Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023406.1 Corchorus olitorius cultivar O-4 contig23439, 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: 101831
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2630 original size:41 final size:43
Alignment explanation
Indices: 2531--2630 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 43
2521 TTTCACTCTG
* * *
2531 AAGTCCCCAAGCACATATATAACACAGGGGCAACTCTCTCTAA
1 AAGTCCCTAAGCACATATATAACACAGAGGCAACTCTATCTAA
*
2574 AAGT-CCTCAAGCACATATATAACACAGAGGC-A-TCTATAC-CA
1 AAGTCCCT-AAGCACATATATAACACAGAGGCAACTCTAT-CTAA
*
2615 AAGTCCCTAAACACAT
1 AAGTCCCTAAGCACAT
2631 GTAACACAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
41 16 0.33
42 7 0.14
43 26 0.53
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (43 bp):
AAGTCCCTAAGCACATATATAACACAGAGGCAACTCTATCTAA
Found at i:6730 original size:34 final size:33
Alignment explanation
Indices: 6682--6745 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
6672 TTTTTTGACC
*
6682 TCTATGTTGGACACACATAAAAAGGAACCTTTCT
1 TCTATGTTGAACACACAT-AAAAGGAACCTTTCT
*
6716 TCTATGTTGAACACACATAAAAGGATCCTT
1 TCTATGTTGAACACACATAAAAGGAACCTT
6746 AGGCCCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (33 bp):
TCTATGTTGAACACACATAAAAGGAACCTTTCT
Found at i:7418 original size:5 final size:5
Alignment explanation
Indices: 7408--7473 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
7398 TTATGTATGT
* *
7408 ATATA ATATA ATA-A A-ATA ATATT ATGT- ATATAA TATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA
7456 ATAGTA ATAATA ATATA A
1 ATA-TA AT-ATA ATATA A
7474 AATATAACTA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
3 1 0.02
4 10 0.20
5 27 0.54
6 7 0.14
7 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:7429 original size:31 final size:29
Alignment explanation
Indices: 7382--7477 Score: 96
Period size: 31 Copynumber: 3.4 Consensus size: 29
7372 CTGTTTTAGA
*
7382 ATAATACATAATAATATTATGTATGTATATAAT
1 ATAATA-A-AATAATATTATGTATATA-AT-AT
7415 ATAATAAAATAATATTATGTATATAATAT
1 ATAATAAAATAATATTATGTATATAATAT
*
7444 ATAATATAAT-ATA-TA-GTA-ATAATA-
1 ATAATAAAATAATATTATGTATATAATAT
7468 AT-ATAAAATA
1 ATAATAAAATA
7478 TAACTATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
23 6 0.10
24 2 0.03
25 6 0.10
26 3 0.05
27 2 0.03
28 3 0.05
29 11 0.19
30 2 0.03
31 17 0.29
32 1 0.02
33 6 0.10
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (29 bp):
ATAATAAAATAATATTATGTATATAATAT
Found at i:7454 original size:34 final size:33
Alignment explanation
Indices: 7382--7449 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 33
7372 CTGTTTTAGA
*
7382 ATAATACATAATAATATTATGTATGTATATAAT
1 ATAATACATAATAATATTATGTATATATATAAT
7415 ATAATA-A-AATAATATTATGTATATA-AT-AT
1 ATAATACATAATAATATTATGTATATATATAAT
7444 ATAATA
1 ATAATA
7450 TAATATATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.24
30 2 0.06
31 17 0.50
32 1 0.03
33 6 0.18
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (33 bp):
ATAATACATAATAATATTATGTATATATATAAT
Found at i:7470 original size:16 final size:14
Alignment explanation
Indices: 7408--7486 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 14
7398 TTATGTATGT
7408 ATATAATATA-ATA
1 ATATAATATATATA
*
7421 AAATAATAT-TAT-
1 ATATAATATATATA
*
7433 GTAT-ATAATATATA
1 ATATAAT-ATATATA
7447 ATATAATATATAGTA
1 ATATAATATATA-TA
7462 ATAATAATATA-A-A
1 AT-ATAATATATATA
7475 ATATAACTATAT
1 ATATAA-TATAT
7487 TCACCAGAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
13 20 0.38
14 8 0.15
15 7 0.13
16 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:7472 original size:21 final size:20
