Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003171.1 Kokia drynarioides strain JFW-HI SEQ_115773, 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: 40302
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2268 original size:24 final size:24
Alignment explanation
Indices: 2229--2291 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
2219 TAGACTAATA
* * *
2229 AGAGTTTGACTCAAACAACTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
2253 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
2277 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
2292 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:4247 original size:24 final size:24
Alignment explanation
Indices: 4210--4270 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
4200 GACTAATAAG
* * * * *
4210 AGTTTGACTCAAACAACTAAATAG
1 AGTTTAACTGAAACAAATAAACAA
*
4234 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
4258 AGTTTAACTGAAA
1 AGTTTAACTGAAA
4271 GATTATTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:4561 original size:20 final size:20
Alignment explanation
Indices: 4536--4573 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4526 ACCATTACTA
*
4536 ATTAATTAGGTTTGAATTCC
1 ATTAATGAGGTTTGAATTCC
*
4556 ATTAATGAGGTTTTAATT
1 ATTAATGAGGTTTGAATT
4574 TAGTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTAATGAGGTTTGAATTCC
Found at i:4875 original size:9 final size:9
Alignment explanation
Indices: 4861--4913 Score: 63
Period size: 10 Copynumber: 5.6 Consensus size: 9
4851 AAAAAAGTTT
4861 TTTTTATAA
1 TTTTTATAA
4870 TTTTTATATA
1 TTTTTATA-A
4880 TTTTTAATAA
1 TTTTT-ATAA
4890 TTTTTATAAA
1 TTTTTAT-AA
4900 TTTTT-TGAA
1 TTTTTAT-AA
4909 TTTTT
1 TTTTT
4914 GAATATTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
9 18 0.45
10 19 0.47
11 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:4889 original size:20 final size:20
Alignment explanation
Indices: 4860--4904 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4850 AAAAAAAGTT
* *
4860 TTTTTTATAATTTTTATATA
1 TTTTTAATAATTTTTATAAA
4880 TTTTTAATAATTTTTATAAA
1 TTTTTAATAATTTTTATAAA
4900 TTTTT
1 TTTTT
4905 TGAATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAATAATTTTTATAAA
Found at i:8990 original size:2 final size:2
Alignment explanation
Indices: 8983--9012 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8973 TAAGACTGAA
8983 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
9013 GATGATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10970 original size:40 final size:40
Alignment explanation
Indices: 10915--10996 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
10905 GAATTTAATG
10915 GCAACAAAACAAAATGTGATGATTGCAATATGGCTATAAA
1 GCAACAAAACAAAATGTGATGATTGCAATATGGCTATAAA
10955 GCAACAAAACAAAATGTGATGATTGCAATATGGCTATAAA
1 GCAACAAAACAAAATGTGATGATTGCAATATGGCTATAAA
10995 GC
1 GC
10997 CGAATTTGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.22
