Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006440.1 Corchorus capsularis cultivar CVL-1 contig06461, 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: 48130
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--85 Score: 70
Period size: 2 Copynumber: 43.5 Consensus size: 2
* * *
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA AA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
44 -A T- TC T- TCA TT TA TA TA TA T- TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83 TA T
1 TA T
86 TCAATTAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
1 4 0.06
2 65 0.92
3 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7677 original size:3 final size:3
Alignment explanation
Indices: 7669--7697 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7659 AAATTTTGAA
7669 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7698 AGAAGAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9182 original size:104 final size:104
Alignment explanation
Indices: 9002--9201 Score: 328
Period size: 104 Copynumber: 1.9 Consensus size: 104
8992 CCTCATTTGT
* *
9002 ATTTTTCTAAGTTCTGGATCAAAAGTTATGAATTTTCTTCTAAAACTACTCTTGTGAAGTCCTCC
1 ATTTTTCTAAGTTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTACTCTTATGAAGTCCTCC
**
9067 TTTAAATAGGATTTAACAATGTTGCATCATGGCCGAATC
66 TTTAAATAGGATTTAACAATACTGCATCATGGCCGAATC
* * *
9106 ATTTTTCTAAGTTCTGGATCCAAAGTTATGAATTTTCTTCCAAAATTGCTCTTATGAAGTCCTCC
1 ATTTTTCTAAGTTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTACTCTTATGAAGTCCTCC
*
9171 TTTAAATAGGATTTAGCAATACTGCATCATG
66 TTTAAATAGGATTTAACAATACTGCATCATG
9202 TCTAAATCAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 88 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (104 bp):
ATTTTTCTAAGTTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTACTCTTATGAAGTCCTCC
TTTAAATAGGATTTAACAATACTGCATCATGGCCGAATC
Found at i:11594 original size:22 final size:22
Alignment explanation
Indices: 11569--11734 Score: 99
Period size: 22 Copynumber: 7.6 Consensus size: 22
11559 GGAGATTAAC
* *
11569 AAAATCTCATAGGGAGGTTATT
1 AAAATTTCATAGGAAGGTTATT
* * **
11591 AAAA-ATCATAAGAAGGTTACA
1 AAAATTTCATAGGAAGGTTATT
11612 AAAATTTCATAGGAAGGTTTATT
1 AAAATTTCATAGGAAGG-TTATT
*** *
11635 AAAATTTCATATTTAGGTTATC
1 AAAATTTCATAGGAAGGTTATT
* * *
11657 AAAGTTTCATATGG-AGTTTATC
1 AAAATTTCATA-GGAAGGTTATT
* *
11679 ACAATTTCATAGGTAA--TTATC
1 AAAATTTCATAGG-AAGGTTATT
* *
11700 AAAATTTCATAGCG-TGGTTATC
1 AAAATTTCATAG-GAAGGTTATT
*
11722 AAAATTTAATAGG
1 AAAATTTCATAGG
11735 GTAGTTGGTA
Statistics
Matches: 114, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
21 35 0.31
22 61 0.54
23 18 0.16
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATT
Found at i:11607 original size:21 final size:22
Alignment explanation
Indices: 11569--11645 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
11559 GGAGATTAAC
* *
11569 AAAATCTCATAGGGAGGTTATTA
1 AAAAT-TCATAAGAAGGTTATTA
*
11592 AAAA-TCATAAGAAGGTTA-CA
1 AAAATTCATAAGAAGGTTATTA
*
11612 AAAATTTCATAGGAAGGTTTATTA
1 AAAA-TTCATAAGAAGG-TTATTA
*
11636 AAATTTCATA
1 AAAATTCATA
11646 TTTAGGTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.11
21 12 0.27
22 10 0.23
23 13 0.30
24 4 0.09
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (22 bp):
AAAATTCATAAGAAGGTTATTA
Found at i:11721 original size:43 final size:43
Alignment explanation
Indices: 11612--11734 Score: 106
Period size: 43 Copynumber: 2.8 Consensus size: 43
11602 GAAGGTTACA
* * ** *
