Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold731
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: 143317
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10677 original size:14 final size:15
Alignment explanation
Indices: 10658--10688 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10648 GTTTAGTTTA
10658 TTTATAT-TAATTTT
1 TTTATATATAATTTT
10672 TTTATATATAATTTT
1 TTTATATATAATTTT
10687 TT
1 TT
10689 AAAATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATATATAATTTT
Found at i:10712 original size:20 final size:20
Alignment explanation
Indices: 10673--10712 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
10663 ATTAATTTTT
** *
10673 TTATATATAATTTTTTAAAA
1 TTATATATAATTAATAAAAA
10693 TTATATATAATTAATAAAAA
1 TTATATATAATTAATAAAAA
10713 AATACTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATATATAATTAATAAAAA
Found at i:10940 original size:22 final size:21
Alignment explanation
Indices: 10915--10955 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
10905 TAGCAAAATG
10915 ACAACAAAACAATGAGAAAACA
1 ACAACAAAACAATG-GAAAACA
* *
10937 ACAAGAAAACAGTGGAAAA
1 ACAACAAAACAATGGAAAA
10956 ATAGTAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.66, C:0.15, G:0.15, T:0.05
Consensus pattern (21 bp):
ACAACAAAACAATGGAAAACA
Found at i:12955 original size:11 final size:12
Alignment explanation
Indices: 12927--12958 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12917 GCCCGCCCAC
12927 ATTAATTTTTAT
1 ATTAATTTTTAT
12939 ATTAATTTTTAT
1 ATTAATTTTTAT
12951 A-TAATTTT
1 ATTAATTTT
12959 AAATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTAATTTTTAT
Found at i:15383 original size:16 final size:16
Alignment explanation
Indices: 15362--15397 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
15352 CCTCCTATGA
15362 CCAAGTTTCCTCCGCT
1 CCAAGTTTCCTCCGCT
15378 CCAAGTTTCCTCCGCT
1 CCAAGTTTCCTCCGCT
15394 CCAA
1 CCAA
15398 ACGAGTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.44, G:0.11, T:0.28
Consensus pattern (16 bp):
CCAAGTTTCCTCCGCT
Found at i:21646 original size:16 final size:17
Alignment explanation
Indices: 21625--21657 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21615 CTACAAATAT
21625 AATAAAATAT-TAAAAA
1 AATAAAATATATAAAAA
*
21641 AATAAATTATATAAAAA
1 AATAAAATATATAAAAA
21658 TTACGCCGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAATATATAAAAA
Found at i:33682 original size:2 final size:2
Alignment explanation
Indices: 33677--33702 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33667 AAGAAAAAAT
33677 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
33703 CTGCTTTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35050 original size:174 final size:172
Alignment explanation
Indices: 34592--35225 Score: 820
Period size: 174 Copynumber: 3.7 Consensus size: 172
34582 CTGTAAATTA
* * * * * * * *
34592 TTGTCGTGTTTTAAATGAATGTACGAAACGTTCCAAGAAAGAAATAAGTTAGTTTTAAACTTTGA
1 TTGTCGTATTTTAAAT-AAAGCACGGAACGTTTCAA-AAAGAAATGAGTTAATTTTAAATTTTGA
* * ** * * *
34657 ACATATTTTTAAGTTTGATATATAAATTAAACGTTCACTGAAATTTTAAATAAATTTTTCATTTT
64 ACATCTTTTTAAGTTTGATGTATATGTTAAACGTTCACTGAAAATTTAAATAAACTCTTCATTTT
*
34722 ATTTATGACTATTTAATGCACACAAATATCGTTTTTATTATATT
129 ATTTATGACTATTTAATGCACACAGATATCGTTTTTATTATATT
* *
34766 TTGTCGTATTTTAAATTAA--A--G--CGTTTCAAAAATGAAATGAGTTGATTTTAAATTTTGAA
1 TTGTCGTATTTTAAATAAAGCACGGAACGTTTCAAAAA-GAAATGAGTTAATTTTAAATTTTGAA
* *
34825 CATCTTTTAAAGTTTGATGTATATGTTAAACGTTCACGGAAAATTTAAATAAACTCTTCATTTTA
65 CATCTTTTTAAGTTTGATGTATATGTTAAACGTTCACTGAAAATTTAAATAAACTCTTCATTTTA
*
34890 TTTATGACTATTTAATGCGCACAGATATCGTTTTTATTATATT
130 TTTATGACTATTTAATGCACACAGATATCGTTTTTATTATATT
*
34933 TTGTCGTATTTTAAACTAAAGCACGGAACGTTTCAAAAACGAAATGAGTTAATTTTCAATTTTGA
1 TTGTCGTATTTTAAA-TAAAGCACGGAACGTTTCAAAAA-GAAATGAGTTAATTTTAAATTTTGA
* * *
34998 ACATCTTTTTAAGTTTGATGTATATGTTAAATGTTCACT-AGAAATCTAAATAAATTCTTCATTT
64 ACATCTTTTTAAGTTTGATGTATATGTTAAACGTTCACTGA-AAATTTAAATAAACTCTTCATTT
*
35062 TATTTATGACTATTTAATGCACACAGATATCATTTTTATTATATT
128 TATTTATGACTATTTAATGCACACAGATATCGTTTTTATTATATT
* * * * *
35107 TTGTCGTATTTTAAACTAAAGCACAGAATGTTTCAAAAA-AAATGAATTGATTTTGAATTTTGAA
1 TTGTCGTATTTTAAA-TAAAGCACGGAACGTTTCAAAAAGAAATGAGTTAATTTTAAATTTTGAA
* *
35171 CATCTTTTTGAGTTTTGATGTATTTGTTAATA--TTCACTGAAAATTTAAATAAACT
65 CATCTTTTTAAG-TTTGATGTATATGTTAA-ACGTTCACTGAAAATTTAAATAAACT
35226 TGACAGCAAA
Statistics
Matches: 408, Mismatches: 40, Indels: 26
0.86 0.08 0.05
Matches are distributed among these distances:
166 3 0.01
167 141 0.35
168 3 0.01
170 1 0.00
171 1 0.00
172 53 0.13
173 19 0.05
174 187 0.46
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (172 bp):
TTGTCGTATTTTAAATAAAGCACGGAACGTTTCAAAAAGAAATGAGTTAATTTTAAATTTTGAAC
ATCTTTTTAAGTTTGATGTATATGTTAAACGTTCACTGAAAATTTAAATAAACTCTTCATTTTAT
TTATGACTATTTAATGCACACAGATATCGTTTTTATTATATT
Found at i:35556 original size:201 final size:201
Alignment explanation
Indices: 35189--37049 Score: 1709
Period size: 201 Copynumber: 9.4 Consensus size: 201
35179 TGAGTTTTGA
* ** * *
35189 TGTATTTGTTAATATTCACT-GAAAATTTAAATAAACTTGACAGCAAACAAATTATTCTTTTTAT
1 TGTATATGTTAACGTTCACTAG-AAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTAT
* * * * *
35253 TTATAACTATTAAAT--ACACATATATTATTTTTGTTATATTTTGTCATGTATTAAATGAAAGCA
65 TTATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGCA
* * * * * * * * *
35316 CGAGATATTTCAAAAAATATATGAGTTAATATGAAAATTTGAATATCTTTCTAAGTTTTGATAAA
130 CGAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAA
35381 CAAGGCTTT
195 -AA-GCTTT
* * * *
35390 TGTATATGTTAACATTCACTAGAATTTTAAATAAATTTGGCAACAAACAAATTATTC-TTTT-CT
1 TGTATATGTTAACGTTCACTAGAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTATT
* * *
35453 TATAACTATTAAATACATACATATATCATTTTTATTGTATTTTGTCATGTCTTAAATGAAAGCAC
66 TATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGCAC
** * * **
35518 GAAGCGTTTCAAGAAATATATGAGTTAATTTTAAAATTTGAACATCTTTCTAAGCATTGATGAAC
131 GAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAA-
35583 AAGGCTTT
195 AA-GCTTT
** * * * * *
35591 TGTATATGTTAACGTTCACCGGAAATTTAAATAAAATTGGCAACAATCAGATTATTCTTATTATT
1 TGTATATGTTAACGTTCACTAGAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTATT
* * * * * *
35656 TATAACTATTAAATACACACGTGTGTCATTTTTATTGTATCTTGTCGTGTTTCAAATGAAAACAC
66 TATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGCAC
* *
35721 -AAATGTTTCAAGAAATATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTT--T----
131 GAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAAA
35779 A-----
196 AGCTTT
* * * * * *
35780 TGTATAGGTTAACATTCA-TTGAAAATTTAAATGAATTTGACAACAAA-TAATTTTTC-TTTTAT
1 TGTATATGTTAACGTTCACTAG-AAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTAT
* * * *
35842 TTATAATTATTAAAT--ACACATATATCATTTTTATTGCATTTTGCCGTGTTTTAAATGAAAGAA
65 TTATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGCA
* ** *** **
35905 CAAAATGTTTCAAGAAAGATATTG-GTTTTTTTTTTTTTTTGAACATCTTTCTAAACTTTGATGA
130 CGAAATGTTTCAAGAAAGATA-TGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATG-
*
35969 ATAAAACTTT
193 A-AAAGCTTT
* * * * *
35979 TGTATATGTTAACCTTCACTA-AAAGTTTAAATAAATTTGGCAACAAATATATTCTTCTTTTTTA
1 TGTATATGTTAACGTTCACTAGAAA-TTTAAATAAATTTGACAACAAACAAATTATTC-TTTTTA
* * * * * *
36043 TTTATAGCTATTAAATACACATAAATGTAATTTTTATTATATTTTGTCGTGTTTTAAATG-AAGA
64 TTTATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAG-
* * *
36107 CACAAAATGTTTTAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTTTAAGTTTTGATG
128 CACGAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATG
*
36172 AACGAGGCTTT
193 AA--AAGCTTT
* * * * **
36183 TGCATATGTTAATGTTCACT-GAAAATTTAAATAAAATTGGCAACAAACAGGTTATTCTTTTTAT
1 TGTATATGTTAACGTTCACTAG-AAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTAT
* * *
36247 TTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAGTGAAAACA
65 TTATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGCA
*
36312 -G-AATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTT--T---
130 CGAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAA
36370 -A-----
195 AAGCTTT
* * * *
36371 TGTATGTGTTAACTTTAACTA-AAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTAT
1 TGTATATGTTAACGTTCACTAGAAA-TTTAAATAAATTTGACAACAAACAAATTATTCTTTTTAT
* * * *
36435 TTATAACTATTAAATACACATAGATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAGAA-A
65 TTATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGA-AAGC
* * * * *
36499 ACGAAAGGTTTCAATAAAGATATGAGTTGATATTTTAAAATTTGAACATCTTTTTAAGCTTTGAT
129 ACGAAATGTTTCAAGAAAGATATGAGTT-A-ATTTTAAATTTTGAACATCTTTCTAAGTTTTGAT
36564 GAATAAGACTTT
192 GAA-AAG-CTTT
* * * * * *
36576 TATATATGCTAACGTTCACT-GAAAATTTAAATAAAATTGACAACAAATAGATTCTTCTTTTTTA
1 TGTATATGTTAACGTTCACTAG-AAATTTAAATAAATTTGACAACAAACAAATTATTC-TTTTTA
* * *** *
36640 TTTATAACTATTGAATACACTCGGGTATCATTTTTATTGTATTCTGTCGTGTTTTAAATGAAAGC
64 TTTATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGC
*
36705 AC-AGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTT--T-
129 ACGA-AATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATG
36766 ---A-----
193 AAAAGCTTT
* * *
36767 TGTATATTTTAACGTTCATTA-AAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTAT
1 TGTATATGTTAACGTTCACTAGAAA-TTTAAATAAATTTGACAACAAACAAATTATTCTTTTTAT
* * * * *
36831 TTATAACTCTTAAAT--ACACATATATCATTTTTATTGTATGGTAGTTGTGTTTTAAATGAAAGT
65 TTATAACTATTAAATACACACATATATCATTTTTATTGTAT-TTTGTCGTGTTTTAAATGAAAGC
* * * * * * * * * *
36894 ACCAAATG-ATCTAAGAATGAAATAAATTAGTTATAAATTTTGTACAAAT-TTTTTAAGATTTTG
129 ACGAAATGTTTC-AAGAAAGATATGAGTTAATTTTAAATTTTG-A-ACATCTTTCTAAG-TTTTG
*
36957 AAGAATAAGACTTT
190 ATGAA-AAG-CTTT
* * * * * * * *
36971 TGTATATGTTAACATCCATTATAAATTTAAATAAATTCGACAA-AATCAAAATATTCATTTTATT
1 TGTATATGTTAACGTTCACTAGAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTATT
*
37035 AATAACTATTAAATA
66 TATAACTATTAAATA
37050 TATACAAATT
Statistics
Matches: 1367, Mismatches: 210, Indels: 163
0.79 0.12 0.09
Matches are distributed among these distances:
185 40 0.03
186 45 0.03
187 24 0.02
188 135 0.10
189 88 0.06
190 53 0.04
191 53 0.04
192 27 0.02
194 2 0.00
195 1 0.00
197 1 0.00
198 4 0.00
199 53 0.04
200 12 0.01
201 258 0.19
202 76 0.06
203 154 0.11
204 200 0.15
205 54 0.04
206 87 0.06
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (201 bp):
TGTATATGTTAACGTTCACTAGAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTATT
TATAACTATTAAATACACACATATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGCAC
GAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAAA
AGCTTT
Found at i:36192 original size:204 final size:202
Alignment explanation
Indices: 35780--37013 Score: 1186
Period size: 204 Copynumber: 6.2 Consensus size: 202
35770 TAAGTTTTTA
* * * * *
35780 TGTATAGGTTAACATTCATTGAAAATTTAAATGAATTTGACAACAAATA-ATT-TT-TCTTTTAT
1 TGTATATGTTAACGTTCACTGAAAATTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTAT
* * *
35842 TTATAATTATTAAATACACAT-ATATCATTTTTATTGCATTTTGCCGTGTTTTAAATGAAAGAAC
66 TTATAACTATTAAATACACATAATATCATTTTTATTGTATTTTGTCGTGTTTTAAATG-AAGAAC