Consensus pattern (40 bp):
GCAACAAAACAAAATGTGATGATTGCAATATGGCTATAAA
Found at i:12366 original size:30 final size:31
Alignment explanation
Indices: 12330--12722 Score: 278
Period size: 30 Copynumber: 13.1 Consensus size: 31
12320 ACTCAAAAAG
* **
12330 CCCCCAAACTTTTC-AAAAATCAAAAATTAA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
*
12360 CCCCCAAAC-ATTCTAAAAATCACATTTTAA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
* * *
12390 CCCTCAAA-ATTTCAAAAAAATCACATTTTAA
1 CCCCCAAACTTTTC-TAAAAATCACATTTTAA
12421 CCCCCAAAC-TTTCTAAAAATCACATTTTAA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
* * * * *
12451 -CCCTAAAATTTTCTAAGAATAACACTTTAA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
*
12481 CCCCTCAAACTTCT-TAAAAATCACATTTTAA
1 CCCC-CAAACTTTTCTAAAAATCACATTTTAA
* *
12512 CCCCTCAAACTTCTC-AAAAATAACATTTTAA
1 CCCC-CAAACTTTTCTAAAAATCACATTTTAA
** *
12543 -CCCCAAACTACTC-AAAAATCACATTTTGA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
** * *
12572 CCCTTAAACTTCTC-AAAAATCGCATTTTAA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
* * * * ** *
12602 CCCTCGAACTTCTC-CAAAATTTCATTTTGA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
* * *
12632 CCCTCAAACTTCTCT-AAAATCACATTTTGA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
* * * * *
12662 -TCGCAAACTCTCCT-AAAATTACAATTTT-A
1 CCCCCAAACTTTTCTAAAAATCAC-ATTTTAA
* * *
12691 CGCCCAAAATTTTCT-AAAATTACATTTTAA
1 CCCCCAAACTTTTCTAAAAATCACATTTTAA
12721 CC
1 CC
12723 TTGAATTCTC
Statistics
Matches: 300, Mismatches: 50, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
29 54 0.18
30 167 0.56
31 73 0.24
32 6 0.02
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (31 bp):
CCCCCAAACTTTTCTAAAAATCACATTTTAA
Found at i:12412 original size:31 final size:29
Alignment explanation
Indices: 12334--12659 Score: 303
Period size: 30 Copynumber: 10.8 Consensus size: 29
12324 AAAAAGCCCC
* ** *
12334 CAAACTTTTCAAAAATCAAAAATTAACCCC
1 CAAAC-TTTCAAAAATCACATTTTAACCCT
*
12364 CAAACATTCTAAAAATCACATTTTAACCCT
1 CAAACTTTC-AAAAATCACATTTTAACCCT
* *
12394 CAAAATTTCAAAAAAATCACATTTTAACCCC
1 CAAACTTTC--AAAAATCACATTTTAACCCT
12425 CAAACTTTCTAAAAATCACATTTTAACCCT
1 CAAACTTTC-AAAAATCACATTTTAACCCT
* * * * *
12455 AAAATTTTCTAAGAATAACACTTTAACCCCT
1 CAAACTTTC-AAAAATCACATTTTAA-CCCT
*
12486 CAAACTTCTTAAAAATCACATTTTAACCCCT
1 CAAACTT-TCAAAAATCACATTTTAA-CCCT
*
12517 CAAACTTCTCAAAAATAACATTTTAACCC-
1 CAAACTT-TCAAAAATCACATTTTAACCCT
* *
12546 CAAACTACTCAAAAATCACATTTTGACCCT
1 CAAACT-TTCAAAAATCACATTTTAACCCT
* *
12576 TAAACTTCTCAAAAATCGCATTTTAACCCT
1 CAAACTT-TCAAAAATCACATTTTAACCCT
* * ** *
12606 CGAACTTCTCCAAAATTTCATTTTGACCCT
1 CAAACTT-TCAAAAATCACATTTTAACCCT
*
12636 CAAACTTCTCTAAAATCACATTTT
1 CAAACTT-TCAAAAATCACATTTT
12660 GATCGCAAAC
Statistics
Matches: 247, Mismatches: 42, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
29 28 0.11
30 140 0.57
