Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024095.1 Corchorus olitorius cultivar O-4 contig24128, 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: 57919
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2384 original size:21 final size:21
Alignment explanation
Indices: 2358--2428 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
2348 TGCTAGGAGA
2358 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
2379 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
2400 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2421 TCATTGGA
1 TCATTGGA
2429 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:9508 original size:27 final size:27
Alignment explanation
Indices: 9434--9510 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
9424 AAGACAACTC
* *
9434 TTGATTCATGAAAAATCACAATATTAA
1 TTGATTCATGAATAATCACATTATTAA
*
9461 TTAATTCATGAATAATCACATTATTAA
1 TTGATTCATGAATAATCACATTATTAA
9488 TTGATTCATGAATAATCACATTA
1 TTGATTCATGAATAATCACATTA
9511 GTCATTAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (27 bp):
TTGATTCATGAATAATCACATTATTAA
Found at i:12300 original size:19 final size:18
Alignment explanation
Indices: 12272--12307 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12262 AGAATTAAAT
12272 TAAAAGAAAACATAAAAAC
1 TAAAAGAAAA-ATAAAAAC
*
12291 TAAAATAAAAATAAAAA
1 TAAAAGAAAAATAAAAA
12308 TAAGTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
TAAAAGAAAAATAAAAAC
Found at i:14844 original size:23 final size:24
Alignment explanation
Indices: 14809--14862 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
14799 TAAAATAAAA
*
14809 AAAAAAAAGAAGATCA-AACGAAA-T
1 AAAAATAAGAAGAT-AGAAC-AAATT
14833 AAAAATAA-AAGATAGAACAAATT
1 AAAAATAAGAAGATAGAACAAATT
14856 AAAAATA
1 AAAAATA
14863 GAAATTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.15
23 16 0.59
24 7 0.26
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAATAAGAAGATAGAACAAATT
Found at i:15062 original size:15 final size:16
Alignment explanation
Indices: 15034--15064 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
15024 GAGAGTGATC
15034 AAAGCAATTTAAATTA
1 AAAGCAATTTAAATTA
15050 AAAGCAA-TTAAATTA
1 AAAGCAATTTAAATTA
15065 TAAAAGCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAGCAATTTAAATTA
Found at i:17886 original size:59 final size:58
Alignment explanation
Indices: 17783--17912 Score: 224
Period size: 59 Copynumber: 2.2 Consensus size: 58
17773 GTACTCGATG
* * *
17783 GCACGACCTAGTGGGCATCCCTACACGAGCAATAAGAACGATCGAGCATCCCTCGGTC
1 GCACGGCCTAGTGGGCATCCCCACACGAGCAATAAGAACAATCGAGCATCCCTCGGTC
17841 GCACGGCCTAGTGGGCATCCCCCACACGAGCAATAAGAACAATCGAGCATCCCTCGGTC
1 GCACGGCCTAGTGGGCAT-CCCCACACGAGCAATAAGAACAATCGAGCATCCCTCGGTC
17900 GCACGGCCTAGTG
1 GCACGGCCTAGTG
17913 ATGCCTACAT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
58 17 0.25
59 51 0.75
ACGTcount: A:0.26, C:0.34, G:0.25, T:0.15
Consensus pattern (58 bp):
GCACGGCCTAGTGGGCATCCCCACACGAGCAATAAGAACAATCGAGCATCCCTCGGTC
Found at i:18468 original size:18 final size:18
Alignment explanation
Indices: 18435--18486 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
18425 AAAAAAGCGG
* *
18435 AGAGCACATGACGCCATA
1 AGAGCACACGATGCCATA
*
18453 AGAGCGCACGATGCCATA
1 AGAGCACACGATGCCATA
18471 AGAGCACACGATGCCA
1 AGAGCACACGATGCCA
18487 CGCTTTGGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.37, C:0.29, G:0.25, T:0.10
Consensus pattern (18 bp):
AGAGCACACGATGCCATA
