Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000952.1 Hibiscus syriacus cultivar Beakdansim tig00001906_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: 64793
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1484 original size:38 final size:36
Alignment explanation
Indices: 1394--1497 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 36
1384 GTGCTCACCA
1394 TTGTCTCTCTTGAGACAGTTT-CCTTGAAAC-AACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
1428 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA-CT
* * *
1466 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1498 TAAACATTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 21 0.34
35 9 0.15
37 3 0.05
38 29 0.47
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:1560 original size:36 final size:36
Alignment explanation
Indices: 1513--1598 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
1503 ATTGAAAACA
** * * *
1513 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
1549 TTTCCCTTGAAACAAATTTTTTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
1585 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1599 TAAACTTGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:1593 original size:101 final size:102
Alignment explanation
Indices: 1427--1867 Score: 627
Period size: 101 Copynumber: 4.3 Consensus size: 102
1417 TTGAAACAAC
*
1427 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTTCTCCCTTGAGACAGTTTCTCTT
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTTTTCTCCCTTGAGACAGTTTCTCTT
*
1492 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
65 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
1530 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
*
1594 AAACATAAAC-TTGGAAACATTTCCCTTGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
* *
1630 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCCTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
*
1695 AAACATAAACATTGAAAACATTTCCCTAGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
* * * **
1732 TTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAACTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
* * * ** * **
1796 AAACACAAAACCTTTGAGATTATTTCCCTCGAAACAAAT
66 AAACA-TAAA-CATTGAAAACATTTCCCTTGAAATGAAT
* * * *
1835 TTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1868 CAAAATCTTT
Statistics
Matches: 306, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
100 56 0.18
101 112 0.37
102 60 0.20
103 78 0.25
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
Found at i:1680 original size:37 final size:37
Alignment explanation
Indices: 1613--1699 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
1603 CTTGGAAACA
** * * *
1613 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
1649 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
1686 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
1700 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 12 0.27
37 30 0.68
38 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
Found at i:1769 original size:36 final size:36
Alignment explanation
Indices: 1714--1867 Score: 104
Period size: 36 Copynumber: 4.4 Consensus size: 36
1704 CATTGAAAAC
* ** * *
1714 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
1750 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* * ** **
1786 ACTTCTCTTGAAACACAA-AAC--CT---TTGAGATT
1 ATTTCCCTTGAAACA-AATTTCGTCTCCCTTGAGACA
* * *
1817 ATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
1853 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
1868 CAAAATCTTT
Statistics
Matches: 86, Mismatches: 25, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
30 2 0.02
31 18 0.21
33 2 0.02
34 2 0.02
36 60 0.70
37 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:1850 original size:67 final size:67
Alignment explanation
Indices: 1742--1879 Score: 222
Period size: 67 Copynumber: 2.1 Consensus size: 67
1732 TTCGTCTCTC
* *
1742 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAAAC
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
1807 CT
66 CT
* ** *
1809 TTGAGATTATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
1874 CT
66 CT
1876 TTGA
1 TTGA
1880 ATTTATCTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (67 bp):
TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
CT
Found at i:1891 original size:67 final size:67
Alignment explanation
Indices: 1742--1900 Score: 221
Period size: 67 Copynumber: 2.4 Consensus size: 67
1732 TTCGTCTCTC
* * *
1742 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAAAC
1 TTGAGATTATCTCCCTTGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
1807 CT
66 CT
* * ** *
1809 TTGAGATTATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTATCTCCCTTGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
1874 CT
66 CT
*
1876 TTGA-ATTTATCTCCCTTAAAACAAA
1 TTGAGA-TTATCTCCCTTGAAACAAA
1901 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 1 0.01
67 81 0.99
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (67 bp):
TTGAGATTATCTCCCTTGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
CT
Found at i:3197 original size:105 final size:105
Alignment explanation
Indices: 2727--3698 Score: 1423
Period size: 105 Copynumber: 9.3 Consensus size: 105
2717 GCCATCCGCG
* * * * * *
2727 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
2792 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAAC-AACAACTTTC-CAATCTCAGAGCCA
*
2836 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
2901 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAA-CAACAACTTT-CCAATCTCAGAGCCA
*
2943 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3008 ACCGCTGGTTGTCAAC-ACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
3047 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
3112 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
* *
3152 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3217 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
3257 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3322 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCC-
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
* *
3361 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
3426 ACCGCTGTTTATCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
**
3466 ATTTCAACTTCACAACGAAATATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
3531 ACCGCTGCTTGTCAAC-A-AA-TTT-C-AT-TCAGATTCA
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
* * *
3565 ATTTCAACTTCACAAC---GGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
3627 ACGGCTGGTTGTCAACAAACAA-TTTCCCGGT-TCCAGAGCCA
66 ACCGCTGGTTGTCAAC-AACAACTTT-CCAATCT-CAGAGCCA
* *
3668 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
3699 TGGAACAATG
Statistics
Matches: 799, Mismatches: 49, Indels: 33
0.91 0.06 0.04
Matches are distributed among these distances:
96 55 0.07
98 1 0.00
99 27 0.03
100 2 0.00
101 2 0.00
102 4 0.01
103 23 0.03
104 194 0.24
105 305 0.38
106 66 0.08
107 97 0.12
108 1 0.00
109 22 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
Found at i:3367 original size:209 final size:210
Alignment explanation
Indices: 2727--3698 Score: 1414
Period size: 209 Copynumber: 4.6 Consensus size: 210
2717 GCCATCCGCG
* * * * * *
2727 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
2792 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
63 GGGACCGCTGGTTGTCAAC-AACAACTTTC-CAATCTCAGAGCCAATTTCAACTTCACAACGAAG
* *
2856 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAAC
126 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAAC
* *
2921 AATTTTCCCAATTTCAGAGCCA
190 AA-CTTCCCAATCTCAGAGCCA
*
2943 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3008 ACCGCTGGTTGTCAAC-ACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
3072 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTT
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
3137 CCAATCTCAGAGCCA
196 CCAATCTCAGAGCCA
* *
3152 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3217 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
3282 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
3347 CCAATCTCAGAGCC-
196 CCAATCTCAGAGCCA
* *
3361 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * **
3426 ACCGCTGTTTATCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAATATAT
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
3491 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-A-AA-TT-
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
* **
