Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006350.1 Hibiscus syriacus cultivar Beakdansim tig00015187_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: 66442
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:539 original size:38 final size:40
Alignment explanation
Indices: 450--597 Score: 212
Period size: 40 Copynumber: 3.8 Consensus size: 40
440 TTGCAGGTTT
** *
450 ACTTCGGTGTATATGGTGGGCACGCCCTTTTGTGTAATAC
1 ACTTCGGTGTATATGGTGGGCACAACCTTATGTGTAATAC
*
490 ACTTCGGTGTATATAGTGGGCACAACCTTATGTGT-A-AC
1 ACTTCGGTGTATATGGTGGGCACAACCTTATGTGTAATAC
* *
528 ACTTCGGTGTATATGGTGGGCACGACCTTATTTGTAATAC
1 ACTTCGGTGTATATGGTGGGCACAACCTTATGTGTAATAC
*
568 ACTTCGCTGTATATGGT-GGCACAACCTTAT
1 ACTTCGGTGTATATGGTGGGCACAACCTTAT
598 ATATAGCACG
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
38 34 0.35
39 14 0.14
40 49 0.51
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (40 bp):
ACTTCGGTGTATATGGTGGGCACAACCTTATGTGTAATAC
Found at i:579 original size:78 final size:77
Alignment explanation
Indices: 450--597 Score: 244
Period size: 78 Copynumber: 1.9 Consensus size: 77
440 TTGCAGGTTT
* *
450 ACTTCGGTGTATATGGTGGGCACGCCCTTTTGTGTAATACACTTCGGTGTATATAGTGGGCACAA
1 ACTTCGGTGTATATGGTGGGCACGACCTTTTGTGTAATACACTTCGCTGTATATAGT-GGCACAA
515 CCTTATGTGTAAC
65 CCTTATGTGTAAC
*
528 ACTTCGGTGTATATGGTGGGCACGACCTTATT-TGTAATACACTTCGCTGTATATGGTGGCACAA
1 ACTTCGGTGTATATGGTGGGCACGACCTT-TTGTGTAATACACTTCGCTGTATATAGTGGCACAA
592 CCTTAT
65 CCTTAT
598 ATATAGCACG
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
77 13 0.20
78 51 0.77
79 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (77 bp):
ACTTCGGTGTATATGGTGGGCACGACCTTTTGTGTAATACACTTCGCTGTATATAGTGGCACAAC
CTTATGTGTAAC
Found at i:750 original size:44 final size:44
Alignment explanation
Indices: 700--861 Score: 218
Period size: 44 Copynumber: 3.7 Consensus size: 44
690 GGTAAGCATG
*
700 AAAATAAGCTTCCGAGCTTATGGAATAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGT
* *
744 AAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGTT
1 AAAATAAGCTTACGAGCTTATGGAA-TAATGGTAAGTATATTGGT
* ** *
789 AAAAT-AGCTTACGAGATTATGGGTTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGT
* *
833 AAAATAAGCTTACAAGCTTATGGGATAAT
1 AAAATAAGCTTACGAGCTTATGGAATAAT
862 TGATACAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
44 64 0.62
45 39 0.38
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (44 bp):
AAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGT
Found at i:2410 original size:22 final size:22
Alignment explanation
Indices: 2384--2439 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2374 CCATCAGAGG
*
2384 GTATCGATACCACTATATAGTA
1 GTATCAATACCACTATATAGTA
2406 GTATCAATACCACTATATAGTA
1 GTATCAATACCACTATATAGTA
2428 GTATCAATACCA
1 GTATCAATACCA
2440 TCTGAGGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (22 bp):
GTATCAATACCACTATATAGTA
Found at i:17332 original size:18 final size:18
Alignment explanation
Indices: 17309--17350 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
17299 GCCCTTATCA
*
17309 TGTTGAAAGAATTAATTT
1 TGTTGAAAGAATTAATTC
17327 TGTTGAAAGAATTAATTC
1 TGTTGAAAGAATTAATTC
17345 TGTTGA
1 TGTTGA
17351 TATTTTAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (18 bp):
TGTTGAAAGAATTAATTC
Found at i:20498 original size:5 final size:5
Alignment explanation
Indices: 20472--20603 Score: 85
Period size: 5 Copynumber: 25.8 Consensus size: 5
20462 TCGTTCTATT
* * *
20472 TTTTA GTTTA TTTCA -TTCA TTTTA TTTTCA TTTTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A --TTTTA TTTTA TTTTA
* *
20519 TTTTA TTTCA TTTTA TTTT- TGTTT- TTTTA -TTTA TTTTAGCA CTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTT---A TTTTA
* * *
20565 TTTTTA TTCTA -TTTA TTTTG TTTTA ATTTA TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
20604 TCTCTGAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
4 15 0.15
5 72 0.71
6 5 0.05
7 1 0.01
8 8 0.08
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:20505 original size:32 final size:32
Alignment explanation
Indices: 20458--20538 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
20448 GGAGGCAACC
* *
20458 CATTTCGTTCTATTTTTTAGTTTATTTCA-TT
1 CATTTCATTTTATTTTTTAGTTTATTTCATTT
* * *
20489 CATTTTATTTTCATTTTTTATTTTATTTTATTT
1 CATTTCATTTT-ATTTTTTAGTTTATTTCATTT
*
20522 TATTTCATTTTATTTTT
1 CATTTCATTTTATTTTT
20539 GTTTTTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 8 0.20
32 22 0.54
33 11 0.27
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (32 bp):
CATTTCATTTTATTTTTTAGTTTATTTCATTT
Found at i:20508 original size:27 final size:27
Alignment explanation
Indices: 20478--20532 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
20468 TATTTTTTAG
20478 TTTATTTCA-TTCATTTTATTTTCATTT
1 TTTATTTCATTTCATTTTA-TTTCATTT
* *
20505 TTTATTTTATTTTATTTTATTTCATTT
1 TTTATTTCATTTCATTTTATTTCATTT
20532 T
1 T
20533 ATTTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTATTTCATTTCATTTTATTTCATTT
Found at i:20544 original size:38 final size:36
Alignment explanation
