Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013006.1 Kokia drynarioides strain JFW-HI SEQ_128024, 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: 49400
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:366 original size:29 final size:29
Alignment explanation
Indices: 319--484 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 29
309 CCCTATAGGT
319 CCCTAAACTGTCCAAAAATTCAATTTTCAA
1 CCCTAAACT-TCCAAAAATTCAATTTTCAA
* * **
349 CCCTAAACTTCCAAAAATCCTATTTTTGA
1 CCCTAAACTTCCAAAAATTCAATTTTCAA
** * *
378 CCCCGAACCTCCAAAAATTCCATTTTC-A
1 CCCTAAACTTCCAAAAATTCAATTTTCAA
* * * * * *
406 CCCTCGAACATCCAAAAATCCCATTTTTGAC
1 CCCT-AAACTTCCAAAAAT-TCAATTTTCAA
* * * *
437 CCCAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCAATTTTCAA
*
466 CCCTCGAACTTCCAAAAAT
1 CCCT-AAACTTCCAAAAAT
485 CCCATTTTGA
Statistics
Matches: 106, Mismatches: 26, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
28 4 0.04
29 60 0.57
30 39 0.37
31 3 0.03
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.28
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCAATTTTCAA
Found at i:492 original size:29 final size:30
Alignment explanation
Indices: 354--581 Score: 202
Period size: 30 Copynumber: 7.7 Consensus size: 30
344 TTCAACCCTA
*
354 AACTTCCAAAAATCCTATTTTTGA-CCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCCG
* * * *
383 AACCTCCAAAAATTCCA-TTTTCACCCTCG
1 AACTTCCAAAAATCCCATTTTTGACCCCCG
* **
412 AACATCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCCG
*
442 AACTTCCAAAAATTCCATTTTT-ACCCCTCG
1 AACTTCCAAAAATCCCATTTTTGACCCC-CG
****
472 AACTTCCAAAAATCCCA-TTTTGACCTAAA
1 AACTTCCAAAAATCCCATTTTTGACCCCCG
* ** *
501 AACTT-CAAAAAACTCCATTTTTTTCCCCCA
1 AACTTCCAAAAATC-CCATTTTTGACCCCCG
*
531 AAATTCC-AAAATCCCATTTTTGA-CCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCCG
559 AAACTTCCAAAAATTCCC-TTTTT
1 -AACTTCCAAAAA-TCCCATTTTT
582 AAACCTAAAT
Statistics
Matches: 157, Mismatches: 32, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
28 16 0.10
29 64 0.41
30 72 0.46
31 5 0.03
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTGACCCCCG
Found at i:493 original size:59 final size:60
Alignment explanation
Indices: 323--582 Score: 298
Period size: 59 Copynumber: 4.4 Consensus size: 60
313 ATAGGTCCCT
* * * *
323 AAACTGTCCAAAAATTCAATTTTCAACCCT-AAACTTCCAAAAATCCTATTTTTGACCCC-
1 AAACT-TCCAAAAATTCCATTTTTACCCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * *
382 GAACCTCCAAAAATTCCATTTTCA-CCCTCGAACATCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* **
441 AAACTTCCAAAAATTCCATTTTTACCCCTCGAACTTCCAAAAATCCCA-TTTTGACCTAA
1 AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * *
500 AAACTTCAAAAAACTCCATTTTTTTCCCC-CAAAATTCC-AAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCA-TTTTTACCCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
*
559 AAACTTCCAAAAATTCCCTTTTTA
1 AAACTTCCAAAAATTCCATTTTTA
583 AACCTAAATT
Statistics
Matches: 172, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
57 4 0.02
58 58 0.34
59 79 0.46
60 31 0.18
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:11528 original size:44 final size:44
Alignment explanation
Indices: 11479--11570 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
11469 AAAAATACTT
* **
11479 CGTCTAAAAATAAAAGGGGAATTGAGATGAAAACCCACAAAGGG
1 CGTCTAAAAAAAAAAGGGGAATCAAGATGAAAACCCACAAAGGG
** **
11523 CGTCTAAAAAAAAAAGGGGGGTCAAGATGAAAACCTGCAAAGGG
1 CGTCTAAAAAAAAAAGGGGAATCAAGATGAAAACCCACAAAGGG
11567 CGTC
1 CGTC
11571 CTGGAACCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.13
Consensus pattern (44 bp):
CGTCTAAAAAAAAAAGGGGAATCAAGATGAAAACCCACAAAGGG
Found at i:12860 original size:206 final size:206
Alignment explanation
Indices: 12495--13097 Score: 859
Period size: 206 Copynumber: 2.9 Consensus size: 206
12485 TCAGGACTCG
*
12495 ATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAA
1 ATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * *
12559 ACGGTTATCTTCTTGATGAGATACTGAGAAGTGAACCAAATTTGTCTTCTTGATGAGATACAGAG
66 ATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAG
* * ** * * *
12624 AAGCGGATTGAAACAAACGACGCAGTCATCTTCTTGATGAGATACTGAAAAGAAGACCAAATCAA
131 AAGTGGATTAAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAA
12689 ACCCACGCTCA
196 ACCCACGCTCA
* * * * *
12700 ATGCGAGCAAATATTCGAACCCCAACGTCCTGATGAGATACTGAGAAGCGGGTCGAAGTAATAAA
1 ATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * *
12765 ATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGGG
66 ATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAG
* * * * *
12830 AAATGAATTAAAACAAGTGATGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAAACCAAATCAA
131 AAGTGGATTAAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAA
* *
12895 ACCCAGGCTCG
196 ACCCACGCTCA
*
12906 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
1 ATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * * *
12971 GTGGTTAGCTTCTTGATGAGATAC-GAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACAGA
66 ATGGTTAGCTTCTTGATGAGATACTG-AGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGA
* **
13035 GAAGTGGATCAAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTGGACCAAAT
130 GAAGTGGATTAAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAAT
13098 TCGTCTTCCT
Statistics
Matches: 346, Mismatches: 50, Indels: 3
0.87 0.13 0.01
Matches are distributed among these distances:
205 19 0.05
206 327 0.95
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (206 bp):
ATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
ATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAG
AAGTGGATTAAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAA
ACCCACGCTCA
Found at i:13076 original size:86 final size:86
Alignment explanation
Indices: 12979--13169 Score: 231
Period size: 86 Copynumber: 2.2 Consensus size: 86
12969 AAGTGGTTAG
* * **
12979 CTTCTTGATGAGATAC-GAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACAGAGAAGTGGA
1 CTTCTTGATGAGATACTG-AAAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAATAAA
13043 TCAAAACAAGTGATGCGGTCAT
65 TCAAAACAAGTGATGCGGTCAT
* * * * * * *
13065 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGATATATAGGGAAATAAAT
1 CTTCTTGATGAGATACTGAAAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAATAAAT
**
13130 TGAAACAAGTGATGCGGTCAT
66 CAAAACAAGTGATGCGGTCAT
* *
13151 CTTCCTGAAGAGATACTGA
1 CTTCTTGATGAGATACTGA
13170 GAAGAAAACT
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 88 0.99
87 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (86 bp):
CTTCTTGATGAGATACTGAAAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAATAAAT
CAAAACAAGTGATGCGGTCAT
Found at i:13142 original size:292 final size:292
Alignment explanation
Indices: 12773--13379 Score: 1106
Period size: 292 Copynumber: 2.1 Consensus size: 292
12763 AAATGGTTAG
*
12773 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGGGAAATGAAT
1 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGGGAAATAAAT
*
12838 TAAAACAAGTGATGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAAACCAAATCAAACCCAGGC
66 TAAAACAAGTGATGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAAACCAAATCAAACCCACGC
* *
12903 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAAT
*
12968 AAAGTGGTTAGCTTCTTGATGAGATACGAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACA
196 AAAGTGGTTAGCTTCCTGATGAGATACGAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACA
*
13033 GAGAAGTGGATCAAAACAAGTGATGCGGTCAT
261 GAGAAGTGGATCAAAACAAGTGATGCAGTCAT
*
13065 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGATATATAGGGAAATAAAT
1 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGGGAAATAAAT
* *
13130 TGAAACAAGTGATGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAAACTAAATCAAACCCACGC
66 TAAAACAAGTGATGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAAACCAAATCAAACCCACGC
*
13195 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGTAAT
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAAT
13260 AAAGTGGTTAGCTTCCTGATGAGATACGAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACA
196 AAAGTGGTTAGCTTCCTGATGAGATACGAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACA
13325 GAGAAGTGGATCAAAACAAGTGATGCAGTCAT
261 GAGAAGTGGATCAAAACAAGTGATGCAGTCAT
* *
13357 CTTCATGATGAGATACTAAGAAG
1 CTTCTTGATGAGATACTGAGAAG
13380 AAGGCCAAGT
Statistics
Matches: 303, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
292 303 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (292 bp):
CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGGGAAATAAAT
TAAAACAAGTGATGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAAACCAAATCAAACCCACGC
TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAAT
AAAGTGGTTAGCTTCCTGATGAGATACGAAAAAGTGAACCAAATCCGTCTTCTTGATGAAACACA
GAGAAGTGGATCAAAACAAGTGATGCAGTCAT
Found at i:13785 original size:11 final size:12
Alignment explanation
Indices: 13769--13854 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 12
13759 TTTCTAAAAA
*
13769 TTAAATTT-ACT
1 TTAAATTTAAAT
13780 TTAAATTTAAAT
1 TTAAATTTAAAT
*
13792 TTAAA-TTAATTTT
1 TTAAATTTAA--AT
13805 TTAAATTT-AAT
1 TTAAATTTAAAT
*
13816 TT-AGTTTAAAT
1 TTAAATTTAAAT
*
13827 TTGAAA--TAATT
1 TT-AAATTTAAAT
*
13838 TTAAACTTAAAT
1 TTAAATTTAAAT
13850 TTAAA
1 TTAAA
13855 ATCAATTACA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
10 7 0.12
11 26 0.44
12 16 0.27
13 8 0.14
