Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010057.1 Corchorus capsularis cultivar CVL-1 contig10078, 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: 102750
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:13369 original size:62 final size:61
Alignment explanation
Indices: 13297--13415 Score: 220
Period size: 62 Copynumber: 1.9 Consensus size: 61
13287 CCAAGTGAAA
*
13297 GCAGGTCCAAAAAGCCCCAAGTCCTTTTCTCTTGTTATATATATTTAAGAAGATTGTAAGT
1 GCAGGTCCAAAAACCCCCAAGTCCTTTTCTCTTGTTATATATATTTAAGAAGATTGTAAGT
13358 GCAGGTCCCAAAAACCCCCAAGTCCTTTTCTCTTGTTATATATATTTAAGAAGATTGT
1 GCAGGT-CCAAAAACCCCCAAGTCCTTTTCTCTTGTTATATATATTTAAGAAGATTGT
13416 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 6 0.11
62 50 0.89
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (61 bp):
GCAGGTCCAAAAACCCCCAAGTCCTTTTCTCTTGTTATATATATTTAAGAAGATTGTAAGT
Found at i:27082 original size:25 final size:25
Alignment explanation
Indices: 27053--27111 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
27043 CATCATCTGG
*
27053 GTTTACATTATTGTTCCAAAATCTT
1 GTTTACATTATTGTTACAAAATCTT
*
27078 GTTTACAATATTGTTACAAAATCTT
1 GTTTACATTATTGTTACAAAATCTT
27103 GTTTACATT
1 GTTTACATT
27112 GTTCCCACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (25 bp):
GTTTACATTATTGTTACAAAATCTT
Found at i:37388 original size:32 final size:31
Alignment explanation
Indices: 37352--37459 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 31
37342 AATGGATATT
37352 AAACTAAACTACTATTTTATGGCCAAAAAAAA
1 AAACTAAACTACTATTTT-TGGCCAAAAAAAA
37384 AAACTAAACTACTATTTTTGGCC--AAAAAA
1 AAACTAAACTACTATTTTTGGCCAAAAAAAA
** *
37413 AAACTAAACTACTAAAGTTGGTGCCAAAAAAAA
1 AAACTAAACTACT-ATTTTTG-GCCAAAAAAAA
*
37446 AAACTAAACCACTA
1 AAACTAAACTACTA
37460 AAGTTGTTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
29 19 0.28
30 4 0.06
31 8 0.12
32 19 0.28
33 18 0.26
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.22
Consensus pattern (31 bp):
AAACTAAACTACTATTTTTGGCCAAAAAAAA
Found at i:37444 original size:33 final size:32
Alignment explanation
Indices: 37372--37465 Score: 122
Period size: 33 Copynumber: 3.0 Consensus size: 32
37362 ACTATTTTAT
** *
37372 GGCCAAAAAAAAAAACTAAACTACT-ATTTTT
1 GGCCAAAAAAAAAAACTAAACTACTAAAGTTG
37403 GGCC--AAAAAAAAACTAAACTACTAAAGTTG
1 GGCCAAAAAAAAAAACTAAACTACTAAAGTTG
*
37433 GTGCCAAAAAAAAAAACTAAACCACTAAAGTTG
1 G-GCCAAAAAAAAAAACTAAACTACTAAAGTTG
37466 TTATATGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 19 0.35
30 4 0.07
31 7 0.13
33 25 0.45
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (32 bp):
GGCCAAAAAAAAAAACTAAACTACTAAAGTTG
Found at i:38376 original size:21 final size:21
Alignment explanation
Indices: 38333--38376 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
38323 TAAGGTTTAG
* *
38333 AAACAATTAATTAAAAGCCTT
1 AAACAATTAATTAAAAACATT
38354 AAAC-ATTAATTAAAAACAATT
1 AAACAATTAATTAAAAAC-ATT
38375 AA
1 AA
38377 GGAAGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (21 bp):
AAACAATTAATTAAAAACATT
Found at i:38552 original size:2 final size:2
Alignment explanation
Indices: 38539--38568 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
38529 GTTAAAAATA
38539 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
38569 ACAAATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40445 original size:30 final size:30
Alignment explanation
Indices: 40411--40490 Score: 135
Period size: 29 Copynumber: 2.7 Consensus size: 30
40401 AAATTGAAAC
40411 GTTTGGCCCCAAATCGAGCATAGCAGCAAG
1 GTTTGGCCCCAAATCGAGCATAGCAGCAAG
40441 GTTTGG-CCCAAATCGAGCATAGCAGCAAG
