Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017933.1 Corchorus olitorius cultivar O-4 contig17966, 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: 21442
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:3152 original size:41 final size:42
Alignment explanation
Indices: 3072--3154 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
3062 AACTAATGAC
** *
3072 TTTATTTTCTTAACTAAATTTTCTTAAAAGCACTTATAAAAT
1 TTTATTTTCTTAACTAAATTTTCTTAAAAAAACTCATAAAAT
* *
3114 TTTA-TTTCTTAACTTAATTTTTTTAAAAAAACTCATAAAAT
1 TTTATTTTCTTAACTAAATTTTCTTAAAAAAACTCATAAAAT
3155 AAAACAATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (42 bp):
TTTATTTTCTTAACTAAATTTTCTTAAAAAAACTCATAAAAT
Found at i:4658 original size:11 final size:12
Alignment explanation
Indices: 4619--4674 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
4609 TATTAACCTT
*
4619 AATTAAAATTTA
1 AATTAAAAATTA
4631 CAATTAAAAATTA
1 -AATTAAAAATTA
*
4644 AATTAATAA-TA
1 AATTAAAAATTA
*
4655 AATTAAAAAAT-
1 AATTAAAAATTA
4666 AATTAAAAA
1 AATTAAAAA
4675 AAAGGGGCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
11 19 0.49
12 9 0.23
13 11 0.28
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AATTAAAAATTA
Found at i:8474 original size:21 final size:21
Alignment explanation
Indices: 8450--8491 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8440 ACCTTCGACA
8450 TCTTGCTAGTTGACCTAATTT
1 TCTTGCTAGTTGACCTAATTT
*
8471 TCTTTCTAGTTGACCTAATTT
1 TCTTGCTAGTTGACCTAATTT
8492 CCTTTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (21 bp):
TCTTGCTAGTTGACCTAATTT
Found at i:8496 original size:21 final size:21
Alignment explanation
Indices: 8455--8497 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
8445 CGACATCTTG
*
8455 CTAGTTGACCTAATTTTCTTT
1 CTAGTTGACCTAATTTCCTTT
8476 CTAGTTGACCTAATTTCCTTT
1 CTAGTTGACCTAATTTCCTTT
8497 C
1 C
8498 AATGGGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.49
Consensus pattern (21 bp):
CTAGTTGACCTAATTTCCTTT
Found at i:9475 original size:59 final size:59
Alignment explanation
Indices: 9315--9488 Score: 231
Period size: 59 Copynumber: 2.8 Consensus size: 59
9305 CCCTGTAAGG
* *
9315 CTGGAAGAGTGATTTGCTTGAAAGAGGCTAATCTAAATGAGGCAGCAATCTAGGATTGTTC
1 CTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAA--AGGCAGCAATCTAGGATTGTTC
*
9376 CTGGAAGTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAACGGCAGCAATCTAGGATTGTTC
1 C------TGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAAAGGCAGCAATCTAGGATTGTTC
* *
9441 CTGGAAGAGTGATTTGCTTGAGAGAGGTTAACCTAAATGGCAGCAATC
1 CTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAAAGGCAGCAATC
9489 GAGGGCATTT
Statistics
Matches: 102, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
59 45 0.44
61 1 0.01
65 22 0.22
67 34 0.33
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (59 bp):
CTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAAAGGCAGCAATCTAGGATTGTTC
Found at i:9529 original size:203 final size:197
Alignment explanation
Indices: 9173--9627 Score: 793
Period size: 203 Copynumber: 2.3 Consensus size: 197
9163 GTAGGATCAG
*
9173 TTGTTCCTGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGGCAGCAATCTAGGATTGATC
1 TTGTTCCTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCTAGGATTGATC
*
9238 CTGGAAGAGTGATTTGCTTGAGAGAGGCTAACTTAAATGGCAGCAATCGAGGGCATTTCAATCCA
66 CTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCGAGGGCATTTCAATCCA
9303 ATCCCTGTAAGGCTGGAAGAGTGATTTGCTTGAAAGAGGCTAATCTAAATGAGGCAGCAATCTAG
131 ATCCCTGTAAGGCTGGAAGAGTGATTTGCTTGAAAGAGGCTAATCTAAATGAGGCAGCAATCTAG
9368 GA
196 GA
*
9370 TTGTTCCTGGAAGTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAACGGCAGCAATCTAGGA
1 TTGTTCC------TGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCTAGGA
* *
9435 TTGTTCCTGGAAGAGTGATTTGCTTGAGAGAGGTTAACCTAAATGGCAGCAATCGAGGGCATTTC
60 TTGATCCTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCGAGGGCATTTC
*
9500 AATCCAATCCCTGTAAGGCTGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGGCAGCA
125 AATCCAATCCCTGTAAGGCTGGAAGAGTGATTTGCTTGAAAGAGGCTAATCTAAATGAGGCAGCA
9565 ATCTAGGA
190 ATCTAGGA
9573 TTGTTCCTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTTAAATGGCAGCAATC
1 TTGTTCCTGGAAGAGTGATTTGCTTGAGAGAGGCTAACC-TAAATGGCAGCAATC
9628 GAGGGCATTT
Statistics
Matches: 244, Mismatches: 7, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
197 39 0.16
198 14 0.06
203 191 0.78
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (197 bp):
TTGTTCCTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCTAGGATTGATC
CTGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCGAGGGCATTTCAATCCA
ATCCCTGTAAGGCTGGAAGAGTGATTTGCTTGAAAGAGGCTAATCTAAATGAGGCAGCAATCTAG
GA
Found at i:9671 original size:139 final size:138
Alignment explanation
Indices: 9383--9698 Score: 582
Period size: 139 Copynumber: 2.3 Consensus size: 138
9373 TTCCTGGAAG
* *
9383 TGGAAGAGTGATTTGCTTGAGAGAGGCTAACCTAAA--CGGCAGCAATCTAGGATTGTTCCTGGA
1 TGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGGCAGCAATCTAGGATTGTTCCTGGA
*
9446 AGAGTGATTTGCTTGAGAGAGGTTAACCTAAATGGCAGCAATCGAGGGCATTTCAATCCAATCCC
66 AGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCGAGGGCATTTCAATCCAATCCC
9511 TGTAAGGC
131 TGTAAGGC
9519 TGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGGCAGCAATCTAGGATTGTTCCTGGA
1 TGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGGCAGCAATCTAGGATTGTTCCTGGA
9584 AGAGTGATTTGCTTGAGAGAGGCTAACCTTAAATGGCAGCAATCGAGGGCATTTCAATCCAATCC
66 AGAGTGATTTGCTTGAGAGAGGCTAACC-TAAATGGCAGCAATCGAGGGCATTTCAATCCAATCC
9649 CTGTAAGGC
130 CTGTAAGGC
9658 TGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGG
1 TGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGG
9699 GCATTTCAAT
Statistics
Matches: 174, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
136 35 0.20
138 53 0.30
139 86 0.49
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (138 bp):
TGGAAGAGTGATTTGCTTGAGAGAGGCTAATCTAAATGAGGCAGCAATCTAGGATTGTTCCTGGA
AGAGTGATTTGCTTGAGAGAGGCTAACCTAAATGGCAGCAATCGAGGGCATTTCAATCCAATCCC
TGTAAGGC
Found at i:13656 original size:7 final size:7
Alignment explanation
Indices: 13652--13948 Score: 88
Period size: 8 Copynumber: 41.7 Consensus size: 7
13642 TTTTTATTAT
13652 TTATTTA
1 TTATTTA
*
13659 CTATTTA
1 TTATTTA
13666 TT-TTTA
1 TTATTTA
13672 TT-TTTA
1 TTATTTA
13678 TT-TTT-
1 TTATTTA
13683 TTATTT-
1 TTATTTA
13689 TTACATTT-
1 TT--ATTTA
13697 TTAACTATTA
1 TT-A-T-TTA
13707 TCTATTTA
1 T-TATTTA
*
13715 -TATTCA
