Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009160.1 Hibiscus syriacus cultivar Beakdansim tig00112688_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: 458650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:228805 original size:23 final size:23
Alignment explanation
Indices: 228775--228825 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
228765 ATTACCTATT
*
228775 TTACATTATATAAGCGCTACCTA
1 TTACATTATATAAGCGATACCTA
228798 TTACATTATATAAGCGATACCTA
1 TTACATTATATAAGCGATACCTA
228821 TTACA
1 TTACA
228826 ATAAGCGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (23 bp):
TTACATTATATAAGCGATACCTA
Found at i:228831 original size:19 final size:21
Alignment explanation
Indices: 228781--228841 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
228771 TATTTTACAT
*
228781 TATATAAGCGCTACCTATTAC
1 TATATAAGCGATACCTATTAC
228802 ATTATATAAGCGATACCTATTAC
1 --TATATAAGCGATACCTATTAC
* *
228825 -A-ATAAGCGCTACATATT
1 TATATAAGCGATACCTATT
228842 GTAAAGGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.40
20 1 0.03
23 20 0.57
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (21 bp):
TATATAAGCGATACCTATTAC
Found at i:234407 original size:14 final size:15
Alignment explanation
Indices: 234375--234407 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
234365 CTAGATCGCA
234375 TTTATTTTATTCGAG
1 TTTATTTTATTCGAG
*
234390 TTTATTTTTTTC-AG
1 TTTATTTTATTCGAG
234404 TTTA
1 TTTA
234408 CATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (15 bp):
TTTATTTTATTCGAG
Found at i:235034 original size:21 final size:20
Alignment explanation
Indices: 235007--235104 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
234997 AATCAGTTTC
235007 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
235028 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
235049 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
235069 CCAGAATCGCAACGCGA-TAT
1 -CAAAATCGCAACGCGATTTT
*
235089 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
235105 ACACATAATC
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 14 0.24
20 3 0.05
21 42 0.71
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:235150 original size:20 final size:20
Alignment explanation
Indices: 235073--235260 Score: 185
Period size: 19 Copynumber: 9.6 Consensus size: 20
235063 GATTTTCCAG
*
235073 AATCGCAACGCGATAT--GAA
1 AATCGCAACGCG-TATCCGTA
* *
235092 AATCGCAACGCG-AACACAT-
1 AATCGCAACGCGTATC-CGTA
235111 AATCGCAACGCGTA-CCGTA
1 AATCGCAACGCGTATCCGTA
*
235130 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
235150 AATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
*
235169 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
235189 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
235209 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
* *
235230 AATCGCAACGAGAATCCGT-
1 AATCGCAACGCGTATCCGTA
235249 AATCGCAACGCG
1 AATCGCAACGCG
235261 ATATTTAAAG
Statistics
Matches: 141, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
17 1 0.01
18 2 0.01
19 68 0.48
20 55 0.39
21 15 0.11
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:235160 original size:39 final size:40
Alignment explanation
Indices: 235073--235260 Score: 185
Period size: 39 Copynumber: 4.8 Consensus size: 40
235063 GATTTTCCAG
* * *
235073 AATCGCAACGCGATAT--GAAAATCGCAACGCG-AACACAT-
1 AATCGCAACGCG-TATCCGTAAATCGCAACGCGTATC-CGTA
*
235111 AATCGCAACGCGTA-CCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
235150 AATCGCAACGCGTATCCGT-AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* * * *
235189 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGT-A
* *
235230 AATCGCAACGAGAATCCGT-AATCGCAACGCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG
235261 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
37 2 0.02
38 27 0.21
39 53 0.42
40 27 0.21
41 17 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:235676 original size:33 final size:33
Alignment explanation
Indices: 235637--235707 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
235627 TTCACTTAGA
235637 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
235670 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
235703 TTTCA
1 TTTCA
235708 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:235845 original size:14 final size:14
Alignment explanation
Indices: 235826--235882 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
235816 TTTGGTTTCG
235826 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
235840 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
235859 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
235873 CGTTGCGATT
1 CGTTGCGATT
235883 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:235851 original size:33 final size:33
Alignment explanation
Indices: 235809--235931 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
235799 AAATGAAAAA
**
235809 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
235842 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
235875 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
235916 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
235932 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 43 0.54
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.27
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:235893 original size:21 final size:21
Alignment explanation
Indices: 235867--235931 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
235857 CGCGTTGCGA
235867 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
235888 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
235908 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
235929 TTC
1 TTC
235932 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:237917 original size:93 final size:93
Alignment explanation
Indices: 237615--238267 Score: 1249
Period size: 93 Copynumber: 7.1 Consensus size: 93
237605 TAGATTGCTT
* *
237615 AGTAAATTTATTCGGTTGCTGCCATTTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
237680 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
237708 AGTAAATTTGTTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
237772 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
237799 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
237864 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
237892 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
237957 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
237985 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
238050 TTTATCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238078 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238143 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238171 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238236 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238263 AGTAA
1 AGTAA
238268 TGCAATCCAT
Statistics
Matches: 552, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 46 0.08
92 96 0.17
93 410 0.74
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:238352 original size:19 final size:19
Alignment explanation
Indices: 238312--238440 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
238302 TAGTTTACTT
* *
238312 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
238332 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
238351 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
238370 TCGCAA--C-AAA--AGAA
1 TCGCAACGCGAAACCAAAA
238384 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
238403 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
238417 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
238436 TCGCA
1 TCGCA
238441 TTGCGATTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 46 0.49
20 13 0.14
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:238386 original size:33 final size:33
Alignment explanation
Indices: 238347--238440 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
238337 ACGCGAAACC
**
238347 AAAATCGCAACGCGAAATGAAAATCGCAAC-AA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAA
*
238379 AAGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AA-AATCGCAACGCGAAACCAAAATCGCAACGAA
238413 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