1 GTTTGGCCCCAAATCGAGCATAGCAGCAAG
* *
40470 GTTTGGCCCTAAATTGAGCAT
1 GTTTGGCCCCAAATCGAGCAT
40491 TTTGCCCTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 29 0.62
30 18 0.38
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (30 bp):
GTTTGGCCCCAAATCGAGCATAGCAGCAAG
Found at i:41201 original size:2 final size:2
Alignment explanation
Indices: 41154--41186 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
41144 TCTTTCCCTA
41154 AT AT -T AT AT -T 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
41187 AGTACAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:42475 original size:2 final size:2
Alignment explanation
Indices: 42468--42513 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
42458 AGAATTACAT
* * *
42468 TA TA TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42510 TA TA
1 TA TA
42514 AAGATCGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:43549 original size:55 final size:55
Alignment explanation
Indices: 43462--43748 Score: 267
Period size: 55 Copynumber: 5.2 Consensus size: 55
43452 ATTAAAGATT
*
43462 ACACCATCAGGACCAACTTT-TT-GATCCAGATGATCTGAATGATAAATAGAAGGCA
1 ACACCATCAGGACCAA-TTTATTAG-TCCAGATGATCTGAATGATAAATAGAAGACA
* * * * * *** *
43517 ACACCATCAGGATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTA-ATTGACA
1 ACACCATCAGGACCAATTTATTAGTCCAGATGATCTGAATGATAAATAGA-AGACA
* * * *
43572 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
1 ACACCATCAGGACCAATTTATTAGTCCAGATGATCTGAATGATAAATAGAAGACA
* * * * * *** *
43627 ACACCATCAGGATCAATTTATTAGTCCCGATGATTTGAGTAATTTTTA-ATTGACA
1 ACACCATCAGGACCAATTTATTAGTCCAGATGATCTGAATGATAAATAGA-AGACA
* * * *
43682 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAATACA
1 ACACCATCAGGACCAATTTATTAGTCCAGATGATCTGAATGATAAATAGAAGACA
43737 ACACCATCAGGA
1 ACACCATCAGGA
43749 TCAAGCTATT
Statistics
Matches: 177, Mismatches: 49, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
54 5 0.03
55 169 0.95
56 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (55 bp):
ACACCATCAGGACCAATTTATTAGTCCAGATGATCTGAATGATAAATAGAAGACA
Found at i:43659 original size:110 final size:110
Alignment explanation
Indices: 43462--43752 Score: 528
Period size: 110 Copynumber: 2.6 Consensus size: 110
43452 ATTAAAGATT
* * *
43462 ACACCATCAGGACCAACTTTTTGATCCAGATGATCTGAATGATAAATAGAAGGCAACACCATCAG
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
*
43527 GATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATTGACA
66 GATCAATTTATTAGTCCCGATGATTTGAGTAATTTTTAATTGACA
43572 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
43637 GATCAATTTATTAGTCCCGATGATTTGAGTAATTTTTAATTGACA
66 GATCAATTTATTAGTCCCGATGATTTGAGTAATTTTTAATTGACA
**
43682 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAATACAACACCATCAG
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
43747 GATCAA
66 GATCAA
43753 GCTATTTATC
Statistics
Matches: 175, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 175 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (110 bp):
ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
GATCAATTTATTAGTCCCGATGATTTGAGTAATTTTTAATTGACA
Found at i:48738 original size:23 final size:23
Alignment explanation
Indices: 48708--48876 Score: 80
Period size: 23 Copynumber: 7.3 Consensus size: 23
48698 AAAACTTTGT
48708 AAGAAATTGGTTCTGATGGTGTG
1 AAGAAATTGGTTCTGATGGTGTG
** * * *
48731 AAGAAATTTATAC-CATCAGG-ATG
1 AAGAAATTGGTTCTGAT--GGTGTG
*
48754 ATGAAATTGGTTCTGATGGTGTG
1 AAGAAATTGGTTCTGATGGTGTG
** * * *
48777 AAGAAATTTATAC-CATCAGG-ATG
1 AAGAAATTGGTTCTGAT--GGTGTG
* *
48800 ATGAAATTGGTTCTGATGGTGTC
1 AAGAAATTGGTTCTGATGGTGTG
