Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold803
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: 54279
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:4037 original size:16 final size:16
Alignment explanation
Indices: 4013--4051 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4003 ACCAAACTTG
* *
4013 AAATAATTTGAATCTA
1 AAATGATTTAAATCTA
*
4029 AAATGATTTAAATTTA
1 AAATGATTTAAATCTA
4045 AAATGAT
1 AAATGAT
4052 CCAAACCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (16 bp):
AAATGATTTAAATCTA
Found at i:5151 original size:19 final size:20
Alignment explanation
Indices: 5127--5179 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
5117 ATGCTTTGAA
*
5127 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCTCAAT
*
5146 TGTATCGATACATACTCAAT
1 TGTATCGATACATGCTCAAT
*
5166 CGTATCGATACATG
1 TGTATCGATACATG
5180 AAATTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:10379 original size:20 final size:20
Alignment explanation
Indices: 10354--10397 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
10344 ATCGGCGAGT
*
10354 GGCGGTTGATGGTGATTACC
1 GGCGGTCGATGGTGATTACC
*
10374 GGCGGTCGATGGTGGTTACC
1 GGCGGTCGATGGTGATTACC
10394 GGCG
1 GGCG
10398 ACCGACGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.45, T:0.25
Consensus pattern (20 bp):
GGCGGTCGATGGTGATTACC
Found at i:17155 original size:27 final size:28
Alignment explanation
Indices: 17116--17184 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
17106 AGTGACATTT
*
17116 CTTTTCAAAGTCCATAACTCTATGGCAT-
1 CTTTT-AAAGTCCACAACTCTATGGCATC
* * *
17144 TTTTTTAAGTCCACAACTCTGTGGCATC
1 CTTTTAAAGTCCACAACTCTATGGCATC
17172 CTTTTAAAGTCCA
1 CTTTTAAAGTCCA
17185 AAAGTCCACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 19 0.56
28 15 0.44
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.38
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCTATGGCATC
Found at i:17224 original size:27 final size:27
Alignment explanation
Indices: 17186--17348 Score: 110
Period size: 28 Copynumber: 5.9 Consensus size: 27
17176 TAAAGTCCAA
* * *
17186 AAGTCCACAACTCTGTGGTACCCTTTT
1 AAGTCTACAACTCCGTGGCACCCTTTT
* *
17213 AAGTCTACAACTCCGTGGCATCTTTTT
1 AAGTCTACAACTCCGTGGCACCCTTTT
* * *
17240 AAGTCTATAACTTCGTGGCATCCTTTTT
1 AAGTCTACAACTCCGTGGCA-CCCTTTT
* * * ** **
17268 AAGCCCACAAGTCAATGGCACCCTTCCA
1 AAGTCTACAACTCCGTGGCACCCTT-TT
* * *
17296 AAGTCCACAACTTCGTGGCATCCTTTTT
1 AAGTCTACAACTCCGTGGCA-CCCTTTT
* * *
17324 AAGCCTACAAGTCAGTGGCACCCTT
1 AAGTCTACAACTCCGTGGCACCCTT
17349 CCAATTATGT
Statistics
Matches: 101, Mismatches: 32, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
27 48 0.48
28 49 0.49
29 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGTCTACAACTCCGTGGCACCCTTTT
Found at i:17470 original size:27 final size:28
Alignment explanation
Indices: 17425--17495 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
17415 TCAGTGACAT
*
17425 TTCTTTTCAAAGTCCATAACTCTATGGCA
1 TTCTTTT-AAAGTCCATAACTCCATGGCA
*
17454 TTCTTTT-AAGTCCATAACTCCGTGGCA
1 TTCTTTTAAAGTCCATAACTCCATGGCA
*
17481 TTTTTTTAAAGTCCA
1 TTCTTTTAAAGTCCA
17496 AAAGTCCACA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.63
28 7 0.18
29 7 0.18
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (28 bp):
TTCTTTTAAAGTCCATAACTCCATGGCA
Found at i:17535 original size:27 final size:27
Alignment explanation
Indices: 17497--17577 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
17487 TAAAGTCCAA
* *
17497 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCAACAACTCTGTGGCATCCTTTT
* *
17524 AAGTCTACAACTCCGTGGCATCCTTTT
1 AAGTCAACAACTCTGTGGCATCCTTTT
*
17551 AAGTCAATAACT-TCGTGGCATCCTTTT
1 AAGTCAACAACTCT-GTGGCATCCTTTT