238441 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 52 0.91
34 3 0.05
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAA
Found at i:238417 original size:14 final size:14
Alignment explanation
Indices: 238398--238424 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
238388 AACGCGAAAC
238398 CAAAATCGCAACGA
1 CAAAATCGCAACGA
238412 CAAAATCGCAACG
1 CAAAATCGCAACG
238425 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:238438 original size:52 final size:52
Alignment explanation
Indices: 238312--238440 Score: 147
Period size: 52 Copynumber: 2.5 Consensus size: 52
238302 TAGTTTACTT
** *
238312 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACAAAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
* *
238364 T-G-AAAATCGCAACAAAAGAATCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACA-CGAAACAAAA-AATCGCAACGCGAAACCAAAATCGCAACG-CAAAA
* *
238417 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACAAAAAATCGCA
238441 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
50 3 0.05
51 8 0.13
52 37 0.59
53 7 0.11
54 6 0.10
55 2 0.03
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACAAAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
Found at i:238458 original size:19 final size:19
Alignment explanation
Indices: 238436--238608 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
238426 GAAACCAAAA
*
238436 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
238455 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
238471 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
238488 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
238504 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
238521 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
238540 TCGCGTTGCGATTTTTGTT
1 TCGCGTTGCGATTTTCATT
* *
238559 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
238578 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
238598 TCGTGTTGCGA
1 TCGCGTTGCGA
238609 AAGTAAACTA
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 78 0.61
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:238477 original size:14 final size:14
Alignment explanation
Indices: 238458--238514 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
238448 TTTCATTTCG
238458 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
238472 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
238489 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
238505 CGTTGCGATT
1 CGTTGCGATT
238515 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:238566 original size:38 final size:38
Alignment explanation
Indices: 238436--238608 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
238426 GAAACCAAAA
*
238436 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
238471 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
238504 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
238540 TCGCGTTGCGATTTTTGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
238578 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
238609 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:240538 original size:14 final size:14
Alignment explanation
Indices: 240519--240557 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
240509 ATTGTTTAAT
240519 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
240533 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
240547 TGATTGTGTAA
1 TGATT-TGTAA
240558 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:240667 original size:19 final size:19
Alignment explanation
Indices: 240643--240763 Score: 145
Period size: 19 Copynumber: 6.8 Consensus size: 19
240633 GCATTATGTT
240643 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
240662 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
240679 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
240695 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
240712 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
240728 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
240747 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
240764 CGAGAGAATC
Statistics
Matches: 87, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
14 20 0.23
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 39 0.45
20 16 0.18
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:240689 original size:14 final size:14
Alignment explanation
Indices: 240670--240724 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
240660 GCGAAATGAA
240670 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
240684 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
240703 AATCGCAACGAGAG
1 AATCGCAACGAGAG
240717 AATCGCAA
1 AATCGCAA
240725 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:240693 original size:33 final size:33
Alignment explanation
Indices: 240651--240743 Score: 186
Period size: 33 Copynumber: 2.8 Consensus size: 33
240641 TTGAAATGAA
240651 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
240684 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
240717 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
240744 TGCGGAAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:240835 original size:14 final size:14
Alignment explanation
Indices: 240816--240870 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
240806 CATTTCCGCA
240816 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
240830 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
240847 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
240863 TTGCGATT
1 TTGCGATT
240871 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:240841 original size:53 final size:53
Alignment explanation
Indices: 240830--240995 Score: 291
Period size: 53 Copynumber: 3.2 Consensus size: 53
240820 GATTCTCTCG
240830 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
240882 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* *
240935 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
240988 TTGCGATT
1 TTGCGATT
240996 CTCTCGTTGC
Statistics
Matches: 110, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
52 15 0.14
53 94 0.85
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:240848 original size:86 final size:86
Alignment explanation
Indices: 240758--240934 Score: 273
Period size: 86 Copynumber: 2.1 Consensus size: 86
240748 GAAATGAAAA
240758 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
240823 TCTCTCGTTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATT
** * *** * **
240844 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
240909 TCTCTCGTTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATT
240930 TCGCA
1 TCGCA
240935 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.41
Consensus pattern (86 bp):
TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
TCTCTCGTTGCGATTTTCATT
Found at i:240935 original size:86 final size:90
Alignment explanation
Indices: 240778--241009 Score: 358
Period size: 86 Copynumber: 2.7 Consensus size: 90
240768 AGAATCGCAA
240778 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
240843 TTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTCATCTCCGAT
240864 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
240929 TTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGA-TTTCATCTCCG-AT
*
240956 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
241010 GTAATTTCCG
Statistics
Matches: 138, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
86 103 0.75
87 14 0.10
88 3 0.02
89 3 0.02
90 3 0.02
92 12 0.09
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (90 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTCATCTCCGAT
Found at i:241017 original size:33 final size:33
Alignment explanation
Indices: 240796--241009 Score: 220
Period size: 33 Copynumber: 6.2 Consensus size: 33
240786 TCATTTCGCA
240796 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
240830 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
240863 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
240900 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
240935 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
240969 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
241002 TTGCGATT
1 TTGCGATT
241010 GTAATTTCCG
Statistics