14 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:13790 original size:6 final size:6
Alignment explanation
Indices: 13769--13854 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
13759 TTTCTAAAAA
* *
13769 TTAAAT TT-ACT TTAAAT TTAAAT TTAAA- TTAATTTT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA--AT TTAAAT TTAAAT
* * *
13816 TT-AGT TTAAAT TTGAAA- -TAATT TTAAAC TTAAAT TTAAA
1 TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAA
13855 ATCAATTACA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
4 2 0.03
5 18 0.29
6 35 0.56
7 3 0.05
8 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:13809 original size:36 final size:35
Alignment explanation
Indices: 13769--13839 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
13759 TTTCTAAAAA
*
13769 TTAAATTTACTTTAAATTTAAATTT-AAATTAATTTT
1 TTAAATTTAATTT-AATTTAAATTTGAAA-TAATTTT
*
13805 TTAAATTTAATTTAGTTTAAATTTGAAATAATTTT
1 TTAAATTTAATTTAATTTAAATTTGAAATAATTTT
13840 AAACTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
TTAAATTTAATTTAATTTAAATTTGAAATAATTTT
Found at i:14613 original size:13 final size:13
Alignment explanation
Indices: 14595--14629 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
14585 ACTTTAATGC
14595 TATTAATAAATAT
1 TATTAATAAATAT
*
14608 TATTAATTAATAT
1 TATTAATAAATAT
*
14621 TAATAATAA
1 TATTAATAA
14630 TAATAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAATAAATAT
Found at i:15674 original size:29 final size:29
Alignment explanation
Indices: 15636--16063 Score: 249
Period size: 30 Copynumber: 14.7 Consensus size: 29
15626 GAGGTCCCTA
*
15636 AACTGTCCAAAAATTCCATTTTCACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
15666 AACTTCCAAAAA-TCCTATTTTTGA-CCTCG
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTCG
* * * *
15695 AAACCTCCAAAAATTCCATTTTCACCCCCA
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
15725 AACTTCCAAAAATCCCA--TTT----T-G
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
15747 -AC-CCCAAAATTTCCAATTTTACCCCT-A
1 AACTTCCAAAAATTCCATTTTTA-CCCTCG
* * *
15774 AAATTCCAAAAATACCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
15803 AAACTTCCAAAAATTCCATTTTTACCCCCTG
1 -AACTTCCAAAAATTCCATTTTTACCCTC-G
* * * **
15834 AACTACTAAAAATCCCATTTTTACCCTTA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
15863 AATTTTCAAAAATACCATTTTTAACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* * *
15893 AACTTCCAAAAATTCCTTTTTTACCCCCTA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* * * *
15923 AACTACTAAAAATCCCATTTTTAACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* * *
15953 AACTTCCAAAAATCCCATTTTTACCCCCTT
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
*
15983 AACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
16012 AAATTTCCAAAAATACCATTTTTTACCCT-G
1 -AACTTCCAAAAATTCCA-TTTTTACCCTCG
* *
16042 AAACTTCCAAAAAATCCCTTTT
1 -AACTTCCAAAAATTCCATTTT
16064 AAACCTAAAT
Statistics
Matches: 313, Mismatches: 59, Indels: 53
0.74 0.14 0.12
Matches are distributed among these distances:
20 10 0.03
21 2 0.01
22 3 0.01
27 3 0.01
28 7 0.02
29 78 0.25
30 193 0.62
31 17 0.05
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:15761 original size:49 final size:49
Alignment explanation
Indices: 15701--15794 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
15691 CTCGAAACCT
* *
15701 CCAAAAATTCC-ATTTTCACCCCCAAACTTCCAAAAATCCCATTTTGACC
1 CCAAAAATTCCAATTTT-ACCCCCAAAATTCCAAAAATACCATTTTGACC
* *
15750 CCAAAATTTCCAATTTTACCCCTAAAATTCCAAAAATACCATTTT
1 CCAAAAATTCCAATTTTACCCCCAAAATTCCAAAAATACCATTTT
15795 TAACCTCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 35 0.88
50 5 0.12
ACGTcount: A:0.37, C:0.32, G:0.01, T:0.30
Consensus pattern (49 bp):
CCAAAAATTCCAATTTTACCCCCAAAATTCCAAAAATACCATTTTGACC
Found at i:15776 original size:21 final size:20
Alignment explanation
Indices: 15730--15782 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
15720 CCCCAAACTT
* *
15730 CCAAAAATCCCATTTTGACC
1 CCAAAATTCCAATTTTGACC
15750 CCAAAATTTCCAATTTT-ACC
1 CCAAAA-TTCCAATTTTGACC
15770 CCTAAAATTCCAA
1 CC-AAAATTCCAA
15783 AAATACCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.28
Consensus pattern (20 bp):
CCAAAATTCCAATTTTGACC
Found at i:15817 original size:60 final size:59
Alignment explanation
Indices: 15763--16068 Score: 289
Period size: 60 Copynumber: 5.1 Consensus size: 59
15753 AAATTTCCAA
* * * *
15763 TTTT-ACCCCTAAAATTCCAAAAATACCATTTTTAACCTCGAAACTTCCAAAAATTCCAT
1 TTTTAACCCC-AAAATTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* * * * * * * * * *
15822 TTTTACCCCCTGAACTACTAAAAATCCCATTTTTA-CCCTTAAATTTTCAAAAATACCAT
1 TTTTAACCCC-AAAATTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* * * *
15881 TTTTAACCCCAAAACTTCCAAAAATTCCTTTTTTACCCCCTAAACTACTAAAAATCCCAT