** *** **
35906 AAAATGTTTCAAGAAAGATATTG-GTTTTTTTTTTTTTTTGAACATCTTTCTAAACTTTGATGAA
130 AAAATGTTTCAAGAAAGATA-TGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAA
*
35970 TAAAACTTT
194 TAAGACTTT
* * *
35979 TGTATATGTTAACCTTCACT-AAAAGTTTAAATAAATTTGGCAACAAATATATTCTTCTTTTTTA
1 TGTATATGTTAACGTTCACTGAAAA-TTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTA
* * * *
36043 TTTATAGCTATTAAATACACATAAATGTAATTTTTATTATATTTTGTCGTGTTTTAAATGAAGAC
65 TTTATAACTATTAAATACACAT-AATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAGA-
* *
36108 ACAAAATGTTTTAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTTTAAGTTTTGATGA
128 ACAAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGA
** *
36173 ACGAGGCTTT
193 ATAAGACTTT
* * * * * * *
36183 TGCATATGTTAATGTTCACTGAAAATTTAAATAAAATTGGCAACAAACAGGTTATTC-TTTTTAT
1 TGTATATGTTAACGTTCACTGAAAATTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTAT
* * *
36247 TTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAGTGAA-AAC
66 TTATAACTATTAAATACACATA-ATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAGAAC
* *
36311 AGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAG-TTT--T---T
130 AAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAAT
36370 ---A----
195 AAGACTTT
* * * * *
36371 TGTATGTGTTAACTTTAACT-AAAATTTTAAATAAATTTGACAACAAACAAATTCTTC-TTTTTA
1 TGTATATGTTAACGTTCACTGAAAA-TTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTA
* *
36434 TTTATAACTATTAAATACACATAGATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAGAAA
65 TTTATAACTATTAAATACACATA-ATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGA-AGA
* * * * * *
36499 ACGAAAGGTTTCAATAAAGATATGAGTTGATATTTTAAAATTTGAACATCTTTTTAAGCTTTGAT
128 ACAAAATGTTTCAAGAAAGATATGAGTT-A-ATTTTAAATTTTGAACATCTTTCTAAGTTTTGAT
36564 GAATAAGACTTT
191 GAATAAGACTTT
* * *
36576 TATATATGCTAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATTCTTCTTTTTTAT
1 TGTATATGTTAACGTTCACTGAAAATTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTAT
* ** * *
36641 TTATAACTATTGAATACAC-TCGGGTATCATTTTTATTGTATTCTGTCGTGTTTTAAATGAAAGC
66 TTATAACTATTAAATACACAT--AATATCATTTTTATTGTATTTTGTCGTGTTTTAAATG-AAGA
* *
36705 ACAGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAG-TTT--T--
128 ACAAAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGA
36765 -T---A----
193 ATAAGACTTT
* * * *
36767 TGTATATTTTAACGTTCA-TTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTC-TTTTTA
1 TGTATATGTTAACGTTCACTGAAAA-TTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTA
* * * * *
36830 TTTATAACTCTTAAATACACAT-ATATCATTTTTATTGTATGGTAGTTGTGTTTTAAATGAAAGT
65 TTTATAACTATTAAATACACATAATATCATTTTTATTGTAT-TTTGTCGTGTTTTAAATG-AAGA
* * * * * * * * * *
36894 ACCAAATG-ATCTAAGAATGAAATAAATTAGTTATAAATTTTGTACAAAT-TTTTTAAGATTTTG
128 ACAAAATGTTTC-AAGAAAGATATGAGTTAATTTTAAATTTTG-A-ACATCTTTCTAAG-TTTTG
*
36957 AAGAATAAGACTTT
189 ATGAATAAGACTTT
* * * *
36971 TGTATATGTTAACATCCA-TTATAAATTTAAATAAATTCGACAA
1 TGTATATGTTAACGTTCACTGA-AAATTTAAATAAATTTGACAA
37014 AATCAAAATA
Statistics
Matches: 860, Mismatches: 121, Indels: 103
0.79 0.11 0.10
Matches are distributed among these distances:
187 4 0.00
188 123 0.14
189 49 0.06
190 61 0.07
191 49 0.06
192 27 0.03
193 3 0.00
195 2 0.00
197 1 0.00
198 7 0.01
199 39 0.05
200 7 0.01
201 56 0.07
202 28 0.03
203 70 0.08
204 193 0.22
205 53 0.06
206 87 0.10
207 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (202 bp):
TGTATATGTTAACGTTCACTGAAAATTTAAATAAATTTGACAACAAATAGATTCTTCTTTTTTAT
TTATAACTATTAAATACACATAATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAGAACA
AAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTTGATGAATA
AGACTTT
Found at i:36744 original size:597 final size:593
Alignment explanation
Indices: 35059--36891 Score: 2190
Period size: 592 Copynumber: 3.1 Consensus size: 593
35049 AAATTCTTCA
* * * * *
35059 TTTTATTTATGACTATTTAATGCACACAGATATCATTTTTATTATATTTTGTCGTATTTTAAACT
1 TTTTATTTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAA-T
* * * * ** *
35124 -AAAGCACAGAATGTTTCAA-AAAAAATGAATTGATTTTGAATTTTGAACATCTTTTTGAGTTTT
65 GAAA--ACAGAATGTTTCAAGAAAATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTT
* * * *
35187 GATGTATTTGTTAA-TATTCACTGAAAATTTAAATAAACTTGACAGCAAACAAATTATTCTTTTT
128 TATGTATGTGTTAACT-TTCACTGAAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTT
* * * * *
35251 ATTTATAACTATTAAATACACATATATTATTTTTGTTATATTTTGTCATGTATTAAATGAAAGCA
192 ATTTATAACTATTAAATACACATATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAAAGAA
* * * * * * * *
35316 CGAGATATTTCAAAAAATATATGAGTTA-ATATGAAAATTTGAATATCTTTCTAAGTTTTGATAA
257 CGAAATGTTTCAAAAAAGATATGAGTTATATTTTAAAATTTGAACATCTTTCTAAGCTTTGATGA
* * * * *
35380 ACAAGGCTTTTGTATATGTTAACATTCACTAGAATTTTAAATAAATTTGGCAACAAACAAATTAT
322 ATAAGACTTTTGTATATGTTAACATTCACTA-AAATTTAAATAAATTTGGCAACAAATAAATTCT
* * * *
35445 TC--TTTT-CTTATAACTATTAAATACA-TACATATATCATTTTTATTGTATTTTGTCATGTCTT
386 TCTTTTTTATTTATAACTATTAAATACACTACATGTATCATTTTTATTGTATTTTGTCGTGTTTT
* * *
35506 AAATGAAAGCAC-GAAGCGTTTCAAGAAATATATGAGTTAATTTTAAAATTTGAACATCTTTCTA
451 AAATGAAAGCACAGAA-TGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTA
** * *
35570 AGCATTGATGAACAAGGCTTTTGTATATGTTAACGTTCACCGGAAATTTAAATAAAATTGGCAAC
515 AGTTTTGATGAACAAGGCTTTTGCATATGTTAACGTTCACCGAAAATTTAAATAAAATTGGCAAC
*
35635 AATCAGATTATTCT
580 AAACAGATTATTCT
* * * * * * *
35649 TATTATTTATAACTATTAAATACACACGTGTGTCATTTTTATTGTATCTTGTCGTGTTTCAAATG