Alignment explanation
Indices: 7408--7479 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
7398 TTATGTATGT
7408 ATATAATATA-ATAA-AATA
1 ATATAATATATATAATAATA
* *
7426 ATATTATGTATATAATATATA
1 ATATAATATATATAATA-ATA
7447 ATATAATATATAGTAATAATA
1 ATATAATATATA-TAATAATA
*
7468 ATATAAAATATA
1 ATATAATATATA
7480 ACTATATTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.18
19 4 0.09
20 1 0.02
21 27 0.60
22 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
ATATAATATATATAATAATA
Found at i:7480 original size:7 final size:7
Alignment explanation
Indices: 7407--7479 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
7397 ATTATGTATG
7407 TATATAA
1 TATATAA
7414 TATAATAA
1 TAT-ATAA
7422 -A-ATAA
1 TATATAA
*
7427 TAT-TATG
1 TATATA-A
7434 TATATAA
1 TATATAA
7441 TATATAA
1 TATATAA
7448 TATA-ATA
1 TATATA-A
7455 TATAGTAA
1 TATA-TAA
7463 TA-ATAA
1 TATATAA
*
7469 TATAAAA
1 TATATAA
7476 TATA
1 TATA
7480 ACTATATTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
5 4 0.07
6 9 0.17
7 31 0.57
8 9 0.17
9 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (7 bp):
TATATAA
Found at i:10706 original size:70 final size:67
Alignment explanation
Indices: 10593--10728 Score: 209
Period size: 70 Copynumber: 2.0 Consensus size: 67
10583 CGCGTTAATT
*
10593 GCTAAATATAATTCCTAGTAGTAATGCTAATACTTATACTACAAATGCCAATTTTACATTTATCA
1 GCTAAATATAATTCCTAGTAATAATGCTAATACTTATACTACAAATGCCAATTTTACATTTATCA
10658 TC
66 TC
** *
10660 GCTAAATATAATTCCTAGTAATAATACTGCTAATACTTATACTACAAATGTTAATTTTCCATTTA
1 GCTAAATATAATTCCTAGTAAT-A-A-TGCTAATACTTATACTACAAATGCCAATTTTACATTTA
10725 TCAT
63 TCAT
10729 ATTATATTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
67 21 0.34
68 1 0.02
69 1 0.02
70 39 0.63
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.39
Consensus pattern (67 bp):
GCTAAATATAATTCCTAGTAATAATGCTAATACTTATACTACAAATGCCAATTTTACATTTATCA
TC
Found at i:14239 original size:17 final size:17
Alignment explanation
Indices: 14217--14250 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
14207 AACTTCTCTG
14217 GTCCCTAAATTAAATCC
1 GTCCCTAAATTAAATCC
14234 GTCCCTAAATTAAATCC
1 GTCCCTAAATTAAATCC
14251 ATTAAGATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (17 bp):
GTCCCTAAATTAAATCC
Found at i:14981 original size:178 final size:177
Alignment explanation
Indices: 14618--15008 Score: 502
Period size: 178 Copynumber: 2.2 Consensus size: 177
14608 CCGATCAAGG
* * *
14618 TGATTTAAGTGT-TTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGATTCGAAAACT
1 TGATTCAAGTGTCTT-TTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACT
* *
14682 AAATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAACAGGAATGG
65 AAATTTAATGTTTCAAGTATCAAAAATGCTTACGAAAAATTAGTTGTTTCGATTAACAGGAATGG
* * * *
14747 ACTGTCCACTTAATATTACATAACTTTTACTCCAGATGTTTGATGAGG
130 ACGGTCCACTTAATATTACATAACTTTTACTCAAGATGTCTGATGAGA
* *
14795 TGATTCAAGTGTCTTTTAAAAGGTTGTTTCATGATCTACAACTTTTATGAAGGACTCGAAAGA-T
1 TGATTCAAGTGTCTTTTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAA-ACT
* * * ** *
14859 AAATTTAATGTTTGAAGTATAGAAAAATGCTTACGAAGAATTAGTTGTTTCGATTGGCGGGAATG
65 AAATTTAATGTTTCAAGTAT-CAAAAATGCTTACGAAAAATTAGTTGTTTCGATTAACAGGAATG
* * * *
14924 TG-CGGTCTACTTAATATTACAT-ATTTTTGCTCAATATGTCTGATTGAGA
129 -GACGGTCCACTTAATATTACATAACTTTTACTCAAGATGTCTGA-TGAGA
* *
14973 TTATTCAAGTGTCTGTTAAAAGGTTGTTCCATGATC
1 TGATTCAAGTGTCTTTTAAAAGGTTGTTCCATGATC
15009 CGCAACCGAA
Statistics
Matches: 185, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
177 89 0.48
178 95 0.51
