Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015003.1 Kokia drynarioides strain JFW-HI SEQ_130047, 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: 198370
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 146 characters in sequence are not A, C, G, or T
Found at i:3039 original size:15 final size:16
Alignment explanation
Indices: 3019--3053 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3009 AGAACTCAAC
3019 AAATATTTTTCT-TTT
1 AAATATTTTTCTGTTT
*
3034 AAATATTTTTTTGTTT
1 AAATATTTTTCTGTTT
3050 AAAT
1 AAAT
3054 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (16 bp):
AAATATTTTTCTGTTT
Found at i:3822 original size:163 final size:163
Alignment explanation
Indices: 3631--4117 Score: 888
Period size: 161 Copynumber: 3.0 Consensus size: 163
3621 AAATATGTAT
* * * * *
3631 TTTTTTAACTTAACAGTTTAAGAGTGTAAGTAGTAATGAGAAATATATCAAAATAAATTTTAATG
1 TTTTTTAACTTAATAGTTTAAAAGTGTAAGTAGTAACGAGAATTATATCGAAATAAATTTTAATG
3696 ACATAATTTTTTTAACACGTTGGATCAAAACAATAAATTAAATATTTACAATTTGATACAACCTA
66 ACATAATTTTTTTAACACGTTGGATCAAAACAATAAATTAAATATTTACAATTTGATACAACCTA
3761 AAACGTTTTAAAAATTATATGAAGAAATTAAAA
131 AAACGTTTTAAAAATTATATGAAGAAATTAAAA
3794 TTTTTTAACTTAATAGTTTAAAAGTGTAAGTAGTAACGAGAATTATATCGAAATAAATTTTAATG
1 TTTTTTAACTTAATAGTTTAAAAGTGTAAGTAGTAACGAGAATTATATCGAAATAAATTTTAATG
3859 ACATAATTTTTTTAACACGTTGGATCAAAAC--TAAATTAAATATTTACAATTTGATACAACCTA
66 ACATAATTTTTTTAACACGTTGGATCAAAACAATAAATTAAATATTTACAATTTGATACAACCTA
3922 AAACGTTTTAAAAATTATATGAAGAAATTAAAA
131 AAACGTTTTAAAAATTATATGAAGAAATTAAAA
*
3955 ATTTTTAACTTAATAGTTTAAAAGTGTAAGTAGTAACGAGAATTATATCGAAATAAATTTTAATG
1 TTTTTTAACTTAATAGTTTAAAAGTGTAAGTAGTAACGAGAATTATATCGAAATAAATTTTAATG
*
4020 ACATAATTTTTTTAACACGTTGGGTCAAAACAATAAATTAAATATTTACAATTTGATACAACCTA
66 ACATAATTTTTTTAACACGTTGGATCAAAACAATAAATTAAATATTTACAATTTGATACAACCTA
*
4085 AAACGTTTTAAAAATTACATGAAGAAATTAAAA
131 AAACGTTTTAAAAATTATATGAAGAAATTAAAA
4118 ATTGAACCGC
Statistics
Matches: 314, Mismatches: 8, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
161 159 0.51
163 155 0.49
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (163 bp):
TTTTTTAACTTAATAGTTTAAAAGTGTAAGTAGTAACGAGAATTATATCGAAATAAATTTTAATG
ACATAATTTTTTTAACACGTTGGATCAAAACAATAAATTAAATATTTACAATTTGATACAACCTA
AAACGTTTTAAAAATTATATGAAGAAATTAAAA
Found at i:15585 original size:4 final size:4
Alignment explanation
Indices: 15576--15613 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
15566 TTATTTCTTA
15576 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
15614 ATACATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:32168 original size:13 final size:13
Alignment explanation
Indices: 32152--32178 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32142 TTTTTCTCTT
32152 TTTTTATTTTTTA
1 TTTTTATTTTTTA
32165 TTTTTATTTTTTA
1 TTTTTATTTTTTA
32178 T
1 T
32179 GATGCATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:32820 original size:18 final size:18
Alignment explanation
Indices: 32799--32846 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
32789 TAGGCCCAGT
* *
32799 GATTACTCCCGGCCTAGC
1 GATTACTCCAGACCTAGC
* *
32817 GATTACTCTAGACCTAGT
1 GATTACTCCAGACCTAGC
32835 GATTACTCCAGA
1 GATTACTCCAGA
32847 TGGGGTTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (18 bp):
GATTACTCCAGACCTAGC
Found at i:37879 original size:27 final size:25
Alignment explanation
Indices: 37834--37898 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 25
37824 TGTTCACTTT
*
37834 TTTTTTTTTTAATATAAAATTCTATAA
1 TTTTTTTTTCAA-A-AAAATTCTATAA
37861 TTATTTTCTTTCAAAAAAATTCTATAA
1 TT-TTTT-TTTCAAAAAAATTCTATAA
37888 TTTTTTTTTCA
1 TTTTTTTTTCA
37899 TTTGTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 5 0.14
26 4 0.11
27 16 0.46
28 5 0.14
29 5 0.14
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTTTTTTCAAAAAAATTCTATAA
Found at i:39406 original size:2 final size:2
Alignment explanation
Indices: 39399--39429 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