3552 TC-AT-TCAGATTCA
196 CCAATCTCAGAGCCA
* * *
3565 ATTTCAACTTCACAAC---GGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* ** * *
3627 ACGGCTGGTTGTCAACAAACAA-TTTCCCGGT-TCCAGAGCCAATTTCAACTTCACGACGGAGGA
66 ACCGCTGGTTGTCAAC-AACAACTTT-CCAATCT-CAGAGCCAATTTCAACTTCACAACGAAGGA
3690 TATTGGACT
128 TATTGGACT
3699 TGGAACAATG
Statistics
Matches: 701, Mismatches: 49, Indels: 26
0.90 0.06 0.03
Matches are distributed among these distances:
201 57 0.08
202 43 0.06
203 6 0.01
204 17 0.02
205 1 0.00
206 2 0.00
207 2 0.00
208 1 0.00
209 270 0.39
210 130 0.19
211 97 0.14
212 2 0.00
213 49 0.07
214 3 0.00
216 21 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (210 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
CCAATCTCAGAGCCA
Found at i:3367 original size:314 final size:313
Alignment explanation
Indices: 2727--3698 Score: 1453
Period size: 314 Copynumber: 3.1 Consensus size: 313
2717 GCCATCCGCG
* * * * * *
2727 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
2792 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
63 GGGACCGCTGGTTGTCAAC-AACAACTTTC-CAATCTCAGAGCCAATTTCAACTTCACAACGAAG
* * *
2856 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAAC
126 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAAC
*
2921 AATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
190 AA-TTT-CCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
2986 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-ACAACTTCCCAATCTCAGAGCCA
252 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
3047 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
3112 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
3177 TGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTT
3242 CCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
195 CCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
3307 CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCC-
259 CTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
3361 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * **
3426 ACCGCTGTTTATCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAATATAT
66 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
3491 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-A-AATTT-
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTC
** * *
3553 C-ATTCAGATTCAATTTCAACTTCACAAC---GGATATTGGACTCGAGACAACACAAGTTCAACT
196 CAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * **
3614 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGT-TCCAGAGCCA
261 TCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCA
* *
3668 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
3699 TGGAACAATG
Statistics
Matches: 609, Mismatches: 37, Indels: 25
0.91 0.06 0.04
Matches are distributed among these distances:
305 59 0.10
306 18 0.03
307 28 0.05
308 23 0.04
309 2 0.00
310 1 0.00
311 3 0.00
312 2 0.00
313 2 0.00
314 269 0.44
315 30 0.05
316 95 0.16
317 52 0.09
318 3 0.00
320 22 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (313 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTC
CAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:4711 original size:17 final size:18
Alignment explanation
Indices: 4685--4724 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4675 TTATTATGGA
4685 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
4701 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
4719 TATTAT
1 TATTAT
4725 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:4729 original size:2 final size:2
Alignment explanation
Indices: 4722--4775 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
4712 ATGTTATTAT
4722 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4763 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
4776 TAATTATTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5246 original size:2 final size:2
Alignment explanation
Indices: 5239--5266 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5229 TAATACTTTG
5239 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
5267 TTTCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5341 original size:14 final size:16
Alignment explanation
Indices: 5311--5344 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
5301 CTTTACTATT
