Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003093.1 Hibiscus syriacus cultivar Beakdansim tig00006452_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: 128598
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:960 original size:48 final size:48
Alignment explanation
Indices: 905--1000 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 48
895 TCAGGGGGAG
*
905 AGTTACAA-AGAATTTC-CTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGA-AATTTCAATGTTCAAACCGAT-TTTCTTTACAGCCTATT
953 AGTTACAAGAAATTTCAAATGTTCAAACCGATTTTCTTTACAGCCTAT
1 AGTTACAAGAAATTTC-AATGTTCAAACCGATTTTCTTTACAGCCTAT
1001 CCTTTCCTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
48 14 0.32
49 17 0.39
50 13 0.30
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (48 bp):
AGTTACAAGAAATTTCAATGTTCAAACCGATTTTCTTTACAGCCTATT
Found at i:3224 original size:16 final size:16
Alignment explanation
Indices: 3195--3235 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3185 CAGACTTGTT
3195 TGTTTTCT--ACAGTC
1 TGTTTTCTACACAGTC
3209 TGTTTTCTACACAGTC
1 TGTTTTCTACACAGTC
3225 TGTTTTCTACA
1 TGTTTTCTACA
3236 AATACAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.32
16 17 0.68
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (16 bp):
TGTTTTCTACACAGTC
Found at i:11495 original size:18 final size:18
Alignment explanation
Indices: 11472--11514 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
11462 GAATGTCCAT
11472 ATTGATTAAGTCATCCTA
1 ATTGATTAAGTCATCCTA
11490 ATTGATTAAGTCATCCTA
1 ATTGATTAAGTCATCCTA
*
11508 GTTGATT
1 ATTGATT
11515 CTAGTGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (18 bp):
ATTGATTAAGTCATCCTA
Found at i:13462 original size:24 final size:24
Alignment explanation
Indices: 13427--13545 Score: 132
Period size: 24 Copynumber: 5.0 Consensus size: 24
13417 AAACATAATT
* *
13427 CATGACAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* * * * *
13451 CAGGTCATGTATGAGATTAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
13475 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
13499 CATGTC-AGATATCATATTAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
13523 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
13546 TAAATCGAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
23 2 0.03
24 73 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:13499 original size:48 final size:48
Alignment explanation
Indices: 13432--13545 Score: 158
Period size: 48 Copynumber: 2.4 Consensus size: 48
13422 TAATTCATGA
* *
13432 CAAGTATCATATCAAAATCCAGGTCATG-TATGAGATTAGAATCCAAGT
1 CAAGTATCATATCAGAATCCAGGTCA-GATATCAGATTAGAATCCAAGT
* * *
13480 CAAGTATCATATCAGAATCCATGTCAGATATCATATTAGAATCCATGT
1 CAAGTATCATATCAGAATCCAGGTCAGATATCAGATTAGAATCCAAGT
*
13528 CAAGTATCAGATCAGAAT
1 CAAGTATCATATCAGAAT
13546 TAAATCGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 58 0.98
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (48 bp):
CAAGTATCATATCAGAATCCAGGTCAGATATCAGATTAGAATCCAAGT
Found at i:30133 original size:17 final size:18
Alignment explanation
Indices: 30101--30134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30091 GAAGGTTAAA
*
30101 TTATTTTTTGACAATTTT
1 TTATTTTTTGAAAATTTT
30119 TTATTTTTT-AAAATTT
1 TTATTTTTTGAAAATTT
30135 AATGGTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTATTTTTTGAAAATTTT
Found at i:33189 original size:30 final size:30
Alignment explanation
Indices: 33155--33228 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
33145 TCCCGAGCAA
*
33155 GATGCTACTGCTGCTCCCGCCGCAGCCAAG
1 GATGCTACTGCTGCTACCGCCGCAGCCAAG
*
33185 GATGCTACTGCTGCTACCGCCGCTGCCAAG
1 GATGCTACTGCTGCTACCGCCGCAGCCAAG
33215 GATGCTACTGCTGC
1 GATGCTACTGCTGC
33229 CAAGGACGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.20
Consensus pattern (30 bp):
GATGCTACTGCTGCTACCGCCGCAGCCAAG
Found at i:34748 original size:21 final size:20
Alignment explanation
Indices: 34702--34749 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
34692 GATTCTGACT
34702 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
34722 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
34744 ATCGCA
1 ATCGCA
34750 ACGCGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:34755 original size:21 final size:20
Alignment explanation
Indices: 34740--34777 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34730 TGCGATTTTC
34740 CTAAATCGCAACGCGATTAT
1 CTAAATCGCAACGCGATTAT
* *
34760 GTAAATCGCAACGAGATT
1 CTAAATCGCAACGCGATT
34778 CTGACTATCG
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:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (20 bp):
CTAAATCGCAACGCGATTAT
Found at i:35661 original size:25 final size:24
Alignment explanation
Indices: 35633--35687 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
35623 GTATTCGAAA
35633 TTTGATCTTGGTCAATACCCGGACT
1 TTTGATCTTGGTCAATACCCGGA-T
*
35658 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAT
35682 TTTGAT
1 TTTGAT
35688 GATTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAT
Found at i:38225 original size:20 final size:19
Alignment explanation
Indices: 38197--38240 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
38187 CAATCATCTT
*
38197 AATGTCTATCACAACGCGGA
1 AATGACTATCACAACGC-GA
* *
38217 AATGACTATCGCAATGCGA
1 AATGACTATCACAACGCGA
38236 AATGA
1 AATGA
38241 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGACTATCACAACGCGA
Found at i:38246 original size:19 final size:18
Alignment explanation
Indices: 38224--38321 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 18
38214 GGAAATGACT
