Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008116.1 Hibiscus syriacus cultivar Beakdansim tig00110655_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: 363508
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2266 original size:16 final size:15
Alignment explanation
Indices: 2245--2278 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
2235 TATGTTGTGA
2245 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
2261 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
2276 GTT
1 GTT
2279 AGATTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:5222 original size:30 final size:30
Alignment explanation
Indices: 5186--5253 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
5176 ACTGCAAGTC
*
5186 CCATCAACGTGCGTTCCACCAGTGCCTGCT
1 CCATCAACGTGCGTTCCACCAGTACCTGCT
5216 CCATCAACGTGCGTTCCACCAGTACCTGCT
1 CCATCAACGTGCGTTCCACCAGTACCTGCT
5246 CCATCAAC
1 CCATCAAC
5254 ACATCTGCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.41, G:0.16, T:0.22
Consensus pattern (30 bp):
CCATCAACGTGCGTTCCACCAGTACCTGCT
Found at i:5265 original size:30 final size:31
Alignment explanation
Indices: 5195--5288 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 31
5185 CCCATCAACG
* *
5195 TGCGTTCCACCAGTGCCTGCTCCATC-A-ACG
1 TGCGTGCCACCAGT-CCTGCTCCATCAACACA
*
5225 TGCGTTCCACCAGTACCTGCTCCATCAACACA
1 TGCGTGCCACCAGT-CCTGCTCCATCAACACA
* *
5257 T-C-TGCCACCATGTGCTTCTCCATCAACACA
1 TGCGTGCCACCA-GTCCTGCTCCATCAACACA
5287 TG
1 TG
5289 ACTCATCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
30 48 0.87
31 4 0.07
32 3 0.05
ACGTcount: A:0.21, C:0.39, G:0.15, T:0.24
Consensus pattern (31 bp):
TGCGTGCCACCAGTCCTGCTCCATCAACACA
Found at i:7945 original size:16 final size:15
Alignment explanation
Indices: 7924--7957 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
7914 TATGTTGTGA
7924 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
7940 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
7955 GTT
1 GTT
7958 AGATTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:12356 original size:2 final size:2
Alignment explanation
Indices: 12351--12376 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12341 ACACACACAC
12351 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
12377 CTTAAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15535 original size:19 final size:20
Alignment explanation
Indices: 15511--15561 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
15501 AATGACCAAT
15511 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
15530 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
15550 AAAATCGCAACG
1 AAAATCGCAACG
15562 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:15571 original size:20 final size:20
Alignment explanation
Indices: 15548--15601 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
15538 AACGCGATTT
*
15548 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
15568 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
15588 AGAAAATCGCAACG
1 AGAAAATCGCAACG
15602 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:15889 original size:20 final size:20
Alignment explanation
Indices: 15636--15887 Score: 324
Period size: 20 Copynumber: 12.4 Consensus size: 20
15626 TTTAGAAGAA
*
15636 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
15656 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
15676 AATCGCAATTGCGATTGAGAG
1 AATCGCAA-TGCGATTGAGAG
* * *
15697 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
15720 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
15740 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
15760 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
15780 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
15800 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
15820 ATTCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
15840 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
15860 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
15880 AATCGCAA
1 AATCGCAA
15888 CGTTGAAAAT
Statistics
Matches: 212, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
20 176 0.83
21 20 0.09
22 2 0.01
23 14 0.07
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:15904 original size:60 final size:60
Alignment explanation
Indices: 15530--15907 Score: 194
Period size: 60 Copynumber: 6.2 Consensus size: 60
15520 ACGCGATATC
* * * ** *** * *
15530 AAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAACGGTCAAAAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCGCAACGTTGAAAAG
* * *
15590 AAAATCGCAACGCGAGCTTCCA-AG-TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTG-
1 AAAATCGCAATGCGA--TT-GAGAGAATCGCAACGCGA-TT-G-AGAAAATCGCAA--CG-TTGA
*
15652 ATAG
57 AAAG
* * * * * * *
15656 --AATCGCAATGCGATTTATAGAATCGCAATTGCGATTGAGAGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAA-CGCGATTGAGAAAATCGCAA--CG-TTGAAAAG
* * * * * * **
15718 AAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATG-CGACTGAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCGCAACGTTGA-AAAG
* * * * * * * * **
15778 AGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGATTCGCAATG-CGACTGAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCGCAACGTTGA-AAAG
* * *
15838 AGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTGAAAAT
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCGCAACGTTGAAAAG
15898 AAAATCGCAA
1 AAAATCGCAA
15908 CGGTCAAAAG
Statistics
Matches: 256, Mismatches: 45, Indels: 34
0.76 0.13 0.10
Matches are distributed among these distances:
59 1 0.00
60 130 0.51
61 29 0.11
62 10 0.04
63 27 0.11
64 53 0.21
66 5 0.02
67 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (60 bp):
AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCGCAACGTTGAAAAG
Found at i:15916 original size:20 final size:20
Alignment explanation
Indices: 15878--15916 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15868 CGCGATTTAG
* *
15878 AAAATCGCAACGTTGAAAAT
1 AAAATCGCAACGGTCAAAAT
15898 AAAATCGCAACGGTCAAAA
1 AAAATCGCAACGGTCAAAA
15917 GAATAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAT
Found at i:16018 original size:6 final size:6
Alignment explanation
Indices: 16007--16051 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
15997 ACCACGTATT
16007 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
16052 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:16631 original size:20 final size:20
Alignment explanation
Indices: 16608--16778 Score: 198
Period size: 20 Copynumber: 8.4 Consensus size: 20
16598 ATTTTCAACG
* *
16608 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
16628 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
16648 TTGCGATTCTCTCAGTCGCG
1 TTGCGATTCTCTCAATCGCA
* *
16668 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
* *
16691 TTGCGACTCTCTCAATCGCG
1 TTGCGATTCTCTCAATCGCA
*
16711 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
16731 TTGCGATTATATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
16751 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
16771 TTGCGATT
1 TTGCGATT
16779 TTCTTCTAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
20 115 0.85
21 2 0.01
22 3 0.02
23 15 0.11
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:16709 original size:83 final size:83
Alignment explanation
Indices: 16606--16758 Score: 216
Period size: 83 Copynumber: 1.8 Consensus size: 83
16596 TTATTTTCAA
* * * * * * *
16606 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTG
1 CGTTGCGACTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
16671 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
* * *
16689 CGTTGCGACTCTCTCAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
16754 CGATT
66 CGATT
16759 CTATCAATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 60 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (83 bp):
CGTTGCGACTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:16775 original size:103 final size:103
Alignment explanation
Indices: 16606--16799 Score: 307
Period size: 103 Copynumber: 1.9 Consensus size: 103
16596 TTATTTTCAA
* * * * * * *
16606 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
16671 CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
66 CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
* *
16709 CGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
16774 CGATTTTCTTCTAAATCGCGTTGCGA
66 CGATTTTCTTCTAAATCGCGTTGCGA
16800 ACTTGGAAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (103 bp):
CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
Found at i:16791 original size:83 final size:81
Alignment explanation
Indices: 16608--16799 Score: 208
Period size: 83 Copynumber: 2.3 Consensus size: 81
16598 ATTTTCAACG
* * * * * * * * *
16608 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTGCG
1 TTGCGACTCTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
*
16673 ATTTTCTTCTAAATCGCG
66 A-TTTCTTC-AAATCGCA
*
16691 TTGCGACTCTCTCAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
1 TTGCGACTCTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
16756 A-TTCTATC-AATCGCA
66 ATTTCT-TCAAATCGCA
*
16771 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--CTC-TCTAAATCGCGTTGCGA
16800 ACTTGGAAGC
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
80 12 0.13
81 4 0.04
82 4 0.04
83 72 0.78
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (81 bp):
TTGCGACTCTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
ATTTCTTCAAATCGCA
Found at i:16840 original size:20 final size:20
Alignment explanation
Indices: 16815--16866 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
16805 GAAGCTCGCA
*
16815 TTGCGATTTTCTTTTGACCG
1 TTGCGATTTTCTTTTGAACG
*
16835 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACG
16855 TTGCGATTTTCT
1 TTGCGATTTTCT
16867 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACG
Found at i:16893 original size:19 final size:20
Alignment explanation
Indices: 16853--16903 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
16843 TTCTTTTTAA
*
16853 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
16873 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
16892 CGTTGCGATTTT
1 CGTTGCGATTTT
16904 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:18267 original size:18 final size:19
Alignment explanation
Indices: 18246--18281 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18236 TATAACAAAA
18246 TACAAA-AAACTAAATATT
1 TACAAATAAACTAAATATT
*
18264 TACAAATAAATTAAATAT
1 TACAAATAAACTAAATAT
18282 AACATAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
TACAAATAAACTAAATATT
Found at i:18302 original size:17 final size:17
Alignment explanation
Indices: 18280--18313 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18270 TAAATTAAAT
18280 ATAACATAATACAAAAA
1 ATAACATAATACAAAAA
*
18297 ATAACATAATATAAAAA
1 ATAACATAATACAAAAA
18314 CCAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAACATAATACAAAAA
Found at i:18409 original size:51 final size:50
Alignment explanation
Indices: 18307--18412 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 50
18297 ATAACATAAT
* * * *
18307 ATAAAAACCAAATATATAAATATAATATTCAATTAAAATATAAAATTAAAC
1 ATAAAAACCAAATATAAAAATATAACATTCAATTAAAAGACAAAA-TAAAC
* *
18358 ATAAAAACTAAATATAAAAAATATAACCTTCAATTAAAAGACATAAA-AAAC
1 ATAAAAACCAAATAT-AAAAATATAACATTCAATTAAAAGACA-AAATAAAC
18409 ATAA
1 ATAA
18413 GATAAAATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 22 0.47
52 22 0.47
53 3 0.06
ACGTcount: A:0.64, C:0.09, G:0.01, T:0.25
Consensus pattern (50 bp):
ATAAAAACCAAATATAAAAATATAACATTCAATTAAAAGACAAAATAAAC
Found at i:20655 original size:15 final size:15
Alignment explanation
Indices: 20635--20685 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
20625 TAGGATTTTA
20635 ATTTTTATTATTAAG
1 ATTTTTATTATTAAG
20650 ATTTTTAGTT-TT-A-
1 ATTTTTA-TTATTAAG
20663 ATTATTTATTATTAAG
1 ATT-TTTATTATTAAG
20679 ATTTTTA
1 ATTTTTA
20686 GTTTACTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 14 0.45
16 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
ATTTTTATTATTAAG
Found at i:20674 original size:29 final size:28
Alignment explanation
Indices: 20630--20689 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
20620 TAAATTAGGA
20630 TTTTAATTTTTATTATTAAGATTTTTAG
1 TTTTAATTTTTATTATTAAGATTTTTAG
20658 TTTTAATTATTTATTATTAAGATTTTTAG
1 TTTTAATT-TTTATTATTAAGATTTTTAG
20687 TTT
1 TTT
20690 ACTATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (28 bp):
TTTTAATTTTTATTATTAAGATTTTTAG
Found at i:23273 original size:15 final size:15
Alignment explanation
Indices: 23253--23290 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
23243 AATGAATTCA
23253 TCAAAATTCAAAGGT
1 TCAAAATTCAAAGGT
23268 TCAAAATTCAAAGGT
1 TCAAAATTCAAAGGT
23283 TCAAAATT
1 TCAAAATT
23291 TATACATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (15 bp):
TCAAAATTCAAAGGT
Found at i:28611 original size:11 final size:11
Alignment explanation
Indices: 28595--28626 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
28585 TAAAGAGAAC
28595 TAAACTAAATA
1 TAAACTAAATA
28606 TAAACTAAATA
1 TAAACTAAATA
28617 TAAACTAAAT
1 TAAACTAAAT
28627 GCCATGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAACTAAATA
Found at i:32416 original size:37 final size:37
Alignment explanation
Indices: 32366--32439 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
32356 GAGATCAGTT
32366 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
1 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
32403 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
1 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
32440 ATCAAACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
Found at i:39023 original size:23 final size:23
Alignment explanation
Indices: 39005--39070 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
38995 CATAGATTTG
39005 TCCCGAAGGACCGCGTAGAATTA
1 TCCCGAAGGACCGCGTAGAATTA
* *
39028 TCTCGAAGGACCAG-ATAGAATTA
1 TCCCGAAGGACC-GCGTAGAATTA
*
39051 TCCCGAAAGACCGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
39071 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTA
Found at i:39237 original size:57 final size:58
Alignment explanation
Indices: 39142--39259 Score: 150
Period size: 57 Copynumber: 2.0 Consensus size: 58
39132 ACCATATAAA
* * *
39142 TATTTCACATAGCATTATTCAATTTATTATTTTCTCACATAGA-ACATATACTCATAG
1 TATTTCACATAGCATTATTCAAATGATCATTTTCTCACATAGACACATATACTCATAG
* * *
39199 TATTTCACCTAGCATTATTCAAATGATCATTTAT-TCACATAGAGCACATTTATTCATAG
1 TATTTCACATAGCATTATTCAAATGATCATTT-TCTCACATAGA-CACATATACTCATAG
39258 TA
1 TA
39260 ACGAAATCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 37 0.71
58 1 0.02
59 14 0.27
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.41
Consensus pattern (58 bp):
TATTTCACATAGCATTATTCAAATGATCATTTTCTCACATAGACACATATACTCATAG
Found at i:39933 original size:43 final size:43
Alignment explanation
Indices: 39872--40005 Score: 268
Period size: 43 Copynumber: 3.1 Consensus size: 43
39862 TTGACCCAAT
39872 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
1 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
39915 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
1 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
39958 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
1 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
40001 ACTCA
1 ACTCA
40006 AAAACTCTTA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (43 bp):
ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
Found at i:45137 original size:3 final size:3
Alignment explanation
Indices: 45129--45243 Score: 212
