Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011991.1 Kokia drynarioides strain JFW-HI SEQ_126989, 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: 106967
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--25 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
26 TTGTTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1231 original size:3 final size:3
Alignment explanation
Indices: 1225--1267 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1215 TTTCTTCTTC
1225 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1268 GTGGGTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3347 original size:2 final size:2
Alignment explanation
Indices: 3340--3368 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3330 TAATTAACTA
3340 AT AT AT 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 A
3369 GTGGGAGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3809 original size:9 final size:9
Alignment explanation
Indices: 3795--3867 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 9
3785 TTGGTTCAAG
3795 TTTTTATAA
1 TTTTTATAA
3804 TTTTTATAA
1 TTTTTATAA
*
3813 GTTTATATCAA
1 -TTTTTAT-AA
* *
3824 TTTTAATATT
1 TTTTTATA-A
*
3834 TTTTTAAAA
1 TTTTTATAA
* *
3843 TTTCTATGA
1 TTTTTATAA
3852 TTTTTAATAA
1 TTTTT-ATAA
3862 TTTTTA
1 TTTTTA
3868 AGAATTTTAA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
9 21 0.44
10 25 0.52
11 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3816 original size:19 final size:19
Alignment explanation
Indices: 3792--3867 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
3782 GATTTGGTTC
3792 AAGTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
* *
3811 AAGTTTATATCAATTTTAAT
1 AAGTTTTTAT-AATTTTTAT
** * *
3831 ATTTTTTTAAAATTTCTAT
1 AAGTTTTTATAATTTTTAT
*
3850 GA-TTTTTAATAATTTTTA
1 AAGTTTTT-ATAATTTTTA
3868 AGAATTTTAA
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 5 0.12
19 24 0.56
20 14 0.33
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (19 bp):
AAGTTTTTATAATTTTTAT
Found at i:3875 original size:19 final size:19
Alignment explanation
Indices: 3835--3879 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3825 TTTAATATTT
* *
3835 TTTTAA-AATTTCTATGAT
1 TTTTAATAATTTCTAAGAA
*
3853 TTTTAATAATTTTTAAGAA
1 TTTTAATAATTTCTAAGAA
3872 TTTTAATA
1 TTTTAATA
3880 TGTTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTAATAATTTCTAAGAA
Found at i:4016 original size:25 final size:23
Alignment explanation
Indices: 3979--4052 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
3969 ATTTTCATAA
*
3979 GTTTATATCAATTTTAATATTTTTG
1 GTTTTTAT-AATTTT-ATATTTTTG
*
4004 GTTTTTAATAATTTTATATTTTTTT
1 GTTTTT-ATAATTTTATA-TTTTTG
4029 GTTTTTATAATTTTTATGATTTTT
1 GTTTTTATAA-TTTTAT-ATTTTT
4053 AATCATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 7 0.16
25 33 0.77
26 3 0.07
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.68
Consensus pattern (23 bp):
GTTTTTATAATTTTATATTTTTG
Found at i:4033 original size:24 final size:25
Alignment explanation
Indices: 3988--4052 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
3978 AGTTTATATC
3988 AATTTTA-ATATTTTTGGTTTTTAAT
1 AATTTTATAT-TTTTTGGTTTTTAAT
*
4013 AATTTTATATTTTTTTGTTTTT-AT
1 AATTTTATATTTTTTGGTTTTTAAT
4037 AATTTTTATGATTTTT
1 AA-TTTTAT-ATTTTT
4053 AATCATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 4 0.11
25 24 0.67
26 8 0.22
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (25 bp):
AATTTTATATTTTTTGGTTTTTAAT