Matches: 150, Mismatches: 15, Indels: 31
0.77 0.08 0.16
Matches are distributed among these distances:
31 4 0.03
32 7 0.05
33 77 0.51
34 31 0.21
35 4 0.03
36 3 0.02
37 2 0.01
38 2 0.01
39 8 0.05
40 3 0.02
41 9 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:241024 original size:53 final size:53
Alignment explanation
Indices: 240830--241028 Score: 196
Period size: 53 Copynumber: 3.8 Consensus size: 53
240820 GATTCTCTCG
* *
240830 TTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GTTGCGATTTTCATTTCGCA
* *
240882 TTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GTTGCGATTTTCATTTCGCA
* * * *
240935 TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
* * *
240988 TTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTGCGAT
1 TTGCGATT-T-TCAGTTCCGCATTGCAATTTCCATGTTGCGAT
241029 AGTCAAATGC
Statistics
Matches: 132, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
52 12 0.09
53 110 0.83
54 8 0.06
55 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
Found at i:244241 original size:20 final size:20
Alignment explanation
Indices: 244213--244441 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
244203 AAATTTCAGT
* * *
244213 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
244233 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
244253 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
244273 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
244293 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
244313 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
244333 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
244353 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
244373 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
244393 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
244413 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
244433 GTTGCGATT
1 GTTGCGATT
244442 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:245030 original size:23 final size:23
Alignment explanation
Indices: 245004--245057 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
244994 AACAAGTTAG
*
245004 AAAATATTTATA-TATTTTCTTTA
1 AAAATATTTAAATTATTTT-TTTA
245027 AAAA-ATTTAAATTATTTTTTTA
1 AAAATATTTAAATTATTTTTTTA
* *
245049 TATATATTT
1 AAAATATTT
245058 TTTTACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAAATATTTAAATTATTTTTTTA
Found at i:252534 original size:6 final size:6
Alignment explanation
Indices: 252516--252584 Score: 77
Period size: 6 Copynumber: 11.5 Consensus size: 6
252506 TATATGGTAA
* * * *
252516 TGTATG T-TAATG TGTATG TGTGTG TGAATG TGTATG TGTTTG TATATG
1 TGTATG TGT-ATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
*
252564 TGTATG TGTACG TGTATG TGT
1 TGTATG TGTATG TGTATG TGT
252585 TGGTCTTTCG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
5 1 0.02
6 49 0.96
7 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.49
Consensus pattern (6 bp):
TGTATG
Found at i:253501 original size:20 final size:20
Alignment explanation
Indices: 253476--253529 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
253466 GACTAACAAA
253476 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
253496 TTCGCAAC-CCAATTTCTAAT
1 TTCGCAACGCGAA-TTCCAAT
253516 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
253530 ATGTAAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:253561 original size:21 final size:21
Alignment explanation
Indices: 253537--253580 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
253527 AATATGTAAA
*
253537 TCACATTGTGATTTTCCAAAT
1 TCACATTGCGATTTTCCAAAT
*
253558 TCACGTTGCGATTTTCCAAAT
1 TCACATTGCGATTTTCCAAAT
253579 TC
1 TC
253581 GCAACGCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (21 bp):
TCACATTGCGATTTTCCAAAT
Found at i:253589 original size:21 final size:21
Alignment explanation
Indices: 253472--253590 Score: 55
Period size: 20 Copynumber: 5.8 Consensus size: 21
253462 AAATGACTAA
*
253472 CAAATTCGCAACGCGA-ATTC
1 CAAATTCGCAACGCGATTTTC
* * *
253492 CAATTTCGCAAC-CCAATTTC
1 CAAATTCGCAACGCGATTTTC
* * * * *
253512 TAATTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGATTTTC
* * ** *
253533 TAAA-TCACATTGTGATTTTC
1 CAAATTCGCAACGCGATTTTC
* ***
253553 CAAATTCACGTTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
253574 CAAATTCGCAACGCGAT
1 CAAATTCGCAACGCGAT
253591 AGTCAAATTC
Statistics
Matches: 74, Mismatches: 22, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
19 2 0.03
20 37 0.50
21 35 0.47
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:253599 original size:20 final size:19
Alignment explanation
Indices: 253574--253639 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
253564 TGCGATTTTC
*
253574 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACGA-AGT
*
253594 CAAATTCACAACAC-AAGT
1 CAAATTCGCAACACGAAGT
*
253612 CAAATTCGCAACTCGAAAGT
1 CAAATTCGCAACACG-AAGT
*
253632 CAATTTCG
1 CAAATTCG
253640 GAACTGAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
20 23 0.59
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACACGAAGT
Found at i:254445 original size:12 final size:12
Alignment explanation
Indices: 254424--254457 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
254414 ACCACATTTC
*
254424 CAATACCAAACA
1 CAATATCAAACA
254436 CAATATCAAACA
1 CAATATCAAACA
*
254448 CAATCTCAAA
1 CAATATCAAA
254458 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:254633 original size:24 final size:24
Alignment explanation
Indices: 254582--254635 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
254572 GTATTCGAAA
* *
254582 TTTGATCTTGGTCAATATCCGGAC
1 TTTGATCTTGATCAATATCCAGAC
*
254606 TTTGATCTTGATCAATA-CTCAGAT
1 TTTGATCTTGATCAATATC-CAGAC
254630 TTTGAT
1 TTTGAT
254636 GATGTGATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGATCAATATCCAGAC
Found at i:256918 original size:18 final size:18
Alignment explanation
Indices: 256885--256920 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
256875 AAGCAAAAGG
* *
256885 AAATCAAAATCGCAATCA
1 AAATCAAAACCCCAATCA
256903 AAATCAAAACCCCAATCA
1 AAATCAAAACCCCAATCA
256921 CAACCGGCTT
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:0.56, C:0.28, G:0.03, T:0.14
Consensus pattern (18 bp):
AAATCAAAACCCCAATCA
Found at i:257295 original size:20 final size:20
Alignment explanation
Indices: 257246--257303 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
257236 TAAGCGTTGT
257246 GATAGTCAAATTTGCAACGC
1 GATAGTCAAATTTGCAACGC
* * *
257266 AAAAGACAAATTTGCAACGC
1 GATAGTCAAATTTGCAACGC
*
257286 GATAGTCAAATTCGCAAC
1 GATAGTCAAATTTGCAAC
257304 TCGAAATCAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
GATAGTCAAATTTGCAACGC
Found at i:257448 original size:25 final size:25
Alignment explanation
Indices: 257410--257463 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
257400 AAATCAATTA
*
257410 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
257435 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
257460 AACA
1 AACA
257464 AATAATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:257867 original size:18 final size:18
Alignment explanation
Indices: 257846--257882 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
257836 GTAATTGGAG
257846 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
257864 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
257882 T
1 T
257883 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:257889 original size:24 final size:24
Alignment explanation
Indices: 257838--257890 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
257828 TTTCATATGT
* * *
257838 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
257862 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
257886 AATTT
1 AATTT
257891 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:258236 original size:39 final size:39
Alignment explanation
Indices: 258193--258279 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
258183 TCTGATGCTC
*
258193 ATCAAAATCCAAAGCTCATATGGTTCCAAGCAAAAAGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
* *
258232 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
258271 ATCAAAATC
1 ATCAAAATC
258280 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
Found at i:258663 original size:14 final size:14
Alignment explanation