17578 TAAGCCCACA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (27 bp):
AAGTCAACAACTCTGTGGCATCCTTTT
Found at i:17551 original size:63 final size:63
Alignment explanation
Indices: 17433--17552 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
17423 ATTTCTTTTC
* ** * **
17433 AAAGTCCATAACTCTATGGCATTCTTTTAAGTCCATAACTCCGTGGCATTTTTTTAAAGTCCA
1 AAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCA
* *
17496 AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCTACAACTCCGTGGCATCCTTTTAA
1 AAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAA
17553 GTCAATAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (63 bp):
AAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCA
Found at i:17602 original size:311 final size:311
Alignment explanation
Indices: 17039--17663 Score: 1151
Period size: 311 Copynumber: 2.0 Consensus size: 311
17029 TCACTCATCA
*
17039 CAATTATGTCAAATCCCTAGAGAGCTTGACCTCCCTAGTACTGTGACCCCTTCAAAGTCCACGAT
1 CAATTATGTCAAATCCCTAGAGAACTTGACCTCCCTAGTACTGTGACCCCTTCAAAGTCCACGAT
* *
17104 TCAGTGACATTTCTTTTCAAAGTCCATAACTCTATGGCATTTTTTTAAGTCCACAACTCTGTGGC
66 TCAGTGACATTTCTTTTCAAAGTCCATAACTCTATGGCATTCTTTTAAGTCCACAACTCCGTGGC
*
17169 ATCCTTTTAAAGTCCAAAAGTCCACAACTCTGTGGTACCCTTTTAAGTCTACAACTCCGTGGCAT
131 ATCCTTTTAAAGTCCAAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCTACAACTCCGTGGCAT
* *
17234 CTTTTTAAGTCTATAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAG
196 CCTTTTAAGTCAATAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAG
* *
17299 TCCACAACTTCGTGGCATCCTTTTTAAGCCTACAAGTCAGTGGCACCCTTC
261 TCCACAACTTCGTGGCATCCTTTTTAAACCCACAAGTCAGTGGCACCCTTC
17350 CAATTATGTCAAATCCCTAGAGAACTTGACCTCCCTAGTACTGTGACCCCTTCAAAGTCCACGAT
1 CAATTATGTCAAATCCCTAGAGAACTTGACCTCCCTAGTACTGTGACCCCTTCAAAGTCCACGAT
*
17415 TCAGTGACATTTCTTTTCAAAGTCCATAACTCTATGGCATTCTTTTAAGTCCATAACTCCGTGGC
66 TCAGTGACATTTCTTTTCAAAGTCCATAACTCTATGGCATTCTTTTAAGTCCACAACTCCGTGGC
**
17480 ATTTTTTTAAAGTCCAAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCTACAACTCCGTGGCAT
131 ATCCTTTTAAAGTCCAAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCTACAACTCCGTGGCAT
17545 CCTTTTAAGTCAATAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAG
196 CCTTTTAAGTCAATAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAG
17610 TCCACAACTTCGTGGCATCCTTTTTAAACCCACAAGTCAGTGGCACCCTTC
261 TCCACAACTTCGTGGCATCCTTTTTAAACCCACAAGTCAGTGGCACCCTTC
17661 CAA
1 CAA
17664 AACCCACAAG
Statistics
Matches: 303, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
311 303 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (311 bp):
CAATTATGTCAAATCCCTAGAGAACTTGACCTCCCTAGTACTGTGACCCCTTCAAAGTCCACGAT
TCAGTGACATTTCTTTTCAAAGTCCATAACTCTATGGCATTCTTTTAAGTCCACAACTCCGTGGC
ATCCTTTTAAAGTCCAAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCTACAACTCCGTGGCAT
CCTTTTAAGTCAATAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAG
TCCACAACTTCGTGGCATCCTTTTTAAACCCACAAGTCAGTGGCACCCTTC
Found at i:17755 original size:32 final size:32
Alignment explanation
Indices: 17697--18004 Score: 286
Period size: 32 Copynumber: 10.1 Consensus size: 32
17687 TTTTTAGGCC
*
17697 CACAAGTCAGTGGC-A-TCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
* *
17727 CACAAGTCGGTGGTAACTCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
*
17759 CACAAGTTGGTGGCAA-TCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACT-CATTTCAAAGCCCA
* *
17791 CACAAGTCGGTGGAAACCCATTTCAAAG--C-
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
* * **
17820 CACAAGTCAGTGGC-A-TCCTTTTTAAG-CC-
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
* * **
17848 CACAAGTCAGTGGC-ACCCATTTTTAAG-CC-
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