Found at i:4034 original size:16 final size:18
Alignment explanation
Indices: 4015--4053 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4005 TTTTTAATAA
*
4015 TTTTAT-ATTTTTTTG-T
1 TTTTATAATTTTTATGAT
4031 TTTTATAATTTTTATGAT
1 TTTTATAATTTTTATGAT
4049 TTTTA
1 TTTTA
4054 ATCATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTATAATTTTTATGAT
Found at i:6655 original size:20 final size:19
Alignment explanation
Indices: 6602--6656 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
6592 TATAAAATAC
*
6602 TATTAATATATTATGATAAAT
1 TATTAA-AT-TTATTATAAAT
**
6623 TATTAAAAATATTATAGAAT
1 TATTAAATTTATTATA-AAT
6643 TATTAAATTTATTA
1 TATTAAATTTATTA
6657 AATATAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.21
20 16 0.57
21 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATTAAATTTATTATAAAT
Found at i:6785 original size:39 final size:40
Alignment explanation
Indices: 6706--6794 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
6696 AAAGAATTAT
6706 AAATATTATAAAAATGTCACAAGTTAAAAAATGTTAATAA
1 AAATATTATAAAAATGTCACAAGTTAAAAAATGTTAATAA
* * * * *
6746 AAATATTA-AAAAGTGTCATAATTTTAAAGA-GTTATATAA
1 AAATATTATAAAAATGTCACAAGTTAAAAAATGTTA-ATAA
*
6785 AAATAGTATA
1 AAATATTATA
6795 TTGATAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.10
39 28 0.68
40 9 0.22
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (40 bp):
AAATATTATAAAAATGTCACAAGTTAAAAAATGTTAATAA
Found at i:6829 original size:12 final size:10
Alignment explanation
Indices: 6792--6847 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
6782 TAAAAATAGT
6792 ATATTGATAAA
1 ATATT-ATAAA
6803 ATATTATAAA
1 ATATTATAAA
6813 A-ATTATTAAA
1 ATATTA-TAAA
6823 ATTATTA-AAA
1 A-TATTATAAA
6833 AT-TTATAAA
1 ATATTATAAA
6842 AT-TTAT
1 ATATTAT
6848 TTTGAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.07
9 14 0.34
10 15 0.37
11 5 0.12
12 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATTATAAA
Found at i:6833 original size:19 final size:18
Alignment explanation
Indices: 6805--6844 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6795 TTGATAAAAT
6805 ATTATAAAAA-TTATTAAA
1 ATTATAAAAATTTA-TAAA
6823 ATTATTAAAAATTTATAAA
1 ATTA-TAAAAATTTATAAA
6842 ATT
1 ATT
6845 TATTTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATAAAAATTTATAAA
Found at i:6862 original size:29 final size:29
Alignment explanation
Indices: 6799--6862 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
6789 AGTATATTGA
*
6799 TAAAATATTATAAAAATTATTAAAATTAT
1 TAAAATATTATAAAAATTATTAAAATAAT
* **
6828 TAAAA-ATTTATAAAATTTATTTTGAATAAT
1 TAAAATA-TTATAAAAATTA-TTAAAATAAT
6858 TAAAA
1 TAAAA
6863 AATGAGAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 16 0.55
30 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
TAAAATATTATAAAAATTATTAAAATAAT
Found at i:7201 original size:21 final size:21
Alignment explanation
Indices: 7158--7201 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7148 TTACCACTCC
**
7158 TTTTATAAATTTATAATTTTT
1 TTTTATAAATTTATAATCATT
7179 TTTTATAAATTT-TAATACATT
1 TTTTATAAATTTATAAT-CATT
7200 TT
1 TT
7202 AAATAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATAAATTTATAATCATT
Found at i:14500 original size:339 final size:339
Alignment explanation
Indices: 13877--14892 Score: 1780
Period size: 339 Copynumber: 3.0 Consensus size: 339
13867 TTTACGGATT
13877 CAGTATTCAAGGGGTCTACGACAGCCATCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