5311 TTTTATCTTACTTTTA
1 TTTTATCTTACTTTTA
5327 TTTTAT-TTA-TTTTA
1 TTTTATCTTACTTTTA
5341 TTTT
1 TTTT
5345 TTCCTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 3 0.17
16 6 0.33
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATCTTACTTTTA
Found at i:6060 original size:21 final size:21
Alignment explanation
Indices: 6034--6077 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6024 TAGTTTAGTA
6034 TCCCACAAATATAAGCCTTCT
1 TCCCACAAATATAAGCCTTCT
6055 TCCCACAAATATAAGCCTTCT
1 TCCCACAAATATAAGCCTTCT
6076 TC
1 TC
6078 ACTATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.30
Consensus pattern (21 bp):
TCCCACAAATATAAGCCTTCT
Found at i:8263 original size:23 final size:23
Alignment explanation
Indices: 8237--8305 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
8227 CACCACAGCT
*
8237 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
8260 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
8283 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
8306 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:14945 original size:20 final size:20
Alignment explanation
Indices: 14908--14947 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
14898 ACCGAGACAT
* *
14908 GTCCCTACACGTAGCAAGAC
1 GTCCCTACACGCAACAAGAC
*
14928 GTCCCTACATGCAACAAGAC
1 GTCCCTACACGCAACAAGAC
14948 ATGATTTTTA
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:0.33, C:0.35, G:0.17, T:0.15
Consensus pattern (20 bp):
GTCCCTACACGCAACAAGAC
Found at i:24161 original size:29 final size:28
Alignment explanation
Indices: 24041--24286 Score: 157
Period size: 29 Copynumber: 8.5 Consensus size: 28
24031 TATTGTAAGT
*
24041 TTAAAAATATATTTTATTTTCTTATCCAAC
1 TTAAAAATATATTTTATTTT-TTAT-TAAC
*
24071 TTATTAAATATA-TTTATTTTTTA-T---
1 TTA-AAAATATATTTTATTTTTTATTAAC
* * * *
24095 TTAAAAA-ATGTTTTATTCTTATCTTATC
1 TTAAAAATATATTTTATT-TTTTATTAAC
*
24123 TTTAAATATATATTTTATTTTTTATTAAC
1 -TTAAAAATATATTTTATTTTTTATTAAC
* * *
24152 TT-AAAATATATATTTCTTATATATTAAC
1 TTAAAAATATAT-TTTATTTTTTATTAAC
*
24180 TT-TAAATATATTTTATTCTTTTATTAAC
1 TTAAAAATATATTTTATT-TTTTATTAAC
* * *
24208 TTAAAAATATATTTTGTTATTATCTTAAC
1 TTAAAAATATATTTTATT-TTTTATTAAC
24237 TTCAAATATATACATATATATTATTTTTTATTAAC
1 TT-AAA-A-AT--ATAT-T-TTATTTTTTATTAAC
* *
24272 TTAAAATTGTATTTT
1 TTAAAAATATATTTT
24287 TTATTATTAC
Statistics
Matches: 168, Mismatches: 29, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
22 2 0.01
23 9 0.05
24 6 0.04
25 1 0.01
27 13 0.08
28 37 0.22
29 40 0.24
30 26 0.15
31 8 0.05
32 3 0.02
33 1 0.01
34 7 0.04
35 11 0.07
36 4 0.02
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (28 bp):
TTAAAAATATATTTTATTTTTTATTAAC
Found at i:24171 original size:24 final size:24
Alignment explanation
Indices: 24138--24235 Score: 90
Period size: 24 Copynumber: 3.8 Consensus size: 24
24128 ATATATATTT
24138 TATTTTTTATTAACTTAAAATATA
1 TATTTTTTATTAACTTAAAATATA
*
24162 TATTTCTTATATATTAACTTTAAATATATTT
1 TA-TT-TT-T-TATTAAC-TTAAA-ATA-TA
24193 TATTCTTTTATTAACTTAAAA-ATA
1 TATT-TTTTATTAACTTAAAATATA
*
24217 TATTTTGTTATTATCTTAA
1 TATTTT-TTATTAACTTAA
24236 CTTCAAATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
23 2 0.03
24 18 0.29
25 3 0.05
26 3 0.05
27 6 0.10
28 14 0.22
29 6 0.10
30 8 0.13
31 3 0.05
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (24 bp):
TATTTTTTATTAACTTAAAATATA
Found at i:24176 original size:28 final size:29
Alignment explanation
Indices: 24126--24248 Score: 128
Period size: 28 Copynumber: 4.3 Consensus size: 29
24116 TCTTATCTTT
* * *
24126 AAATATATATTTTATTTTTTATTAACTTA
1 AAATATATATTTTCTTATATATTAACTTA
*
24155 AAATATATA-TTTCTTATATATTAACTTT
1 AAATATATATTTTCTTATATATTAACTTA
*
24183 AAATATATTTTATTCTT-T-TATTAACTTA
1 AAATATATATT-TTCTTATATATTAACTTA
* * *
24211 AAA-ATATATTTTGTTATTATCTTAACTTC
1 AAATATATATTTTCTTA-TATATTAACTTA
24240 AAATATATA
1 AAATATATA
24249 CATATATATT
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
26 4 0.05
27 6 0.08
28 36 0.46
29 22 0.28
30 10 0.13
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.54
Consensus pattern (29 bp):
AAATATATATTTTCTTATATATTAACTTA
Found at i:24183 original size:57 final size:57
Alignment explanation
Indices: 24122--24301 Score: 192
Period size: 56 Copynumber: 3.1 Consensus size: 57
24112 CTTATCTTAT