* ** *
17877 CATAAGTTAGTGAC-A-TCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
** *
17907 CACAAGTCGGTAACAACTCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
* *
17939 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
*
17971 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
18003 CA
1 CA
18005 AGTAAGTGGC
Statistics
Matches: 234, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
27 7 0.03
28 25 0.11
29 37 0.16
30 23 0.10
31 3 0.01
32 139 0.59
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
Found at i:17871 original size:29 final size:28
Alignment explanation
Indices: 17565--18389 Score: 668
Period size: 28 Copynumber: 28.2 Consensus size: 28
17555 CAATAACTTC
**
17565 GTGGCATCCTTTTTAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * *
17593 ATGGCACCCTTCCAAAGTCCACAACTTC-
1 GTGGCATCCTTTCAAAGCCCACAA-GTCA
*
17621 GTGGCATCCTTTTTAAA-CCCACAAGTCA
1 GTGGCATCC-TTTCAAAGCCCACAAGTCA
* * *
17649 GTGGCACCCTTCCAAAACCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * ** *
17677 ATGGCACCCCTTTTTAGGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
17706 GTGGCATCATTTCAAAGCCCACACAAGTCG
1 GTGGCATCCTTTCAAAG-CC-CACAAGTCA
* * * **
17736 GTGGTAACTCATTTGAAAGCCCACACAAGTTG
1 GTGG-CA-TCCTTTCAAAG-CC-CACAAGTCA
*
17768 GTGGCAATCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ATCC-TTTCAAAG-CC-CACAAGTCA
* *
17800 GTGGAAACCCATTTCAAAG-CCACAAGTCA
1 GTGG-CATCC-TTTCAAAGCCCACAAGTCA
**
17829 GTGGCATCCTTTTTAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* ** * *
17857 GTGGCACCCATTTTTAAGCCCATAAGTTA
1 GTGGCATCC-TTTCAAAGCCCACAAGTCA
* * *
17886 GTGACATCATTTCAAAGCCCACACAAGTCG
1 GTGGCATCCTTTCAAAG-CC-CACAAGTCA
** * * **
17916 GTAACAACTCATTTGAAAGCCCACACAAGTTG
1 GTGGC-A-TCCTTTCAAAG-CC-CACAAGTCA
* *
17948 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ATCC-TTTCAAAG-CC-CACAAGTCA
* *
17980 GTGGCAACCCATTTCAAAGCCCACAAGTAA
1 GTGGC-ATCC-TTTCAAAGCCCACAAGTCA
* * *
18010 GTGGCATCTTTTCAAAGCCCATAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
18038 GTGGCATCCTTCTTAAAACCCACAAGTCA
1 GTGGCATCCTT-TCAAAGCCCACAAGTCA
18067 GTGGCATCCTTCTCAAAGCCCACAAG-CAA
1 GTGGCATCCTT-TCAAAGCCCACAAGTC-A
* *
18096 GTGGCATCATTCTCAAAGCCCACACAAATCA
1 GTGGCATCCTT-TCAAAG-CC-CACAAGTCA
* *
18127 GTGGCATCTTTTCAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
18155 GTGGCATCCTTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
18183 GTGGCATCCTTTCGAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
18211 GTGGCATCCTTCTCAAAGCCCATAAGTCA
1 GTGGCATCCTT-TCAAAGCCCACAAGTCA
*
18240 GTGGCATCCTTCTCAAAGCCCACACAGATTA
1 GTGGCATCCTT-TCAAAGCCCACA-AG-TCA
* *
18271 GTGGTATCTTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
18299 GTGGCATCCTTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
18327 ATGGCATCCTTTCAAAGCCCGCAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
18355 GTGGCATCCTTTCAAAGCCTACACAAGTCA
1 GTGGCATCCTTTCAAAGCC--CACAAGTCA
*
18385 ATGGC
1 GTGGC
18390 TTCAAAACCC
Statistics
Matches: 666, Mismatches: 102, Indels: 56
0.81 0.12 0.07
Matches are distributed among these distances:
27 13 0.02
28 254 0.38
29 168 0.25
30 69 0.10
31 34 0.05
32 128 0.19
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:17941 original size:180 final size:179
Alignment explanation
Indices: 17638--18389 Score: 744
Period size: 180 Copynumber: 4.2 Consensus size: 179
17628 CCTTTTTAAA
* * * * * *
17638 CCCACAAGTCAGTGGCACCCTTCCAAAACCCACAAGTCAATGGCACCCCTT-TTTAGGCCCACAA
1 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTCTTAAAGCCCACAA
*
17702 GTCAGTGGCATCATT-TCAAAGCCCACACAAGTCGGTGGTAACTCATTTGAAAGCCCACACAAGT
