Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009646.1 Corchorus capsularis cultivar CVL-1 contig09667, 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: 96389
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:456 original size:27 final size:27
Alignment explanation
Indices: 418--1608 Score: 1403
Period size: 27 Copynumber: 44.0 Consensus size: 27
408 TTTAGCCAAA
418 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
445 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
472 ATGTGACCCTACTGAATATGCAAC--T
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
497 ATGTGGCCCTACTGAATATGCAACCAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
524 ACGAGCCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
551 AT-ATGGCCCTACTGAATATGCAACTAT
1 ATGA-GGCCCTACTGAATATGCAACTAT
*
578 ATGTGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
605 ATGTA-TCCCTACTGAATATGCAACTAT
1 ATG-AGGCCCTACTGAATATGCAACTAT
*
632 ATGAGGCCCTACTGAATATGCAACTAC
1 ATGAGGCCCTACTGAATATGCAACTAT
*
659 A--AGACCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
684 ATGA-GCCATACTGATTATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
710 ATGA-GCCATACTGATTATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
736 ATGATGTGACCTTACTGAATATGCAACTAT
1 ATGA-G-G-CCCTACTGAATATGCAACTAT
*
766 ATGAGGCCCTACTGAATATGGAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
793 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
820 AT-ATGGCCCTATTGAATATGCAACTAT
1 ATGA-GGCCCTACTGAATATGCAACTAT
* * * *
847 ATGTGGTCATACTGAATATGCAACTAC
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
874 ATGTA-ACCCTACTGAATATGCAGCTAT
1 ATG-AGGCCCTACTGAATATGCAACTAT
901 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
928 ATGTTGTGGTCCTACTGAATATGCAACTAT
1 A---TGAGGCCCTACTGAATATGCAACTAT
* *
958 ATG-GCCCCTACTAAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
984 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
1011 AT--GGCCTTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
1036 ATGATGTGGTCCTACTGAATATGCAACTAT
1 ATGA---GGCCCTACTGAATATGCAACTAT
1066 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
1093 ATGTGGCCCTACTGAATATACAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* * *
1120 ATGTGGCCCTACTGAATACGCAACTAC
1 ATGAGGCCCTACTGAATATGCAACTAT
*
1147 ATGTA-ACCCTACTGAATATGCAACTAT
1 ATG-AGGCCCTACTGAATATGCAACTAT
*
1174 ACGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
1201 ATGATGTGGTCCTACTGAATATACAACTAT
1 ATGA---GGCCCTACTGAATATGCAACTAT
1231 ATGAGGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
1258 AT--GGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
1283 ATGATGTGGCCCTACTGAACCTACTGAATATGCAACTAT
1 ATGA---GG-----C----CCTACTGAATATGCAACTAT
*
1322 AT--TGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
1347 ATGATGTGATCCTACTGAATATGCAACTAT
1 ATGA-G-G-CCCTACTGAATATGCAACTAT
* *
1377 ATAAGGCCCTACTGAATATGCAACTAC
1 ATGAGGCCCTACTGAATATGCAACTAT
**
1404 ATGAGGTTCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
**
1431 ATGCTGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