Indices: 258629--258682 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
258619 ATAATTCTTA
*
258629 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
258643 TAAACAAATCAACT
1 TTTACAAATCAACT
*
258657 TTTACAAATCATCT
1 TTTACAAATCAACT
258671 TTTACAAATCAA
1 TTTACAAATCAA
258683 TAAATCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:260161 original size:21 final size:22
Alignment explanation
Indices: 260137--260185 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
260127 GGATTCTTCG
*
260137 ATGATGA-GATGG-GCCTCTTTA
1 ATGATGAGGA-GGCGCCTCTTGA
260158 ATGAT-AGGAGGCGCCTCTTGA
1 ATGATGAGGAGGCGCCTCTTGA
260179 ATGATGA
1 ATGATGA
260186 TAGGTGCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (22 bp):
ATGATGAGGAGGCGCCTCTTGA
Found at i:260619 original size:21 final size:21
Alignment explanation
Indices: 260595--260642 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
260585 CATTATCTTC
* *
260595 ACGTAAAGTACCGACCTCATA
1 ACGTAAAGCACCAACCTCATA
*
260616 ACGTAAAGCACCAACCTCATC
1 ACGTAAAGCACCAACCTCATA
260637 ACGTAA
1 ACGTAA
260643 TTCCCCTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (21 bp):
ACGTAAAGCACCAACCTCATA
Found at i:262380 original size:13 final size:13
Alignment explanation
Indices: 262362--262393 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
262352 GGGTTACTTC
262362 AACAAAAAGACAA
1 AACAAAAAGACAA
262375 AACAAAAAGACAA
1 AACAAAAAGACAA
262388 AACAAA
1 AACAAA
262394 GACAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:262396 original size:11 final size:12
Alignment explanation
Indices: 262366--262399 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
262356 TACTTCAACA
262366 AAAAGACAAAAC
1 AAAAGACAAAAC
262378 AAAAAGACAAAAC
1 -AAAAGACAAAAC
262391 -AAAGACAAA
1 AAAAGACAAA
262400 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:262620 original size:20 final size:20
Alignment explanation
Indices: 262595--262662 Score: 100
Period size: 20 Copynumber: 3.3 Consensus size: 20
262585 TATGAGAGAT
*
262595 GGAGATAGACAGATTTCGTC
1 GGAGATAGACGGATTTCGTC
262615 GGAGATAGACGGATTTCGTC
1 GGAGATAGACGGATTTCGTC
*
262635 GGAGATGGGGACGGATTTCGTC
1 GGAGAT--AGACGGATTTCGTC
262657 GGAGAT
1 GGAGAT
262663 GGGGACGGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 25 0.57
22 19 0.43
ACGTcount: A:0.25, C:0.13, G:0.38, T:0.24
Consensus pattern (20 bp):
GGAGATAGACGGATTTCGTC
Found at i:262650 original size:22 final size:22
Alignment explanation
Indices: 262606--262672 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
262596 GAGATAGACA
*
262606 GATTTCGTCGGAGAT--AGACG
1 GATTTCGTCGGAGATGGGGACG
262626 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGACG
262648 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGACG
262670 GAT
1 GAT
262673 GTCGCCGTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 15 0.34
22 29 0.66
ACGTcount: A:0.21, C:0.13, G:0.42, T:0.24
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACG
Found at i:262825 original size:20 final size:20
Alignment explanation
Indices: 262800--262844 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
262790 GCGTAAAAAC
*
262800 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
262820 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
262840 ATTTG
1 ATTTG
262845 GAAACTGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:263616 original size:18 final size:19
Alignment explanation
Indices: 263593--263633 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
263583 TCAACAGATG
263593 ATATAA-AAATCATTAAAA
1 ATATAATAAATCATTAAAA
**
263611 ATATAATATTTCATTAAAA
1 ATATAATAAATCATTAAAA
263630 ATAT
1 ATAT
263634 TGTAGTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAATAAATCATTAAAA
Found at i:264291 original size:18 final size:18
Alignment explanation
Indices: 264268--264305 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
264258 AGGCGGCGGT
264268 GGCGGAGCAGACAA-AGGA
1 GGCGGAGCAGA-AAGAGGA
*
264286 GGCGGAGGAGAAAGAGGA
1 GGCGGAGCAGAAAGAGGA
264304 GG
1 GG
264306 AAACGATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.37, C:0.11, G:0.53, T:0.00
Consensus pattern (18 bp):
GGCGGAGCAGAAAGAGGA
Found at i:269738 original size:25 final size:25
Alignment explanation
Indices: 269704--269755 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
269694 ATATTGATCC
* *
269704 CCCGTCCCCGTCCCCATTTAAAAAA
1 CCCGTACCCGTCCCCACTTAAAAAA
*
269729 CCCGTACCCGTCCCCGCTTAAAAAA
1 CCCGTACCCGTCCCCACTTAAAAAA
269754 CC
1 CC
269756 GCAAGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.46, G:0.10, T:0.17
Consensus pattern (25 bp):
CCCGTACCCGTCCCCACTTAAAAAA
Found at i:269858 original size:12 final size:12
Alignment explanation
Indices: 269843--269873 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
269833 GTTATTTAAA
*
269843 CGGGTATCGGGT
1 CGGGTATCGGGC
269855 CGGGTATCGGGC
1 CGGGTATCGGGC
269867 CGGGTAT
1 CGGGTAT
269874 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:269925 original size:38 final size:38
Alignment explanation
Indices: 269871--269965 Score: 131
Period size: 38 Copynumber: 2.5 Consensus size: 38
269861 TCGGGCCGGG
*
269871 TATATATATA-TATATATATTTATTT-ATTTAAATTAAA
1 TATATAAATATTATATATATTT-TTTAATTTAAATTAAA
*
269908 TATATAAATATTATATATATTTTTTAATTTAATTTAAA
1 TATATAAATATTATATATATTTTTTAATTTAAATTAAA
* *
269946 TTTATTAATATTATATATAT
1 TATATAAATATTATATATAT
269966 AATAATAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 12 0.23
38 40 0.77
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
TATATAAATATTATATATATTTTTTAATTTAAATTAAA
Found at i:270098 original size:29 final size:30
Alignment explanation
Indices: 270028--270101 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
270018 CAAACCCGTC
* * *
270028 CCCGTCCCCGTTTAGCATAAACGGTTTTTT
1 CCCGTCACCGTTTAACATAAACGGATTTTT
270058 CCCGTCACCGTTTAACATAAAC-GATTTTT
1 CCCGTCACCGTTTAACATAAACGGATTTTT
**
270087 CCCGTCGTCGTTTAA
1 CCCGTCACCGTTTAA
270102 TTCGATTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (30 bp):
CCCGTCACCGTTTAACATAAACGGATTTTT
Found at i:274775 original size:27 final size:28
Alignment explanation
Indices: 274736--274805 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
274726 TTATTATTAT
* *
274736 TTAACTTAAATTTTAATAATAA-TATAA
1 TTAATTTAAATTTTAATAAAAATTATAA
* *
274763 TTAATTTATATTTTTATTAAAAATTATAA
1 TTAATTTA-AATTTTAATAAAAATTATAA
* *
274792 TTATTTTAGATTTT
1 TTAATTTAAATTTT
274806 TTTTTATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
27 7 0.21
28 15 0.44
29 12 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTAAATTTTAATAAAAATTATAA
Found at i:275762 original size:20 final size:20
Alignment explanation
Indices: 275717--275762 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
275707 GACCAACAAA
* *
275717 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
275737 -TCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATCTCCAAT
275756 ATCGCAA
1 ATCGCAA
275763 ATTCGCGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:275796 original size:20 final size:20
Alignment explanation
Indices: 275773--275849 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
275763 ATTCGCGCTG
*
275773 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTA
* *
275793 CATTTTGCGTTGCGATAGTGTA
1 CATTTCGCGTTGCGAT--TTTA
* *
275815 CA-GT-GTCGTTGCGATTTTC
1 CATTTCG-CGTTGCGATTTTA
275834 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
275850 AGTCTACAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.09
20 26 0.58
21 11 0.24
22 4 0.09
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTA
Found at i:275825 original size:41 final size:41
Alignment explanation
Indices: 275780--275859 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
275770 CTGCATTTCG
* * *
275780 CGTTGCGATTTTTCATTTTGCGTTGCGATAGTGTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
275821 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
275860 AAATTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:277027 original size:21 final size:21
Alignment explanation
Indices: 277001--277215 Score: 98
Period size: 21 Copynumber: 10.4 Consensus size: 21
276991 AAGAAACAAA
*
277001 ATCGCAACGACACTGTAGATT
1 ATCGCAACGACACTGTAGACT
* **
277022 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
