Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012114.1 Corchorus capsularis cultivar CVL-1 contig12135, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55600
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:175 original size:44 final size:44
Alignment explanation
Indices: 126--245 Score: 174
Period size: 44 Copynumber: 2.8 Consensus size: 44
116 CTCCATGTGG
126 AATGTTGGTAAGCACTCTACGAAATTTTGATAAGC-TTCCTATAA
1 AATGTTGGTAAGCACTCTACGAAATTTTGATAA-CTTTCCTATAA
* *
170 AATGTTGGTAAGCACACTACGAAATTTTGATCACTTTCCTATAA
1 AATGTTGGTAAGCACTCTACGAAATTTTGATAACTTTCCTATAA
* *
214 AATGTTGGTAATCACTAT-C-AAATTTTGATAAC
1 AATGTTGGTAAGCACTCTACGAAATTTTGATAAC
246 CTCATTATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 12 0.17
43 2 0.03
44 55 0.80
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (44 bp):
AATGTTGGTAAGCACTCTACGAAATTTTGATAACTTTCCTATAA
Found at i:279 original size:21 final size:20
Alignment explanation
Indices: 208--375 Score: 104
Period size: 22 Copynumber: 8.1 Consensus size: 20
198 GATCACTTTC
* * * *
208 CTATAAAATGTTGGTAATCA
1 CTATAAAATTTTGATAACCT
*
228 CTATCAAATTTTGATAACCT
1 CTATAAAATTTTGATAACCT
248 CATTATAAAATTTTGATAAACCT
1 C--TATAAAATTTTGAT-AACCT
*
271 CTGTAAAATTTTGATAACCT
1 CTATAAAATTTTGATAACCT
* * * *
291 CTTTTGAAATTTTGTTAATCT
1 C-TATAAAATTTTGATAACCT
* ** *
312 C-ATGATGTTTCGATAACCAT
1 CTATAAAATTTTGATAACC-T
* *
332 CTCATGAAATTTTGATAACTACC
1 CT-ATAAAATTTTGATAAC--CT
*
355 CTATGAAATTTTGATAACCT
1 CTATAAAATTTTGATAACCT
375 C
1 C
376 CCTCTTAAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
19 11 0.09
20 26 0.22
21 29 0.25
22 42 0.36
23 8 0.07
24 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
CTATAAAATTTTGATAACCT
Found at i:348 original size:22 final size:21
Alignment explanation
Indices: 233--375 Score: 114
Period size: 22 Copynumber: 6.8 Consensus size: 21
223 AATCACTATC
* *
233 AAATTTTGATAACCTCATTATA
1 AAATTTTGATAACCTC-TCATG
* *
255 AAATTTTGATAAACCTCT-GTA
1 AAATTTTGAT-AACCTCTCATG
**
276 AAATTTTGATAACCTCTTTTG
1 AAATTTTGATAACCTCTCATG
*
297 AAATTTTGTTAA--TCTCATG
1 AAATTTTGATAACCTCTCATG
** *
316 ATGTTTCGATAACCATCTCATG
1 AAATTTTGATAACC-TCTCATG
*
338 AAATTTTGATAA-CTACCCTATG
1 AAATTTTGATAACCT-CTC-ATG
360 AAATTTTGATAACCTC
1 AAATTTTGATAACCTC
376 CCTCTTAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
19 13 0.13
20 8 0.08
21 27 0.27
22 43 0.43
23 8 0.08
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACCTCTCATG
Found at i:378 original size:22 final size:22
Alignment explanation
Indices: 146--378 Score: 99
Period size: 22 Copynumber: 10.9 Consensus size: 22
136 AGCACTCTAC
* *
146 GAAATTTTGATAAGCTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * * * * *
168 AAAATGTTGGTAAGCACACTAC
1 GAAATTTTGATAACCTCCCTAT
* * *
190 GAAATTTTGATCACTTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * *
212 AAAATGTTGGTAA--TCACTAT
1 GAAATTTTGATAACCTCCCTAT
* **
232 CAAATTTTGATAACCTCATTAT
1 GAAATTTTGATAACCTCCCTAT
* *
254 AAAATTTTGATAAACCT--CTGT
1 GAAATTTTGAT-AACCTCCCTAT
* * *
275 AAAATTTTGATAACCT-CTTTT
1 GAAATTTTGATAACCTCCCTAT
* *
296 GAAATTTTGTTAA--TCTC-AT
1 GAAATTTTGATAACCTCCCTAT
** * *
315 GATGTTTCGATAACCATCTC-AT
1 GAAATTTTGATAACC-TCCCTAT
337 GAAATTTTGATAA-CTACCCTAT
1 GAAATTTTGATAACCT-CCCTAT
359 GAAATTTTGATAACCTCCCT
1 GAAATTTTGATAACCTCCCT
379 CTTAAAAATC
Statistics
Matches: 155, Mismatches: 45, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
19 11 0.07
20 21 0.14
21 29 0.19
22 87 0.56
23 7 0.05
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAT
Found at i:404 original size:22 final size:22
Alignment explanation
Indices: 379--421 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
369 TAACCTCCCT
*
379 CTTAAAAATCACACTATGAAAA
1 CTTAAAAACCACACTATGAAAA
* *
401 CTTAATAACCACATTATGAAA
1 CTTAAAAACCACACTATGAAA
422 TTTTGATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (22 bp):