1458 AT--GGCCTTACTGAATATGCAACTAA
1 ATGAGGCCCTACTGAATATGCAACTAT
*
1483 AT--GGCCCTACTGAATATGCAACTGT
1 ATGAGGCCCTACTGAATATGCAACTAT
*
1508 AT--GGCCCTACTGAATATGCAACTGT
1 ATGAGGCCCTACTGAATATGCAACTAT
1533 AT--GGCCCTACTGAATATGCAACTAT
1 ATGAGGCCCTACTGAATATGCAACTAT
* * *
1558 ATGA-GCCATACTGATTATGCAACTAC
1 ATGAGGCCCTACTGAATATGCAACTAT
* *
1584 ATGA-ACCCTACTGAATATGTAACTA
1 ATGAGGCCCTACTGAATATGCAACTA
1609 CATGGCCCTA
Statistics
Matches: 1020, Mismatches: 93, Indels: 103
0.84 0.08 0.08
Matches are distributed among these distances:
25 211 0.21
26 117 0.11
27 538 0.53
28 2 0.00
29 5 0.00
30 123 0.12
34 1 0.00
35 1 0.00
39 22 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (27 bp):
ATGAGGCCCTACTGAATATGCAACTAT
Found at i:1334 original size:34 final size:38
Alignment explanation
Indices: 1263--1335 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
1253 ACTATATGGC
1263 CCTACTGAATATGCAACTATATGATGTGGCCCTACTGAA
1 CCTACTGAATATGCAAC-ATATGATGTGGCCCTACTGAA
1302 CCTACTGAATATGCAAC-TAT-AT-T-GCCCTACTGAA
1 CCTACTGAATATGCAACATATGATGTGGCCCTACTGAA
1336 TATGCAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
34 11 0.32
35 1 0.03
36 2 0.06
37 3 0.09
39 17 0.50
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (38 bp):
CCTACTGAATATGCAACATATGATGTGGCCCTACTGAA
Found at i:1511 original size:50 final size:51
Alignment explanation
Indices: 1304--1608 Score: 373
Period size: 50 Copynumber: 5.8 Consensus size: 51
1294 CTACTGAACC
*
1304 TACTGAATATGCAACTATATTGCCCTACTGAATATGCAACTATATGATGTGATCC-
1 TACTGAATATGCAACTATATGGCCCTACTGAATATGCAACTATATGA---G--CCT
* **
1359 TACTGAATATGCAACTATATAAGGCCCTACTGAATATGCAACTACATGAGGTT
1 TACTGAATATGCAACTATAT--GGCCCTACTGAATATGCAACTATATGAGCCT
1412 CTACTGAATATGCAACTATATGCTGCCCTACTGAATATGCAACTATATG-GCCT
1 -TACTGAATATGCAACTATATG--GCCCTACTGAATATGCAACTATATGAGCCT
* * *
1465 TACTGAATATGCAACTAAATGGCCCTACTGAATATGCAACTGTATG-GCCC
1 TACTGAATATGCAACTATATGGCCCTACTGAATATGCAACTATATGAGCCT
* *
1515 TACTGAATATGCAACTGTATGGCCCTACTGAATATGCAACTATATGAGCCA
1 TACTGAATATGCAACTATATGGCCCTACTGAATATGCAACTATATGAGCCT
* * * *
1566 TACTGATTATGCAACTACATGAACCCTACTGAATATGTAACTA
1 TACTGAATATGCAACTATATG-GCCCTACTGAATATGCAACTA
1609 CATGGCCCTA
Statistics
Matches: 223, Mismatches: 19, Indels: 19
0.85 0.07 0.07
Matches are distributed among these distances:
50 70 0.31
51 21 0.09
52 40 0.18
53 2 0.01
54 45 0.20
55 20 0.09
57 25 0.11
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (51 bp):
TACTGAATATGCAACTATATGGCCCTACTGAATATGCAACTATATGAGCCT
Found at i:8114 original size:68 final size:69
Alignment explanation
Indices: 8003--8135 Score: 214
Period size: 68 Copynumber: 1.9 Consensus size: 69
7993 TCGAAATCTG
* *
8003 GGATGGACAGGGTGGGATTATTGGAAAGGAGATAACTACCTCCTATTGTGTAGTCCATTTCAATA
1 GGATGGACAGGGTGGGATTATGGGAAAGGAGAGAACTACCTCCTATTGTGTAGTCCATTTCAATA
8068 CCTA
66 CCTA
* * *
8072 GGATGGAC-GGGTGGGATTATGGGAAATGAGAGGACTATCTCCTATTGTGTAGTCCATTTCAATA
1 GGATGGACAGGGTGGGATTATGGGAAAGGAGAGAACTACCTCCTATTGTGTAGTCCATTTCAATA