31 78 0.32
32 1 0.00
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.31
Consensus pattern (29 bp):
CAAACTTTCAAAAATCACATTTTAACCCT
Found at i:12690 original size:90 final size:89
Alignment explanation
Indices: 12330--12661 Score: 291
Period size: 91 Copynumber: 3.7 Consensus size: 89
12320 ACTCAAAAAG
* ** * *
12330 CCCC-CAAACTTTTCAAAAATCAA-AAATTAACCCCCAAAC-ATTCTAAAAATCACATTTTAACC
1 CCCCTCAAACTTCTCAAAAAT-AACATTTTAA-CCCCAAACTACTC-AAAAATCACATTTTGACC
*
12392 CTCAAAATT-TCAAAAAAATCACATTTTAA
63 CT-AAACTTCTC--AAAAATCACATTTTAA
* * * ** * * * *
12421 CCCC-CAAACTT-TCTAAAAATCACATTTTAACCCTAAAATTTTCTAAGAATAACACTTTAACCC
1 CCCCTCAAACTTCTC-AAAAATAACATTTTAACCCCAAACTACTC-AAAAATCACATTTTGA-CC
*
12484 CTCAAACTTCTTAAAAATCACATTTTAA
63 CT-AAACTTCTCAAAAATCACATTTTAA
12512 CCCCTCAAACTTCTCAAAAATAACATTTTAACCCCAAACTACTCAAAAATCACATTTTGACCCTT
1 CCCCTCAAACTTCTCAAAAATAACATTTTAACCCCAAACTACTCAAAAATCACATTTTGACCC-T
*
12577 AAACTTCTCAAAAATCGCATTTTAA
65 AAACTTCTCAAAAATCACATTTTAA
* * ** * * *
12602 -CCCTCGAACTTCTCCAAAATTTCATTTTGACCCTCAAACTTCTCTAAAATCACATTTTGA
1 CCCCTCAAACTTCTCAAAAATAACATTTTAACCC-CAAACTACTCAAAAATCACATTTTGA
12662 TCGCAAACTC
Statistics
Matches: 203, Mismatches: 29, Indels: 19
0.81 0.12 0.08
Matches are distributed among these distances:
89 28 0.14
90 59 0.29
91 72 0.35
92 41 0.20
93 3 0.01
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.30
Consensus pattern (89 bp):
CCCCTCAAACTTCTCAAAAATAACATTTTAACCCCAAACTACTCAAAAATCACATTTTGACCCTA
AACTTCTCAAAAATCACATTTTAA
Found at i:18482 original size:40 final size:39
Alignment explanation
Indices: 18427--18504 Score: 147
Period size: 40 Copynumber: 2.0 Consensus size: 39
18417 TTATGATTTG
18427 TTTTTTTTTTTTTTTTGTTTTGAATTTATATAGAGGAANT
1 TTTTTTTTTTTTTTTTGTTTTGAATTTATATAGAGGAA-T
18467 TTTTTTTTTTTTTTTTGTTTTGAATTTATATAGAGGAA
1 TTTTTTTTTTTTTTTTGTTTTGAATTTATATAGAGGAA
18505 CATATTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.65
Consensus pattern (39 bp):
TTTTTTTTTTTTTTTTGTTTTGAATTTATATAGAGGAAT
Found at i:19213 original size:2 final size:2
Alignment explanation
Indices: 19206--19238 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19196 ATTATTTAAC
19206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19239 ATGGTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19627 original size:10 final size:11
Alignment explanation
Indices: 19598--19622 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19588 TAATCTAACT
19598 AAATATCTATA
1 AAATATCTATA
19609 AAATATCTATA
1 AAATATCTATA
19620 AAA
1 AAA
19623 GTCTAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATCTATA
Found at i:23369 original size:33 final size:33
Alignment explanation
Indices: 23312--23376 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
23302 TATTTTTATT
23312 TTTTAATAAAATTTTCGAATTTTTATAGAAAAATGA
1 TTTTAATAAAATTTTC-AATTTTTA-A-AAAAATGA
*
23348 TTTTAA-ATAATTTTC-ATTTTTAAAAAAAT