39389 CTATATTCCT
39399 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39430 AACTTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41233 original size:18 final size:17
Alignment explanation
Indices: 41212--41245 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
41202 AGAGAGAGAA
41212 GAAGAAGAAGAGGAAAGT
1 GAAGAAGAAGA-GAAAGT
41230 GAAGAAGAAGAGAAAG
1 GAAGAAGAAGAGAAAG
41246 AACAAAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (17 bp):
GAAGAAGAAGAGAAAGT
Found at i:42491 original size:6 final size:6
Alignment explanation
Indices: 42462--42498 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
42452 ACAAGGACAA
42462 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAA-AG GA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GA
42499 GAAGTGGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:43819 original size:2 final size:2
Alignment explanation
Indices: 43812--43849 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
43802 TCAAACCTTT
* *
43812 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43850 GCCAAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43960 original size:26 final size:26
Alignment explanation
Indices: 43931--43987 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
43921 TGATGCAAAC
*
43931 GTAATGATAACGGTGAAATTAAAATA
1 GTAATGATAACGATGAAATTAAAATA
*
43957 GTAACGATAACGATGAAATTAAAATA
1 GTAATGATAACGATGAAATTAAAATA
*
43983 ATAAT
1 GTAAT
43988 TATGAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (26 bp):
GTAATGATAACGATGAAATTAAAATA
Found at i:45999 original size:16 final size:17
Alignment explanation
Indices: 45965--46001 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
45955 GTTTTAAAAT
45965 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
45983 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
45999 TTT
1 TTT
46002 TCATTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:50037 original size:6 final size:6
Alignment explanation
Indices: 50028--50054 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
50018 TAATTATAAA
50028 AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAA
50055 ATATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:50320 original size:12 final size:13
Alignment explanation
Indices: 50303--50332 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50293 GTCTAAATTT
50303 AATTTG-ATTTAA
1 AATTTGAATTTAA
50315 AATTTGAATTTAA
1 AATTTGAATTTAA
50328 AATTT
1 AATTT
50333 TATTCAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
AATTTGAATTTAA
Found at i:50466 original size:28 final size:28
Alignment explanation
Indices: 50422--50481 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
50412 ATATTTATAT
*
50422 TATATTATTTTAATATTTAATAA-TTTTA
1 TATATTATTTTAATATTGAA-AATTTTTA
*
50450 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAATTTTTA
50478 TATA
1 TATA
50482 ATGATCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAATTTTTA
Found at i:50479 original size:26 final size:27
Alignment explanation
Indices: 50421--50480 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
50411 AATATTTATA
*
50421 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
50448 TATATATT-TTTTATTTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
50475 TTATAT
1 TTATAT
50481 AATGATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 12 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:53335 original size:3 final size:3
Alignment explanation
Indices: 53327--53361 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
53317 AGCAGTGAGT
53327 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53362 TATTTCTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54034 original size:26 final size:27
Alignment explanation
Indices: 54005--54055 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
53995 TCAAAAAGTT
54005 AAAATTTAAT-TTTTGTTTA-TTTTTCA
1 AAAATTTAATCTTTT-TTTACTTTTTCA
