Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2458
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: 101580
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:316 original size:6 final size:6
Alignment explanation
Indices: 307--341 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
297 CTAGCACTAG
307 CACTGA CACTGA CACTGA CACTGA CACTGA CACTG
1 CACTGA CACTGA CACTGA CACTGA CACTGA CACTG
342 GGGAGACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (6 bp):
CACTGA
Found at i:322 original size:18 final size:17
Alignment explanation
Indices: 287--341 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
277 AATACTACCT
*
287 TGCACTGGCACT-AGCAC
1 TGCACTGACACTGA-CAC
304 TAGCACTGACACTGACAC
1 T-GCACTGACACTGACAC
322 TGACACTGACACTGACAC
1 TG-CACTGACACTGACAC
340 TG
1 TG
342 GGGAGACATC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.06
18 31 0.91
19 1 0.03
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (17 bp):
TGCACTGACACTGACAC
Found at i:12076 original size:2 final size:2
Alignment explanation
Indices: 12069--12115 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12059 TGTCAAGTAC
12069 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
12111 AT AT A
1 AT AT A
12116 GGAGGAGATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12790 original size:2 final size:2
Alignment explanation
Indices: 12783--12809 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12773 TAAGTCCCTT
12783 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12810 TGATACCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15455 original size:2 final size:2
Alignment explanation
Indices: 15409--15440 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15399 GATTATTATT
15409 TA 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 TA
15441 ATAATTAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15913 original size:2 final size:2
Alignment explanation
Indices: 15906--15935 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15896 CGTCGCTTAT
15906 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
15936 AAGAAGGGGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:21227 original size:88 final size:88
Alignment explanation
Indices: 21078--21252 Score: 350
Period size: 88 Copynumber: 2.0 Consensus size: 88
21068 GTGTCATATG
21078 GCATTTACTAATCATAGGATTTATGCATAGCTTTGGCAGGTATGATCATTTGATATTGTGGCTGA
1 GCATTTACTAATCATAGGATTTATGCATAGCTTTGGCAGGTATGATCATTTGATATTGTGGCTGA
21143 CAAATTAATTTCTTACTAAAATA
66 CAAATTAATTTCTTACTAAAATA
21166 GCATTTACTAATCATAGGATTTATGCATAGCTTTGGCAGGTATGATCATTTGATATTGTGGCTGA
1 GCATTTACTAATCATAGGATTTATGCATAGCTTTGGCAGGTATGATCATTTGATATTGTGGCTGA
21231 CAAATTAATTTCTTACTAAAAT
66 CAAATTAATTTCTTACTAAAAT
21253 TGTAACCGTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (88 bp):
GCATTTACTAATCATAGGATTTATGCATAGCTTTGGCAGGTATGATCATTTGATATTGTGGCTGA
CAAATTAATTTCTTACTAAAATA
Found at i:27045 original size:50 final size:50
Alignment explanation
Indices: 26970--27076 Score: 196
Period size: 50 Copynumber: 2.1 Consensus size: 50
26960 GGCAACATAC
*
26970 CTTGGAGATAGCTTGCACGAATGCTGTTTGAATTGACTGAGCATCAGCCT
1 CTTGGAGATAGCTTGCACGAATGCTGTTTGAATTGACTGAACATCAGCCT
*
27020 CTTGGAGATAGCTTGCACGAATGCTGTTTGAATTGACTGAACATTAGCCT
1 CTTGGAGATAGCTTGCACGAATGCTGTTTGAATTGACTGAACATCAGCCT
27070 CTTGGAG
1 CTTGGAG
27077 TTTTTGTGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
CTTGGAGATAGCTTGCACGAATGCTGTTTGAATTGACTGAACATCAGCCT
Found at i:33653 original size:40 final size:40
Alignment explanation
Indices: 33593--33672 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
33583 CTAAACAGAC
*
33593 TCCTAACATACTAATGCCACTACCATATTATTTGCAACAA
1 TCCTAACATACTAATACCACTACCATATTATTTGCAACAA
* *
33633 TCCTAACATATTGATACCACTACCATATTATTTGCAACAA
1 TCCTAACATACTAATACCACTACCATATTATTTGCAACAA
33673 CTGATTTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (40 bp):
TCCTAACATACTAATACCACTACCATATTATTTGCAACAA
Found at i:34630 original size:2 final size:2
Alignment explanation
Indices: 34623--34669 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
34613 GACTTGTGAA
34623 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
34665 CT CT C
1 CT CT C
34670 CTATTAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:43162 original size:2 final size:2
Alignment explanation
Indices: 43155--43188 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
43145 AAGTTTGGAT
*
43155 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43189 TTGTGTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45733 original size:3 final size:3
Alignment explanation
Indices: 45727--45769 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
45717 CAATTTCATG
45727 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
45770 TGTCCTTGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:47353 original size:23 final size:23