1 CAGTATTCAAGGGGTCTACGACAGCCATCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
* *
13942 GTTGCAGTATTGAGATCAGTAGCTTGTTCTCCATTTTCTATTAAAGAATTGTCATTAAAAGCTTT
66 GTTGCAGTATTGAGATCAGCAGCTTGTTCTCCATTTTCTATTAAAGAATTGTCATTAAAATCTTT
*
14007 CTTCTCGGCTATGCGCTTTTTCTTTGATGCAGGCCGGGATTGAAAGGAATCTTCTTTTGACTCAT
131 CTTCTCGGCTTTGCGCTTTTTCTTTGATGCAGGCCGGGATTGAAAGGAATCTTCTTTTGACTCAT
14072 GTTCCTGGTCCTTGTGAGCAACATCTTTATGTTTATTAGTTTCCAATTCAGAATGTTCTCCTGGA
196 GTTCCTGGTCCTTGTGAGCAACATCTTTATGTTTATTAGTTTCCAATTCAGAATGTTCTCCTGGA
* *
14137 ACGTTTATTCCCACATCAGCCATCCTTTTCCCAGCAGTTGACCTCTTATTTCTATCAGAAGACAA
261 ACGTTTATTCCCCCATCGGCCATCCTTTTCCCAGCAGTTGACCTCTTATTTCTATCAGAAGACAA
*
14202 TCTCCGAGAGGTTG
326 ACTCCGAGAGGTTG
* *
14216 CAGTATTCAAGGGGTCTACAACAGCCCTCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
1 CAGTATTCAAGGGGTCTACGACAGCCATCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
* *
14281 GTTGCAGTATTGAGATCAGCAGCTTGTACTCCATTTTCTATTAAAGAACTGTCATTAAAATCTTT
66 GTTGCAGTATTGAGATCAGCAGCTTGTTCTCCATTTTCTATTAAAGAATTGTCATTAAAATCTTT
14346 CTTCTCGGCTTTGCGCTTTTTCTTTGATGCAGGCCGGGATTGAAAGGAATCTTCTTTTGACTCAT
131 CTTCTCGGCTTTGCGCTTTTTCTTTGATGCAGGCCGGGATTGAAAGGAATCTTCTTTTGACTCAT
* *
14411 GTTCCTGGTCCTTGTAAGCAACATCTTTATGTTTTTTAGTTTCCAATTCAGAATGTTCTCCTGGA
196 GTTCCTGGTCCTTGTGAGCAACATCTTTATGTTTATTAGTTTCCAATTCAGAATGTTCTCCTGGA
* * *
14476 ACGGTTATTCCCCCATCGGCCATCCTTTTCCCAGCAGTTGAGCTCTTATTTCTATTAGAAGACAA
261 ACGTTTATTCCCCCATCGGCCATCCTTTTCCCAGCAGTTGACCTCTTATTTCTATCAGAAGACAA
14541 ACTCCGAGAGGTTG
326 ACTCCGAGAGGTTG
* * *
14555 AAGTATTCAAGGGGTCTGCGACAGCCGTCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
1 CAGTATTCAAGGGGTCTACGACAGCCATCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
*
14620 GTTGCAGTATTGAGATCAGCAGCTTGTTCTCTATTTTCTATTAAAGAATTGTCATTAAAATCTTT
66 GTTGCAGTATTGAGATCAGCAGCTTGTTCTCCATTTTCTATTAAAGAATTGTCATTAAAATCTTT
* * * *
14685 CTTCTCGGCTTTGCGCTTTTTCTTTGATACAGGACGAGATTGAAAGGAATCATCTTTTGACTCAT
131 CTTCTCGGCTTTGCGCTTTTTCTTTGATGCAGGCCGGGATTGAAAGGAATCTTCTTTTGACTCAT
* *
14750 GTTCCAGGTCCTTGTGAGCAACATCTTTATGTTTATTACTTTCCAATTCAGAATGTTCTCCTGGA
196 GTTCCTGGTCCTTGTGAGCAACATCTTTATGTTTATTAGTTTCCAATTCAGAATGTTCTCCTGGA
** *
14815 ACGTTTATTCCCCCATCGGCCATCCTTTTCGTAGCAATTGACCTCTTATTTCTATCAGAAGACAA
261 ACGTTTATTCCCCCATCGGCCATCCTTTTCCCAGCAGTTGACCTCTTATTTCTATCAGAAGACAA
14880 ACTCCGAGAGGTT
326 ACTCCGAGAGGTT
14893 TCATCCACAC
Statistics
Matches: 641, Mismatches: 36, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
339 641 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (339 bp):
CAGTATTCAAGGGGTCTACGACAGCCATCGTATTTTCCAGTTTCTGACCTAAAGTGCACTCAGAG
GTTGCAGTATTGAGATCAGCAGCTTGTTCTCCATTTTCTATTAAAGAATTGTCATTAAAATCTTT
CTTCTCGGCTTTGCGCTTTTTCTTTGATGCAGGCCGGGATTGAAAGGAATCTTCTTTTGACTCAT
GTTCCTGGTCCTTGTGAGCAACATCTTTATGTTTATTAGTTTCCAATTCAGAATGTTCTCCTGGA
ACGTTTATTCCCCCATCGGCCATCCTTTTCCCAGCAGTTGACCTCTTATTTCTATCAGAAGACAA
ACTCCGAGAGGTTG
Found at i:17228 original size:12 final size:12
Alignment explanation
Indices: 17207--17248 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
17197 TCATTAACAT
*
17207 TGTTCGTGAATA
1 TGTTCATGAATA
*
17219 TGTTCATGAACA
1 TGTTCATGAATA
*
17231 TGTTCGTGAATA
1 TGTTCATGAATA
17243 TGTTCA
1 TGTTCA
17249 CGAAAACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (12 bp):
TGTTCATGAATA
Found at i:17239 original size:24 final size:25
Alignment explanation
Indices: 17196--17248 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
17186 TTCTTTATTA
*