*
54031 AAAATTTAGTCTTTTTTTACTTTTT
1 AAAATTTAATCTTTTTTTACTTTTT
54056 AGATTTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (27 bp):
AAAATTTAATCTTTTTTTACTTTTTCA
Found at i:60689 original size:18 final size:17
Alignment explanation
Indices: 60666--60706 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
60656 TTGAATCAAG
*
60666 TTTTATATTTTTAATAAA
1 TTTTATATTTTCAA-AAA
60684 TTTTAT-TTTTCAAAAA
1 TTTTATATTTTCAAAAA
60700 TTTTATA
1 TTTTATA
60707 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATATTTTCAAAAA
Found at i:61928 original size:64 final size:61
Alignment explanation
Indices: 61815--61956 Score: 176
Period size: 63 Copynumber: 2.3 Consensus size: 61
61805 TTTACATAAT
* * *
61815 AACAAATTTAGCTCTAAAATAATTACAAATTTATCAATTTCATCTTAATTCTAAAAAAATTC
1 AACAAATTTAACTCTAAAATAATTACAAATTTATCAATTTAATCCTAATTCT-AAAAAATTC
* * * *
61877 AACAAATTTAACTTCTATAATATTTATAGATTCTATCAATTTAATCCTAATTCTAAAAAATTC
1 AACAAATTTAAC-TCTAAAATAATTACAAATT-TATCAATTTAATCCTAATTCTAAAAAATTC
* *
61940 AACAAAATTAACCCTAA
1 AACAAATTTAACTCTAA
61957 TACGTTCTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 14 0.21
63 35 0.51
64 19 0.28
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.37
Consensus pattern (61 bp):
AACAAATTTAACTCTAAAATAATTACAAATTTATCAATTTAATCCTAATTCTAAAAAATTC
Found at i:71657 original size:15 final size:15
Alignment explanation
Indices: 71637--71673 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
71627 TATACATGTT
*
71637 TTTTTTTTTTTTTTC
1 TTTTTTTCTTTTTTC
71652 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
*
71667 TCTTTTT
1 TTTTTTT
71674 GAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:71657 original size:17 final size:17
Alignment explanation
Indices: 71635--71673 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
71625 TATATACATG
* *
71635 TTTTTTTTTTTTTTTTC
1 TTTTTTTCTTTTTTCTC
71652 TTTTTTTCTTTTTTCTC
1 TTTTTTTCTTTTTTCTC
71669 TTTTT
1 TTTTT
71674 GAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (17 bp):
TTTTTTTCTTTTTTCTC
Found at i:71670 original size:9 final size:8
Alignment explanation
Indices: 71636--71673 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
71626 ATATACATGT
*
71636 TTTTTTTT
1 TTTTTTTC
71644 TTTTTTTC
1 TTTTTTTC
71652 TTTTTTTC
1 TTTTTTTC
71660 TTTTTTCTC
1 TTTTTT-TC
71669 TTTTT
1 TTTTT
71674 GAATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:86361 original size:3 final size:3
Alignment explanation
Indices: 86353--86384 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
86343 ATGTATATAA
86353 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
86385 GTCTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:90397 original size:14 final size:16
Alignment explanation
Indices: 90372--90405 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
90362 CATATGTATA
90372 AAATTATAATTTTT-T
1 AAATTATAATTTTTAT
90387 AAATT-TAATTTTTAT
1 AAATTATAATTTTTAT
90402 AAAT
1 AAAT
90406 AAATAGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTATAATTTTTAT
Found at i:90805 original size:3 final size:3
Alignment explanation
Indices: 90797--90857 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
90787 AATAAATCAC
*
90797 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
90845 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
90858 TTTTAAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:100610 original size:2 final size:2
Alignment explanation
Indices: 100603--100627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100593 CAAATATGAA
100603 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
100628 CGGAAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104495 original size:15 final size:17
Alignment explanation
Indices: 104475--104524 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
104465 AACTTAAAAC
104475 AACCT-AAATGA-TCAA
1 AACCTAAAATGATTCAA
104490 AACCTAAAATGATTC-A
1 AACCTAAAATGATTCAA
* *