65 GTCAGTGGCATCATTCTCAAAGCCCACACAAGTCGGT--CAACTCATTTGAAAGCCCACACAAGT
17766 TGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGAAACCCATTTCAAAG
128 TGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGG-AACCCATTTCAAAG
** * *
17819 -CCACAAGTCAGTGGCATCCTTTTTAAGCCCACAAGTCAGTGGCACCCATT-TTTAAGCCCATAA
1 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTCTTAAAGCCCACAA
* *
17882 GTTAGTGACATCATT-TCAAAGCCCACACAAGTCGGTAACAACTCATTTGAAAGCCCACACAAGT
65 GTCAGTGGCATCATTCTCAAAGCCCACACAAGTCGGT--CAACTCATTTGAAAGCCCACACAAGT
*
17946 TGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAG
128 TGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGG-AACCCATTTCAAAG
* * * * * *
17999 CCCACAAGTAAGTGGCATCTTTTCAAAGCCCATAAGTTAGTGGCATCCTTCTTAAAACCCACAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCTTAAAGCCCACAAG
* * *
18064 TCAGTGGCATCCTTCTCAAAGCCCACAAGCAAGT-GG-C-A-TCATTCTCAAAGCCCACACAAAT
66 TCAGTGGCATCATTCTCAAAGCCCAC-A-CAAGTCGGTCAACTCATT-TGAAAGCCCACACAAGT
** * * * * *
18125 CAGTGGC-AT-CTTTTCAAAG-CC-CATAAGTCAGTGGCATCC-TTTCAAAG
128 TGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGAACCCATTTCAAAG
* * * * * *
18172 CCCACAAGTTAGTGGCATCCTTTCGAAGCCCATAAGTCAGTGGCATCCTTCTCAAAGCCCATAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCTTAAAGCCCACAAG
* * *
18237 TCAGTGGCATCCTTCTCAAAGCCCACACAGATTAGT-GGT--A-TCTTTTCAAAG-CC-CACAAG
66 TCAGTGGCATCATTCTCAAAGCCCACAC--A--AGTCGGTCAACTCATTTGAAAGCCCACACAAG
** *** * *
18296 TCAGTGGC-ATCC-TTTCAAAG-CC-CACAAGTTAATGGCATCC-TTTCAAAG
127 TTGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGAACCCATTTCAAAG
* *
18344 CCCGCAAGTCAGTGGCATCCTTTCAAAGCCTACACAAGTCAATGGC
1 CCCACAAGTCAGTGGCATCCTTTCAAAGCC--CACAAGTCAGTGGC
18390 TTCAAAACCC
Statistics
Matches: 501, Mismatches: 55, Indels: 37
0.84 0.09 0.06
Matches are distributed among these distances:
171 1 0.00
172 76 0.15
173 96 0.19
174 21 0.04
175 21 0.04
176 2 0.00
177 9 0.02
178 6 0.01
179 24 0.05
180 164 0.33
181 62 0.12
182 11 0.02
183 3 0.01
184 5 0.01
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (179 bp):
CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCTTAAAGCCCACAAG
TCAGTGGCATCATTCTCAAAGCCCACACAAGTCGGTCAACTCATTTGAAAGCCCACACAAGTTGG
TGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGAACCCATTTCAAAG
Found at i:18261 original size:144 final size:144
Alignment explanation
Indices: 17565--18373 Score: 628
Period size: 144 Copynumber: 5.5 Consensus size: 144
17555 CAATAACTTC
** * * * * * *
17565 GTGGCATCCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAGTCCACAACTTC-GTGGCATC
1 GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAA-GTCAGTGGCATC
* * * * * * * *
17629 CTTTTTAAA-CCCACAAGTC-AGTGGCACCCTTC-CAAA-ACC-CACAAGTCAATGGCACCCCTT
65 CTTCTCAAAGCCCACAAG-CAAGTGGCATCATTCTCAAAGCCCACACAAATCAGTGGCA--TCTT
* *
17689 TT-TAGGCCCACAAGTCA
127 TTCAAAGCCCACAAGTCA
* ** * * * **
17706 GTGGCATCATTTCAAAGCCCACACAAGTCGGTGGTAACTCATTTGAAAGCCCACACAAGTTGGTG
1 GTGGCATCCTTTCAAAG-CC-CACAAGTTAGTGG-CA-TCCTTTCAAAG-CC-CACAAGTCAGTG
* * * *
17771 GCAATCCATT-TCAAAGCCCACACAAGTC-GGTGGAAACCCATT-TCAAAG--C-CACAAGTCAG
60 GC-ATCC-TTCTCAAAG-CC-CACAAG-CAAGTGG-CA-TCATTCTCAAAGCCCACACAAATCAG
*
17830 TGGCATCCTTTT-TAAGCCCACAAGTCA
118 TGGCAT-CTTTTCAAAGCCCACAAGTCA
* ** * * * * **
17857 GTGGCACCCATTTTTAAGCCCATAAGTTAGTGACATCATTTCAAAGCCCACACAAGTCGGTAACA
1 GTGGCATCC-TTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAG-CC-CACAAGTCAGTGGC-
* * *** * * *
17922 ACTCATT-TGAAAGCCCACACAAGTTGGTGGCAACCCATT-TCAAAGCCCACACAAGTCGGTGGC
62 A-TCCTTCTCAAAG-CC-CACAAGCAAGTGGC-A-TCATTCTCAAAGCCCACACAAATCAGTGGC
* * *
17985 AACCCATTTCAAAGCCCACAAGTAA
122 -A-TCTTTTCAAAGCCCACAAGTCA
* * * *
18010 GTGGCATCTTTTCAAAGCCCATAAGTTAGTGGCATCCTTCTTAAAACCCACAAGTCAGTGGCATC
