Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022840.1 Corchorus olitorius cultivar O-4 contig22873, 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: 36201
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3081 original size:21 final size:22
Alignment explanation
Indices: 3057--3097 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3047 TTACCTCATA
*
3057 CATTCATTCAT-CATGCCATGG
1 CATTCATTCATGCATCCCATGG
3078 CATTCATTCATGCATCCCAT
1 CATTCATTCATGCATCCCAT
3098 TTAACTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (22 bp):
CATTCATTCATGCATCCCATGG
Found at i:5600 original size:15 final size:15
Alignment explanation
Indices: 5573--5622 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5563 AGAAGTTCAA
5573 AAAAAATCAATCAATC
1 AAAAAATC-ATCAATC
**
5589 AAAAAATCATCAAAA
1 AAAAAATCATCAATC
**
5604 AAAAAATCAAAAATC
1 AAAAAATCATCAATC
5619 AAAA
1 AAAA
5623 TCAAAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAATCATCAATC
Found at i:6296 original size:50 final size:50
Alignment explanation
Indices: 6221--6411 Score: 276
Period size: 50 Copynumber: 3.8 Consensus size: 50
6211 GACAAGATTT
* *
6221 CTTTCCATTT-ATGTGTTCAAGATCAAAATTCGCTGTTCAAAATAAAATTG
1 CTTTCCATTTGA-GAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
6271 CTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
1 CTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* * * *
6321 CTTTCCATTTGAGAGTTCAAGATTAAAGTTCGCTTTTCAAAGTAAGATTG
1 CTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* * * *
6371 CATTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
1 CTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAA
6412 TGGCATTTAA
Statistics
Matches: 128, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
50 127 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (50 bp):
CTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
Found at i:7071 original size:50 final size:50
Alignment explanation
Indices: 7012--7444 Score: 681
Period size: 50 Copynumber: 8.7 Consensus size: 50
7002 CGAATGTTTT
* * * *
7012 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAATCGATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
* *
7062 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
7112 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
7162 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
** *
7212 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAATTATCAATATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
* *
7262 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAATATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
* *
7312 GGCTTTTCTACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
* * *
7362 GGTTTTTCCACAAGCCAAATTCGTTTCCATACGAGTC-AGTTATCAACGTA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGA-TTATCAACATA
*
7412 GGCTTTTCCACAAGCCACA-TCCGTTTCCATACG
1 GGCTTTTCCACAAGCCAAACT-CGTTTCCATACG
7445 GTGCATTACC
Statistics
Matches: 361, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 2 0.01
50 359 0.99
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
Found at i:7533 original size:50 final size:50
Alignment explanation
Indices: 7456--7636 Score: 220
Period size: 50 Copynumber: 3.6 Consensus size: 50
7446 TGCATTACCT
* * *
7456 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGTGGAAGATGGTCC
1 TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAAGGTCC
** * * *
7506 CCTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCAGAAGAAGGACC
1 TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAAGGTCC
* ** *
7556 TTTTGAGATTGAATTGGAATTCAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAAGGTCC
* *
7606 TTTTAATATT-AGATTGGAAGACAATTCAAAG
1 TTTTAAGATTGA-ATTGGAAGACAGTTCAAAG
7637 AAGTTGATCG
Statistics
Matches: 110, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 109 0.99
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAAGGTCC
Found at i:7634 original size:100 final size:100
Alignment explanation
Indices: 7456--7636 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 100
7446 TGCATTACCT
* * *
7456 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGTGGAAGATGGTCCCCTTAAGATTGAATT
1 TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCCCTTAAGATTGAATT
* *
7521 GGTAGACAGTTCAAAGGATAAGCAGAAGAAGGACC
66 GGAAGACAATTCAAAGGATAAGCAGAAGAAGGACC
* ** ** *
7556 TTTTGAGATTGAATTGGAATTCAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAATATT-AGAT
1 TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCCCTTAAGATTGA-AT
7620 TGGAAGACAATTCAAAG
65 TGGAAGACAATTCAAAG
7637 AAGTTGATCG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
99 1 0.01
100 68 0.99
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.28
Consensus pattern (100 bp):
TTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCCCTTAAGATTGAATT
GGAAGACAATTCAAAGGATAAGCAGAAGAAGGACC
Found at i:7977 original size:27 final size:27
Alignment explanation
Indices: 7903--7977 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
7893 ATTATCAAAA
* *
7903 ATCCAGGGGCATTTTGGTCATTTTCAC
1 ATCCAGGGGCATTTTGGTCAGTTGCAC
* * *
7930 ATTCAGGGGGTATTTTAGTCAGTTGCAC
1 ATCCA-GGGGCATTTTGGTCAGTTGCAC
*
7958 GTCCAGGGGCATTTTGGTCA
1 ATCCAGGGGCATTTTGGTCA
7978 TTTATACTTC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (27 bp):
ATCCAGGGGCATTTTGGTCAGTTGCAC
Found at i:13207 original size:27 final size:26
Alignment explanation
Indices: 13169--13250 Score: 110
Period size: 27 Copynumber: 3.1 Consensus size: 26
13159 TTGAATACCC
13169 TTACTCTTTTTACTGATTACCAATTTT
1 TTACTCTTTTTACTGATTACC-ATTTT
*
13196 TTACTCTTTTTACTCATTACCATTTT
1 TTACTCTTTTTACTGATTACCATTTT
* * *
13222 CTTACTTTTTTTACTGGTTTCCATTTT
1 -TTACTCTTTTTACTGATTACCATTTT
13249 TT
1 TT
13251 GCATGTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 7 0.14
27 42 0.86
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.60
Consensus pattern (26 bp):
TTACTCTTTTTACTGATTACCATTTT
Found at i:13271 original size:35 final size:34
Alignment explanation
Indices: 13254--13329 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 34
13244 ATTTTTTGCA
13254 TGTTTTACTTTAATTACTGAATACCATTTTTACTC
1 TGTTTTACTTTAATTACTGAATACCATTTTTA-TC
*
13289 TTTTTTACTTTAATTACTGAATACCATTTTTACTC
1 TGTTTTACTTTAATTACTGAATACCATTTTTA-TC
13324 T-TTTTA
1 TGTTTTA
13330 ATCTTTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (34 bp):
TGTTTTACTTTAATTACTGAATACCATTTTTATC
Found at i:13466 original size:21 final size:21
Alignment explanation
Indices: 13363--13689 Score: 155
Period size: 21 Copynumber: 15.5 Consensus size: 21
13353 TGAATTTTAA
*
13363 TTACTGATTACCATTAC-CATT
1 TTACTGATTACTATTACTC-TT
* *
13384 TTATTGATTACTCTTTACTC-T
1 TTACTGATTACT-ATTACTCTT
* * *
13405 TTACTGATAACAATGAC-CATT
1 TTACTGATTACTATTACTC-TT
* * *
13426 TTGCTGTTTACTGTTTACTCTT
1 TTACTGATTACT-ATTACTCTT
*
13448 TTAATGATTACTATTACTC-T