8136 TCATGTTCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
68 51 0.86
69 8 0.14
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (69 bp):
GGATGGACAGGGTGGGATTATGGGAAAGGAGAGAACTACCTCCTATTGTGTAGTCCATTTCAATA
CCTA
Found at i:14816 original size:19 final size:21
Alignment explanation
Indices: 14770--14817 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
14760 TGTGACACGC
*
14770 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAAGTC-TGA
14792 CACATGTACCAAAAAGT-T-A
1 CACATGTACCAAAAAGTCTGA
14811 CACATGT
1 CACATGT
14818 CACGCGTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 7 0.28
20 1 0.04
22 17 0.68
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (21 bp):
CACATGTACCAAAAAGTCTGA
Found at i:14822 original size:53 final size:54
Alignment explanation
Indices: 14737--14840 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 54
14727 GACGTGGCAC
* **
14737 GCCACGTGTACCAAAAAGTGACATGTGACACGC-CACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGACACGCGCACATGTACCAAAAAGTCGT
* * * *
14790 GCCACATGTACCAAAAAGTTACACATGTCACGCGTACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGACACGCGCACATGTACCAAAAAGT
14841 GACACATGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 28 0.65
54 15 0.35
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (54 bp):
GCCACATGTACCAAAAAGTGACACATGACACGCGCACATGTACCAAAAAGTCGT
Found at i:15914 original size:57 final size:57
Alignment explanation
Indices: 15845--15958 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
15835 GGTTGTATAT
*
15845 TGGGAATTTGGGATTAAACATTTTCCCTGGTTAATTACAAGTAGTGCTGCAAAGGAA
1 TGGGAATTTGGGATTAAACATTTTCCCTGGTTAATTACAAGTAGTGCTACAAAGGAA
*
15902 TGGGAATTTGGGATTAAACATTTTCCCTGGTTAATTATAAGTAGTGCTACAAAGGAA
1 TGGGAATTTGGGATTAAACATTTTCCCTGGTTAATTACAAGTAGTGCTACAAAGGAA
15959 CAACGTGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (57 bp):
TGGGAATTTGGGATTAAACATTTTCCCTGGTTAATTACAAGTAGTGCTACAAAGGAA
Found at i:16412 original size:18 final size:18
Alignment explanation
Indices: 16389--16435 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
16379 TCAAATATCG
16389 TATTATATATAATTAGTA
1 TATTATATATAATTAGTA
*
16407 TATTATATGTAATTAGTA
1 TATTATATATAATTAGTA
16425 T-TATATATATA
1 TAT-TATATATA
16436 CTAATCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TATTATATATAATTAGTA
Found at i:34272 original size:29 final size:29
Alignment explanation
Indices: 34239--34310 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
34229 GTAGTGTTTA
34239 GACGTTTTGTCCCCTAAACTTCAATTTT-G
1 GACGTTTTG-CCCCTAAACTTCAATTTTGG
*
34268 GACGTTTTGCCCCCTGAACTTCAATTTTGG
1 GACGTTTTG-CCCCTAAACTTCAATTTTGG
*
34298 GACATTTTGCCCC
1 GACGTTTTGCCCC
34311 GCCTGATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 30 0.77
30 9 0.23
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.38
Consensus pattern (29 bp):
GACGTTTTGCCCCTAAACTTCAATTTTGG
Found at i:34671 original size:23 final size:23
Alignment explanation
Indices: 34645--34688 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
34635 AATTCACAAC
*
34645 ACAACAGCCCAACAGACAAAAAG