1 TTTTATTTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAATG
*
35714 AAAACACAAATGTTTCAAGAAATATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTT
66 AAAACA-GAATGTTTCAAGAAA-ATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTT
* * * * *
35779 ATGTATAG-GTTAACATTCATTGAAAATTTAAATGAATTTGACAACAAA-TAATTTTTC-TTTTA
129 ATGTAT-GTGTTAACTTTCACTGAAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTA
* * * *
35841 TTTATAATTATTAAATACACATATATCATTTTTATTGCATTTTGCCGTGTTTTAAATGAAAGAAC
193 TTTATAACTATTAAATACACATATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAAAGAAC
* * * **** *
35906 AAAATGTTTCAAGAAAGATATTG-GTT-TTTTTTTTTTTTTGAACATCTTTCTAAACTTTGATGA
258 GAAATGTTTCAAAAAAGATA-TGAGTTATATTTTAAAATTTGAACATCTTTCTAAGCTTTGATGA
* * *
35969 ATAAAACTTTTGTATATGTTAACCTTCACTAAAAGTTTAAATAAATTTGGCAACAAATATATTCT
322 ATAAGACTTTTGTATATGTTAACATTCACTAAAA-TTTAAATAAATTTGGCAACAAATAAATTCT
* * *
36034 TCTTTTTTATTTATAGCTATTAAATACACATAAATGTA--ATTTTTATTATATTTTGTCGTGTTT
386 TCTTTTTTATTTATAACTATTAAATACAC-TACATGTATCATTTTTATTGTATTTTGTCGTGTTT
* * *
36097 TAAATG-AAGACACAAAATGTTTTAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTTT
450 TAAATGAAAG-CACAGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCT
* * *
36161 AAGTTTTGATGAACGAGGCTTTTGCATATGTTAATGTTCACTGAAAATTTAAATAAAATTGGCAA
514 AAGTTTTGATGAACAAGGCTTTTGCATATGTTAACGTTCACCGAAAATTTAAATAAAATTGGCAA
*
36226 CAAACAGGTTATTCT
579 CAAACAGATTATTCT
*
36241 TTTTATTTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAGTG
1 TTTTATTTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAATG
36306 AAAACAGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTA
66 AAAACAGAATGTTTCAAGAAA-ATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTA
* *
36371 TGTATGTGTTAACTTTAACT-AAAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTAT
130 TGTATGTGTTAACTTTCACTGAAAA-TTTAAATAAATTTGACAACAAACAAATTATTCTTTTTAT
36435 TTATAACTATTAAATACACATAGATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAGAA-A
194 TTATAACTATTAAATACACAT--ATATCATTTTTATTGTATTTTGTCATGTTTTAAATGA-AAGA
* * *
36499 ACGAAAGGTTTCAATAAAGATATGAGTTGATATTTTAAAATTTGAACATCTTTTTAAGCTTTGAT
256 ACGAAATGTTTCAAAAAAGATATGAGTT-ATATTTTAAAATTTGAACATCTTTCTAAGCTTTGAT
* * * * * *
36564 GAATAAGACTTTTATATATGCTAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATT
320 GAATAAGACTTTTGTATATGTTAACATTCACT-AAAATTTAAATAAATTTGGCAACAAATAAATT
* ** *
36629 CTTCTTTTTTATTTATAACTATTGAATACACT-CGGGTATCATTTTTATTGTATTCTGTCGTGTT
384 CTTCTTTTTTATTTATAACTATTAAATACACTACATGTATCATTTTTATTGTATTTTGTCGTGTT
*
36693 TTAAATGAAAGCACAGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCT
449 TTAAATGAAAGCACAGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCT
* * ** * *
36758 AAGTTTT--T-----A------TGTATATTTTAACGTTCA-TTAAAATTTTAAATAAATTTGACA
514 AAGTTTTGATGAACAAGGCTTTTGCATATGTTAACGTTCACCGAAAA-TTTAAATAAAATTGGCA
* *
36809 ACAAACAAATTCTTCT
578 ACAAACAGATTATTCT
* * * * *
36825 TTTTATTTATAACTCTTAAAT--ACACATATATCATTTTTATTGTATGGTAGTTGTGTTTTAAAT
1 TTTTATTTATAACTATTAAATACACACATATATCATTTTTATTATAT-TTTGTCGTGTTTTAAAT
36888 GAAA
65 GAAA
36892 GTACCAAATG
Statistics
Matches: 1064, Mismatches: 147, Indels: 71
0.83 0.11 0.06
Matches are distributed among these distances:
582 23 0.02
583 22 0.02
584 63 0.06
588 5 0.00
589 171 0.16
590 72 0.07
591 174 0.16
592 231 0.22
593 28 0.03
594 8 0.01
595 61 0.06
596 3 0.00
597 196 0.18
598 7 0.01
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (593 bp):
TTTTATTTATAACTATTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAATG
AAAACAGAATGTTTCAAGAAAATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTAT
GTATGTGTTAACTTTCACTGAAAATTTAAATAAATTTGACAACAAACAAATTATTCTTTTTATTT
ATAACTATTAAATACACATATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAAAGAACGAA
ATGTTTCAAAAAAGATATGAGTTATATTTTAAAATTTGAACATCTTTCTAAGCTTTGATGAATAA
GACTTTTGTATATGTTAACATTCACTAAAATTTAAATAAATTTGGCAACAAATAAATTCTTCTTT
TTTATTTATAACTATTAAATACACTACATGTATCATTTTTATTGTATTTTGTCGTGTTTTAAATG
AAAGCACAGAATGTTTCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTCTAAGTTTT
GATGAACAAGGCTTTTGCATATGTTAACGTTCACCGAAAATTTAAATAAAATTGGCAACAAACAG
ATTATTCT
Found at i:36792 original size:396 final size:389
Alignment explanation
Indices: 35789--36869 Score: 1350
Period size: 396 Copynumber: 2.7 Consensus size: 389
35779 ATGTATAGGT
* * * * * *
35789 TAACATTCATTGAAAATTTAAATGAATTTGACAACAAATA-ATTTT-TCTTTTATTTATAATTAT
1 TAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATTTTCTTTTTTATTTATAACTAT
* * *
35852 TAAATACACAT-ATATCATTTTTATTGCATTTTGCCGTGTTTTAAATGAAAGAACAAAATGTTTC
66 TAAATACAC-TCATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAG-ACAGAATGTTTC
** *** * *
35916 AAGAAAGATATTG-GTTTTTTTTTTTTTTTGAACATCTTTCTAAACTTTGATGAATAAAACTTTT
129 AAGAAAGATA-TGAGTTAATTTTAAATTTTGAACATCTTCCT-AAGTTT--T---T---A----T
* * * *
35980 GTATATGTTAACCTTCACTAAAAGTTTAAATAAATTTGGCAACAAATATATTCTTCTTTTTTATT
180 GTATATGTTAACCTTCACTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTC-TTTTTATT
* * * * * *
36045 TATAGCTATTAAATACACATAAATGTAATTTTTATTATATTTTGTCGTGTTTTAAATGAAGACAC
244 TATAACTATTAAATACACAT-AATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAAGAAAC
* * * *
36110 AAAATGTTTTAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTTTTAAGTTTTGATGAAC
308 AAAAGGTTTCAAGAAAGATATGAGTTAATTTTAAAATTTGAACATCTTTTTAAGCTTTGATGAAC
* * * *
36175 GAGGCTTTTGCATATGT
373 AAGACTTTTACATATGC
* * * *
36192 TAATGTTCACTGAAAATTTAAATAAAATTGGCAACAAACAGGTTATTC-TTTTTATTTATAACTA