Indices: 20470--20556 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 36
20460 TTTCGTTCTA
*
20470 TTTTTTAGTTTATTTCATTCATTTTATTTTCATTTT
1 TTTTTTATTTTATTTCATTCATTTTATTTTCATTTT
* **
20506 TTATTTTATTTTATTTTATTTCATTTTATTTTTGTTTT
1 TT-TTTTATTTTATTTCA-TTCATTTTATTTTCATTTT
20544 TTTATTTATTTTA
1 TTT-TTTATTTTA
20557 GCACTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 2 0.05
37 14 0.32
38 28 0.64
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (36 bp):
TTTTTTATTTTATTTCATTCATTTTATTTTCATTTT
Found at i:25652 original size:10 final size:10
Alignment explanation
Indices: 25637--25672 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
25627 TTACAACAAG
25637 CTAGTACCAT
1 CTAGTACCAT
25647 CTAGTACCAT
1 CTAGTACCAT
*
25657 CTAGTA-CTT
1 CTAGTACCAT
25666 CTAGTAC
1 CTAGTAC
25673 TTCTAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (10 bp):
CTAGTACCAT
Found at i:26889 original size:183 final size:183
Alignment explanation
Indices: 26577--26926 Score: 628
Period size: 183 Copynumber: 1.9 Consensus size: 183
26567 ATTAAATCCG
26577 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
26642 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCAACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCAACTGCTT
*
26707 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTATCCCTC
131 TTATCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTATCCCTC
*
26760 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGGAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
26825 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCAACTGCTT
*
26890 TTATCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTATCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
26927 TAGTTAAACC
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 159 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCAACTGCTT
TTATCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTATCCCTC
Found at i:28305 original size:102 final size:105
Alignment explanation
Indices: 28121--28368 Score: 369
Period size: 102 Copynumber: 2.4 Consensus size: 105
28111 TTTTTCTTAA
* * * *
28121 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
*
28186 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
28225 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGAC
28287 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* *
28328 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
28369 TAAACATTGA
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 55 0.42
103 40 0.31
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:28358 original size:66 final size:66
Alignment explanation
Indices: 28252--28431 Score: 278
Period size: 66 Copynumber: 2.8 Consensus size: 66
28242 CTTGAGATAG
*
28252 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
28317 A
66 A
*
28318 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
28383 A
66 A
* * *
28384 TTTCCCTT-GAA-ATAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
28432 AAATTTTGTC
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
63 29 0.27
64 1 0.01
65 6 0.06
66 72 0.67
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:28461 original size:166 final size:169
Alignment explanation
Indices: 28148--28531 Score: 604
Period size: 166 Copynumber: 2.3 Consensus size: 169
28138 CTTGAGATAG
* * *
28148 TTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGAAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
*
28213 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
65 ACATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
*
28278 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
130 CCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* *
28318 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
28382 CATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
66 CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
28445 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
28484 TTTCCCTT-GAA-ATG-AA-TTT-TCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
28532 AATTTTGTCT
Statistics
Matches: 202, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
163 26 0.13
164 4 0.02
165 5 0.02
166 91 0.45
167 2 0.01
168 59 0.29
169 3 0.01
170 12 0.06
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:28527 original size:34 final size:35
Alignment explanation
Indices: 28484--28567 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
28474 ATTGAAAACA
** *
28484 TTTCCCTTGAAATGAATTTTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAATTTTCTCTCATTGAGACAG
*
28518 TTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAG
1 TTTCCCTTGAAACAAATTTTCTCTCA-TTGAGACAG
**
28554 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
28568 TAAACTTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 22 0.52
36 20 0.48
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTTCTCTCATTGAGACAG
Found at i:28556 original size:36 final size:34
Alignment explanation
Indices: 28216--28736 Score: 138
Period size: 37 Copynumber: 15.4 Consensus size: 34