Found at i:19112 original size:27 final size:27
Alignment explanation
Indices: 19074--19125 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
19064 AAGACAACTC
*
19074 TTGATTCATGAATAATCACATTATTAA
1 TTGATTAATGAATAATCACATTATTAA
19101 TTGATTAATGAATAATCACATTATT
1 TTGATTAATGAATAATCACATTATT
19126 CATTAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (27 bp):
TTGATTAATGAATAATCACATTATTAA
Found at i:19130 original size:23 final size:25
Alignment explanation
Indices: 19081--19132 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
19071 CTCTTGATTC
*
19081 ATGAATAATCACATTATTAATTGATTA
1 ATGAATAATCAC--TATTAATTCATTA
19108 ATGAATAATCAC-ATT-ATTCATTA
1 ATGAATAATCACTATTAATTCATTA
19131 AT
1 AT
19133 ATCTTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.38
24 3 0.12
27 12 0.50
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (25 bp):
ATGAATAATCACTATTAATTCATTA
Found at i:22752 original size:32 final size:33
Alignment explanation
Indices: 22696--22758 Score: 119
Period size: 32 Copynumber: 1.9 Consensus size: 33
22686 TTAGAAATTG
22696 CGGCGTTTCCGTACAAAAAACGCCACTATTTAT
1 CGGCGTTTCCGTACAAAAAACGCCACTATTTAT
22729 CGGCGTTTCCGTAC-AAAAACGCCACTATTT
1 CGGCGTTTCCGTACAAAAAACGCCACTATTT
22759 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (33 bp):
CGGCGTTTCCGTACAAAAAACGCCACTATTTAT
Found at i:28941 original size:21 final size:21
Alignment explanation
Indices: 28916--28955 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28906 TAAAACACAC
28916 TTAATCATAAATATAAAAAAT
1 TTAATCATAAATATAAAAAAT
28937 TTAATCATAAATATAAAAA
1 TTAATCATAAATATAAAAA
28956 TAGTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAATCATAAATATAAAAAAT
Found at i:29676 original size:20 final size:20
Alignment explanation
Indices: 29651--29690 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29641 TGAAACACAC
29651 TTAATCATAAATATAAAAAT
1 TTAATCATAAATATAAAAAT
29671 TTAATCATAAATATAAAAAT
1 TTAATCATAAATATAAAAAT
29691 AGTAAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAATCATAAATATAAAAAT
Found at i:30073 original size:22 final size:22
Alignment explanation
Indices: 30047--30093 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
30037 CCAATATAAC
* *
30047 ACATAATTAAAAGACATAATTA
1 ACATAATTAAAAGACAAAATCA
30069 ACATAATTAAAAGACAAAATCA
1 ACATAATTAAAAGACAAAATCA
30091 ACA
1 ACA
30094 AAATAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (22 bp):
ACATAATTAAAAGACAAAATCA
Found at i:32410 original size:2 final size:2
Alignment explanation
Indices: 32403--32439 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
32393 GCTCTACAAT
32403 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32440 ATTATCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32791 original size:181 final size:180
Alignment explanation
Indices: 32477--32838 Score: 634
Period size: 181 Copynumber: 2.0 Consensus size: 180
32467 CTAAAAATTA
* *
32477 TTAAATTTTCTAAACCTAATCCCTAATTTCCTCTTTTGCTCGAGCTCTCGCAACTCTCTTTCACT
1 TTAAATTTTCTAAACCTAATCCCTAATTCCCTCTTTTGCTCGACCTCTCGCAACTCTCTTTCACT
* *
32542 CTCTCCCTCCACCTCCTTCATTTTCAAATCCACGATGGTCGCCCCTCCGTTCGCCCACCGTCGAC
66 CTCTCCCACCACCTCCTTCATTTCCAAATCCACGATGGTCGCCCCTCCGTTCGCCCACCGTCGAC
*
32607 GGATCTTAATGCCTGAGACTTGAGGTATTCTTCCCCTTTCTTCTCCTTTC
131 GGATCTGAATGCCTGAGACTTGAGGTATTCTTCCCCTTTCTTCTCCTTTC
* *
32657 TTAAATTTTCATAAACCTAATCCCTAATTCCCTCTTTTGCTTGACCTCTCTCAACTCTCTTTCAC