38224 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
38243 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
38257 ATCGCAATGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
38276 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
38290 ATCGCAAAGCGAAATAAAA
1 ATCGC-AAGCGAAATGAAA
38309 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
38322 TTTAGTTTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
14 18 0.30
15 4 0.07
16 3 0.05
17 3 0.05
18 4 0.07
19 29 0.48
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:38271 original size:33 final size:33
Alignment explanation
Indices: 38224--38317 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
38214 GGAAATGACT
38224 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
38257 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
38290 ATCGCAAAGCGAAATAAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
38318 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:38339 original size:19 final size:19
Alignment explanation
Indices: 38317--38354 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38307 AAATCGCAAC
38317 GCGAATTTAGTTTCACGTT
1 GCGAATTTAGTTTCACGTT
* *
38336 GCGATTTTAGTTTCGCGTT
1 GCGAATTTAGTTTCACGTT
38355 CTCTCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (19 bp):
GCGAATTTAGTTTCACGTT
Found at i:38376 original size:27 final size:28
Alignment explanation
Indices: 38332--38411 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 28
38322 TTTAGTTTCA
38332 CGTTGCGATTTT-AGTTTCGCG-TTCTCT
1 CGTTGCGATTTTCA-TTTCGCGATTCTCT
*
38359 CGTTGCGCTTTTCATTTCACGTTGCGATTCTCT
1 CGTTGCGATTTTCATTT--C---GCGATTCTCT
38392 CGTTGCGATTTTCATTTCGC
1 CGTTGCGATTTTCATTTCGC
38412 ATTGCGATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
27 14 0.32
28 3 0.07
29 1 0.02
31 1 0.02
32 3 0.07
33 22 0.50
ACGTcount: A:0.09, C:0.25, G:0.20, T:0.46
Consensus pattern (28 bp):
CGTTGCGATTTTCATTTCGCGATTCTCT
Found at i:38395 original size:33 final size:33
Alignment explanation
Indices: 38353--38419 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
38343 TAGTTTCGCG
* *
38353 TTCTCTCGTTGCGCTTTTCATTTCACGTTGCGA
1 TTCTCTCGTTGCGATTTTCATTTCACATTGCGA
*
38386 TTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 TTCTCTCGTTGCGATTTTCATTTCACATTGCGA
38419 T
1 T
38420 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.10, C:0.25, G:0.18, T:0.46
Consensus pattern (33 bp):
TTCTCTCGTTGCGATTTTCATTTCACATTGCGA
Found at i:38524 original size:14 final size:14
Alignment explanation
Indices: 38505--38542 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
38495 GAATTATGTT
38505 CAAATCAATTTTTA
1 CAAATCAATTTTTA
38519 CAAATC-ATCTTTTA
1 CAAATCAAT-TTTTA
38533 CAAATCAATT
1 CAAATCAATT
38543 AAACAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (14 bp):
CAAATCAATTTTTA
Found at i:39935 original size:21 final size:21
Alignment explanation
Indices: 39911--39986 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
39901 GTGAGAGGGA
39911 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * **
39932 CCTCTTGAACGGTGGGAGTGG
1 CCTCTTCAACGATGACAGTGG
* * * * *
39953 ACTC-TCGAGGAATGATAGAGG
1 CCTCTTCAACG-ATGACAGTGG
39974 CCTCTTCAACGAT
1 CCTCTTCAACGAT
39987 AGGAGTGGAC
Statistics
Matches: 38, Mismatches: 15, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
20 3 0.08
21 31 0.82
22 4 0.11
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:40494 original size:20 final size:20
Alignment explanation
Indices: 40469--40506 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40459 CGCGATTATA
40469 GTTTCGCGTTACGATTTTTG
1 GTTTCGCGTTACGATTTTTG
*
40489 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTACGATTTT
40507 ATCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTCGCGTTACGATTTTTG
Found at i:40523 original size:15 final size:14
Alignment explanation
Indices: 40495--40553 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
40485 TTTGGTTTCG
40495 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
40509 CGTTGCGATTTTTATTT
1 CGTTGCGA-TTTTA--T
* *
40526 CGCGTTGCGATTCTCT
1 --CGTTGCGATTTTAT
40542 CGTTGCGATTTT
1 CGTTGCGATTTT
40554 CATTTCGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 19 0.51
15 5 0.14
16 1 0.03
17 1 0.03
18 3 0.08
19 8 0.22
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:40530 original size:33 final size:33
Alignment explanation
Indices: 40475--40569 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
40465 TATAGTTTCG
* * *
40475 CGTTACGATTTTTGGTTTCGCGTTGCGATTTTAT
1 CGTTGCGATTTTT-ATTTCGCGTTGCGATTCTAT
*
40509 CGTTGCGATTTTTATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTTATTTCGCGTTGCGATTCTAT
*
40542 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTTATTTCGCGTTGCGAT
40570 AGTTATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 44 0.79
34 12 0.21
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTTATTTCGCGTTGCGATTCTAT
Found at i:40580 original size:26 final size:25
Alignment explanation
Indices: 40549--40599 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 25
40539 TCTCGTTGCG
40549 ATTTTCATTTCGCGTTGCGATAGTT
1 ATTTTCATTTCGCGTTGCGATAGTT
40574 A--TT--TTTCGCGTTGCGATAGTT
1 ATTTTCATTTCGCGTTGCGATAGTT
40595 ATTTT
1 ATTTT
40600 TCACGTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 19 0.79
23 4 0.17
25 1 0.04
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.51
Consensus pattern (25 bp):
ATTTTCATTTCGCGTTGCGATAGTT
Found at i:40582 original size:21 final size:21
Alignment explanation
Indices: 40556--40611 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
40546 GCGATTTTCA
