 4 0.10
18 14 0.36
19 10 0.26
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:220627 original size:14 final size:14
Alignment explanation
Indices: 220608--220662 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
220598 TTTCATTTCG
220608 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
220622 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
220638 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
220654 CGTTGCGAT
1 CGTTGCGAT
220663 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 20 0.57
16 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:220638 original size:32 final size:32
Alignment explanation
Indices: 220591--220681 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
220581 ACAAATCGCA
220591 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
220624 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
* *
220656 TTGCGATAGTCATTTTCGTGTTGCGA
1 TTGCGAT-TTCA-TTTCGCGTTGCGA
220682 AAGTAAACTA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.61
33 9 0.17
34 12 0.22
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:221180 original size:18 final size:18
Alignment explanation
Indices: 221154--221198 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
221144 GTCGATCAGA
*
221154 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
221172 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
221190 TGATGGCTC
1 TGATGGCTC
221199 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:222541 original size:20 final size:20
Alignment explanation
Indices: 222516--222553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
222506 AATAGTTTTT
222516 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
222536 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
222554 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:222842 original size:22 final size:22
Alignment explanation
Indices: 222817--222860 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
222807 GATTTAGATA
222817 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
222839 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
222861 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:223071 original size:20 final size:20
Alignment explanation
Indices: 223046--223139 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
223036 GATTATGTAT
223046 TATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTTAG
*
223066 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTTAG
* *** *
223086 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTTAG
* * *
223107 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTTAG
*
223127 TATCGCATTGCGA
1 TATCGCGTTGCGA
223140 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTTAG
Found at i:223111 original size:41 final size:41
Alignment explanation
Indices: 223066--223143 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
223056 CGAAAGTTAG
* * *
223066 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
223107 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
223144 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:223140 original size:20 final size:20
Alignment explanation
Indices: 223026--223140 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
223016 CGCTTTGAAA
*
223026 ATCGCATTGCGATTA-TGTATT
1 ATCGCATTGCGA-TAGT-TAGT
* *
223047 ATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATAGTTAGT
* * *
223067 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTTAGT
* * ** *
223087 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTTAGT
*
223108 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTTAGT
223128 ATCGCATTGCGAT
1 ATCGCATTGCGAT
223141 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
20 51 0.67
21 25 0.33
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTTAGT
Found at i:223159 original size:41 final size:41
Alignment explanation
Indices: 223066--223161 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
223056 CGAAAGTTAG
* * * ** *
223066 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
223107 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
223149 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
223162 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:223755 original size:6 final size:6
Alignment explanation
Indices: 223740--223772 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
223730 TCTCGTCTCG
*
223740 GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
223773 AATACGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.15, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:225340 original size:2 final size:2
Alignment explanation
Indices: 225333--225570 Score: 93
Period size: 2 Copynumber: 130.0 Consensus size: 2
225323 TTAGTATTAC
* * * *
225333 AT AT AT AT AT AT A- AT GT TT AT AT AT AT AT -T AT TT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