17196 TTCATTAACATTGTTCGTGAATATG
1 TTCATGAACATTGTTCGTGAATATG
17221 TTCATGAACA-TGTTCGTGAATATG
1 TTCATGAACATTGTTCGTGAATATG
17245 TTCA
1 TTCA
17249 CGAAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (25 bp):
TTCATGAACATTGTTCGTGAATATG
Found at i:18312 original size:71 final size:71
Alignment explanation
Indices: 18196--18338 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
18186 AAAATCACGG
*
18196 GTAGAAGAGAAGAAAGACAGTAATGTTGAATTTGAATGATAGAAAATAAGTTTCGACTACATCTA
1 GTAGAAGAGAAAAAAGACAGTAATGTTGAATTTGAATGATAGAAAATAAGTTTCGACTACATCTA
18261 TTTATA
66 TTTATA
* *
18267 GTAGAAGAGAAAAAAGACAGTAATGTTGAATTTGAATGATAGAAAATGAGTTTCGACTGCATCTA
1 GTAGAAGAGAAAAAAGACAGTAATGTTGAATTTGAATGATAGAAAATAAGTTTCGACTACATCTA
18332 TTTATA
66 TTTATA
18338 G
1 G
18339 GTTTAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (71 bp):
GTAGAAGAGAAAAAAGACAGTAATGTTGAATTTGAATGATAGAAAATAAGTTTCGACTACATCTA
TTTATA
Found at i:24314 original size:44 final size:44
Alignment explanation
Indices: 24264--24348 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
24254 TAATTGTAAT
* * * * * *
24264 TTAAATTCTAATTATTTTTATATGTATATTTATGACAACTTCTA
1 TTAAATTATAATTATTTTCAAATGAATAATTATCACAACTTCTA
24308 TTAAATTATAATTATTTTCAAATGAATAATTATCACAACTT
1 TTAAATTATAATTATTTTCAAATGAATAATTATCACAACTT
24349 TGATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (44 bp):
TTAAATTATAATTATTTTCAAATGAATAATTATCACAACTTCTA
Found at i:24693 original size:25 final size:25
Alignment explanation
Indices: 24665--24722 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
24655 TTTACATATT
24665 TTTATAAA-TTAT-TATAATTAAAATA
1 TTTATAAATTTATGTA-AATTAAAA-A
24690 TTTATAAATTTATGTAAATTAAAAA
1 TTTATAAATTTATGTAAATTAAAAA
*
24715 TATATAAA
1 TTTATAAA
24723 AGTATTTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 16 0.53
26 12 0.40
27 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTATAAATTTATGTAAATTAAAAA
Found at i:25107 original size:14 final size:15
Alignment explanation
Indices: 25079--25107 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25069 TTAATTTATA
25079 TATTTTTAAAGATTT
1 TATTTTTAAAGATTT
25094 TATTTTTAAA-ATTT
1 TATTTTTAAAGATTT
25108 ATACTTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTTTTAAAGATTT
Found at i:33746 original size:17 final size:17
Alignment explanation
Indices: 33724--33757 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33714 ATATTTTATT
* *
33724 TTTAAAATTAGTTTTTA
1 TTTAAAAATAATTTTTA
33741 TTTAAAAATAATTTTTA
1 TTTAAAAATAATTTTTA
33758 AAAAATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAAAATAATTTTTA
Found at i:33993 original size:2 final size:2
Alignment explanation
Indices: 33949--33978 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33939 TAATGATTTA
33949 AT 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
33979 TATTTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34004 original size:18 final size:18
Alignment explanation
Indices: 33950--34005 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
33940 AATGATTTAA
*
33950 TATATATATATATATATATA
1 TATATATAT-TATATA-ATT
*
33970 TATATATATTATTTAATT
1 TATATATATTATATAATT
33988 TATATA-ATTAATATAATT
1 TATATATATT-ATATAATT
34006 ATTTTTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 3 0.09
18 15 0.47
19 5 0.16
20 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATATTATATAATT
Found at i:39229 original size:81 final size:78
Alignment explanation
Indices: 39067--39231 Score: 190
