Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002658.1 Hibiscus syriacus cultivar Beakdansim tig00005437_pilon, 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: 65502
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1707 original size:106 final size:106
Alignment explanation
Indices: 1466--2042 Score: 860
Period size: 106 Copynumber: 5.5 Consensus size: 106
1456 ATGAAATTTG
* * * * * * *
1466 TTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAGATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
* *
1531 CTGAGAAGTTGAAA-TGGCTCTGAAATTGGGAAGTTGTTTA
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
* *
1571 TTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
1636 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
*
1677 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT-CAATA--CTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
* * * * * *
1739 TTGTGAAGCTGAAATTGGCTCTAAAATTGAGAAGTTGTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
* * *
1780 TTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTAGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
1845 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
*
1886 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
* *
1951 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATT-ATTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTGTTTA
* * *
1992 TTGACAACCAGCTGT-CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGT
2043 GACACGATAT
Statistics
Matches: 429, Mismatches: 38, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
103 89 0.21
104 5 0.01
105 108 0.25
106 222 0.52
107 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
Found at i:1812 original size:209 final size:210
Alignment explanation
Indices: 1332--2042 Score: 957
Period size: 209 Copynumber: 3.4 Consensus size: 210
1322 ATCCTCCATC
* ** * *
1332 GTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTG---ACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* * *
1394 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC-G-AA
66 GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
* * * * * * *
1457 -T--GAAA---TTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG
131 TTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
*
1516 GTCCAAGATCCTTCGCT
196 GTCC-A-ATACTTCGCT
* * * *
1533 GAGAAGTTGAAA-TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAACGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
*
1597 GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAA
66 GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
*
1662 TTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGA
131 TTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
*
1727 GT-CAATACTTCGTT
196 GTCCAATACTTCGCT
* * * * *
1741 GTGAAGCTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCAT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
* *
1806 GAAGTTGAACTTGCATTGTCTAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
66 GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
*
1871 TTGGGAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
131 TTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
1936 GTCCAATATCCTTCGCT
196 GTCCAATA--CTTCGCT
* * *
1953 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATT-ATTGTTGACAACCAGCTGT-CCTTCGTTG
1 GTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
2016 TGAAGTTGAACTTGTGTTGTCTTGAGT
65 TGAAGTTGAACTTGCGTTGTCTTGAGT
2043 GACACGATAT
Statistics
Matches: 447, Mismatches: 47, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
200 24 0.05
201 11 0.02
203 73 0.16
204 1 0.00
205 2 0.00
206 1 0.00
208 22 0.05
209 175 0.39
210 6 0.01
211 79 0.18
212 49 0.11
213 4 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (210 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
TTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
GTCCAATACTTCGCT
Found at i:1919 original size:315 final size:308
Alignment explanation
Indices: 1332--2042 Score: 1004
Period size: 315 Copynumber: 2.3 Consensus size: 308
1322 ATCCTCCATC
* **
1332 GTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTG---ACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
* * *
1394 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCGAATG
66 GAAGTTGAACTTGTGTTGTCTAGAGTCCAATA-CCTTCGCTGTGAAGCTGAAATTGACTCAAATG
* * * ** * *
1459 AAATTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAGA
130 AAATTTGTTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAACTTGCATTGTCTAGAGTCCAAGA
*
1524 TCCTTCGCTGAGAAGTTGAAATGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAACGGTCCC
195 TCCTTCGCTGAGAAGTTGAAATGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAACGGTCCC
1589 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCT
260 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCT
* * *
1638 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
* * *
1703 GAAGTTGAACTTGCGTTGTCTAGAGT-CAATA-CTTCGTTGTGAAGCTGAAATTGGCTCTAAAAT
66 GAAGTTGAACTTGTGTTGTCTAGAGTCCAATACCTTCGCTGTGAAGCTGAAATTGACTC--AAA-
* *
1766 TGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTAGAG
128 TGA-AA----TTTGTTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAACTTGCATTGTCTAGAG
* *
1831 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCA
188 TCCAAGATCCTTCGCTGAGAAGTTGAAA-TGGCTCTGAAATTGGGAAATTGTTTATTGACAACCA
** *
1896 GTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCT
252 ACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCT
* *
1953 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATT-ATTGTTGACAACCAGCTGT-CCTTCGTTG
1 GTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTG
*
2016 TGAAGTTGAACTTGTGTTGTCTTGAGT
65 TGAAGTTGAACTTGTGTTGTCTAGAGT
2043 GACACGATAT
Statistics
Matches: 359, Mismatches: 33, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
306 61 0.17
308 7 0.02
309 45 0.13
310 2 0.01
314 105 0.29
315 134 0.37
316 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (308 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
GAAGTTGAACTTGTGTTGTCTAGAGTCCAATACCTTCGCTGTGAAGCTGAAATTGACTCAAATGA
AATTTGTTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAACTTGCATTGTCTAGAGTCCAAGAT
CCTTCGCTGAGAAGTTGAAATGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAACGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCT
Found at i:3597 original size:171 final size:173
Alignment explanation
Indices: 3275--3620 Score: 592
Period size: 171 Copynumber: 2.0 Consensus size: 173
3265 TAAATAGGCC
*
3275 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
3340 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
* *
3405 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTAAAGCTTGATGTGCCATTT
*
3450 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
3512 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTC-AGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
3576 ATTGTGCTTGATCAATCTCATAGTTTAAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTAAAGCTTGATGTGCCATTT
3621 TTTAGGGAAT
Statistics
Matches: 165, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
170 14 0.08
171 71 0.43
172 28 0.17
174 1 0.01
175 51 0.31
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGAT
TGTGCTTGATCAATCTCATAGTTTAAAGCTTGATGTGCCATTT
Found at i:3735 original size:16 final size:16
Alignment explanation
Indices: 3709--3742 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3699 TCTTTGTTTT
3709 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
3726 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
3741 TT
1 TT
3743 GATTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:7060 original size:20 final size:19