24122 CTTTAAATATATATTTTATTTTTTATTAACTTAAAATATATATTTCTTATATATTAA
1 CTTTAAATATATATTTTATTTTTTATTAACTTAAAATATATATTTCTTATATATTAA
* *
24179 CTTT-AA-ATATATTTTATTCTTTTATTAACTTAAAA-ATATATTTTGTTATTATCTTAA
1 CTTTAAATATATATTTTATT-TTTTATTAACTTAAAATATATA-TTTCTTA-TATATTAA
* * *
24236 CTTCAAATATATACATATATATTATTTTTTATTAACTTAAAAT-TGTATTTTTTAT-TATT-A
1 CTT-TAA-ATAT--ATAT-T-TTATTTTTTATTAACTTAAAATATATATTTCTTATATATTAA
24296 CTTTAA
1 CTTTAA
24302 GTTAAAAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
55 17 0.16
56 24 0.23
57 14 0.13
59 3 0.03
60 5 0.05
61 5 0.05
62 1 0.01
63 10 0.10
64 20 0.19
65 5 0.05
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.56
Consensus pattern (57 bp):
CTTTAAATATATATTTTATTTTTTATTAACTTAAAATATATATTTCTTATATATTAA
Found at i:24189 original size:55 final size:57
Alignment explanation
Indices: 24130--24247 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 57
24120 ATCTTTAAAT
*
24130 ATATATTTTATT-TTTTATTAACTT-AAAATATATATTTCTTA-TATATTAACTTTAA
1 ATATATTTTATTCTTTTATTAACTTAAAAATATAT-TTTCTTATTATATTAACTTCAA
* *
24185 ATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTATTATCTTAACTTCAA
1 ATATATTTTATTCTTTTATTAACTTAAAAATATATTTTCTTATTATATTAACTTCAA
24242 ATATAT
1 ATATAT
24248 ACATATATAT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
55 12 0.21
56 18 0.32
57 27 0.47
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (57 bp):
ATATATTTTATTCTTTTATTAACTTAAAAATATATTTTCTTATTATATTAACTTCAA
Found at i:24409 original size:57 final size:56
Alignment explanation
Indices: 24297--24443 Score: 140
Period size: 59 Copynumber: 2.5 Consensus size: 56
24287 TTATTATTAC
* * *
24297 TTTAAGTTAAAAAAAAGAATAAAATATACTATTTGAAGATAAGTTAATAAAAAAT-ATT
1 TTTAAGTT--AAAAAAGAATAAAATATA-TTTTTAAAGATAAGATAATAAAAAATAATT
24355 TTTAAGTTAATAAAAGAATAAAATATATTTTTAAAG-TCAAGATAA-AAATTAAATACATT
1 TTTAAGTTAA-AAAAGAATAAAATATATTTTTAAAGAT-AAGATAATAAA--AAATA-ATT
*
24414 TTAAAGTTAGAATAAA-AATAAAATATATTT
1 TTTAAGTTA-AA-AAAGAATAAAATATATTT
24444 AATAAGTTGA
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
55 4 0.05
56 15 0.19
57 20 0.26
58 8 0.10
59 26 0.34
60 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (56 bp):
TTTAAGTTAAAAAAGAATAAAATATATTTTTAAAGATAAGATAATAAAAAATAATT
Found at i:24470 original size:31 final size:30
Alignment explanation
Indices: 24363--24474 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 30
24353 TTTTTAAGTT
* * *
24363 AATAAAAGAATAAAATATATTTTTAAAGTCA-
1 AATAAAA-ATTAAAATATA-TTTAAAAGTTAG
* *
24394 AGATAAAAATT-AAATACATTTTAAAGTTAG
1 A-ATAAAAATTAAAATATATTTAAAAGTTAG
24424 AATAAAAA-TAAAATATATTTAATAAGTT-G
1 AATAAAAATTAAAATATATTTAA-AAGTTAG
24453 AATAAAAAGTTAAAATATATTT
1 AATAAAAA-TTAAAATATATTT
24475 TTTCTTGCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.01
29 36 0.51
30 12 0.17
31 15 0.21
32 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (30 bp):
AATAAAAATTAAAATATATTTAAAAGTTAG
Found at i:31046 original size:21 final size:21
Alignment explanation
Indices: 30988--31047 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
30978 TGATCGTTAT
** *
30988 AATATTAACGCGATAATT-AC
1 AATATTAACATGATGATTAAC
*
31008 AATATTAATATGGA-GATTAAC
1 AATATTAACAT-GATGATTAAC
31029 AATATTAACATGATGATTA
1 AATATTAACATGATGATTA
31048 CCATGGTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
AATATTAACATGATGATTAAC
Found at i:39204 original size:21 final size:21
Alignment explanation
Indices: 39179--39221 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39169 GGAAATGTTA
*
39179 AAAAACATTAATGTTTTAGGT
1 AAAAACAATAATGTTTTAGGT
*
39200 AAAAATAATAATGTTTTAGGT
1 AAAAACAATAATGTTTTAGGT
39221 A
1 A
39222 TTTTTACCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (21 bp):
AAAAACAATAATGTTTTAGGT
Found at i:39911 original size:2 final size:2
Alignment explanation
Indices: 39899--39968 Score: 124
Period size: 2 Copynumber: 35.0 Consensus size: 2
39889 AAGTATCAAA
39899 AT AT AT CAT 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
39942 AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39969 TAAATCAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 63 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40339 original size:201 final size:197
Alignment explanation
Indices: 40097--40494 Score: 706