Period size: 81 Copynumber: 2.1 Consensus size: 78
39057 ATTTTATTTT
* * * * *
39067 TTTTTATTTTTTTCTTGTGAATTTTGTGTATACATTTTGAAAGTAATGCTTTCAATGAATTTATA
1 TTTTTATTTTTTTCTGGTGAAATTTGTATACACATTTTGAAAGTAATGCTTTCAATGAATTCATA
* *
39132 AATTTATTAATTTA
66 AATGTATCAA-TTA
*
39146 TTTTTATTTTTTTTCTGGTGAAATTTGTATACACATTTTTGGAAGTAATGCTTTCAATGGAA-TC
1 TTTTTA-TTTTTTTCTGGTGAAATTTGTATACACA-TTTTGAAAGTAATGCTTTCAAT-GAATTC
39210 ATAAGATGTAGTCAA-TA
63 ATAA-ATGTA-TCAATTA
39227 TTTTT
1 TTTTT
39232 TCTTAAAATT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
79 6 0.08
80 24 0.33
81 33 0.45
82 7 0.10
83 3 0.04
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (78 bp):
TTTTTATTTTTTTCTGGTGAAATTTGTATACACATTTTGAAAGTAATGCTTTCAATGAATTCATA
AATGTATCAATTA
Found at i:40594 original size:16 final size:18
Alignment explanation
Indices: 40555--40588 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40545 TAAATTTATA
40555 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
40572 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
40589 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:40946 original size:2 final size:2
Alignment explanation
Indices: 40939--40968 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40929 ATCTTTATTG
40939 AT 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
40969 TGGATCACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41519 original size:31 final size:30
Alignment explanation
Indices: 41468--41536 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
41458 ATAGTTAGAT
* * *
41468 TTAAATTTTAAAATCTAAAAAGTAGAAGGA
1 TTAAATTTTAAAATCAAAAAAATACAAGGA
41498 TTAAATTCTTAAAAAT-AAAAAAATACAAGGA
1 TTAAATT-TT-AAAATCAAAAAAATACAAGGA
41529 TTAAATTT
1 TTAAATTT
41537 CATATTTCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.24
31 21 0.62
32 5 0.15
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (30 bp):
TTAAATTTTAAAATCAAAAAAATACAAGGA
Found at i:52443 original size:16 final size:18
Alignment explanation
Indices: 52408--52445 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
52398 AAAATATTTA
*
52408 TTTTAATGATTTTAATAT
1 TTTTAATGATATTAATAT
52426 TTTTAATG-TATT-ATAT
1 TTTTAATGATATTAATAT
52442 TTTT
1 TTTT
52446 TTAATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAATGATATTAATAT
Found at i:52446 original size:18 final size:17
Alignment explanation
Indices: 52401--52450 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
52391 TGTTGGGAAA
52401 ATATTTATTTTAATGATT
1 ATATTT-TTTTAATGATT
* *
52419 TTAATATTTTTAATGTATT
1 AT-ATTTTTTTAATG-ATT
52438 ATATTTTTTTAAT
1 ATATTTTTTTAAT
52451 TTTGTATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
ATATTTTTTTAATGATT
Found at i:54614 original size:49 final size:49
Alignment explanation
Indices: 54542--54644 Score: 206
Period size: 49 Copynumber: 2.1 Consensus size: 49
54532 TTGAAGAAGT
54542 GGAAGGCTAATGCAGGCAAGGCTATGTTTGCAATTAAAACCACTGTAGA
1 GGAAGGCTAATGCAGGCAAGGCTATGTTTGCAATTAAAACCACTGTAGA
54591 GGAAGGCTAATGCAGGCAAGGCTATGTTTGCAATTAAAACCACTGTAGA
1 GGAAGGCTAATGCAGGCAAGGCTATGTTTGCAATTAAAACCACTGTAGA
54640 GGAAG
1 GGAAG
54645 AAATGTTAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (49 bp):
GGAAGGCTAATGCAGGCAAGGCTATGTTTGCAATTAAAACCACTGTAGA
Found at i:59149 original size:3 final size:3
Alignment explanation
Indices: 59135--59222 Score: 59
Period size: 3 Copynumber: 29.3 Consensus size: 3
59125 AAGAACATAT
* * * * * * *