Alignment explanation
Indices: 7024--7061 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
7014 TGCAGATGAT
*
7024 GGAAATAAAATAAAAGAGA
1 GGAAAAAAAATAAAAGAGA
7043 GGAAAAAAAATAAAA-AGA
1 GGAAAAAAAATAAAAGAGA
7061 G
1 G
7062 TTAGTAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (19 bp):
GGAAAAAAAATAAAAGAGA
Found at i:8445 original size:10 final size:11
Alignment explanation
Indices: 8341--8450 Score: 52
Period size: 10 Copynumber: 10.1 Consensus size: 11
8331 ACATAATGAA
8341 AATAAATAAAT
1 AATAAATAAAT
8352 AGTATAAATAAAAT
1 A--ATAAAT-AAAT
*
8366 AAAAAAATAAA-
1 -AATAAATAAAT
*
8377 AATATATAAA-
1 AATAAATAAAT
** **
8387 AATGTATGTAT
1 AATAAATAAAT
8398 AATATAATAAAT
1 AATA-AATAAAT
* *
8410 ACTAAAT-AGT
1 AATAAATAAAT
*
8420 AA-CAAT-AAT
1 AATAAATAAAT
8429 AATAAATAAAT
1 AATAAATAAAT
8440 AA-AAATAAAT
1 AATAAATAAAT
8450 A
1 A
8451 TACATATATA
Statistics
Matches: 75, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
9 7 0.09
10 30 0.40
11 12 0.16
12 10 0.13
13 11 0.15
14 4 0.05
15 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:8566 original size:20 final size:19
Alignment explanation
Indices: 8527--8573 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
8517 ATACGTTAGG
8527 AAAATATAGTAAAAAAATAA
1 AAAATA-AGTAAAAAAATAA
* *
8547 TAAATAAGTAAAATAGATAA
1 AAAATAAGTAAAA-AAATAA
8567 AAAATAA
1 AAAATAA
8574 TAATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAATAAGTAAAAAAATAA
Found at i:8604 original size:61 final size:61
Alignment explanation
Indices: 8539--8656 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 61
8529 AATATAGTAA
** * * * *
8539 AAAAATAATA-AATAAGTAAAATAGATAAAAAATAAT-AATATATATATATATATAATAATAG
1 AAAAATAATATAA-AAAAAAAAT-GAAAAAAAATAATAAATAAATAAATAAATATAATAATAG
8600 AAAAATAATATAAAAAAAAAATGAAAAAAAATAATAAATAAATAAATAAATATAATA
1 AAAAATAATATAAAAAAAAAATGAAAAAAAATAATAAATAAATAAATAAATATAATA
8657 TATATATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 12 0.24
61 35 0.71
62 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (61 bp):
AAAAATAATATAAAAAAAAAATGAAAAAAAATAATAAATAAATAAATAAATATAATAATAG
Found at i:8639 original size:4 final size:4
Alignment explanation
Indices: 8536--8656 Score: 55
Period size: 4 Copynumber: 31.5 Consensus size: 4
8526 GAAAATATAG
* * * *
8536 TAAA AAAA T-AA TAAA TAAG TAAAA TAGA TAAA -AAA T-AA T-AA TATA
1 TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * *
8581 TATA TATA TATAA T-AA TAGAA -AAA TAATA TAAA -AAA AAAA TGAA -AAA
1 TAAA TAAA TA-AA TAAA TA-AA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA
8628 -AAA T-AA TAAA TAAA TAAA TAAA TATAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TA
8657 TATATATATA
Statistics
Matches: 93, Mismatches: 11, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
3 28 0.30
4 50 0.54
5 15 0.16
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:8642 original size:21 final size:21
Alignment explanation
Indices: 8599--8656 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
8589 TATAATAATA
*
8599 GAAAAATAATATAAAAAAAAAAT
1 GAAAAA-AA-ATAATAAAAAAAT
*
8622 GAAAAAAAATAATAAATAAAT
1 GAAAAAAAATAATAAAAAAAT
*
8643 -AAATAAATATAATA
1 GAAA-AAAAATAATA
8657 TATATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 20 0.65
22 2 0.06
23 6 0.19
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (21 bp):
GAAAAAAAATAATAAAAAAAT
Found at i:8661 original size:2 final size:2
Alignment explanation
Indices: 8649--8706 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
8639 AAATAAATAA
8649 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8690 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
8707 GAAATAATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24284 original size:29 final size:29
Alignment explanation
Indices: 24250--24337 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 29
24240 AAAGGACCTA