179 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (177 bp):
TGATTCAAGTGTCTTTTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATCAAAAATGCTTACGAAAAATTAGTTGTTTCGATTAACAGGAATGGA
CGGTCCACTTAATATTACATAACTTTTACTCAAGATGTCTGATGAGA
Found at i:26017 original size:28 final size:28
Alignment explanation
Indices: 25975--26045 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
25965 GTACTTGAGG
* * **
25975 TGACTAAAATACCCCTGGATGCGCAAAA
1 TGACCAAAATGCCCCTGGACACGCAAAA
*
26003 TGACCAAAATGCCCCTGGACATGCAAAA
1 TGACCAAAATGCCCCTGGACACGCAAAA
26031 TGACCAAAATGCCCC
1 TGACCAAAATGCCCC
26046 CTTAAGTGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (28 bp):
TGACCAAAATGCCCCTGGACACGCAAAA
Found at i:31817 original size:25 final size:24
Alignment explanation
Indices: 31789--31847 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
31779 GTAATGTTGC
31789 ATTTTAATCATGTAGCTCAAATCT
1 ATTTTAATCATGTAGCTCAAATCT
* *
31813 AATTTCATTCATGTAGCTCAAATCT
1 -ATTTTAATCATGTAGCTCAAATCT
*
31838 ACTTTAATCA
1 ATTTTAATCA
31848 ACTAATTGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (24 bp):
ATTTTAATCATGTAGCTCAAATCT
Found at i:35631 original size:46 final size:46
Alignment explanation
Indices: 35447--35770 Score: 310
Period size: 46 Copynumber: 6.8 Consensus size: 46
35437 TCTTATCACT
* *
35447 TTCCAAAACTGCCCTTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCT-
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTC--T-T-T-TA
* * *
35497 TTCGAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTTTTTTCTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAG-TTTTCTTT-TA
* * * *
35545 TTCCAAGAATGCCCCTTCCTGGTTGGAATGTCCTTA-TTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCC-CAGTTTTCTTTTA
* * * * *
35591 TACCAAAAATGCTCCTTCCCGGTCGGAAGGTCCCAGTTTTCAAGATCTCA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTC----TTTTA
* * *
35641 TCCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTTA
* * * * *
35687 TTCCAAAAAAGCCCCATCTTGGTTGGAAGGTCCCCGTTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTTA
**
35733 TTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCCAGTT
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTT
35771 GTCTACTTTT
Statistics
Matches: 226, Mismatches: 40, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
45 1 0.00
46 109 0.48
47 10 0.04
48 30 0.13
49 1 0.00
50 71 0.31
51 4 0.02
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (46 bp):
TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTTA
Found at i:35693 original size:96 final size:95
Alignment explanation
Indices: 35449--35766 Score: 286
Period size: 96 Copynumber: 3.3 Consensus size: 95
35439 TTATCACTTT
* * * * *
35449 CCAAAACTGCCCTTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCT-TTCGAAAAATGCCCCT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTC--T-T-T-TATTCCAAAAATGCCCCT
* **** *
35513 TCCTGGTCGGAAGGTCCCTGTTTT-TTTTTCTATT
61 TCCTGGTCGGAAGGTCCCAGTTTTCAAGATCTATC
* * * * * * *
35547 CCAAGAATGCCCCTTCCTGGTTGGAATGTCCTTATTTTCTTTTATACCAAAAATGCTCCTTCCCG
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTTATTCCAAAAATGCCCCTTCCTG
35612 GTCGGAAGGTCCCAGTTTTCAAGATCTCATC
66 GTCGGAAGGTCCCAGTTTTCAAGATCT-ATC
* * *
35643 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTTATTCCAAAAAAGCCCCATCTTG
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTTATTCCAAAAATGCCCCTTCCTG
* * * * *
35708 GTTGGAAGGTCCCCGTTTTC---TTTTATT
66 GTCGGAAGGTCCCAGTTTTCAAGATCTATC
** *
35735 CCAAAAATGCCCCTTCCCAGTCGGAAGGTCCC
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
35767 AGTTGTCTAC
Statistics