40556 TTTCGCGTTGCGATAGTTATT
1 TTTCGCGTTGCGATAGTTATT
40577 TTTCGCGTTGCGATAGTTATT
1 TTTCGCGTTGCGATAGTTATT
*
40598 TTTCACGTTGCGAT
1 TTTCGCGTTGCGAT
40612 TTTAAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.46
Consensus pattern (21 bp):
TTTCGCGTTGCGATAGTTATT
Found at i:40872 original size:93 final size:94
Alignment explanation
Indices: 40681--40965 Score: 457
Period size: 93 Copynumber: 3.1 Consensus size: 94
40671 ATAGATTATA
* * *
40681 TTACTTT-AACCAAAAGACAAAACAAAGATAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* **
40745 TTAACAGAATTGGCAGCAATAGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
40774 TTACTTTCAACCAAAATACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG-
1 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
40838 TTAGCAGAATTGACAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
40867 TTACTTTCAACCAAAAGGCAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
40932 TTAGCAGAATTGGCAGCAACCAAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
40961 TTACT
1 TTACT
40966 AAACAATCTA
Statistics
Matches: 177, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
93 93 0.53
94 84 0.47
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:42578 original size:20 final size:20
Alignment explanation
Indices: 42553--42615 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
42543 TTTTGGTTGA
*
42553 AATGAAAATCGTAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
42573 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
42592 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
42613 AAT
1 AAT
42616 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:43224 original size:20 final size:20
Alignment explanation
Indices: 43199--43283 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
43189 GCTATGTAAA
43199 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
*
43219 TCGCATTGCGAT--TTACGTAT
1 TCGCATTGCGATAGTCA-G-AT
**
43239 TCGCATTGCGATTTTCCTA-AT
1 TCGCATTGCGATAGT-C-AGAT
* *
43260 TCGCAATGCGATAGTCAGAA
1 TCGCATTGCGATAGTCAGAT
43280 TCGC
1 TCGC
43284 GTTACGAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 32 0.62
21 14 0.27
22 1 0.02
24 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:43263 original size:21 final size:20
Alignment explanation
Indices: 43217--43271 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
43207 CGATAGTCAG
*
43217 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
43237 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
*
43257 AATTCGCAATGCGAT
1 -ATTCGCATTGCGAT
43272 AGTCAGAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:49913 original size:3 final size:3
Alignment explanation
Indices: 49907--49981 Score: 69
Period size: 3 Copynumber: 24.7 Consensus size: 3
49897 CATTTTAATG
* * * * * * *
49907 TTA TTA TTA TTA TTA TAA TTA TTA TAA TTA TAA TTA TAA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
49955 TTA TTA TTA TTA TTA ATA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TT
49982 TAATATTACA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:51110 original size:23 final size:23
Alignment explanation
Indices: 51084--51130 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
51074 TTAATTATGA
51084 ATTAGATTTTTAATC-TTAATTTT
1 ATTAGA-TTTTAATCATTAATTTT
* *
51107 ATTATATTTTAGTCATTAATTTT
1 ATTAGATTTTAATCATTAATTTT
51130 A
1 A
51131 AATGTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTAGATTTTAATCATTAATTTT
Found at i:51138 original size:22 final size:22
Alignment explanation
Indices: 51091--51138 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
51081 TGAATTAGAT
*
51091 TTTTAATCTTAATTTTATTATA
1 TTTTAATCTTAATTTTATAATA
* *
51113 TTTTAGTCATTAATTTTA-AATG
1 TTTTAATC-TTAATTTTATAATA
51135 TTTT
1 TTTT
51139 CATTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTAATCTTAATTTTATAATA
Found at i:62614 original size:11 final size:11
Alignment explanation
Indices: 62594--62655 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 11
62584 ATGTTTGAAG
62594 AAAA-AAAGAA
1 AAAAGAAAGAA
62604 AAAAGAAAG--
1 AAAAGAAAGAA
*
62613 AAAAGAAAAAA
1 AAAAGAAAGAA
62624 AAAAGAAA-AA
1 AAAAGAAAGAA
62634 AAAAG--AGAA
1 AAAAGAAAGAA
62643 AAAAG-AAGAA
1 AAAAGAAAGAA
62653 AAA
1 AAA
62656 GGGGGGGTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
8 1 0.02
9 15 0.33
10 18 0.39
11 12 0.26
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:62995 original size:16 final size:16
Alignment explanation
Indices: 62969--63013 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
62959 TTTGAATACA
*
62969 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
62986 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
63001 ATTCAATTTATTT
1 ATTCAATTTATTT
63014 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:63890 original size:83 final size:83
Alignment explanation
Indices: 63784--64610 Score: 1447
Period size: 83 Copynumber: 10.0 Consensus size: 83
63774 ATATCCCAGT
*
63784 CCAATCATTGAACTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
63849 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
* *
63867 CCAATCATTGAATTTGAGAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTCGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
63932 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
* * * **
63950 CCAGTTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64015 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
64033 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64098 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