1 TTACTGATTACTATTACTCTT
*
13468 TT-CTTGATTACTCTTTACTC-T
1 TTAC-TGATTACT-ATTACTCTT
* *
13489 TTACTGACTATTATTACTC-T
1 TTACTGATTACTATTACTCTT
*
13509 TT-CTTGATTACTTCTTACTC-T
1 TTAC-TGATTAC-TATTACTCTT
* **
13530 TTACTTACAACTATTACTCTT
1 TTACTGATTACTATTACTCTT
** * *
13551 TTACTCTTTACTCTTAC-CAT
1 TTACTGATTACTATTACTCTT
*
13571 TTACTG------ATTGCTCTT
1 TTACTGATTACTATTACTCTT
*
13586 TAACTGATTACTATTACTCTT
1 TTACTGATTACTATTACTCTT
*
13607 TTACTGATTACTCTTTACTCTT
1 TTACTGATTACT-ATTACTCTT
13629 TTACTGATTACCATTTACTGATTACTCTT
1 TTACTG------A-TTACT-ATTACTCTT
* *
13658 TAACTAATTACTATTACTCTT
1 TTACTGATTACTATTACTCTT
13679 TTACTGATTAC
1 TTACTGATTAC
13690 CATTTTACTG
Statistics
Matches: 228, Mismatches: 50, Indels: 56
0.68 0.15 0.17
Matches are distributed among these distances:
14 3 0.01
15 7 0.03
19 2 0.01
20 42 0.18
21 114 0.50
22 39 0.17
23 3 0.01
28 1 0.00
29 17 0.07
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (21 bp):
TTACTGATTACTATTACTCTT
Found at i:13514 original size:41 final size:40
Alignment explanation
Indices: 13433--13551 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 40
13423 ATTTTGCTGT
* *
13433 TTACTGTTTACTCTTTTAATGATTACTATTACTCTTTCTTGA
1 TTACT-TTTACTC-TTTACTGACTACTATTACTCTTTCTTGA
*
13475 TTACTCTTTACTCTTTACTGACTATTATTACTCTTTCTTGA
1 TTACT-TTTACTCTTTACTGACTACTATTACTCTTTCTTGA
* *
13516 TTACTTCTTACTCTTTACTTACAACTATTACTCTTT
1 TTACTT-TTACTCTTTACTGACTACTATTACTCTTT
13552 TACTCTTTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.01
41 56 0.81
42 12 0.17
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (40 bp):
TTACTTTTACTCTTTACTGACTACTATTACTCTTTCTTGA
Found at i:13566 original size:41 final size:39
Alignment explanation
Indices: 13457--13577 Score: 129
Period size: 41 Copynumber: 2.9 Consensus size: 39
13447 TTTAATGATT
*
13457 ACTATTACTCTTTCTTGATTACTCTTTACTCTTTACTGACT
1 ACTATTACTCTTTCTT-ATTACTC-TTACTCTTTACTGACA
* *
13498 ATTATTACTCTTTCTTGATTACTTCTTACTCTTTACTTACA
1 ACTATTACTCTTTCTT-ATTAC-TCTTACTCTTTACTGACA
13539 ACTATTACTCTTTTACTCT-TTACTCTTAC-CATTTACTGA
1 ACTATTACTC-TTT-CT-TATTACTCTTACTC-TTTACTGA
13578 TTGCTCTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
40 1 0.01
41 57 0.81
42 9 0.13
43 2 0.03
44 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.51
Consensus pattern (39 bp):
ACTATTACTCTTTCTTATTACTCTTACTCTTTACTGACA
Found at i:13618 original size:15 final size:15
Alignment explanation
Indices: 13593--13711 Score: 73
Period size: 15 Copynumber: 8.2 Consensus size: 15
13583 CTTTAACTGA
13593 TTACT-ATTACTCTT
1 TTACTGATTACTCTT
13607 TTACTGATTACTC-T
1 TTACTGATTACTCTT
13621 TTAC-------TCTT
1 TTACTGATTACTCTT
*
13629 TTACTGATTAC-CAT
1 TTACTGATTACTCTT
13643 TTACTGATTACTCTTTAACT
1 TTACTGATTACTC--T---T
13663 AATTACT-ATTACTCTT
1 --TTACTGATTACTCTT
13679 TTACTGATTAC-CATT
1 TTACTGATTACTC-TT
13694 TTACTGATTACTCTT
1 TTACTGATTACTCTT
13709 TTA
1 TTA
13712 TTCTTTACTG
Statistics
Matches: 83, Mismatches: 2, Indels: 39
0.67 0.02 0.31
Matches are distributed among these distances:
7 2 0.02
8 5 0.06
14 29 0.35
15 31 0.37
16 2 0.02
19 1 0.01
20 1 0.01
21 7 0.08
22 5 0.06
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (15 bp):
TTACTGATTACTCTT
Found at i:13621 original size:36 final size:36
Alignment explanation
Indices: 13542--13752 Score: 177
Period size: 36 Copynumber: 5.9 Consensus size: 36
13532 ACTTACAACT
* ** *
13542 ATTACTCTTTTACTCTTTACTCTTAC-CATTTACTG