CTTAAAAACCACACTATGAAAA
Found at i:1369 original size:31 final size:31
Alignment explanation
Indices: 1331--1391 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1321 CAATTTAGAA
* *
1331 ATATATGAAAATAAAGGGTATAATCGGAAAT
1 ATATATGAAAATAAAGAGTACAATCGGAAAT
1362 ATATATGAAAATAAAGAGTACAATCGGAAA
1 ATATATGAAAATAAAGAGTACAATCGGAAA
1392 ACAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (31 bp):
ATATATGAAAATAAAGAGTACAATCGGAAAT
Found at i:6981 original size:31 final size:29
Alignment explanation
Indices: 6924--6985 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
6914 AACATATAAA
*
6924 AAACAAGCCAAATTGAAGCAATCAAACAT
1 AAACAAGCCAAATTGAAGCAAACAAACAT
6953 AAACAAGTCTCAAATTGGAA-CAAACAAACAT
1 AAACAAG-C-CAAATT-GAAGCAAACAAACAT
6984 AA
1 AA
6986 TCAACCCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 1 0.03
31 18 0.62
32 3 0.10
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.15
Consensus pattern (29 bp):
AAACAAGCCAAATTGAAGCAAACAAACAT
Found at i:29944 original size:2 final size:2
Alignment explanation
Indices: 29937--29961 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29927 CTTTTATCCT
29937 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 T
29962 GATCCTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30196 original size:15 final size:15
Alignment explanation
Indices: 30168--30210 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
30158 GATTAAAAGC
*
30168 AACAGATTATATAGAA
1 AACA-ATTAAATAGAA
*
30184 AGCAATTAAATAGAA
1 AACAATTAAATAGAA
*
30199 AACAATAAAATA
1 AACAATTAAATA
30211 AAGGCAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (15 bp):
AACAATTAAATAGAA
Found at i:32411 original size:37 final size:38
Alignment explanation
Indices: 32361--32564 Score: 217
Period size: 37 Copynumber: 5.5 Consensus size: 38
32351 GATGCCCTCT
32361 AAGATCCCTGTTTAGGTGTCTCATTCAAAT-CTGGTTC
1 AAGATCCCTGTTTAGGTGTCTCATTCAAATCCTGGTTC
* ** *
32398 AAGATCCCTGTTTAGGT-T-TCTTGTCAAATCCTTATTT
1 AAGATCCCTGTTTAGGTGTCTCAT-TCAAATCCTGGTTC
* *
32435 AAGATCCCGGTTTAGGTGTCTCA-TCGAAAT-TTGGTTC
1 AAGATCCCTGTTTAGGTGTCTCATTC-AAATCCTGGTTC
*
32472 AAGATCCCTGTTTAGGT-T-TCTTGTCAAATCCTGGTTC
1 AAGATCCCTGTTTAGGTGTCTCAT-TCAAATCCTGGTTC
* **
32509 AAGGTCCCTGTTTAGGTGTCTCA-TCAAATCCTTATTC
1 AAGATCCCTGTTTAGGTGTCTCATTCAAATCCTGGTTC
* *
32546 CAGATTCCTGTTTAGGTGT
1 AAGATCCCTGTTTAGGTGT
32565 GATCGTGTCA
Statistics
Matches: 137, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
35 5 0.04
36 12 0.09
37 110 0.80
38 6 0.04
39 4 0.03
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (38 bp):
AAGATCCCTGTTTAGGTGTCTCATTCAAATCCTGGTTC
Found at i:32481 original size:74 final size:73
Alignment explanation
Indices: 32360--32562 Score: 289
Period size: 74 Copynumber: 2.7 Consensus size: 73
32350 GGATGCCCTC
32360 TAAGATCCCTGTTTAGGTGTCTCATTCAAATCTGGTTCAAGATCCCTGTTTAGGTTTCTTGTCAA
1 TAAGATCCCTGTTTAGGTGTCTCA-TCAAATCTGGTTCAAGATCCCTGTTTAGGTTTCTTGTCAA
*
32425 ATCCTTATT
65 ATCCTGATT
* *
32434 TAAGATCCCGGTTTAGGTGTCTCATCGAAATTTGGTTCAAGATCCCTGTTTAGGTTTCTTGTCAA
1 TAAGATCCCTGTTTAGGTGTCTCATC-AAATCTGGTTCAAGATCCCTGTTTAGGTTTCTTGTCAA
*
32499 ATCCTGGTT
65 ATCCTGATT
* * ** * *
32508 CAAGGTCCCTGTTTAGGTGTCTCATCAAATCCTTATTCCAGATTCCTGTTTAGGT
1 TAAGATCCCTGTTTAGGTGTCTCATCAAAT-CTGGTTCAAGATCCCTGTTTAGGT
32563 GTGATCGTGT
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
73 6 0.05
74 109 0.95
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (73 bp):
TAAGATCCCTGTTTAGGTGTCTCATCAAATCTGGTTCAAGATCCCTGTTTAGGTTTCTTGTCAAA
TCCTGATT
Found at i:32559 original size:111 final size:111
Alignment explanation
Indices: 32361--32564 Score: 295
Period size: 111 Copynumber: 1.8 Consensus size: 111
32351 GATGCCCTCT
* **
32361 AAGATCCCTGTTTAGGTGTCTCATTCAAATCTGGTTCAAGATCCCTGTTTAGGTTTCTTGTCAAA
1 AAGATCCCTGTTTAGGTGTCTCATTCAAATCTGGTTCAAGATCCCTGTTTAGGTGTCTCATCAAA
*