64116 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64181 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
64199 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64264 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
64282 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
64347 TGATCTGGTTCGGTAAAA
66 TGATCTGGTTTGGTAAAA
*
64365 CCAATCATTGAATTTGAGAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64430 TGATCTGGTTTGGTAAAA
66 TGATCTGGTTTGGTAAAA
* * * ** *
64448 CCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
64513 TGATCTGGTTTAGTAAAA
66 TGATCTGGTTTGGTAAAA
* * * ** *
64531 CCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
64596 TGATCTGGTTTGGTA
66 TGATCTGGTTTGGTA
64611 GGAACTACAG
Statistics
Matches: 717, Mismatches: 27, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 717 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
CCAATCATTGAATTTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGTAAAA
Found at i:65609 original size:113 final size:112
Alignment explanation
Indices: 65317--65825 Score: 754
Period size: 113 Copynumber: 4.5 Consensus size: 112
65307 TTAAATTCAC
* * *
65317 CACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATTATCTTTTCCAGTAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGA
* * *
65381 AGAAGTTCATAATGAGAAGAATTTGTTCGACTTTTTGCTCAAATCCAT
65 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
* *
65429 CACTTGATGGGTCAGT-TTTTCCAG-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATG
1 CACTTGATGGATTA-TCTTTTCCAGTA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATG
65492 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
64 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
* *
65541 CACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATATGAAGAAGGATGA
1 CACTTGATGGATTATCTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGA
65606 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
65 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
*** *
65654 CACTTGATGGATTAAAATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATTACTTGAAGAAGGA
1 CACTTGATGGATTATCTTTTCCA-GTAGAGTTCATAATGAGAAGAACTCA-T-C-TGAAGAAGGA
* *
65719 TGAAGAAGTTCATAACGAGAAGAATTTGTTCAACCTTTTGTTCAAATCTAT
62 TGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
* *
65770 CACTTGATGGACTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 CACTTGATGGATTATCTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAA
65826 AAAAGAAGAA
Statistics
Matches: 363, Mismatches: 24, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
111 1 0.00
112 123 0.34
113 133 0.37
114 3 0.01
115 2 0.01
116 101 0.28
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (112 bp):
CACTTGATGGATTATCTTTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAA
GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTAT
Found at i:65799 original size:229 final size:225
Alignment explanation
Indices: 65344--65835 Score: 788
Period size: 229 Copynumber: 2.2 Consensus size: 225
65334 TTTCCAGAGA
65344 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * *** *
65409 GACTTTTTGCTCAAATCCATCACTTGATGGGTCAGTTTTTCCAGAGGAGTTCATAATGAGAAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAAAATTGCCAGAGGAGTTCATAATGAGAAGAA
*
65474 CTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCT
131 CTCATCTGAAGAAGGATGAAGAAGTTCATAACGAGAAGAATTTGTTCAACCTTTTGCTCAAATCT
*
65539 ATCACTTGATGGATTATCTTTTCCAGTTCG
196 ATCACTTGATGGACTATCTTTTCCAGTTCG
* *
65569 AGTTCATAATGAGAAGAACTCATATGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
65634 AACCTTTTGCTCAAATCTATCACTTGATGGATTAAAATTGCCAG-GTAGAGTTCATAATGAGAAG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAAAATTGCCAGAG--GAGTTCATAATGAGAAG
*
65698 AACTCATTACTTGAAGAAGGATGAAGAAGTTCATAACGAGAAGAATTTGTTCAACCTTTTGTTCA
129 AACTCA-T-C-TGAAGAAGGATGAAGAAGTTCATAACGAGAAGAATTTGTTCAACCTTTTGCTCA
65763 AATCTATCACTTGATGGACTATCTTTTCCAGTTCG
191 AATCTATCACTTGATGGACTATCTTTTCCAGTTCG
* *
65798 AGTTCATAATGAGAAGAACTCATCTGAAAAAAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
65836 TTTGTTCAAC
Statistics
Matches: 244, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
224 1 0.00
225 98 0.40
226 23 0.09
227 1 0.00
228 1 0.00
229 120 0.49
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (225 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAAAATTGCCAGAGGAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGATGAAGAAGTTCATAACGAGAAGAATTTGTTCAACCTTTTGCTCAAATCT
ATCACTTGATGGACTATCTTTTCCAGTTCG
Found at i:65910 original size:92 final size:93
Alignment explanation
Indices: 65736--65913 Score: 288
Period size: 93 Copynumber: 1.9 Consensus size: 93
65726 GTTCATAACG
* *
65736 AGAAGAATTTGTTCAACCTTTTGTTCAAATCTATCACTTGATGGACTATCTTTTCCAGTTCGAGT
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGACTATCTTTTCCAGTTCGAGT
65801 TCATAATGAGAAGAACTCATCTGAAAAA
66 TCATAATGAGAAGAACTCATCTGAAAAA
* * *
65829 AGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGG-GTCA-GTTTTCCAGTTCGAG
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGACT-ATCTTTTCCAGTTCGAG
65892 TTCATAATGAGAAGAACTCATC
65 TTCATAATGAGAAGAACTCATC
65914 AGGAGAAGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
92 37 0.47
93 42 0.53
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (93 bp):
AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGACTATCTTTTCCAGTTCGAGT
TCATAATGAGAAGAACTCATCTGAAAAA
Found at i:66189 original size:3 final size:3
Alignment explanation
Indices: 66183--66254 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
66173 CATTTTAATG
* * * * * * *