1 TTAAATTTTC-TAAACCTAATCCCTAATTCCCTCTTTTGCTCGACCTCTCGCAACTCTCTTTCAC
*
32722 TCTCTCCCACCGCCTCCTTCATTTCCAAATCCACGATGGTCGCCCCTCCGTTCGCCCACCGTCGA
65 TCTCTCCCACCACCTCCTTCATTTCCAAATCCACGATGGTCGCCCCTCCGTTCGCCCACCGTCGA
*
32787 CGGATCTGAATGCCTGAGACTTGAGGTATTCTTCCCCTTTCTTCTCGTTTC
130 CGGATCTGAATGCCTGAGACTTGAGGTATTCTTCCCCTTTCTTCTCCTTTC
32838 T
1 T
32839 GGTAATAAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
180 10 0.06
181 162 0.94
ACGTcount: A:0.17, C:0.36, G:0.11, T:0.36
Consensus pattern (180 bp):
TTAAATTTTCTAAACCTAATCCCTAATTCCCTCTTTTGCTCGACCTCTCGCAACTCTCTTTCACT
CTCTCCCACCACCTCCTTCATTTCCAAATCCACGATGGTCGCCCCTCCGTTCGCCCACCGTCGAC
GGATCTGAATGCCTGAGACTTGAGGTATTCTTCCCCTTTCTTCTCCTTTC
Found at i:38437 original size:27 final size:27
Alignment explanation
Indices: 38405--38476 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
38395 AGTGATCCTA
*
38405 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACACGC
* **
38432 AAATGACCAAAATGCCCCTGGATGCGC
1 AAATGACCAAAATGCCCCTGAACACGC
*
38459 AAATGACTAAAATGCCCC
1 AAATGACCAAAATGCCCC
38477 CTAGGTGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACACGC
Found at i:38969 original size:30 final size:30
Alignment explanation
Indices: 38933--39487 Score: 577
Period size: 30 Copynumber: 18.9 Consensus size: 30
38923 AACTACAATG
* *
38933 ATGATCCTAAACTAGGATTAAAATAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * * * *
38963 ATGATCCTAAATCAGGATTGAAAGAAAGCT
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
38993 ACGATCCTCAACCAGGATTAACATAGAGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
*
39024 AT-ATCCTCAACCAGGATAAAAAT-AAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
**
39052 ATGATCCTCAACCAGGATTAAAATGGAGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
**
39083 AT-ATCCTCAACCAGGATTAAAATGGAGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
**
39113 AT-ATCCTCAATTAGGATTAAAATAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
39142 ACGATCCTCAACCAGGATTAAAATAATGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
39172 ACGATCCTCAACCAGGATTAAAACAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
39202 ACGATCCTCAACCAGGATTAAAACAAAGTA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
39232 ACGATCCTCAACCAGGATTAAAATAAAGTA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
39262 ACGATCCTCAACCAGGATTAAAATGATGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
39293 AT-ATCCTCAACCAGGATTAAAAT-AA-C-
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
39319 --GATCCTCAACCAGGATTAAAATAAAGTA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * * *
39347 ACGATCCTCAACCACGATTAAAATGATGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
39378 AT-ATCCTCAACCAGGATTAAAAT-AA-C-
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
39404 --GATCCTTAACCAGGATTAAAATAAAGTA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * * *
39432 ACGATCCCCAACCAGGATTAAAATGATGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
39463 AT-ATCCTCAACCAGGATTAAAATAA
1 ATGATCCTCAACCAGGATTAAAATAA
39488 CGATAAAAAT
Statistics
Matches: 451, Mismatches: 54, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
25 41 0.09
26 4 0.01
28 5 0.01
29 27 0.06
30 364 0.81
31 10 0.02
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (30 bp):
ATGATCCTCAACCAGGATTAAAATAAAGCA
Found at i:39358 original size:85 final size:85
Alignment explanation
Indices: 38965--39491 Score: 673
Period size: 85 Copynumber: 6.0 Consensus size: 85