Period size: 3 Copynumber: 38.3 Consensus size: 3
45119 TTAAAGTTAT
45129 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
45177 TTA TCA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45225 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
45244 GCAAATAAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:48268 original size:31 final size:29
Alignment explanation
Indices: 48206--48274 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
48196 TTTATCTAAG
48206 TACCTAAAG-TATTTTTAGTCAAAATAAA
1 TACCTAAAGTTATTTTTAGTCAAAATAAA
* * *
48234 TACCTAAAGTTATCATTTTGGTCAAGATAGA
1 TACCTAAAGTTAT--TTTTAGTCAAAATAAA
48265 TACCTAAAGT
1 TACCTAAAGT
48275 ATTCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 9 0.26
29 3 0.09
31 23 0.66
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (29 bp):
TACCTAAAGTTATTTTTAGTCAAAATAAA
Found at i:49731 original size:14 final size:14
Alignment explanation
Indices: 49712--49748 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
49702 TTCTTCGATG
49712 AGAGGGAGAGTTAC
1 AGAGGGAGAGTTAC
49726 AGAGGGAGAGTTAC
1 AGAGGGAGAGTTAC
*
49740 AGAGAGAGA
1 AGAGGGAGA
49749 AGAGAGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.43, T:0.11
Consensus pattern (14 bp):
AGAGGGAGAGTTAC
Found at i:50667 original size:36 final size:36
Alignment explanation
Indices: 50596--50667 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
50586 GTTAGAAAAT
**
50596 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAACATAAA
* *
50632 ATTTATATAATTTT-TTTACAAAATTAAAAAGATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAACATAAA
50668 TAGGTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAACATAAA
Found at i:51678 original size:15 final size:15
Alignment explanation
Indices: 51660--51708 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
51650 AAATTACCTG
51660 AAAATTGTTTTACGT
1 AAAATTGTTTTACGT
** *
51675 AAAA-TGAATTACCT
1 AAAATTGTTTTACGT
*
51689 AAAATTGTTTTAGGT
1 AAAATTGTTTTACGT
51704 AAAAT
1 AAAAT
51709 GAATTATATT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (15 bp):
AAAATTGTTTTACGT
Found at i:51692 original size:29 final size:30
Alignment explanation
Indices: 51638--51714 Score: 120
Period size: 29 Copynumber: 2.6 Consensus size: 30
51628 TAAAAAATAA
* *
51638 TTTACATAAAATAAATTACCTGAAAATTGT
1 TTTACGTAAAATGAATTACCTGAAAATTGT
51668 TTTACGTAAAATGAATTACCT-AAAATTGT
1 TTTACGTAAAATGAATTACCTGAAAATTGT
*
51697 TTTAGGTAAAATGAATTA
1 TTTACGTAAAATGAATTA
51715 TATTAATGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 25 0.57
30 19 0.43
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACCTGAAAATTGT
Found at i:52112 original size:25 final size:26
Alignment explanation
Indices: 52041--52117 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 26
52031 TATTACTCAT
52041 TATTAATAATTTAATAATATTAGATTTA
1 TATTAATAATTT-ATAATATTA-ATTTA
** **
52069 TAAAAATAATAGATAATATT-ATTTA
1 TATTAATAATTTATAATATTAATTTA
*
52094 TATTAATAATTTATTATATATAAT
1 TATTAATAATTTATAATAT-TAAT
52118 AATATATTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
25 19 0.50
26 1 0.03
27 10 0.26
28 8 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TATTAATAATTTATAATATTAATTTA
Found at i:55407 original size:21 final size:22
Alignment explanation
Indices: 55369--55421 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
55359 AAACATACCA
* * *
55369 AAAGATAGATGAAA-GTGTCAT
1 AAAGATAAAAGAAAGGTGTCAC
*
55390 AAAGATAAAAGAACGTGTGTCAC
1 AAAGATAAAAGAAAG-GTGTCAC
55413 AAAGATAAA
1 AAAGATAAA
55422 GTTACTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 11 0.42
23 15 0.58
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.19
Consensus pattern (22 bp):
AAAGATAAAAGAAAGGTGTCAC
Found at i:61376 original size:2 final size:2
Alignment explanation
Indices: 61371--61400 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61361 AAATTACAAT
61371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61401 AAGAAAACAA
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):
TA
Found at i:62179 original size:37 final size:37
Alignment explanation
Indices: 62129--62204 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
62119 GTAAGTTAAG
*
62129 TTAGATCTGTTTATCATCTTCCATGGATCTTCTGAGA
1 TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
62166 TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
1 TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
62203 TT
1 TT
62205 TGAGCTCATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (37 bp):
TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
Found at i:64468 original size:35 final size:35
Alignment explanation
Indices: 64407--64478 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
64397 AATTTCAAAT
**
64407 TAATTTAATTTTATTCTAAATCTTAAATTCTAAAA
1 TAATTTAATTACATTCTAAATCTTAAATTCTAAAA
*
64442 TAATTTAATTACATTTTAAAAT-TTAAATTCTAAAA
1 TAATTTAATTACATTCT-AAATCTTAAATTCTAAAA
64477 TA
1 TA
64479 CTTCAATTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (35 bp):
TAATTTAATTACATTCTAAATCTTAAATTCTAAAA
Found at i:65678 original size:35 final size:35
Alignment explanation
Indices: 65533--65679 Score: 179
Period size: 35 Copynumber: 4.2 Consensus size: 35
65523 ATTCCTCCTT
* * * * *
65533 AAATTGAAATATTTTAGAATTT-GGGTTTTATATTG
1 AAATTGAATTACTTTGGAATTTAGGG-TTTAGAATG
* * *
65568 TAATTAAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
65603 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
* * *
65638 AAATTGAATTGCTTTGGAATTTGGGGTTTAAAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
65673 AAATTGA
1 AAATTGA
65680 GGAATGTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
35 96 0.97
36 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (35 bp):
AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
Found at i:66430 original size:9 final size:9
Alignment explanation
Indices: 66418--66443 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
66408 TAATATTTTA
66418 TATTTAATT
1 TATTTAATT
66427 TATTTAATT
1 TATTTAATT
66436 TATTTAAT
1 TATTTAAT
66444 ATGTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:66439 original size:25 final size:25
Alignment explanation
Indices: 66411--66465 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
66401 ATATTTTTAA
*
66411 TATTTTATAT-TTAATTTATTTAATT
1 TATTTTATATGTT-ACTTATTTAATT
*
66436 TATTTAATATGTTACTTATTTAATT
1 TATTTTATATGTTACTTATTTAATT
66461 T-TTTT
1 TATTTT
66466 GCAGATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 3 0.12
25 21 0.81
26 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TATTTTATATGTTACTTATTTAATT
Found at i:70613 original size:17 final size:17
Alignment explanation
Indices: 70591--70625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
70581 AATAAGAAAA
70591 TAATTTATTTTTCAAAT
1 TAATTTATTTTTCAAAT
* *
70608 TAATTTTTTTTTGAAAT
1 TAATTTATTTTTCAAAT
70625 T
1 T
70626 TGTTCATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
TAATTTATTTTTCAAAT
Found at i:71766 original size:22 final size:22
Alignment explanation
Indices: 71724--71766 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
71714 TTTACAATAT
* *
71724 TTTAATATTGTATAAATCAATG
1 TTTAATATTATATAAAACAATG
71746 TTTAATA-TATATAAAAACAAT
1 TTTAATATTATAT-AAAACAAT
71767 CCATCTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (22 bp):
TTTAATATTATATAAAACAATG
Found at i:75013 original size:2 final size:2
Alignment explanation
Indices: 75006--75047 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
74996 TTAATAAGTA
75006 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
75048 TTCCTTTATT
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:77914 original size:62 final size:62
Alignment explanation
Indices: 77817--77941 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
77807 TTTGTAAGGT
77817 TACTCTTTGTCCTCAAAAGAAAGACTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGG
1 TACTCTTTGTCCTCAAAAGAAAGACTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGG
*
77879 TACTCTTTGTCTTCAAAAGAAAGACTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGG
1 TACTCTTTGTCCTCAAAAGAAAGACTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGG
77941 T
1 T
77942 TGAGAAAGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (62 bp):
TACTCTTTGTCCTCAAAAGAAAGACTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGG
Found at i:83149 original size:20 final size:21
Alignment explanation
Indices: 83113--83173 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
83103 TTTTGGTGTA
*
83113 GAGGGAA-TCGATACCCCC-AT
1 GAGGGAACT-GATTCCCCCTAT
*
83133 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACTGATTCCCCCTAT
*
83154 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACTGATTCCCCC
83174 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 15 0.44
21 3 0.09
22 1 0.03
23 15 0.44
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACTGATTCCCCCTAT
Found at i:83182 original size:21 final size:21
Alignment explanation
Indices: 83156--83195 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83146 CCCCCTTTGA
*
83156 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
83177 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
83196 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:85480 original size:13 final size:13
Alignment explanation
Indices: 85462--85507 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
85452 AGGGGGAGTA
85462 ATTTCAAAACTTG
1 ATTTCAAAACTTG
*
85475 ATTTC-AAA--TA
1 ATTTCAAAACTTG
85485 ATTTCAAAAACTTG
1 ATTTC-AAAACTTG
85499 ATTTCAAAA
1 ATTTCAAAA
85508 TCTTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 6 0.22
12 6 0.22
13 9 0.33
14 6 0.22
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:85490 original size:23 final size:24
Alignment explanation
Indices: 85460--85506 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
85450 TAAGGGGGAG
85460 TAATTTC-AAAACTTGATTTCAAA
1 TAATTTCAAAAACTTGATTTCAAA
85483 TAATTTCAAAAACTTGATTTCAAA
1 TAATTTCAAAAACTTGATTTCAAA
85507 ATCTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (24 bp):
TAATTTCAAAAACTTGATTTCAAA
Found at i:86921 original size:26 final size:25
Alignment explanation
Indices: 86892--86951 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
86882 CATTTATTTA
86892 CTCGTTTA-TACTCATTCATGAACAAG
1 CTCGTTTATTA-T-ATTCATGAACAAG
*
86918 CTCGTTTATTTATTTTCATGAACAAG
1 CTCGTTTA-TTATATTCATGAACAAG
86944 CTCGTTTA
1 CTCGTTTA
86952 CTCGTTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 28 0.90
27 1 0.03
28 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.42
Consensus pattern (25 bp):
CTCGTTTATTATATTCATGAACAAG
Found at i:91023 original size:51 final size:51
Alignment explanation
Indices: 90947--91103 Score: 187
Period size: 50 Copynumber: 3.1 Consensus size: 51
90937 TTAGCAGTAA
* *
90947 AGCGCGCCCCCTGTACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGATATGGCGCCACGTGGGGTAT
* * **
90998 AGCGCTCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGATATGGCGCCACGTGGGGTAT
* * *
91048 AGCGCGGCCCCTGCAGCGCGCTATAC-ATGTATAT--CTGACACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATG-ATATGGC-GCCACGTGGGGTAT
91098 AGCGCG
1 AGCGCG
91104 GTGCAGGGGG
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 8 0.09
50 43 0.47
51 39 0.43
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.20
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGATATGGCGCCACGTGGGGTAT
Found at i:91068 original size:50 final size:51
Alignment explanation
Indices: 90947--91073 Score: 184
Period size: 51 Copynumber: 2.5 Consensus size: 51
90937 TTAGCAGTAA
* **
90947 AGCGCGCCCCCTGTACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* *
90998 AGCGCTCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* *
91048 AGCGCGGCCCCTGCAGCGCGCTATAC
1 AGCGCGCCCCCTGCACCGCGCTATAC
91074 ATGTATATCT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 29 0.43
51 39 0.57
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.18
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
Found at i:91222 original size:12 final size:10
Alignment explanation
Indices: 91181--91221 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
91171 TTTATCACAC
91181 CAAATTCTCT
1 CAAATTCTCT
91191 CAAATTCTCT
1 CAAATTCTCT
91201 -AAATTTCTCT
1 CAAA-TTCTCT
*
91211 CAAATACTCT
1 CAAATTCTCT
91221 C
1 C
91222 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:91270 original size:13 final size:14
Alignment explanation
Indices: 91242--91270 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
91232 ATATTTTATA
91242 ATATTTTTACTATT
1 ATATTTTTACTATT
91256 ATATTTTTACT-TT
1 ATATTTTTACTATT
91269 AT
1 AT
91271 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:91480 original size:107 final size:108
Alignment explanation
Indices: 91345--91547 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 108
91335 TGAAAATCAT
*
91345 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
91410 TATTTAGTT-ATTTATTTAATGCATGATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATATTAATAATTAA
* *
91452 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
91517 TAATTAGTTGATTCATTTAATGCATGATTAT
66 TAATTAGTTGATTCATTTAATGCATGATTAT
91548 TAGATTAAGA
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 70 0.78
108 20 0.22
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (108 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATATTAATAATTAA
Found at i:93094 original size:18 final size:18
Alignment explanation
Indices: 93071--93105 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
93061 AGCAGCCACC
93071 GCAGCCATATATGATGCT
1 GCAGCCATATATGATGCT
93089 GCAGCCATATATGATGC
1 GCAGCCATATATGATGC
93106 CGCCATCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (18 bp):
GCAGCCATATATGATGCT
Found at i:97281 original size:48 final size:46
Alignment explanation
Indices: 97190--97283 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 46
97180 CGATATTTGC
* **
97190 CCCGCGCTATATAAAATTATGGAGTAAAGGTATGTCGCGGTACCTG
1 CCCGCGCTATATAAAATTATGGAGTAAAAGTATGAAGCGGTACCTG
*
97236 CCCGCGTTATATAAAATTATTAGGAGTAAAAGTAT-AAGACGGTACCTG
1 CCCGCGCTATATAAAATTA-T-GGAGTAAAAGTATGAAG-CGGTACCTG
97284 ATCTGCGCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 18 0.44
47 2 0.05
48 21 0.51
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
CCCGCGCTATATAAAATTATGGAGTAAAAGTATGAAGCGGTACCTG
Found at i:99186 original size:22 final size:23
Alignment explanation
Indices: 99143--99186 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
99133 TTTAATGTTG
*
99143 AATCATTTAACAATATTTTATTA
1 AATCATTCAACAATATTTTATTA
*
99166 AATCATTCAATAAT-TTTTATT
1 AATCATTCAACAATATTTTATT
99187 TAGATGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (23 bp):
AATCATTCAACAATATTTTATTA
Found at i:100990 original size:2 final size:2
Alignment explanation
Indices: 100983--101026 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
100973 CATTATAAAC
100983 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
101025 AT
1 AT
101027 GAGAATATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101070 original size:5 final size:5
Alignment explanation
Indices: 101060--101098 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
101050 TTGATGAAAT
*
101060 GTATA GTATA G--TA GTATA GTATA ATATA GTATA GTATA G
1 GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTATA G
101099 CATATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
5 27 0.90
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
GTATA
Found at i:107422 original size:27 final size:27
Alignment explanation
Indices: 107392--107445 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
107382 TATATTTTCT
* * * *
107392 AATTTATTTGTATTTTAAAATTTTATA