1 TTTTAATAAAATTTTCAATTTTTAAAAAAAT
23377 CTTCAAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 6 0.21
32 1 0.04
33 7 0.25
35 8 0.29
36 6 0.21
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (33 bp):
TTTTAATAAAATTTTCAATTTTTAAAAAAATGA
Found at i:31879 original size:17 final size:17
Alignment explanation
Indices: 31857--31898 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
31847 AGCCCAACAG
*
31857 ATTTAAATTTATTTTAA
1 ATTTAAATTTATATTAA
*
31874 ATTTAAGTTTATATTAA
1 ATTTAAATTTATATTAA
*
31891 ATCTAAAT
1 ATTTAAAT
31899 CCATTTGGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATATTAA
Found at i:32722 original size:3 final size:3
Alignment explanation
Indices: 32714--32781 Score: 57
Period size: 3 Copynumber: 22.0 Consensus size: 3
32704 TTGATAACAT
* * * * *
32714 TAA TAA TAA TAT TAA TAA TAA TAA -ATA TAA TAC TAA TTA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
32759 TTAA TTAA TAA TAA TAA TAA TAA
1 -TAA -TAA TAA TAA TAA TAA TAA
32782 GTAAAAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 1 0.02
3 43 0.83
4 8 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:33901 original size:29 final size:29
Alignment explanation
Indices: 33862--34143 Score: 123
Period size: 29 Copynumber: 9.6 Consensus size: 29
33852 CACTTGAATT
*
33862 TTTCCAGAATTCCATTTTTGACCCT-AAAC
1 TTTCCAAAATTCCATTTTT-ACCCTCAAAC
* * *
33891 TTTCTAAAATTACATTTTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAAC
* ** **
33920 TTTCCAAAATTCCATTTTTAACCTTGATT
1 TTTCCAAAATTCCATTTTTACCCTCAAAC
* *
33949 TTTCAAAAATTACCA-TTTTACCCTCGAAC
1 TTTCCAAAATT-CCATTTTTACCCTCAAAC
* * * **** * *
33978 -CTCTAAAAATTCAATTTTTTGGTTCAGAT
1 TTTC-CAAAATTCCATTTTTACCCTCAAAC
34007 TTCTCCAAAATTACCA-TTTTACCCTCAAAC
1 TT-TCCAAAATT-CCATTTTTACCCTCAAAC
* * **
34037 -TTCCAAAAATTCCACTTTTAACC-CAATT
1 TTTCC-AAAATTCCATTTTTACCCTCAAAC
* *
34065 TTTCCAAAAATTACCA-TTTTACCCCCTAA-
1 TTTCC-AAAATT-CCATTTTTACCCTCAAAC
* * **
34094 TGTCTAAAATTTATATTTTTAACCC-CAAAC
1 TTTCCAAAA-TTCCATTTTT-ACCCTCAAAC
34124 TTTCCCAAAATTACCATTTT
1 TTT-CCAAAATT-CCATTTT
34144 ATCCCCGAGT
Statistics
Matches: 187, Mismatches: 48, Indels: 34
0.70 0.18 0.13
Matches are distributed among these distances:
28 23 0.12
29 120 0.64
30 30 0.16
31 14 0.07
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTCCAAAATTCCATTTTTACCCTCAAAC
Found at i:33931 original size:58 final size:58
Alignment explanation
Indices: 33862--34144 Score: 191
Period size: 58 Copynumber: 4.8 Consensus size: 58
33852 CACTTGAATT
* * *
33862 TTTCCAGAATTCCATTTTTGACCCTAAACTTTCTAAAATTA-CATTTTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTAACCCTAAACTTTCAAAAATTACCA-TTTTACCCTCGAAC
* * **
33920 TTTCCAAAATTCCATTTTTAACCTTGATTTTTCAAAAATTACCATTTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTAACCCTAAACTTTCAAAAATTACCATTTTACCCTCGAAC
* * * **** * * * *
33978 -CTCTAAAAATTCAATTTTT-TGGTTCAGATTTCTCCAAAATTACCATTTTACCCTCAAAC