38955 ATAAAGCAAT
* * * * *
38965 GATCCTAAATCAGGATTGAAAGAAAGCT-ACGATCCTCAACCAGGATTAACATAGA-GCAAATAT
1 GATCCTCAACCAGGATTAAAATAAAG-TAACGATCCTCAACCAGGATTAAAAT-GATGCAAATAT
*
39028 CCTCAACCAGGATAAAAATAAGC
64 CCTCAACCAGGATTAAAATAA-C
** * **
39051 AATGATCCTCAACCAGGATTAAAATGGAGCAAATATCCTCAACCAGGATTAAAATGGA-GCAAAT
1 ---GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAAT-GATGCAAAT
**
39115 ATCCTCAATTAGGATTAAAATAAAGCAAC
62 ATCCTCAACCAGGATTAAAAT-----AAC
* * ** * **
39144 GATCCTCAACCAGGATTAAAATAATGCAACGATCCTCAACCAGGATTAAAACAAAGCAACGATCC
1 GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAATGATGCAAATATCC
39209 TCAACCAGGATTAAAACAAAGTAAC
66 TCAACCAGGATT---A-AAA-TAAC
39234 GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAATGATGCAAATATCC
1 GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAATGATGCAAATATCC
39299 TCAACCAGGATTAAAATAAC
66 TCAACCAGGATTAAAATAAC
*
39319 GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCACGATTAAAATGATGCAAATATCC
1 GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAATGATGCAAATATCC
39384 TCAACCAGGATTAAAATAAC
66 TCAACCAGGATTAAAATAAC
* *
39404 GATCCTTAACCAGGATTAAAATAAAGTAACGATCCCCAACCAGGATTAAAATGATGCAAATATCC
1 GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAATGATGCAAATATCC
39469 TCAACCAGGATTAAAATAAC
66 TCAACCAGGATTAAAATAAC
39489 GAT
1 GAT
39492 AAAAATAGAA
Statistics
Matches: 390, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
85 173 0.44
86 3 0.01
87 1 0.00
89 68 0.17
90 137 0.35
93 2 0.01
94 5 0.01
95 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (85 bp):
GATCCTCAACCAGGATTAAAATAAAGTAACGATCCTCAACCAGGATTAAAATGATGCAAATATCC
TCAACCAGGATTAAAATAAC
Found at i:39823 original size:73 final size:72
Alignment explanation
Indices: 39699--39928 Score: 313
Period size: 73 Copynumber: 3.2 Consensus size: 72
39689 CAATTTGCGG
** *
39699 TCAACTGAAATAAA-CTGCCGAAAAGATCGCCCTAGATCAACTGGAATAAACTGAAGAAAAGGAT
1 TCAACTGAAATAAATC-GAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTGAAG-AAAGGAT
39763 CGCCCTGGA
64 CGCCCTGGA
* * *
39772 TCCATTGAAATAAATCGAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTAAAGAAAGAGATC
1 TCAACTGAAATAAATCGAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAG-GATC
39837 GCCCTGGA
65 GCCCTGGA
* * * * *
39845 TCAACTGAAATAAATTGAAG-AAAGATCGCCCTGGATCAATTAAAATAAACTGAATAAA-GATCG
1 TCAACTGAAATAAATCGAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAGGATCG
39908 CCCTGGA
66 CCCTGGA
39915 TCAACTGAAATAAA
1 TCAACTGAAATAAA
39929 CTGAATAAGG
Statistics
Matches: 141, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
70 26 0.18
72 37 0.26
73 77 0.55
74 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (72 bp):
TCAACTGAAATAAATCGAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAGGATCG
CCCTGGA
Found at i:39878 original size:35 final size:36
Alignment explanation
Indices: 39699--39969 Score: 316
Period size: 35 Copynumber: 7.6 Consensus size: 36
39689 CAATTTGCGG
** *
39699 TCAACTGAAATAAACTGCCGAAAAGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
39735 TCAACTGGAATAAACTGAAGAAAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAA-GATCGCCCTGGA
* * *
39772 TCCATTGAAATAAA-TCGAAGAAAAGATCGCCCTAGA
1 TCAACTGAAATAAACT-GAAGAAAAGATCGCCCTGGA
*
39808 TCAACTGAAATAAACTAAAGAAAGAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-AGATCGCCCTGGA
*
39845 TCAACTGAAATAAATTGAAG-AAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