32426 TCCTTATTTAAGATCCCGGTTTAGGTGTCTCATCGAAATTTGGTTC
66 TCCTTATTCAAGATCCCGGTTTAGGTGTCTCATCGAAATTTGGTTC
* *
32472 AAGATCCCTGTTTAGGT-T-TCTTGTCAAATCCTGGTTCAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAGATCCCTGTTTAGGTGTCTCAT-TCAAAT-CTGGTTCAAGATCCCTGTTTAGGTGTCTCATCA
* * *
32535 AATCCTTATTCCAGATTCCTGTTTAGGTGT
64 AATCCTTATTCAAGATCCCGGTTTAGGTGT
32565 GATCGTGTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
109 3 0.04
110 7 0.09
111 72 0.88
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (111 bp):
AAGATCCCTGTTTAGGTGTCTCATTCAAATCTGGTTCAAGATCCCTGTTTAGGTGTCTCATCAAA
TCCTTATTCAAGATCCCGGTTTAGGTGTCTCATCGAAATTTGGTTC
Found at i:34514 original size:37 final size:37
Alignment explanation
Indices: 34375--34563 Score: 184
Period size: 37 Copynumber: 5.1 Consensus size: 37
34365 AGCTCGATCA
* * *
34375 AGGTGTCTTATCAAATCCTTATTTAAGGTCCATGTTT
1 AGGTGTCTTATCAAATCCTTGTTTAAGATCCCTGTTT
* *
34412 AGGTGTCTTATCAAATCCTTGTTTAAGGTCCTTGCTTT
1 AGGTGTCTTATCAAATCCTTGTTTAAGATCCCTG-TTT
* *
34450 -GGTGTCTCATCGAATCCTTGTTTAAGATCCCTGTTT
1 AGGTGTCTTATCAAATCCTTGTTTAAGATCCCTGTTT
* * * * *
34486 AGGTGTCTCATCGAATTCTTGTTCAAGATCCCTGCTT
1 AGGTGTCTTATCAAATCCTTGTTTAAGATCCCTGTTT
* * * * * *
34523 AGCTTTCTTGTCAAAAT-CTTGTTCAAGATCTCTGCTT
1 AGGTGTCTTATC-AAATCCTTGTTTAAGATCCCTGTTT
34560 AGGT
1 AGGT
34564 TTAAGGCTGT
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
36 3 0.02
37 124 0.93
38 6 0.05
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (37 bp):
AGGTGTCTTATCAAATCCTTGTTTAAGATCCCTGTTT
Found at i:34970 original size:8 final size:8
Alignment explanation
Indices: 34959--35223 Score: 80
Period size: 8 Copynumber: 33.5 Consensus size: 8
34949 AAGTAAAAAT
34959 AATAGATA
1 AATAGATA
*
34967 AATAGGTA
1 AATAGATA
* *
34975 TATGGATA
1 AATAGATA
34983 AATAGATA
1 AATAGATA
* *
34991 AATGGGTA
1 AATAGATA
** * *
34999 GGTAAAAA
1 AATAGATA
*
35007 AATATATA
1 AATAGATA
35015 AATAGAT-
1 AATAGATA
35022 AATAGA-A
1 AATAGATA
35029 AATAGATA
1 AATAGATA
35037 AATA-AGTA
1 AATAGA-TA
** *
35045 GGTAAATA
1 AATAGATA
*
35053 AAAAGATA
1 AATAGATA
35061 AAT--A-A
1 AATAGATA
35066 AATAGAT-
1 AATAGATA
*
35073 AATA-ACTG
1 AATAGA-TA
*
35081 AATAGACA
1 AATAGATA
35089 AATAAAAGGATA
1 AAT---A-GATA
35101 AATAG-TA
1 AATAGATA
*
35108 AATAAATAA
1 AATAGAT-A
35117 ATAGTAGATA
1 A-A-TAGATA
35127 AATAGAT-
1 AATAGATA
35134 AATA-ATA
1 AATAGATA
35141 AATA-AT-
1 AATAGATA
*
35147 AATA-ACA
1 AATAGATA
35154 AATAGATA
1 AATAGATA
*
35162 ATTA-AGTA
1 AATAGA-TA
35170 AATA-ATA
1 AATAGATA
35177 AATAAAGAAACTA
1 AAT--AG--A-TA
*
35190 AGTAGATA
1 AATAGATA
*
35198 GATAGAT-
1 AATAGATA
35205 AATA-ATA
1 AATAGATA
35212 AATAGATA
1 AATAGATA
35220 AATA
1 AATA
35224 AAATAACTTA
Statistics
Matches: 188, Mismatches: 39, Indels: 60
0.66 0.14 0.21
Matches are distributed among these distances:
5 4 0.02
6 11 0.06
7 52 0.28
8 92 0.49
9 8 0.04
10 3 0.02
11 7 0.04
12 7 0.04
13 4 0.02
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.25
Consensus pattern (8 bp):
AATAGATA
Found at i:35009 original size:24 final size:24
Alignment explanation
Indices: 34951--35064 Score: 90
Period size: 24 Copynumber: 4.8 Consensus size: 24
34941 AATAAAAAAA
*
34951 GTAAAAATAATAGATAAATAGGTAT
1 GTAAAAA-AATAGATAAATAGGTAG
* ** * *
34976 ATGGATAAATAGATAAATGGGTAG
1 GTAAAAAAATAGATAAATAGGTAG
* *
35000 GTAAAAAAATATATAAATAGATA-
1 GTAAAAAAATAGATAAATAGGTAG
* * *
35023 AT-AGAAAATAGATAAATAAGTAG
1 GTAAAAAAATAGATAAATAGGTAG
35046 GTAAATAAAA-AGATAAATA
1 GTAAA-AAAATAGATAAATA
35065 AAATAGATAA
Statistics
Matches: 66, Mismatches: 20, Indels: 7
0.71 0.22 0.08
Matches are distributed among these distances:
22 16 0.24
23 2 0.03
24 41 0.62
25 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.25
Consensus pattern (24 bp):
GTAAAAAAATAGATAAATAGGTAG
Found at i:35033 original size:46 final size:46
Alignment explanation
Indices: 34951--35076 Score: 141