1 TTATTTA
*
13721 CTATTTA
1 TTATTTA
13728 TCTATTTA
1 T-TATTTA
*
13736 TT-TACTA
1 TTAT-TTA
13743 TTTATTT-
1 -TTATTTA
13750 TT-TTTA
1 TTATTTA
*
13756 TTATCTA
1 TTATTTA
13763 CTTATTTA
1 -TTATTTA
**
13771 CCATTTA
1 TTATTTA
13778 TCTATTTA
1 T-TATTTA
13786 TTTATTT-
1 -TTATTTA
**
13793 TTAACTA
1 TTATTTA
*
13800 TTATCTA
1 TTATTTA
13807 TTTATTTA
1 -TTATTTA
*
13815 CTATTTA
1 TTATTTA
*
13822 TTTATCT-
1 -TTATTTA
**
13829 TTAACTA
1 TTATTTA
*
13836 TTATCTA
1 TTATTTA
13843 TTTATTTA
1 -TTATTTA
*
13851 CTATTTA
1 TTATTTA
13858 TCT-TTTA
1 T-TATTTA
13865 TTTATTT-
1 -TTATTTA
*
13872 TTAATTA
1 TTATTTA
**
13879 TTACCTA
1 TTATTTA
13886 TTTATTTA
1 -TTATTTA
*
13894 CTATTTA
1 TTATTTA
*
13901 -TCTTT-
1 TTATTTA
13906 TTATTTA
1 TTATTTA
13913 TTAATTTA
1 TT-ATTTA
13921 GTTA-TTA
1 -TTATTTA
13928 TCTATTTA
1 T-TATTTA
13936 TTTATTTA
1 -TTATTTA
13944 TTATT
1 TTATT
13949 ATTTTTTTAA
Statistics
Matches: 222, Mismatches: 34, Indels: 68
0.69 0.10 0.21
Matches are distributed among these distances:
5 5 0.02
6 53 0.24
7 76 0.34
8 77 0.35
9 8 0.04
10 2 0.01
11 1 0.00
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATTTA
Found at i:13697 original size:14 final size:14
Alignment explanation
Indices: 13665--13699 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13655 TTTACTATTT
*
13665 ATTTTTATTTTTAT
1 ATTTTTATTTTTAC
*
13679 TTTTTTATTTTTAC
1 ATTTTTATTTTTAC
13693 ATTTTTA
1 ATTTTTA
13700 ACTATTATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTTATTTTTAC
Found at i:13739 original size:4 final size:4
Alignment explanation
Indices: 13722--13957 Score: 90
Period size: 4 Copynumber: 61.5 Consensus size: 4
13712 TTATATTCAC
* * * * *
13722 TATT TATC TATT TATT TA-C TATT TATT T-TT TTTAT TATC TACT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT
* * * * * *
13769 TA-C CATT TATC TATT TATT TATT T-TT AACTAT TATC TATT TATT TA-C
1 TATT TATT TATT TATT TATT TATT TATT TA-T-T TATT TATT TATT TATT
* * * * *
13816 TATT TATT TATC T-TT AACTAT TATC TATT TATT TA-C TATT TATC T-TT
1 TATT TATT TATT TATT TA-T-T TATT TATT TATT TATT TATT TATT TATT
* ** *
13863 TATT TA-T T-TT TAAT TA-T TACC TATT TATT TA-C TATT TATCT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT
* * *
13907 TATT TATT AATT TAGT TA-T TATC TATT TATT TATT TA-T TA-T TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
*
13952 TTTT TA
1 TATT TA
13958 ACTACCTATT
Statistics
Matches: 167, Mismatches: 44, Indels: 42
0.66 0.17 0.17
Matches are distributed among these distances:
3 35 0.21
4 119 0.71
5 9 0.05
6 4 0.02
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:13788 original size:43 final size:43
Alignment explanation
Indices: 13722--13939 Score: 220
Period size: 43 Copynumber: 5.1 Consensus size: 43
13712 TTATATTCAC
* * * *
13722 TATTTATCTATTTATTTA-CTATTTATTTTTTTTATTATCTACT
1 TATTTA-CTATTTATCTATTTATTTATTTTTATTATTATCTATT
* *
13765 TATTTACCATTTATCTATTTATTTATTTTTAACTATTATCTATT
1 TATTTACTATTTATCTATTTATTTATTTTT-ATTATTATCTATT
* * *
13809 TATTTACTA--T-T-TATTTA--T-CTTTAACTATTATCTATT
1 TATTTACTATTTATCTATTTATTTATTTTTATTATTATCTATT
*
13845 TATTTACTATTTATCT-TTTATTTATTTTTAATTATTACCTATT
1 TATTTACTATTTATCTATTTATTTATTTTT-ATTATTATCTATT
*
13888 TATTTACTATTTATCTTTTTATTTATTAATTTAGTTATTATCTATT