1 TTTC-CAAAATTCCATTTTTAACCCT-AAACTT-TCAAAAATTACCATTTTACCCTCGAAC
* ** * *
34037 -TTCCAAAAATTCCACTTTTAACCC-AATTTTTCCAAAAATTACCATTTTACCCCCTAA-
1 TTTCC-AAAATTCCATTTTTAACCCTAAACTTT-CAAAAATTACCATTTTACCCTCGAAC
* * ** * *
34094 TGTCTAAAATTTATATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTA
1 TTTCCAAAA-TTCCATTTTTAACCCTAAACTTT-CAAAAATTACCATTTTA
34145 TCCCCGAGTG
Statistics
Matches: 176, Mismatches: 39, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
57 9 0.05
58 104 0.59
59 63 0.36
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (58 bp):
TTTCCAAAATTCCATTTTTAACCCTAAACTTTCAAAAATTACCATTTTACCCTCGAAC
Found at i:34132 original size:117 final size:117
Alignment explanation
Indices: 33869--34144 Score: 294
Period size: 117 Copynumber: 2.4 Consensus size: 117
33859 ATTTTTCCAG
* * * * *
33869 AATTCCATTTTTGACCCTAAACTTT-CTAAAATTA-CATTTTTACCCTCGAACTTTCCAAAATTC
1 AATTCAATTTTTAACCCCAAACTTTCCCAAAATTACCA-TTTTACCCTCAAACTTTCCAAAATTC
* ** *
33932 CATTTTTAACCTTGATTTTTCAAAAATTACCATTTTACCCTCGAACCTCTAAA
65 CACTTTTAACCTCAATTTTTCAAAAATTACCATTTTACCCCCGAACCTCTAAA
***** *
33985 AATTCAATTTTTTGGTTCAGA-TTTCTCCAAAATTACCATTTTACCCTCAAAC-TTCCAAAAATT
1 AATTCAATTTTTAACCCCAAACTTTC-CCAAAATTACCATTTTACCCTCAAACTTTCC-AAAATT
* **
34048 CCACTTTTAACC-CAATTTTTCCAAAAATTACCATTTTACCCCCTAATGTCT-AA
64 CCACTTTTAACCTCAATTTTT-CAAAAATTACCATTTTACCCCCGAACCTCTAAA
*
34101 AATTTATATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTA
1 AATTCA-ATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTA
34145 TCCCCGAGTG
Statistics
Matches: 129, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
115 3 0.02
116 30 0.23
117 90 0.70
118 6 0.05
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (117 bp):
AATTCAATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCC
ACTTTTAACCTCAATTTTTCAAAAATTACCATTTTACCCCCGAACCTCTAAA
Found at i:34171 original size:59 final size:58
Alignment explanation
Indices: 33869--34171 Score: 174
Period size: 59 Copynumber: 5.2 Consensus size: 58
33859 ATTTTTCCAG
* * * * *
33869 AATT-CCATTTTTGACCCTAAACTTT-CTAAAATTA-CATTTTTACCCTCGAACTTTCCAA
1 AATTACCATTTTTAACCC-AAACTTTCCAAAAATTACCA-TTTTACCCCCGAA-TGTCTAA
*** * * * **
33927 AATT-CCATTTTTAACCTTGATTTTTCAAAAATTACCATTTTACCCTCGAACCTCTAAA
1 AATTACCATTTTTAACCCAAACTTTCCAAAAATTACCATTTTACCCCCGAATGTCT-AA
* **** * * * * *
33985 AATT-CAATTTTTTGGTTCAGA-TTTCTCCAAAATTACCATTTTACCCTCAAACT-TCCAAA
1 AATTACCA-TTTTTAACCCAAACTTTC-CAAAAATTACCATTTTACCCCCGAA-TGT-CTAA
* ** *
34044 AATT-CCACTTTTAACCCAATTTTTCCAAAAATTACCATTTTACCCCCTAATGTCTAA
1 AATTACCATTTTTAACCCAAACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAA
* * * *
34101 AATTTA-TATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTATCCCCGAGTGTCTAA
1 AA-TTACCATTTTTAA-CCCAAACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAA
34160 AATTACCATTTT
1 AATTACCATTTT
34172 GGCCCAGAGT
Statistics