104506 AACTTAAAATGATCCAA
1 AACCTAAAATGATTCAA
104523 AA
1 AA
104525 AAATTAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.22
Consensus pattern (17 bp):
AACCTAAAATGATTCAA
Found at i:105081 original size:17 final size:15
Alignment explanation
Indices: 105036--105093 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
105026 TATAAGGGTA
105036 ATAATTAAAAGA-TAT
1 ATAATTAAAA-ATTAT
*
105051 ATAATTAATAATTAT
1 ATAATTAAAAATTAT
105066 ATAAATTAAAATATTAT
1 AT-AATTAAAA-ATTAT
*
105083 AT-GTTAAAAAT
1 ATAATTAAAAAT
105094 AAAAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.08
15 20 0.54
16 7 0.19
17 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATAATTAAAAATTAT
Found at i:105411 original size:17 final size:17
Alignment explanation
Indices: 105389--105421 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
105379 TAAGTACATA
105389 ATTATATTAAAA-ATTAT
1 ATTATA-TAAAATATTAT
105406 ATTATATAAAATATTA
1 ATTATATAAAATATTA
105422 ATATGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATATAAAATATTAT
Found at i:111359 original size:36 final size:34
Alignment explanation
Indices: 111281--111367 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 34
111271 CATTCTAGAG
* * *
111281 CTTTAACCGTTACTCCATCTATGTCAGATGAGAA
1 CTTTAACCGTTACTCCATCGATGTCACATAAGAA
* *
111315 CTTCAACCGTTACTCCATCCAGATGTTACATAAGAA
1 CTTTAACCGTTACTCCAT-C-GATGTCACATAAGAA
*
111351 CTTTAACCGCTACTCCA
1 CTTTAACCGTTACTCCA
111368 ATTTAGGGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 17 0.39
35 1 0.02
36 26 0.59
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (34 bp):
CTTTAACCGTTACTCCATCGATGTCACATAAGAA
Found at i:116932 original size:5 final size:5
Alignment explanation
Indices: 116916--116949 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
116906 AGAATTGAGC
116916 AAACA GAAACA AAACA AAACA AAACA AAACA AAA
1 AAACA -AAACA AAACA AAACA AAACA AAACA AAA
116950 AGAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:116940 original size:15 final size:16
Alignment explanation
Indices: 116916--116958 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
116906 AGAATTGAGC
116916 AAACAGAAACAAAACA
1 AAACAGAAACAAAACA
116932 AAACA-AAACAAAACA
1 AAACAGAAACAAAACA
116947 AAA-AGAAA-AAAA
1 AAACAGAAACAAAA
116959 AAACTTACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.19
15 16 0.62
16 5 0.19
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (16 bp):
AAACAGAAACAAAACA
Found at i:117123 original size:81 final size:81
Alignment explanation
Indices: 116976--117132 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 81
116966 CTCTGGAAAC
* * *
116976 AGATCTTGATGAATATCTATATGTGGACTACCCACATCATTAGGGTTTTCAGTATGAGGGGGAGT
1 AGATCTTGATGAATATCTATATGTGAACTACCCACATCATGAGGGTTATCAGTATGAGGGGGAGT
117041 ATCCATATGAGAGTTG
66 ATCCATATGAGAGTTG
* * ** *
117057 AGATCTTGTTGAATATCTATGTGTGAACTACCCATGTCATGAGGGTTATCA-TGA-GAGGGAGTA
1 AGATCTTGATGAATATCTATATGTGAACTACCCACATCATGAGGGTTATCAGT-ATGAGGG-GGA
117120 GTATCCATATGAG
64 GTATCCATATGAG
117133 GGTTCTCAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
80 6 0.09
81 60 0.91
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (81 bp):
AGATCTTGATGAATATCTATATGTGAACTACCCACATCATGAGGGTTATCAGTATGAGGGGGAGT
ATCCATATGAGAGTTG
Found at i:117836 original size:20 final size:19
Alignment explanation
Indices: 117789--117838 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
117779 TGAACTCGAA
*
117789 TAAATTTTAAATATTAAAT
1 TAAATTTAAAATATTAAAT
*
117808 TAAATTTTAAAATTTTAAAT
1 TAAA-TTTAAAATATTAAAT
*
117828 ATCAATTTAAA
1 -TAAATTTAAA
117839 CGTTGAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 19 0.73
21 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTTAAAATATTAAAT
Found at i:117847 original size:27 final size:27
Alignment explanation
Indices: 117790--117847 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
117780 GAACTCGAAT
* **
117790 AAATTTTAAATATTAAATTAAATTTTA
1 AAATTTTAAATATCAAATTAAACGTTA