28206 ATTGAAAACA
* * *
28216 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAA-CAAATTT-TCTCTCTTGAGACAG
*
28252 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAA-TTT-TCTCTCTTGAGACAG
* * * *
28289 TTTCTCTTGAAACATAA-----AC-ATTGAAAACA-
1 TTTCCCTTGAAACA-AATTTTCTCTCTTG-AGACAG
* *
28318 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAA-TTT-TCTCTCTTGAGACAG
* * * *
28355 TTTCTCTTGAAACATAA-----AC-ATTGAAAGCA-
1 TTTCCCTTGAAACA-AATTTTCTCTCTTGAGA-CAG
* * *
28384 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTCTCTCTTGAGACAG
* *
28418 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAA
1 TTTCCCTTGAAAC-AAA-TTT-TCTCTCTTGAGACAG
* * * *
28455 TTTCTCTTGAAACATAA-----AC-ATTGAAAACA-
1 TTTCCCTTGAAACA-AATTTTCTCTCTTG-AGACAG
** *
28484 TTTCCCTTGAAATGAATTTTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTCTCTCTTGAGACAG
*
28518 TTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAG
1 TTTCCCTTGAAACAAATTTTCTCTC--TTGAGACAG
** * *
28554 TTTCTATTGAAACATAA-----ACT-TTGAAAACAG
1 TTTCCCTTGAAACA-AATTTTCTCTCTTG-AGACAG
* *
28584 TTTCCCTTGAAACAAA----ATCT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTCTCTCTTGAGACA-G
* *
28613 TTTTACATT-AAACAAATTTCGTCTCTCTTGAGACAG
1 -TTTCCCTTGAAACAAATTT--TCTCTCTTGAGACAG
** *
28649 TTTCTTTTGAAACAAATTTTGTCTCTCTTAAGACATG
1 TTTCCCTTGAAACAAA-TTT-TCTCTCTTGAGACA-G
** * *
28686 TTTTTCTTAAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAA-TTT-TCTCTCTTGAGACAG
*
28723 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
28737 TCAATCCTTG
Statistics
Matches: 364, Mismatches: 67, Indels: 108
0.68 0.12 0.20
Matches are distributed among these distances:
28 6 0.02
29 61 0.17
30 42 0.12
32 2 0.01
33 6 0.02
34 42 0.12
35 11 0.03
36 71 0.20
37 103 0.28
38 20 0.05
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (34 bp):
TTTCCCTTGAAACAAATTTTCTCTCTTGAGACAG
Found at i:28581 original size:99 final size:100
Alignment explanation
Indices: 28318--28595 Score: 459
Period size: 100 Copynumber: 2.8 Consensus size: 100
28308 ATTGAAAACA
* *
28318 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
28383 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
*
28418 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
28483 ATTTCCCTTGAAATGAATTTTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
** * *
28518 TTTCCCTTGAAAC-AAATTTTGTCTCATTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
28582 AGTTTCCCTTGAAA
66 A-TTTCCCTTGAAA
28596 CAAAATCTTT
Statistics
Matches: 167, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
99 47 0.28
100 120 0.72
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (100 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
Found at i:28584 original size:30 final size:30
Alignment explanation
Indices: 28550--28608 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28540 CTCATTTGAG
*
28550 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
28580 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
28609 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:28701 original size:268 final size:262
Alignment explanation
Indices: 28146--28737 Score: 700
Period size: 268 Copynumber: 2.2 Consensus size: 262
28136 CGCTTGAGAT
** * *
28146 AGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGA
1 AGTTTCCCTTAAAACA-AAA-TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
28211 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
64 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
* * *
28276 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAACAAAATTTTGT
129 TCACTTGAGACAGTTTCTATTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAAA---T-T
*
28341 CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCATTTCCCTTGAAATAAATTGTCT
190 CT--CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCATTTCCCTTGAAACAAATTGTCT
* *
28406 CTCTTGAGAT
253 CTCTTAAGAC
* *
28416 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAA
1 AGTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
28481 ACATTTCCCTTGAAATGAA-TTT-TCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTC
66 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
* *
28543 ATTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAACAGTTTCCCTTGAAACAAAA-TCT-TT
131 ACTTGAGACAGTTTCTATTGAAACATAAACATTGAAAACA-TTTCCCTTGAAACAAAATTCTCTT
* * * * **
28606 GA-ATATGTTT-TACATT-AAACA-AATTTCGTCTCTCTTGAGA-CAGTTTCTTTTGAAACAAAT
195 GAGACA-GTTTCT-C-TTGAAACATAA-------AC-ATTGAAAGCA-TTTCCCTTGAAACAAA-
28666 TTTGTCTCTCTTAAGAC
247 -TTGTCTCTCTTAAGAC
**
28683 ATGTTTTTCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT
1 A-GTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT
28738 CAATCCTTGA
Statistics
Matches: 284, Mismatches: 22, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
257 5 0.02
258 14 0.05
259 2 0.01
261 3 0.01
264 3 0.01
265 66 0.23
266 44 0.15
267 18 0.06
268 111 0.39
269 3 0.01
270 15 0.05
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (262 bp):
AGTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
ACTTGAGACAGTTTCTATTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAAATTCTCTTG
AGACAGTTTCTCTTGAAACATAAACATTGAAAGCATTTCCCTTGAAACAAATTGTCTCTCTTAAG
AC
Found at i:28704 original size:38 final size:36
Alignment explanation
Indices: 28622--28736 Score: 151
Period size: 36 Copynumber: 3.1 Consensus size: 36
28612 GTTTTACATT
*
28622 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTT-TTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTT-TTCTTG
* *
28658 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTTTCTTG
* *
28695 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTTTCTTG
28732 AAACA
1 AAACA
28737 TCAATCCTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
36 27 0.39
37 22 0.32
38 20 0.29
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTTCTTG
Found at i:28841 original size:34 final size:34
Alignment explanation
Indices: 28776--28891 Score: 166
Period size: 34 Copynumber: 3.4 Consensus size: 34
28766 CCTTGATACA
28776 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC-AAAA-AAACCTTTGAAATT
*
28812 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
28846 GTTTCTCTTGAAACAC---AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
28877 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
28892 AATTTCGTCT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
34 29 0.38
35 4 0.05
36 16 0.21
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
Found at i:28938 original size:67 final size:67
Alignment explanation
Indices: 28846--29032 Score: 239
Period size: 67 Copynumber: 2.7 Consensus size: 67
28836 CTTTGAAAAT
*
28846 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
28911 CA
66 CA
* * * *
28913 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAG
* *
28978 GCC
65 ACA
* * * * *
28981 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
29033 CTGTCTTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
67 41 0.40
68 32 0.31
69 7 0.07
70 22 0.22
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:29541 original size:106 final size:107
Alignment explanation
Indices: 29350--29582 Score: 324
Period size: 106 Copynumber: 2.2 Consensus size: 107
29340 GGTTTTAGCT
*
29350 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAAAACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAAAACAAGTTCAACTTCACAA
*** *
29415 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTAACTGTCAACAAAACAATTTCCCAATTCC
* ** * * **
29456 GGAGCCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAAAACAAGTTCAACTTCACAA
*
29521 CGAAGGGACGGCTAACTGTCAACAAAACAATTTCCCAGTTCC
66 CGAAGGGACGGCTAACTGTCAACAAAACAATTTCCCAATTCC
* *
29563 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
29583 GACAGAAGAT
Statistics
Matches: 110, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
106 77 0.70
107 33 0.30
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAAAACAAGTTCAACTTCACAA
CGAAGGGACGGCTAACTGTCAACAAAACAATTTCCCAATTCC
Found at i:30949 original size:2 final size:2
Alignment explanation
Indices: 30942--30999 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
30932 ATTAATATTA
30942 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
30984 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
31000 TTAAGTATAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35860 original size:39 final size:39
Alignment explanation
Indices: 35817--35901 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
35807 GCATGAGAAA
35817 GCAGTTTTCATGAGTAGGATAAGAGCACATGAATGTAGT
1 GCAGTTTTCATGAGTAGGATAAGAGCACATGAATGTAGT
35856 GCAGTTTTCATGAGTAGGATAAGAGCACATGAATGTAGT
1 GCAGTTTTCATGAGTAGGATAAGAGCACATGAATGTAGT
35895 GCAGTTT
1 GCAGTTT
35902 CCAGGACAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (39 bp):
GCAGTTTTCATGAGTAGGATAAGAGCACATGAATGTAGT
Found at i:36243 original size:90 final size:89
Alignment explanation
Indices: 36131--36302 Score: 299
Period size: 90 Copynumber: 1.9 Consensus size: 89
36121 ATTTGCATCT
* *
36131 GCACACAACTTTCCATCATCTAGCACTTGGACTTTTTAGCCCTAACTCCATCATTCATCTACCAC
1 GCACACAACATTCCATCATCTAGCACTTGGACTTTTTAGCCCTAACTCCAT-ATACATCTACCAC
36196 CTGTATTCAGGGATGGATAAATCCA
65 CTGTATTCAGGGATGGATAAATCCA
* *
36221 GCACACAACATTCCATCTTCTAGTACTTGGACTTTTTAGCCCTAACTCCATATACATCTACCACC
1 GCACACAACATTCCATCATCTAGCACTTGGACTTTTTAGCCCTAACTCCATATACATCTACCACC
36286 TGTATTCAGGGATGGAT
66 TGTATTCAGGGATGGAT
36303 GGATCAAGAG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 48 0.62
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (89 bp):
GCACACAACATTCCATCATCTAGCACTTGGACTTTTTAGCCCTAACTCCATATACATCTACCACC
TGTATTCAGGGATGGATAAATCCA
Found at i:36711 original size:26 final size:27
Alignment explanation
Indices: 36682--36738 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
36672 CAATAATCTT
36682 TTTTAACAAGCATGA-ATAGAGTAA-AA
1 TTTTAACAAGCATGACA-AGAGTAACAA
* * *
36708 TTTTATCGAGCTTGACAAGAGTAACAA
1 TTTTAACAAGCATGACAAGAGTAACAA
36735 TTTT
1 TTTT
36739 TTGACAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (27 bp):
TTTTAACAAGCATGACAAGAGTAACAA
Found at i:37305 original size:3 final size:3