1 TAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATT-TTCTTTTTTATTTATAACTA
* * *
36256 TTAAATACACACATATATCATTTTTATTATATTTTGTCGTGTTTTAAGTGAAA-ACAGAATGTTT
65 TTAAATACACTC--ATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGACAGAATGTTT
* *
36320 CAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTATGTATGTGTTAACT
128 CAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTATGTATATGTTAACC
*
36385 TTAACTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTATTTATAACTATTAAAT
193 TTCACTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTATTTATAACTATTAAAT
* *
36450 ACACATAGATATCATTTTTATTGTATTTTGTCATGTTTTAAATG-AGAAAACGAAAGGTTTCAAT
258 ACACATA-ATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAAG-AAACAAAAGGTTTCAAG
* *
36514 AAAGATATGAGTTGATATTTTAAAATTTGAACATCTTTTTAAGCTTTGATGAATAAGACTTTTAT
321 AAAGATATGAGTT-A-ATTTTAAAATTTGAACATCTTTTTAAGCTTTGATGAACAAGACTTTTAC
36579 ATATGC
384 ATATGC
36585 TAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATTCTTCTTTTTTATTTATAACTA
1 TAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATT-TTCTTTTTTATTTATAACTA
* * *
36650 TTGAATACACTCGGGTATCATTTTTATTGTATTCTGTCGTGTTTTAAATGAAAGCACAGAATGTT
65 TTAAATACACTC--ATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAG-ACAGAATGTT
*
36715 TCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTATGTATATTTTAAC
127 TCAAGAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTATGTATATGTTAAC
* * *
36780 GTTCATTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTATTTATAACTCTTAAA
192 CTTCACTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTATTTATAACTATTAAA
36845 TACACAT-ATATCATTTTTATTGTAT
257 TACACATAATATCATTTTTATTGTAT
36870 GGTAGTTGTG
Statistics
Matches: 597, Mismatches: 67, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
390 3 0.01
391 84 0.14
392 51 0.09
393 90 0.15
394 79 0.13
396 142 0.24
399 1 0.00
402 1 0.00
403 33 0.06
404 9 0.02
405 69 0.12
407 35 0.06
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (389 bp):
TAACGTTCACTGAAAATTTAAATAAAATTGACAACAAATAGATTTTCTTTTTTATTTATAACTAT
TAAATACACTCATATCATTTTTATTGTATTTTGTCGTGTTTTAAATGAAAGACAGAATGTTTCAA
GAAAGATATGAGTTAATTTTAAATTTTGAACATCTTCCTAAGTTTTTATGTATATGTTAACCTTC
ACTAAAATTTTAAATAAATTTGACAACAAACAAATTCTTCTTTTTATTTATAACTATTAAATACA
CATAATATCATTTTTATTGTATTTTGTCATGTTTTAAATGAAGAAACAAAAGGTTTCAAGAAAGA
TATGAGTTAATTTTAAAATTTGAACATCTTTTTAAGCTTTGATGAACAAGACTTTTACATATGC
Found at i:37790 original size:6 final size:6
Alignment explanation
Indices: 37781--37808 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
37771 ATTGTTATTG
37781 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
37809 TTAATTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:38794 original size:2 final size:2
Alignment explanation
Indices: 38787--38817 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38777 ATGGGTAAAT
38787 TA 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 TA T
38818 GTCAACATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39755 original size:18 final size:19
Alignment explanation
Indices: 39732--39769 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
39722 CTTGTTTAGA
*
39732 ATTTTTTATCGT-ATTAAT
1 ATTTTTTATAGTAATTAAT
39750 A-TTTTTATAGTAATTAAT
1 ATTTTTTATAGTAATTAAT
39768 AT
1 AT
39770 ATTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTTTATAGTAATTAAT
Found at i:39756 original size:17 final size:18
Alignment explanation
Indices: 39734--39774 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39724 TGTTTAGAAT
*
39734 TTTTTATCGT-ATTAATA
1 TTTTTATAGTAATTAATA
39751 TTTTTATAGTAATTAATA
1 TTTTTATAGTAATTAATA
*
39769 TATTTA
1 TTTTTA
39775 AAAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTTTATAGTAATTAATA
Found at i:40262 original size:30 final size:30
Alignment explanation
Indices: 40218--40280 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
40208 ACTTAACAAG
*
40218 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATGAA
* *
40248 CAAATGTCTTTAAAATAATAACAAAATGAA
1 CAAATGCCTCTAAAATAATAACAAAATGAA
40278 CAA
1 CAA
40281 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATGAA
Found at i:40335 original size:22 final size:22
Alignment explanation
Indices: 40310--40352 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40300 TATCGAAACA
40310 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
**
40332 ATAATAGTAAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
40353 AACAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:40365 original size:22 final size:22
Alignment explanation
Indices: 40318--40365 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
40308 CAATAATAAC
* * *
40318 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAACAAAAGT
40340 AAAATAGTAGCAAAACAAGAAG-
1 AAAATAGTAGCAAAACAA-AAGT
40362 AAAA
1 AAAA
40366 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (22 bp):
AAAATAGTAGCAAAACAAAAGT
Found at i:41715 original size:46 final size:46
Alignment explanation
Indices: 41647--41736 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
41637 ATTGTTGGTG
* * * *
41647 TGTGGGGATAAAATGAATTTATGAGAAATTAATGAAAGCTTCAAAA
1 TGTGGAGATAAAATAAAATTATGAGAAATTAACGAAAGCTTCAAAA
*
41693 TGTGGAGATAAAATAAAATTATGATAAATTAACGAAAGCTTCAA
1 TGTGGAGATAAAATAAAATTATGAGAAATTAACGAAAGCTTCAA
41737 GACGTGTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.28
Consensus pattern (46 bp):
TGTGGAGATAAAATAAAATTATGAGAAATTAACGAAAGCTTCAAAA
Found at i:43365 original size:2 final size:2
Alignment explanation