** * * *
48823 AAGAAATTTATAC-CATCAGG-ATG
1 AAGAAATTGGTTCTGAT--GGTGTG
48846 AAGAAATTGGTTCTGATGGTGTG
1 AAGAAATTGGTTCTGATGGTGTG
48869 AAGAAATT
1 AAGAAATT
48877 TATACCATCA
Statistics
Matches: 98, Mismatches: 36, Indels: 24
0.62 0.23 0.15
Matches are distributed among these distances:
22 12 0.12
23 74 0.76
24 12 0.12
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (23 bp):
AAGAAATTGGTTCTGATGGTGTG
Found at i:48777 original size:46 final size:46
Alignment explanation
Indices: 48710--48891 Score: 346
Period size: 46 Copynumber: 4.0 Consensus size: 46
48700 AACTTTGTAA
48710 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGAT
1 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGAT
48756 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGAT
1 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGAT
* *
48802 GAAATTGGTTCTGATGGTGTCAAGAAATTTATACCATCAGGATGAA
1 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGAT
48848 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATG
1 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATG
48892 CAGATGTCGA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (46 bp):
GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGAT
Found at i:49545 original size:55 final size:55
Alignment explanation
Indices: 49458--49854 Score: 382
Period size: 55 Copynumber: 7.2 Consensus size: 55
49448 ATTAAAGATT
*
49458 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGACA
* * * * * * *
49513 ACACCATCAGGATCAATTTATTAGTCCTGATGATTTG-A-G-TAATTTTTAATTGACA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAA-ATTGAA--GACA
*
49568 ACATCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAATG-CA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAA-GACA
* * * * * ** *
49623 ACACCATCAGGATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATT-AA-A-A
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCT--G-AATGATAAATTGAAGACA
* * *
49678 CCACCATCAGGACCAATTTTTTGGTCCAGATGATCTAAATGATAAATTGAAGGCA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGACA
* * * * * * *
49733 ACACCATCAGGATCAATTTATTAGTCCCGATGATTTG-A-G-TAATTTTTAATTGACA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAA-ATTGAA--GACA
*
49788 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAATACA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGACA
49843 ACACCATCAGGA
1 ACACCATCAGGA
49855 TCAAGCTATT
Statistics
Matches: 269, Mismatches: 54, Indels: 38
0.75 0.15 0.11
Matches are distributed among these distances:
52 14 0.05
53 12 0.04
54 2 0.01
55 210 0.78
56 4 0.01
57 13 0.05
58 14 0.05
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (55 bp):
ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGACA
Found at i:49655 original size:110 final size:110
Alignment explanation
Indices: 49458--49858 Score: 723
Period size: 110 Copynumber: 3.6 Consensus size: 110
49448 ATTAAAGATT
49458 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
49523 GATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATTGACA
66 GATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATTGACA
* *
49568 ACATCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAATGCAACACCATCAG
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
*
49633 GATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATT-AAA
66 GATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATTGACA
*
49677 ACCACCATCAGGACCAATTTTTTGGTCCAGATGATCTAAATGATAAATTGAAGGCAACACCATCA
1 A-CACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCA
*
49742 GGATCAATTTATTAGTCCCGATGATTTGAGTAATTTTTAATTGACA