Alignment explanation
Indices: 37297--37405 Score: 175
Period size: 3 Copynumber: 36.7 Consensus size: 3
37287 TTTTTATCCA
* *
37297 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
37345 TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37393 TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TA
37406 AATATATTAA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 95 0.98
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39533 original size:24 final size:24
Alignment explanation
Indices: 39506--39577 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
39496 TAATTCTTTC
39506 TTTTCAAATTTTTTATATTTATTA
1 TTTTCAAATTTTTTATATTTATTA
* *
39530 TTTTTATAA-TATTTATATGTT-TTA
1 TTTTCA-AATTTTTTATAT-TTATTA
* * * *
39554 TTTGCAAGTATTTTATTTTTATTA
1 TTTTCAAATTTTTTATATTTATTA
39578 GTTATTTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
23 3 0.08
24 29 0.81
25 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTCAAATTTTTTATATTTATTA
Found at i:39543 original size:18 final size:18
Alignment explanation
Indices: 39520--39554 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39510 CAAATTTTTT
39520 ATATTTATTAT-TTTTATA
1 ATATTTA-TATGTTTTATA
39538 ATATTTATATGTTTTAT
1 ATATTTATATGTTTTAT
39555 TTGCAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTTATATGTTTTATA
Found at i:50180 original size:18 final size:16
Alignment explanation
Indices: 50155--50235 Score: 85
Period size: 17 Copynumber: 4.9 Consensus size: 16
50145 TTATGCTTGA
*
50155 AGAAAAGAAAGAAGAAG
1 AGAAAA-AAAAAAGAAG
50172 AGAAAAAGAAAAAGAA-
1 AGAAAAA-AAAAAGAAG
*
50188 AGAAACAAAAAAAAGAAA
1 AG-AA-AAAAAAAAGAAG
50206 AGAAAAAAAAAAGAAG
1 AGAAAAAAAAAAGAAG
*
50222 A-AAAAAAAATAGAA
1 AGAAAAAAAAAAGAA
50236 AAAGAAAAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
15 12 0.21
16 15 0.26
17 25 0.44
18 5 0.09
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (16 bp):
AGAAAAAAAAAAGAAG
Found at i:50181 original size:14 final size:12
Alignment explanation
Indices: 50154--50244 Score: 73
Period size: 13 Copynumber: 7.7 Consensus size: 12
50144 ATTATGCTTG
*
50154 AAGAAAAGAAAG
1 AAGAAAAGAAAA
*
50166 AAGAAGAG-AAA
1 AAGAAAAGAAAA
*
50177 AAG-AAA-AAGA
1 AAGAAAAGAAAA
*
50187 AAGAAACAAAAAA
1 AAGAAA-AGAAAA
50200 AAGAAAAGAAAA
1 AAGAAAAGAAAA
50212 AA-AAAAGAAGAA
1 AAGAAAAGAA-AA
* *
50224 AAAAAAATAGAAA
1 AAGAAAAGA-AAA
50237 AAGAAAAG
1 AAGAAAAG
50245 GGTCAAGGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
10 7 0.11
11 14 0.22
12 19 0.30
13 22 0.35
14 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (12 bp):
AAGAAAAGAAAA
Found at i:50186 original size:29 final size:26
Alignment explanation
Indices: 50154--50244 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 26
50144 ATTATGCTTG
50154 AAGAAAAGAAAGAAGAAGAGAAAAAGAAA
1 AAGAAAAGAAAGAA-AA-A-AAAAAGAAA
*
50183 AAG-AAAGAAACAAAAAAAAGAAAAGAAA
1 AAGAAAAG-AA-AGAAAAAA-AAAAGAAA
*
50211 AAAAAAAG-AAGAAAAAAAAATAGAAA
1 AAGAAAAGAAAGAAAAAAAAA-AGAAA
50237 AAGAAAAG
1 AAGAAAAG
50245 GGTCAAGGTG
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
25 3 0.06
26 19 0.36
27 2 0.04
28 15 0.28
29 11 0.21
30 3 0.06
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (26 bp):
AAGAAAAGAAAGAAAAAAAAAAGAAA
Found at i:50202 original size:13 final size:12
Alignment explanation
Indices: 50157--50243 Score: 61
Period size: 12 Copynumber: 7.2 Consensus size: 12
50147 ATGCTTGAAG
* *
50157 AAAAGAAAGAAG
1 AAAAGAAAAAAA
* *
50169 AAGAGAAAAAGA
1 AAAAGAAAAAAA
50181 AAAAGAAAGAAACA
1 AAAAGAAA-AAA-A
*
50195 AAAA-AAAGAAA
1 AAAAGAAAAAAA
*
50206 AGAA-AAAAAAA
1 AAAAGAAAAAAA
*
50217 AGAAGAAAAAAA
1 AAAAGAAAAAAA
*
50229 AATAGAAAAAGAA
1 AAAAGAAAAA-AA
50242 AA
1 AA
50244 GGGTCAAGGT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
11 14 0.23
12 32 0.53
13 9 0.15
14 5 0.08
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:50240 original size:18 final size:17
Alignment explanation
Indices: 50157--50243 Score: 86
Period size: 18 Copynumber: 4.9 Consensus size: 17
50147 ATGCTTGAAG
* *
50157 AAAAGAAAGAAGAAGAGA
1 AAAAGAAA-AAGAAAAAA
50175 AAAAGAAAAAGAAAGAAA
1 AAAAGAAAAAGAAA-AAA
*
50193 CAAA-AAAAAGAAAAGAA
1 AAAAGAAAAAGAAAA-AA
*
50210 AAAAAAAAGAAGAAAAAA
1 AAAAGAAA-AAGAAAAAA
50228 AAATAGAAAAAGAAAA
1 AAA-AGAAAAAGAAAA
50244 GGGTCAAGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
16 1 0.02
17 19 0.32
18 28 0.47
19 11 0.19
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAA
Found at i:51403 original size:82 final size:83
Alignment explanation
Indices: 51266--51818 Score: 863
Period size: 82 Copynumber: 6.7 Consensus size: 83
51256 AAACATTAAC
*
51266 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTTAGTTATCTGATCTGGTTGGA
1 TAGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
51330 CAGAA-CAATCATTGAATT
65 CAGAACCAATCATTGAATT
* *
51348 TAGAAAATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTTAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
* *
51413 AGAA-CAAACATT-AA-C
66 AGAACCAATCATTGAATT
*
51428 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTGGA
1 TAGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
51492 CAGAA-CAATCATTGAATT
65 CAGAACCAATCATTGAATT
51510 TAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
51575 AGAACCAATCATTGTGAGTT
66 AGAACCAATCA-T-TGAATT
*
51595 TAGAAGATGAATTTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
51660 AGAACCAATCATTGAGTT
66 AGAACCAATCATTGAATT
51678 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TAGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGG
51742 -CAGAACCAATCATTGAATT
64 ACAGAACCAATCATTGAATT
** * * *
51761 CGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 TAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
51819 ATTTAGTAGG
Statistics
Matches: 442, Mismatches: 18, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
79 1 0.00
80 71 0.16
81 4 0.01
82 140 0.32
83 139 0.31
84 7 0.02
85 80 0.18
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
TAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAACCAATCATTGAATT
Found at i:51522 original size:162 final size:163
Alignment explanation
Indices: 51254--51818 Score: 861
Period size: 162 Copynumber: 3.4 Consensus size: 163
51244 ATATCCTAGT
*
51254 CCAAACATT-AACTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTTAGTTATCT
1 CCAAACATTGAACTAGAAGATGAATTTGCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
*
51318 GATCTGGTTGGACAGAACAATCATTGAATTTAGAAAATGAATTTGCTCATAGCATCTTCTGGAAG
65 GATCTGGTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAG
*
51383 TGTTCTTTTAGTTATCTGATCTGGTTGGACAGAA
130 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
51417 -CAAACATT-AACTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATAT
1 CCAAACATTGAACTAGAAGATGAATTTGCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
51480 GATCTGGTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAG
65 GATCTGGTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAG
51545 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
130 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* ** *
51579 CCAATCATTGTGAGTTTAGAAGATGAATTTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTA
1 CCAAACA-T-TGA-ACTAGAAGATGAATTTGC-CATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
51644 TCTGATCTGGTTGGACAGAACCAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCT
62 TCTGATCTGGTTGGACAGAA-CAATCATTGAATTTAGAAGATGAATTTGCTC-ATAGCATCTTCT
51708 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAA
125 GGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAA
* * * * * *
51747 CCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAAACATTGAACT-AGAAGATGAATTTG-CCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
51812 TGATCTG
64 TGATCTG
51819 ATTTAGTAGG
Statistics
Matches: 375, Mismatches: 16, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
162 158 0.42
163 5 0.01
164 1 0.00
165 3 0.01
166 55 0.15
167 67 0.18
168 82 0.22
169 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (163 bp):
CCAAACATTGAACTAGAAGATGAATTTGCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGGTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGT
GTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:52732 original size:113 final size:114
Alignment explanation
Indices: 52534--53190 Score: 1108
Period size: 113 Copynumber: 5.7 Consensus size: 114
52524 TTAGCAAAGA
52534 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
52598 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
52647 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
52711 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
52760 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
52824 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
52873 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-T
52938 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
61 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
52992 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAG-AA-AGTTCATAATGAGAAGAA--C-T
*
53057 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG
61 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * ** *
53111 CTTGAATTCATC-ATTTGATGGAACATCATCCCCAGCAGAAAGTTCGTAATGAGAAGAACTCATC
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATC
* *
53175 TGGAGAA-AAAGAAGAA
65 TGAAGAAGGAAGAAGAA
53191 TTTATTCAAT
Statistics
Matches: 528, Mismatches: 8, Indels: 16
0.96 0.01 0.03
Matches are distributed among these distances:
113 271 0.51
114 12 0.02
115 2 0.00
116 18 0.03
117 17 0.03
118 23 0.04
119 185 0.35
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (114 bp):
CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:53334 original size:3 final size:3
Alignment explanation
Indices: 53326--53414 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
53316 TTTTTATCCA
* *
53326 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
53374 TAT TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53415 AAATATATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56071 original size:34 final size:36
Alignment explanation
