Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020904.1 Corchorus olitorius cultivar O-4 contig20937, 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: 59666
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2365 original size:14 final size:14
Alignment explanation
Indices: 2346--2372 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2336 TTGCTGCTTC
2346 TGTTTAATCCTTAT
1 TGTTTAATCCTTAT
2360 TGTTTAATCCTTA
1 TGTTTAATCCTTA
2373 CTGAATTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (14 bp):
TGTTTAATCCTTAT
Found at i:2632 original size:1 final size:1
Alignment explanation
Indices: 2626--2657 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
2616 TTAGTTCCAT
2626 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2658 CTAGTGCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4831 original size:84 final size:83
Alignment explanation
Indices: 4708--4869 Score: 288
Period size: 84 Copynumber: 1.9 Consensus size: 83
4698 TAGGATTTCT
* *
4708 TTTGGCTTTTGATACCATAAAAGAGTTTAAAGAATGGTTATCTCGCTTAGATTGGGAGATAGAAT
1 TTTGGCTTTTGATACCATAAAAGAGTTTAAAGAATGGTTATCTCCCTTAGATTGAGAGATAGAAT
4773 CCCATTCTATTTAAATCC
66 CCCATTCTATTTAAATCC
*
4791 TTTGGCTTTTGATACCATAAAAAGAGTTTAAAGAATGGTTATCTCCCTTTGATTGAGAGATAGAA
1 TTTGGCTTTTGATACCAT-AAAAGAGTTTAAAGAATGGTTATCTCCCTTAGATTGAGAGATAGAA
4856 TCCCATTCTATTTA
65 TCCCATTCTATTTA
4870 TACAGGGGTT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 18 0.24
84 57 0.76
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (83 bp):
TTTGGCTTTTGATACCATAAAAGAGTTTAAAGAATGGTTATCTCCCTTAGATTGAGAGATAGAAT
CCCATTCTATTTAAATCC
Found at i:6423 original size:19 final size:18
Alignment explanation
Indices: 6399--6434 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6389 TAAAGACTCA
6399 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
6418 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
6435 ATTATTTCAA
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:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:7101 original size:15 final size:16
Alignment explanation
Indices: 7074--7103 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7064 CACAAGGAAC
7074 AATTAATTTCTATTAT
1 AATTAATTTCTATTAT
7090 AATTAA-TTCTATTA
1 AATTAATTTCTATTA
7104 AGAAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAATTTCTATTAT
Found at i:14407 original size:21 final size:21
Alignment explanation
Indices: 14381--14456 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
14371 GAGGAAGGTA
14381 CGGATGACCGGGCAAGCGGCG
1 CGGATGACCGGGCAAGCGGCG
14402 CGGATGACCGGGCAAGCGGCG
1 CGGATGACCGGGCAAGCGGCG
* * * * * *
14423 GGGATGGCCGGGCATGTGACT
1 CGGATGACCGGGCAAGCGGCG
14444 CGGATGACCGGGC
1 CGGATGACCGGGC
14457 CATGTCCGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.17, C:0.26, G:0.47, T:0.09
Consensus pattern (21 bp):
CGGATGACCGGGCAAGCGGCG
Found at i:17357 original size:20 final size:21
Alignment explanation
Indices: 17321--17360 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
17311 CAAAAACAAA
17321 TTTTTTTTTATGACGCAAAAAC
1 TTTTTTTTTAT-ACGCAAAAAC
17343 TTTTTTTTTAT-CGCAAAA
1 TTTTTTTTTATACGCAAAA
17361 CCGAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTTTTTTATACGCAAAAAC
Found at i:24869 original size:15 final size:15
Alignment explanation
Indices: 24849--24880 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
24839 AAACTAAGTG
24849 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
24864 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
24879 GA
1 GA
24881 ACCCCCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:27810 original size:37 final size:37
Alignment explanation
Indices: 27755--27867 Score: 217
Period size: 37 Copynumber: 3.1 Consensus size: 37
27745 GAATACTTGA
*
27755 TAGGTTTATTGCTTGAATAATTGAGTCATATGCTAGT
1 TAGGGTTATTGCTTGAATAATTGAGTCATATGCTAGT
27792 TAGGGTTATTGCTTGAATAATTGAGTCATATGCTAGT
1 TAGGGTTATTGCTTGAATAATTGAGTCATATGCTAGT
27829 TAGGGTTATTGCTTGAATAATTGAGTCATATGCTAGT
1 TAGGGTTATTGCTTGAATAATTGAGTCATATGCTAGT
27866 TA