* *
117817 AAATTTTAAATATCAATTTAAACGTTG
1 AAATTTTAAATATCAAATTAAACGTTA
117844 AAAT
1 AAAT
117848 CAAATTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
AAATTTTAAATATCAAATTAAACGTTA
Found at i:118678 original size:49 final size:49
Alignment explanation
Indices: 118619--118718 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 49
118609 CTATAATTGA
*
118619 ATAGAACTTTCAATCAACAATTTACGAATAGTACAATTTCTATGTATTT
1 ATAGAACTTTCAATCAACAATTTACAAATAGTACAATTTCTATGTATTT
* ** * *
118668 ATAGAGCTTTCAATCAACAATTTACAAATAGTTTAATTTTTATTTATTT
1 ATAGAACTTTCAATCAACAATTTACAAATAGTACAATTTCTATGTATTT
118717 AT
1 AT
118719 GCTTGTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (49 bp):
ATAGAACTTTCAATCAACAATTTACAAATAGTACAATTTCTATGTATTT
Found at i:120896 original size:81 final size:82
Alignment explanation
Indices: 120730--120886 Score: 198
Period size: 81 Copynumber: 1.9 Consensus size: 82
120720 GCTAGCCCCA
*
120730 AAAATGAAAAATTATATTTTAATTTTCTTAAAAATTAAAAATTTATAAATTTATATATAATAAAA
1 AAAATGAAAAATTATATTTTAATTTTCTTAAAAATTAAAAATTTATAAATTAATATATAATAAAA
*
120795 ATTGCATTTTAACGTTT
66 ATTACATTTTAACGTTT
* * *
120812 AAAATGAAAATATTGTA-TTTAATTTT-TTTAAAA-TAATGGAA-TTATAAATTAATATATAAT-
1 AAAATGAAAA-ATTATATTTTAATTTTCTTAAAAATTAA--AAATTTATAAATTAATATATAATA
*
120872 AAAATTATATTTTAA
63 AAAATTACATTTTAA
120887 TTTTTTAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
80 16 0.24
81 24 0.36
82 21 0.32
83 5 0.08
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (82 bp):
AAAATGAAAAATTATATTTTAATTTTCTTAAAAATTAAAAATTTATAAATTAATATATAATAAAA
ATTACATTTTAACGTTT
Found at i:126577 original size:6 final size:6
Alignment explanation
Indices: 126524--126577 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
126514 ATATCTATCT
* * * * *
126524 TCCTAT TCCCAC TCCTAT TCCTAT TCCTAT TCCTAC TCCTAC TCCTAC
1 TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC
126572 TCCTAC
1 TCCTAC
126578 ACATTTCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.17, C:0.44, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCTAC
Found at i:126577 original size:12 final size:12
Alignment explanation
Indices: 126524--126576 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
126514 ATATCTATCT
*
126524 TCCTATTCCCAC
1 TCCTATTCCTAC
*
126536 TCCTATTCCTAT
1 TCCTATTCCTAC
126548 TCCTATTCCTAC
1 TCCTATTCCTAC
*
126560 TCCTACTCCTAC
1 TCCTATTCCTAC
126572 TCCTA
1 TCCTA
126577 CACATTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (12 bp):
TCCTATTCCTAC
Found at i:126577 original size:18 final size:18
Alignment explanation
Indices: 126524--126577 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
126514 ATATCTATCT
* *
126524 TCCTATTCCCACTCCTAT
1 TCCTATTCCTACTCCTAC
*
126542 TCCTATTCCTATTCCTAC
1 TCCTATTCCTACTCCTAC
*
126560 TCCTACTCCTACTCCTAC
1 TCCTATTCCTACTCCTAC
126578 ACATTTCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.44, G:0.00, T:0.39
Consensus pattern (18 bp):
TCCTATTCCTACTCCTAC
Found at i:139852 original size:20 final size:20
Alignment explanation
Indices: 139819--139876 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
139809 ATTCTCTTAA
139819 CAAAAATTACAAAATAATTTT
1 CAAAAATT-CAAAATAATTTT
*
139840 CAAAAATTGAAAATAATTTT
1 CAAAAATTCAAAATAATTTT
*
139860 -TAAAATTCAAAA-AATTT
1 CAAAAATTCAAAATAATTT
139877 ATAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 11 0.32
21 8 0.24
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
CAAAAATTCAAAATAATTTT
Found at i:139881 original size:18 final size:19
Alignment explanation
Indices: 139821--139882 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
139811 TCTCTTAACA
139821 AAAATTACAAAATAATTT-T
1 AAAATT-CAAAATAATTTAT
* *
139840 CAAAAATTGAAAATAATTTTT
1 --AAAATTCAAAATAATTTAT
139861 AAAATTCAAAA-AATTTAT
1 AAAATTCAAAATAATTTAT
139879 AAAA
1 AAAA
139883 AAAAAATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.27
19 10 0.27
20 10 0.27
21 7 0.19