24250 TCCATATGTTCTGAGAACATAGGTAACTG
1 TCCATATGTTCTGAGAACATAGGTAACTG
* * **
24279 TCCATATGTCCTGAAGGACATATATAAACTG
1 TCCATATGTTCTG-AGAACATAGGT-AACTG
*
24310 TCCATATG-TCTCGAAAGACATAGGTAAC
1 TCCATATGTTCT-GAGA-ACATAGGTAAC
24338 CCTCGACTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
29 12 0.26
30 14 0.30
31 20 0.43
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (29 bp):
TCCATATGTTCTGAGAACATAGGTAACTG
Found at i:29609 original size:2 final size:2
Alignment explanation
Indices: 29602--29646 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29592 CTGTATACCC
29602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29644 AT A
1 AT A
29647 CAATAAAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30098 original size:27 final size:27
Alignment explanation
Indices: 30068--30120 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
30058 AAGATTTTAG
*
30068 AGAACTGAAATATAAGTGTTCTAAAAT
1 AGAACTGAAATAAAAGTGTTCTAAAAT
*
30095 AGAAGTGAAATAAAAGTGTTCTAAAA
1 AGAACTGAAATAAAAGTGTTCTAAAA
30121 AGGCTAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (27 bp):
AGAACTGAAATAAAAGTGTTCTAAAAT
Found at i:31348 original size:66 final size:66
Alignment explanation
Indices: 31250--31410 Score: 202
Period size: 66 Copynumber: 2.4 Consensus size: 66
31240 TATATTTCTA
* * *
31250 TTGAAACAAATTTTATCTCCCTCT-AGACAGTTTCTCGTGAAACACC-AACATTTGAGATCGTTT
1 TTGAAACAAATTTTGTCTCCCT-TGAGACAGTTTCTCATAAAACACCAAAC-TTTGAGATCGTTT
31313 CCC
64 CCC
* * *
31316 TTGAAA-ATAATTTTGTCTCCCTTGAGATAGTTTCTCATAAAATACCAAACTTTGAGATTGTTTC
1 TTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCATAAAACACCAAACTTTGAGATCGTTTC
31380 CC
65 CC
**
31382 TTGAAACAAGCTTTGTCTCCCTTGAGACA
1 TTGAAACAAATTTTGTCTCCCTTGAGACA
31411 ACTTCTCTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
65 2 0.02
66 76 0.93
67 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (66 bp):
TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATAAAACACCAAACTTTGAGATCGTTTCC
C
Found at i:32302 original size:7 final size:7
Alignment explanation
Indices: 32275--32327 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
32265 TTATTCGGGA
32275 AAAAAAG
1 AAAAAAG
**
32282 ACCAAAG
1 AAAAAAG
*
32289 AGAAAAAT
1 A-AAAAAG
* *
32297 AGAAAAC
1 AAAAAAG
32304 AAAAAAG
1 AAAAAAG
32311 AAAAAAG
1 AAAAAAG
32318 AAAAAAG
1 AAAAAAG
32325 AAA
1 AAA
32328 GAATGTGAGG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.89
8 4 0.11
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:32708 original size:2 final size:2
Alignment explanation
Indices: 32701--32747 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
32691 TGGTTTAAGG
32701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32743 CAT AT
1 -AT AT
32748 TCGAAACAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36809 original size:85 final size:85
Alignment explanation
Indices: 36699--37322 Score: 741
Period size: 85 Copynumber: 7.3 Consensus size: 85
36689 CAGACAGTTA
* * * * * *
36699 TTCTCGCCTTGCGCTATGCTATAAATTTGACATGCCCTTGAGCTGAATGGT-ATCAAACTCGAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAAT-GTAATCGAACTCGAAG
** * *
36763 GTATTCATTGAAAAATAACCC
65 GTATTTGTTGACAGATAACCC
* *
36784 TTATCGCCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
*
36849 TCTTTGTTGACAGATAA-CC
66 TATTTGTTGACAGATAACCC
* * * * *
36868 TTCTCGTCTTGAGCTATGCTGTAGATTTGATATGCCCTTGAGCTGAATAG-AATCGAACTCAAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAAT-GTAATCGAACTCGAAG
36932 GTATTTGTTGACAGATAACCC
65 GTATTTGTTGACAGATAACCC
* ** * *
36953 TTTTTTCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCAAACTTGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
* *
37018 TCTTTGTTGACAGGTAACCC
66 TATTTGTTGACAGATAACCC
* * * * **
37038 TTCTTGCCTTGAGTTATGCTGTAGATTTGATATGCCCTTGAGCTGAATGCAATCGAACTTAAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