66183 TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TAA TAA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
66231 TTA TTA TTA TTA ATA TATA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TT
66255 TAATATTACA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:67407 original size:23 final size:23
Alignment explanation
Indices: 67381--67427 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
67371 TTAATTATGA
67381 ATTAGATTTTTAATC-TTAATTTT
1 ATTAGA-TTTTAATCATTAATTTT
* *
67404 ATTATATTTTAGTCATTAATTTT
1 ATTAGATTTTAATCATTAATTTT
67427 A
1 A
67428 AATGTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTAGATTTTAATCATTAATTTT
Found at i:67435 original size:22 final size:22
Alignment explanation
Indices: 67388--67435 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
67378 TGAATTAGAT
*
67388 TTTTAATCTTAATTTTATTATA
1 TTTTAATCTTAATTTTATAATA
* *
67410 TTTTAGTCATTAATTTTA-AATG
1 TTTTAATC-TTAATTTTATAATA
67432 TTTT
1 TTTT
67436 CATTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTAATCTTAATTTTATAATA
Found at i:70094 original size:10 final size:10
Alignment explanation
Indices: 70079--70152 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
70069 CATTTAATAA
70079 ATAAACGAAC
1 ATAAACGAAC
70089 ATAAACGAAC
1 ATAAACGAAC
70099 ----ACGAAC
1 ATAAACGAAC
*
70105 ATAAATGAAC
1 ATAAACGAAC
* *
70115 ATGAAC-ATAA
1 ATAAACGA-AC
70125 ATGAACACGAAC
1 AT-AA-ACGAAC
70137 ATAAACGAAC
1 ATAAACGAAC
70147 ATAAAC
1 ATAAAC
70153 ATTGGAGACC
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:70154 original size:16 final size:16
Alignment explanation
Indices: 70083--70147 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
70073 TAATAAATAA
70083 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
70099 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
* *
70115 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
70131 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
70147 A
1 A
70148 TAAACATTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:70517 original size:10 final size:10
Alignment explanation
Indices: 70504--70558 Score: 56
Period size: 10 Copynumber: 5.1 Consensus size: 10
70494 TTAAACATAA
70504 ATAAACGAAC
1 ATAAACGAAC
70514 ATAAACGAAC
1 ATAAACGAAC
70524 ATAACCGAACGAAC
1 AT-A---AACGAAC
*
70538 ATAAACAAAC
1 ATAAACGAAC
*
70548 ATAACCGAAC
1 ATAAACGAAC
70558 A
1 A
70559 AACATAACCG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 27 0.71
11 1 0.03
13 1 0.03
14 9 0.24
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:70534 original size:14 final size:14
Alignment explanation
Indices: 70517--70572 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
70507 AACGAACATA
70517 AACGAACATAACCG
1 AACGAACATAACCG
70531 AACGAACAT-A---
1 AACGAACATAACCG
*
70541 AACAAACATAACCG
1 AACGAACATAACCG
*
70555 AACAAACATAACCG
1 AACGAACATAACCG
70569 AACG
1 AACG
70573 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.55, C:0.27, G:0.11, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:70534 original size:24 final size:24
Alignment explanation
Indices: 70507--70571 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
70497 AACATAAATA
70507 AACGAACATAAACGAACATAACCG
1 AACGAACATAAACGAACATAACCG
*
70531 AACGAACATAAACAAACATAACCG
1 AACGAACATAAACGAACATAACCG
* *
70555 AACAAACATAACCGAAC
1 AACGAACATAAACGAAC
70572 GTTCACGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.57, C:0.26, G:0.09, T:0.08
Consensus pattern (24 bp):
AACGAACATAAACGAACATAACCG
Found at i:71237 original size:14 final size:14
Alignment explanation
Indices: 71218--71247 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71208 GAACTCAACT
*
71218 TTTCCAGCTTACCA
1 TTTCCAGATTACCA
71232 TTTCCAGATTACCA
1 TTTCCAGATTACCA
71246 TT
1 TT
71248 CGTCGGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (14 bp):
TTTCCAGATTACCA
Found at i:72412 original size:34 final size:34
Alignment explanation
Indices: 72369--72446 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
72359 TTCCGCAAAA
*
72369 ATTAATATTTCGTATTCTCAATTTGTTCTCATCG
1 ATTAATATTTCATATTCTCAATTTGTTCTCATCG
*
72403 ATTAATATTTCATATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCATATTCTCAATTTGTTCTCATCG
72437 ATTAATATTT
1 ATTAATATTT
72447 ATGTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (34 bp):
ATTAATATTTCATATTCTCAATTTGTTCTCATCG
Found at i:73297 original size:36 final size:37
Alignment explanation
Indices: 73249--73347 Score: 152
Period size: 36 Copynumber: 2.8 Consensus size: 37
73239 AATTACATCC
*
73249 ACTTTAGC-TTAGGTAAAAGCTTAA-ATGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAATACGTAATATGA
73284 ACTTT-GACTTTAGGTAAAAGC-TAATACGTAATATGA
1 ACTTTAG-CTTTAGGTAAAAGCTTAATACGTAATATGA
73320 ACTTTAGCTTTAGGTAAAAGCTTAATAC
1 ACTTTAGCTTTAGGTAAAAGCTTAATAC
73348 TTATGAAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
34 1 0.02
35 9 0.16
36 41 0.71
37 7 0.12
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.34
Consensus pattern (37 bp):
ACTTTAGCTTTAGGTAAAAGCTTAATACGTAATATGA
Found at i:73370 original size:13 final size:13
Alignment explanation
Indices: 73352--73389 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
73342 TAATACTTAT
73352 GAAATAAAATTGA
1 GAAATAAAATTGA
73365 GAAATAAAATTGA
1 GAAATAAAATTGA
73378 GAAATAAAATTG
1 GAAATAAAATTG
73390 TTTAGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
GAAATAAAATTGA
Found at i:74373 original size:162 final size:159
Alignment explanation
Indices: 74100--74422 Score: 603
Period size: 162 Copynumber: 2.0 Consensus size: 159
74090 GTATATGCAC
74100 TACTCCCTAAGTCCAAGTAATATATCAAATAGGAAAAGGAACCCAAGGTTTGATGCAGAACACAA