11612 AAAATTTCATA-GGAAGGTTTATTAAAATTTCATATTTAGGTTATC
1 AAAATTTCATATGG-AGG-TTATCAAAATTTAATAGGTA-ATTATC
* * * *
11657 AAAGTTTCATATGGAGTTTATCACAATTTCATAGGTAATTATC
1 AAAATTTCATATGGAGGTTATCAAAATTTAATAGGTAATTATC
*
11700 AAAATTTCATA-GCGTGGTTATCAAAATTTAATAGG
1 AAAATTTCATATG-GAGGTTATCAAAATTTAATAGG
11735 GTAGTTGGTA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.02
43 33 0.52
44 16 0.25
45 12 0.19
46 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (43 bp):
AAAATTTCATATGGAGGTTATCAAAATTTAATAGGTAATTATC
Found at i:13460 original size:37 final size:37
Alignment explanation
Indices: 13417--13620 Score: 175
Period size: 37 Copynumber: 5.5 Consensus size: 37
13407 CACTCTTCAT
*
13417 CGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTCC
1 CGCAGAGCTCTCCTTACCGCGGCAGCACCCTCTTTCC
* *
13454 CACAGAGCTCTCCTTACTGCGGC-G-ACTCC-CATATTCAC
1 CGCAGAGCTCTCCTTACCGCGGCAGCAC-CCTC-T-TTC-C
* * *
13492 TGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTAC
1 CGCAGAGCTCTCCTTACCGCGGCAGCACCCTCTTTCC
* *** * * *
13529 CGCAGAGCTCTGCTTATAACAGCGGCTCCCATC-TTCAC
1 CGCAGAGCTCTCCTTACCGCGGCAGCACCC-TCTTTC-C
*
13567 CGCAGAGCTCTCCTT-CCTGCGGCAGCACCCTCTTTAC
1 CGCAGAGCTCTCCTTACC-GCGGCAGCACCCTCTTTCC
*
13604 CGCAGTGCTCTCCTTAC
1 CGCAGAGCTCTCCTTAC
13621 AAATCACTGC
Statistics
Matches: 128, Mismatches: 27, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
35 3 0.02
36 4 0.03
37 64 0.50
38 50 0.39
39 4 0.03
40 3 0.02
ACGTcount: A:0.17, C:0.40, G:0.18, T:0.25
Consensus pattern (37 bp):
CGCAGAGCTCTCCTTACCGCGGCAGCACCCTCTTTCC
Found at i:13558 original size:75 final size:75
Alignment explanation
Indices: 13412--13620 Score: 287
Period size: 75 Copynumber: 2.8 Consensus size: 75
13402 GATAGCACTC
* * * * *
13412 TTCATCGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTCCCACAGAGCTCTCCTTACTGCGGC
1 TTCACCGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTACCGCAGAGCTCTCCTTACTACAGC
13477 GACTCCCATA
66 GACTCCCATA
* *
13487 TTCACTGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTACCGCAGAGCTCTGCTTA-TAACAG
1 TTCACCGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTACCGCAGAGCTCTCCTTACT-ACAG
* *
13551 CGGCTCCCATC
65 CGACTCCCATA
* *
13562 TTCACCGCAGAGCTCTCCTT-CCTGCGGCAGCACCCTCTTTACCGCAGTGCTCTCCTTAC
1 TTCACCGCAGAGCTCTCCTTACC-GCGGTAGCACCCTCTTTACCGCAGAGCTCTCCTTAC
13621 AAATCACTGC
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
74 3 0.03
75 115 0.97
ACGTcount: A:0.17, C:0.40, G:0.18, T:0.26
Consensus pattern (75 bp):
TTCACCGCAGAGCTCTCCTTACCGCGGTAGCACCCTCTTTACCGCAGAGCTCTCCTTACTACAGC
GACTCCCATA
Found at i:14915 original size:29 final size:30
Alignment explanation
Indices: 14880--14947 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
14870 GGTCTTTAAT
* *
14880 GTGTGTGTGAAAT-TCA-TGGGTCTCTTTTA
1 GTGTGTGTGAAATAT-ATTGGGCCCCTTTTA
14909 GTGTGTGTGAAATATATTGGGCCCCTTTTA
1 GTGTGTGTGAAATATATTGGGCCCCTTTTA
14939 GTGTGTGTG
1 GTGTGTGTG
14948 GATCAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 14 0.40
30 21 0.60
ACGTcount: A:0.16, C:0.10, G:0.31, T:0.43
Consensus pattern (30 bp):
GTGTGTGTGAAATATATTGGGCCCCTTTTA
Found at i:16229 original size:149 final size:148
Alignment explanation
Indices: 15979--16404 Score: 723
Period size: 149 Copynumber: 2.9 Consensus size: 148
15969 TCGTTACAAT
* * * * *
15979 AAGGCCCACCGATGCCAAATCTGAAAACA-TTTAGAAGGCCAACCGATGCCAACTTTAGAAA-C-
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
* * *
16041 TTTTTCAAGAAGGCCAACCGATACCAAATTTAAAAACATTTTAGAAGGCTAACCGATGCCAACTT