1 GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCATC
18075 CTTCTCAAAGCCCACAAGCAAGTGGCATCATTCTCAAAGCCCACACAAATCAGTGGCATCTTTTC
65 CTTCTCAAAGCCCACAAGCAAGTGGCATCATTCTCAAAGCCCACACAAATCAGTGGCATCTTTTC
*
18140 AAAGCCCATAAGTCA
130 AAAGCCCACAAGTCA
* *
18155 GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCGAAGCCCATAAGTCAGTGGCATCC
1 GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
18220 TTCTCAAAGCCCATAAGTC-AGTGGCATCCTTCTCAAAGCCCACACAGATTAGTGGTATCTTTTC
66 TTCTCAAAGCCCACAAG-CAAGTGGCATCATTCTCAAAGCCCACACAAATCAGTGGCATCTTTTC
18284 AAAGCCCACAAGTCA
130 AAAGCCCACAAGTCA
* *
18299 GTGGCATCCTTTCAAAGCCCACAAGTTAATGGCATCCTTTCAAAGCCCGCAAGTCAGTGGCATCC
1 GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
18364 TT-TCAAAGCC
66 TTCTCAAAGCC
18374 TACACAAGTC
Statistics
Matches: 556, Mismatches: 81, Indels: 60
0.80 0.12 0.09
Matches are distributed among these distances:
141 14 0.03
142 2 0.00
143 19 0.03
144 157 0.28
145 63 0.11
146 7 0.01
147 33 0.06
148 81 0.15
149 11 0.02
150 18 0.03
151 64 0.12
152 55 0.10
153 32 0.06
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (144 bp):
GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
TTCTCAAAGCCCACAAGCAAGTGGCATCATTCTCAAAGCCCACACAAATCAGTGGCATCTTTTCA
AAGCCCACAAGTCA
Found at i:18580 original size:48 final size:48
Alignment explanation
Indices: 18525--18656 Score: 201
Period size: 48 Copynumber: 2.8 Consensus size: 48
18515 GGCACCTTTA
* *
18525 TTAGCTCAATGTCGGTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
1 TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* *
18573 TTAGCTCAATGTCGTTGACCTTGAATCAGCACATTGTCCACTTTTGCC
1 TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* **
18621 TTAGCTCGATGTCGTTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTG
18657 GCACTCCTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (48 bp):
TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:19979 original size:33 final size:33
Alignment explanation
Indices: 19942--20008 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
19932 TTCAACGATT
19942 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
19975 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
20008 T
1 T
20009 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:19980 original size:13 final size:13
Alignment explanation
Indices: 19962--19986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19952 CATAAAATGT
19962 TGTATCGATACAA
1 TGTATCGATACAA
19975 TGTATCGATACA
1 TGTATCGATACA
19987 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:20068 original size:13 final size:13
Alignment explanation
Indices: 20050--20074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20040 ATTACTCAAA
20050 TGTATCGATACAT
1 TGTATCGATACAT
20063 TGTATCGATACA
1 TGTATCGATACA
20075 CCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20139 original size:52 final size:52
Alignment explanation
Indices: 20083--20203 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
20073 CACCGATCTT
*
20083 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
20135 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
20187 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
20204 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:38535 original size:27 final size:27
Alignment explanation
Indices: 38463--39000 Score: 725
Period size: 27 Copynumber: 19.6 Consensus size: 27
38453 ACTGTGACCT
*
38463 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
38490 TTTTTAGAGTCCATAACTCCGTGGCACC
1 CTTTTA-AGTCCACAACTCCGTGGCACC
* * *
38518 CTTTTAAGTCCATAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