277042 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* * *
277063 ATCACAACG-CGATTTTCA-ACT
1 ATCGCAACGAC-ACTGT-AGACT
277084 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* * *
277105 ATCGTAACG-CGATTTTCA-ACT
1 ATCGCAACGAC-ACTGT-AGACT
* **
277126 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
*
277146 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTGTAGACT
* *
277167 ATCGCAACG-CGAAATG-A-A-A
1 ATCGCAACGAC--ACTGTAGACT
277186 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
277207 ATCGCAACG
1 ATCGCAACG
277216 CGATTTTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 44
0.66 0.13 0.20
Matches are distributed among these distances:
18 3 0.02
19 16 0.11
20 29 0.20
21 84 0.59
22 11 0.08
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:277055 original size:41 final size:41
Alignment explanation
Indices: 276997--277116 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
276987 TCTTAAGAAA
*
276997 CAAAATCGCAACGACACTGTAGATTATCGCAACGCGAAATG
1 CAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
* * ** *
277038 GAAAATCGCAACGACACTGTAGACTATCACAACGCGATTTT
1 CAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
* *
277079 CAACTATCGCAACGACACTGTAGACTATCGTAACGCGA
1 CAA-AATCGCAACGACACTGTAGACTATCGCAACGCGA
277117 TTTTCAACTA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 37 0.54
42 31 0.46
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
Found at i:277101 original size:42 final size:42
Alignment explanation
Indices: 277001--277134 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
276991 AAGAAACAAA
* ** ** *
277001 ATCGCAACGACACTGTAGATTATCGCAACGCGAAATGGAA-A
1 ATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAACT
*
277042 ATCGCAACGACACTGTAGACTATCACAACGCGATTTTCAACT
1 ATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAACT
*
277084 ATCGCAACGACACTGTAGACTATCGTAACGCGATTTTCAACT
1 ATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAACT
277126 ATCGCAACG
1 ATCGCAACG
277135 CGAAATGGAA
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 34 0.41
42 49 0.59
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCAACT
Found at i:277197 original size:40 final size:41
Alignment explanation
Indices: 277123--277218 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 41
277113 GCGATTTTCA
277123 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
*
277164 ACTATCGCAACGCGAAAT-GAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
277204 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
277219 TTTTCAACTA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 36 0.67
41 18 0.33
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
Found at i:277243 original size:102 final size:104
Alignment explanation
Indices: 277021--277235 Score: 353
Period size: 104 Copynumber: 2.1 Consensus size: 104
277011 CACTGTAGAT
* ** *
277021 TATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCACAACGCGATTTTCAACTAT
1 TATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCACAACGCGATAATCAACAAT
*
277086 CGCAACGACACTGTAGACTATCGTAACGCGATTTTCAAC
66 CGCAACGACACTGTAGACTATCGCAACGCGATTTTCAAC
* *
277125 TATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA-AATGAA-AAT
1 TATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCACAACGCGATAATCAACAAT
277188 CGCAACGACACTGTAGACTATCGCAACGCGATTTTCAAC
66 CGCAACGACACTGTAGACTATCGCAACGCGATTTTCAAC
277227 TATCGCAAC
1 TATCGCAAC
277236 ATGAAATGTA
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 49 0.47
103 3 0.03
104 52 0.50
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (104 bp):
TATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCACAACGCGATAATCAACAAT
CGCAACGACACTGTAGACTATCGCAACGCGATTTTCAAC
Found at i:278786 original size:38 final size:37
Alignment explanation
Indices: 278710--278782 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
278700 AAAATATAAT
* *
278710 ATATTAATATTTTTTTTAAAAAATATTAATAATATTA
1 ATATTAATATTTTTTCTAAAAAATATTAATAAGATTA
* *
278747 ATATTTATATATTTTTCTAAAAAATA-TAGTAAGATT
1 ATATTAATAT-TTTTTCTAAAAAATATTAATAAGATT
278783 TAATGTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATATTAATATTTTTTCTAAAAAATATTAATAAGATTA
Found at i:281293 original size:12 final size:13
Alignment explanation
Indices: 281264--281290 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
281254 TCTTGATAGG
281264 AATCAAAAGGAAA
1 AATCAAAAGGAAA
281277 AATCAAAAGGAAA
1 AATCAAAAGGAAA
281290 A
1 A
281291 TCATTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (13 bp):
AATCAAAAGGAAA
Found at i:283445 original size:12 final size:13
Alignment explanation
Indices: 283416--283442 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
283406 TCTTGATAGG
283416 AATCAAAAGGAAA
1 AATCAAAAGGAAA
283429 AATCAAAAGGAAA
1 AATCAAAAGGAAA
283442 A
1 A
283443 TCATTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (13 bp):
AATCAAAAGGAAA
Found at i:285597 original size:12 final size:13
Alignment explanation
Indices: 285568--285594 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
285558 TCTTGATAGG
285568 AATCAAAAGGAAA
1 AATCAAAAGGAAA
285581 AATCAAAAGGAAA
1 AATCAAAAGGAAA
285594 A
1 A
285595 TCATTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (13 bp):
AATCAAAAGGAAA
Found at i:289947 original size:22 final size:22
Alignment explanation
Indices: 289919--289964 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
289909 TGGTTTCCCT
289919 TTCCTGGCTTAAGCCCCACATA
1 TTCCTGGCTTAAGCCCCACATA
*
289941 TTCCTGGCTTCAGCCCCACATA
1 TTCCTGGCTTAAGCCCCACATA
289963 TT
1 TT
289965 TGTTTGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (22 bp):
TTCCTGGCTTAAGCCCCACATA
Found at i:296847 original size:7 final size:7
Alignment explanation
Indices: 296816--296914 Score: 71
Period size: 7 Copynumber: 14.1 Consensus size: 7
296806 GAGGGGCACC
296816 AAGAAGA
1 AAGAAGA
296823 AA-AAGA
1 AAGAAGA
296829 AA-AAGA
1 AAGAAGA
* *
296835 GGAGAAGG
1 -AAGAAGA
296843 AAGAAAGA
1 AAG-AAGA
296851 AAGGAA-A
1 AA-GAAGA
296858 AAGAAGA
1 AAGAAGA
296865 AAGAAGA
1 AAGAAGA
* *
296872 AATAAAA
1 AAGAAGA
296879 GAAGAAGA
1 -AAGAAGA
296887 AAGAAGA
1 AAGAAGA
* *
296894 AGGAGGA
1 AAGAAGA
*
296901 AAAAAG-
1 AAGAAGA
296907 AAGAAGA
1 AAGAAGA
296914 A
1 A
296915 TAAGAGATGA
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
6 18 0.25
7 37 0.52
8 15 0.21
9 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (7 bp):
AAGAAGA
Found at i:296848 original size:18 final size:19
Alignment explanation
Indices: 296825--296884 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
296815 CAAGAAGAAA
* *
296825 AAGAAA-AAGAGGAGAAGG
1 AAGAAAGAAGAGGAAAAAG
296843 AAGAAAGAA-AGGAAAAAG
1 AAGAAAGAAGAGGAAAAAG
*
296861 AAGAAAGAAGA-AATAAAAG
1 AAGAAAGAAGAGGA-AAAAG
296880 AAGAA
1 AAGAA
296885 GAAAGAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 23 0.64
19 13 0.36
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (19 bp):
AAGAAAGAAGAGGAAAAAG
Found at i:296892 original size:22 final size:21
Alignment explanation
Indices: 296816--296894 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
296806 GAGGGGCACC
*
296816 AAGAAGAAA-AAGAAAAAGAG
1 AAGAAGAAAGAAGAAAAAAAG
* * *
296836 GAGAAGGAAGAAAGAAAGGAAA-
1 AAGAAGAAAG-AAGAAA-AAAAG
296858 AAGAAGAAAGAAGAAATAAAAG
1 AAGAAGAAAGAAGAAA-AAAAG
296880 AAGAAGAAAGAAGAA
1 AAGAAGAAAGAAGAA
296895 GGAGGAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.15
21 9 0.19
22 29 0.62
23 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (21 bp):
AAGAAGAAAGAAGAAAAAAAG
Found at i:296919 original size:29 final size:29
Alignment explanation
Indices: 296837--296919 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
296827 GAAAAAGAGG
* *
296837 AGAAGGAAGAAAGAA-AGGAAAAAGAAGAA
1 AGAAGGAAAAAAGAAGAAG-AAAAGAAGAA
*
296866 AGAAGAAATAAAAGAAGAAG-AAAGAAG-A
1 AGAAGGAA-AAAAGAAGAAGAAAAGAAGAA
*
296894 AGGAGGAAAAAAGAAGAAGAATAAGA
1 AGAAGGAAAAAAGAAGAAGAA-AAGA
296920 GATGAAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
27 11 0.24
28 8 0.18
29 18 0.40
30 6 0.13
31 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (29 bp):
AGAAGGAAAAAAGAAGAAGAAAAGAAGAA
Found at i:298018 original size:24 final size:24
Alignment explanation
Indices: 297991--298074 Score: 168
Period size: 24 Copynumber: 3.5 Consensus size: 24
297981 GCATGAGTAG