1 ACAACAACCCAACAGACAAAAAG
34668 ACAACAACCCAACAGACAAAA
1 ACAACAACCCAACAGACAAAA
34689 TGATCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.32, G:0.09, T:0.00
Consensus pattern (23 bp):
ACAACAACCCAACAGACAAAAAG
Found at i:36394 original size:2 final size:2
Alignment explanation
Indices: 36389--36427 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
36379 TTTTTGCCAA
* *
36389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36428 AAAGAGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:36882 original size:27 final size:28
Alignment explanation
Indices: 36847--36914 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
36837 ATCCTAGGGA
*
36847 ACTAACTTTGAATGGGA-AACTATTTTG
1 ACTAACTTTGAATGGGAGAACTATCTTG
* *
36874 ACTAGCTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTATCTTG
*
36901 ACTAACTTGGAATG
1 ACTAACTTTGAATG
36915 AGAGTCTGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTATCTTG
Found at i:41320 original size:27 final size:28
Alignment explanation
Indices: 41284--41351 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
41274 ATCCTAGGGA
* *
41284 ACTAATTTTGAATGGGA-AACTGTTTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
41311 ACTAGCTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
41338 ACTAACTTGGAATG
1 ACTAACTTTGAATG
41352 AGAGTCTGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTGTCTTG
Found at i:41534 original size:2 final size:2
Alignment explanation
Indices: 41527--41587 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
41517 TTCGAAGCTT
41527 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
41569 AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
41588 TATATATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:42648 original size:22 final size:22
Alignment explanation
Indices: 42620--42668 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
42610 TTCATCAATG
42620 GAGCTTTTGATTGGGTAGGCTA
1 GAGCTTTTGATTGGGTAGGCTA
42642 GAGCTTTTGATTGGGTAGGCTA
1 GAGCTTTTGATTGGGTAGGCTA
42664 GAGCT
1 GAGCT
42669 GATTAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.10, G:0.37, T:0.35
Consensus pattern (22 bp):
GAGCTTTTGATTGGGTAGGCTA
Found at i:46062 original size:31 final size:31
Alignment explanation
Indices: 46024--46121 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
46014 CAAAGCAGAG
46024 GAAAAAGAAAAACTAATGGAAGAATGAAGAT
1 GAAAAAGAAAAACTAATGGAAGAATGAAGAT
* * * * *
46055 GAAAAAGAAAGA--AA---AACAAAGTAGAG
1 GAAAAAGAAAAACTAATGGAAGAATGAAGAT
46081 GAAAAAGAAAAACTAATGGAAGAATGAAGAT
1 GAAAAAGAAAAACTAATGGAAGAATGAAGAT
46112 GAAAAAGAAA
1 GAAAAAGAAA
46122 GAAAAACAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
26 19 0.37
28 2 0.04
29 2 0.04
31 29 0.56
ACGTcount: A:0.65, C:0.03, G:0.22, T:0.09
Consensus pattern (31 bp):
GAAAAAGAAAAACTAATGGAAGAATGAAGAT
Found at i:46081 original size:57 final size:57
Alignment explanation
Indices: 46006--46131 Score: 234
Period size: 57 Copynumber: 2.2 Consensus size: 57
45996 TGGAGTTGAG
46006 AGAAAACACAAAGCAGAGGAAAAAGAAAAACTAATGGAAGAATGAAGATGAAAAAGAA