38545 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
38572 CTTTTAAGTCCACAATTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
38599 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
38627 CTTTTAAGTCCACAATTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* ***
38654 CTTTTAAAGTCTACAACTTTATGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
38682 CTTTTTAAGTCCACAACTCCGTGGCACA
1 C-TTTTAAGTCCACAACTCCGTGGCACC
38710 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
38738 CTTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
38766 CTTTTAAGTCCACAAGTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
38793 CTTTTAAGTCCACAAGTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
38820 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
38847 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
38875 CTTTTAAGTTCACGATTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
38902 CTTTTAAAGTCCACAACTCCGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
38930 CTTTTAAAGTCCACAACTCTGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
38958 CTTTTAAGTTCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
38985 CTTTTTAAGTCCACAA
1 C-TTTTAAGTCCACAA
39001 GGCGGTGGCA
Statistics
Matches: 455, Mismatches: 48, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
27 228 0.50
28 223 0.49
29 4 0.01
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:38904 original size:248 final size:248
Alignment explanation
Indices: 38464--39000 Score: 790
Period size: 248 Copynumber: 2.2 Consensus size: 248
38454 CTGTGACCTC
* * *
38464 TTTAAAGTCCACAACTCCGTGGCACCTTTTTAGAGTCCATAACTCCGTGGCACCCTTTTAAGTCC
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * * * * * *
38529 ATAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAATTTCGTG
66 ACAACTCCGTGACACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
*
38594 GCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCCATGGCACCCTTTT
131 GCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCCATGACACCCTTTT
* ** *
38659 AAAGTCTACAACTTTATGGCACCCTTTTTAAGTCCACAACTCCGTGGCACACT
196 AAAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACACT
*
38712 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCC
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
38777 ACAAGTCCGTGACACCCTTTTAAGTCCACAAGTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
66 ACAACTCCGTGACACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
* * *
38842 GCACCCTTTT-AAGTCCACAACTCCGTGGCATCCCTTTTAAGTTCACGATTCCGTGACACCCTTT
131 GCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAATTCCATGACACCCTTT
* * * * *
38906 TAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCTGTGGTACCCT
195 TAAAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACACT
* * *
38960 TTT-AAGTTCACAACTTCGTGGCACCCTTTTTAAGTCCACAA
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAA
39001 GGCGGTGGCA
Statistics
Matches: 258, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
247 54 0.21
248 204 0.79
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.29
Consensus pattern (248 bp):
TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGACACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
GCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCCATGACACCCTTTT
AAAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACACT
Found at i:39010 original size:28 final size:28
Alignment explanation
Indices: 38468--39000 Score: 674
Period size: 28 Copynumber: 19.4 Consensus size: 28
38458 GACCTCTTTA
38468 AAGTCCACAACTCCGTGGCA-CCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
*
38495 AGAGTCCATAACTCCGTGGCACCC-TTTT
1 A-AGTCCACAACTCCGTGGCACCCTTTTT