297991 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
298015 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
298039 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
298063 TGCATCGATGCA
1 TGCATCGATGCA
298075 TGGTATAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGGA
Found at i:299301 original size:17 final size:17
Alignment explanation
Indices: 299275--299314 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
299265 GTTTGAGCAT
*
299275 TTCAAGCCTATTTTTCA
1 TTCAATCCTATTTTTCA
299292 TTCAATCCTATTTTTCA
1 TTCAATCCTATTTTTCA
299309 TTCAAT
1 TTCAAT
299315 ATTCATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.03, T:0.50
Consensus pattern (17 bp):
TTCAATCCTATTTTTCA
Found at i:303880 original size:49 final size:49
Alignment explanation
Indices: 303821--303980 Score: 284
Period size: 49 Copynumber: 3.3 Consensus size: 49
303811 TCTGTAACGC
**
303821 CAGACGTGCTAAATCATCATCAATCGCAGCACCACCGTCACAAAGATGT
1 CAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAGATGT
*
303870 CAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAGACGT
1 CAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAGATGT
*
303919 CAGACGTGCTAAATCATCATCAATCATAGCACCACAGTCACAAAGATGT
1 CAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAGATGT
303968 CAGACGTGCTAAA
1 CAGACGTGCTAAA
303981 AGCTCCACCT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 106 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.19
Consensus pattern (49 bp):
CAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAGATGT
Found at i:304117 original size:53 final size:53
Alignment explanation
Indices: 304044--304150 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 53
304034 TAAATCATTT
* * * *
304044 ATCATTCACCTATCAGAATCTTTTTCAAATATCATC-AAAATCAAGTATCATAC
1 ATCATTCACCTATCAAAATCTTTTT-AAACATCAACAAAAATCAAGTATAATAC
*
304097 ATCATTCA-CTCATCAAAATCTTTTTAAACATTAACAAAAATCAAGTATAATAC
1 ATCATTCACCT-ATCAAAATCTTTTTAAACATCAACAAAAATCAAGTATAATAC
304150 A
1 A
304151 ATATAAATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 9 0.19
53 38 0.81
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (53 bp):
ATCATTCACCTATCAAAATCTTTTTAAACATCAACAAAAATCAAGTATAATAC
Found at i:306235 original size:29 final size:30
Alignment explanation
Indices: 306188--306248 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
306178 TTTTGGTCCT
** *
306188 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTCTAGCCAC
*
306218 TAAAC-TTTCAAAACTTATACTCTAGTCAC
1 TAAACTTTTCAAAACTTATACTCTAGCCAC
306247 TA
1 TA
306249 GACAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTCTAGCCAC
Found at i:306804 original size:21 final size:21
Alignment explanation
Indices: 306779--306821 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
306769 TTTTAAATCA
306779 GCATAAGATTTCTGTCTATCT
1 GCATAAGATTTCTGTCTATCT
306800 GCATAAGATTTCTGTCTATCT
1 GCATAAGATTTCTGTCTATCT
306821 G
1 G
306822 AAGCTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (21 bp):
GCATAAGATTTCTGTCTATCT
Found at i:310567 original size:22 final size:22
Alignment explanation
Indices: 310526--310606 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
310516 CTCGTATAAA
310526 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
310549 TGCATCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
310571 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
310593 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
310607 ATATAATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 44 0.80
23 11 0.20
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:311266 original size:2 final size:2
Alignment explanation
Indices: 311259--311288 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
311249 TCTCTTAAAC
311259 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
311289 TCACATGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:312330 original size:21 final size:21
Alignment explanation
Indices: 312306--312350 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
312296 TCTTGTTCGT
* *
312306 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
312327 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
312348 TTG
1 TTG
312351 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:315563 original size:22 final size:22
Alignment explanation
Indices: 315522--315602 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
315512 CTCGTATAAA
315522 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
315545 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
315567 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
* *
315589 TGCACTGTAGTGCC
1 TGCACCGAAGTGCC
315603 ATATAATGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 44 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:316256 original size:2 final size:2
Alignment explanation
Indices: 316249--316290 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
316239 TCTCTTAAAC
316249 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
316291 TCACATGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317326 original size:21 final size:21
Alignment explanation
Indices: 317302--317346 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
317292 TCTTGTTCGT
* *
317302 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
317323 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
317344 TTG
1 TTG
317347 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:318322 original size:21 final size:21
Alignment explanation
Indices: 318285--318329 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
318275 GATTTCTGGG
*
318285 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
318306 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
318327 CAA
1 CAA
318330 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:320030 original size:25 final size:26
Alignment explanation
Indices: 319996--320046 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
319986 GAGTAGAGGG
319996 TCTACGCGGTCCTTCGGGATA-ATAT
1 TCTACGCGGTCCTTCGGGATATATAT
320021 TCTACGCGGTCCTTCGGGATATATAT
1 TCTACGCGGTCCTTCGGGATATATAT
320047 ATATTCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (26 bp):
TCTACGCGGTCCTTCGGGATATATAT
Found at i:320198 original size:23 final size:23
Alignment explanation
Indices: 320154--320198 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
320144 ATCATTATAT
*
320154 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
320177 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
320199 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:323222 original size:23 final size:23
Alignment explanation
Indices: 323178--323222 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
323168 ATCATTATAT
* *
323178 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGATGCAATTATACGC
* *
323201 GGCACTTCGATGCATTTATACG
1 GGCACTACGATGCAATTATACG
323223 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGC
Found at i:326541 original size:21 final size:21
Alignment explanation
Indices: 326498--326542 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
326488 GATTTCTGGG
* *
326498 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
326519 CAAGGGGAACCGATACTCC-TT
1 CAAGGGGAACCGATAC-CCATT
326540 CAA
1 CAA
326543 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:328415 original size:23 final size:23
Alignment explanation
Indices: 328371--328415 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
328361 ATCATTATAT
*
328371 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
328394 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
328416 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:330882 original size:49 final size:48
Alignment explanation
Indices: 330826--330989 Score: 256
Period size: 49 Copynumber: 3.4 Consensus size: 48
330816 TACATCTGTA
*
330826 ACGTCAGACGTGCTAAATCATCATCAACCGTAGCACCATCGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCA-CGTCACAAAG
* *
330875 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTTACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCA-CGTCACAAAG
*
330924 ATGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACAGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCAC-GTCACAAAG
*
330973 ATGTCAGACGTGCTAAA
1 ACGTCAGACGTGCTAAA