Period size: 46 Copynumber: 2.7 Consensus size: 46
34941 AATAAAAAAA
* * **
34951 GTAAAAATAATAGATAAATAGGTATATGGATAAATAGATAAATGGGTAG
1 GTAAAAA-AATAGATAAATAGATA-ATAGA-AAATAGATAAATAAGTAG
*
35000 GTAAAAAAATATATAAATAGATAATAGAAAATAGATAAATAAGTAG
1 GTAAAAAAATAGATAAATAGATAATAGAAAATAGATAAATAAGTAG
*
35046 GTAAATAAAA-AGATAAATA-A-AATAGATAATA
1 GTAAA-AAAATAGATAAATAGATAATAGAAAATA
35077 ACTGAATAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
44 10 0.14
45 1 0.01
46 29 0.42
47 8 0.12
48 14 0.20
49 7 0.10
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.25
Consensus pattern (46 bp):
GTAAAAAAATAGATAAATAGATAATAGAAAATAGATAAATAAGTAG
Found at i:35054 original size:4 final size:4
Alignment explanation
Indices: 35001--35225 Score: 57
Period size: 4 Copynumber: 59.0 Consensus size: 4
34991 AATGGGTAGG
* * * * * * **
35001 TAAA AAAA TATA TAAA TAGA T-AA TAGA -AAA TAGA TAAA TAAG TAGG
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
35047 TAAA TAAA -AAGA TAAA TAAAA TAGA T-AA TAAC TGAA TAGA CAAA TAAA
1 TAAA TAAA TAA-A TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
35095 -AGGA TAAA T-AG TAAA TAAA TAAA T-AG TAGA TAAA TAGA T-AA T-AA
1 TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * *
35139 TAAA T-AA T-AA T-AA CAAA TAGA TAAT TAAG TAAA T-AA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * * *
35183 GAAA CTAAG TAGA TAGA TAGA T-AA T-AA TAAA TAGA TAAA TAAA
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
35226 ATAACTTAAT
Statistics
Matches: 157, Mismatches: 49, Indels: 30
0.67 0.21 0.13
Matches are distributed among these distances:
3 34 0.22
4 114 0.73
5 9 0.06
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:35076 original size:24 final size:23
Alignment explanation
Indices: 35001--35226 Score: 79
Period size: 25 Copynumber: 9.2 Consensus size: 23
34991 AATGGGTAGG
* *
35001 TAAAAAAATATATAAATAGATAA
1 TAAAAAGATAAATAAATAGATAA
* *
35024 TAGAAAATAGATAAATAAGTAGGTAAA
1 T--AAAA-AGATAAATAAATAGAT-AA
35051 TAAAAAGATAAATAAAATAGATAA
1 TAAAAAGATAAAT-AAATAGATAA
*
35075 TAACTGAATAGACAAATAAA-AGGATAAA
1 TAA---AA-AGATAAATAAATA-GAT-AA
**
35103 TAGTAA-ATAAATAAATAG-TAGA
1 TAAAAAGATAAATAAATAGATA-A
*
35125 TAAATAGATAATAATAAATA-ATAA
1 TAAAAAGAT-A-AATAAATAGATAA
* * *
35149 TAACAAATAGATAATTAAGTAAATAA
1 T-A-AAA-AGATAAATAAATAGATAA
* *
35175 TAAATAAAGA-AACTAAGTAGATAGA
1 T-AA-AAAGATAAATAAATAGATA-A
* *
35200 TAGATA-AT-AATAAATAGATAAA
1 TAAAAAGATAAATAAATAGAT-AA
35222 TAAAA
1 TAAAA
35227 TAACTTAATA
Statistics
Matches: 154, Mismatches: 24, Indels: 51
0.67 0.10 0.22
Matches are distributed among these distances:
21 1 0.01
22 19 0.12
23 15 0.10
24 30 0.19
25 38 0.25
26 25 0.16
27 15 0.10
28 11 0.07
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.24
Consensus pattern (23 bp):
TAAAAAGATAAATAAATAGATAA
Found at i:35116 original size:15 final size:15
Alignment explanation
Indices: 35098--35145 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
35088 AAATAAAAGG
35098 ATAAATAGTAAATAA
1 ATAAATAGTAAATAA
*
35113 ATAAATAGTAGATAA
1 ATAAATAGTAAATAA
* *
35128 ATAGATAAT-AATAA
1 ATAAATAGTAAATAA
35142 ATAA
1 ATAA
35146 TAATAACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (15 bp):
ATAAATAGTAAATAA
Found at i:35144 original size:7 final size:7
Alignment explanation
Indices: 35124--35224 Score: 59
Period size: 7 Copynumber: 14.1 Consensus size: 7
35114 TAAATAGTAG
35124 ATAAATA
1 ATAAATA
35131 GAT-AATA
1 -ATAAATA
35138 ATAAATA
1 ATAAATA
35145 AT-AATA
1 ATAAATA
*
35151 ACAAATA
1 ATAAATA
*
35158 GATAATTA
1 -ATAAATA
35166 AGTAAATA
1 A-TAAATA
35174 ATAAATA
1 ATAAATA
35181 A-AGAA-A
1 ATA-AATA
* *
35187 CTAAGTA
1 ATAAATA
*
35194 GATAGATA
1 -ATAAATA
35202 GAT-AATA
1 -ATAAATA
35209 ATAAATA
1 ATAAATA
35216 GATAAATA
1 -ATAAATA
35224 A
1 A
35225 AATAACTTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
6 12 0.16
7 34 0.47
8 27 0.37