* * *
38523 AAGTCCATAACTCTGTGGCATCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
*
38550 AAGTCCACAACTCCGTGGCATCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* * *
38577 AAGTCCACAATTTCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTT
38605 AAGTCCACAACTCCGTGGCACCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* * *
38632 AAGTCCACAATTCCATGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* ***
38660 AAGTCTACAACTTTATGGCACCCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* *
38688 AAGTCCACAACTCCGTGGCACACTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTT
*
38716 AAGTCCACAACTCCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTT
*
38744 AAGCCCACAACTCCGTGGCACCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* *
38771 AAGTCCACAAGTCCGTGACACCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
*
38798 AAGTCCACAAGTCCGTGGCACCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
38825 AAGTCCACAACTCCGTGGCACCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
38852 AAGTCCACAACTCCGTGGCATCCC-TTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTTT
* * * * *
38880 AAGTTCACGATTCCGTGACACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* *
38908 AAGTCCACAACTCCGTGGCACTCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* *
38936 AAGTCCACAACTCTGTGGTACCC-TTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
* *
38963 AAGTTCACAACTTCGTGGCACCCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTT
38991 AAGTCCACAA
1 AAGTCCACAA
39001 GGCGGTGGCA
Statistics
Matches: 446, Mismatches: 53, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
27 218 0.49
28 226 0.51
29 2 0.00
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.29
Consensus pattern (28 bp):
AAGTCCACAACTCCGTGGCACCCTTTTT
Found at i:39256 original size:32 final size:32
Alignment explanation
Indices: 38996--39477 Score: 417
Period size: 32 Copynumber: 15.8 Consensus size: 32
38986 TTTTTAAGTC
* * *
38996 CACAAGGCGGTGGCATTCCCTTCT-AAAG-CC-
1 CACAAGTCGGTGGCA-ACCCTTTTCAAAGCCCA
**
39026 CACAAGTTAGTGGC-ACCCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
** *
39055 CACAAGTTAGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
39083 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
39111 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
** * *
39139 CACAAGTTAGTCGC-A-CCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
39167 CACAAGTCAGTGGC-A-CCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
39197 CACAAGTTGGTGGC-A-CCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
39227 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
39259 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * *
39291 CACAAGTCAGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
39323 CACAAGTCGGTGGCAATCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
39355 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * * *
39387 CACAAGTTGATGGGAA-CCTCTTTCAAGAGTCCA
1 CACAAGTCGGTGGCAACCCT-TTTCAA-AGCCCA
** *
39420 CAC-TTTCGGTGGCAACCCTTTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * *
39451 CGCAAGTCAGTGGCAACCTTTTTCAAA
1 CACAAGTCGGTGGCAACCCTTTTCAAA
39478 TCACCATTTT
Statistics
Matches: 398, Mismatches: 43, Indels: 20
0.86 0.09 0.04
Matches are distributed among these distances:
27 2 0.01
28 115 0.29
29 24 0.06
30 52 0.13
31 11 0.03
32 183 0.46
33 11 0.03
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
Found at i:41071 original size:21 final size:18
Alignment explanation
Indices: 41038--41080 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
41028 TGATGTTTGC
41038 ATTTGTTTTTTTATTATCAT
1 ATTTGTTTTTTTATT-T-AT
*