330990 AGCTCCACCT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 1 0.01
49 106 0.99
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (48 bp):
ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACGTCACAAAG
Found at i:333266 original size:29 final size:30
Alignment explanation
Indices: 333219--333279 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
333209 TTTTGGTCCT
**
333219 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
* *
333249 TAAAC-TTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
333278 TA
1 TA
333280 GACAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGCCAC
Found at i:335275 original size:22 final size:22
Alignment explanation
Indices: 335249--335329 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 22
335239 ATAAGGCAGA
*
335249 GGGAATCGATACCCCCTTTAAG
1 GGGAACCGATACCCCCTTTAAG
*
335271 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCTTT-AAG
* * *
335294 AGGAACCGATTCCCCC---CAG
1 GGGAACCGATACCCCCTTTAAG
*
335313 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
335330 GAGGGTTCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 15 0.30
22 17 0.34
23 18 0.36
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTTAAG
Found at i:335298 original size:23 final size:22
Alignment explanation
Indices: 335250--335309 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 22
335240 TAAGGCAGAG
* * *
335250 GGAATCGATACCCCCTTTAAGG
1 GGAACCGATTCCCCCTTTAAGA
335272 GGAACCGATTCCCCCTTTGAAGA
1 GGAACCGATTCCCCCTTT-AAGA
335295 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
335310 CAGGGGAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (22 bp):
GGAACCGATTCCCCCTTTAAGA
Found at i:340075 original size:18 final size:19
Alignment explanation
Indices: 340052--340100 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
340042 GCGATGGTGT
340052 TATTATTATTT-AATAAAA
1 TATTATTATTTGAATAAAA
*
340070 TATTATTATTTGAGAATAAAT
1 TATTATTATTT--GAATAAAA
340091 TATTATTATT
1 TATTATTATT
340101 AAATGGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.41
21 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTATTATTTGAATAAAA
Found at i:341099 original size:10 final size:10
Alignment explanation
Indices: 341086--341135 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
341076 AATATAATAA
*
341086 TAATACTATT
1 TAATTCTATT
*
341096 TAATTTTATT
1 TAATTCTATT
*
341106 TAATTCGATT
1 TAATTCTATT
341116 TAATTC-ATT
1 TAATTCTATT
341125 TATATT-TATT
1 TA-ATTCTATT
341135 T
1 T
341136 CTTTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 5 0.15
10 29 0.85
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (10 bp):
TAATTCTATT
Found at i:342745 original size:120 final size:121
Alignment explanation
Indices: 342445--342930 Score: 686
Period size: 120 Copynumber: 4.0 Consensus size: 121
342435 ATTCAAAGAT
* * * *
342445 TAAATTAATTTTAATTTATTAAAATTATGACTAAATTGATATAATATATAAGTAAAAGTGATCAA
1 TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCAA
* * *
342510 ATGTGTAATTATATCAATTTTATTAAGTTTTCAAAGTTAAGACGAGATAAAATATA
66 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
* * * ** *
342566 TAAATTAATTATAATTTTTTAAAATTACAACTAAATTGATAGAATATAAAAGTGTAAGTGACCAT
1 TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCAA
342631 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAA-ATA
66 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
* * * *
342686 TAAAGTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGAAAAAGTGACCAA
1 TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCAA
342751 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
66 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
* * * *** * * *
342807 TATATATATTTTTAATTTTTTAAAATTACTTTTAAATTGATAAAATATAAAAGTATAAGTGACAA
1 TAAAT-TAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCA
* * *
342872 AATGTATAATTATATCAATTTTATTAAATTTTAAAAATTAGGATGAGATAAATATATA
65 AATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAA-ATATA
342930 T
1 T
342931 TTTTATGTTA
Statistics
Matches: 323, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
120 110 0.34
121 110 0.34
122 97 0.30
123 6 0.02
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (121 bp):
TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCAA
ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
Found at i:342745 original size:241 final size:242
Alignment explanation
Indices: 342445--342929 Score: 765
Period size: 241 Copynumber: 2.0 Consensus size: 242
342435 ATTCAAAGAT
* * * * *
342445 TAAATTAATTTTAATTTATTAAAATTATGACTAAATTGATATAATATATAAGTAAAAGTGATCAA
1 TAAAGTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGAAAAAGTGACCAA
* *
342510 ATGTGTAATTATATCAATTTTATTAAGTTTTCAAAGTTAAGACGAGATAAAATATATAAAT-TAA
66 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGACGAGATAAAATATATAAATATAA
* * * * *
342574 TTATAATTTTTTAAAATTACAACTAAATTGATAGAATATAAAAGTGTAAGTGACCATATGTGTAA
131 TTATAATTTTTTAAAATTACAACTAAATTGATAAAATATAAAAGTATAAGTGACAAAATGTATAA
*
342639 TTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAAATA
196 TTATATCAATTTTATTAAATTTTAAAAATTAAGATGAGATAAAAATA
342686 TAAAGTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGAAAAAGTGACCAA
1 TAAAGTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGAAAAAGTGACCAA
* * *
342751 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATATATATATAT
66 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGACGAGATAAAATATATAAATATAA
* ***
342816 TTTTAATTTTTTAAAATTACTTTTAAATTGATAAAATATAAAAGTATAAGTGACAAAATGTATAA
131 TTATAATTTTTTAAAATTACAACTAAATTGATAAAATATAAAAGTATAAGTGACAAAATGTATAA
* *
342881 TTATATCAATTTTATTAAATTTTAAAAATTAGGATGAGATAAATATA
196 TTATATCAATTTTATTAAATTTTAAAAATTAAGATGAGATAAAAATA
342928 TA
1 TA
342930 TTTTTATGTT
Statistics
Matches: 221, Mismatches: 22, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
241 117 0.53
242 104 0.47
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (242 bp):
TAAAGTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGAAAAAGTGACCAA
ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGACGAGATAAAATATATAAATATAA
TTATAATTTTTTAAAATTACAACTAAATTGATAAAATATAAAAGTATAAGTGACAAAATGTATAA
TTATATCAATTTTATTAAATTTTAAAAATTAAGATGAGATAAAAATA
Found at i:343394 original size:56 final size:55
Alignment explanation
Indices: 343309--343415 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 55
343299 CTTTATTTAT
343309 AATTATTATAAATAAAGTTAATTATTAATACAGTATGATATCAAATATATACATA
1 AATTATTATAAATAAAGTTAATTATTAATACAGTATGATATCAAATATATACATA
*
343364 AATTATTATAAAATAAAGTTAATTATTAATATAGTATGATATCAAATATATA
1 AATTATTAT-AAATAAAGTTAATTATTAATACAGTATGATATCAAATATATA
343416 TGTAATCCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 9 0.18
56 41 0.82
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (55 bp):
AATTATTATAAATAAAGTTAATTATTAATACAGTATGATATCAAATATATACATA
Found at i:359558 original size:27 final size:27
Alignment explanation
Indices: 359528--359580 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
359518 AAAAAAAGAA
359528 GAAAAAAATCTAACAATAAAATAAAAT
1 GAAAAAAATCTAACAATAAAATAAAAT
359555 GAAAAAAATCTAACAATAAAATAAAA
1 GAAAAAAATCTAACAATAAAATAAAA
359581 AGAAGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.17
Consensus pattern (27 bp):
GAAAAAAATCTAACAATAAAATAAAAT
Found at i:360472 original size:16 final size:14
Alignment explanation
Indices: 360432--360470 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
360422 TATCTTTTAA
360432 TTTTTAAAAATATT
1 TTTTTAAAAATATT
*
360446 TTATTAAAAATATT
1 TTTTTAAAAATATT
360460 TTTTTATAAAA
1 TTTTTA-AAAA
360471 ATTAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTTAAAAATATT
Found at i:361315 original size:18 final size:16
Alignment explanation
Indices: 361283--361315 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
361273 CGTTGTAAGG
361283 TAATTTTTTTAATATA
1 TAATTTTTTTAATATA
361299 TAATGTTTTTT-ATATA
1 TAAT-TTTTTTAATATA
361315 T
1 T
361316 GATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTTTTAATATA
Found at i:367949 original size:18 final size:17
Alignment explanation
Indices: 367923--367958 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
367913 ATAATAAGAC
367923 TAAAATTAAAAAAATTAA
1 TAAAATT-AAAAAATTAA
*
367941 TAAAGTTAAAAAATTAA
1 TAAAATTAAAAAATTAA
367958 T
1 T