1 AATTCATTTGTAATATAAAATTCTATA
*
107419 AATTCATTTTTAATATAAAATTCTATA
1 AATTCATTTGTAATATAAAATTCTATA
107446 TTCGTTCATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (27 bp):
AATTCATTTGTAATATAAAATTCTATA
Found at i:108315 original size:15 final size:17
Alignment explanation
Indices: 108290--108363 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 17
108280 CTCAAAATTA
*
108290 AATATTATTTT-A-AAT
1 AATAATATTTTAACAAT
*
108305 AATTATATTTTAACAAT
1 AATAATATTTTAACAAT
*
108322 AATAATATTTTCAC-AT
1 AATAATATTTTAACAAT
* * * *
108338 CATAAAATTATAAAAAT
1 AATAATATTTTAACAAT
108355 AATTAATAT
1 AA-TAATAT
108364 AATATATACT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
15 9 0.20
16 12 0.27
17 18 0.41
18 5 0.11
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATATTTTAACAAT
Found at i:117412 original size:17 final size:17
Alignment explanation
Indices: 117378--117409 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
117368 AGTCTATGTT
117378 ATTTACATATTATTTTA
1 ATTTACATATTATTTTA
117395 ATTTA-ATATTATTTT
1 ATTTACATATTATTTT
117410 TAACATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTACATATTATTTTA
Found at i:117724 original size:27 final size:27
Alignment explanation
Indices: 117694--117749 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
117684 TTTATATATC
117694 TTTAAAAATATTTTACTT-TT-ACTTAAT
1 TTTAAAAATA-TTTA-TTATTAACTTAAT
*
117721 TTTAAATATATTTATTATTAACTTAAT
1 TTTAAAAATATTTATTATTAACTTAAT
117748 TT
1 TT
117750 AAAGATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.08
26 6 0.23
27 18 0.69
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAAAAATATTTATTATTAACTTAAT
Found at i:117761 original size:27 final size:27
Alignment explanation
Indices: 117713--117779 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
117703 ATTTTACTTT
* * *
117713 TACTTAATTTTAAATATATTTATTATTA
1 TACTTAA-TTTAAAGATATTTATCACTA
*
117741 -ACTTAATTTAAAGATGTTTTATCACTA
1 TACTTAATTTAAAGAT-ATTTATCACTA
117768 TA-TTAATTTAAA
1 TACTTAATTTAAA
117780 ATTATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 8 0.24
27 24 0.73
28 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (27 bp):
TACTTAATTTAAAGATATTTATCACTA
Found at i:117940 original size:31 final size:31
Alignment explanation
Indices: 117905--117964 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
117895 AAAAATTAAA
*
117905 ATATATATTTAAACTAAGATAAGAATAAAAT
1 ATATATATTTAAACTAAAATAAGAATAAAAT
* * *
117936 ATATATTTTTAAATTAAAATAATAATAAA
1 ATATATATTTAAACTAAAATAAGAATAAA
117965 TAGTCTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (31 bp):
ATATATATTTAAACTAAAATAAGAATAAAAT
Found at i:118734 original size:39 final size:39
Alignment explanation
Indices: 118691--118788 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 39
118681 TTCTAAATAT
* *
118691 GAAGATTTCACAACTTCACGGCATATTAAGGTAAATGAA
1 GAAGACTTCACAACTGCACGGCATATTAAGGTAAATGAA
* * * * *
118730 GAAGACTCCACGACTGGATGGCATATTCAGGTAAATGAA
1 GAAGACTTCACAACTGCACGGCATATTAAGGTAAATGAA
* * *
118769 AAAGACTTCACGATTGCACG
1 GAAGACTTCACAACTGCACG
118789 ACGTCTTCAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (39 bp):
GAAGACTTCACAACTGCACGGCATATTAAGGTAAATGAA
Found at i:126913 original size:18 final size:18
Alignment explanation
Indices: 126890--126926 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
126880 ATTGATGTGA
*
126890 TATTTTTAAATTATTTAT
1 TATTTTTAAATTAATTAT
126908 TATTTTTAAATTAATTAT
1 TATTTTTAAATTAATTAT
126926 T
1 T
126927 CTTTCATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTTAAATTAATTAT
Found at i:136431 original size:2 final size:2
Alignment explanation
Indices: 136424--136462 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
136414 TTTTAAGAAA
*
136424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
136463 AATAAGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:136829 original size:17 final size:17
Alignment explanation
Indices: 136809--136848 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
136799 TAAAAGCAAT
136809 AATAAAATAAT-ATTACA
1 AATAAAATAATGATTA-A
136826 AAT-AAATAATGATTAA
1 AATAAAATAATGATTAA
136842 AATAAAA
1 AATAAAA
136849 GAAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
AATAAAATAATGATTAA
Found at i:138300 original size:30 final size:30
Alignment explanation
Indices: 138266--138327 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
138256 GGGCCACCGA
* *
138266 TGTTGGGCTTGGAATTGATTGGG-CTGGTTC
1 TGTTGGGCCTGGAATAGATTGGGTC-GGTTC
*
138296 TGTTGGGCCTGGACTAGATTGGGTCGGTTC
1 TGTTGGGCCTGGAATAGATTGGGTCGGTTC
138326 TG
1 TG
138328 GTTTTGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.10, C:0.13, G:0.40, T:0.37
Consensus pattern (30 bp):
TGTTGGGCCTGGAATAGATTGGGTCGGTTC
Found at i:138382 original size:3 final size:3
Alignment explanation
Indices: 138374--138458 Score: 66
Period size: 3 Copynumber: 28.3 Consensus size: 3
138364 TGTATTTATT
* * * *
138374 TAA TAA TAA TAA TAAA TAA -ATA TAA TAA TAT TAA TAT TAA TAT TTA
1 TAA TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
138420 -AA TAA TAA TAA TAA TAA TAG TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
138459 TTAAGTAATT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
2 2 0.03
3 56 0.90
4 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:141322 original size:2 final size:2
Alignment explanation
Indices: 141315--141371 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
141305 ATATCAAAGC
141315 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
141357 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
141372 GTGTTTTGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:144066 original size:18 final size:18
Alignment explanation
Indices: 144045--144102 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
144035 TCGTTTTGGT
144045 GAAAATTTTGTTTTTCTA
1 GAAAATTTTGTTTTTCTA
** * **
144063 GAAAGACATCGTTTTGGT-
1 GAAA-ATTTTGTTTTTCTA
144081 GAAAATTTTGTTTTTCTA
1 GAAAATTTTGTTTTTCTA
144099 GAAA
1 GAAA
144103 GACATCATTT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
17 8 0.29
18 12 0.43
19 8 0.29
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (18 bp):
GAAAATTTTGTTTTTCTA
Found at i:144078 original size:36 final size:36
Alignment explanation
Indices: 144031--144114 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 36
144021 GGTGTAAAAC
144031 GACATCGTTTTGGTGAAAATTTTGTTTTTCTAGAAA
1 GACATCGTTTTGGTGAAAATTTTGTTTTTCTAGAAA
144067 GACATCGTTTTGGTGAAAATTTTGTTTTTCTAGAAA
1 GACATCGTTTTGGTGAAAATTTTGTTTTTCTAGAAA
*
144103 GACATCATTTTG
1 GACATCGTTTTG
144115 ACGATGTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (36 bp):
GACATCGTTTTGGTGAAAATTTTGTTTTTCTAGAAA
Found at i:145273 original size:14 final size:14
Alignment explanation
Indices: 145256--145289 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
145246 CTCGTTTACA
* *
145256 TTCGTTCGTTTTTG
1 TTCGTTCATTTATG
145270 TTCGTTCATTTATG
1 TTCGTTCATTTATG
145284 TTCGTT
1 TTCGTT
145290 TGTCATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.15, G:0.18, T:0.62
Consensus pattern (14 bp):
TTCGTTCATTTATG
Found at i:146417 original size:58 final size:58
Alignment explanation
Indices: 146306--146417 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
146296 AACGATAGGT
* * * **
146306 GACCAAAACGAAATCAAAATGTAACACTAAGTATGATTTTTTTTTTAAATAGTTTGAC
1 GACCAAAACGAAACCAAAATATAACACTAAGTATGAGTTTTTTTAAAAATAGTTTGAC
*
146364 GACCAAAACGAAACCAAAATATAACATTAAGTAT-AGTTTTTTTAAAAAGTAGTT
1 GACCAAAACGAAACCAAAATATAACACTAAGTATGAGTTTTTTTAAAAA-TAGTT
146418 GGGTTACCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 11 0.23
58 36 0.77
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (58 bp):
GACCAAAACGAAACCAAAATATAACACTAAGTATGAGTTTTTTTAAAAATAGTTTGAC
Found at i:146857 original size:105 final size:105
Alignment explanation
Indices: 146669--146867 Score: 326