41058 ATTTTTTTATTTTATTTAT
1 ATTTGTTT-TTTTATTTAT
41077 ATTT
1 ATTT
41081 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTGTTTTTTTATTTAT
Found at i:45952 original size:28 final size:27
Alignment explanation
Indices: 45926--45978 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
45916 AATGTTTTAA
45926 ATAAATTTGTTTTATA-AAATAAATTT
1 ATAAATTTGTTTTATATAAATAAATTT
* * *
45952 ATTAATTTTTTTTTTATAAATAAATTT
1 ATAAATTTGTTTTATATAAATAAATTT
45979 GTTTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
ATAAATTTGTTTTATATAAATAAATTT
Found at i:46635 original size:19 final size:20
Alignment explanation
Indices: 46608--46658 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
46598 TTATGTTTTG
* *
46608 TATCAATACATGTTC-ATTA
1 TATCGATACATGCTCAATTA
* *
46627 TATCGATACATACTCAATTG
1 TATCGATACATGCTCAATTA
46647 TATCGATACATG
1 TATCGATACATG
46659 AAACTGGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (20 bp):
TATCGATACATGCTCAATTA
Found at i:46652 original size:20 final size:19
Alignment explanation
Indices: 46605--46657 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
46595 ACATTATGTT
* **
46605 TTGTATCAATACATGTTCA
1 TTGTATCGATACATACTCA
*
46624 TTATATCGATACATACTCAA
1 TTGTATCGATACATACTC-A
46644 TTGTATCGATACAT
1 TTGTATCGATACAT
46658 GAAACTGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (19 bp):
TTGTATCGATACATACTCA
Found at i:46726 original size:13 final size:13
Alignment explanation
Indices: 46708--46732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46698 CATGGCACAT
46708 TGTATCGATACAG
1 TGTATCGATACAG
46721 TGTATCGATACA
1 TGTATCGATACA
46733 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:46732 original size:33 final size:32
Alignment explanation
Indices: 46688--46752 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
46678 TATCATTGTT
46688 TGTATCAATACATG-GCACATTGTATCGATACAG
1 TGTATCAATACATGAG-A-ATTGTATCGATACAG
*
46721 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCAATACATG-AGAATTGTATCGATACA
46753 TTATACCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTATCAATACATGAGAATTGTATCGATACAG
Found at i:52228 original size:21 final size:21
Alignment explanation
Indices: 52202--52250 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
52192 ATTTAATTTT
52202 TTAA-TTAAATAATAATTCAAA
1 TTAATTTAAATAA-AATTCAAA
* *
52223 TTAATTTAATTAAAATTTAAA
1 TTAATTTAAATAAAATTCAAA
*
52244 TTTATTT
1 TTAATTT
52251 CATTTAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTTAAATAAAATTCAAA
Found at i:52544 original size:23 final size:23
Alignment explanation
Indices: 52518--52598 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 23
52508 TTAAAGTTAC
52518 ATAAATTTTATAAAAAATAAAAT
1 ATAAATTTTATAAAAAATAAAAT
** ** * * *
52541 ATAAAATCAATATTTAAAGTTACAT
1 AT-AAAT-TTTATAAAAAATAAAAT
52566 --AAATTTTATAAAAAATAAAAT
1 ATAAATTTTATAAAAAATAAAAT
*
52587 ATAAAATTTATA
1 ATAAATTTTATA
52599 TTTGTAAGTG
Statistics
Matches: 39, Mismatches: 15, Indels: 8
0.63 0.24 0.13
Matches are distributed among these distances:
21 10 0.26
22 4 0.10
23 11 0.28
24 4 0.10
25 10 0.26
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (23 bp):
ATAAATTTTATAAAAAATAAAAT
Found at i:52601 original size:46 final size:46
Alignment explanation
Indices: 52500--52593 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
52490 TAATTAATCG
52500 ATCAATATTTAAAGTTACATAAATTTTATAAAAAATAAAATATAAA
1 ATCAATATTTAAAGTTACATAAATTTTATAAAAAATAAAATATAAA
52546 ATCAATATTTAAAGTTACATAAATTTTATAAAAAATAAAATATAAA
1 ATCAATATTTAAAGTTACATAAATTTTATAAAAAATAAAATATAAA
52592 AT
1 AT
52594 TTATATTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (46 bp):
ATCAATATTTAAAGTTACATAAATTTTATAAAAAATAAAATATAAA
Done.