1 TA
27868 TTATTTACAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (37 bp):
TAGGGTTATTGCTTGAATAATTGAGTCATATGCTAGT
Found at i:29184 original size:11 final size:10
Alignment explanation
Indices: 29168--29214 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
29158 AAGCTCTTGT
29168 TTGAAGACTCA
1 TTGAAGA-TCA
*
29179 TTGAAGATAA
1 TTGAAGATCA
29189 TTTGAAGAT--
1 -TTGAAGATCA
29198 TTGAAGATCA
1 TTGAAGATCA
29208 TTGAAGA
1 TTGAAGA
29215 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:29203 original size:19 final size:18
Alignment explanation
Indices: 29179--29214 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29169 TGAAGACTCA
29179 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
29198 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
29215 ATTATTTCAA
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:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:32325 original size:52 final size:52
Alignment explanation
Indices: 32247--32523 Score: 432
Period size: 52 Copynumber: 5.3 Consensus size: 52
32237 AATCGAACAC
* * * *
32247 ACTTTTCCACTTTGGAAAGACCTAAATCAAACGCTTTGAAAACTTGATGGGA
1 ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTGATGGGA
* *
32299 ACTTTTCCACTTTGAAAAGACCTAAATCGAACGCTTTGAAAACTTGATGGGA
1 ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTGATGGGA
* *
32351 ACTTTCCCACTTTCAAAAGACCTAAATCGAACACATTGAAAACTTGATGGGA
1 ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTGATGGGA
*
32403 ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAACACTTGATGGGA
1 ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTGATGGGA
* *
32455 ACTTTCCCACTTTG-AAA-ACCTAAATCGAATACTTTGAAAACTGGATGGGA
1 ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTGATGGGA
32505 ACTTTCCCCACTTTGAAAA
1 ACTTT-CCCACTTTGAAAA
32524 TTTTGAATGT
Statistics
Matches: 211, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
50 35 0.17
51 12 0.06
52 164 0.78
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (52 bp):
ACTTTCCCACTTTGAAAAGACCTAAATCGAACACTTTGAAAACTTGATGGGA
Found at i:36864 original size:34 final size:37
Alignment explanation
Indices: 36826--36911 Score: 97
Period size: 43 Copynumber: 2.2 Consensus size: 37
36816 GTCTAATTAG
36826 ATGCAAATTT-TGC-ATA-AAGATGGTCCAATTAAAC
1 ATGCAAATTTATGCAATAGAAGATGGTCCAATTAAAC
36860 ATGCAAATTCTGATTATGCAATATGAAGATGGTCCAATTAAAC
1 ATGCAAA---T--TTATGCAATA-GAAGATGGTCCAATTAAAC
36903 ATGCAAATT
1 ATGCAAATT
36912 CTGATTATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
34 7 0.16
37 1 0.02
38 1 0.02
39 2 0.05
40 4 0.09
41 3 0.07
43 25 0.58
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
ATGCAAATTTATGCAATAGAAGATGGTCCAATTAAAC
Found at i:36903 original size:43 final size:43
Alignment explanation
Indices: 36842--36929 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
36832 ATTTTGCATA
36842 AAGATGGTCCAATTAAACATGCAAATTCTGATTATGCAATATG
1 AAGATGGTCCAATTAAACATGCAAATTCTGATTATGCAATATG
36885 AAGATGGTCCAATTAAACATGCAAATTCTGATTATGCAATATG
1 AAGATGGTCCAATTAAACATGCAAATTCTGATTATGCAATATG
36928 AA
1 AA
36930 TAGGAACCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (43 bp):
AAGATGGTCCAATTAAACATGCAAATTCTGATTATGCAATATG
Found at i:39111 original size:26 final size:26
Alignment explanation
Indices: 39082--39145 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
39072 GAAATCTGGC
39082 CCAACCCATGCATGGGGTACCCTCGA
1 CCAACCCATGCATGGGGTACCCTCGA
39108 CCAACCCATGCATGGGGTACCCTCGA
1 CCAACCCATGCATGGGGTACCCTCGA
39134 CCAACCCATGCA
1 CCAACCCATGCA
39146 AGGGCTAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.25, C:0.41, G:0.20, T:0.14
Consensus pattern (26 bp):
CCAACCCATGCATGGGGTACCCTCGA
Found at i:39702 original size:15 final size:15
Alignment explanation
Indices: 39682--39713 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39672 TGTTGAAGTC
39682 TTATCATATATCTCA
1 TTATCATATATCTCA
39697 TTATCATATATCTCA
1 TTATCATATATCTCA
39712 TT
1 TT
39714 TCTTCTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATCATATATCTCA
Found at i:42594 original size:12 final size:12
Alignment explanation
Indices: 42579--42604 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42569 AACAAAATTG
42579 TATTAGGCTAAC
1 TATTAGGCTAAC
42591 TATTAGGCTAAC
1 TATTAGGCTAAC
42603 TA
1 TA
42605 AGGGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
TATTAGGCTAAC
Found at i:44370 original size:21 final size:21
Alignment explanation
Indices: 44346--44416 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
44336 CTTAGGCAAT
*
44346 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
44367 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
44388 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
44409 TCCAATGA
1 TCCAATGA
44417 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:45150 original size:21 final size:24
Alignment explanation
Indices: 45121--45171 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
45111 TTTTGAACTC
45121 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
45144 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
45167 ATTAT
1 ATTAT
45172 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:45166 original size:25 final size:25
Alignment explanation
Indices: 45121--45169 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
45111 TTTTGAACTC
*
45121 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
45146 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
45170 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:46392 original size:36 final size:36
Alignment explanation
Indices: 46343--46882 Score: 690
Period size: 36 Copynumber: 15.2 Consensus size: 36
46333 TAAGCTCAAA
46343 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* * * * *
46379 TAAATAACTAAAATCA-ACAAAAAACTTAATTTAGGG
1 TAATTAAGTAAAATCAGTC-AAAGACTTAATTCAGGG
*
46415 TAATTAAGTAAATTCAGT-AAAG---T-A--CAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* *
46444 TAATTAAGTAAAATCAGCCAAAGACTTAATTTAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
46480 TAATTAAGTAAAATCAGT-AAAGGACTTAATTCTGGG
1 TAATTAAGTAAAATCAGTCAAA-GACTTAATTCAGGG
* * *
46516 TAATTAAGTAAGAGCAGTCCAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* * * *
46552 TAATTAAATAAAATCAGTCAAAGGCTTAATTTAGCG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* *
46588 TAAATAAGTAGAATCAGTCAAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* *
46624 TAATTAAGTAAAATCAGTAAAAGACTTAATTCTGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
46660 TAATTAAGT-AAATCAATCAAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* *
46695 TAATTAAGTAAAACCAGTCAAAGATTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
46731 TAATTAAGTAAAATCAGT-AAAGGACTTAATTCAAGG
1 TAATTAAGTAAAATCAGTCAAA-GACTTAATTCAGGG
* * *
46767 TAATTAAGTAAAGTCAGTCAAAGACCTAATCCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
*
46803 TAATTAAGTAAAATCGGT-AAAGTACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGG
* *
46839 TAATTAAGTAAAGTCAGTCAAAGATTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
46875 TAATTAAG
1 TAATTAAG
46883 GGGTCGTTTG
Statistics
Matches: 430, Mismatches: 58, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.05
30 4 0.01
31 1 0.00
32 1 0.00
33 1 0.00
34 1 0.00
35 46 0.11
36 347 0.81
37 9 0.02
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
Found at i:47316 original size:36 final size:36
Alignment explanation
Indices: 47275--47694 Score: 614
Period size: 36 Copynumber: 11.7 Consensus size: 36
47265 AATAAAAAAG
* *
47275 GACTTAATTCATGGTAATTAAGTAGAATCAGTCAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
47311 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
47347 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
* * * *
47383 AACTTAATTCAGGGTAATTAAGT-AAATAAATAAAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGT-CAAA
*
47419 GACTTAATTTAGGGTAATTAAGTAAAATCAGTCAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
* *
47455 GACTTAATTCAGGGTAATTAAGTAAAATCAATCAAG
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
*