367959 GTGTTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAATTAAAAAATTAA
Found at i:368041 original size:20 final size:21
Alignment explanation
Indices: 368007--368047 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
367997 CTGAATTTAA
368007 AAATTTAACTCAATTA-ATTT
1 AAATTTAACTCAATTAGATTT
* *
368027 AAATTTAATTTAATTAGATTT
1 AAATTTAACTCAATTAGATTT
368048 GATAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATTTAACTCAATTAGATTT
Found at i:369290 original size:16 final size:17
Alignment explanation
Indices: 369240--369293 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
369230 TAAAATAAAA
369240 TAATTTGAAAGTTAGAG
1 TAATTTGAAAGTTAGAG
* *
369257 TGA-TT-AAAATTAGGAG
1 TAATTTGAAAGTTA-GAG
369273 TAATTTGAAAGTTA-AG
1 TAATTTGAAAGTTAGAG
369289 TAATT
1 TAATT
369294 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 6 0.20
16 14 0.47
17 4 0.13
18 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (17 bp):
TAATTTGAAAGTTAGAG
Found at i:376583 original size:15 final size:16
Alignment explanation
Indices: 376563--376594 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
376553 AACCTTTCAT
376563 ATTT-AAAATTATATC
1 ATTTAAAAATTATATC
376578 ATTTAAAAATTATATC
1 ATTTAAAAATTATATC
376594 A
1 A
376595 ATTTTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAAATTATATC
Found at i:378825 original size:15 final size:15
Alignment explanation
Indices: 378807--378835 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
378797 AAAGATACTC
378807 CTAATAAAGTAATAG
1 CTAATAAAGTAATAG
378822 CTAATAAAGTAATA
1 CTAATAAAGTAATA
378836 TTTTCACCTG
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:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (15 bp):
CTAATAAAGTAATAG
Found at i:387033 original size:20 final size:22
Alignment explanation
Indices: 387010--387053 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
387000 GTAAGTTACG
387010 AATTTAATT-TT-TATATTTTT
1 AATTTAATTATTATATATTTTT
387030 AATTTAATTATTATATATTTTT
1 AATTTAATTATTATATATTTTT
387052 AA
1 AA
387054 ATTTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATTTAATTATTATATATTTTT
Found at i:387184 original size:60 final size:60
Alignment explanation
Indices: 387112--387235 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
387102 TAAAGAATAC
* ** ** *
387112 AAATGGTCCCCCAACTATAGGGTGTTGTTTTATTGAGTCTCAT-GACTATTAAAAGTTACA
1 AAATAGTCCCCCAACTATAGGACGTTACTTTATTGAGTC-CATCGACTATCAAAAGTTACA
* *
387172 AAATAGTCCCCCAACTATAGGACGTTACTTTGTTGAGTCCATCGACTATCAAAAGTTATA
1 AAATAGTCCCCCAACTATAGGACGTTACTTTATTGAGTCCATCGACTATCAAAAGTTACA
387232 AAAT
1 AAAT
387236 GGTAACCCGA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 3 0.05
60 52 0.95
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (60 bp):
AAATAGTCCCCCAACTATAGGACGTTACTTTATTGAGTCCATCGACTATCAAAAGTTACA
Found at i:387545 original size:60 final size:60
Alignment explanation
Indices: 387463--387579 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
387453 ACCATTTTGC
* ** * * *
387463 AACTTTTAATAGTCGGGGGACTCAACAAAGTAATACCCTATAATCAAGGGACCATTTCAT
1 AACTTTTAATAATCGAAGGACTCAACAAAGCAAAACCATATAATCAAGGGACCATTTCAT
* * * **
387523 AACTTTTAATAATCGAATGACTCAATAAAGCAAAACCATATAGTTGAGGGACCATTT
1 AACTTTTAATAATCGAAGGACTCAACAAAGCAAAACCATATAATCAAGGGACCATTT
387580 GTATACTTTA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (60 bp):
AACTTTTAATAATCGAAGGACTCAACAAAGCAAAACCATATAATCAAGGGACCATTTCAT
Found at i:388020 original size:8 final size:9
Alignment explanation
Indices: 388001--388035 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
387991 TATATATAAT
388001 AAAAATTAA
1 AAAAATTAA
388010 AAAAATT-A
1 AAAAATTAA
388018 AAAAATTAA
1 AAAAATTAA
388027 AAAAATTAA
1 AAAAATTAA
388036 TTTAAGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:388023 original size:17 final size:17
Alignment explanation
Indices: 388001--388035 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
387991 TATATATAAT
388001 AAAAATTAAAAAAATTA
1 AAAAATTAAAAAAATTA
388018 AAAAATTAAAAAAATTA
1 AAAAATTAAAAAAATTA
388035 A
1 A
388036 TTTAAGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATTAAAAAAATTA
Found at i:390624 original size:15 final size:15
Alignment explanation
Indices: 390604--390653 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
390594 TCTTGGTTTG
390604 TTTAATATATTATTA
1 TTTAATATATTATTA
* * *
390619 TTTAATAGATTGTGA
1 TTTAATATATTATTA
390634 TTATAAATATATTATTA
1 TT-T-AATATATTATTA
390651 TTT
1 TTT
390654 GGTTGGTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 14 0.52
16 2 0.07
17 11 0.41
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTAATATATTATTA
Found at i:396037 original size:3 final size:3
Alignment explanation
Indices: 396029--396079 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
396019 ATGTAAATTA
* * *
396029 AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAC GAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
396078 AA
1 AA
396080 AAAAAAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:396349 original size:46 final size:44
Alignment explanation
Indices: 396229--396522 Score: 182
Period size: 46 Copynumber: 6.7 Consensus size: 44
396219 GTTGGGGACG
* * * * *
396229 ACACTGCTCATACGTGATGAAGAGTTCGGGTCATTTTAAGGT--TA
1 ACACGGCTCCTACGTGATGAGGAG-TCTGGTCA-TCTAAGGTGATA
* * * *
396273 ACGCGGTTCCTACGTGATGAAGAAGTCTGGTCGTCTAAAGGTGATA
1 ACACGGCTCCTACGTGATG-AGGAGTCTGGTCATCT-AAGGTGATA
* * * * *
396319 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAGGA-GTCTGGTCATCTAAGGTGATA
* *
396362 ACATGGCTCCTACGTGATGAGGAGATCTGG---TCT--GG-GAATG
1 ACACGGCTCCTACGTGATGAGGAG-TCTGGTCATCTAAGGTG-ATA
* * *
396402 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTGAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAG-TCTGGTCATCT-AAGGTGATA
* * * *
396448 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATA-GT--TG
1 ACACGGCTCCTACGTGATGAGGA-GTCTGGTCATCTA-AGGTGATA
396491 ACACGGCTCCTACGTGATGAGGAGATCTGGTC
1 ACACGGCTCCTACGTGATGAGGAG-TCTGGTC
396523 TGAGAATGAT
Statistics
Matches: 197, Mismatches: 34, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
38 2 0.01
40 31 0.16
42 2 0.01
43 59 0.30
44 26 0.13
45 13 0.07
46 62 0.31
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (44 bp):
ACACGGCTCCTACGTGATGAGGAGTCTGGTCATCTAAGGTGATA
Found at i:396384 original size:43 final size:43
Alignment explanation
Indices: 396319--396521 Score: 166
Period size: 43 Copynumber: 4.7 Consensus size: 43
396309 AAAGGTGATA
*
396319 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* * * *
396362 ACATGGCTCCTACGTGATGAGGAGATCTGG---TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
* * ** ** * *
396402 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTGAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT--TG
* *
396448 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATAGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
*
396491 ACACGGCTCCTACGTGATGAGGAGATCTGGT
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGT
396522 CTGAGAATGA
Statistics
Matches: 126, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
39 2 0.02
40 31 0.25
42 2 0.02
43 56 0.44
45 5 0.04
46 29 0.23
47 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGTTG
Found at i:396416 original size:40 final size:41
Alignment explanation
Indices: 396360--396550 Score: 156
Period size: 40 Copynumber: 4.5 Consensus size: 41
396350 TATCTATGGT
* *
396360 TGACATGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGATCTGAGAA
* * * *
396400 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTGAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGG--ATCTG-A-G-AA
* * * * *
396446 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATAGT
1 TGACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTGAGA-A
396489 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGAGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGATCTGAGAA
* *
396529 TGATACGGCTCATACGTGATGA
1 TGACACGGCTCCTACGTGATGA
396551 AGAGGGCTGG
Statistics
Matches: 118, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
40 51 0.43
41 2 0.02
42 1 0.01
43 31 0.26
44 1 0.01
45 1 0.01
46 30 0.25
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (41 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGATCTGAGAA
Done.