Alignment explanation
Indices: 47327--47407 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
47317 CATTATTAAT
*
47327 TAAATTTATAATTTTTACATAAA
1 TAAAATTATAATTTTTACATAAA
*
47350 TAAAATTATAAATATTTTTCATAAA
1 TAAAATTAT-AAT-TTTTACATAAA
* **
47375 T-AACTTATAATTTTTACACGAA
1 TAAAATTATAATTTTTACATAAA
47397 TAAAATTATAA
1 TAAAATTATAA
47408 ACTCTCACCA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 9 0.19
23 19 0.40
24 9 0.19
25 11 0.23
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (23 bp):
TAAAATTATAATTTTTACATAAA
Found at i:47373 original size:25 final size:25
Alignment explanation
Indices: 47337--47408 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 25
47327 TAAATTTATA
47337 ATTTTTACATAAATAAAATTATAAAT
1 ATTTTT-CATAAATAAAATTATAAAT
*
47363 ATTTTTCATAAAT-AACTTAT-AAT
1 ATTTTTCATAAATAAAATTATAAAT
* **
47386 -TTTTACACGAATAAAATTATAAA
1 ATTTTTCATAAATAAAATTATAAA
47409 CTCTCACCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 9 0.23
23 9 0.23
24 8 0.21
25 7 0.18
26 6 0.15
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (25 bp):
ATTTTTCATAAATAAAATTATAAAT
Found at i:47420 original size:47 final size:47
Alignment explanation
Indices: 47332--47457 Score: 141
Period size: 47 Copynumber: 2.7 Consensus size: 47
47322 TTAATTAAAT
* * ***
47332 TTATAATTTTTACATAAATAAAATTATAAA-TATTTTTCATAAATAAC
1 TTATAATTTTTACA-GAATAAAATTATAAACTACTCACCATAAATAAC
*
47379 TTATAATTTTTACACGAATAAAATTATAAACT-CTCACCATAATTAAC
1 TTATAATTTTTACA-GAATAAAATTATAAACTACTCACCATAAATAAC
*
47426 TTATAACTTTATACAG-ATAAAATTATAAACTA
1 TTATAA-TTTTTACAGAATAAAATTATAAACTA
47458 TCTAATATAC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 15 0.22
47 45 0.66
48 8 0.12
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.40
Consensus pattern (47 bp):
TTATAATTTTTACAGAATAAAATTATAAACTACTCACCATAAATAAC
Found at i:47784 original size:3 final size:3
Alignment explanation
Indices: 47778--47816 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
47768 AAAAAAAAAG
47778 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
47817 ATCTCAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:48632 original size:11 final size:11
Alignment explanation
Indices: 48616--48643 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
48606 ACAATGCAGT
48616 CCAACATCATA
1 CCAACATCATA
48627 CCAACATCATA
1 CCAACATCATA
48638 CCAACA
1 CCAACA
48644 GAAGCAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.14
Consensus pattern (11 bp):
CCAACATCATA
Found at i:53734 original size:2 final size:2
Alignment explanation
Indices: 53727--53752 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53717 TTAAGAATGA
53727 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
53753 TTACTGTAAC
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:61548 original size:2 final size:2
Alignment explanation
Indices: 61543--61571 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61533 TAAGTGTGTG
61543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61572 TTAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62258 original size:21 final size:21
Alignment explanation
Indices: 62217--62256 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
62207 TAGATTTTCC
62217 TGTTATTTTATATTAATTTTA
1 TGTTATTTTATATTAATTTTA
62238 TGTT-TTTTA-ATGTAATTTT
1 TGTTATTTTATAT-TAATTTT
62257 TACATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TGTTATTTTATATTAATTTTA
Found at i:63710 original size:17 final size:17
Alignment explanation
Indices: 63673--63724 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
63663 AAATATTTCG
*
63673 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
63688 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
63704 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
63721 AATT
1 AATT
63725 GCATTTCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 2 0.06
17 10 0.31
18 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:68873 original size:20 final size:18
Alignment explanation
Indices: 68844--68891 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
68834 ATTTCAAATT
68844 AAATATTAATAAATAAATAAA
1 AAATA-TAAT-AA-AAATAAA
*
68865 AAATATAATTAAAATAAA
1 AAATATAATAAAAATAAA
68883 AAATATAAT
1 AAATATAAT
68892 TGCATCTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 16 0.62
19 1 0.04
20 4 0.15
21 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATAATAAAAATAAA
Found at i:68879 original size:18 final size:18
Alignment explanation
Indices: 68858--68892 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
68848 ATTAATAAAT
68858 AAATAAAAAATATAATTA
1 AAATAAAAAATATAATTA
68876 AAATAAAAAATATAATT
1 AAATAAAAAATATAATT
68893 GCATCTCTAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAAAATATAATTA
Found at i:72547 original size:2 final size:2
Alignment explanation
Indices: 72542--72570 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