47491 GACTTAATTTAGGGTAATTAAGTAAAATCAGTCAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
*
47527 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAG
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
* * * *
47563 GACTTAATTAAGGGTAATTAAGGAAAGTCAGTAAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
47599 GACTTAATTCAGGGTAATTAAGTAAAATCAG-CAAA
1 GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
* * *
47634 GTACTTAACTCAGCGTAATTAAGTAAAATTAGT-AAA
1 G-ACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
*
47670 TAAC-TAATTCAGGGTAATTAAGTAA
1 -GACTTAATTCAGGGTAATTAAGTAA
47695 GTAGCTTAAT
Statistics
Matches: 345, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
35 29 0.08
36 310 0.90
37 6 0.02
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (36 bp):
GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAA
Found at i:47913 original size:56 final size:55
Alignment explanation
Indices: 47753--47935 Score: 233
Period size: 55 Copynumber: 3.3 Consensus size: 55
47743 AGATAAAGTA
* * * *
47753 AATAAAATGGCTTAATTCAGAGTAAATTGTGTCTGTAGAAAAGAAAAAAAAAAGAT
1 AATAAAAGGGCTTAATTCAGGGTAAATTGAGTCTGTAGAAAAG-AAAAAAAAGGAT
*
47809 AATAAAAGGGCTTAATTCAGGGTAAATTGAGTTTGTAGAAAAGAAAAAAAAGGAT
1 AATAAAAGGGCTTAATTCAGGGTAAATTGAGTCTGTAGAAAAGAAAAAAAAGGAT
* * * * *
47864 AATAAAAGGGCTTAATTCGGGGTAAATTGAGTCAGTCA-AAGAGATAAAAAGGGAT
1 AATAAAAGGGCTTAATTCAGGGTAAATTGAGTCTGT-AGAAAAGAAAAAAAAGGAT
* *
47919 AATCAAACGGCTTAATT
1 AATAAAAGGGCTTAATT
47936 TAGATTTAAT
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
55 73 0.65
56 40 0.35
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.24
Consensus pattern (55 bp):
AATAAAAGGGCTTAATTCAGGGTAAATTGAGTCTGTAGAAAAGAAAAAAAAGGAT
Found at i:55958 original size:107 final size:105
Alignment explanation
Indices: 55814--56084 Score: 328
Period size: 98 Copynumber: 2.6 Consensus size: 105
55804 AAATTAAAGG
* * * *
55814 TTTATTATTATAGAGTTCTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGGCCTAAATTA
1 TTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACT-AGTTTA-GCCCAAATTA
* *
55879 AAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAA
64 AAATTTTATTTTTATTTCAAGGGTAAATTACAAAATTAATAA
* * * *
55921 TTTATTGTTATAGGGTTTTATAAATAAAATACAAAACTAATGTCAC-------CCCCAAATTAAA
1 TTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAGTTTAGCCCAAATTAAA
*
55979 ATTTTATTTTTATTTCAAGGGTAAATTACATAATTAATAA
66 ATTTTATTTTTATTTCAAGGGTAAATTACAAAATTAATAA
* *
56019 --TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTTAGTTTAGTCCAAATTAA
1 TTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCAC-TAGTTTAGCCCAAATTAA
56081 AATT
65 AATT
56085 AAAATATTAG
Statistics
Matches: 139, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
95 4 0.03
96 35 0.25
98 47 0.34
103 13 0.09
107 40 0.29
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
TTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAGTTTAGCCCAAATTAAA
ATTTTATTTTTATTTCAAGGGTAAATTACAAAATTAATAA
Found at i:58312 original size:17 final size:16
Alignment explanation
Indices: 58281--58327 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
58271 TAGGGTTTAG
58281 TTATATATA-TATATA
1 TTATATATATTATATA
58296 TTATATTATATTATATA
1 TTATA-TATATTATATA
* *
58313 TAATAATAAATTATA
1 TTAT-ATATATTATA
58328 AATGCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 17 0.63
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATATATTATATA
Found at i:58371 original size:2 final size:2
Alignment explanation
Indices: 58247--58356 Score: 58
Period size: 2 Copynumber: 58.5 Consensus size: 2
58237 TTTCTGATAC
* * * *
58247 AT AT AC AT AT AT AT AT AT AT AT AT -T AGG GT TT AGT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
*
58289 AT AT AT AT -T AT AT -T AT AT -T AT AT AT A- AT A- AT AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** *
58325 AT AA AT GC AA AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58357 ATTAAAAAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
1 9 0.11
2 71 0.88
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Done.