Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011235.1 Corchorus capsularis cultivar CVL-1 contig11256, 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: 17435
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3622 original size:21 final size:21
Alignment explanation
Indices: 3594--3647 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3584 ACTAGCGCTG
3594 GGCG-CCCATGTGGTAAGCCT
1 GGCGCCCCATGTGGTAAGCCT
**
3614 GGCGCCCCA-GCTGGTTTGCCT
1 GGCGCCCCATG-TGGTAAGCCT
*
3635 CGCGCCCCATGTG
1 GGCGCCCCATGTG
3648 CTCCAGTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.09, C:0.37, G:0.33, T:0.20
Consensus pattern (21 bp):
GGCGCCCCATGTGGTAAGCCT
Found at i:4062 original size:35 final size:35
Alignment explanation
Indices: 3998--4125 Score: 132
Period size: 35 Copynumber: 3.7 Consensus size: 35
3988 GGTCTGATCA
* * *
3998 ATCTTCAAAGTTGGTTTCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGGATTCAGATAACTCGGTGCAGC
* * *
4033 ATCTTCAAAATTGGATTCGGATAAGTCGGTGCAGC
1 ATCTTCAAAGTTGGATTCAGATAACTCGGTGCAGC
* * * * *
4068 ATATTTAAAGTTGGATTAAGATGACTCGGTGAAGC
1 ATCTTCAAAGTTGGATTCAGATAACTCGGTGCAGC
* *
4103 ATTTTCGAAGTTGGATT-AGATAA
1 ATCTTCAAAGTTGGATTCAGATAA
4126 ATCAGATGAC
Statistics
Matches: 75, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
34 5 0.07
35 70 0.93
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (35 bp):
ATCTTCAAAGTTGGATTCAGATAACTCGGTGCAGC
Found at i:4517 original size:90 final size:89
Alignment explanation
Indices: 4149--4959 Score: 901
Period size: 90 Copynumber: 9.0 Consensus size: 89
4139 GTGCAGTATC
* *
4149 TTCAAGTGATTCGGTGAATCAAG-TAATGCGGTGC---ATTTCTTCAAAGATTGGAATTCGGTGA
1 TTCAGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAG-TCGG-ATTCGGTGA
* *
4210 GCTCGGTGCAGCACATTTTCAAATAG
64 GCTCGGTGCAGCAGATTTTCAAACAG
* * * * *
4236 ATCATGGTGATTCGGTGAATCAGGTAAATGCGGTGC---ATTTCTTCAAAGATTGGAATTCCGTG
1 TTCA-GGTGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAG-TCGG-ATTCGGTG
* **
4298 AGCTCGGTGCAGCAAATTTTCAAATGG
63 AGCTCGGTGCAGCAGATTTTCAAACAG
* * * * *
4325 TT-ATAGTGATTCGGTGAATCAAGTTAAAGTGGTGCATTATTTTTTTTCAAGAAT-GGATTCGGT
1 TTCA-GGTGATTCGGTGAATCAAGTTAATGCGGTGCATTA--TTTCTTCAA-AGTCGGATTCGGT
* * *
4388 GAGCTCAGTGCAGCACATTTTCAAAAAG
62 GAGCTCGGTGCAGCAGATTTTCAAACAG
* *
4416 TTCAGGACGATTCGGTGAAACAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAG
1 TTCAGG-TGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAG
*
4481 CTCGGTGTAGCAGATTTTCAAACAG
65 CTCGGTGCAGCAGATTTTCAAACAG
*
4506 TTTAGGTCGATTCGGTGAATCAAGTTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGA
1 TTCAGGT-GATTCGGTGAATCAAG-TTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGA
4571 GCTCGGTGCAGCAGATTTTCAAACAG
64 GCTCGGTGCAGCAGATTTTCAAACAG
* * * * *
4597 TTCAGGATGATTCAGTGAATCAAGTTGAGGCAGTGCCTTATTTCTTCAAAGTCGGATTCGGTGAG
1 TTCAGG-TGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAG
*
4662 CTCTGTGCAGCAGATTTTCAAACAG
65 CTCGGTGCAGCAGATTTTCAAACAG
* * * * * *
4687 TTCAGGATGATTCAGTGAATCAAGTTGAGGCAGTGCCTTATTTCTTC-AAGATTGGATTCGGTGA
1 TTCAGG-TGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAG-TCGGATTCGGTGA
*
4751 GCTCGGTGTAGCAGATATTT-AAACAG
64 GCTCGGTGCAGCAGAT-TTTCAAACAG
* * *** * * *
4777 TTCAAGATCATTCGGTGAATCAAGTTGGGGCGGTGCCTTACTTCTTCCAAA-TTGGATTCGGTGA
1 TTC-AGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTT-CAAAGTCGGATTCGGTGA
4841 GCTCGGTGCAGCAGATTTTCAAACAG
64 GCTCGGTGCAGCAGATTTTCAAACAG
* * * *
4867 TTCAAGATGATTCGGTGAATCGAGTTAATGTGGTGCATTATTTCTTCAAAGTC-GATTTGGTGAG