66 TTTTTCAAGAAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
16106 TGGAAACCTTTTTTCAAG
131 TGGAAACCTTTTTTCAAG
16124 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
*
16189 ATTTTTCAAGAAGGCCAACCGATACCAACTTTGAAGACATTTTAGAAGGCCAACCGATGCCAACT
66 -TTTTTCAAGAAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACT
16254 TTGGAAACCTTTTTTCAAG
130 TTGGAAACCTTTTTTCAAG
*
16273 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAATGCCAACCGATGCCAACTTTGGAAACCC
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAA-CC
16338 TTTTTTCAAGAAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACT
65 TTTTTTCAAGAAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACT
16403 TT
130 TT
16405 TGATGAAGGC
Statistics
Matches: 265, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
145 25 0.09
146 31 0.12
147 1 0.00
149 205 0.77
150 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (148 bp):
AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
TTTTTCAAGAAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
TGGAAACCTTTTTTCAAG
Found at i:16231 original size:75 final size:74
Alignment explanation
Indices: 15979--16404 Score: 723
Period size: 75 Copynumber: 5.8 Consensus size: 74
15969 TCGTTACAAT
* * * * *
15979 AAGGCCCACCGATGCCAAATCTGAAAACA-TTTAGAAGGCCAACCGATGCCAACTTTAGAAA-C-
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
16041 TTTTTCAAG
66 TTTTTCAAG
* * *
16050 AAGGCCAACCGATACCAAATTTAAAAACATTTTAGAAGGCTAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
16115 TTTTTCAAG
66 TTTTTCAAG
16124 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
16189 ATTTTTCAAG
66 -TTTTTCAAG
*
16199 AAGGCCAACCGATACCAACTTTGAAGACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
16264 TTTTTCAAG
66 TTTTTCAAG
*
16273 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAATGCCAACCGATGCCAACTTTGGAAACCC
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAA-CC
16338 TTTTTTCAAG
65 TTTTTTCAAG
16348 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTT
16405 TGATGAAGGC
Statistics
Matches: 337, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
71 25 0.07
72 30 0.09
73 1 0.00
74 140 0.42
75 141 0.42
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (74 bp):
AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
TTTTTCAAG
Found at i:16935 original size:2 final size:2
Alignment explanation
Indices: 16928--16972 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
16918 TAATAAGGAA
* * * *
16928 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16970 AT A
1 AT A
16973 AGTAGAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29431 original size:21 final size:20
Alignment explanation
Indices: 29407--29453 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
29397 ATCATATATT
29407 ATATTTATTTT-ATACTAAAAA
1 ATATTTATTTTCATA--AAAAA
*
29428 ATATTTTTTTTCATAAAAAA
1 ATATTTATTTTCATAAAAAA
29448 AT-TTTA
1 ATATTTA
29454 AAACAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 7 0.30
21 10 0.43
22 3 0.13
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTATTTTCATAAAAAA
Found at i:30012 original size:17 final size:17
Alignment explanation
Indices: 29980--30029 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
29970 CGTGGCATAA
*
29980 GAAATAAATATTTTTATT
1 GAAATATAT-TTTTTATT
**
29998 TTAATATATTTTTTATT
1 GAAATATATTTTTTATT
*
30015 GAAATTTATTTTTTA
1 GAAATATATTTTTTA
30030 ATAATAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GAAATATATTTTTTATT