1 TATTTACTATTTATCTATTTATTTATT--TTTA-TTATTATCTATT
13934 TATTTA
1 TATTTA
13940 TTTATTATTA
Statistics
Matches: 147, Mismatches: 14, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
36 22 0.15
37 3 0.02
38 2 0.01
39 5 0.03
40 7 0.05
41 2 0.01
42 13 0.09
43 44 0.30
44 28 0.19
45 1 0.01
46 20 0.14
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.64
Consensus pattern (43 bp):
TATTTACTATTTATCTATTTATTTATTTTTATTATTATCTATT
Found at i:13826 original size:36 final size:36
Alignment explanation
Indices: 13720--13901 Score: 181
Period size: 36 Copynumber: 4.8 Consensus size: 36
13710 ATTTATATTC
13720 ACTATTTATCTATTTATTTACTATTTATTT-TTTTT-
1 ACTA-TTATCTATTTATTTACTATTTATTTATTTTTA
*
13755 ATTATCTA-CTTATTTACCATTTATCTATTTATTTATTTTTA
1 ACTAT-TATC-TATTT---ATTTA-CTATTTATTTATTTTTA
*
13796 ACTATTATCTATTTATTTACTATTTATTTATCTTTA
1 ACTATTATCTATTTATTTACTATTTATTTATTTTTA
13832 ACTATTATCTATTTATTTACTATTTATCTTTTATTTATTTTTA
1 ACTATTATCTATTTATTTAC----TA---TTTATTTATTTTTA
* *
13875 ATTATTACCTATTTATTTACTATTTAT
1 ACTATTATCTATTTATTTACTATTTAT
13902 CTTTTTATTT
Statistics
Matches: 125, Mismatches: 6, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
34 2 0.02
35 10 0.08
36 41 0.33
37 5 0.04
38 5 0.04
39 12 0.10
40 14 0.11
41 5 0.04
43 31 0.25
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.63
Consensus pattern (36 bp):
ACTATTATCTATTTATTTACTATTTATTTATTTTTA
Found at i:13870 original size:79 final size:75
Alignment explanation
Indices: 13720--13907 Score: 270
Period size: 79 Copynumber: 2.4 Consensus size: 75
13710 ATTTATATTC
13720 ACTATTTATCTATTTATTTACTATTTATTTTTTTTATTATCTACTTATTTACCATTTATCTATTT
1 ACTA-TTATCTATTTATTTACTATTTATTTTTTTTATTATCTACTTATTTACCATTTATCTATTT
13785 ATTTATTTTTA
65 ATTTATTTTTA
* *
13796 ACTATTATCTATTTATTTACTATTTATTTATCTTTAACTATTATCTATTTATTTACTATTTATCT
1 ACTATTATCTATTTATTTACTATTTATTT-T-TTT---TATTATCTACTTATTTACCATTTATCT
13861 -TTTATTTATTTTTA
61 ATTTATTTATTTTTA
* * *
13875 ATTATTACCTATTTATTTACTATTTATCTTTTT
1 ACTATTATCTATTTATTTACTATTTATTTTTTT
13908 ATTTATTAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
75 25 0.25
76 5 0.05
77 6 0.06
78 1 0.01
79 40 0.39
80 25 0.25
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (75 bp):
ACTATTATCTATTTATTTACTATTTATTTTTTTTATTATCTACTTATTTACCATTTATCTATTTA
TTTATTTTTA
Found at i:13928 original size:19 final size:19
Alignment explanation
Indices: 13906--13948 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
13896 ATTTATCTTT
13906 TTATTTATTAATTTAGTTA
1 TTATTTATTAATTTAGTTA
* * *
13925 TTATCTATTTATTTATTTA
1 TTATTTATTAATTTAGTTA
13944 TTATT
1 TTATT
13949 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTTATTAATTTAGTTA
Found at i:13947 original size:11 final size:11
Alignment explanation
Indices: 13639--13957 Score: 132
Period size: 11 Copynumber: 28.8 Consensus size: 11
13629 GACCAAAAAG
*
13639 ATTTTTTTATT
1 ATTTATTTATT
*
13650 ATTTATTTACT
1 ATTTATTTATT
13661 ATTTATTT-TT
1 ATTTATTTATT
*
13671 ATTTTTATTTTTTT
1 A--TTTA-TTTATT
*
13685 ATTT-TTACATT
1 ATTTATT-TATT
**
13696 -TTTAACTATT
1 ATTTATTTATT
*
13706 ATCTATTTA-T
1 ATTTATTTATT
13716 ATTCACTATTTATCT
1 ATT---TATTTAT-T
*
13731 ATTTATTTACT
1 ATTTATTTATT
13742 ATTTATTT-TT
1 ATTTATTTATT
13752 -TTTA-TTATCT