65 GGATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATTGACA
**
49788 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAATACAACACCATCAG
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
49853 GATCAA
66 GATCAA
49859 GCTATTTATC
Statistics
Matches: 278, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
109 3 0.01
110 272 0.98
111 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (110 bp):
ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACACCATCAG
GATCAATTTATTAGTCCTGATGATTTGAGTAATTTTTAATTGACA
Found at i:52460 original size:2 final size:2
Alignment explanation
Indices: 52444--52480 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
52434 TCTATACAGC
*
52444 AT AT AG AT A- 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
52481 TCATAGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:52780 original size:2 final size:2
Alignment explanation
Indices: 52773--52798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52763 TGGGAACTTC
52773 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
52799 TTCATATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55100 original size:3 final size:3
Alignment explanation
Indices: 55092--55133 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
55082 TTTTAGACAA
55092 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55134 TTGGATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56204 original size:3 final size:3
Alignment explanation
Indices: 56191--56230 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
56181 AACCCTCTTG
56191 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56231 AATACAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:62831 original size:14 final size:14
Alignment explanation
Indices: 62814--62855 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
62804 AAAAAGCTTT
62814 AAAGAAGAAAACAA
1 AAAGAAGAAAACAA
*
62828 AAAGAAGAAAAAAA
1 AAAGAAGAAAACAA
62842 AAAGAAGAAGAACA
1 AAAGAAGAA-AACA
62856 GCGTGCGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAACAA
Found at i:62969 original size:4 final size:4
Alignment explanation
Indices: 62960--62999 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
62950 CCGACTGTTC
*
62960 TTCT TTCT TTCT TTCT TTCTT TTCT CTCT TTCT CTTCT TT
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT -TTCT TT
63000 AAACTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:62989 original size:13 final size:12
Alignment explanation
Indices: 62957--62998 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
62947 GACCCGACTG
62957 TTCTTCTTTC-T
1 TTCTTCTTTCTT
62968 TTCTTTCTTTCTT
1 TTC-TTCTTTCTT
*
62981 TTCTCTCTTTCTC
1 TTCT-TCTTTCTT
62994 TTCTT
1 TTCTT
62999 TAAACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.11
12 9 0.33
13 15 0.56
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCTTCTTTCTT
Found at i:70382 original size:59 final size:59
Alignment explanation
Indices: 70290--70412 Score: 246
Period size: 59 Copynumber: 2.1 Consensus size: 59
70280 GGAATTATGG
70290 TTTGATGCTCATAGAATTTTGTGTAAGGTTATAGGTCACTTTCTAAACATCTTATGTAA
1 TTTGATGCTCATAGAATTTTGTGTAAGGTTATAGGTCACTTTCTAAACATCTTATGTAA
70349 TTTGATGCTCATAGAATTTTGTGTAAGGTTATAGGTCACTTTCTAAACATCTTATGTAA
1 TTTGATGCTCATAGAATTTTGTGTAAGGTTATAGGTCACTTTCTAAACATCTTATGTAA
70408 TTTGA
1 TTTGA
70413 AAAAGAAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (59 bp):
TTTGATGCTCATAGAATTTTGTGTAAGGTTATAGGTCACTTTCTAAACATCTTATGTAA
Found at i:83605 original size:21 final size:21
Alignment explanation
Indices: 83571--83634 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