Indices: 56031--56132 Score: 145
Period size: 34 Copynumber: 2.9 Consensus size: 36
56021 TTTCGTCCTA
* *
56031 CTAGGATTCAAACTACTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAAGATAGAATTTT
* *
56066 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAAGATAGAATTTT
56101 GCTAGGATTCAAACTCCTAAAAATAAGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAAGATAGA
56133 GTTATACTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 28 0.47
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAAGATAGAATTTT
Found at i:56563 original size:18 final size:17
Alignment explanation
Indices: 56524--56566 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
56514 ATTATATGGA
56524 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
56540 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
56558 TATTATTAT
1 TATTATTAT
56567 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:56597 original size:62 final size:62
Alignment explanation
Indices: 56531--56647 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 62
56521 GGATATTTTA
* * *
56531 TTCATTTA-TTTTTATTATTCATGTTATTA-TTATTATATGTATATATATATATATAAATTATT
1 TTCATTTATTTTTTACTA-T-ATGTTACTATTTATTATATATATATATATATATATAAATTATT
*
56593 TTCATTTATTTTTTACTATATTTTACTATTTATTATATATATATATATATATATA
1 TTCATTTATTTTTTACTATATGTTACTATTTATTATATATATATATATATATATA
56648 TATATATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 7 0.14
62 34 0.69
63 8 0.16
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (62 bp):
TTCATTTATTTTTTACTATATGTTACTATTTATTATATATATATATATATATATAAATTATT
Found at i:56633 original size:2 final size:2
Alignment explanation
Indices: 56626--56660 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56616 TACTATTTAT
56626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56661 TCTTTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60851 original size:16 final size:16
Alignment explanation
Indices: 60825--60900 Score: 61
Period size: 16 Copynumber: 4.8 Consensus size: 16
60815 AGATCCAATC
60825 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAGAA
60840 AAGAAGCAAAAAAGCAA
1 AAGAAGCAAAAAAG-AA
**
60857 AA-AAAAAAACAAAGAA
1 AAGAAGCAAA-AAAGAA
*
60873 AAGAAAG-AACAAAAAAA
1 AAG-AAGCAA-AAAAGAA
60890 AAG-AGCAAAAA
1 AAGAAGCAAAAA
60901 TCAAAAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
15 10 0.20
16 19 0.38
17 18 0.36
18 3 0.06
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:60865 original size:13 final size:13
Alignment explanation
Indices: 60847--60913 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
60837 GAAAAGAAGC
60847 AAAAAAGCAAAAA
1 AAAAAAGCAAAAA
60860 AAAAAA-CAAAGAA
1 AAAAAAGCAAA-AA
*
60873 AAGAAAGAACAAAAA
1 AA-AAA-AGCAAAAA
*
60888 AAAAGAGCAAAAA
1 AAAAAAGCAAAAA
*
60901 TCAAAAAG-AAAAA
1 -AAAAAAGCAAAAA
60914 GGGACAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 4 0.09
13 22 0.49
14 10 0.22
15 5 0.11
16 4 0.09
ACGTcount: A:0.81, C:0.07, G:0.10, T:0.01
Consensus pattern (13 bp):
AAAAAAGCAAAAA
Found at i:60874 original size:9 final size:8
Alignment explanation
Indices: 60831--60891 Score: 54
Period size: 8 Copynumber: 7.5 Consensus size: 8
60821 AATCAAGAAC
60831 AAAAAAGA
1 AAAAAAGA
* *
60839 AAAGAAGC
1 AAAAAAGA
60847 AAAAAAGCA
1 AAAAAAG-A
60856 AAAAAA-A
1 AAAAAAGA
60863 AAACAAAGA
1 AAA-AAAGA
60872 AAAGAAAGA
1 AAA-AAAGA
*
60881 ACAAAA-A
1 AAAAAAGA
60888 AAAA
1 AAAA
60892 GAGCAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
7 8 0.19
8 18 0.42
9 17 0.40
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:60885 original size:28 final size:26
Alignment explanation
Indices: 60825--60891 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
60815 AGATCCAATC
* * *
60825 AAGAACAAAAAAGAAAAGAAGCAAAA
1 AAGAACAAAAAAAAAAAAAAGAAAAA
60851 AAG--CAAAAAAAAAAACAAAGAAAAGA
1 AAGAACAAAAAAAAAAA-AAAGAAAA-A
60877 AAGAACAAAAAAAAA
1 AAGAACAAAAAAAAA
60892 GAGCAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 11 0.32
25 6 0.18
26 7 0.21
28 10 0.29
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (26 bp):
AAGAACAAAAAAAAAAAAAAGAAAAA
Found at i:60899 original size:25 final size:24
Alignment explanation
Indices: 60825--60900 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 24
60815 AGATCCAATC
60825 AAGAACAAAAAAGAAAAGAAGC-AAAA
1 AAGAAC-AAAAA-AAAAG-AGCAAAAA
* *
60851 AAGCAAAAAAAAAAACAAAG-AAAAGA
1 AAG-AACAAAAAAAA-AGAGCAAAA-A
60877 AAGAACAAAAAAAAAGAGCAAAAA
1 AAGAACAAAAAAAAAGAGCAAAAA
60901 TCAAAAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
24 4 0.10
25 22 0.54
26 13 0.32
27 2 0.05
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (24 bp):
AAGAACAAAAAAAAAGAGCAAAAA
Found at i:61561 original size:22 final size:22
Alignment explanation
Indices: 61533--61587 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
61523 GCTATCCCAT
61533 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
61555 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
61577 CAAACCTTTGA
1 CAAACCTTTGA
61588 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:62017 original size:17 final size:18