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:139884 original size:20 final size:19
Alignment explanation
Indices: 139820--139883 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
139810 TTCTCTTAAC
139820 AAAAATTACAAAATAATTTT
1 AAAAATT-CAAAATAATTTT
*
139840 CAAAAATTGAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
139860 TAAAATTCAAAA-AATTTAT
1 AAAAATTCAAAATAATTT-T
139879 AAAAA
1 AAAAA
139884 AAAAATCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 5 0.13
19 15 0.39
20 11 0.29
21 7 0.18
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:156193 original size:21 final size:21
Alignment explanation
Indices: 156167--156210 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
156157 TATAAAATTG
156167 AAAATTAAAAAAAAAAACAAA
1 AAAATTAAAAAAAAAAACAAA
*
156188 AAAATTAAAAACAAAAACAAA
1 AAAATTAAAAAAAAAAACAAA
156209 AA
1 AA
156211 CAAAGCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (21 bp):
AAAATTAAAAAAAAAAACAAA
Found at i:156197 original size:27 final size:28
Alignment explanation
Indices: 156160--156214 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
156150 TTGTGTATAT
**
156160 AAAATTGAAAATTAAAAAAAAAAACAAA
1 AAAATTGAAAAACAAAAAAAAAAACAAA
*
156188 AAAATT-AAAAACAAAAACAAAAACAAA
1 AAAATTGAAAAACAAAAAAAAAAACAAA
156215 GCAAAGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (28 bp):
AAAATTGAAAAACAAAAAAAAAAACAAA
Found at i:156712 original size:24 final size:25
Alignment explanation
Indices: 156680--156729 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
156670 CTCTATGTTT
* *
156680 AAAATTTAATTTTTC-AATATTTAA
1 AAAAATTAATTTTTCGAATATATAA
156704 AAAAATTAATTTTTCGAATATATAA
1 AAAAATTAATTTTTCGAATATATAA
156729 A
1 A
156730 TTCAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAATTAATTTTTCGAATATATAA
Found at i:162804 original size:2 final size:2
Alignment explanation
Indices: 162799--162829 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
162789 ACACACACAC
162799 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
162830 TTTAAGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:163901 original size:20 final size:20
Alignment explanation
Indices: 163853--163902 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
163843 GTCGAGCTAG
**
163853 TAATATTTAAGAATGGACTT
1 TAATATTTTGGAATGGACTT
163873 TAATATTTTGGAATGGACTT
1 TAATATTTTGGAATGGACTT
163893 TAATATTTTG
1 TAATATTTTG
163903 ATATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (20 bp):
TAATATTTTGGAATGGACTT
Found at i:167577 original size:23 final size:22
Alignment explanation
Indices: 167550--167676 Score: 96
Period size: 23 Copynumber: 5.5 Consensus size: 22
167540 GAACTCTAGC
*
167550 GTGCTTACTGTTTCACACTTCGT
1 GTGCTTACTGTTTCGCACTT-GT
*
167573 GTGCTTACTATTTCGCACTTTGT
1 GTGCTTACTGTTTCGCAC-TTGT
*
167596 GTGCTTATTGTTTCGCATCTTGT
1 GTGCTTACTGTTTCGCA-CTTGT
* *
167619 GTGCCTACTGATTT-GCGCTATGT
1 GTGCTTACTG-TTTCGCACT-TGT
* * *
167642 GCGCCTACTGGATT-GCACTGTGT
1 GTGCTTACT-GTTTCGCACT-TGT
*
167665 GTCCTTACTGTT
1 GTGCTTACTGTT
167677 AAGTACTTCG
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
22 4 0.05
23 73 0.87
24 7 0.08
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (22 bp):
GTGCTTACTGTTTCGCACTTGT
Found at i:172427 original size:12 final size:12
Alignment explanation
Indices: 172407--172440 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
172397 ATTTGTGATC
*
172407 AAAATTGAAAGT
1 AAAAGTGAAAGT
172419 AAAAGTGAAAGT
1 AAAAGTGAAAGT
*
172431 GAAAGTGAAA
1 AAAAGTGAAA
172441 TTGGAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (12 bp):
AAAAGTGAAAGT
Found at i:172429 original size:6 final size:6
Alignment explanation
Indices: 172412--172456 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
172402 TGATCAAAAT
* * * *
172412 TGAAAG TAAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
172457 TATGAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:172451 original size:18 final size:18
Alignment explanation