Period size: 201 Copynumber: 2.0 Consensus size: 197
40087 CATTTTAAAA
40097 ATTAAAATAATATATTTGAATCAAAGGATTAGAATCTATAAATACTTTTGAATAATTAATAAAAA
1 ATTAAAATAATATATTTGAATCAAAGGATTAGAATCTATAAATACTTTTGAATAATTAATAAAAA
*
40162 TATTAATATTAAAGATCATAATTTATTTTTTAATGAATCATGACATTCTTGACGAAACCTAAAAC
66 TATTAATATTAAAGATCATAATTTATTTTTTAATGAACCATGACATTCTTGACGAAACCTAAAAC
* *
40227 GTTAATCGTATCCATAACATTTATCGATTATAACTCATTTTCCATGTGCAAAGATTGAATCATAG
131 GTTAATCGTATCCATAACATTTATCGACTATAACTCATTTTCCATGTGCAAAGATTGAACCATAG
40292 AT
196 AT
40294 ATTAAAATAATATATTTGAATCAATCAAAGGATTAGAATCTATAAATACTTTTGAATAATTAATA
1 ATTAAAATAATATATTTG----AATCAAAGGATTAGAATCTATAAATACTTTTGAATAATTAATA
*
40359 AAAATATTAATATTAAAGATCATAATTTATTTTTTAATGAACCATGACGTTCTTGACGAAACCTA
62 AAAATATTAATATTAAAGATCATAATTTATTTTTTAATGAACCATGACATTCTTGACGAAACCTA
* *
40424 AAATGTTAATCGTATCCATAACATTTATCGACTATAACTCATTTTCCATGTGTAAAGATTGAACC
127 AAACGTTAATCGTATCCATAACATTTATCGACTATAACTCATTTTCCATGTGCAAAGATTGAACC
40489 ATAGAT
192 ATAGAT
40495 TGAAAGATTA
Statistics
Matches: 191, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
197 18 0.09
201 173 0.91
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (197 bp):
ATTAAAATAATATATTTGAATCAAAGGATTAGAATCTATAAATACTTTTGAATAATTAATAAAAA
TATTAATATTAAAGATCATAATTTATTTTTTAATGAACCATGACATTCTTGACGAAACCTAAAAC
GTTAATCGTATCCATAACATTTATCGACTATAACTCATTTTCCATGTGCAAAGATTGAACCATAG
AT
Found at i:40791 original size:53 final size:52
Alignment explanation
Indices: 40695--40799 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 52
40685 AGTTTTCATC
*
40695 GAATTTAATATAATTAGTGTTTTTTATCATTCAGCTGTTAAATATTTAACGG
1 GAATTTAATATAATTAGTGTTTTTTATCATTCAGCTATTAAATATTTAACGG
*
40747 GAATTTATTATAATTAGTGTTTTTTTATCATTCAGCTATTAAATATTTAACGG
1 GAATTTAATATAATTAGTG-TTTTTTATCATTCAGCTATTAAATATTTAACGG
40800 TGTTAAAACG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 18 0.36
53 32 0.64
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (52 bp):
GAATTTAATATAATTAGTGTTTTTTATCATTCAGCTATTAAATATTTAACGG
Found at i:41046 original size:20 final size:21
Alignment explanation
Indices: 40985--41047 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
40975 TGTCGTCTGA
*
40985 TTCATTCGTACCTACCTTAAT
1 TTCATTTGTACCTACCTTAAT
* * *
41006 TTCATTTGTGCCCACCCTAAT
1 TTCATTTGTACCTACCTTAAT
41027 TT-ATTTGTACCTACCTTAAT
1 TTCATTTGTACCTACCTTAAT
41047 T
1 T
41048 GATCTTGATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.22, C:0.27, G:0.06, T:0.44
Consensus pattern (21 bp):
TTCATTTGTACCTACCTTAAT
Found at i:44526 original size:21 final size:21
Alignment explanation
Indices: 44502--44541 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44492 TATTTGAATT
*
44502 AATTAATATATATCAAACACA
1 AATTAATAAATATCAAACACA
*
44523 AATTTATAAATATCAAACA
1 AATTAATAAATATCAAACA
44542 TAATATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATATCAAACACA
Found at i:49032 original size:12 final size:12
Alignment explanation
Indices: 49005--49035 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
48995 TGTAATTATA
49005 AAAAAATAAAAT
1 AAAAAATAAAAT
49017 -AAAAATAAAAT
1 AAAAAATAAAAT
49028 AAAAAATA
1 AAAAAATA
49036 TTTAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:49433 original size:29 final size:29
Alignment explanation
Indices: 49396--49454 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
49386 AATAATTTAT
49396 ATTTATATTTTTAGTTAATTTGTAATTAC
1 ATTTATATTTTTAGTTAATTTGTAATTAC
49425 ATTTATATTTTTAGTTAATTTGTAATTAC
1 ATTTATATTTTTAGTTAATTTGTAATTAC
49454 A
1 A
49455 CATCTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (29 bp):
ATTTATATTTTTAGTTAATTTGTAATTAC
Found at i:50925 original size:18 final size:18
Alignment explanation
Indices: 50898--50937 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50888 AGTAAGTTCA
* *
50898 AATTAGATAAGATATCTT
1 AATTAGATAAGAAATATT
*
50916 AATTATATAAGAAATATT
1 AATTAGATAAGAAATATT
50934 AATT
1 AATT
50938 TATTCAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (18 bp):
AATTAGATAAGAAATATT
Found at i:61909 original size:2 final size:2
Alignment explanation
Indices: 61902--61936 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61892 CCATGTTTGC
61902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61937 AGCAATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.