* * *
37103 TTTTTATTGATAGATAACCC
66 TATTTGTTGACAGATAACCC
*
37123 TTCTCGTCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
* * *
37188 TTTTTTGCTGACATATAACCC
66 -TATTTGTTGACAGATAACCC
* * *
37209 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATATCCTTGAGCTGAGTGTAATTGAACTCGGAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTC-GAAG
* * * *
37274 GTTTTTTTTCTAGCAGATAGCCC
65 GTATTTGTT-GA-CAGATAACCC
* * *
37297 TTTTCGCCTTGAGCTATGCTGCAAAT
1 TTCTCGCCTTGAGTTATGCTGTAAAT
37323 GGTTCCTTTA
Statistics
Matches: 466, Mismatches: 65, Indels: 13
0.86 0.12 0.02
Matches are distributed among these distances:
84 77 0.17
85 274 0.59
86 78 0.17
87 6 0.01
88 31 0.07
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
TATTTGTTGACAGATAACCC
Found at i:36990 original size:169 final size:169
Alignment explanation
Indices: 36699--37322 Score: 766
Period size: 169 Copynumber: 3.7 Consensus size: 169
36689 CAGACAGTTA
* * * * * *
36699 TTCTCGCCTTGCGCTATGCTATAAATTTGACATGCCCTTGAGCTGAATGGTATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT-GAATCGAACTCAAAGG
* * * * *
36764 TATTCATTGAAAAATAACCCTTATCGCCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTG
65 TATTTATTGAAAGATAACCCTTTTCTCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTG
36829 AATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA-CC
130 AATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCC
* *
36868 TTCTCGTCTTGAGCTATGCTGTAGATTTGATATGCCCTTGAGCTGAATAGAATCGAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT-GAATCGAACTCAAAGG
* * *
36933 TATTTGTTGACAGATAACCCTTTTTTCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTG
65 TATTTATTGAAAGATAACCCTTTTCTCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTG
* * *
36998 AATGTAATCAAACTTGAAGGTCTTTGTTGACAGGTAACCC
130 AATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCC
* * * *
37038 TTCTTGCCTTGAGTTATGCTGTAGATTTGATATGCCCTTGAGCTGAATGCAATCGAACTTAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATG-AATCGAACTCAAAGG
* * *
37103 TTTTTATTGATAGATAACCCTTCTCGT-CTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCT
65 TATTTATTGAAAGATAACCCTTTTC-TCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCT
* * *
37167 GAATGTAATCGAACTCGAAGGTTTTTTGCTGACATATAACCC
129 GAATGTAATCGAACTCGAAGG-TCTTTGTTGACAGATAACCC
* ** * * *
37209 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATATCCTTGAGCTGAGTGTAATTGAACTCGGAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATG-AATCGAACTC-AAAG
* * * * * * * *
37274 GTTTTTTTTCTAGCAGATAGCCCTTTTCGCCTTGAGCTATGCTGCAAAT
64 GTATTTATT-GA-AAGATAACCCTTTTCTCCTTGAGTTATGCTGTAAAT
37323 GGTTCCTTTA
Statistics
Matches: 395, Mismatches: 52, Indels: 11
0.86 0.11 0.02
Matches are distributed among these distances:
169 148 0.37
170 137 0.35
171 69 0.17
172 11 0.03
173 1 0.00
174 29 0.07
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (169 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGAATCGAACTCAAAGGT
ATTTATTGAAAGATAACCCTTTTCTCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGA
ATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCC
Found at i:38130 original size:13 final size:13
Alignment explanation
Indices: 38112--38136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38102 AAAATTGCAT
38112 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
38125 TTCTTTTTTTTT
1 TTCTTTTTTTTT
38137 ATTATCGCAA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:39447 original size:24 final size:24
Alignment explanation
Indices: 39417--39466 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
39407 ATGGGGGCTT
39417 CATGGGTTCCACCCGGTATGGTGA
1 CATGGGTTCCACCCGGTATGGTGA
39441 CATGGGTTCCACCCGGTATGGTGA
1 CATGGGTTCCACCCGGTATGGTGA
39465 CA
1 CA
39467 CTACGTGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (24 bp):
CATGGGTTCCACCCGGTATGGTGA