1 TTC-AGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAG
* *
4931 CTAGGTGCAGCAGATTTTCAGACAG
65 CTCGGTGCAGCAGATTTTCAAACAG
4956 TTCA
1 TTCA
4960 AGCTTTCAAG
Statistics
Matches: 639, Mismatches: 64, Indels: 41
0.86 0.09 0.06
Matches are distributed among these distances:
87 3 0.00
88 46 0.07
89 109 0.17
90 311 0.49
91 125 0.20
92 35 0.05
93 9 0.01
94 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (89 bp):
TTCAGGTGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAGC
TCGGTGCAGCAGATTTTCAAACAG
Found at i:4865 original size:361 final size:359
Alignment explanation
Indices: 4149--4959 Score: 986
Period size: 361 Copynumber: 2.3 Consensus size: 359
4139 GTGCAGTATC
*
4149 TTCAAG-TGATTCGGTGAATCAAG-TAATGCGGTGC---ATTTCTTCAAAGATTGGAATTCGGTG
1 TTCAAGATGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAG-TCGG-ATTCGGTG
* * * * * * *
4209 AGCTCGGTGCAGCACATTTTCAAATAGATCATGGTGATTCGGTGAATCAGGTAAATGCGGTGCAT
64 AGCTCGGTGCAGCAGATTTTCAAACAGTTCATGGTGATTCAGTGAATCAAGTAAAGGCAGTGCAT
* ** * *
4274 TTCTTCAAAGATTGGAATTCCGTGAGCTCGGTGCAGCAAATTTTCAAATGGTTATAGTGATTCGG
129 TTCTTCAAAGATCGGAATTCCGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTAGAGTGATTCAG
** *
4339 TGAATCAAGTTAAAGTGGTGCATTATTTTTTTTCAAGAATGGATTCGGTGAGCTCAGTGCAGCAC
194 TGAATCAAGTTAAAGCAGTGCATTA-TTTTCTTCAAGAATGGATTCGGTGAGCTCAGTGCAGCAC
* * *
4404 ATTTTCAAAAAGTTCAGGACGATTCGGTGAAACAAGTTAATGCGGTGCATTATTTCTTCAAAGTC
258 ATTTTCAAAAAGTTCAAGACGATTCGGTGAAACAAGTTAAGGCGGTGCATTACTTCTTCAAAGTC
*
4469 GGATTCGGTGAGCTCGGTGTAGCAGATTTTCAAACAG
323 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAG
* *
4506 TT-TAGGTCGATTCGGTGAATCAAGTTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTG
1 TTCAAGAT-GATTCGGTGAATCAAG-TTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTG
**
4570 AGCTCGGTGCAGCAGATTTTCAAACAGTTCA-GGATGATTCAGTGAATCAAGTTGAGGCAGTGCC
64 AGCTCGGTGCAGCAGATTTTCAAACAGTTCATGG-TGATTCAGTGAATCAAGTAAAGGCAGTG-C
* * *
4634 TTATTTCTTCAAAG-TCGG-ATTCGGTGAGCTCTGTGCAGCAGATTTTCAAACAGTTCAG-GATG
127 --ATTTCTTCAAAGATCGGAATTCCGTGAGCTCGGTGCAGCAAATTTTCAAACAGTT-AGAG-TG
* * * * * *
4696 ATTCAGTGAATCAAGTTGAGGCAGTGCCTTA-TTTCTTCAAGATTGGATTCGGTGAGCTCGGTGT
188 ATTCAGTGAATCAAGTTAAAGCAGTGCATTATTTTCTTCAAGAATGGATTCGGTGAGCTCAGTGC
* * * ** *
4760 AGCAGATATTT-AAACAGTTCAAGATC-ATTCGGTGAATCAAGTTGGGGCGGTGCCTTACTTCTT
253 AGCACAT-TTTCAAAAAGTTCAAGA-CGATTCGGTGAAACAAGTTAAGGCGGTGCATTACTTCTT
*
4823 CCAAA-TTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAG
316 -CAAAGTCGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAG
* * *
4867 TTCAAGATGATTCGGTGAATCGAGTTAATGTGGTGCATTATTTCTTCAAAGTC-GATTTGGTGAG
1 TTCAAGATGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAG
* *
4931 CTAGGTGCAGCAGATTTTCAGACAGTTCA
66 CTCGGTGCAGCAGATTTTCAAACAGTTCA
4960 AGCTTTCAAG
Statistics
Matches: 391, Mismatches: 46, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
356 2 0.01
357 3 0.01
358 16 0.04
359 37 0.09
360 41 0.10
361 189 0.48
362 48 0.12
363 43 0.11
364 12 0.03
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (359 bp):
TTCAAGATGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGTCGGATTCGGTGAG
CTCGGTGCAGCAGATTTTCAAACAGTTCATGGTGATTCAGTGAATCAAGTAAAGGCAGTGCATTT
CTTCAAAGATCGGAATTCCGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTAGAGTGATTCAGTG
AATCAAGTTAAAGCAGTGCATTATTTTCTTCAAGAATGGATTCGGTGAGCTCAGTGCAGCACATT
TTCAAAAAGTTCAAGACGATTCGGTGAAACAAGTTAAGGCGGTGCATTACTTCTTCAAAGTCGGA
TTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAG
Found at i:5297 original size:47 final size:47
Alignment explanation
Indices: 5220--5517 Score: 411
Period size: 47 Copynumber: 6.3 Consensus size: 47
5210 ATCCAGACAA
* *
5220 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTCAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * * *
5267 TCTTCTCTCGCTTCCACGCGATTTTGCAATTTAGTGGCCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
*
5314 -CATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTGACCAAAGTTGG
1 TC-TTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * *
5361 TCTTCTCTCGCTTCCATGCGAATTTTCAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* ** * *
5408 TCTTCTCTCGCTTCCACACGAGTTTGCAATTTAGTGGCCAAAGGTGG
1 TCTTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
*
5455 -CATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTGACCAAAGTTGG
1 TC-TTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
*
5502 TCTTTTCTCACTTCCA
1 TCTTTTCTCGCTTCCA
5518 CGCAAATTTG
Statistics
Matches: 219, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
46 2 0.01
47 215 0.98
48 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCATGCGAGTTTGCAATTTAGTGACCAAAGTTGG
Found at i:5479 original size:141 final size:141
Alignment explanation
Indices: 5220--5526 Score: 533
Period size: 141 Copynumber: 2.2 Consensus size: 141
5210 ATCCAGACAA
* *
5220 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTCAGTGACCAAAGTTGGTCTTCTCTCGCTTCCACG
1 TCTTTTCTCGCTTCCATGCGAATTTTCAATTCAGTGACCAAAGTTGGTCTTCTCTCGCTTCCACA
* *
5285 CGATTTTGCAATTTAGTGGCCAAAGTTGGCATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTG
66 CGAGTTTGCAATTTAGTGGCCAAAGGTGGCATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTG
5350 ACCAAAGTTGG
131 ACCAAAGTTGG
* *
5361 TCTTCTCTCGCTTCCATGCGAATTTTCAATTTAGTGACCAAAGTTGGTCTTCTCTCGCTTCCACA
1 TCTTTTCTCGCTTCCATGCGAATTTTCAATTCAGTGACCAAAGTTGGTCTTCTCTCGCTTCCACA
5426 CGAGTTTGCAATTTAGTGGCCAAAGGTGGCATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTG
66 CGAGTTTGCAATTTAGTGGCCAAAGGTGGCATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTG
5491 ACCAAAGTTGG
131 ACCAAAGTTGG
* * *
5502 TCTTTTCTCACTTCCACGCAAATTT
1 TCTTTTCTCGCTTCCATGCGAATTT
5527 GCATTTGGAA
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 156 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (141 bp):
TCTTTTCTCGCTTCCATGCGAATTTTCAATTCAGTGACCAAAGTTGGTCTTCTCTCGCTTCCACA
CGAGTTTGCAATTTAGTGGCCAAAGGTGGCATTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTG
ACCAAAGTTGG
Found at i:5618 original size:22 final size:22
Alignment explanation
Indices: 5535--5629 Score: 61
Period size: 21 Copynumber: 4.3 Consensus size: 22
5525 TTGCATTTGG
* *
5535 AAAAAACAAAACAAAAAAA--AG
1 AAAAAAGAAAA-AAAAAAAGCAA
*
5556 AAAAAAGAAAAAGAAAAAGTGACAA
1 AAAAAAGAAAAA-AAAAA-AG-CAA
*** *
5581 AAAAAAGAAGCTAAAAAAGCCA
1 AAAAAAGAAAAAAAAAAAGCAA
*
5603 AAAAAAGAAAAAAAAAAA-CTA
1 AAAAAAGAAAAAAAAAAAGCAA
5624 AAAAAA
1 AAAAAA
5630 TGCAAACACA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.02
21 23 0.40
22 17 0.30
23 1 0.02
24 5 0.09
25 10 0.18
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.03
Consensus pattern (22 bp):
AAAAAAGAAAAAAAAAAAGCAA
Found at i:5620 original size:13 final size:13
Alignment explanation
Indices: 5535--5573 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5525 TTGCATTTGG
*
5535 AAAAAACAAAACAA
1 AAAAAAGAAAA-AA
5549 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
*
5562 GAAAAAGAAAAA
1 AAAAAAGAAAAA