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (7 bp):
ATAAATA
Found at i:35151 original size:35 final size:35
Alignment explanation
Indices: 35112--35225 Score: 101
Period size: 35 Copynumber: 3.2 Consensus size: 35
35102 ATAGTAAATA
35112 AATAAATAGTAGATAAATAGATAATAATAAATAAT
1 AATAAATAGTAGATAAATAGATAATAATAAATAAT
* *
35147 AATAACA-AATAGATAATTA-AGTAAATAATAAATAA-
1 AATAA-ATAGTAGATAAATAGA-T-AATAATAAATAAT
* *
35182 AGA-AACTAAGTAGATAGATAGATAATAATAAATAGAT
1 A-ATAAAT-AGTAGATAAATAGATAATAATAAATA-AT
35219 AAATAAA
1 -AATAAA
35226 ATAACTTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
34 1 0.02
35 30 0.49
36 25 0.41
37 2 0.03
38 3 0.05
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (35 bp):
AATAAATAGTAGATAAATAGATAATAATAAATAAT
Found at i:35196 original size:36 final size:34
Alignment explanation
Indices: 35099--35215 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 34
35089 AATAAAAGGA
*
35099 TAAATAGTAAATAAATAAA-T-AGTAGATAAATAG
1 TAAATAATAAATAAA-AAACTAAGTAGATAAATAG
* *
35132 -ATAATAATAAATAATAATAAC-AAATAGATAATTAAG
1 TA-AATAATAAATAA-AA-AACTAAGTAGATAAAT-AG
*
35168 TAAATAATAAATAAAGAAACTAAGTAGATAGATAG
1 TAAATAATAAATAAA-AAACTAAGTAGATAAATAG
35203 -ATAATAATAAATA
1 TA-AATAATAAATA
35216 GATAAATAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
32 1 0.01
33 12 0.18
34 4 0.06
35 26 0.38
36 24 0.35
37 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.26
Consensus pattern (34 bp):
TAAATAATAAATAAAAAACTAAGTAGATAAATAG
Found at i:35236 original size:13 final size:14
Alignment explanation
Indices: 35220--35253 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
35210 TAAATAGATA
35220 AATAAAATAAC-TT
1 AATAAAATAACTTT
35233 AATAAAATAACTTT
1 AATAAAATAACTTT
35247 AATAAAA
1 AATAAAA
35254 ACAAAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAAATAACTTT
Found at i:35671 original size:16 final size:16
Alignment explanation
Indices: 35642--35672 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35632 ATAAAATCAA
35642 TTCCTAAATAAATTAG
1 TTCCTAAATAAATTAG
*
35658 TTCCTAAATTAATTA
1 TTCCTAAATAAATTA
35673 TGGCATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
TTCCTAAATAAATTAG
Found at i:41457 original size:27 final size:27
Alignment explanation
Indices: 41410--41477 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
41400 ATCCTAGGGA
*
41410 ACTAACTTTGACTGGGAAACTGT-TCTG
1 ACTAACTTTGAATGGGAAACTGTCT-TG
*
41437 ACTAGCTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGA-AACTGTCTTG
41464 ACTAA-TTTGGAATG
1 ACTAACTTT-GAATG
41478 AGAGTCTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 6 0.18
27 27 0.79
28 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.34
Consensus pattern (27 bp):
ACTAACTTTGAATGGGAAACTGTCTTG
Found at i:41844 original size:24 final size:24
Alignment explanation
Indices: 41816--41898 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 24
41806 CCATAGAGAA
41816 CTTCTTGGAATGACCGCACTAGAT
1 CTTCTTGGAATGACCGCACTAGAT
* * * * *
41840 CTTCTAGGGATCAACTCTGACCACTGAAAA
1 CTTCTTGGAAT-GAC-C-G--CACT-AGAT
*
41870 CTTCTTGGAATGACCGCATTAGAT
1 CTTCTTGGAATGACCGCACTAGAT
41894 CTTCT
1 CTTCT
41899 AGGGATCAAC
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
24 16 0.38
25 5 0.12
26 1 0.02
27 2 0.05
28 1 0.02
29 6 0.14
30 11 0.26
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (24 bp):
CTTCTTGGAATGACCGCACTAGAT
Found at i:41943 original size:54 final size:53
Alignment explanation
Indices: 41524--41970 Score: 470
Period size: 54 Copynumber: 8.3 Consensus size: 53
41514 ATTAATTGGA
* * * * * *
41524 GATCAACTCTAATCATCGAAAACTTATTGGAAAT-ACCACACTGGATCATCT-GAA
1 GATCAACTCTGACCAT-GAAAACTTCTTGG-AATGACCGCACTGGATCTTCTAG-G
* * *
41578 GATCAACTTTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCAAT-T-GG
1 GATCAACTCTGACCA-TGAAAACTTCTTGGAATGACCGCACTGGATC-TTCTAGG
* * * * * * *