Matches: 181, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
92 31 0.17
93 3 0.02
94 36 0.20
95 4 0.02
96 76 0.42
98 31 0.17
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (95 bp):
CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTTATTCCAAAAATGCCCCTTCCTG
GTCGGAAGGTCCCAGTTTTCAAGATCTATC
Found at i:35766 original size:142 final size:144
Alignment explanation
Indices: 35447--35770 Score: 454
Period size: 144 Copynumber: 2.3 Consensus size: 144
35437 TCTTATCACT
* * * * * * *
35447 TTCCAAAACTGCCCTTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCTTTCGAAAAATGCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCAAGATCTCATCCCAAAAATGCCCC
* * * * *
35512 TTCCTGGTCGGAAGGTCCCTGTTTTTTTTTCTATTCCAAGAATGCCCCTTCCTGGTTGGAATGTC
66 TTCCTGGTCGGAAGGTCCCTGTTTTTCTTTCTATTCCAAAAAAGCCCCATCCTGGTTGGAAGGTC
**
35577 CTTATTTTCTTTTA
131 CCCATTTTCTTTTA
* *
35591 TACCAAAAATGCTCCTTCCCGGTCGGAAGGTCCCAGTTTTCAAGATCTCATCCCAAAAATGCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCAAGATCTCATCCCAAAAATGCCCC
* *
35656 TTCCTGGTTGGAAGGTCCCTG-TTTTCTTT-TATTCCAAAAAAGCCCCATCTTGGTTGGAAGGTC
66 TTCCTGGTCGGAAGGTCCCTGTTTTTCTTTCTATTCCAAAAAAGCCCCATCCTGGTTGGAAGGTC
*
35719 CCCGTTTTCTTTTA
131 CCCATTTTCTTTTA
*
35733 TTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCCAGTT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTT
35771 GTCTACTTTT
Statistics
Matches: 158, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
142 75 0.47
143 7 0.04
144 76 0.48
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (144 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCAAGATCTCATCCCAAAAATGCCCC
TTCCTGGTCGGAAGGTCCCTGTTTTTCTTTCTATTCCAAAAAAGCCCCATCCTGGTTGGAAGGTC
CCCATTTTCTTTTA
Found at i:35910 original size:39 final size:36
Alignment explanation
Indices: 35826--35935 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 36
35816 TTTAATTCCC
**
35826 AGTTTGCCCTTCCCAGTCGAAAGGTGTTGTTCAATTTCG
1 AGTTTGCCCTTCCCA-TCG-AAGGTGTTG-TCAATACCG
35865 AGTTTGCCCTTCCCACTCAGAAGGTGTTGTCAGTATACCG
1 AGTTTGCCCTTCCCA-TC-GAAGGTGTTGTCA--ATACCG
35905 A-TTTGCCCTTTCCTCATCGAGAGGTGTTGTC
1 AGTTTGCCC-TTCC-CATCGA-AGGTGTTGTC
35936 GCCATTGTCC
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
38 3 0.05
39 35 0.56
40 22 0.35
41 2 0.03
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (36 bp):
AGTTTGCCCTTCCCATCGAAGGTGTTGTCAATACCG
Found at i:36179 original size:80 final size:82
Alignment explanation
Indices: 35988--36190 Score: 295
Period size: 80 Copynumber: 2.5 Consensus size: 82
35978 TATTTACCAA
* *
35988 TGCCTTTGTCCGGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTTACCAGTTTGCCCTTCC
1 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTGACCAGTTTGCCCTTCC
36053 TCATCAGGAGGTGTTGT
66 TCATCAGGAGGTGTTGT
* * * * *
36070 TACCTTTGTTCATTTTGCCCTTCCTCATCGGAAGGTATTGTCAGTA-TGCCCTA-TTTGCCCTTC
1 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTGACC-AGTTTGCCCTTC
* *
36133 CTCAT-TGGGGGTGTTGT
65 CTCATCAGGAGGTGTTGT
36150 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
1 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
36191 TGCCTTTGTC
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
80 47 0.44
81 18 0.17
82 42 0.39
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (82 bp):
TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTGACCAGTTTGCCCTTCC
TCATCAGGAGGTGTTGT
Found at i:36197 original size:41 final size:41
Alignment explanation
Indices: 35988--36202 Score: 226
Period size: 41 Copynumber: 5.3 Consensus size: 41
35978 TATTTACCAA
*
35988 TGCCTTTGTCCGGTTTGCCCTTCCTCATCGGAAGGTGTTGT