Indices: 43358--43383 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43348 TAAATTGATT
43358 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
43384 AACAGCTGCT
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):
TA
Found at i:45873 original size:64 final size:64
Alignment explanation
Indices: 45794--45923 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
45784 TGAAAGAAGT
45794 CTTTACAATTTTGTTTCAATCATTTTGATAATACCACATGGTGGGATAGTGGCTCAAAACTGAC
1 CTTTACAATTTTGTTTCAATCATTTTGATAATACCACATGGTGGGATAGTGGCTCAAAACTGAC
*
45858 CTTTACAATTTTGTTTCAATCATTTTGATAATCCCACATGGTGGGATAGTGGCTCAAAACTGAC
1 CTTTACAATTTTGTTTCAATCATTTTGATAATACCACATGGTGGGATAGTGGCTCAAAACTGAC
45922 CT
1 CT
45924 GTCCTTATAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (64 bp):
CTTTACAATTTTGTTTCAATCATTTTGATAATACCACATGGTGGGATAGTGGCTCAAAACTGAC
Found at i:50580 original size:133 final size:134
Alignment explanation
Indices: 50327--50623 Score: 372
Period size: 133 Copynumber: 2.2 Consensus size: 134
50317 ATCCATTCAT
* * * *
50327 TCAAAGTTTTTCCTCAAATTAGATATTTTTACTGGCGTTTCTCCAATAACGCCACTATATCCCAA
1 TCAAATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTCTCCAATAACGCCACTATATCCCAA
* * * * *
50392 TATTTGCGGCGTCTTTTACAATGCGCCACTAAAGAAATAAAATGGAGCAATAAAACGGTAGC-GT
66 TATTTCCGGCGTCTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGCA-CTGT
50456 TTTG-
130 TTTGC
* *
50460 TCCAAATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTC-CCTGAA-AACGCCGCTA-AT-T
1 T-CAAATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTCTCC--AATAACGCCACTATATCC
* *
50521 CAATCTTTTCCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGCAC
63 CAAT-ATTTCCGGCGTCTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGCAC
50586 TGTTTTGC
127 TGTTTTGC
* *
50594 TCAGATTTTTTCCTCAAATTCGTTATCTTT
1 TCAAATTTTTTCCTCAAATTAGTTATCTTT
50624 GTTGCGGAAG
Statistics
Matches: 143, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
132 5 0.03
133 90 0.63
134 46 0.32
135 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (134 bp):
TCAAATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTCTCCAATAACGCCACTATATCCCAA
TATTTCCGGCGTCTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGCACTGTT
TTGC
Found at i:53301 original size:21 final size:22
Alignment explanation
Indices: 53275--53321 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
53265 CTCTGCTCAA
*
53275 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
53296 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
53318 ACTC
1 ACTC
53322 ACTCCTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:56938 original size:30 final size:29
Alignment explanation
Indices: 56902--56996 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
56892 AACTAAATTC
56902 CATATTTATGAATAATACAGGGACTTATGT
1 CATATTTATGAATAATA-AGGGACTTATGT
* * *
56932 CATATTT-TGACATTATAA--AACTAAAT-T
1 CATATTTATGA-ATAATAAGGGACT-TATGT
*
56959 CCATATTTATGATTAATATAGGGACTTATGT
1 -CATATTTATGAATAATA-AGGGACTTATGT
56990 CATATTT
1 CATATTT
56997 TAACATTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
27 4 0.08
28 13 0.26
29 8 0.16
30 21 0.42
31 4 0.08
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (29 bp):
CATATTTATGAATAATAAGGGACTTATGT
Found at i:56953 original size:58 final size:58
Alignment explanation
Indices: 56891--57008 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
56881 AATAGAACAT
*
56891 AAACTAAATTCCATATTTATGAATAATACAGGGACTTATGTCATATTTTGACATTATA
1 AAACTAAATTCCATATTTATGAATAATACAGGGACTTATGTCATATTTTAACATTATA
* *
56949 AAACTAAATTCCATATTTATGATTAATATAGGGACTTATGTCATATTTTAACATTATA
1 AAACTAAATTCCATATTTATGAATAATACAGGGACTTATGTCATATTTTAACATTATA
57007 AA
1 AA
57009 TATATTAGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (58 bp):
AAACTAAATTCCATATTTATGAATAATACAGGGACTTATGTCATATTTTAACATTATA
Found at i:57148 original size:23 final size:24
Alignment explanation
Indices: 57122--57166 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
57112 GATTAAGAAA
57122 TTAAAACTAAAT-AATATATGTGT
1 TTAAAACTAAATAAATATATGTGT
***
57145 TTAATTTTAAATAAATATATGT
1 TTAAAACTAAATAAATATATGT
57167 ATCAAGTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (24 bp):
TTAAAACTAAATAAATATATGTGT
Found at i:59306 original size:22 final size:22
Alignment explanation
Indices: 59235--59306 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 22
59225 AAATGCCCTC
** * *
59235 TAAAATAATAACAAAATAACAA
1 TAAAATAATAGTAATATAATAA
* * * * *
59257 TAAAGTAAGAGTTATACAATAT
1 TAAAATAATAGTAATATAATAA
*
59279 TCAAATAATAGTAATATAATAA
1 TAAAATAATAGTAATATAATAA
59301 TAAAAT
1 TAAAAT
59307 GATGGGTAAC
Statistics
Matches: 34, Mismatches: 16, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAAATAATAGTAATATAATAA
Found at i:60704 original size:13 final size:14
Alignment explanation
Indices: 60678--60711 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
60668 TCAAAATTTA
60678 AAAATAATATTATT
1 AAAATAATATTATT
60692 AAAATAA-ATTATT
1 AAAATAATATTATT
60705 ATAAATA
1 A-AAATA
60712 TTAAACACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATAATATTATT
Found at i:61631 original size:26 final size:24
Alignment explanation
Indices: 61592--61639 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
61582 AATCACTTGA
61592 AAAAAAATATAAAATC-TAAAAATT
1 AAAAAAATATAAAA-CATAAAAATT
61616 AAAAAAATATTCAAAACATAAAAA
1 AAAAAAATA-T-AAAACATAAAAA
61640 AAATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAAAAATATAAAACATAAAAATT
Found at i:66489 original size:2 final size:2
Alignment explanation