1 TTTTAACCCCAAAA-TTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* *
15941 TTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCTTAACTTCCAAAAATCCCAT
1 TTTTAACCCCAAAA-TTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* * *
16001 TTTTGACCTCGAAATTTCCAAAAATACCATTTTTTA--CCCTGAAACTTCCAAAAAATCCC-T
1 TTTTAACC-CCAAAATTCCAAAAATACCA-TTTTTACCCCCT-AAACTTCC-AAAAATCCCAT
*
16061 TTTAAACC
1 TTTTAACC
16069 TAAATTTTCC
Statistics
Matches: 203, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
58 2 0.01
59 51 0.25
60 131 0.65
61 19 0.09
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
TTTTAACCCCAAAATTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
Found at i:15875 original size:89 final size:89
Alignment explanation
Indices: 15763--16004 Score: 351
Period size: 89 Copynumber: 2.7 Consensus size: 89
15753 AAATTTCCAA
* *
15763 TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTAC
1 TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
*
15828 CCCCTGAACTACTAAAAATCCCAT
66 CCCCTAAACTACTAAAAATCCCAT
* * * *
15852 TTTTACCCTTAAATTTTCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCTTTTTTAC
1 TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
15917 CCCCTAAACTACTAAAAATCCCAT
66 CCCCTAAACTACTAAAAATCCCAT
* * ** *
15941 TTTTAACCCC-AAAACTTCCAAAAATCCCATTTTTACCCCCTTAACTTCCAAAAATCCCATTTTT
1 TTTT-ACCCCTAAAA-TTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTT
16005 GACCTCGAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
89 89 0.66
90 46 0.34
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (89 bp):
TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
CCCCTAAACTACTAAAAATCCCAT
Found at i:18023 original size:20 final size:21
Alignment explanation
Indices: 17979--18025 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
17969 AATTTTAAAA
17979 TTTT-AATTTTTTATATATAT
1 TTTTAAATTTTTTATATATAT
* *
17999 ATTTAAATTTTTTATA-ATGT
1 TTTTAAATTTTTTATATATAT
18019 TTTTAAA
1 TTTTAAA
18026 ATATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAAATTTTTTATATATAT
Found at i:18048 original size:33 final size:30
Alignment explanation
Indices: 17968--18048 Score: 76
Period size: 33 Copynumber: 2.6 Consensus size: 30
17958 TTATTTCAGA
* *
17968 AAATTTTAAAATTT-TAATTTTTTATATAT
1 AAATTTTAAATTTTATAATTTTTTAAATAT
*
17997 ATA-TTTAAATTTTTTATAATGTTTTTAAAATAT
1 AAATTTTAAA--TTTTATAAT-TTTTT-AAATAT
18030 AAATTTTAAATTTGTATAA
1 AAATTTTAAATTT-TATAA
18049 ATATTTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 6 0.15
29 2 0.05
30 3 0.07
31 4 0.10
32 8 0.20
33 12 0.29
34 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
AAATTTTAAATTTTATAATTTTTTAAATAT
Found at i:18078 original size:18 final size:18
Alignment explanation
Indices: 18032--18080 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
18022 TAAAATATAA
*
18032 ATTTTAAATTTGTATAAAT
1 ATTTTAAATTT-TAAAAAT
*
18051 ATTTTGAATTTTAAAAATT
1 ATTTTAAATTTTAAAAA-T
18070 ATTTT-AATTTT
1 ATTTTAAATTTT
18081 TTTTGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTTTAAATTTTAAAAAT
Found at i:18081 original size:19 final size:20
Alignment explanation
Indices: 18018--18081 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
18008 TTTTATAATG
*
18018 TTTTTAAAATATAAATTTTAAA
1 TTTTTAAAA-AT-TATTTTAAA
* * *
18040 TTTGTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTAAA
18059 -TTTTAAAAATTATTTT-AA
1 TTTTTAAAAATTATTTTAAA
18077 TTTTT
1 TTTTT
18082 TTTGTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 9 0.26
19 17 0.50
21 1 0.03
22 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTAAA
Found at i:19003 original size:11 final size:12
Alignment explanation
Indices: 18987--19072 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 12
18977 TTTCTAAAAA
*
18987 TTAAATTT-ACT
1 TTAAATTTAAAT
18998 TTAAATTTAAAT
1 TTAAATTTAAAT
*
19010 TTAAA-TTAATTTT
1 TTAAATTTAA--AT
19023 TTAAATTT-AAT
1 TTAAATTTAAAT
*
19034 TT-AGTTTAAAT
1 TTAAATTTAAAT
*
19045 TTGAAA--TAATT
1 TT-AAATTTAAAT
*
19056 TTAAACTTAAAT
1 TTAAATTTAAAT
19068 TTAAA
1 TTAAA
19073 ATCAATTACA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
10 7 0.12
11 26 0.44
12 16 0.27
13 8 0.14
14 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:19008 original size:6 final size:6
Alignment explanation
Indices: 18987--19072 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
18977 TTTCTAAAAA
* *
18987 TTAAAT TT-ACT TTAAAT TTAAAT TTAAA- TTAATTTT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA--AT TTAAAT TTAAAT
* * *
19034 TT-AGT TTAAAT TTGAAA- -TAATT TTAAAC TTAAAT TTAAA
1 TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAA
19073 ATCAATTACA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