Found at i:43030 original size:8 final size:7
Alignment explanation
Indices: 43019--43076 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
43009 GAAATAAAAT
43019 TAAATGAA
1 TAAAT-AA
43027 TAAATAA
1 TAAATAA
43034 TAAA-AA
1 TAAATAA
43040 -ACAATAA
1 TA-AATAA
43047 TAAATAA
1 TAAATAA
*
43054 TACA-AA
1 TAAATAA
43060 TAAAATAA
1 T-AAATAA
43068 TAAA-AA
1 TAAATAA
43074 TAA
1 TAA
43077 TATTATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 1 0.02
6 12 0.28
7 21 0.49
8 9 0.21
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.22
Consensus pattern (7 bp):
TAAATAA
Found at i:43050 original size:20 final size:20
Alignment explanation
Indices: 43011--43076 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
43001 GAAAAAAAGA
*
43011 AATAAAATTAAATGAATAAAT
1 AATAAAATAAAAT-AATAAAT
43032 AATAAAA-AACAATAATAAAT
1 AATAAAATAA-AATAATAAAT
43052 AATACAAATAAAATAATAAA-
1 AATA-AAATAAAATAATAAAT
43072 AATAA
1 AATAA
43077 TATTATTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 1 0.02
20 16 0.39
21 22 0.54
22 2 0.05
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.23
Consensus pattern (20 bp):
AATAAAATAAAATAATAAAT
Found at i:43067 original size:14 final size:14
Alignment explanation
Indices: 43014--43076 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
43004 AAAAAGAAAT
*
43014 AAAATTAAATGAATA
1 AAAATAAAAT-AATA
*
43029 AATAATAAAA-AACA
1 AA-AATAAAATAATA
*
43043 ATAAT-AAATAATA
1 AAAATAAAATAATA
*
43056 CAAATAAAATAATA
1 AAAATAAAATAATA
43070 AAAATAA
1 AAAATAA
43077 TATTATTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
12 3 0.08
13 9 0.24
14 18 0.47
15 2 0.05
16 6 0.16
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (14 bp):
AAAATAAAATAATA
Found at i:43186 original size:38 final size:38
Alignment explanation
Indices: 43131--43534 Score: 419
Period size: 38 Copynumber: 10.3 Consensus size: 38
43121 TCTAACACCA
*
43131 TATATTATATATTTTCAAAATATTTTAAAAACTATATAT
1 TATA-TATATATTTTCAAAATGTTTTAAAAACTATATAT
43170 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
*
43208 TATATATATATTTTCAAAATGTTTTAAAAATTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
* *
43246 TATATATATATTTTCAAAATATTTTAAAAGCTATATA-
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
**
43283 T-TATATAGGTTTTCAAAATGTTTTAAAAACTATATATT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATA-T
43321 ATATATATATATTTTTCAAAATGTTTTAAAAACTATATAT
1 -TATATATATA-TTTTCAAAATGTTTTAAAAACTATATAT
*
43361 TACATA-A-ATTTTCAAAATGTTTTAAAAACTATATTAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATA-TAT
* **
43398 ATATATATATATATATAT-ATATAT-TTTTCAAAATGTTTTGAAAACTATAT
1 -TATATATATAT-T-T-TCA-AAATGTTTT-AAAA-------ACTA-TATAT
* * *
43448 TATATATATATATTCAAAATGTTTTTAAAATTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
* * *
43486 TATATA-A-GTTTTCAAAATGTTGTAAAAACCATATTAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATA-TAT
43523 ATATATATATAT
1 -TATATATATAT
43535 ATATATATTC
Statistics
Matches: 309, Mismatches: 28, Indels: 55
0.79 0.07 0.14
Matches are distributed among these distances:
36 76 0.25
37 9 0.03
38 127 0.41
39 14 0.05
40 10 0.03
41 28 0.09
42 6 0.02
43 8 0.03
46 7 0.02
47 6 0.02
49 11 0.04
50 5 0.02
51 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:43402 original size:2 final size:2
Alignment explanation
Indices: 43390--43421 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
43380 TTTTAAAAAC
43390 TA TA T- 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 TA T
43422 TTTTCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:43420 original size:89 final size:86
Alignment explanation
Indices: 43313--43491 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 86
43303 TTTTAAAAAC
*
43313 TATATATTATATATATATATTTTTCAAAATGTTTTAAAAACTATA-TATTACATAAATTTTCAAA
1 TATATATTATATATATATATTTTTCAAAATGTTTTAAAAACTATATTA-TACATAAATATTCAAA