Matches: 190, Mismatches: 42, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
57 12 0.06
58 88 0.46
59 89 0.47
60 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
AATTACCATTTTTAACCCAAACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAA
Found at i:34189 original size:28 final size:28
Alignment explanation
Indices: 34128--34189 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
34118 CCAAACTTTC
* * *
34128 CCAAAATTACCATTTTATCCCCGAGTGT
1 CCAAAATTACCATTTTAGCCCAGAGTAT
* *
34156 CTAAAATTACCATTTTGGCCCAGAGTAT
1 CCAAAATTACCATTTTAGCCCAGAGTAT
34184 CCAAAA
1 CCAAAA
34190 ATCACATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTAGCCCAGAGTAT
Found at i:34570 original size:97 final size:97
Alignment explanation
Indices: 34404--34597 Score: 259
Period size: 97 Copynumber: 2.0 Consensus size: 97
34394 GAAAACTTTC
* * *
34404 AAATCAAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCAAGAT
1 AAATCAAGGCAATATTCTTTTATCTCGAGTTCTGAAAATTTGTGCCTTAACTTACTAGGCAAGAG
34469 TTTTCTTCAAATCG-GAATAATCGAATACCCTT
66 TTTTCTTCAAATCGAG-ATAATCGAATACCCTT
* * ***
34501 AAATCAAGGCAATGTT-TCTTTATCTCTGA-TTCTGAAAATTTGTGTCTTAACTTACTAGGTGCG
1 AAATCAAGGCAATATTCT-TTTATCTC-GAGTTCTGAAAATTTGTGCCTTAACTTACTAGGCAAG
*
34564 AGTTTTCTTCAAATCGAGATAATCGAATATCCTT
64 AGTTTTCTTCAAATCGAGATAATCGAATACCCTT
34598 TTCCAAAGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
96 1 0.01
97 81 0.95
98 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (97 bp):
AAATCAAGGCAATATTCTTTTATCTCGAGTTCTGAAAATTTGTGCCTTAACTTACTAGGCAAGAG
TTTTCTTCAAATCGAGATAATCGAATACCCTT
Found at i:37062 original size:31 final size:31
Alignment explanation
Indices: 37019--37079 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
37009 GGCCTATAGC
*
37019 GGCGCTTATAAGTGCCATTAAAACATTTAGT
1 GGCGCTTATAAGTGCCACTAAAACATTTAGT
* *
37050 GGCGTTTATAAGTGCCGCTAAAACATTTAG
1 GGCGCTTATAAGTGCCACTAAAACATTTAG
37080 CGACGCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (31 bp):
GGCGCTTATAAGTGCCACTAAAACATTTAGT
Found at i:37103 original size:32 final size:31
Alignment explanation
Indices: 37037--37103 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
37027 TAAGTGCCAT
* * *
37037 TAAAACATTTAGTGGCGTTTATAAGTGCCGC
1 TAAAACATTTAGCGACGTTTATAAATGCCGC
37068 TAAAACATTTAGCGACGCTTGT-TAAATGCCGC
1 TAAAACATTTAGCGACG-TT-TATAAATGCCGC
37100 TAAA
1 TAAA
37104 GATAACGCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.48
32 15 0.48
33 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
TAAAACATTTAGCGACGTTTATAAATGCCGC
Found at i:38012 original size:15 final size:15
Alignment explanation
Indices: 37992--38028 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
37982 GAAGTATCGC
37992 AAATGCTATTTGAAG
1 AAATGCTATTTGAAG
38007 AAATGCTATTTGAAG
1 AAATGCTATTTGAAG
38022 AAATGCT
1 AAATGCT
38029 TCAAGAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (15 bp):
AAATGCTATTTGAAG
Done.