Period size: 105 Copynumber: 1.9 Consensus size: 105
146659 GCTTTCAACC
* ** *
146669 GAACGTTCAAATACCCTATGCAATCTCTGGTGCTTGAATCTGGGACCTTTAAAGATAACAATCAT
1 GAACGCTCAAATACCCTATGCAATCTCTGGTGCTTGAAAATGAGACCTTTAAAGATAACAATCAT
* *
146734 TCCTTTAATAAGTTAGATCACTTGGTTCACATTTGATAAT
66 TCATTTAATAAGTGAGATCACTTGGTTCACATTTGATAAT
*
146774 GAACGCTCAAATACCCTATGCAATCTCTGGTGCTTGAAAATGAGACCTTTAAGGATAACAATCAT
1 GAACGCTCAAATACCCTATGCAATCTCTGGTGCTTGAAAATGAGACCTTTAAAGATAACAATCAT
*
146839 TCATTTAATCAGTGAGATCACTTGGTTCA
66 TCATTTAATAAGTGAGATCACTTGGTTCA
146868 TGTTACAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 86 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (105 bp):
GAACGCTCAAATACCCTATGCAATCTCTGGTGCTTGAAAATGAGACCTTTAAAGATAACAATCAT
TCATTTAATAAGTGAGATCACTTGGTTCACATTTGATAAT
Found at i:153980 original size:12 final size:12
Alignment explanation
Indices: 153963--153988 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
153953 TTGTTGTGCT
153963 TGCTCCTCGGGC
1 TGCTCCTCGGGC
153975 TGCTCCTCGGGC
1 TGCTCCTCGGGC
153987 TG
1 TG
153989 TTCAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.35, T:0.27
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:158826 original size:20 final size:21
Alignment explanation
Indices: 158788--158827 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
158778 GAAGTTTTAA
* *
158788 GATCATCAATTGTCTTTTGAT
1 GATCATCAATTGACCTTTGAT
158809 GATCATC-ATTGACCTTTGA
1 GATCATCAATTGACCTTTGA
158828 AAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
GATCATCAATTGACCTTTGAT
Found at i:166512 original size:31 final size:31
Alignment explanation
Indices: 166474--166532 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
166464 AGTATTTAAA
* *
166474 ATATTTTTAATTAAAATAAATATTTAAAATT
1 ATATTTTTAATCAAAATAAATAATTAAAATT
166505 ATATTTTTAATCAAAATAAATAATTAAA
1 ATATTTTTAATCAAAATAAATAATTAAA
166533 TAATCATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATTTTTAATCAAAATAAATAATTAAAATT
Found at i:179208 original size:60 final size:60
Alignment explanation
Indices: 179135--179253 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
179125 ATATGTCACA
* * ** *
179135 AAACTATAACTCTCATTTTAAGTTGGTCCTTAAACTTTT-AATTATTCTAATTTCATCCCT
1 AAACTATAACTCTCATTCTAAATCAGTCCTTAAACTTTTGAA-AATTCTAATTTCATCCCT
* *
179195 AAACTATGACTCTCATTCTAAATCAGTCCTTAAACTTTTGAAAATTCTGATTTCATCCC
1 AAACTATAACTCTCATTCTAAATCAGTCCTTAAACTTTTGAAAATTCTAATTTCATCCC
179254 AAAATTCATC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (60 bp):
AAACTATAACTCTCATTCTAAATCAGTCCTTAAACTTTTGAAAATTCTAATTTCATCCCT
Found at i:179479 original size:60 final size:59
Alignment explanation
Indices: 179386--179558 Score: 168
Period size: 60 Copynumber: 2.9 Consensus size: 59
179376 GTCTATACGT
* * * * * **
179386 ATAGTTTGGGATGAAATTGGAATGTTCAAAAAGTATGGGGATTAATTTGGAATGA-AGATC
1 ATAGTTTGGGATGAAATTGAAATATT-TAAAAGTATGAGGACTAATTTAAAATGATAG-TC
* * *
179446 ATAGTTTGGGGATGGAATTGAAATATTTAAAAGTTTGAGGACTGATTTAAAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGTATGAGGACTAATTTAAAATGATAGTC
* * * * *
179506 ATAGTTTAGGGATGAAACTGAAACATTTAAAAGTTTAAGGACCAATTTAAAAT
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGTATGAGGACTAATTTAAAAT
179559 AAAGATTGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
60 76 0.81
61 18 0.19
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATATTTAAAAGTATGAGGACTAATTTAAAATGATAGTC
Found at i:179901 original size:31 final size:28
Alignment explanation
Indices: 179852--179920 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
179842 ATACATGTTT
*
179852 TGACCAAAAATACTTTAGGTCTTTATTA
1 TGACCAAAAATACTTTAGGTATTTATTA
*
179880 TGACCAAAATGATAACTTTAGGTATTTATTT
1 TGACCAAAA--AT-ACTTTAGGTATTTATTA
*
179911 TGACAAAAAA
1 TGACCAAAAA
179921 ATTGGATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 9 0.26
29 1 0.03
30 2 0.06
31 23 0.66
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (28 bp):
TGACCAAAAATACTTTAGGTATTTATTA
Found at i:180444 original size:29 final size:30
Alignment explanation
Indices: 180378--180453 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
180368 AAAAAATTGA
* * *
180378 ATACTTTAGATACATATTTTGACCAAAAAGT
1 ATACTTTAGATACTTACTTTGA-CAAAAAAT
*
180409 AAACTTTAGATACTTACTTTGA-AAAAAAT
1 ATACTTTAGATACTTACTTTGACAAAAAAT
180438 ATACTTT-GAGTACTTA
1 ATACTTTAGA-TACTTA
180454 AAATAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 18 0.46
31 19 0.49
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (30 bp):
ATACTTTAGATACTTACTTTGACAAAAAAT
Found at i:180563 original size:11 final size:12
Alignment explanation
Indices: 180500--180568 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 12
180490 ATATAAATCT
180500 TTATAATATAATAA
1 TTATAA-ATAA-AA
180514 TTAATAAATAAAA
1 TT-ATAAATAAAA
**
180527 TTATATTTAATAA
1 TTATAAATAA-AA
* *
180540 TTATTAATTAAA
1 TTATAAATAAAA
180552 -TATAAATAAAA
1 TTATAAATAAAA
180563 TT-TAAA
1 TTATAAA
180569 AATTTAGGGG
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
11 13 0.30
12 9 0.20
13 12 0.27
14 6 0.14
15 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTATAAATAAAA
Found at i:181179 original size:9 final size:9
Alignment explanation
Indices: 181165--181191 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
181155 CTGCTCTCCT
181165 CTTCTTCTC
1 CTTCTTCTC
181174 CTTCTTCTC
1 CTTCTTCTC
181183 CTTCTTCTC
1 CTTCTTCTC
181192 GTTGCTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:183580 original size:35 final size:35
Alignment explanation
Indices: 183524--183593 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
183514 GTTGAGTCTT
*
183524 CTTCTTCTTTTCTTATAACCCAATCTCATCAACAC
1 CTTCTTCTTTTCTTACAACCCAATCTCATCAACAC
* *
183559 CTTCTTCTTCTTCTT-CCACCCATTCTCATCAACAC
1 CTTCTTCTT-TTCTTACAACCCAATCTCATCAACAC
183594 TCTTACCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 26 0.84
36 5 0.16
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.40
Consensus pattern (35 bp):
CTTCTTCTTTTCTTACAACCCAATCTCATCAACAC
Found at i:194397 original size:23 final size:24
Alignment explanation
Indices: 194370--194414 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
194360 AAATTTAATA
194370 TTAAT-AAAATATTTAA-TATTATT
1 TTAATCAAAATA-TTAATTATTATT
194393 TTAATCAAAATATTAATTATTA
1 TTAATCAAAATATTAATTATTA
194415 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATCAAAATATTAATTATTATT
Found at i:194456 original size:20 final size:20
Alignment explanation
Indices: 194416--194457 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
194406 TAATTATTAA
194416 AATATTTAAAATATATTTATT
1 AATATTTAAAATATA-TTATT
194437 AATATTTAATAATATA-TATT
1 AATATTTAA-AATATATTATT
194457 A
1 A
194458 TTTTTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATTTAAAATATATTATT
Found at i:194458 original size:23 final size:22
Alignment explanation
Indices: 194364--194459 Score: 70
Period size: 23 Copynumber: 4.1 Consensus size: 22
194354 ATTTATAAAT
194364 TTAATA-TTAATAAAATATTTA
1 TTAATATTTAATAAAATATTTA
* *
194385 ATATTATTTTAATCAAAATATTAATTA
1 TTAATA-TTTAAT-AAAATA-T--TTA
*
194412 TTAAAATATTTAA-AATATATTTA
1 TT--AATATTTAATAAAATATTTA
*
194435 TTAATATTTAATAATATATATTA
1 TTAATATTTAATAAAATAT-TTA
194458 TT
1 TT
194460 TTTGTAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
21 13 0.22
22 7 0.12
23 15 0.25
24 6 0.10
25 2 0.03
26 5 0.08
27 4 0.07
28 5 0.08
29 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATATTTAATAAAATATTTA
Found at i:194623 original size:13 final size:13
Alignment explanation
Indices: 194599--194640 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
194589 AAATTATTAA
194599 TAATTT-ATATATT
1 TAATTTAATATA-T
194612 TAATATTAATATAT
1 TAAT-TTAATATAT
194626 TAATTTAATAATAT
1 TAATTTAAT-ATAT
194640 T
1 T
194641 TTAATAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTTAATATAT
Found at i:194627 original size:8 final size:8