1 TACTCCCTAAGTCCAAGTAATATATCAAATAGGAAAAGGAACCCAAGGTTTGATGCAGAACACAA
74165 CATAGATGTTTATCTTTCAAACAAACCCCTTTCTTTATACAGATGATGCAATAATGTCCAATTAG
66 CATAGATGTTTATCTTTCAAACAAACCCCTTTCTTTATACAGATGATGCAATAATGTCCAATTAG
74230 TCAGATGGTGACGTTGTTTGATTATATAA
131 TCAGATGGTGACGTTGTTTGATTATATAA
74259 TACTCCCTAAGTCCAAGTAATATATCAAATAGGAAAAGGAACCCAAGGTTTTGATGCAGAAGACA
1 TACTCCCTAAGTCCAAGTAATATATCAAATAGGAAAAGGAACCCAAGG-TTTGATGCAG-A-ACA
74324 CAACATAGATGTTTATCTTT-ACAACAAACCCCTTTCTTTATACAGATGATGCAATAATGTCCAA
63 CAACATAGATGTTTATCTTTCA-AACAAACCCCTTTCTTTATACAGATGATGCAATAATGTCCAA
74388 TTAGTCAGATGGTGACGTTGTTTGATTATATAA
127 TTAGTCAGATGGTGACGTTGTTTGATTATATAA
74421 TA
1 TA
74423 AATCCTTATT
Statistics
Matches: 160, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
159 48 0.30
160 10 0.06
161 2 0.01
162 100 0.62
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (159 bp):
TACTCCCTAAGTCCAAGTAATATATCAAATAGGAAAAGGAACCCAAGGTTTGATGCAGAACACAA
CATAGATGTTTATCTTTCAAACAAACCCCTTTCTTTATACAGATGATGCAATAATGTCCAATTAG
TCAGATGGTGACGTTGTTTGATTATATAA
Found at i:74576 original size:36 final size:36
Alignment explanation
Indices: 74529--74601 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
74519 TTCAAAATTT
74529 ATGGCATTTCAATTTCATCTTCCAAAGGAAAAAGTA
1 ATGGCATTTCAATTTCATCTTCCAAAGGAAAAAGTA
74565 ATGGCATTTCAATTTCATCTTCCAAAGGAAAAAGTA
1 ATGGCATTTCAATTTCATCTTCCAAAGGAAAAAGTA
74601 A
1 A
74602 CAAATGCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (36 bp):
ATGGCATTTCAATTTCATCTTCCAAAGGAAAAAGTA
Found at i:75048 original size:34 final size:34
Alignment explanation
Indices: 74965--75048 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
74955 CAATGCAGCA
* *
74965 TCCAAACAACGTAATTGGTTTTCTGGAATTGGTTT
1 TCCAAAAAAC-TAATTGGTTTTCTGGAATTGATTT
* **
75000 TCCAGAAATGTAATTGGTTTTCTGGAATTGATTT
1 TCCAAAAAACTAATTGGTTTTCTGGAATTGATTT
75034 TCCAAAAAACTAATT
1 TCCAAAAAACTAATT
75049 ACAGCCAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 35 0.85
35 6 0.15
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (34 bp):
TCCAAAAAACTAATTGGTTTTCTGGAATTGATTT
Found at i:80039 original size:20 final size:21
Alignment explanation
Indices: 79996--80039 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
79986 TGAGATGGTA
* *
79996 GTATCGATACATGTTCTTTGG
1 GTATCGATACATGTTCCTTAG
*
80017 GTATCGATA-TTGTTCCTTAG
1 GTATCGATACATGTTCCTTAG
80037 GTA
1 GTA
80040 ATGATACCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (21 bp):
GTATCGATACATGTTCCTTAG
Found at i:80657 original size:22 final size:22
Alignment explanation
Indices: 80632--80713 Score: 137
Period size: 22 Copynumber: 3.7 Consensus size: 22
80622 AGTGTGATAA
*
80632 CACTTTTGTATCAGTGCAGAGG
1 CACTTTTGTATCAGTGCTGAGG
80654 CACTTTTGTATCAGTGCTGAGG
1 CACTTTTGTATCAGTGCTGAGG
80676 CACTTTTGTATCAGTGCTGAGG
1 CACTTTTGTATCAGTGCTGAGG
* *
80698 CACTTTAGTATAAGTG
1 CACTTTTGTATCAGTG
80714 TTATGGCGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (22 bp):
CACTTTTGTATCAGTGCTGAGG
Found at i:83863 original size:25 final size:24
Alignment explanation
Indices: 83827--83890 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
83817 TCATTTCAAA
*
83827 ATTATAATTATATAA-AAAATATTT
1 ATTATATTTATA-AATAAAATATTT
83851 ATATATATTTATAAATAAAATATTT
1 AT-TATATTTATAAATAAAATATTT
*
83876 ATT-TATTTAGAAATA
1 ATTATATTTATAAATA
83891 TCAGAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 11 0.31
24 5 0.14
25 20 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTATATTTATAAATAAAATATTT
Found at i:85551 original size:3 final size:3
Alignment explanation
Indices: 85538--85589 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
85528 TAATTTTTTT
* * * * *
85538 TAA TAA CAA TAA TAA TATA TAA TAA TAA TTA TTA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
85584 TAA TAA
1 TAA TAA
85590 AATGGGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:85946 original size:124 final size:119
Alignment explanation
Indices: 85733--86013 Score: 336
Period size: 124 Copynumber: 2.3 Consensus size: 119
85723 TAAATTCTTC
* * * * *
85733 TCTT-TCTTCAGATGAGTTCTTCTCATTATGAAATTTTCGCTGGGGATGATGTTGACCTATTTCC
1 TCTTCTCTTCAGATGAGTTCTTCTCATTATG-AACTTTCTCTGGGGATGATGCTAACCTATATCC
* * *
85797 TTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTAT
65 TTCTATGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTAT
* * *
85852 TCTTTCTCCTTCATATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTAT
1 TC-TTCT-CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG---GGATGATGCTAACCTAT
* * * *
85917 ATGCTTCTATGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTT
61 ATCCTTCTATGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTAT
*
85976 TCTTCT-TT-AGATAAGTTCTTCTCATTATGAAC-TTCTCT
1 TCTTCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
86014 AAAATAAACT
Statistics
Matches: 139, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
119 8 0.06
120 24 0.17
121 13 0.09
122 24 0.17
123 4 0.03
124 66 0.47
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (119 bp):
TCTTCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGGGATGATGCTAACCTATATCCT
TCTATGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTAT
Found at i:86283 original size:116 final size:113
Alignment explanation
Indices: 85938--86543 Score: 692
Period size: 113 Copynumber: 5.4 Consensus size: 113
85928 ATAGAATTAT
* * ** * * *
85938 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-CTTCTTTAGATAAGTTCTTCTC
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * *
85999 ATTATGAACTTCT--CT-AAAATAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAAC-TCTAACTGGTAAT--GCTGATCCATCAAGTGATGAATTTAA