4 2 0.03
5 18 0.29
6 35 0.56
7 3 0.05
8 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:19027 original size:36 final size:35
Alignment explanation
Indices: 18987--19057 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
18977 TTTCTAAAAA
*
18987 TTAAATTTACTTTAAATTTAAATTT-AAATTAATTTT
1 TTAAATTTAATTT-AATTTAAATTTGAAA-TAATTTT
*
19023 TTAAATTTAATTTAGTTTAAATTTGAAATAATTTT
1 TTAAATTTAATTTAATTTAAATTTGAAATAATTTT
19058 AAACTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
TTAAATTTAATTTAATTTAAATTTGAAATAATTTT
Found at i:19831 original size:13 final size:13
Alignment explanation
Indices: 19813--19847 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
19803 ACTTTAATGC
19813 TATTAATAAATAT
1 TATTAATAAATAT
*
19826 TATTAATTAATAT
1 TATTAATAAATAT
*
19839 TAATAATAA
1 TATTAATAA
19848 TAATAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAATAAATAT
Found at i:20892 original size:29 final size:29
Alignment explanation
Indices: 20854--21281 Score: 249
Period size: 30 Copynumber: 14.7 Consensus size: 29
20844 GAGGTCCCTA
*
20854 AACTGTCCAAAAATTCCATTTTCACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
20884 AACTTCCAAAAA-TCCTATTTTTGA-CCTCG
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTCG
* * * *
20913 AAACCTCCAAAAATTCCATTTTCACCCCCA
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
20943 AACTTCCAAAAATCCCA--TTT----T-G
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
20965 -AC-CCCAAAATTTCCAATTTTACCCCT-A
1 AACTTCCAAAAATTCCATTTTTA-CCCTCG
* * *
20992 AAATTCCAAAAATACCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
21021 AAACTTCCAAAAATTCCATTTTTACCCCCTG
1 -AACTTCCAAAAATTCCATTTTTACCCTC-G
* * * **
21052 AACTACTAAAAATCCCATTTTTACCCTTA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
21081 AATTTTCAAAAATACCATTTTTAACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* * *
21111 AACTTCCAAAAATTCCTTTTTTACCCCCTA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* * * *
21141 AACTACTAAAAATCCCATTTTTAACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* * *
21171 AACTTCCAAAAATCCCATTTTTACCCCCTT
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
*
21201 AACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
21230 AAATTTCCAAAAATACCATTTTTTACCCT-G
1 -AACTTCCAAAAATTCCA-TTTTTACCCTCG
* *
21260 AAACTTCCAAAAAATCCCTTTT
1 -AACTTCCAAAAATTCCATTTT
21282 AAACCTAAAT
Statistics
Matches: 313, Mismatches: 59, Indels: 53
0.74 0.14 0.12
Matches are distributed among these distances:
20 10 0.03
21 2 0.01
22 3 0.01
27 3 0.01
28 7 0.02
29 78 0.25
30 193 0.62
31 17 0.05
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:20979 original size:49 final size:49
Alignment explanation
Indices: 20919--21012 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
20909 CTCGAAACCT
* *
20919 CCAAAAATTCC-ATTTTCACCCCCAAACTTCCAAAAATCCCATTTTGACC
1 CCAAAAATTCCAATTTT-ACCCCCAAAATTCCAAAAATACCATTTTGACC
* *
20968 CCAAAATTTCCAATTTTACCCCTAAAATTCCAAAAATACCATTTT
1 CCAAAAATTCCAATTTTACCCCCAAAATTCCAAAAATACCATTTT
21013 TAACCTCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 35 0.88
50 5 0.12
ACGTcount: A:0.37, C:0.32, G:0.01, T:0.30
Consensus pattern (49 bp):
CCAAAAATTCCAATTTTACCCCCAAAATTCCAAAAATACCATTTTGACC
Found at i:20994 original size:21 final size:20
Alignment explanation
Indices: 20948--21000 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
20938 CCCCAAACTT
* *
20948 CCAAAAATCCCATTTTGACC
1 CCAAAATTCCAATTTTGACC
20968 CCAAAATTTCCAATTTT-ACC
1 CCAAAA-TTCCAATTTTGACC
20988 CCTAAAATTCCAA
1 CC-AAAATTCCAA
21001 AAATACCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.28
Consensus pattern (20 bp):
CCAAAATTCCAATTTTGACC
Found at i:21035 original size:60 final size:59
Alignment explanation
Indices: 20981--21286 Score: 289
Period size: 60 Copynumber: 5.1 Consensus size: 59
20971 AAATTTCCAA
* * * *
20981 TTTT-ACCCCTAAAATTCCAAAAATACCATTTTTAACCTCGAAACTTCCAAAAATTCCAT
1 TTTTAACCCC-AAAATTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* * * * * * * * * *
21040 TTTTACCCCCTGAACTACTAAAAATCCCATTTTTA-CCCTTAAATTTTCAAAAATACCAT
1 TTTTAACCCC-AAAATTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* * * *
21099 TTTTAACCCCAAAACTTCCAAAAATTCCTTTTTTACCCCCTAAACTACTAAAAATCCCAT
1 TTTTAACCCCAAAA-TTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* *
21159 TTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCTTAACTTCCAAAAATCCCAT
1 TTTTAACCCCAAAA-TTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
* * *
21219 TTTTGACCTCGAAATTTCCAAAAATACCATTTTTTA--CCCTGAAACTTCCAAAAAATCCC-T
1 TTTTAACC-CCAAAATTCCAAAAATACCA-TTTTTACCCCCT-AAACTTCC-AAAAATCCCAT
*
21279 TTTAAACC
1 TTTTAACC
21287 TAAATTTTCC
Statistics