Alignment explanation
Indices: 61995--62029 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
61985 TCAACATCAA
*
61995 ATATTGGGGCAT-TTTGG
1 ATATTGAGGCATCTTTGG
62012 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
62030 GGATTCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:62594 original size:36 final size:36
Alignment explanation
Indices: 62503--62783 Score: 321
Period size: 36 Copynumber: 8.0 Consensus size: 36
62493 ACTAGAAGAG
62503 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
62539 -TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
62574 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
62610 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
62646 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* ** * *
62675 TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
62712 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
62747 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
62784 CTTTAAATTT
Statistics
Matches: 205, Mismatches: 27, Indels: 25
0.80 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 40 0.20
36 106 0.52
37 36 0.18
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:62908 original size:66 final size:65
Alignment explanation
Indices: 62741--62911 Score: 197
Period size: 66 Copynumber: 2.6 Consensus size: 65
62731 GTTTCTCTTG
** * *
62741 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAAC--AAACTTTAAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAACTTCAAATTTATTTCCCCT
62803 A
65 A
* * *
62804 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACAAAAATCTTCAAATTTA-TTCCCTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAA-CTTCAAATTTATTTCCCCT
62868 A
65 A
* * *
62869 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
62912 CAGATATCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
63 28 0.31
64 6 0.07
65 15 0.16
66 42 0.46
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAACTTCAAATTTATTTCCCCTA
Found at i:63934 original size:104 final size:104
Alignment explanation
Indices: 63507--64193 Score: 993
Period size: 103 Copynumber: 6.6 Consensus size: 104
63497 GCCATCTGCG
* * * * * * *
63507 ATTTCAACTCCACGACGGAGGATATCGGGCACTCGAGACAACACAAGTTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT-TGG-ACTCCAGACAACGCAAG-TTCAACTTCACGACGAA
*
63572 GGGA-CGACTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAACAACAACTTC-CAATTTCAGAGCCA
*
63615 ATTTCAACTTCACAACGAA--ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63678 ACCGCTGCCTGTCAACAACAACTTCTCAATTTC--AGCCA
66 ACCGCTGCTTGTCAACAACAACTTC-CAATTTCAGAGCCA
63716 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
63781 ACCGCTGCTTGTCAACAATAACTTCTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTTCAGAGCCA
*
63820 ATTTCAACTTCACAAC-AAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63884 ACCGCTGCTTGTCAACAACAACTTCCCATTCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATT-TCAGAGCCA
* *
63924 ATTTCAACTTCACAACGAAGGATATTGGACTCCATAC-ATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
63988 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTT-CCAATTTCAGAGCCA
* *
64028 ATTTCAATTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
64093 ACCGCTGCTTGTCAACAA-AA-TTTC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTTCAGAGCCA
* * *
64128 ATTTCAACTTCACAACGAAGGAT-TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
64192 AC
66 AC
64194 GACTTTGACA
Statistics
Matches: 534, Mismatches: 36, Indels: 27
0.89 0.06 0.05
Matches are distributed among these distances:
99 39 0.07
100 29 0.05
101 25 0.05
102 7 0.01
103 188 0.35
104 158 0.30
105 68 0.13
106 4 0.01
108 16 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCAATTTCAGAGCCA
Found at i:64820 original size:37 final size:36
Alignment explanation
Indices: 64741--64839 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 36
64731 TTTCGTCCTA
* *
64741 CTAGGATTCAAACTACTAAAAAT-GGAT-AGAGTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAAGTTT
*
64775 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAAGTTT
64810 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
64840 GTTATACTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
33 21 0.36
34 4 0.07
35 5 0.09
37 28 0.48
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAAGTTT
Found at i:64861 original size:70 final size:69
Alignment explanation
Indices: 64741--64871 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 69
64731 TTTCGTCCTA
* *
64741 CTAGGATTCAAACTACTAAAAATGGATAGAGTTTTAGGATTCAAACTCCTAAAAATAGGATAAAA
1 CTAGGATTCAAACTACTAAAAATGGATA-AGTTATACGATTCAAACTCCTAAAAATAGGATAAAA
64806 TTTTG
65 TTTTG
* * * * *
64811 CTAGGATTCAAACTCCTAAAAATAGGAT-AGTTATACTATTATAAATTCCTAAAGATAGGAT
1 CTAGGATTCAAACTACTAAAAAT-GGATAAGTTATACGATT-CAAACTCCTAAAAATAGGAT
64872 CCACAAGCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 9 0.17
70 39 0.75
71 4 0.08
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (69 bp):
CTAGGATTCAAACTACTAAAAATGGATAAGTTATACGATTCAAACTCCTAAAAATAGGATAAAAT
TTTG
Done.