41631 AGATCAACTCTGATCATCGAAAACTTATTGGAAAGACCACACTGGATCGTCAAGA
1 -GATCAACTCTGACCAT-GAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
* * * *
41686 TATCAACTCTGATCATTGAAAACTTCTTGGAATGACTGCACTGGATCTTCTTGG
1 GATCAACTCTGACCA-TGAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
* * *
41740 GATCAACTTTGACCATAGAAAACTTCTTGGAATGACCACACTGGATCTTCTGGG
1 GATCAACTCTGACCAT-GAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
* * *
41794 GAGCAACTCTGACCATAGAGAACTTCTTGGAATGACCGCACTAGATCTTCTAGG
1 GATCAACTCTGACCAT-GAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
* *
41848 GATCAACTCTGACCACTGAAAACTTCTTGGAATGACCGCATTAGATCTTCTAGG
1 GATCAACTCTGACCA-TGAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
* * * *
41902 GATCAACTCTGACCACTGAAAACTTCTTGAAATGACTGCATTGGATATTCTAGG
1 GATCAACTCTGACCA-TGAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
41956 GATCAACTCTGACCA
1 GATCAACTCTGACCA
41971 ATGGATCTTC
Statistics
Matches: 343, Mismatches: 40, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
53 6 0.02
54 331 0.97
55 6 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (53 bp):
GATCAACTCTGACCATGAAAACTTCTTGGAATGACCGCACTGGATCTTCTAGG
Found at i:41985 original size:29 final size:29
Alignment explanation
Indices: 41943--41999 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
41933 ATGACTGCAT
41943 TGGATATTCTAGGGATCAACTCTGACCAA
1 TGGATATTCTAGGGATCAACTCTGACCAA
*
41972 TGGATCTTCTAGGGATCAACTCTGACCA
1 TGGATATTCTAGGGATCAACTCTGACCA
42000 TTGAAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (29 bp):
TGGATATTCTAGGGATCAACTCTGACCAA
Found at i:41985 original size:137 final size:136
Alignment explanation
Indices: 41837--42104 Score: 419
Period size: 136 Copynumber: 2.0 Consensus size: 136
41827 GACCGCACTA
*
41837 GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGGAATGACCGCATTAGATCTTCTAGG
1 GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGGAATGACCGCACTAGATCTTCT-GG
* *
41902 GATCAACTCTGACCACTGAAAACTTCTTGAAATGACTGCATTGGATATTCTAGGGATCAACTCTG
65 GATCAACTCTGACCACTGAAAACTTCTTGAAATGACCGCACTGGATATTCTAGGGATCAACTCTG
41967 ACCAATG
130 ACCAATG
* * * *
41974 GATCTTCTAGGGATCAACTCTGACCATTGAAAGCTTCTTGGAATGACTGCACTGGATCTTCTGGG
1 GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGGAATGACCGCACTAGATCTTCTGGG
* * * * *
42039 ATCAACTCTGACCATTGAAAATTTCTTGGAATGACCGCACTGGATCTTCTGGGGATCAACTCTGA
66 ATCAACTCTGACCACTGAAAACTTCTTGAAATGACCGCACTGGATATTCTAGGGATCAACTCTGA
42104 C
131 C
42105 GATTGAAAAC
Statistics
Matches: 119, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
136 62 0.52
137 57 0.48
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (136 bp):
GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGGAATGACCGCACTAGATCTTCTGGG
ATCAACTCTGACCACTGAAAACTTCTTGAAATGACCGCACTGGATATTCTAGGGATCAACTCTGA
CCAATG
Found at i:41988 original size:83 final size:82
Alignment explanation
Indices: 41891--42052 Score: 270
Period size: 83 Copynumber: 2.0 Consensus size: 82
41881 GACCGCATTA
*
41891 GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGAAATGACTGCATTGGATATTCTAGG
1 GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGAAATGACTGCACTGGATATTCT-GG
41956 GATCAACTCTGACCAATG
65 GATCAACTCTGACCAATG
* * * *
41974 GATCTTCTAGGGATCAACTCTGACCATTGAAAGCTTCTTGGAATGACTGCACTGGATCTTCTGGG
1 GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGAAATGACTGCACTGGATATTCTGGG
42039 ATCAACTCTGACCA
66 ATCAACTCTGACCA
42053 TTGAAAATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 17 0.23
83 57 0.77
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (82 bp):
GATCTTCTAGGGATCAACTCTGACCACTGAAAACTTCTTGAAATGACTGCACTGGATATTCTGGG
ATCAACTCTGACCAATG
Found at i:42045 original size:53 final size:54
Alignment explanation
Indices: 41972--42194 Score: 267
Period size: 53 Copynumber: 4.1 Consensus size: 54
41962 CTCTGACCAA
* *