1 ATTACTCTTTAACTGATTACTATTACTCATTTACTG
* *
13577 ATTGCTCTTTAACTGATTACTATTACTCTTTTACTG
1 ATTACTCTTTAACTGATTACTATTACTCATTTACTG
**
13613 ATTACTCTTT-ACTCTTTTACTGATTAC-CATTTACTG
1 ATTACTCTTTAACT-GATTACT-ATTACTCATTTACTG
* *
13649 ATTACTCTTTAACTAATTACTATTACTCTTTTACTG
1 ATTACTCTTTAACTGATTACTATTACTCATTTACTG
* * *
13685 ATTAC-CATTTTACTGATTACTCTTTTATTC-TTTACTG
1 ATTACTC-TTTAACTGATTA--CTATTACTCATTTACTG
*
13722 ATTACT-ATT-ACTGAATTACTACTTA-TCATTT
1 ATTACTCTTTAACTG-ATTACTA-TTACTCATTT
13753 TCTTTTTGAA
Statistics
Matches: 145, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
34 4 0.03
35 40 0.28
36 74 0.51
37 20 0.14
38 7 0.05
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (36 bp):
ATTACTCTTTAACTGATTACTATTACTCATTTACTG
Found at i:13646 original size:29 final size:28
Alignment explanation
Indices: 13613--13679 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
13603 TCTTTTACTG
* *
13613 ATTACTCTTTACTCTTTTACTGATTACC
1 ATTACTCTTTACTCTTTAACTAATTACC
** *
13641 ATTTACTGATTACTCTTTAACTAATTACT
1 A-TTACTCTTTACTCTTTAACTAATTACC
13670 ATTACTCTTT
1 ATTACTCTTT
13680 TACTGATTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.25, C:0.21, G:0.03, T:0.51
Consensus pattern (28 bp):
ATTACTCTTTACTCTTTAACTAATTACC
Found at i:13651 original size:72 final size:71
Alignment explanation
Indices: 13542--13698 Score: 246
Period size: 72 Copynumber: 2.2 Consensus size: 71
13532 ACTTACAACT
* * *
13542 ATTACTCTTTTACTCTTTACTCTTACCATTTACTGATTGCTCTTTAACTGATTACTATTACTCTT
1 ATTACTCTTTTACTCTTTACTATTACCATTTACTGATTACTCTTTAACTAATTACTATTACTCTT
13607 TTACTG
66 TTACTG
13613 ATTACTC-TTTACTCTTTTACTGATTACCATTTACTGATTACTCTTTAACTAATTACTATTACTC
1 ATTACTCTTTTACTC-TTTACT-ATTACCATTTACTGATTACTCTTTAACTAATTACTATTACTC
13677 TTTTACTG
64 TTTTACTG
13685 ATTAC-CATTTTACT
1 ATTACTC-TTTTACT
13699 GATTACTCTT
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
70 7 0.09
71 14 0.18
72 52 0.66
73 6 0.08
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.50
Consensus pattern (71 bp):
ATTACTCTTTTACTCTTTACTATTACCATTTACTGATTACTCTTTAACTAATTACTATTACTCTT
TTACTG
Found at i:13668 original size:51 final size:51
Alignment explanation
Indices: 13593--13709 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
13583 CTTTAACTGA
* * *
13593 TTACT-ATTACTCTTTTACTGATTACTCTTTACTCTTTTACTGATTACCA-T
1 TTACTGATTACTCTTTAACTAATTACT-ATTACTCTTTTACTGATTACCATT
13643 TTACTGATTACTCTTTAACTAATTACTATTACTCTTTTACTGATTACCATT
1 TTACTGATTACTCTTTAACTAATTACTATTACTCTTTTACTGATTACCATT
13694 TTACTGATTACTCTTT
1 TTACTGATTACTCTTT
13710 TATTCTTTAC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
50 26 0.42
51 36 0.58
ACGTcount: A:0.24, C:0.21, G:0.04, T:0.51
Consensus pattern (51 bp):
TTACTGATTACTCTTTAACTAATTACTATTACTCTTTTACTGATTACCATT
Found at i:22259 original size:23 final size:25
Alignment explanation
Indices: 22212--22258 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
22202 AGAAATTTTT
*
22212 TTTTTTTTTTAGAAAACGTAAAAAC
1 TTTTTTTTTCAGAAAACGTAAAAAC
*
22237 TTTTTTTTTCA-AAAACGCAAAA
1 TTTTTTTTTCAGAAAACGTAAAA
22259 CACAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (25 bp):
TTTTTTTTTCAGAAAACGTAAAAAC
Found at i:29120 original size:69 final size:69
Alignment explanation
Indices: 29020--29453 Score: 622
Period size: 69 Copynumber: 6.3 Consensus size: 69
29010 CTCATTAAAC
* * * * * * *
29020 TTGGCTTATGGAAAAGCCTATGCT-G-TATGGATGGACCCGATGTTTAAACTGACTCGCATGGAA