43377 ATGTTTTAAAAACTATATTATATA
65 ATGTTTTAAAAACTATA-TAT-TA
* * *
43401 TATATATATATATATATATATTTTTCAAAATGTTTTGAAAACTATATTATATATATATATTCAAA
1 TATATAT-TATATATATATATTTTTCAAAATGTTTTAAAAACTATATTATACATAAATATTCAAA
* *
43466 ATGTTTTTAAAATTATATATTA
65 ATGTTTTAAAAACTATATATTA
43488 TATA
1 TATA
43492 AGTTTTCAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
87 6 0.07
88 10 0.12
89 65 0.78
90 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (86 bp):
TATATATTATATATATATATTTTTCAAAATGTTTTAAAAACTATATTATACATAAATATTCAAAA
TGTTTTAAAAACTATATATTA
Found at i:43464 original size:36 final size:37
Alignment explanation
Indices: 43405--43529 Score: 139
Period size: 36 Copynumber: 3.4 Consensus size: 37
43395 TATATATATA
* * *
43405 TATATATATATATATATTTTTCAAAATGTTTTGAAAAC
1 TATAT-TATATATATAGTATTCAAAATGTTTTAAAAAC
* *
43443 TATATTATATATATA-TATTCAAAATGTTTTTAAAAT
1 TATATTATATATATAGTATTCAAAATGTTTTAAAAAC
* *
43479 TATA-TAT-TATATAAGTTTTCAAAATGTTGTAAAAAC
1 TATATTATATATAT-AGTATTCAAAATGTTTTAAAAAC
*
43515 CATATTATATATATA
1 TATATTATATATATA
43530 TATATATATA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
34 5 0.07
35 4 0.05
36 42 0.56
37 14 0.19
38 10 0.13
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATTATATATATAGTATTCAAAATGTTTTAAAAAC
Found at i:43514 original size:125 final size:128
Alignment explanation
Indices: 43277--43542 Score: 405
Period size: 125 Copynumber: 2.1 Consensus size: 128
43267 TTTTAAAAGC
43277 TATATAT-TATATAGGTTTTCAAAATGTTTTAAAAACTATATATTATATATATATATTTTTCAAA
1 TATATATATATATAGGTTTTCAAAATGTTTTAAAAAC-ATATATTATATATATATA--TTTCAAA
* *
43341 ATGTTTTAAAAACTATATATTACATAAATTTTCAAAATGTTTTAAAAACTATATTATATATATAT
63 ATGTTTTAAAAACTATATATTACATAAATTTTCAAAATGTTGTAAAAACCATATTATATATATAT
43406 A
128 A
* *
43407 TATATATATATATA-TTTTTCAAAATGTTTTGAAAAC-TATATTATATATATATA-TTCAAAATG
1 TATATATATATATAGGTTTTCAAAATGTTTTAAAAACATATATTATATATATATATTTCAAAATG
* * * *
43469 TTTTTAAAATTATATATTATATAAGTTTTCAAAATGTTGTAAAAACCATATTATATATATATA
66 TTTTAAAAACTATATATTACATAAATTTTCAAAATGTTGTAAAAACCATATTATATATATATA
43532 TATATATATAT
1 TATATATATAT
43543 TCAAAAACCG
Statistics
Matches: 127, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
125 77 0.61
128 17 0.13
130 27 0.21
131 6 0.05
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (128 bp):
TATATATATATATAGGTTTTCAAAATGTTTTAAAAACATATATTATATATATATATTTCAAAATG
TTTTAAAAACTATATATTACATAAATTTTCAAAATGTTGTAAAAACCATATTATATATATATA
Found at i:43605 original size:202 final size:199
Alignment explanation
Indices: 43201--43608 Score: 463
Period size: 202 Copynumber: 2.0 Consensus size: 199
43191 TTTTAAAAAC
*
43201 TATATATTATATATATATTTTCAAAATGTTTTAAAAATTATATATTATATATATATTTTCAAAAT
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAA-TATATATTATATATATATATTCAAAAT
* *
43266 ATTTTAAAAGCTATATATTATATAGGTTTTCAAAATGTTTTAAAAACTATATATTATATATATAT
65 ATTTTAAAAGCTATATATTATATAAGTTTTCAAAATGTTGTAAAAACTATATATTATATATATAT
* * * * ** *
43331 ATTTTTCAAAATGTTTTAAAAACTATATATTACATAAATTTTCAAAATGTTTTAAAAACTATATT
130 ATTATTCAAAACGTTTTAAAAACTACATA-TACAAAAATTTTCAAAAACTTATAAAAAC-ATATT
43396 ATATATA
193 ATATATA
* *
43403 TATATATATATATATATATTTTTCAAAATGTTTTGAAAA-CTATATTATATATATATATTCAAAA
1 TATATAT-TATATATATA-TTTTCAAAATGTTTTAAAAATATATATTATATATATATATTCAAAA
* *
43467 TGTTTTTAAAA-TTATATATTATATAAGTTTTCAAAATGTTGTAAAAACCATATTATATATATAT
64 T-ATTTTAAAAGCTATATATTATATAAGTTTTCAAAATGTTGTAAAAA-C-TA-TATAT-TATAT
*
43531 ATATATATATATTCAAAAACCGATTTTTAAAAC-ACA-A-A-AAAAATCTTTCAAAAAC-TATAT
124 ATATATAT-TATTC-AAAA-CG-TTTTAAAAACTACATATACAAAAAT-TTTCAAAAACTTATA-
* *
43591 GATA-ATATTATATATA
183 AAAACATATTATATATA
43607 TA
1 TA
43609 AAAAACTCCA
Statistics
Matches: 176, Mismatches: 17, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
202 64 0.36
203 19 0.11
204 35 0.20
205 13 0.07
206 24 0.14
207 4 0.02
208 5 0.03
209 3 0.02