Alignment explanation
Indices: 194579--194646 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
194569 TTCATAGAAA
194579 TAATATTAT
1 TAATA-TAT
194588 TAA-ATTAT
1 TAATA-TAT
194596 TAATA-AT
1 TAATATAT
*
194603 TTATATAT
1 TAATATAT
*
194611 TTA-ATAT
1 TAATATAT
194618 TAATATAT
1 TAATATAT
* *
194626 TAATTTAA
1 TAATATAT
*
194634 TAATATTT
1 TAATATAT
194642 TAATA
1 TAATA
194647 AAGATGTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.24
8 33 0.67
9 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAATATAT
Found at i:194644 original size:30 final size:28
Alignment explanation
Indices: 194577--194646 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
194567 ATTTCATAGA
194577 AATAATATTATTAA-ATTATTAATAATTT
1 AATAATATT-TTAATATTATTAATAATTT
*
194605 -AT-ATA-TTTAATATTAATATATTAATTT
1 AATAATATTTTAATATT-AT-TAATAATTT
194632 AATAATATTTTAATA
1 AATAATATTTTAATA
194647 AAGATGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
24 4 0.11
25 4 0.11
26 5 0.14
27 10 0.29
28 2 0.06
29 3 0.09
30 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATAATATTTTAATATTATTAATAATTT
Found at i:197093 original size:17 final size:17
Alignment explanation
Indices: 197068--197101 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
197058 GAAGACTAAA
* *
197068 TTTATTTTAATTTATTT
1 TTTAATTTAATATATTT
197085 TTTAATTTAATATATTT
1 TTTAATTTAATATATTT
197102 ATTTCTACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATTTAATATATTT
Found at i:197383 original size:29 final size:29
Alignment explanation
Indices: 197350--197420 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
197340 TATCTCTTTA
*
197350 ATTTTGTTTTAACTTATTAAATAT-TTTT
1 ATTTTTTTTTAACTTATTAAATATATTTT
*
197378 ATTTTTTTCTTAATTTATTAAATATATTTT
1 ATTTTTTT-TTAACTTATTAAATATATTTT
197408 ATTTTTATTTTAA
1 ATTTTT-TTTTAA
197421 TGTAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 7 0.18
29 15 0.39
30 14 0.37
31 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (29 bp):
ATTTTTTTTTAACTTATTAAATATATTTT
Found at i:197434 original size:31 final size:31
Alignment explanation
Indices: 197368--197446 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
197358 TTAACTTATT
* **
197368 AAATAT-TTTTATTTTT-TTCTTAATTTATT
1 AAATATATTTTATTTTTATTCTTAATGTAAA
197397 AAATATATTTTATTTTTATT-TTAATGTAAA
1 AAATATATTTTATTTTTATTCTTAATGTAAA
*
197427 AATATATATTTTATCTTTAT
1 AA-ATATATTTTATTTTTAT
197447 CGTCACTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.14
30 19 0.44
31 18 0.42
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (31 bp):
AAATATATTTTATTTTTATTCTTAATGTAAA
Found at i:197608 original size:64 final size:55
Alignment explanation
Indices: 197538--197684 Score: 146
Period size: 51 Copynumber: 2.6 Consensus size: 55
197528 TATATTACAA
*
197538 TTATTTTAAATTAAAAAATATATAATATTTTATTCTTATCTTTACTTAAAAATATATTTTATTC
1 TTATTTTAAATTAAAAAATATAT-ATATTTTA---TTAT-TAT-CTT---AATATATTTTATTC
197602 TTATTTTAAA-T--AAAA-ATATATATTTTATTATTATCTTAATATATTTTATTC
1 TTATTTTAAATTAAAAAATATATATATTTTATTATTATCTTAATATATTTTATTC
*
197653 TTATTTTCAATT--AAAATATATAT-TTTTATTAT
1 TTATTTTAAATTAAAAAATATATATATTTTATTAT
197685 CTTAACTTTT
Statistics
Matches: 79, Mismatches: 2, Indels: 16
0.81 0.02 0.16
Matches are distributed among these distances:
51 23 0.29
52 14 0.18
53 6 0.08
54 3 0.04
55 2 0.03
56 4 0.05
59 8 0.10
60 4 0.05
61 4 0.05
63 1 0.01
64 10 0.13
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (55 bp):
TTATTTTAAATTAAAAAATATATATATTTTATTATTATCTTAATATATTTTATTC
Found at i:197625 original size:30 final size:30
Alignment explanation
Indices: 197515--197640 Score: 103
Period size: 30 Copynumber: 4.0 Consensus size: 30
197505 CTATTAAATT
* **
197515 AATATAAAATATATATATTACAATTATTTTA
1 AATA-AAAATATATATTTTATTATTATTTTA
*
197546 AATTAAAAAATATATAATATTTTATTCTTATCTTT-
1 AA-T--AAAA-ATAT-ATATTTTATTATTAT-TTTA
* * *
197581 ACTTAAAA-ATATATTTTATTCTTATTTTA
1 AATAAAAATATATATTTTATTATTATTTTA
*
197610 AATAAAAATATATATTTTATTATTATCTTA
1 AATAAAAATATATATTTTATTATTATTTTA
197640 A
1 A
197641 TATATTTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.04
29 21 0.27
30 22 0.29
31 3 0.04
32 4 0.05
33 3 0.04
34 6 0.08
35 12 0.16
36 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (30 bp):
AATAAAAATATATATTTTATTATTATTTTA
Found at i:197645 original size:51 final size:49
Alignment explanation
Indices: 197588--197689 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 49
197578 TTTACTTAAA
197588 AATATATTTTATTCTTATTTTAAATAAAAATATATATTTTATTATTATCTT
1 AATATATTTTATTCTTATTTTAAATAAAAATATATA-TTT-TTATTATCTT
* *
197639 AATATATTTTATTCTTATTTTCAATTAAAATATATATTTTTATTATCTT
1 AATATATTTTATTCTTATTTTAAATAAAAATATATATTTTTATTATCTT
197688 AA
1 AA
197690 CTTTTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 12 0.24
50 3 0.06
51 34 0.69
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (49 bp):
AATATATTTTATTCTTATTTTAAATAAAAATATATATTTTTATTATCTT
Found at i:197684 original size:28 final size:28
Alignment explanation
Indices: 197562--197684 Score: 98
Period size: 28 Copynumber: 4.5 Consensus size: 28
197552 AAAATATATA
* *
197562 ATATTTTATTCTTATCTTT-ACTTAAAAAT
1 ATATTTTATTATTAT-TTTCAATT-AAAAT
* * *
197591 ATATTTTATTCTTATTTTAAATAAAAAT
1 ATATTTTATTATTATTTTCAATTAAAAT
* *
197619 ATATATT-TTATTATTATC--TT--AAT
1 ATATTTTATTATTATTTTCAATTAAAAT
*
197642 ATATTTTATTCTTATTTTCAATTAAAAT
1 ATATTTTATTATTATTTTCAATTAAAAT
197670 ATATATTT-TTATTAT
1 ATAT-TTTATTATTAT
197685 CTTAACTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
23 9 0.12
24 9 0.12
25 1 0.01
26 2 0.03
27 8 0.11
28 27 0.36
29 20 0.26
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATTTTATTATTATTTTCAATTAAAAT
Found at i:197714 original size:80 final size:80
Alignment explanation
Indices: 197562--197715 Score: 172
Period size: 80 Copynumber: 1.9 Consensus size: 80
197552 AAAATATATA
* * * *
197562 ATATTTTATTCTTATCTTTACTTAAAAATATATTTTATTCTTATTTTAAATAAAAATATATATTT
1 ATATTTTATTCTTATCTTTAATTAAAAATATATTTTATTATTATCTTAAATAAAAATATATATTA
* *
197627 TATTATTATCTTAAT
66 AAATATTATCTTAAT
* *
197642 ATATTTTATTCTTAT-TTTCAATT-AAAATATATATTT-TTATTATCTTAACTTTTAAAA-ATAT
1 ATATTTTATTCTTATCTTT-AATTAAAAATATAT-TTTATTATTATCTTAA--ATAAAAATATAT
197703 ATTAAAATATTAT
62 ATTAAAATATTAT
197716 ATATTTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
79 22 0.35
80 35 0.56
81 5 0.08
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (80 bp):
ATATTTTATTCTTATCTTTAATTAAAAATATATTTTATTATTATCTTAAATAAAAATATATATTA
AAATATTATCTTAAT
Found at i:197748 original size:30 final size:30
Alignment explanation
Indices: 197714--197781 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
197704 TTAAAATATT
197714 ATATATTTTTTA-ATTTAAAATAATAGTAAA
1 ATATATTTTTTATA-TTAAAATAATAGTAAA
*
197744 ATATATATTTTTATATTAAATTAATAGTAAA
1 ATATAT-TTTTTATATTAAAATAATAGTAAA
197775 A-ATATTT
1 ATATATTT
197782 AAATATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 2 0.06
30 10 0.29
31 22 0.63
32 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
ATATATTTTTTATATTAAAATAATAGTAAA
Found at i:198717 original size:45 final size:46
Alignment explanation
Indices: 198656--198760 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 46
198646 TGCATTAAGT
* * * *
198656 GTGCATCTATGCATAAAATG-TATTCAATGTTTTGAAT-AAGCCTAA
1 GTGCATCGATGCATAAAATGCAATT-AATGTTTTCAATAAAACCTAA
* *
198701 GTGCATCGATGCATAAAATGCAATTGATGTTTTCATTAAAACCTAA
1 GTGCATCGATGCATAAAATGCAATTAATGTTTTCAATAAAACCTAA
198747 GTGCATCGATGCAT
1 GTGCATCGATGCAT
198761 GGAGAGTGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.54
46 24 0.46
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCAATTAATGTTTTCAATAAAACCTAA
Found at i:198832 original size:20 final size:20
Alignment explanation
Indices: 198807--198844 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
198797 CAATTTATTC