1 AGAAAA-ACAAAGCAGAGGAAAAAGAAAAACTAATGGAAGAATGAAGATGAAAAAGAA
*
46064 AGAAAAACAAAGTAGAGGAAAAAGAAAAACTAATGGAAGAATGAAGATGAAAAAGAA
1 AGAAAAACAAAGCAGAGGAAAAAGAAAAACTAATGGAAGAATGAAGATGAAAAAGAA
46121 AGAAAAACAAA
1 AGAAAAACAAA
46132 CCGCGCGATC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
57 61 0.91
58 6 0.09
ACGTcount: A:0.66, C:0.06, G:0.21, T:0.07
Consensus pattern (57 bp):
AGAAAAACAAAGCAGAGGAAAAAGAAAAACTAATGGAAGAATGAAGATGAAAAAGAA
Found at i:47619 original size:257 final size:257
Alignment explanation
Indices: 47163--47657 Score: 963
Period size: 257 Copynumber: 1.9 Consensus size: 257
47153 TTTCCGTAAA
47163 AAAGGCCAGCAACAAGTCTTACTTTTTTAGGGGGAGAGTTTTTAATTCTCTAAATTGCCCTCAAG
1 AAAGGCCAGCAACAAGTCTTACTTTTTTAGGGGGAGAGTTTTTAATTCTCTAAATTGCCCTCAAG
*
47228 ATTTCCAAAGGCCTTGGGTTCTTTTGTCACTTGACTTTCAGCCCCTGTTCACACTTGCTAGCCCC
66 ATTTCCAAAGGCCTTGGGTTCTTTTGTCACTTGACTTTCAACCCCTGTTCACACTTGCTAGCCCC
47293 GTTCCCTTCTTGGCGCTTGCTATTTGCTATTTGTTGTTTTTTATCCCCTTTGACTGCTTTCTTGA
131 GTTCCCTTCTTGGCGCTTGCTATTTGCTATTTGTTGTTTTTTATCCCCTTTGACTGCTTTCTTGA
47358 ACCAGGTTTAATTTTTTTTTCTTGGACATATTTCTAATTTTGTAAAAAAGGCCTTGGGTTCC
196 ACCAGGTTTAATTTTTTTTTCTTGGACATATTTCTAATTTTGTAAAAAAGGCCTTGGGTTCC
* *
47420 AAAGGCCAGCAACAAGTCTTACTTTTTTGGGGGGAGAGTTTTTAATTCTCTAAATTGCCCTCGAG
1 AAAGGCCAGCAACAAGTCTTACTTTTTTAGGGGGAGAGTTTTTAATTCTCTAAATTGCCCTCAAG
47485 ATTTCCAAAGGCCTTGGGTTCTTTTGTCACTTGACTTTCAACCCCTGTTCACACTTGCTAGCCCC
66 ATTTCCAAAGGCCTTGGGTTCTTTTGTCACTTGACTTTCAACCCCTGTTCACACTTGCTAGCCCC
47550 GTTCCCTTCTTGGCGCTTGCTATTTGCTATTTGTTGTTTTTTATCCCCTTTGACTGCTTTCTTGA
131 GTTCCCTTCTTGGCGCTTGCTATTTGCTATTTGTTGTTTTTTATCCCCTTTGACTGCTTTCTTGA
47615 ACCAGGTTTAATTTTTTTTTCTTGGACATATTTCTAATTTTGT
196 ACCAGGTTTAATTTTTTTTTCTTGGACATATTTCTAATTTTGT
47658 CTGTTTTGAT
Statistics
Matches: 235, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
257 235 1.00
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.42
Consensus pattern (257 bp):
AAAGGCCAGCAACAAGTCTTACTTTTTTAGGGGGAGAGTTTTTAATTCTCTAAATTGCCCTCAAG
ATTTCCAAAGGCCTTGGGTTCTTTTGTCACTTGACTTTCAACCCCTGTTCACACTTGCTAGCCCC
GTTCCCTTCTTGGCGCTTGCTATTTGCTATTTGTTGTTTTTTATCCCCTTTGACTGCTTTCTTGA
ACCAGGTTTAATTTTTTTTTCTTGGACATATTTCTAATTTTGTAAAAAAGGCCTTGGGTTCC
Found at i:65877 original size:30 final size:30
Alignment explanation
Indices: 65768--65911 Score: 121
Period size: 30 Copynumber: 4.8 Consensus size: 30
65758 GATGTAGTGA
* * * * **
65768 GAGCTGATTTTGTTACAGAAGACGTAGCAG
1 GAGCTGATTTTGATACTGAAGAAGTTGTGG
* * **
65798 GAGTTGATTTT-ATAACTGAAGAACTAATGG
1 GAGCTGATTTTGAT-ACTGAAGAAGTTGTGG
65828 GAGCTGATTTT-ATAACTGAAGAAGTTGTGG
1 GAGCTGATTTTGAT-ACTGAAGAAGTTGTGG
* *
65858 GAGCTGATTTTGGTGCTGAAGAAGTTGTGG
1 GAGCTGATTTTGATACTGAAGAAGTTGTGG
* * *
65888 AAGCTGATCTTGTTACTGAAGAAG
1 GAGCTGATTTTGATACTGAAGAAG
65912 ATCGACCAGT
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
29 1 0.01
30 92 0.98
31 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.31
Consensus pattern (30 bp):
GAGCTGATTTTGATACTGAAGAAGTTGTGG
Found at i:74007 original size:15 final size:16
Alignment explanation