Indices: 172408--172456 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
172398 TTTGTGATCA
*
172408 AAATTGAAAGTAAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
172426 AAAGTGAAAGTGAAATTG
1 AAATTGAAAGTGAAAGTG
*
172444 GAATTGAAAGTGA
1 AAATTGAAAGTGA
172457 TATGAATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:172651 original size:37 final size:38
Alignment explanation
Indices: 172584--172662 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
172574 ATGTCATTAT
* **
172584 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
* **
172622 TTTACTTCGGCTAGA-CCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
172659 TTTA
1 TTTA
172663 TTGCTTCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 21 0.60
38 14 0.40
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (38 bp):
TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
Found at i:176558 original size:22 final size:22
Alignment explanation
Indices: 176527--176568 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
176517 CAATGTTCAA
* *
176527 TTTGAAACTTGTGTGTTTTTAG
1 TTTGAAACTTGAGGGTTTTTAG
*
176549 TTTGATACTTGAGGGTTTTT
1 TTTGAAACTTGAGGGTTTTT
176569 TTTCATGGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.05, G:0.24, T:0.55
Consensus pattern (22 bp):
TTTGAAACTTGAGGGTTTTTAG
Found at i:177937 original size:25 final size:24
Alignment explanation
Indices: 177878--177927 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
177868 AGAAGGGGTG
177878 ATTTAATATTAATATAATTATATTT
1 ATTTAATATTAATATAA-TATATTT
177903 ATTTAATATTAATATAA-A-ATTT
1 ATTTAATATTAATATAATATATTT
177925 ATT
1 ATT
177928 ATCATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.28
23 1 0.04
25 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTAATATTAATATAATATATTT
Found at i:177969 original size:17 final size:18
Alignment explanation
Indices: 177934--177989 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
177924 TATTATCATA
* *
177934 TATTTTTT-GAAAATATT
1 TATTTTTTAGATATTATT
*
177951 TATTTTTTATATATT-TT
1 TATTTTTTAGATATTATT
**
177968 TAAATTTTAGATATTATT
1 TATTTTTTAGATATTATT
177986 TATT
1 TATT
177990 GTCAACAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
17 22 0.76
18 7 0.24
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
TATTTTTTAGATATTATT
Found at i:185289 original size:6 final size:6
Alignment explanation
Indices: 185278--185313 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
185268 AACAGGAAGC
185278 AGGATT AGGATT AGGATT AGGATT AGGATT AGGATT
1 AGGATT AGGATT AGGATT AGGATT AGGATT AGGATT
185314 TGTTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
AGGATT
Found at i:188302 original size:3 final size:3
Alignment explanation
Indices: 188294--188318 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
188284 ATGAACAAGT
188294 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
188319 TCTTTTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:193078 original size:21 final size:21
Alignment explanation
Indices: 193054--193111 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
193044 CTTTTACTGT
*
193054 AAATTCTGAATTTAAATTTCG
1 AAATTCTAAATTTAAATTTCG
193075 AAATTCTAAATTTTAAATTTCG
1 AAATTCTAAA-TTTAAATTTCG
*
193097 -AATTCAAAATTTAAA
1 AAATTCTAAATTTAAA
193112 ATTCTAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 6 0.18
21 17 0.50
22 11 0.32
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (21 bp):
AAATTCTAAATTTAAATTTCG
Found at i:193114 original size:21 final size:21
Alignment explanation
Indices: 193062--193111 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
193052 GTAAATTCTG
193062 AATTTAAATTTCGAAATTCTAA
1 AATTTAAATTTCGAAATTC-AA
*
193084 ATTTTAAATTTCG-AATTCAA
1 AATTTAAATTTCGAAATTCAA
193104 AATTTAAA
1 AATTTAAA
193112 ATTCTAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 9 0.35
21 5 0.19
22 12 0.46
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (21 bp):
AATTTAAATTTCGAAATTCAA
Done.