5574 GTGACAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:6972 original size:36 final size:36
Alignment explanation
Indices: 6932--7005 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
6922 GAGAGAGAGG
6932 GACGTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAA
1 GACGTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAA
6968 GACGTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAA
1 GACGTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAA
7004 GA
1 GA
7006 TGGAAGTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.39, T:0.08
Consensus pattern (36 bp):
GACGTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAA
Found at i:8553 original size:24 final size:25
Alignment explanation
Indices: 8521--8569 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
8511 GTCAAGATTT
*
8521 GAAG-AAAAAGCAAAAATAAAAAAA
1 GAAGAAAAAAGAAAAAATAAAAAAA
*
8545 GAAGGAAAAAGAAAAAATAAAAAAA
1 GAAGAAAAAAGAAAAAATAAAAAAA
8570 TGGAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (25 bp):
GAAGAAAAAAGAAAAAATAAAAAAA
Found at i:14859 original size:2 final size:2
Alignment explanation
Indices: 14852--14879 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14842 ATGACATTGC
14852 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
14880 GTTAATTCTT
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:14943 original size:2 final size:2
Alignment explanation
Indices: 14936--14963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14926 AATAAAATAG
14936 TA 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
14964 CTTGATATAC
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):
TA
Found at i:15060 original size:22 final size:22
Alignment explanation
Indices: 15035--15105 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
15025 AATTTATATT
*
15035 AAATTTTGATAATTACACCATA
1 AAATTTTGATAATCACACCATA
*
15057 AAA-TTT--TAATGACATCCATA
1 AAATTTTGATAATCACA-CCATA
* *
15077 TGAAATTTTGATAATCACACTATG
1 --AAATTTTGATAATCACACCATA
15101 AAATT
1 AAATT
15106 CTGCTAACGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
19 7 0.18
20 5 0.13
21 3 0.08
22 11 0.28
23 3 0.08
24 3 0.08
25 7 0.18
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAATCACACCATA
Found at i:15278 original size:22 final size:23
Alignment explanation
Indices: 15253--15313 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
15243 ATAACAAAAC
*
15253 TATGAAAATTTAATAAGCTA-CT
1 TATGAAAATTTGATAAGCTACCT
*
15275 TATGAAATTTTGATAA-CTACCT
1 TATGAAAATTTGATAAGCTACCT
15297 TATG-AAATTTGATAAGC
1 TATGAAAATTTGATAAGC
15314 AGACTATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (23 bp):
TATGAAAATTTGATAAGCTACCT
Found at i:15322 original size:43 final size:44
Alignment explanation
Indices: 15235--15334 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 44
15225 CAATGAAACA
*
15235 AAATTTTGATAACAAAACTATGAAAATTTAATAAGCTACTTATG
1 AAATTTTGATAACAAAACTATGAAAATTTAATAAGCGACTTATG
* * *
15279 AAATTTTGATAAC-TACCTTATG-AAATTTGATAAGCAGAC-TATG
1 AAATTTTGATAACAAAAC-TATGAAAATTTAATAAGC-GACTTATG
* *
15322 ATATTTTAATAAC
1 AAATTTTGATAAC
15335 CTCCACGTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
43 29 0.60
44 19 0.40
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACAAAACTATGAAAATTTAATAAGCGACTTATG
Found at i:15397 original size:44 final size:45
Alignment explanation
Indices: 15345--15444 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 45
15335 CTCCACGTGG
15345 AATG-TTGGTAAGAACACTAC-AATATTTTGATCACCTTCCTATAA
1 AATGCTTGGTAAGAACACTACGAA-ATTTTGATCACCTTCCTATAA