Matches: 203, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
58 2 0.01
59 51 0.25
60 131 0.65
61 19 0.09
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
TTTTAACCCCAAAATTCCAAAAATACCATTTTTACCCCCTAAACTTCCAAAAATCCCAT
Found at i:21093 original size:89 final size:89
Alignment explanation
Indices: 20981--21222 Score: 351
Period size: 89 Copynumber: 2.7 Consensus size: 89
20971 AAATTTCCAA
* *
20981 TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTAC
1 TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
*
21046 CCCCTGAACTACTAAAAATCCCAT
66 CCCCTAAACTACTAAAAATCCCAT
* * * *
21070 TTTTACCCTTAAATTTTCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCTTTTTTAC
1 TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
21135 CCCCTAAACTACTAAAAATCCCAT
66 CCCCTAAACTACTAAAAATCCCAT
* * ** *
21159 TTTTAACCCC-AAAACTTCCAAAAATCCCATTTTTACCCCCTTAACTTCCAAAAATCCCATTTTT
1 TTTT-ACCCCTAAAA-TTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTT
21223 GACCTCGAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
89 89 0.66
90 46 0.34
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (89 bp):
TTTTACCCCTAAAATTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
CCCCTAAACTACTAAAAATCCCAT
Found at i:23241 original size:20 final size:21
Alignment explanation
Indices: 23197--23243 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
23187 AATTTTAAAA
23197 TTTT-AATTTTTTATATATAT
1 TTTTAAATTTTTTATATATAT
* *
23217 ATTTAAATTTTTTATA-ATGT
1 TTTTAAATTTTTTATATATAT
23237 TTTTAAA
1 TTTTAAA
23244 ATATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAAATTTTTTATATATAT
Found at i:23266 original size:33 final size:30
Alignment explanation
Indices: 23186--23266 Score: 76
Period size: 33 Copynumber: 2.6 Consensus size: 30
23176 TTATTTCAGA
* *
23186 AAATTTTAAAATTT-TAATTTTTTATATAT
1 AAATTTTAAATTTTATAATTTTTTAAATAT
*
23215 ATA-TTTAAATTTTTTATAATGTTTTTAAAATAT
1 AAATTTTAAA--TTTTATAAT-TTTTT-AAATAT
23248 AAATTTTAAATTTGTATAA
1 AAATTTTAAATTT-TATAA
23267 ATATTTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 6 0.15
29 2 0.05
30 3 0.07
31 4 0.10
32 8 0.20
33 12 0.29
34 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
AAATTTTAAATTTTATAATTTTTTAAATAT
Found at i:23296 original size:18 final size:18
Alignment explanation
Indices: 23250--23298 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
23240 TAAAATATAA
*
23250 ATTTTAAATTTGTATAAAT
1 ATTTTAAATTT-TAAAAAT
*
23269 ATTTTGAATTTTAAAAATT
1 ATTTTAAATTTTAAAAA-T
23288 ATTTT-AATTTT
1 ATTTTAAATTTT
23299 TTTTGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTTTAAATTTTAAAAAT
Found at i:23299 original size:19 final size:20
Alignment explanation
Indices: 23236--23299 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
23226 TTTTATAATG
*
23236 TTTTTAAAATATAAATTTTAAA
1 TTTTTAAAA-AT-TATTTTAAA
* * *
23258 TTTGTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTAAA
23277 -TTTTAAAAATTATTTT-AA
1 TTTTTAAAAATTATTTTAAA
23295 TTTTT
1 TTTTT
23300 TTTGTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 9 0.26
19 17 0.50
21 1 0.03
22 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTAAA
Found at i:23797 original size:31 final size:31
Alignment explanation
Indices: 23759--23817 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
23749 GAAGTTATGG
*
23759 TTAAATTTCATATTTAATCCCTATATTTCAC
1 TTAAATTTCAAATTTAATCCCTATATTTCAC
* **
23790 TTAAATTTTAAATTTAATCTTTATATTT
1 TTAAATTTCAAATTTAATCCCTATATTT
23818 TAATTTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAAATTTCAAATTTAATCCCTATATTTCAC
Found at i:31575 original size:17 final size:17
Alignment explanation
Indices: 31545--31626 Score: 103
Period size: 17 Copynumber: 4.8 Consensus size: 17
31535 CTAGGCCCAA
31545 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
31562 TAGAA-TTAAGTTTATTC
1 TA-AATTTAAATTTATTT
31579 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
31596 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
*
31613 TAAATTTTAATTTA
1 TAAATTTAAATTTA
31627 AAATCTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 2 0.04
17 51 0.93
18 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:31588 original size:34 final size:34
Alignment explanation
Indices: 31544--31626 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
31534 TCTAGGCCCA
* *
31544 ATAAATTTAAATTTATTTTAGAA-TTAAGTTTATT
1 ATAAATTTAAATTTATTTGA-AATTTAAATTTATT
*
31578 CTAAATTTAAATTTATTTGAAATTTAAATTTATT
1 ATAAATTTAAATTTATTTGAAATTTAAATTTATT
*
31612 ATAAATTTTAATTTA
1 ATAAATTTAAATTTA
31627 AAATCTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 2 0.05
34 41 0.95
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (34 bp):
ATAAATTTAAATTTATTTGAAATTTAAATTTATT
Found at i:33395 original size:29 final size:29