59135 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATT ATT ATT ATT ATT ATT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
59183 ATT ATT ATT ATT ATT ATT ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
59223 CAAATTGCAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (3 bp):
ATC
Found at i:60190 original size:2 final size:2
Alignment explanation
Indices: 60185--60217 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60175 CATTGGTGTT
60185 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
60218 TATTACATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:67405 original size:14 final size:13
Alignment explanation
Indices: 67385--67422 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
67375 AGATTAGTAC
67385 TATTTTCTATTTG
1 TATTTTCTATTTG
*
67398 TAATTTTCTAATTG
1 T-ATTTTCTATTTG
67412 TATTTT-TATTT
1 TATTTTCTATTT
67423 TCTTGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 12 0.55
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (13 bp):
TATTTTCTATTTG
Found at i:70616 original size:18 final size:18
Alignment explanation
Indices: 70594--70644 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
70584 AATCAAGATC
* *
70594 AAGATCAAGATGGAGGTG
1 AAGATAAAGATGAAGGTG
* **
70612 GAGATTGAGATGAAGGTG
1 AAGATAAAGATGAAGGTG
70630 AAGATAAAGATGAAG
1 AAGATAAAGATGAAG
70645 AGTCGAAACC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.37, T:0.18
Consensus pattern (18 bp):
AAGATAAAGATGAAGGTG
Found at i:70992 original size:74 final size:74
Alignment explanation
Indices: 70881--71020 Score: 217
Period size: 74 Copynumber: 1.9 Consensus size: 74
70871 GAAAATTTAT
* *
70881 TTGTATTGTATTGTATTTTTGCATCAACAATAAACTTATTTACAATTTACAAAAAAATGAAAAAA
1 TTGTATTCTATTGTATTTTTACATCAACAATAAACTTATTTACAATTTACAAAAAAATGAAAAAA
70946 ATGTTTGTG
66 ATGTTTGTG
* * * **
70955 TTGTATTCTATTGTATTTTTACATCAATACTATACTTATTTACAATTTACTCAAAAATGAAAAAA
1 TTGTATTCTATTGTATTTTTACATCAACAATAAACTTATTTACAATTTACAAAAAAATGAAAAAA
71020 A
66 A
71021 AATGAATACA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (74 bp):
TTGTATTCTATTGTATTTTTACATCAACAATAAACTTATTTACAATTTACAAAAAAATGAAAAAA
ATGTTTGTG
Found at i:76597 original size:2 final size:2
Alignment explanation
Indices: 76590--76620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76580 TCTTAAAAAT
76590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76621 TATTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77317 original size:22 final size:24
Alignment explanation
Indices: 77283--77335 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
77273 TAGTTTTTTA
77283 TTTT-TTTTAAATATTT-AT-ATT
1 TTTTATTTTAAATATTTAATAATT
77304 GTTTTATTTT-AATATTTAATAATT
1 -TTTTATTTTAAATATTTAATAATT
77328 TTTTATTT
1 TTTTATTT
77336 ATTAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.39
23 14 0.50
24 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATTTTAAATATTTAATAATT
Found at i:77331 original size:23 final size:21
Alignment explanation
Indices: 77283--77336 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
77273 TAGTTTTTTA
77283 TTTTT-TTTAAATATTTATAT
1 TTTTTATTTAAATATTTATAT
*
77303 TGTTTTATTTTAATATTTAATAAT
1 T-TTTTATTTAAATATTT-AT-AT
77327 TTTTTATTTA
1 TTTTTATTTA
77337 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 4 0.14
22 10 0.36
23 10 0.36
24 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTATTTAAATATTTATAT
Found at i:96545 original size:12 final size:11
Alignment explanation
Indices: 96523--96600 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