83561 TCGGTGAGAG
*
83571 TAAAATTGGTTACTGTAC-GTA
1 TAAAATTTGTTACTGTACAG-A
* *
83592 TTAGATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
*
83613 TAAAATTTGTTACTGTATAGA
1 TAAAATTTGTTACTGTACAGA
83634 T
1 T
83635 GAGAATATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (21 bp):
TAAAATTTGTTACTGTACAGA
Found at i:89773 original size:106 final size:105
Alignment explanation
Indices: 89578--89815 Score: 341
Period size: 106 Copynumber: 2.2 Consensus size: 105
89568 GAGTTTGAAA
* *
89578 CTCGACTCGATCCTATTTGTCATGTTCGAGCTCGGTTCCCATCCAATACATTGTCAGACTCCAAC
1 CTCGAC-CGATCCTATTT-TCATGTTCGAACTCAGTTCCCATCCAATACATTGTCAGACTCCAAC
*
89643 TCGGCTTGATTTTGAAACTTGGAGTTCGAAACTCGACTCAAG
64 TCGGCTCGATTTTGAAACTTGGAGTTCGAAACTCGACTCAAG
* * * * *
89685 CTTGATCGGTCCTACTTTTCATGTTCGAACTCAGTTCCCATCCAATACATTGTTAGACTCGAACT
1 CTCGACCGATCCTA-TTTTCATGTTCGAACTCAGTTCCCATCCAATACATTGTCAGACTCCAACT
* *
89750 CGGCTCGATTTTGAAACTTGGAGTTCGAAACTCGGCTCGAG
65 CGGCTCGATTTTGAAACTTGGAGTTCGAAACTCGACTCAAG
*
89791 CTCGACCGATTCTATTTTTCATGTT
1 CTCGACCGATCCTA-TTTTCATGTT
89816 GAGCTCGGTT
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
106 108 0.94
107 7 0.06
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.33
Consensus pattern (105 bp):
CTCGACCGATCCTATTTTCATGTTCGAACTCAGTTCCCATCCAATACATTGTCAGACTCCAACTC
GGCTCGATTTTGAAACTTGGAGTTCGAAACTCGACTCAAG
Found at i:94218 original size:31 final size:31
Alignment explanation
Indices: 94183--94257 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
94173 ACGGTGTCCG
94183 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
* ** *
94214 ACGTGGCATG-CATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
94244 ACGTGGCATGCCAC
1 ACGTGGCATGCCAC
94258 ATGCACAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGCGAC
Found at i:94267 original size:30 final size:30
Alignment explanation
Indices: 94183--94267 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
94173 ACGGTGTCCG
94183 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTA-CAAAAAGCGAC
* * *
94214 ACGTGGCATG-CATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTG-TACAAAAAGCGAC
* *
94244 ACGTGGCATGCCACATGCACAAAA
1 ACGTGGCATGCCACGTGTACAAAA
94268 GGATACGTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 30 0.67
31 15 0.33
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (30 bp):
ACGTGGCATGCCACGTGTACAAAAAGCGAC
Found at i:96470 original size:53 final size:53
Alignment explanation
Indices: 96390--96496 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
96380 CGGCTGTTTT
96390 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
96443 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
96496 A
1 A
96497 ATGCTAACAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (53 bp):
ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
Found at i:99482 original size:14 final size:13
Alignment explanation
Indices: 99448--99481 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
99438 TTGCAACTTG
99448 ATTTTTTTAATAA
1 ATTTTTTTAATAA
99461 ATTTTTTTAATAA
1 ATTTTTTTAATAA
99474 ATTTTTTT
1 ATTTTTTT
99482 TTGCCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTTTAATAA
Found at i:102354 original size:18 final size:18
Alignment explanation
Indices: 102333--102369 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
102323 AGAGATACAA
102333 AGAGAGACAAACACACAC
1 AGAGAGACAAACACACAC
102351 AGAGAGACAAACACACAC
1 AGAGAGACAAACACACAC
102369 A
1 A
102370 CAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.27, G:0.16, T:0.00
Consensus pattern (18 bp):
AGAGAGACAAACACACAC
Done.