Alignment explanation
Indices: 33356--33744 Score: 476
Period size: 29 Copynumber: 13.2 Consensus size: 29
33346 GGAGGTCCCT
*
33356 AAACTCTCCAAAAATTCCATTTTTACCCCT
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
* *
33386 ATATTTCCAAAAA-TCTCATTTTTAACCCCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCA
*
33416 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
33445 GAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
33474 GAACTTCCAAAAATCCCATTTTTGACTCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
33504 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
33533 AAACTTCCAAAAATTCCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
* * ***
33563 AAACTTCAAAAAATTCTATTTTTACCTTT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
33592 GAACTTCCAAAAATTCTATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
33622 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
33651 AAACTTCCAAAAATTTCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCC-CA
*
33680 AAACTTCCAAAAATTCTATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
33710 AAACTTCCAAAAACTCCATTTTCAACCCCA
1 AAACTTCCAAAAATTCCATTTT-TACCCCA
33740 AAACT
1 AAACT
33745 CTCAAAATTA
Statistics
Matches: 315, Mismatches: 34, Indels: 20
0.85 0.09 0.05
Matches are distributed among these distances:
28 2 0.01
29 173 0.55
30 138 0.44
31 2 0.01
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:33454 original size:59 final size:58
Alignment explanation
Indices: 33356--33744 Score: 485
Period size: 59 Copynumber: 6.6 Consensus size: 58
33346 GGAGGTCCCT
* * * *
33356 AAACTCTCCAAAAATTCCATTTTTACCCCTATATTTCCAAAAA-TCTCATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTC-CATTTTT-ACCCCC
**
33416 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * *
33474 GAACTTCCAAAAATCCCATTTTTGACTCCAAAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * ***
33533 AAACTTCCAAAAATTCCATTTTTTACCCCAAAACTTCAAAAAATTCTATTTTTACCTTT
1 AAACTTCCAAAAATTCCA-TTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * *
33592 GAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * *
33651 AAACTTCCAAAAATTTCATTTTTACCCTC-AAACTTCCAAAAATTCTATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCC-CAAAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
33710 AAACTTCCAAAAACTCCATTTTCAACCCCAAAACT
1 AAACTTCCAAAAATTCCATTTT-TACCCCAAAACT
33745 CTCAAAATTA
Statistics
Matches: 286, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
58 57 0.20
59 208 0.73
60 21 0.07
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:33753 original size:88 final size:87
Alignment explanation
Indices: 33356--33744 Score: 469
Period size: 88 Copynumber: 4.4 Consensus size: 87
33346 GGAGGTCCCT
* * * *
33356 AAACTCTCCAAAAATTCCATTTTTACCCCTATATTTCCAAAAATCTCATTTTTAACCC-CAAAAC
1 AAACT-TCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTTCATTTTT-ACCCTC-AAAC
*
33420 TTCCAAAAATTCCATTTTTACCCCC
63 TTCCAAAAATTCCATTTTTACCCCA
* ** ** *
33445 GAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCC-AAAACT
1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTTCATTTTT-AC-CCTCAAACT
*
33509 TCCAAAAATTCCATTTTTACCCCC
64 TCCAAAAATTCCATTTTTACCCCA
* * **
33533 AAACTTCCAAAAATTCCATTTTTTACCCCAAAACTT-CAAAAAATTCTATTTTTACCTTTGAACT
1 AAACTTCCAAAAATTCCA-TTTTTACCCCAAAACTTCCAAAAATTTC-ATTTTTACCCTCAAACT
* *
33597 TCCAAAAATTCTATTTTTGACCCTA
64 TCCAAAAATTCCATTTTT-ACCCCA
*
33622 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
*
33687 CAAAAATTCTATTTTTAACCCCA
66 CAAAAATTCCATTTTT-ACCCCA
* *
33710 AAACTTCCAAAAACTCCATTTTCAACCCCAAAACT
1 AAACTTCCAAAAATTCCATTTT-TACCCCAAAACT
33745 CTCAAAATTA
Statistics
Matches: 263, Mismatches: 30, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
87 1 0.00
88 194 0.74
89 68 0.26
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (87 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
CAAAAATTCCATTTTTACCCCA
Found at i:33762 original size:88 final size:86
Alignment explanation
Indices: 33356--33821 Score: 438
Period size: 88 Copynumber: 5.3 Consensus size: 86
33346 GGAGGTCCCT
* * * *
33356 AAACTCTCCAAAAATTCCATTTTTACCCCTATATTTCCAAAAATCTCATTTTTAACCC-CAAAAC
1 AAACT-TCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAT-TCACTTTT-ACCCTC-AAAC
*
33420 TTCCAAAAATTCCATTTTTACCCCC
62 TTCCAAAAATTCCATTTTTACCCCA
* ** * * *
33445 GAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCC-AAAACT
1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAT-TCACTTTT-AC-CCTCAAACT
*
33509 TCCAAAAATTCCATTTTTACCCCC
63 TCCAAAAATTCCATTTTTACCCCA
* * * **
33533 AAACTTCCAAAAATTCCATTTTTTACCCCAAAACTTCAAAAAATTCTATTTTTACCTTTGAACTT
1 AAACTTCCAAAAATTCCA-TTTTTACCCCAAAACTTCCAAAAATTC-ACTTTTACCCTCAAACTT