1 TTGGCTTGTGGAAAAGCCTAT-ATGGCT-TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
*
29083 ACAAGT
64 ACGAGT
* * * * * *
29089 TTGACATATGGAAAAGTCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
29154 GAGT
66 GAGT
* *
29158 TTGGCTTATGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACTGACTTGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
29223 GAGT
66 GAGT
*
29227 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
29292 GAGT
66 GAGT
*
29296 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
29361 GTGT
66 GAGT
* *
29365 TTGGCTTGTAGAAAAGCCTATGA-GGCTTGGATGGAACCAAGGCTTAAACTGGCTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTAT-ATGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
29429 CGAGT
65 CGAGT
*
29434 TTGGCCTGTGGAAAAGCCTA
1 TTGGCTTGTGGAAAAGCCTA
29454 ATCATTCGGA
Statistics
Matches: 334, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
68 1 0.00
69 332 0.99
70 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGT
Found at i:29193 original size:23 final size:23
Alignment explanation
Indices: 29165--29262 Score: 60
Period size: 27 Copynumber: 4.3 Consensus size: 23
29155 AGTTTGGCTT
29165 ATGGAAAAGCCTATATGGCTTGG
1 ATGGAAAAGCCTATATGGCTTGG
* * * *
29188 ATGGAACCAAGGCTTAAACTGACTTGT
1 ATGGAA--AA-GCCTATA-TGGCTTGG
* **
29215 ATGGAAACGAGT-T-TGGCTT-G
1 ATGGAAAAGCCTATATGGCTTGG
*
29235 -TGGAAAAGCCTATGTGGCTTGG
1 ATGGAAAAGCCTATATGGCTTGG
29257 ATGGAA
1 ATGGAA
29263 CCAAGGCTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 16
0.65 0.16 0.19
Matches are distributed among these distances:
19 8 0.15
20 1 0.02
21 11 0.20
22 1 0.02
23 11 0.20
24 2 0.04
25 3 0.06
26 5 0.09
27 12 0.22
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.27
Consensus pattern (23 bp):
ATGGAAAAGCCTATATGGCTTGG
Found at i:29810 original size:24 final size:24
Alignment explanation
Indices: 29778--29828 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
29768 ACTTGAATAA
29778 TATGCTTTGAAAGATTCTTTTGCT
1 TATGCTTTGAAAGATTCTTTTGCT
29802 TATGCTTTGAAAGATTCTTTTGCT
1 TATGCTTTGAAAGATTCTTTTGCT
29826 TAT
1 TAT
29829 CCCACTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.51
Consensus pattern (24 bp):
TATGCTTTGAAAGATTCTTTTGCT
Found at i:30187 original size:50 final size:49
Alignment explanation
Indices: 30085--30214 Score: 188
Period size: 50 Copynumber: 2.6 Consensus size: 49
30075 TGGTCTTGGT
* *
30085 CTCACAAATGAAATGCAATCTTATAATAAAAGCGAATTTTGATCTTGGA
1 CTCACAAATGGAATGCAATCTTATAATAAAAGCGAATTTTGATCTTGAA
* **
30134 CTCACAAATGGAATGCCATCTTATTTTGAAAAGCGAATTTTGATCTTGAA
1 CTCACAAATGGAATGCAATCTTATAAT-AAAAGCGAATTTTGATCTTGAA
* *
30184 CTCACAAATGGAATGCACTTTTATAATAAAA
1 CTCACAAATGGAATGCAATCTTATAATAAAA
30215 CTTCTTGTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 27 0.39
50 43 0.61
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (49 bp):
CTCACAAATGGAATGCAATCTTATAATAAAAGCGAATTTTGATCTTGAA
Found at i:31230 original size:15 final size:16
Alignment explanation
Indices: 31197--31249 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
31187 AGTGCATTTA
31197 TTTTTCG-TTTTTCAT
1 TTTTTCGTTTTTTCAT
*
31212 TTTTTCGTTTTTTC-G
1 TTTTTCGTTTTTTCAT
*
31227 TTTTTCATTTTCATTCAT
1 TTTTTCGTTTT--TTCAT
31245 TTTTT
1 TTTTT
31250 ATTATTGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 17 0.55
16 6 0.19
17 3 0.10
18 5 0.16
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTTCGTTTTTTCAT
Done.