210 9 0.05
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (199 bp):
TATATATTATATATATATTTTCAAAATGTTTTAAAAATATATATTATATATATATATTCAAAATA
TTTTAAAAGCTATATATTATATAAGTTTTCAAAATGTTGTAAAAACTATATATTATATATATATA
TTATTCAAAACGTTTTAAAAACTACATATACAAAAATTTTCAAAAACTTATAAAAACATATTATA
TATA
Found at i:45047 original size:30 final size:31
Alignment explanation
Indices: 45008--45066 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
44998 ATCGTTGTTC
45008 AATATTAAAACAAAACAAA-ATTAAATTAAGA
1 AATATTAAAACAAAA-AAACATTAAATTAAGA
* *
45039 AATA-TAAAATAAAAAAACTTTAAATTAA
1 AATATTAAAACAAAAAAACATTAAATTAA
45067 AAGGATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.72
31 4 0.16
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (31 bp):
AATATTAAAACAAAAAAACATTAAATTAAGA
Found at i:46299 original size:9 final size:9
Alignment explanation
Indices: 46251--46304 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
46241 TGAAATATTA
46251 AAAATGAAAT
1 AAAAT-AAAT
* *
46261 GAAATGAAT
1 AAAATAAAT
46270 AAAATAAAT
1 AAAATAAAT
46279 AAAATAATAT
1 AAAATAA-AT
*
46289 AATATAAAT
1 AAAATAAAT
46298 AATAATA
1 AA-AATA
46305 TATGCTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (9 bp):
AAAATAAAT
Found at i:46398 original size:36 final size:36
Alignment explanation
Indices: 46332--46641 Score: 241
Period size: 36 Copynumber: 8.4 Consensus size: 36
46322 AAACTATATA
* * * *
46332 ATATATTACATGTTTTCAAAAACATTTTTTTAAGAAA-T
1 ATATATTATACGTTTTCAAAACCA---TTTTAAAAAACT
* *
46370 ATATATTATACGTTTTTAAAACCATTTTTTTAAAAAACC
1 ATATATTATACGTTTTCAAAACCA---TTTTAAAAAACT
* * * * *
46409 ATATACTATACATTTTCAAAATCATTTT-TAATACT
1 ATATATTATACGTTTTCAAAACCATTTTAAAAAACT
* * * * * *
46444 ATATTTTTTACATTTTCAAAATCATTTTAAAAAGCC
1 ATATATTATACGTTTTCAAAACCATTTTAAAAAACT
** * *
46480 ATATTATATATATATTTTGAAAACCGATTTT-AAAAATT
1 ATA-TAT-TATACGTTTTCAAAACC-ATTTTAAAAAACT
* * *
46518 ATATATCATACGTTTTCGAAACTATTTTAAAAAACT
1 ATATATTATACGTTTTCAAAACCATTTTAAAAAACT
*
46554 ATATATTATACGTTTTCAAAAACTATTTT-AAAAACT
1 ATATATTATACGTTTTC-AAAACCATTTTAAAAAACT
* *
46590 ATATATTATACGTTTTCAAAACTATTTCAAAAAACT
1 ATATATTATACGTTTTCAAAACCATTTTAAAAAACT
* *
46626 ATATTTTATATGTTTT
1 ATATATTATACGTTTT
46642 TTTTCCAAAA
Statistics
Matches: 224, Mismatches: 40, Indels: 18
0.79 0.14 0.06
Matches are distributed among these distances:
35 44 0.20
36 88 0.39
37 15 0.07
38 52 0.23
39 25 0.11
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (36 bp):
ATATATTATACGTTTTCAAAACCATTTTAAAAAACT
Found at i:46595 original size:72 final size:72
Alignment explanation
Indices: 46332--46641 Score: 284
Period size: 72 Copynumber: 4.2 Consensus size: 72
46322 AAACTATATA
* * *
46332 ATATATTACATGTTTTCAAAAACATTTTTTTAAGAAA-TATATATTATACGTTTTTAAAACCATT
1 ATATATTATATGTTTTCAAAAAC--TATTTTAA-AAACTATATATTATACGTTTTCAAAA-C--T
*
46396 TTTTTAAAAAACC
60 ATTTTAAAAAACC
* ** * * * * * *
46409 ATATACTATACATTTTCAAAATC-ATTTTTAATACTATATTTTTTACATTTTCAAAA-TCATTTT
1 ATATATTATATGTTTTCAAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACT-ATTTT
*
46472 AAAAAGCC
65 AAAAAACC
* * * * * * *
46480 ATATTATATATATATTTTGAAAACCGATTTTAAAAATTATATATCATACGTTTTCGAAACTATTT
1 ATA-TAT-TATATGTTTTCAAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACTATTT
*
46545 TAAAAAACT
64 TAAAAAACC
* *
46554 ATATATTATACGTTTTCAAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTCA
1 ATATATTATATGTTTTCAAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTA
*
46619 AAAAACT
66 AAAAACC
*
46626 ATATTTTATATGTTTT
1 ATATATTATATGTTTT
46642 TTTTCCAAAA
Statistics
Matches: 188, Mismatches: 39, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
70 1 0.01
71 14 0.07
72 73 0.39
73 19 0.10
74 62 0.33
75 1 0.01
77 18 0.10
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (72 bp):
ATATATTATATGTTTTCAAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTA
AAAAACC
Done.