39880 TCAATTAAAATAAACTGAA-TAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * * *
39915 TCAACTGAAATAAACTGAA-TAAGGACCACCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
**
39950 TCAACTGAAACGAACTGAAG
1 TCAACTGAAATAAACTGAAG
39970 CATCTGAAAT
Statistics
Matches: 204, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
35 90 0.44
36 53 0.26
37 61 0.30
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (36 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
Found at i:39966 original size:70 final size:70
Alignment explanation
Indices: 39699--39968 Score: 218
Period size: 73 Copynumber: 3.8 Consensus size: 70
39689 CAATTTGCGG
** * * * ** * *
39699 TCAACTGAAATAAACTGCCGAAAAGATCGCCCTAGATCAACTGGAATAAACTGAAGAAAAGGATC
1 TCAACTGAAATAAACTGAAG-AAAGACCACCCTGGATCAACTAAAACAAACTGAA-TAAA-GATC
39764 GCCCTGGA
63 GCCCTGGA
* * * * * * * * *
39772 TCCATTGAAATAAA-TCGAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTAAAGAAAGAGAT
1 TCAACTGAAATAAACT-GAAG-AAAGACCACCCTGGATCAACTAAAACAAACTGAA-TAA-AGAT
39836 CGCCCTGGA
62 CGCCCTGGA
* * * * *
39845 TCAACTGAAATAAATTGAAGAAAGATCGCCCTGGATCAATTAAAATAAACTGAATAAAGATCGCC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTGGATCAACTAAAACAAACTGAATAAAGATCGCC
39910 CTGGA
66 CTGGA
* * * * *
39915 TCAACTGAAATAAACTGAATAAGGACCACCCTGGGTCAACTGAAACGAACTGAA
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTGGATCAACTAAAACAAACTGAA
39969 GCATCTGAAA
Statistics
Matches: 171, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
70 57 0.33
71 2 0.01
72 31 0.18
73 79 0.46
74 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (70 bp):
TCAACTGAAATAAACTGAAGAAAGACCACCCTGGATCAACTAAAACAAACTGAATAAAGATCGCC
CTGGA
Found at i:41950 original size:2 final size:2
Alignment explanation
Indices: 41943--41973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41933 GAACAGTAGA
41943 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 A
41974 ATGGAAAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48196 original size:10 final size:11
Alignment explanation
Indices: 48177--48201 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48167 CAGTGTGCTC
48177 TTTTGTTTTTT
1 TTTTGTTTTTT
48188 TTTTGTTTTTT
1 TTTTGTTTTTT
48199 TTT
1 TTT
48202 AAACTGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:49937 original size:27 final size:27
Alignment explanation
Indices: 49905--49976 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
49895 AGTGACACTA
*
49905 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACACGC
* **
49932 AAATGACCAAAATGCCCCTGGATGCGC
1 AAATGACCAAAATGCCCCTGAACACGC
*
49959 AAATGACTAAAATGCCCC
1 AAATGACCAAAATGCCCC
49977 CTAGGTGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACACGC
Found at i:52881 original size:19 final size:18
Alignment explanation
Indices: 52848--52883 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52838 TCGAAATAAT
52848 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
52866 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
52884 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:55262 original size:19 final size:18
Alignment explanation
Indices: 55229--55266 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
55219 TTGAAATAAT
55229 TCTTCAAAAATCTTCAAA
1 TCTTCAAAAATCTTCAAA
*
55247 TCTTCAAATTATCTTCAAA
1 TCTTCAAA-AATCTTCAAA
55266 T
1 T
55267 GGTCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAA
Done.