Indices: 66484--66515 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
66474 AGAGTTTTTT
66484 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
66516 ATAGTGTATG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:68032 original size:25 final size:27
Alignment explanation
Indices: 67989--68043 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
67979 AATTGGGTCC
67989 TAATTATAAAAAATATAAA-ATTAATTT
1 TAATTATAAAAAATATAAATA-TAATTT
68016 TAATTAT-AAAAA-ATAAATATAATTT
1 TAATTATAAAAAATATAAATATAATTT
68041 TAA
1 TAA
68044 AATTCAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 14 0.52
26 6 0.22
27 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TAATTATAAAAAATATAAATATAATTT
Found at i:68047 original size:27 final size:27
Alignment explanation
Indices: 67989--68043 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
67979 AATTGGGTCC
67989 TAATTATAAAAAATATAAAATTAATTT
1 TAATTATAAAAAATATAAAATTAATTT
*
68016 TAATTATAAAAAATA-AATA-TAATTT
1 TAATTATAAAAAATATAAAATTAATTT
68041 TAA
1 TAA
68044 AATTCAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 9 0.33
26 3 0.11
27 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TAATTATAAAAAATATAAAATTAATTT
Found at i:79593 original size:11 final size:11
Alignment explanation
Indices: 79577--79603 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
79567 AATTGTGCAT
79577 ATTAAATTTAA
1 ATTAAATTTAA
79588 ATTAAATTTAA
1 ATTAAATTTAA
79599 ATTAA
1 ATTAA
79604 CTACTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:81546 original size:21 final size:21
Alignment explanation
Indices: 81486--81546 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
81476 TGGTTGAACG
* * * *
81486 GAAGCTCGTAACAGCTGAATG
1 GAAGCTCGTGAGAGCTAAATA
* * * *
81507 GAAACTCATGAGGGTTAAATA
1 GAAGCTCGTGAGAGCTAAATA
81528 GAAGCTCGTGAGAGCTAAA
1 GAAGCTCGTGAGAGCTAAA
81547 CGAAAAGTAA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GAAGCTCGTGAGAGCTAAATA
Found at i:84573 original size:4 final size:4
Alignment explanation
Indices: 84564--84602 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
84554 AATTTAGCTT
84564 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
84603 TAGATTGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:93066 original size:19 final size:18
Alignment explanation
Indices: 93044--93090 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
93034 ATAAAAGTCA
93044 AAATATTAAAAAAAAGGTT
1 AAATATTAAAAAAAAGG-T
* *
93063 AAAT-TCATAAAAAAATGT
1 AAATATTA-AAAAAAAGGT
93081 AAATATTAAA
1 AAATATTAAA
93091 GCTAACTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (18 bp):
AAATATTAAAAAAAAGGT
Found at i:93775 original size:17 final size:18
Alignment explanation
Indices: 93755--93794 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
93745 ATTAATGTGC
93755 AAAAATTATAAATGAT-A
1 AAAAATTATAAATGATGA
*
93772 AAAAA-TATAAATTATGA
1 AAAAATTATAAATGATGA
93789 AAAAAT
1 AAAAAT
93795 GTTTAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAATGATGA
Found at i:94201 original size:19 final size:19
Alignment explanation
Indices: 94177--94247 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 19
94167 AAATTAGTTT
94177 TTTTTATATTTTTCATATA
1 TTTTTATATTTTTCATATA
*
94196 TTTTTAT-TTTATT-TTATA
1 TTTTTATATTT-TTCATATA
* *
94214 GTTTT-TATTCTTCATATAA
1 TTTTTATATTTTTCATAT-A
94233 TTTTTTATAATTTTT
1 -TTTTTAT-ATTTTT
94248 AATGTTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
17 3 0.08
18 16 0.41
19 10 0.26
20 4 0.10
21 1 0.03
22 5 0.13
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (19 bp):
TTTTTATATTTTTCATATA
Found at i:97283 original size:20 final size:19
Alignment explanation
Indices: 97237--97285 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
97227 AATACAAAAT
*
97237 AATTCAAAATAATTTTCAA
1 AATTCAAAATAATTTTAAA
97256 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
97275 AATTTCAAAAT
1 AA-TTCAAAAT
97286 TTATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 15 0.56
20 8 0.30
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:105644 original size:19 final size:19
Alignment explanation
Indices: 105620--105667 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
105610 AATTTTTCAT
105620 ATATGCTTCATTGGGTCAC
1 ATATGCTTCATTGGGTCAC
105639 ATATGCTTCATTGGGTCAC
1 ATATGCTTCATTGGGTCAC
* *
105658 TTAGGCTTCA
1 ATATGCTTCA
105668 AATAAACAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (19 bp):
ATATGCTTCATTGGGTCAC
Found at i:110106 original size:42 final size:42
Alignment explanation
Indices: 110059--110197 Score: 163
Period size: 42 Copynumber: 3.3 Consensus size: 42
110049 CAAAGGCTGC
* * * *
110059 ACAGAAACACATAAGTGCTAAAC-AGAAACCCGTAAGGGTTGA
1 ACAGAAACTCATAAGAGCTGAACGA-AAACCCATAAGGGTTGA
* * *
110101 ACAGAAGCTCATAAGAGCTGAACGAAAACCTATAAGGGTTAA
1 ACAGAAACTCATAAGAGCTGAACGAAAACCCATAAGGGTTGA
* * * *
110143 ACTGAAGCTCAAAAGAGCTGAACGAAAACCCATTAGGGTTGA
1 ACAGAAACTCATAAGAGCTGAACGAAAACCCATAAGGGTTGA
110185 ACAGAAACTCATA
1 ACAGAAACTCATA
110198 TGAGTTAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 80 0.99
43 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
ACAGAAACTCATAAGAGCTGAACGAAAACCCATAAGGGTTGA
Found at i:110115 original size:21 final size:21
Alignment explanation
Indices: 110091--110214 Score: 65
Period size: 21 Copynumber: 6.0 Consensus size: 21
110081 CAGAAACCCG
*
110091 TAAGGGTTGAACAGAAGCTCA
1 TAAGAGTTGAACAGAAGCTCA
* * *
110112 TAAGAGCTGAACGAAAACCT-A
1 TAAGAGTTGAAC-AGAAGCTCA
* * *
110133 TAAGGGTTAAACTGAAGCTCA
1 TAAGAGTTGAACAGAAGCTCA
* * * *