Indices: 73987--74018 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
73977 GAGCGTAAAC
73987 TTTTTCCTTC-TTTTT
1 TTTTTCCTTCATTTTT
74002 TTTTTCCTTCATTTTT
1 TTTTTCCTTCATTTTT
74018 T
1 T
74019 ACATCTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCCTTCATTTTT
Found at i:86438 original size:82 final size:82
Alignment explanation
Indices: 86312--86477 Score: 269
Period size: 82 Copynumber: 2.0 Consensus size: 82
86302 ACCAAACGAT
* ** * * *
86312 TCATGTTAAGCTATACATGGTATAATTGAGTCGAGTCGAGTAATCAGCTAAACTAAAATCGAGCT
1 TCATGTTAAGCTATACAGGGTATAATCAAGTCGAGTCAAATAATCAGCTAAACTAAAATCAAGCT
86377 CAACACAAAAATCTGAC
66 CAACACAAAAATCTGAC
*
86394 TCATGTTAAGCTATGCAGGGTATAATCAAGTCGAGTCAAATAATCAGCTAAACTAAAATCAAGCT
1 TCATGTTAAGCTATACAGGGTATAATCAAGTCGAGTCAAATAATCAGCTAAACTAAAATCAAGCT
86459 CAACACAAAAATCTGAC
66 CAACACAAAAATCTGAC
86476 TC
1 TC
86478 GATACTTGGC
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (82 bp):
TCATGTTAAGCTATACAGGGTATAATCAAGTCGAGTCAAATAATCAGCTAAACTAAAATCAAGCT
CAACACAAAAATCTGAC
Found at i:86599 original size:7 final size:7
Alignment explanation
Indices: 86587--86612 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
86577 TTAACTCGAG
86587 CTCAATA
1 CTCAATA
86594 CTCAATA
1 CTCAATA
86601 CTCAATA
1 CTCAATA
86608 CTCAA
1 CTCAA
86613 CTCAAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (7 bp):
CTCAATA
Found at i:91484 original size:24 final size:24
Alignment explanation
Indices: 91457--91502 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
91447 GAAAATCAAC
91457 AAGAACAGGACGAGGAAGAGGAGG
1 AAGAACAGGACGAGGAAGAGGAGG
** * *
91481 AAGATGATGACGAGGACGAGGA
1 AAGAACAGGACGAGGAAGAGGA
91503 TTGAAAGCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.43, T:0.04
Consensus pattern (24 bp):
AAGAACAGGACGAGGAAGAGGAGG
Found at i:93756 original size:150 final size:146
Alignment explanation
Indices: 93457--93758 Score: 498
Period size: 150 Copynumber: 2.0 Consensus size: 146
93447 AGAAATTAAC
*
93457 AAAATGATGAACCAAAAATGTAAAGAACTGCACCAAAGGTACCATAGAAGAGCATTCAGAATATG
1 AAAATGATGAACCAAAAATGTAAAGAACTGCACCAAAGGTACCACAGAAGAGCATTCAGAATATG
* * *
93522 TAAAGCAATGTGTCGTCCGTACAGGGTTTAACATCCCTTAGAATAAGATTACACTACCAGAATCA
66 TAAAGCAATGTGTAGTCCCTACAGGGTTTAACATCCCTTAG-A-AAGATTAAACTACCAGAATCA
93587 CACAACCAATACAAAAAA
129 CACAACCAATACAAAAAA
*
93605 AAAATGATGAACCAAAAATGTAAAGAATTGCACCACCAAGGTACCACAGAAGAGCATTCAGAATA
1 AAAATGATGAACCAAAAATGTAAAGAACTGCACCA--AAGGTACCACAGAAGAGCATTCAGAATA
*
93670 TGTAAAGCAATGTGTAGTCCCTACAGGGTTTAATATCCCTTAG-AAGATTAAACTACCAGAATCA
64 TGTAAAGCAATGTGTAGTCCCTACAGGGTTTAACATCCCTTAGAAAGATTAAACTACCAGAATCA
93734 CACAACCAATACAAAAAGA
129 CACAACCAATACAAAAA-A
93753 AAAATG
1 AAAATG
93759 GAAAACTAGA
Statistics
Matches: 145, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
147 37 0.26
148 41 0.28
150 67 0.46
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.20
Consensus pattern (146 bp):
AAAATGATGAACCAAAAATGTAAAGAACTGCACCAAAGGTACCACAGAAGAGCATTCAGAATATG
TAAAGCAATGTGTAGTCCCTACAGGGTTTAACATCCCTTAGAAAGATTAAACTACCAGAATCACA
CAACCAATACAAAAAA
Done.