Found at i:30193 original size:69 final size:72
Alignment explanation
Indices: 30070--30208 Score: 248
Period size: 69 Copynumber: 2.0 Consensus size: 72
30060 TTTTCCACAG
30070 ACAACAAAAACATTTCTCTCTCCTCAATCAATTAAAGATCAAACACCCCCTTTTTCATGAACAAA
1 ACAACAAAAACATTTCTCTCTCCTC-ATCAATTAAAGATCAAACACCCCCTTTTTCATGAACAAA
30135 GAATACAA
65 GAATACAA
30143 ACAACAAAAACATTTCTCTCT-C-C-TCAATTAAAGATCAAACACCCCCTTTTTCATGAACAAAG
1 ACAACAAAAACATTTCTCTCTCCTCATCAATTAAAGATCAAACACCCCCTTTTTCATGAACAAAG
30205 AATA
66 AATA
30209 ATCCTCGATT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
69 43 0.65
71 1 0.02
72 1 0.02
73 21 0.32
ACGTcount: A:0.43, C:0.27, G:0.04, T:0.25
Consensus pattern (72 bp):
ACAACAAAAACATTTCTCTCTCCTCATCAATTAAAGATCAAACACCCCCTTTTTCATGAACAAAG
AATACAA
Found at i:32339 original size:11 final size:10
Alignment explanation
Indices: 32313--32364 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
32303 ATTTCTGTTC
*
32313 CTTTCTTTTT
1 CTTTTTTTTT
32323 CTTTTTCTTTTT
1 C-TTTT-TTTTT
32335 CTTTTTTTTTT
1 C-TTTTTTTTT
*
32346 CTTTTTTTTC
1 CTTTTTTTTT
32356 CTTTTTTTT
1 CTTTTTTTT
32365 AATGAGTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 18 0.47
11 9 0.24
12 11 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:32360 original size:6 final size:6
Alignment explanation
Indices: 32314--32351 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
32304 TTTCTGTTCC
32314 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
32352 TTTCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTCTT
Found at i:32360 original size:17 final size:17
Alignment explanation
Indices: 32314--32362 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
32304 TTTCTGTTCC
*
32314 TTTCTTTTTCTTTTTCTT
1 TTTCTTTCT-TTTTTCTT
*
32332 TTTCTTTTTTTTTTCTT
1 TTTCTTTCTTTTTTCTT
32349 TTT-TTTCCTTTTTT
1 TTTCTTT-CTTTTTT
32363 TTAATGAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.10
17 17 0.59
18 9 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTCTTTCTTTTTTCTT
Found at i:32362 original size:12 final size:11
Alignment explanation
Indices: 32318--32364 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
32308 TGTTCCTTTC
32318 TTTTTCTTTTT
1 TTTTTCTTTTT
32329 CTTTTTCTTTTT
1 -TTTTTCTTTTT
32341 TTTTTC-TTTT
1 TTTTTCTTTTT
*
32351 TTTTCCTTTTT
1 TTTTTCTTTTT
32362 TTT
1 TTT
32365 AATGAGTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 9 0.27
11 13 0.39
12 11 0.33
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:32986 original size:35 final size:35
Alignment explanation
Indices: 32871--33281 Score: 403
Period size: 35 Copynumber: 11.6 Consensus size: 35
32861 TCGTTACAAT
* * * *
32871 AAGGCCCACTGATGCCAAATCTGAAAACA-TTTAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
* * *
32905 AAGGCCAACCGATGTCAACTTTGGAAACTTTTTCAAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTT--AG
* *
32942 AAGGCCAACCGATACCAACTTTAAAAACATTTTAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
* * *
32977 AAGGTCAACCGATGCCAACTTTGGAAACCTTTTTTCAAG
1 AAGGCCAACCGATGCCAACTTT-GAAAAC-ATTTT--AG
*
33016 AAGGCCAACCGATACCAACTTTGAAAACATTTTAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
*
33051 AAGGCCAACCGATGCCAACTTTG---------GA-
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
* *
33076 AAGGCCAACCGATACCAACTTTGAAGACATTTTAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
* *
33111 AAGGCCAACCGATGCCAACTTTGGAAACCTTTTTTCAAG
1 AAGGCCAACCGATGCCAACTTT-GAAAAC-ATTTT--AG
* *
33150 AAAGCCAACCGATACCAACTTTGAAAACATTTTAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