1 ATTTATTTAT-T
* **
13762 ACTTATTTACC
1 ATTTATTTATT
*
13773 ATTTATCTATTT
1 ATTTATTTA-TT
13785 ATTTATTT-TT
1 ATTTATTTATT
**
13795 AACTA-TTATCT
1 ATTTATTTAT-T
*
13806 ATTTATTTACT
1 ATTTATTTATT
13817 ATTTATTTATCT
1 ATTTATTTAT-T
*
13829 -TTAACTATTATCT
1 ATTTA-T-TTAT-T
*
13842 ATTTATTTACT
1 ATTTATTTATT
13853 ATTTATCTT-TT
1 ATTTAT-TTATT
13864 ATTTATTT-TT
1 ATTTATTTATT
* *
13874 AATTA-TTACCT
1 ATTTATTTA-TT
*
13885 ATTTATTTACT
1 ATTTATTTATT
*
13896 ATTTA--TCTT
1 ATTTATTTATT
13905 -TTTATTTATT
1 ATTTATTTATT
*
13915 AATTTAGTTATT
1 -ATTTATTTATT
*
13927 ATCTATTTATTT
1 ATTTATTTA-TT
13939 ATTTA-TTATT
1 ATTTATTTATT
*
13949 ATTTTTTTA
1 ATTTATTTA
13958 ACTACCTATT
Statistics
Matches: 231, Mismatches: 43, Indels: 68
0.68 0.13 0.20
Matches are distributed among these distances:
8 6 0.03
9 11 0.05
10 38 0.16
11 99 0.43
12 51 0.22
13 16 0.07
14 6 0.03
15 4 0.02
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:14074 original size:8 final size:8
Alignment explanation
Indices: 13704--13996 Score: 68
Period size: 8 Copynumber: 37.8 Consensus size: 8
13694 TTTTTAACTA
13704 TTATCTAT
1 TTATCTAT
13712 TTA--TAT
1 TTATCTAT
*
13718 TCA-CTAT
1 TTATCTAT
13725 TTATCTAT
1 TTATCTAT
13733 TTATTTACTAT
1 TTA--T-CTAT
* *
13744 TTATTTTTT
1 TTA-TCTAT
13753 TTAT-TAT
1 TTATCTAT
*
13760 CTA-CTTAT
1 TTATC-TAT
*
13768 TTA-CCAT
1 TTATCTAT
13775 TTATCTAT
1 TTATCTAT
*
13783 TTATTTATTT
1 TTATCTA--T
*
13793 TTAACTA-
1 TTATCTAT
13800 TTATCTAT
1 TTATCTAT
*
13808 TTATTTA-
1 TTATCTAT
* *
13815 CTATTTAT
1 TTATCTAT
13823 TTATC--T
1 TTATCTAT
*
13829 TTAACTA-
1 TTATCTAT
13836 TTATCTAT
1 TTATCTAT
13844 TTATTTACTAT
1 TTA--T-CTAT
13855 TTATCT-T
1 TTATCTAT
*
13862 TTATTTAT
1 TTATCTAT
*
13870 TT-T-TAA
1 TTATCTAT
*
13876 TTAT-TAC
1 TTATCTAT
* *
13883 CTATTTAT
1 TTATCTAT
13891 TTA-CTAT
1 TTATCTAT
*
13898 TTATCTTT
1 TTATCTAT
*
13906 TTATTTAT
1 TTATCTAT
* * *
13914 TAATTTAG
1 TTATCTAT
13922 TTAT-TAT
1 TTATCTAT
* *
13929 CTATTTAT
1 TTATCTAT
*
13937 TTATTTA-
1 TTATCTAT
13944 TTAT-TAT
1 TTATCTAT
* * *
13951 TTTTTTAA
1 TTATCTAT
* *
13959 CTACCTAT
1 TTATCTAT
13967 TTATCTA-
1 TTATCTAT
*
13974 TTATTCTCT
1 TTA-TCTAT
*
13983 GTATCTAT
1 TTATCTAT
13991 TTATCT
1 TTATCT
13997 CTAAACCTAT
Statistics
Matches: 210, Mismatches: 48, Indels: 54
0.67 0.15 0.17
Matches are distributed among these distances:
6 16 0.08
7 66 0.31
8 96 0.46
9 8 0.04
10 10 0.05
11 14 0.07
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.63
Consensus pattern (8 bp):
TTATCTAT
Found at i:18550 original size:54 final size:54
Alignment explanation
Indices: 18450--18996 Score: 605
Period size: 54 Copynumber: 10.1 Consensus size: 54
18440 GGATCTTTTA
* * * * *
18450 AAGTTTTCAGATATCTAAGTTGA-CGTTCAAATGGCCCTGTGTGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATC-TTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
18504 AAGTTTTCAGAGATTTAATTTGTTCTTCAGATGACCCTATGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
18558 AAGTTTTCTGAGGTTTAAGTTGATCTTCAGATGACCCTATGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *
18612 AAGTTTTCAGAGGTTTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * * *
18666 AAGTTTTCAGAGGTTTAAGTTGATCTTCATATAACCTTGTACGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