198807 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
198827 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
198845 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:201463 original size:20 final size:20
Alignment explanation
Indices: 201438--201489 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
201428 ACCCGACGGA
201438 TGCATCGATGCATGGCTTTG
1 TGCATCGATGCATGGCTTTG
*
201458 TGCATCGACGCATGGCTTTG
1 TGCATCGATGCATGGCTTTG
201478 TGCATCGATGCA
1 TGCATCGATGCA
201490 CATTCAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATGGCTTTG
Found at i:201532 original size:44 final size:44
Alignment explanation
Indices: 201481--201577 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
201471 GGCTTTGTGC
* *
201481 ATCGATGCACATTC-AA-GGAGTGCATCGGTGCA-TATTCATGATGT
1 ATCGATGCACATACAAAGGGA-TGCATCGATGCACTATTCA-G-TGT
*
201525 ATCGATGCACATACAAAGGGATGCATCGATGCACTGTTCAGTGT
1 ATCGATGCACATACAAAGGGATGCATCGATGCACTATTCAGTGT
201569 ATCGATGCA
1 ATCGATGCA
201578 TTAAGAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 25 0.53
45 14 0.30
46 8 0.17
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATACAAAGGGATGCATCGATGCACTATTCAGTGT
Found at i:201533 original size:21 final size:23
Alignment explanation
Indices: 201477--201558 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
201467 GCATGGCTTT
201477 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* * *
201500 GTGCATCGGTGCATATTC-ATGA
1 GTGCATCGATGCACATTCAAGGA
* *
201522 -TGTATCGATGCACATACAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
201544 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
201559 TGTTCAGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 13 0.28
22 3 0.07
23 18 0.39
24 12 0.26
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:207404 original size:45 final size:46
Alignment explanation
Indices: 207344--207448 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
207334 TGCACTAAGT
* * *
207344 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAA
1 GTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAA
* * *
207389 GTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAATCTGA
1 GTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAA
207435 GTGCATCGATGCAT
1 GTGCATCGATGCAT
207449 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 34 0.64
46 19 0.36
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAA
Found at i:207520 original size:20 final size:20
Alignment explanation
Indices: 207495--207532 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
207485 CAATTTATTC
207495 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
207515 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
207533 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:221346 original size:3 final size:3
Alignment explanation
Indices: 221338--221380 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
221328 AAAACGTTAA
* * *
221338 AAT AAT AAT AAT AAT AAT AAT TAT TAT TAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
221381 AGAATAGTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:221734 original size:26 final size:28
Alignment explanation
Indices: 221698--221752 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
221688 TTACAATCCC
221698 TAAAATTTTTAAA-TTTTC-TTGTATTT
1 TAAAATTTTTAAATTTTTCTTTGTATTT
*
221724 TAAATTTTTTAAATTTTTCTTTGTATTT
1 TAAAATTTTTAAATTTTTCTTTGTATTT
221752 T
1 T
221753 TTTTAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.46
27 5 0.19
28 9 0.35
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (28 bp):
TAAAATTTTTAAATTTTTCTTTGTATTT
Found at i:222564 original size:29 final size:29
Alignment explanation
Indices: 222522--222588 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
222512 GGGCTCGTGC
222522 TTCGACCATAAAGCTTCAGCACTGTCCAT
1 TTCGACCATAAAGCTTCAGCACTGTCCAT
222551 TTCGACCATAAAGCTTCAGCACTGTCCAT
1 TTCGACCATAAAGCTTCAGCACTGTCCAT
222580 TTCGACCAT
1 TTCGACCAT
222589 GATAGACCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
TTCGACCATAAAGCTTCAGCACTGTCCAT
Found at i:226595 original size:29 final size:29
Alignment explanation
Indices: 226491--226587 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
226481 GTATGATCTT
* *
226491 TATTTTAAATTGAT-CTCTAAACTTTTAAA
1 TATTTTAAATTAATCCTC-AAACTTTTGAA
* * * *
226520 TATTTTAATTTTATCCTTAAAC-TATGACTA
1 TATTTTAAATTAATCCTCAAACTTTTGA--A
226550 TCATTTTAAATTAATCCTCAAACTTTTGAA
1 T-ATTTTAAATTAATCCTCAAACTTTTGAA
226580 TATTTTAA
1 TATTTTAA
226588 TTTCATCCCC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.06
29 23 0.43
30 6 0.11
31 18 0.33
32 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (29 bp):
TATTTTAAATTAATCCTCAAACTTTTGAA
Found at i:226600 original size:29 final size:29
Alignment explanation
Indices: 226491--226600 Score: 78
Period size: 29 Copynumber: 3.7 Consensus size: 29
226481 GTATGATCTT
* * * *
226491 TATTTTAAATTGATCTCTAAACTTTTAAA
1 TATTTTAAATTAATCCCCAAACTTTTGAA
* * ** *
226520 TATTTTAATTTTATCCTTAAAC-TATGACTA
1 TATTTTAAATTAATCCCCAAACTTTTGA--A
*
226550 TCATTTTAAATTAATCCTCAAACTTTTGAA
1 T-ATTTTAAATTAATCCCCAAACTTTTGAA
* *
226580 TATTTTAATTTCATCCCCAAA
1 TATTTTAAATTAATCCCCAAA
226601 TTGTGACATT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
28 3 0.05
29 35 0.55
30 4 0.06
31 18 0.28
32 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.46
Consensus pattern (29 bp):
TATTTTAAATTAATCCCCAAACTTTTGAA
Found at i:226620 original size:60 final size:60
Alignment explanation
Indices: 226496--226664 Score: 146
Period size: 60 Copynumber: 2.8 Consensus size: 60
226486 ATCTTTATTT
* * ** *
226496 TAAATTGATCTCTAAACTTTTAAATATTTTAATTTTATCCTTAAACTATGACTATCATTT
1 TAAATTAATCTCTAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACTATCATTC
* * *
226556 TAAATTAATC-CTCAAACTTTTGAATATTTTAATTTCATCCCCAAATTGTGAC-ATTCATTC
1 TAAATTAATCTCT-AAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACTA-TCATTC
*** * * * **
226616 TAAATCGGTCTCCAAACTTTTGGAACATTCCAATTTCAT-CCCAAACTAT
1 TAAATTAATCTCTAAACTTTT-AAATATTTTAATTTCATCCCCAAACTAT
226665 ACGTATATAC
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 3 0.03
60 70 0.80
61 15 0.17
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (60 bp):
TAAATTAATCTCTAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACTATCATTC
Found at i:229605 original size:20 final size:21
Alignment explanation
Indices: 229566--229608 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
229556 ATTGATTTTA
229566 TATTTTCATAAATAATATATT
1 TATTTTCATAAATAATATATT
*
229587 TATTTTCCTAAAT-ATATATT
1 TATTTTCATAAATAATATATT
229607 TA
1 TA
229609 AAATAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTTCATAAATAATATATT
Found at i:231289 original size:88 final size:88
Alignment explanation
Indices: 231140--231317 Score: 329
Period size: 88 Copynumber: 2.0 Consensus size: 88
231130 ATCGATAGTA
*
231140 TAAAAGAATTGCTCCACTAATGCGATGATATTGTTGCGATGTGACATATTTGGATAACCTTAATC
1 TAAAAGAATTGCTCCACAAATGCGATGATATTGTTGCGATGTGACATATTTGGATAACCTTAATC
231205 CTTAAACATTAAAATCTAACATC
66 CTTAAACATTAAAATCTAACATC
* *
231228 TAAAATAATTGCTCCACAAATGCGATTATATTGTTGCGATGTGACATATTTGGATAACCTTAATC
1 TAAAAGAATTGCTCCACAAATGCGATGATATTGTTGCGATGTGACATATTTGGATAACCTTAATC
231293 CTTAAACATTAAAATCTAACATC
66 CTTAAACATTAAAATCTAACATC
231316 TA
1 TA
231318 GACTATGAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (88 bp):
TAAAAGAATTGCTCCACAAATGCGATGATATTGTTGCGATGTGACATATTTGGATAACCTTAATC
CTTAAACATTAAAATCTAACATC
Found at i:233230 original size:9 final size:8
Alignment explanation
Indices: 233211--233243 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
233201 AAATAATGGG
*
233211 AAAAAAGA
1 AAAAAATA
233219 AAAAAATA
1 AAAAAATA
233227 AAAAAAT-
1 AAAAAATA
233234 AAAAAATA
1 AAAAAATA
233242 AA
1 AA
233244 GCAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (8 bp):
AAAAAATA
Done.