* *
33185 AAGGCCAACCGATGCCAACTTTGGAAACCCTTTTTTCAAG
1 AAGGCCAACCGATGCCAACTTT-GAAA-AC-ATTTT--AG
*
33225 AAGGCCAACCGATACCAACTTTGAAAACATTTTAG
1 AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
33260 AAGGCCAACCGATGCCAACTTT
1 AAGGCCAACCGATGCCAACTTT
33282 TGACGAAGGC
Statistics
Matches: 310, Mismatches: 41, Indels: 51
0.77 0.10 0.13
Matches are distributed among these distances:
25 22 0.07
26 1 0.00
34 23 0.07
35 115 0.37
36 12 0.04
37 51 0.16
38 15 0.05
39 48 0.15
40 23 0.07
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (35 bp):
AAGGCCAACCGATGCCAACTTTGAAAACATTTTAG
Found at i:33037 original size:74 final size:72
Alignment explanation
Indices: 32894--33281 Score: 550
Period size: 74 Copynumber: 5.5 Consensus size: 72
32884 GCCAAATCTG
*
32894 AAAACA-TTTAGAAGGCCAACCGATGTCAACTTTGGAAACTTTTTCAAGAAGGCCAACCGATACC
1 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTCAAGAAGGCCAACCGATACC
32958 AACTTTA
66 AACTTTA
*
32965 AAAACATTTTAGAAGGTCAACCGATGCCAACTTTGGAAACCTTTTTTCAAGAAGGCCAACCGATA
1 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAA-C-TTTTTCAAGAAGGCCAACCGATA
*
33030 CCAACTTTG
64 CCAACTTTA
33039 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGG-----------A-AAGGCCAACCGATACC
1 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTCAAGAAGGCCAACCGATACC
*
33092 AACTTTG
66 AACTTTA
* *
33099 AAGACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCTTTTTTCAAGAAAGCCAACCGATA
1 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAA-C-TTTTTCAAGAAGGCCAACCGATA
*
33164 CCAACTTTG
64 CCAACTTTA
33173 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCCTTTTTTCAAGAAGGCCAACCGAT
1 AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAA--C-TTTTTCAAGAAGGCCAACCGAT
*
33238 ACCAACTTTG
63 ACCAACTTTA
33248 AAAACATTTTAGAAGGCCAACCGATGCCAACTTT
1 AAAACATTTTAGAAGGCCAACCGATGCCAACTTT
33282 TGACGAAGGC
Statistics
Matches: 291, Mismatches: 8, Indels: 32
0.88 0.02 0.10
Matches are distributed among these distances:
60 58 0.20
61 1 0.00
71 6 0.02
72 30 0.10
73 2 0.01
74 126 0.43
75 68 0.23
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (72 bp):
AAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTCAAGAAGGCCAACCGATACC
AACTTTA
Found at i:33079 original size:25 final size:25
Alignment explanation
Indices: 33051--33098 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
33041 AACATTTTAG
*
33051 AAGGCCAACCGATGCCAACTTTGGA
1 AAGGCCAACCGATACCAACTTTGGA
33076 AAGGCCAACCGATACCAACTTTG
1 AAGGCCAACCGATACCAACTTTG
33099 AAGACATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (25 bp):
AAGGCCAACCGATACCAACTTTGGA
Found at i:33086 original size:60 final size:60
Alignment explanation
Indices: 33016--33137 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
33006 TTTTTTCAAG
33016 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGA
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGA
*
33076 AAGGCCAACCGATACCAACTTTGAAGACATTTTAGAAGGCCAACCGATGCCAACTTTGGA
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGA
33136 AA
1 AA
33138 CCTTTTTTCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGA
Found at i:33182 original size:134 final size:134
Alignment explanation
Indices: 32942--33211 Score: 504
Period size: 134 Copynumber: 2.0 Consensus size: 134
32932 CTTTTTCAAG
*
32942 AAGGCCAACCGATACCAACTTTAAAAACATTTTAGAAGGTCAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTAAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