* *
33598 CCAAAAATTCTATTTTTGACCCTA
64 CCAAAAATTCCATTTTT-ACCCCA
* *
33622 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAA-TTCACTTTTACCCTCAAACTTC
*
33687 CAAAAATTCTATTTTTAACCCCA
65 CAAAAATTCCATTTTT-ACCCCA
* * * *
33710 AAACTTCCAAAAACTCCATTTTCAACCCCAAAAC-TCTC-AAAATTACCCTTTTACCCTCGAA-T
1 AAACTTCCAAAAATTCCATTTT-TACCCCAAAACTTC-CAAAAATT-CACTTTTACCCTCAAACT
* * * *
33772 GTCTAAAAACTCAATTTTTAACCCTA
63 -TCCAAAAATTCCATTTTT-ACCCCA
** *
33798 AATTTTCCCAAAATTACCATTTTT
1 AAACTTCCAAAAATT-CCATTTTT
33822 GCCCTCGGGT
Statistics
Matches: 325, Mismatches: 41, Indels: 23
0.84 0.11 0.06
Matches are distributed among these distances:
87 4 0.01
88 245 0.75
89 76 0.23
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (86 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCACTTTTACCCTCAAACTTCC
AAAAATTCCATTTTTACCCCA
Found at i:45359 original size:6 final size:6
Alignment explanation
Indices: 45348--45431 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
45338 CTGGTCCTAA
* *
45348 TAAATT TAAATT T-ATTT TAGAA-T TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT -TAAATT TAAATT
45394 T--ATT TGAAATT TAAATT T--ATT ATAAATT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAATT -TAAATT TAAATT TAAA
45432 ATCTATTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
4 9 0.15
5 7 0.11
6 35 0.56
7 11 0.18
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:45378 original size:17 final size:17
Alignment explanation
Indices: 45348--45429 Score: 112
Period size: 17 Copynumber: 4.8 Consensus size: 17
45338 CTGGTCCTAA
45348 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
45365 TAGAA-TTAAGTTTATTC
1 TA-AATTTAAATTTATTT
45382 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
45399 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
45416 TAAATTTAAATTTA
1 TAAATTTAAATTTA
45430 AAATCTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
16 2 0.04
17 52 0.93
18 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:45442 original size:23 final size:24
Alignment explanation
Indices: 45395--45443 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
45385 ATTTAAATTT
*
45395 ATTTGAAATTTAAATTTATTATAA
1 ATTTGAAATTTAAATCTATTATAA
45419 ATTT-AAATTTAAAATCTATT-TAA
1 ATTTGAAATTT-AAATCTATTATAA
45442 AT
1 AT
45444 AATGTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTGAAATTTAAATCTATTATAA
Found at i:47132 original size:29 final size:29
Alignment explanation
Indices: 47084--47400 Score: 333
Period size: 29 Copynumber: 10.7 Consensus size: 29
47074 GAGGTCCCTA
*
47084 AACTATCCAAAAATTCCATTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
47114 AACTTCCAAAAA-TCTCATTTTTTACCC-CG
1 AACTTCCAAAAATTC-CA-TTTTTACCCTCG
47143 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
47173 AACTTCC-AAAA-TCTCATTTTTGA-CCTCG
1 AACTTCCAAAAATTC-CATTTTT-ACCCTCG
* * *
47201 AAACTTCAAAAAATTCCATTTTTACCCCCA
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* **
47231 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* **
47261 AACTTCCAAAAATTCTATTTTTACCCTTA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
47290 AACTTCCAAAAATTCCATTTTTTTA-CCTTG
1 AACTTCCAAAAATTCCA--TTTTTACCCTCG
47320 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
47350 AACTTCTAAAAATTTCATTTTTGACTC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
47379 AAACTTCCAAAAACTCCATTTT
1 -AACTTCCAAAAATTCCATTTT
47401 CGACCTCTAA
Statistics
Matches: 250, Mismatches: 19, Indels: 36
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.01
28 18 0.07
29 106 0.42
30 97 0.39
31 27 0.11
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:47181 original size:59 final size:59
Alignment explanation
Indices: 47083--47400 Score: 424
Period size: 59 Copynumber: 5.4 Consensus size: 59
47073 AGAGGTCCCT
* *
47083 AAACTATCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTTACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
*
47143 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC-AAAATCTCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
* * * * **
47201 AAACTTCAAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
* ** * **
47260 AAACTTCCAAAAATTCTATTTTTACCCTTAAACTTCCAAAAAT-TCCATTTTTTTACCTTG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCT-CA-TTTTTGACCCCG
* * *
47320 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAATTTCATTTTTGACTCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
*
47379 AAACTTCCAAAAACTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
47401 CGACCTCTAA
Statistics
Matches: 227, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
58 53 0.23
59 118 0.52
60 55 0.24
61 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
Done.