18720 AAGTTTTCAGAGATTTAAATTGATCTTCAGATGACCTTGTGCGGTCTTGCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * *
18774 AAGTTTTAAAAGATTTAAGTTGATCTTCAGATGACCATGTGCCGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * * * *
18828 AAGTTTTCAGGGATCTAAGTTGAT-TTTATGATGACCTTGTGCGGACTTTCATAA
1 AAGTTTTCAGAGATTTAAGTTGATCTTCA-GATGACCCTGTGCGGTCTTTCATAG
* * * * * ** *
18882 AAGCTTTCAAAGATCTAAGTTGATCTTCAGATGACTCAGTGTTGTCTTTCATAA
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
** ** * * * ** *
18936 AAGTTCTT-AGAGATCAAAGTTGATCCCCAGATGATCCAGTGCGATCAATCAAAG
1 AAGTT-TTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
18990 AAGTTTT
1 AAGTTTT
18997 GAATGATCAT
Statistics
Matches: 426, Mismatches: 63, Indels: 9
0.86 0.13 0.02
Matches are distributed among these distances:
53 5 0.01
54 415 0.97
55 6 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (54 bp):
AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
Found at i:19064 original size:53 final size:53
Alignment explanation
Indices: 18947--19335 Score: 349
Period size: 53 Copynumber: 7.3 Consensus size: 53
18937 AGTTCTTAGA
* * * *
18947 GATCAAAGTTGATCCCCAGATGATCCAGTGCGATCA-ATCAAAGAAGTTTTGAAT
1 GATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTTC-AAGAAGTTTTCAAT
* * * *
19001 GATCATAGTTGATCCCTAAATGATCTAGTGCGAT-ATTTCAAGAAGTTTTCAAT
1 GATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAT
* * * **
19054 GATCATAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGTAGTTTTCTTT
1 GATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAT
*
19108 GATCAGAGTTGATCCCAGATGACCCAGTGCGGTCA-TTCGAAGAAGTTTAT-AGA-
1 GATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTC-AAGAAGTTT-TCA-AT
* * * * * **
19161 GATCAGAGTTAATCCTAGATTATCCAGTGCGGTCATTTCAAGTAGTTCTCTTT
1 GATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAT
* * * * * *
19214 GATCAGAGTTGCTCCCAGATGATCTAGTGCAGTCACTCCAAGAAGTTTTTAGA-
1 GATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCA-AT
* * * * * *
19267 GATCAGAGTTGATCTCCAGATGATCCAATGTGGTCCTTCCGAGAAAGTTTTCGAT
1 GATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTTCAAG-AAGTTTTCAAT
19322 GATCAGAGTTGATC
1 GATCAGAGTTGATC
19336 TCATTTTAAG
Statistics
Matches: 272, Mismatches: 49, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
52 3 0.01
53 163 0.60
54 85 0.31
55 21 0.08
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (53 bp):
GATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAAT
Found at i:19151 original size:107 final size:105
Alignment explanation
Indices: 18936--19335 Score: 419
Period size: 107 Copynumber: 3.7 Consensus size: 105
18926 TCTTTCATAA
* * * * **
18936 AAGTTCTTAGAGATCAAAGTTGATCCCCAGATGATCCAGTGCGATCAATCAAAGAAGTTTTGAAT
1 AAGTT-TTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCTAT
* * *
19001 GATCATAGTTGATCCCTAAATGATCTAGTGCGAT-ATTTCAAG
65 GATCAGAGTTGATCCC-AGATGATCTAGTGCGGTCA-TTCAAG
* * *
19043 AAGTTTTCA-ATGATCATAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGTAGTTTTCTT
1 AAGTTTT-AGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCTA
* *
19107 TGATCAGAGTTGATCCCAGATGACCCAGTGCGGTCATTCGAAG
64 TGATCAGAGTTGATCCCAGATGATCTAGTGCGGTCATTC-AAG
* * * * * * *