86047 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
86112 ATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTAACTGGTAATGCTGATCCATCAAGTGATGAATTTAA
* *
86160 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* * * * *
86225 CTCATTATGAACTCT-ACATGGCAATGTTAATCCATCAAATAATGAATTTAA
63 CTCATTATGAACTCTAAC-TGGTAATGCTGATCCATCAAGTGATGAATTTAA
* * *
86276 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
86341 ATTATGAACTCGAACTGGTAATGCTGATCCATTGAA-TGATGAATTCAA
66 ATTATGAACTCTAACTGGTAATGCTGATCCA-TCAAGTGATGAATTTAA
* * *
86389 GCAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGGTGAGTTCTTCT
1 GC-AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
86454 CATTATGAACTCTAACTGGTACTGTTGTTCCA-CTGAGTGATGAATTTAA
65 CATTATGAACTCTAACTGGTAATGCTGATCCATC-AAGTGATGAATTTAA
** *
86503 GCAAAAAGTTGAACATGTTCTTCTCATTATGAACTTTTTCT
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
86544 GGAAAAGTTG
Statistics
Matches: 434, Mismatches: 47, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
109 29 0.07
110 1 0.00
111 2 0.00
112 4 0.01
113 188 0.43
114 106 0.24
115 6 0.01
116 98 0.23
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTAACTGGTAATGCTGATCCATCAAGTGATGAATTTAA
Found at i:86533 original size:73 final size:73
Alignment explanation
Indices: 86445--86608 Score: 186
Period size: 73 Copynumber: 2.2 Consensus size: 73
86435 TCTTTAGGTG
* ** * * *
86445 AGTTCTTCTCATTATGAACTCTAACTGGTACTGTTGTTCC-ACTGAGTGATGAATTTAAGCAAAA
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGTTGATCCAAC-AAATGATGAATTTAAGCAAAA
86509 AGTTGAACA
65 AGTTGAACA
* * ** * * *
86518 TGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCAACAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGTTGATCCAACAAATGATGAATTTAAGCAAAAA
86583 GTTGAACA
66 GTTGAACA
*
86591 AATTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
86609 TTTCTTCTTC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
73 73 0.97
74 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCTAACTGGAAAAGTTGATCCAACAAATGATGAATTTAAGCAAAAA
GTTGAACA
Found at i:88865 original size:8 final size:8
Alignment explanation
Indices: 88852--88904 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
88842 TCTTGACCCC
88852 CTTTTTTT
1 CTTTTTTT
88860 C-TTTTTT
1 CTTTTTTT
88867 CTTTTTTGTT
1 C-TTTTT-TT
*
88877 CTTTTCTT
1 CTTTTTTT
*
88885 CTTTTCTT
1 CTTTTTTT
88893 -TTTTTTT
1 CTTTTTTT
88900 CTTTT
1 CTTTT
88905 CTCTTCAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 13 0.33
8 15 0.38
9 8 0.21
10 3 0.08
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
CTTTTTTT
Found at i:88872 original size:15 final size:15
Alignment explanation
Indices: 88852--88904 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 15
88842 TCTTGACCCC
88852 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
88867 CTTTTTTGTTCTTTTCTT
1 C-TTTTT-TTCTTTT-TT
88885 CTTTTCTTT-TTTTTT
1 CTTTT-TTTCTTTTTT
88900 CTTTT
1 CTTTT
88905 CTCTTCAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.24
16 9 0.26
17 13 0.38
18 4 0.12
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (15 bp):
CTTTTTTTCTTTTTT
Found at i:88889 original size:23 final size:22
Alignment explanation
Indices: 88856--88906 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
88846 GACCCCCTTT
88856 TTTTCTTTTTTCTTTTTTGTTC
1 TTTTCTTTTTTCTTTTTTGTTC
*
88878 TTTTCTTCTTTTCTTTTTTTTTC
1 TTTTCTT-TTTTCTTTTTTGTTC
88901 TTTTCT
1 TTTTCT
88907 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTTTTGTTC
Found at i:88905 original size:15 final size:15
Alignment explanation
Indices: 88856--88906 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
88846 GACCCCCTTT
88856 TTTTCTTTTTTCTT-
1 TTTTCTTTTTTCTTC
*
88870 TTTTGTTCTTTTCTTC
1 TTTTCTT-TTTTCTTC
*
88886 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTCTTC
88901 TTTTCT
1 TTTTCT
88907 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 6 0.19
15 20 0.62
16 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTCTTC
Found at i:96288 original size:16 final size:15
Alignment explanation
Indices: 96256--96284 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
96246 TGAATAATGA
96256 ATGTATGCAAAAAGT
1 ATGTATGCAAAAAGT
96271 ATGTATGCAAAAAG
1 ATGTATGCAAAAAG
96285 GTATTGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (15 bp):
ATGTATGCAAAAAGT
Found at i:99605 original size:32 final size:30
Alignment explanation
Indices: 99569--99633 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
99559 AAATACTTGC
99569 AAATAAAATGAAATATTAATAAGAAAATATAT
1 AAATAAAATGAAA-A-TAATAAGAAAATATAT
** * *
99601 AAATACTATGAAAATAATAAGTATATATAT
1 AAATAAAATGAAAATAATAAGAAAATATAT
99631 AAA
1 AAA
99634 AAATTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 17 0.59
31 1 0.03
32 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (30 bp):
AAATAAAATGAAAATAATAAGAAAATATAT
Found at i:99643 original size:30 final size:30
Alignment explanation
Indices: 99576--99644 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
99566 TGCAAATAAA
* *
99576 ATGAAATATTAATAAGAAAATATATAAATACT
1 ATGAAA-A-TAATAAGAAAATATATAAAAAAT
* *
99608 ATGAAAATAATAAGTATATATATAAAAAAT
1 ATGAAAATAATAAGAAAATATATAAAAAAT
*
99638 TTGAAAA
1 ATGAAAA
99645 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 25 0.78
31 1 0.03
32 6 0.19
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (30 bp):
ATGAAAATAATAAGAAAATATATAAAAAAT
Found at i:100158 original size:25 final size:24
Alignment explanation
Indices: 100122--100185 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