* *
15389 AAT-CTTGGTAAGCACACTACGAAATTTTGATCACTTTCCTATAA
1 AATGCTTGGTAAGAACACTACGAAATTTTGATCACCTTCCTATAA
*
15433 AATGTTTGGTAA
1 AATGCTTGGTAA
15445 TCACTATCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 41 0.82
45 9 0.18
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (45 bp):
AATGCTTGGTAAGAACACTACGAAATTTTGATCACCTTCCTATAA
Found at i:15484 original size:22 final size:22
Alignment explanation
Indices: 15428--15537 Score: 75
Period size: 22 Copynumber: 5.0 Consensus size: 22
15418 ATCACTTTCC
* *
15428 TATAAAATGTTTGGTAA--TCAC
1 TATAAAAT-TTTGATAACCTCAT
* *
15449 TATCAAATTGTGATAACCTCAT
1 TATAAAATTTTGATAACCTCAT
15471 TATAAAATTTTGATAAACCTC-T
1 TATAAAATTTTGAT-AACCTCAT
**
15493 CTGCAAAATTTTGATAACCCTC-T
1 -TATAAAATTTTGATAA-CCTCAT
* * *
15516 TTTGAAATTTTGATAATCTCAT
1 TATAAAATTTTGATAACCTCAT
15538 GATGTTTCAA
Statistics
Matches: 71, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
20 6 0.08
21 10 0.14
22 32 0.45
23 23 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCAT
Found at i:15500 original size:23 final size:23
Alignment explanation
Indices: 15453--15531 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
15443 AATCACTATC
* *
15453 AAATTGTGAT-AACCTCATTAT-A
1 AAATTTTGATAAACCTC-TTCTGA
15475 AAATTTTGATAAACCTC-TCTGCA
1 AAATTTTGATAAACCTCTTCTG-A
* *
15498 AAATTTTGATAACCCTCTTTTG-
1 AAATTTTGATAAACCTCTTCTGA
15520 AAATTTTGATAA
1 AAATTTTGATAA
15532 TCTCATGATG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.04
22 21 0.43
23 23 0.47
24 3 0.06
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCTTCTGA
Found at i:15571 original size:22 final size:22
Alignment explanation
Indices: 15546--15617 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
15536 ATGATGTTTC
15546 AATAACCA-CCTCATGAAATTTT
1 AATAACCACCCT-ATGAAATTTT
*
15568 AATAACTACCCTATGAAATTTT
1 AATAACCACCCTATGAAATTTT
* * *
15590 GATAACCTCCCTATGAATTTTT
1 AATAACCACCCTATGAAATTTT
*
15612 TATAAC
1 AATAAC
15618 ATCCTTACGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 40 0.93
23 3 0.07
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (22 bp):
AATAACCACCCTATGAAATTTT
Found at i:15697 original size:22 final size:22
Alignment explanation
Indices: 15650--15725 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
15640 CTCCCTACAA
* * *
15650 AATTTTGAAAACCATACTAT-T
1 AATTTTGATAACTACACTATGT
15671 AAATTTTGATAACTACACTATGT
1 -AATTTTGATAACTACACTATGT
** *
15694 AATTACGATAACCT-CCCTATGT
1 AATTTTGATAA-CTACACTATGT
15716 AATTTTGATA
1 AATTTTGATA
15726 GCCAAACTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 41 0.93
23 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACTACACTATGT
Found at i:15851 original size:22 final size:22
Alignment explanation
Indices: 15799--15843 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
15789 ATAACATCGC
*
15799 TCTTAAAAACCACACTATGAAA
1 TCTTAATAACCACACTATGAAA
15821 TCTTAATAACCACACTATGAAA
1 TCTTAATAACCACACTATGAAA
15843 T
1 T
15844 TTTGATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (22 bp):
TCTTAATAACCACACTATGAAA
Found at i:16609 original size:33 final size:33
Alignment explanation
Indices: 16567--16636 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
16557 TAATTTAGAT
*
16567 ATTATAATCCGGTTTAAATCGAAAAATTTTATA
1 ATTAGAATCCGGTTTAAATCGAAAAATTTTATA
*
16600 ATTAGAATCCGGTTTAAATTGAAAAATTTTATA
1 ATTAGAATCCGGTTTAAATCGAAAAATTTTATA
16633 ATTA
1 ATTA
16637 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (33 bp):
ATTAGAATCCGGTTTAAATCGAAAAATTTTATA
Done.