72532 ATATATATAT
72542 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 A
72571 TAGACTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:73037 original size:21 final size:21
Alignment explanation
Indices: 73011--73050 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
73001 AATACATACA
73011 TATATTTATATAAATAACATG
1 TATATTTATATAAATAACATG
73032 TATATTTATATAAATAACA
1 TATATTTATATAAATAACA
73051 ACAGGGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (21 bp):
TATATTTATATAAATAACATG
Found at i:75020 original size:3 final size:3
Alignment explanation
Indices: 75012--75036 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
75002 ATCTTCGATA
75012 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
75037 GAATAATTTG
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:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:79330 original size:34 final size:34
Alignment explanation
Indices: 79284--79468 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
79274 GTAAAAACCA
*
79284 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
79318 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
79352 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
79386 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
79420 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
79453 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
79469 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:83561 original size:19 final size:19
Alignment explanation
Indices: 83534--83596 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
83524 TCACGTGTAC
* *
83534 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
83553 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
83572 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
83591 AGTACC
1 AGTACC
83597 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:83947 original size:34 final size:34
Alignment explanation
Indices: 83901--84083 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
83891 GTAAAAACCA
**
83901 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
83935 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
83969 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
84003 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
84037 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
84070 CCATTTAATCAACA
1 CCATTTAATCAACA
84084 GAAAAGGTAT
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 16 0.12
34 112 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:88824 original size:2 final size:2
Alignment explanation
Indices: 88817--88851 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
88807 CGAAGATGCG
* *
88817 GA GA GA GA GA CA CA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
88852 GAAGAGGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:89334 original size:117 final size:115
Alignment explanation
Indices: 89110--89317 Score: 310
Period size: 117 Copynumber: 1.8 Consensus size: 115
89100 AATCCAACAC
* *** * *
89110 AAAATTAAATTTTATTTGTAAGAAGTGATAAATTGCTTAGTGAATATGGGATATCTGAATCTACT
1 AAAATTAAAATTTATTTGTAAGAAGTGATAAATTGCTTACACAATATGGAATATCTGAATCGAC-
89175 TTTTAAAAGGAAGTAAAATCACGCATGAGATGAAAATATAAGGTCTACTAT
65 TTTTAAAAGGAAGTAAAATCACGCATGAGATGAAAATATAAGGTCTACTAT
* *
89226 AAAATTAAAAATTTATTTGTAAGAAGTGATAAATTGTTTACACAATATGGAATATGTGAATCGAC
1 AAAATT-AAAATTTATTTGTAAGAAGTGATAAATTGCTTACACAATATGGAATATCTGAATCGAC
*
89291 -TTTAAAAGGAAGTAAAATCATGCATGA
65 TTTTAAAAGGAAGTAAAATCACGCATGA
89318 ATATCTAAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
115 26 0.32
116 6 0.07
117 50 0.61
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (115 bp):
AAAATTAAAATTTATTTGTAAGAAGTGATAAATTGCTTACACAATATGGAATATCTGAATCGACT
TTTAAAAGGAAGTAAAATCACGCATGAGATGAAAATATAAGGTCTACTAT
Found at i:89974 original size:23 final size:23
Alignment explanation
Indices: 89947--89996 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
89937 TAGTTAGTAG
89947 TTATT-TAAATTCTAATTTT-TTT
1 TTATTATAAATT-TAATTTTATTT
*
89969 ATTATTATAAGTTTAATTTTATTT
1 -TTATTATAAATTTAATTTTATTT
89993 TTAT
1 TTAT
89997 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATTATAAATTTAATTTTATTT
Found at i:90500 original size:5 final size:5
Alignment explanation
Indices: 90490--90516 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
90480 TGATTCATAG
90490 ATGGC ATGGC ATGGC ATGGC ATGGC AT
1 ATGGC ATGGC ATGGC ATGGC ATGGC AT
90517 CCACTTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (5 bp):
ATGGC
Found at i:95787 original size:2 final size:2
Alignment explanation
Indices: 95780--95828 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
95770 TGTTAAATGA
*
95780 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
95822 TC TC TC T
1 TC TC TC T
95829 AATTTTTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Done.