96513 ATAACATCTA
96523 AACAACAAAAAT
1 AACAAC-AAAAT
96535 AACAATCAAAAT
1 AACAA-CAAAAT
* *
96547 AGCAGCAAAAAT
1 AACAAC-AAAAT
*
96559 AACAACAAAAC
1 AACAACAAAAT
**
96570 AAC-ATTAAA-
1 AACAACAAAAT
96579 AACAACAAAAAT
1 AACAAC-AAAAT
*
96591 AACAGCAAAA
1 AACAACAAAA
96601 GCAACAATCA
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
9 3 0.06
10 5 0.10
11 15 0.29
12 27 0.53
13 1 0.02
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.09
Consensus pattern (11 bp):
AACAACAAAAT
Found at i:96558 original size:44 final size:44
Alignment explanation
Indices: 96509--96633 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 44
96499 AAAACGCATA
* * ** *
96509 AAAAATAACATCTAAACAACA-AAAATAACAATCAAAATAGCAGC
1 AAAAATAACAACAAAACAACATAAAA-AACAACAAAAATAACAGC
*
96553 AAAAATAACAACAAAACAACATTAAAAACAACAAAAATAACAGC
1 AAAAATAACAACAAAACAACATAAAAAACAACAAAAATAACAGC
** ** * *
96597 AAAAGCAACAATCAAAACAGTAAAAAAAACACCAAAA
1 AAAAATAACAA-CAAAACAACATAAAAAACAACAAAA
96634 GAGTAAAAAC
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
44 43 0.65
45 23 0.35
ACGTcount: A:0.68, C:0.18, G:0.04, T:0.10
Consensus pattern (44 bp):
AAAAATAACAACAAAACAACATAAAAAACAACAAAAATAACAGC
Found at i:96614 original size:33 final size:33
Alignment explanation
Indices: 96523--96634 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 33
96513 ATAACATCTA
** *
96523 AACAACAAAAATAACAATCAAAATAGCAGCAAAAAT
1 AACAACAAAAGCAACAAT-AAAA-A-CAACAAAAAT
*
96559 AACAACAAAA-CAACATTAAAAACAACAAAAAT
1 AACAACAAAAGCAACAATAAAAACAACAAAAAT
* * ** *
96591 AACAGCAAAAGCAACAATCAAAACAGTAAAAAA
1 AACAACAAAAGCAACAATAAAAACAACAAAAAT
*
96624 AACACCAAAAG
1 AACAACAAAAG
96635 AGTAAAAACC
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
32 18 0.28
33 28 0.43
34 4 0.06
35 5 0.08
36 10 0.15
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (33 bp):
AACAACAAAAGCAACAATAAAAACAACAAAAAT
Found at i:96648 original size:21 final size:20
Alignment explanation
Indices: 96609--96698 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 20
96599 AAGCAACAAT
96609 CAAAACAGTAAAAAAAACAC
1 CAAAACAGTAAAAAAAACAC
* *
96629 CAAAAGAGTAAAAACCAACA-
1 CAAAACAGTAAAAA-AAACAC
**
96649 C-AAATTGTAAAAAAAAAACATC
1 CAAAACAGT--AAAAAAAACA-C
*
96671 CAAAACATTAAAAAAAAGCAC
1 CAAAACAGTAAAAAAAA-CAC
96692 CAAAACA
1 CAAAACA
96699 ACAATATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
19 5 0.09
20 18 0.33
21 25 0.45
22 3 0.05
23 4 0.07
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.09
Consensus pattern (20 bp):
CAAAACAGTAAAAAAAACAC
Found at i:96683 original size:22 final size:21
Alignment explanation
Indices: 96609--96698 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 21
96599 AAGCAACAAT
*
96609 CAAAACAGT-AAAAAAAACAC
1 CAAAACATTAAAAAAAAACAC
* * **
96629 CAAAAGAGTAAAAACCAACA-
1 CAAAACATTAAAAAAAAACAC
*** *
96649 CAAATTGTAAAAAAAAAACATC
1 CAAAACATTAAAAAAAAACA-C
*
96671 CAAAACATTAAAAAAAAGCAC
1 CAAAACATTAAAAAAAAACAC
96692 CAAAACA
1 CAAAACA
96699 ACAATATAAA
Statistics
Matches: 52, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
20 21 0.40
21 16 0.31
22 15 0.29
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.09
Consensus pattern (21 bp):
CAAAACATTAAAAAAAAACAC
Found at i:101142 original size:30 final size:32
Alignment explanation
Indices: 101107--101176 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
101097 TTAACACAAA
101107 AGTCACTGAAC-TT-T-GAAAATGTGACAAAAC