41972 TGGATCTTCTAGGGATCAACTCTGACCATTGAAAGCTTCTTGGAATGACTGCAC
1 TGGATCTTCTAGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCAC
*
42026 TGGATCTTCT-GGGATCAACTCTGACCATTGAAAATTTCTTGGAATGACCGCAC
1 TGGATCTTCTAGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCAC
* * *
42079 TGGATCTTCTGGGGATCAACTCTGACGATTGAAAACTTCTTGGAAATGACCACAC
1 TGGATCTTCTAGGGATCAACTCTGACCATTGAAAACTTCTTGG-AATGACCGCAC
* * * *
42134 TGGCTCAATT-TA-AGATCAACTATGATC-TCT-AGAAACTTCTTTGGAATGACCGCAC
1 TGGATC--TTCTAGGGATCAACTCTGACCAT-TGA-AAACTTC-TTGGAATGACCGCAC
42189 TGGATC
1 TGGATC
42195 ACTTTAAACA
Statistics
Matches: 148, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
53 50 0.34
54 42 0.28
55 49 0.33
56 5 0.03
57 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (54 bp):
TGGATCTTCTAGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCAC
Found at i:42172 original size:245 final size:246
Alignment explanation
Indices: 41727--42193 Score: 638
Period size: 245 Copynumber: 1.9 Consensus size: 246
41717 ATGACTGCAC
* *
41727 TGGATCTTCTTGGGATCAACTTTGACCATAGAAAACTTCTTGGAATGACCACACTGGATCTTCTG
1 TGGATCTTCTAGGGATCAACTCTGACCATAGAAAACTTCTTGGAATGACCACACTGGATCTTCTG
*
41792 GGGAGCAACTCTGACCATAGAGAACTTCTTGGAATGACCGCACTAGATCTTCTAGGGATCAACTC
66 GGGAGCAACTCTGACCATAGAAAACTTCTTGGAATGACCGCACTAGATCTTCTAGGGATCAACTC
* * * *
41857 TGACCACTGAAAACTTCTTGGAATGACCGCATTAGATCTTCTAGGGATCAACTCTGACCACTGAA
131 TGACCACTGAAAACTTCTTGGAATGACCACACTAGATCTTCTAGAGATCAACTATGACCACTGAA
* *
41922 AACTTC-TTGAAATGACTGCATTGGATATTCTAGGGATCAACTCTGACCAA
196 AACTTCTTTGAAATGACCGCACTGGATATTCTAGGGATCAACTCTGACCAA
* * **
41972 TGGATCTTCTAGGGATCAACTCTGACCATTGAAAGCTTCTTGGAATGACTGCACTGGATCTTCT-
1 TGGATCTTCTAGGGATCAACTCTGACCATAGAAAACTTCTTGGAATGACCACACTGGATCTTCTG
* * * * *
42036 GGGATCAACTCTGACCATTGAAAATTTCTTGGAATGACCGCACTGGATCTTCTGGGGATCAACTC
66 GGGAGCAACTCTGACCATAGAAAACTTCTTGGAATGACCGCACTAGATCTTCTAGGGATCAACTC
* * * * * *
42101 TGACGATTGAAAACTTCTTGGAAATGACCACACTGGCTCAATT-TA-AGATCAACTATGATCTCT
131 TGACCACTGAAAACTTCTTGG-AATGACCACACTAGATC--TTCTAGAGATCAACTATGACCACT
*
42164 -AGAAACTTCTTTGGAATGACCGCACTGGAT
193 GA-AAACTTCTTTGAAATGACCGCACTGGAT
42194 CACTTTAAAC
Statistics
Matches: 192, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
244 79 0.41
245 92 0.48
246 19 0.10
247 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (246 bp):
TGGATCTTCTAGGGATCAACTCTGACCATAGAAAACTTCTTGGAATGACCACACTGGATCTTCTG
GGGAGCAACTCTGACCATAGAAAACTTCTTGGAATGACCGCACTAGATCTTCTAGGGATCAACTC
TGACCACTGAAAACTTCTTGGAATGACCACACTAGATCTTCTAGAGATCAACTATGACCACTGAA
AACTTCTTTGAAATGACCGCACTGGATATTCTAGGGATCAACTCTGACCAA
Found at i:42483 original size:52 final size:52
Alignment explanation
Indices: 42391--42489 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 52
42381 CCATCTTCGT
* * * ** *
42391 CCATGTCATGCCCTGATGGCTCTTCTTTCTATGCCTTTGAATTCTTCTTCAC
1 CCATGTCATGCCCTGATGACTCTACTTTATATAACTTTGAATGCTTCTTCAC
*
42443 CCATGTCAT-CCCTGATGACTCTACTTTATGTAACTCTTGAATGCTTC
1 CCATGTCATGCCCTGATGACTCTACTTTATATAACT-TTGAATGCTTC
42490 CTCTGCAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 20 0.51
52 19 0.49
ACGTcount: A:0.17, C:0.29, G:0.13, T:0.40
Consensus pattern (52 bp):
CCATGTCATGCCCTGATGACTCTACTTTATATAACTTTGAATGCTTCTTCAC
Found at i:43324 original size:37 final size:36
Alignment explanation
Indices: 43283--43355 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
43273 TGTCTTAAAA
43283 TCTTTTTGA-AAAACATTTTTTCTCTTTTGAAAAGATT
1 TCTTTTTGAGAAAACA-TTTTTC-CTTTTGAAAAGATT
43320 TCTTTTTGAGGAAAACATTTTTCCTTTTGAAAAGAT
1 TCTTTTTGA-GAAAACATTTTTCCTTTTGAAAAGAT
43356 CACACTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
37 22 0.65
38 6 0.18
39 6 0.18
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (36 bp):
TCTTTTTGAGAAAACATTTTTCCTTTTGAAAAGATT
Found at i:43365 original size:37 final size:39
Alignment explanation
Indices: 43292--43370 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 39