19150 AAGTTTATAGAGATCAGAGTTAAT-CCTAGATTATCCAGTGCGGTCATTTCAAGTAGTTCTCTTT
1 AAGTTT-TAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCTAT
* * *
19214 GATCAGAGTTGCTCCCAGATGATCTAGTGCAGTCACTCCAAG
65 GATCAGAGTTGATCCCAGATGATCTAGTGCGGTCA-TTCAAG
* * * * * *
19256 AAGTTTTTAGAGATCAGAGTTGATCTCCAGATGATCCAATGTGGTCCTTCCGAGAAAGTTTTCGA
1 AAG-TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAG-AAGTTTTCTA
19321 TGATCAGAGTTGATC
64 TGATCAGAGTTGATC
19336 TCATTTTAAG
Statistics
Matches: 245, Mismatches: 38, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
106 108 0.44
107 115 0.47
108 22 0.09
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (105 bp):
AAGTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCTATG
ATCAGAGTTGATCCCAGATGATCTAGTGCGGTCATTCAAG
Found at i:20112 original size:35 final size:35
Alignment explanation
Indices: 19311--20111 Score: 1135
Period size: 35 Copynumber: 22.7 Consensus size: 35
19301 CCTTCCGAGA
*
19311 AAGTTTTCGATGATCAGAGTTGATCTCATTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
19346 AAGTTTTCGATGATCAGAGTTGATCTCATTTTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
19381 AAGATTTCGATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
19416 AAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
1 -AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
19452 AA-TTTT-GTTATGATCAGAGTTGATCTCGTTTCAAG
1 AAGTTTTCG--ATGATCAGAGTTGATCTCATTTCAAG
*
19487 AAGTTTTCGATGATCAGATTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
19522 ATGTTTTCAATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
19557 AAGTTTTCAATGATCAGAGTTGATCTCTTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
19592 AAGTTTTCAATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
19627 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
*
19662 AAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
19697 AAGTTTTCGTTCATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
19732 AAGTTTTCGATGATCAGAGTTGATCTCA-TTCTAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTC-AAG
* * *
19767 AAATTTTCGATGATCAGAGTTGATCTCGTTTCAAA
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
** *
19802 AAGTTTTTTATGATCAGAGTTGATCTCTTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* * *
19837 AAGTTTTTGATGATCAAAGTTGATCTCGTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
19872 AAGTTTTTGATTATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
** *
19907 AAGTTTTTTTATGATCAGAGTTGATATCATTTCAAG
1 AAG-TTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
19943 AAGTTTTCAATGATCAGAGTTGATCTCGTTTCAA-
1 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
* *
19977 AGAGTTATCGTTGATCAGAGTTGATCTCATTTCAAG
1 A-AGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
** *
20013 AAGATTTTTATATGGTCAGAGTTGATCTTC-TTTCAAG
1 AAG--TTTTCGATGATCAGAGTTGATC-TCATTTCAAG
** * *
20050 AAGTTTTTTTATGATCAGATTTGATCTTATTTCAAG
1 AAG-TTTTCGATGATCAGAGTTGATCTCATTTCAAG
20086 AAGTTTTCGATGATCAGAGTTGATCT
1 AAGTTTTCGATGATCAGAGTTGATCT
20112 TCACATTGAT
Statistics
Matches: 696, Mismatches: 56, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
33 1 0.00
34 8 0.01
35 553 0.79
36 104 0.15
37 28 0.04
38 2 0.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
Done.