110154 AAAGAGCTGAAC-GAAAACCCA
1 TAAGAGTTGAACAG-AAGCTCA
* * *
110175 TTAGGGTTGAACAGAAACTCA
1 TAAGAGTTGAACAGAAGCTCA
* *
110196 TATGAGTT-AATAGAAGCTC
1 TAAGAGTTGAACAGAAGCTC
110215 GTGTGAGCTA
Statistics
Matches: 73, Mismatches: 26, Indels: 9
0.68 0.24 0.08
Matches are distributed among these distances:
20 14 0.19
21 53 0.73
22 6 0.08
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (21 bp):
TAAGAGTTGAACAGAAGCTCA
Found at i:111399 original size:21 final size:21
Alignment explanation
Indices: 111375--111416 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
111365 AATTAACTAT
*
111375 CAAAACATTAAAATTTTCTTA
1 CAAAACATTAAAATTATCTTA
* *
111396 CAAAACTTTAATATTATCTTA
1 CAAAACATTAAAATTATCTTA
111417 ATGACACTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
CAAAACATTAAAATTATCTTA
Found at i:112003 original size:51 final size:51
Alignment explanation
Indices: 111927--112029 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
111917 CAAGGAAATT
* *
111927 CAAATCAAAATAATATTTGTTTGCGATTCTAAACAATTTTTCAAAGTACTC
1 CAAATCAAAATAATATTTGTTTGCGATTCCAAACAATTTGTCAAAGTACTC
*
111978 CAAATCAAAATAATCTTTGTTTGCGATTCCAAACAATTTGTCAAAGTACTC
1 CAAATCAAAATAATATTTGTTTGCGATTCCAAACAATTTGTCAAAGTACTC
112029 C
1 C
112030 TTCACCATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (51 bp):
CAAATCAAAATAATATTTGTTTGCGATTCCAAACAATTTGTCAAAGTACTC
Found at i:112204 original size:22 final size:22
Alignment explanation
Indices: 112179--112227 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
112169 CTCTTGCCTT
112179 TAATTTTCTTTATTTCTTCTCC
1 TAATTTTCTTTATTTCTTCTCC
*
112201 TAATTTTCTTTATTTCTTCTCG
1 TAATTTTCTTTATTTCTTCTCC
112223 TAATT
1 TAATT
112228 CTTGATCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.63
Consensus pattern (22 bp):
TAATTTTCTTTATTTCTTCTCC
Found at i:112326 original size:27 final size:27
Alignment explanation
Indices: 112288--112342 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
112278 CTTCCTCCAC
112288 AACTTCCTAGAGATCATTTGCTTCTAA
1 AACTTCCTAGAGATCATTTGCTTCTAA
112315 AACTTCCTAGAGATCATTTGCTTCTAA
1 AACTTCCTAGAGATCATTTGCTTCTAA
112342 A
1 A
112343 TGAGCCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (27 bp):
AACTTCCTAGAGATCATTTGCTTCTAA
Found at i:114258 original size:17 final size:17
Alignment explanation
Indices: 114233--114266 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
114223 ATAACCCATC
114233 CAACCTTTTCCTTGTTT
1 CAACCTTTTCCTTGTTT
*
114250 CAACTTTTTCCTTGTTT
1 CAACCTTTTCCTTGTTT
114267 ACAAGAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.26, G:0.06, T:0.56
Consensus pattern (17 bp):
CAACCTTTTCCTTGTTT
Found at i:118816 original size:19 final size:19
Alignment explanation
Indices: 118794--118856 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
118784 AAAATTACAA
118794 AAAAAATCAAAATAATTTT
1 AAAAAATCAAAATAATTTT
*
118813 AAAAAATTCAAAGTAAATTTT
1 AAAAAA-TCAAAAT-AATTTT
*
118834 -AAAATTCAAAAT-ATTTAT
1 AAAAAATCAAAATAATTT-T
118852 AAAAA
1 AAAAA
118857 TTCCAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 16 0.43
20 10 0.27
21 6 0.16
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATCAAAATAATTTT
Found at i:118818 original size:20 final size:21
Alignment explanation
Indices: 118793--118837 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
118783 AAAAATTACA
118793 AAAAAAATCAAAAT-AATTTT
1 AAAAAAATCAAAATAAATTTT
* *
118813 AAAAAATTCAAAGTAAATTTT
1 AAAAAAATCAAAATAAATTTT
118834 AAAA
1 AAAA
118838 TTCAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAAATCAAAATAAATTTT
Found at i:118857 original size:19 final size:18
Alignment explanation
Indices: 118794--118865 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
118784 AAAATTACAA
*
118794 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAAT-ATTTT
*
118813 AAAAAATTCAAAGTAAATTTT
1 -AAAAATTCAAA--ATATTTT
118834 -AAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTT-T
118852 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
118866 TTATATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.11
18 1 0.02
19 16 0.36
20 16 0.36
21 5 0.11
22 1 0.02
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (18 bp):
AAAAATTCAAAATATTTT
Found at i:118908 original size:27 final size:26
Alignment explanation
Indices: 118861--118913 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
118851 TAAAAATTCC
* *
118861 AAAATTTATATTTTTAAAAATTATAA
1 AAAATTTAAATTTTTAAAAATAATAA
118887 AAAATTTAAAATTTTCT-AAAATAATAA
1 AAAATTT-AAATTTT-TAAAAATAATAA
118914 TTTTGAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 15 0.65
28 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAATTTAAATTTTTAAAAATAATAA
Found at i:138269 original size:6 final size:6
Alignment explanation
Indices: 138258--138285 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
138248 ACTAGTATAC
138258 ACATGT ACATGT ACATGT ACATGT ACAT
1 ACATGT ACATGT ACATGT ACATGT ACAT
138286 AGTCATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (6 bp):
ACATGT
Found at i:140933 original size:33 final size:33
Alignment explanation
Indices: 140878--140941 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
140868 ATTTATTTTT
* *
140878 TATATTAAATAAATATATTA-TTTATGTATATAA
1 TATATAAAATAAATATAATATTTTAT-TATATAA
140911 TATATAAACATAAA-ATAATATTTTATTATAT
1 TATATAAA-ATAAATATAATATTTTATTATAT
140942 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 17 0.63
34 10 0.37
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
TATATAAAATAAATATAATATTTTATTATATAA
Done.