43282 ATCTTTTTGA
** **
43292 AAAACATTTTTTCTCTTTTGAAAAGATTTCTTTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACTTTGAGG
43331 AAAACA-TTTTTC-CTTTTGAAAAGATCACACTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACTTTGAGG
43368 AAA
1 AAA
43371 GTTTCATTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 24 0.67
38 6 0.17
39 6 0.17
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTGAAAAGATCACACTTTGAGG
Found at i:43793 original size:14 final size:14
Alignment explanation
Indices: 43755--43785 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43745 AAAAATCGAT
*
43755 TTTTTAGAAAACCC
1 TTTTTAGAAAACAC
43769 TTTTTAGAAAACAC
1 TTTTTAGAAAACAC
43783 TTT
1 TTT
43786 CTTGAAAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (14 bp):
TTTTTAGAAAACAC
Found at i:47461 original size:20 final size:20
Alignment explanation
Indices: 47438--47497 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
47428 AGCAAATTAT
*
47438 AAAGAAACCCTAAATATATG
1 AAAGAAACCCTAAATATATA
**
47458 AAAGAAACTTTCAAATAT-TA
1 AAAGAAACCCT-AAATATATA
47478 ATAAGAAACCTCTAAATATA
1 A-AAGAAACC-CTAAATATA
47498 AATAAGACAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 11 0.35
21 19 0.61
22 1 0.03
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAGAAACCCTAAATATATA
Found at i:47483 original size:21 final size:21
Alignment explanation
Indices: 47470--47510 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47460 AGAAACTTTC
*
47470 AAATATTAATAAGAAACCTCT
1 AAATATAAATAAGAAACCTCT
*
47491 AAATATAAATAAGACACCTC
1 AAATATAAATAAGAAACCTC
47511 CAACATAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATATAAATAAGAAACCTCT
Found at i:48942 original size:10 final size:10
Alignment explanation
Indices: 48927--48970 Score: 88
Period size: 10 Copynumber: 4.4 Consensus size: 10
48917 AAATTGAGAT
48927 ATAATCAAGC
1 ATAATCAAGC
48937 ATAATCAAGC
1 ATAATCAAGC
48947 ATAATCAAGC
1 ATAATCAAGC
48957 ATAATCAAGC
1 ATAATCAAGC
48967 ATAA
1 ATAA
48971 ATAGACCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.20
Consensus pattern (10 bp):
ATAATCAAGC
Found at i:51406 original size:13 final size:13
Alignment explanation
Indices: 51388--51413 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51378 AACATACTTC
51388 TTCTCCTTTAGGT
1 TTCTCCTTTAGGT
51401 TTCTCCTTTAGGT
1 TTCTCCTTTAGGT
51414 AACTATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (13 bp):
TTCTCCTTTAGGT
Found at i:52642 original size:21 final size:21
Alignment explanation
Indices: 52590--52628 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52580 ACTAACGTTG
52590 GGCA-CCCATGTGGTTTGCTT
1 GGCACCCCATGTGGTTTGCTT
52610 GGCACCCCATGTGGTTTGC
1 GGCACCCCATGTGGTTTGC
52629 CTTGCGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.10, C:0.28, G:0.31, T:0.31
Consensus pattern (21 bp):
GGCACCCCATGTGGTTTGCTT
Found at i:53775 original size:15 final size:15
Alignment explanation
Indices: 53755--53784 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53745 AGGGGATTTT
*
53755 AAGAAAGCAATTAAA
1 AAGAAAACAATTAAA
53770 AAGAAAACAATTAAA
1 AAGAAAACAATTAAA
53785 CTAAATACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (15 bp):
AAGAAAACAATTAAA
Found at i:53818 original size:6 final size:6
Alignment explanation
Indices: 53802--53840 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
53792 CTAAGCAAAG
*
53802 TAAAT- TAAATC TAAATC TAAATC TGAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
53841 GCAAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:55222 original size:11 final size:11
Alignment explanation
Indices: 55205--55236 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
55195 ATTGTCTTCA
55205 AATCTTCAAAT
1 AATCTTCAAAT
*
55216 TATCTTCAAAT
1 AATCTTCAAAT
55227 AATCTTCAAA
1 AATCTTCAAA
55237 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Done.