100112 TTATTTCAAA
*
100122 ATTATAATTATATAA-AAAATATTT
1 ATTATATTTATA-AATAAAATATTT
100146 ATATATATTTATAAATAAAATATTT
1 AT-TATATTTATAAATAAAATATTT
*
100171 ATT-TATTTAGAAATA
1 ATTATATTTATAAATA
100186 TCAGAAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 11 0.31
24 5 0.14
25 20 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTATATTTATAAATAAAATATTT
Found at i:101848 original size:3 final size:3
Alignment explanation
Indices: 101842--101911 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
101832 TATTTTTTTT
* * * *
101842 TAA TAA TAA TAA TAA TAA TATA TAA TAA TTA TAA TTA TTA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
101888 TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
101912 AATGGGTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:102458 original size:2 final size:2
Alignment explanation
Indices: 102446--102483 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
102436 TTAATATTAA
*
102446 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102484 TAACATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103397 original size:9 final size:9
Alignment explanation
Indices: 103366--103399 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
103356 TTAAATATAG
*
103366 TTTATTGAT
1 TTTATTTAT
*
103375 TTTAATTAT
1 TTTATTTAT
103384 TTTATTTAT
1 TTTATTTAT
103393 TTTATTT
1 TTTATTT
103400 CGTGTCCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:103808 original size:29 final size:28
Alignment explanation
Indices: 103776--103855 Score: 71
Period size: 29 Copynumber: 3.0 Consensus size: 28
103766 TTCTTTATAT
*
103776 ATAATCATTAAATTATTTTTATTTTAAAA
1 ATAATCATTAAATTATTTTTATTAT-AAA
* *
103805 ATAAT--TT-AATT-TTTATA-TATAAT
1 ATAATCATTAAATTATTTTTATTATAAA
*
103828 TTAATCATTAAATTATTTTTATATATAA
1 ATAATCATTAAATTATTTTTAT-TATAA
103856 TTTAGTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 7 0.17
26 8 0.20
27 7 0.17
29 10 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATCATTAAATTATTTTTATTATAAA
Found at i:103818 original size:18 final size:18
Alignment explanation
Indices: 103797--103832 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
103787 ATTATTTTTA
103797 TTTTAAAAATAATTTAAT
1 TTTTAAAAATAATTTAAT
* *
103815 TTTTATATATAATTTAAT
1 TTTTAAAAATAATTTAAT
103833 CATTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAAAATAATTTAAT
Found at i:103864 original size:18 final size:18
Alignment explanation
Indices: 103842--103891 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
103832 TCATTAAATT
103842 ATTTTTATATATAATTTA
1 ATTTTTATATATAATTTA
* * *
103860 GTTTTTTTAAATAATTTA
1 ATTTTTATATATAATTTA
**
103878 ATGATTATATATAA
1 ATTTTTATATATAA
103892 AAAATAATTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTTTTATATATAATTTA
Found at i:103921 original size:26 final size:25
Alignment explanation
Indices: 103868--103925 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
103858 TAGTTTTTTT
*
103868 AAATAATTTAATGATTATATATAAA
1 AAATAATTTAATAATTATATATAAA
*
103893 AAATAATTTAAATAATTATTTAATGAAA
1 AAATAATTT-AATAATTATAT-AT-AAA
103921 AAATA
1 AAATA
103926 TTTCAAGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 9 0.32
27 2 0.07
28 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
AAATAATTTAATAATTATATATAAA
Found at i:108151 original size:41 final size:41
Alignment explanation
Indices: 108094--108193 Score: 182
Period size: 41 Copynumber: 2.4 Consensus size: 41
108084 GCTAGTTCCT
*
108094 CGTCTAATTCAATGCATTTAATCCTACTGTTAAATGCAGCA
1 CGTCTAATTCAATGCATTTAATCCTACTATTAAATGCAGCA
108135 CGTCTAATTCAATGCATTTAATCCTACTATTAAATGCAGCA
1 CGTCTAATTCAATGCATTTAATCCTACTATTAAATGCAGCA
*
108176 CGTCTAATTCAACGCATT
1 CGTCTAATTCAATGCATT
108194 ATTTTTCTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (41 bp):
CGTCTAATTCAATGCATTTAATCCTACTATTAAATGCAGCA
Found at i:109959 original size:23 final size:23
Alignment explanation
Indices: 109927--109974 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
109917 AGAATAATTT
* *
109927 TGTCTATGTTGTACATTTATCTA
1 TGTCTATGTTGCACATTTATATA
*
109950 TGTCTGTGTTGCACATTTATATA
1 TGTCTATGTTGCACATTTATATA
109973 TG
1 TG
109975 GCTTTGTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (23 bp):
TGTCTATGTTGCACATTTATATA
Found at i:111226 original size:12 final size:13
Alignment explanation
Indices: 111209--111237 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
111199 TAATATTTAG
111209 CGGGTCGGGT-AT
1 CGGGTCGGGTAAT
111221 CGGGTCGGGTAAT
1 CGGGTCGGGTAAT
111234 CGGG
1 CGGG
111238 ACAGAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.10, C:0.17, G:0.52, T:0.21
Consensus pattern (13 bp):
CGGGTCGGGTAAT
Found at i:111295 original size:29 final size:30
Alignment explanation
Indices: 111253--111326 Score: 132
Period size: 29 Copynumber: 2.5 Consensus size: 30
111243 GATTACTAAA
111253 CCCGTCCCCGTTTAACATAAACGGTTTTT-
1 CCCGTCCCCGTTTAACATAAACGGTTTTTC
*
111282 CCCGTCCCCGTTTAGCATAAACGGTTTTTC
1 CCCGTCCCCGTTTAACATAAACGGTTTTTC
111312 CCCGTCCCCGTTTAA
1 CCCGTCCCCGTTTAA
111327 TTCGATTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 28 0.67
30 14 0.33
ACGTcount: A:0.18, C:0.35, G:0.15, T:0.32
Consensus pattern (30 bp):
CCCGTCCCCGTTTAACATAAACGGTTTTTC
Found at i:114618 original size:2 final size:2
Alignment explanation
Indices: 114611--114666 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
114601 TTCACTCATG
114611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
114653 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
114667 TTCGGTCTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.