225372 AT AT AGT AT AT -T AT GT AT -T AT AT AT -T AT AT A- AT ACT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
225411 AT TT TT AT AT ACT AT AT AT AT -T AT -T AT AT -T A- AT AT TT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
225450 AT -T AT AT -T AT AT AGT AT AT -T AT -T AT AT AGT AT TT AT AT -T
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
225489 GT AT AGT GT -T AT AT -T AT AT -T AT AT AT A- AT AT AT AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
225527 AGT AT A- AT AT -T A- AT AT AT AT -T GC AT A- AT AT AT AT -T AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225564 AT -T AT AT
1 AT AT AT AT
225571 TTTTATTATA
Statistics
Matches: 182, Mismatches: 18, Indels: 72
0.67 0.07 0.26
Matches are distributed among these distances:
1 29 0.16
2 141 0.77
3 12 0.07
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (2 bp):
AT
Found at i:225390 original size:7 final size:7
Alignment explanation
Indices: 225351--225565 Score: 105
Period size: 7 Copynumber: 30.4 Consensus size: 7
225341 ATATAATGTT
225351 TATA-TA
1 TATATTA
225357 TATATTA
1 TATATTA
*
225364 T-TTTTA
1 TATATTA
225370 -ATATATA
1 TATAT-TA
225377 GTATATTA
1 -TATATTA
*
225385 TGTATTA
1 TATATTA
225392 TATATTA
1 TATATTA
225399 TATA--A
1 TATATTA
*
225404 TA-CTTA
1 TATATTA
*
225410 TATTTTTA
1 TA-TATTA
225418 TATACTATA
1 TATA-T-TA
225427 TATATTA
1 TATATTA
225434 TTATATTA
1 -TATATTA
225442 -ATATT-
1 TATATTA
225447 TATATTA
1 TATATTA
225454 TATTATATA
1 TA-TAT-TA
225463 GTATATTA
1 -TATATTA
225471 T-TA-TA
1 TATATTA
225476 TAGTATT-
1 TA-TATTA
*
225483 TATATTG
1 TATATTA
225490 TATAGTGT-
1 TATA-T-TA
225498 TATATTA
1 TATATTA
225505 TAT-TATA
1 TATAT-TA
*
225512 TATAATA
1 TATATTA
225519 TATATTA
1 TATATTA
*
225526 TAGTATAA
1 TA-TATTA
*
225534 TATTAATA
1 TA-TATTA
*
225542 TATATTG
1 TATATTA
* *
225549 CATAATA
1 TATATTA
225556 TATATTA
1 TATATTA
225563 TAT
1 TAT
225566 TATATTTTTA
Statistics
Matches: 162, Mismatches: 20, Indels: 53
0.69 0.09 0.23
Matches are distributed among these distances:
5 6 0.04
6 31 0.19
7 69 0.43
8 38 0.23
9 16 0.10
10 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (7 bp):
TATATTA
Found at i:225400 original size:5 final size:5
Alignment explanation
Indices: 225392--225587 Score: 97
Period size: 5 Copynumber: 38.2 Consensus size: 5
225382 TTATGTATTA
*
225392 TATAT TATAT AATACT TATAT T-T-T TATAT ACTATAT ATATTAT TATAT
1 TATAT TATAT TATA-T TATAT TATAT TATAT --TATAT -TA-TAT TATAT
*
225440 TAATATT TATAT TATAT TATAT AGTATAT TAT-T ATATAG TAT-T TATAT
1 T-ATA-T TATAT TATAT TATAT --TATAT TATAT -TATAT TATAT TATAT
* * *
225488 TGTA- TAGTGT TATAT TATAT TATA- TATAAT ATATAT TATAG TATA-
1 TATAT TA-TAT TATAT TATAT TATAT TAT-AT -TATAT TATAT TATAT
** * *
225533 -ATAT TA-AT ATATAT TGCAT AATA- TATAT TATAT TATATT TTTAT TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT
*
225582 TTTAT T
1 TATAT T
225588 CTTATTATTA
Statistics
Matches: 148, Mismatches: 19, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
3 5 0.03
4 15 0.10
5 86 0.58
6 24 0.16
7 18 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:225577 original size:16 final size:16
Alignment explanation
Indices: 225558--225595 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
225548 GCATAATATA
*
225558 TATTATATTATATTTT
1 TATTATATTATATTCT
*
225574 TATTATATTTTATTCT
1 TATTATATTATATTCT
225590 TATTAT
1 TATTAT
225596 TAGTTTGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATATTATATTCT
Found at i:228423 original size:21 final size:21
Alignment explanation
Indices: 228392--228443 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
228382 GGTCCCATCT
*
228392 GAATTGAAAGTAGCA-AAGAAA
1 GAATTGGAAGTAG-AGAAGAAA
* *
228413 GAATTTGAAGTAGAGAAGAAG
1 GAATTGGAAGTAGAGAAGAAA
228434 GAATTGGAAG
1 GAATTGGAAG
228444 AAAAACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.50, C:0.02, G:0.31, T:0.17
Consensus pattern (21 bp):
GAATTGGAAGTAGAGAAGAAA
Found at i:234331 original size:19 final size:19
Alignment explanation
Indices: 234307--234350 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
234297 TCTCTCAGTA
234307 AATCATAATTTATTTATTT
1 AATCATAATTTATTTATTT
234326 AATCATAATTTATTTATTT
1 AATCATAATTTATTTATTT
*
234345 CATCAT
1 AATCAT
234351 CTTTCACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (19 bp):
AATCATAATTTATTTATTT
Found at i:243403 original size:28 final size:27
Alignment explanation
Indices: 243348--243405 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
243338 ACTGGATCTA
* *
243348 TGTTAAAAAGAGAGAAAATTTTCGATC
1 TGTTAAAAAAAGAGAAAATTTTCAATC
243375 TGTTAAAAAAAGAGAAAATTTTCCAATC
1 TGTTAAAAAAAGAGAAAATTTT-CAATC
243403 TGT
1 TGT
243406 AGAGGTGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.31
Consensus pattern (27 bp):
TGTTAAAAAAAGAGAAAATTTTCAATC
Done.