1 AGTCACTGAACGTTATCGAAAA-GTGACAAAAC
101137 AGTCACT-AACGTTATCGAAAAGTGACAAAAC
1 AGTCACTGAACGTTATCGAAAAGTGACAAAAC
101168 AGTCACTGA
1 AGTCACTGA
101177 TTAATAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.08
30 9 0.25
31 18 0.50
32 6 0.17
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (32 bp):
AGTCACTGAACGTTATCGAAAAGTGACAAAAC
Found at i:101319 original size:22 final size:23
Alignment explanation
Indices: 101294--101371 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 23
101284 ATCATAATCC
101294 AATCAAAATCGAAAT-AACCCTA
1 AATCAAAATCGAAATAAACCCTA
** **
101316 AATCAAAAATAAAAATCAATGTCC-A
1 AATC-AAAATCGAAAT-AA-ACCCTA
101341 AATCAAAATCG-AATAAACCCTA
1 AATCAAAATCGAAATAAACCCTA
101363 AATCAAAAT
1 AATCAAAAT
101372 TCACAATCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
21 2 0.05
22 16 0.37
23 12 0.28
24 5 0.12
25 6 0.14
26 2 0.05
ACGTcount: A:0.58, C:0.19, G:0.04, T:0.19
Consensus pattern (23 bp):
AATCAAAATCGAAATAAACCCTA
Found at i:101380 original size:47 final size:46
Alignment explanation
Indices: 101290--101403 Score: 140
Period size: 47 Copynumber: 2.5 Consensus size: 46
101280 AGCAATCATA
101290 ATCC-AATCAAAATCGAAATAACCCTAAATCAAAAATAAAAATCAAT
1 ATCCAAATCAAAATCGAAA-AACCCTAAATCAAAAATAAAAATCAAT
* * * *
101336 GTCCAAATCAAAATCGAATAAACCCTAAATCAAAATTCACAATCAAT
1 ATCCAAATCAAAATCGAA-AAACCCTAAATCAAAAATAAAAATCAAT
* * *
101383 ATCGACATCAAATTCGAAAAA
1 ATCCAAATCAAAATCGAAAAA
101404 ACACAAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 6 0.10
47 51 0.88
48 1 0.02
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.20
Consensus pattern (46 bp):
ATCCAAATCAAAATCGAAAAACCCTAAATCAAAAATAAAAATCAAT
Found at i:101776 original size:30 final size:32
Alignment explanation
Indices: 101706--101776 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
101696 CCCATCTAAT
* * *
101706 TTCAGTAACTGTTTTATCACTTTTTGATAACG
1 TTCAGTGACTGTTTTATCACATTTTCATAACG
*
101738 TT-AGTGACTGTTTTGTCACATTTTCA-AA-G
1 TTCAGTGACTGTTTTATCACATTTTCATAACG
101767 TTCAGTGACT
1 TTCAGTGACT
101777 TTTGTGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 3 0.09
30 9 0.26
31 20 0.59
32 2 0.06
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (32 bp):
TTCAGTGACTGTTTTATCACATTTTCATAACG
Found at i:102972 original size:15 final size:15
Alignment explanation
Indices: 102952--102982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
102942 TGATCGGCTA
102952 AATTTTTAATTAATT
1 AATTTTTAATTAATT
*
102967 AATTTTTAGTTAATT
1 AATTTTTAATTAATT
102982 A
1 A
102983 TCAACTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
AATTTTTAATTAATT
Found at i:104953 original size:20 final size:20
Alignment explanation
Indices: 104915--104953 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
104905 AAATAACTAT
*
104915 TAATAATTTTTAGAATTTTA
1 TAATAATTTTTACAATTTTA
* *
104935 TAATATTTTTTACAGTTTT
1 TAATAATTTTTACAATTTT
104954 GCGTTCATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (20 bp):
TAATAATTTTTACAATTTTA
Found at i:106895 original size:23 final size:25
Alignment explanation
Indices: 106843--106901 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
106833 AAATGCTGGG
106843 TAACAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
106868 TAACAGAGAGCACA-AGACGTGCT-A
1 TAACAGAGAGCACACACA-GTGCTAA
106892 -AACAGAGAGC
1 TAACAGAGAGC
106902 CCGCTAGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 10 0.31
24 3 0.09
25 19 0.59
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Done.