*
33007 TTTTTCAAGAAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
66 TTTTTCAAGAAAGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
33072 TGGA
131 TGGA
* *
33076 AAGGCCAACCGATACCAACTTTGAAGACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTAAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
33141 TTTTTCAAGAAAGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
66 TTTTTCAAGAAAGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
33206 TGGA
131 TGGA
33210 AA
1 AA
33212 CCCTTTTTTC
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (134 bp):
AAGGCCAACCGATACCAACTTTAAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
TTTTTCAAGAAAGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTT
TGGA
Found at i:33261 original size:75 final size:74
Alignment explanation
Indices: 33076--33281 Score: 385
Period size: 75 Copynumber: 2.8 Consensus size: 74
33066 CAACTTTGGA
*
33076 AAGGCCAACCGATACCAACTTTGAAGACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
33141 TTTTTCAAG
66 TTTTTCAAG
*
33150 AAAGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCC
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAA-CC
33215 TTTTTTCAAG
65 TTTTTTCAAG
33225 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTT
1 AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTT
33282 TGACGAAGGC
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
74 60 0.47
75 68 0.53
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (74 bp):
AAGGCCAACCGATACCAACTTTGAAAACATTTTAGAAGGCCAACCGATGCCAACTTTGGAAACCT
TTTTTCAAG
Found at i:33311 original size:27 final size:27
Alignment explanation
Indices: 33259--33311 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
33249 AAACATTTTA
**
33259 GAAGGCCAACCGATGCCAACTTTTGAC
1 GAAGGCCAACCGATGCCAACGCTTGAC
* *
33286 GAAGGCCCACCGATGGCAACGCTTGA
1 GAAGGCCAACCGATGCCAACGCTTGA
33312 AAGATACTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.15
Consensus pattern (27 bp):
GAAGGCCAACCGATGCCAACGCTTGAC
Found at i:34287 original size:12 final size:12
Alignment explanation
Indices: 34270--34294 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34260 TACATAATTA
34270 TTGGTGTTTATT
1 TTGGTGTTTATT
34282 TTGGTGTTTATT
1 TTGGTGTTTATT
34294 T
1 T
34295 GATCAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TTGGTGTTTATT
Found at i:38873 original size:26 final size:26
Alignment explanation
Indices: 38837--38900 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
38827 TCTGCACTAG
38837 CCCTTGCTTGGGGTGGCTCGGGGTAT
1 CCCTTGCTTGGGGTGGCTCGGGGTAT
38863 CCCTTGCTTGGGGTGGCTCGGGGTAT
1 CCCTTGCTTGGGGTGGCTCGGGGTAT
* *
38889 CCCATGCATGGG
1 CCCTTGCTTGGG
38901 TCGGACTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.06, C:0.25, G:0.41, T:0.28
Consensus pattern (26 bp):
CCCTTGCTTGGGGTGGCTCGGGGTAT
Found at i:41591 original size:33 final size:33
Alignment explanation
Indices: 41512--41621 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 33
41502 TTACAAAGAG
* * *
41512 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTTGATGTTGTTTGCGATGAAACTAAATC
** *
41545 T-AATTTGAGTGTTGTTTGCGATGACACTAAATC
1 TGTTTTTGA-TGTTGTTTGCGATGAAACTAAATC
* * *
41578 TGTTTTTGATGTTGTTTGTGATAAAACAAAATC
1 TGTTTTTGATGTTGTTTGCGATGAAACTAAATC
*
41611 TGTTTTGGATG
1 TGTTTTTGATG
41622 CTAATTATGA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 4 0.06
33 54 0.86
34 5 0.08
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (33 bp):
TGTTTTTGATGTTGTTTGCGATGAAACTAAATC
Done.