1 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
* ** *
36029 CAGTATTT-ACCAGTTTGCCCTTCCTCATCAGG-AGGTGTTGT
1 -TGCCTTTGTCCAGTTTGCCCTTCCTCATC-GGAAGGTGTTGT
* * * *
36070 TACCTTTGTTCATTTTGCCCTTCCTCATCGGAAGGTATTG-
1 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
* * * * *
36110 T-CAGTATGCCCTA-TTTGCCCTTCCTCATTGG-GGGTGTTGT
1 TGC-CTTTGTCC-AGTTTGCCCTTCCTCATCGGAAGGTGTTGT
36150 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
1 TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
36191 TGCCTTTGTCCA
1 TGCCTTTGTCCA
36203 ATTTACCCAA
Statistics
Matches: 139, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
39 8 0.06
40 50 0.36
41 75 0.54
42 6 0.04
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (41 bp):
TGCCTTTGTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
Found at i:36261 original size:40 final size:40
Alignment explanation
Indices: 36217--36449 Score: 328
Period size: 40 Copynumber: 5.8 Consensus size: 40
36207 ACCCAAGCTA
* * *
36217 CCCTTCCCCGCCGGTAGGTGTTGTTTAATTTCCCAGTTTG
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTTTG
*
36257 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGCTTG
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTTTG
* *
36297 -CCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAGGATT-
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCA-GTTTG
36336 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTTTG
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTTTG
36376 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCA-TTCTG
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTT-TG
* * * * *
36416 CCCTTCCTCATCGAAAGGTGTTGTTCATATTCCC
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCC
36450 TTCATGTCAT
Statistics
Matches: 176, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 38 0.22
40 138 0.78
ACGTcount: A:0.17, C:0.30, G:0.19, T:0.33
Consensus pattern (40 bp):
CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTTTG
Found at i:36349 original size:79 final size:80
Alignment explanation
Indices: 36217--36449 Score: 319
Period size: 79 Copynumber: 2.9 Consensus size: 80
36207 ACCCAAGCTA
* * * *
36217 CCCTTCCCCGCCGGTAGGTGTTGTTTAATTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGATTGCCCTTCCCCACCGGAAGGTGTTGTT
36282 TAAATTCCCAGCTTG
66 TAAATTCCCAGCTTG
*
36297 -CCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAGGATT-CCCTTCCCCACCGGAAGGTGTTGT
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCA-GATTGCCCTTCCCCACCGGAAGGTGTTGT
*
36360 TTAAATTCCCAGTTTG
65 TTAAATTCCCAGCTTG
* * * *
36376 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCA-TTCTGCCCTTCCTCATCGAAAGGTGTTGT
1 CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGAT-TGCCCTTCCCCACCGGAAGGTGTTGT
* *
36440 TCATATTCCC
65 TTAAATTCCC
36450 TTCATGTCAT
Statistics
Matches: 136, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
78 1 0.01
79 70 0.51
80 65 0.48
ACGTcount: A:0.17, C:0.30, G:0.19, T:0.33
Consensus pattern (80 bp):
CCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGATTGCCCTTCCCCACCGGAAGGTGTTGTT
TAAATTCCCAGCTTG
Found at i:42417 original size:504 final size:504
Alignment explanation
Indices: 41470--42481 Score: 1790
Period size: 504 Copynumber: 2.0 Consensus size: 504
41460 ACAGGTGCAG
*
41470 GAATCATCATCACATCACCTAATGATGAATGTACCATGATGGCTTTTCACTTAGACTTTGATTGT
1 GAATCATCATCACATCACCTAATGATGAATGTACCATGATGGCTTTTCACTTAGACATTGATTGT
*
41535 ACTAACAATCAAGCTGAGTATGAGGCACTCATCATTGGTTTAGAATTACTCAGAGAAATGAAAGC
66 ACTAACAATCAAGCTGAGTATGAGGCACTCATCACTGGTTTAGAATTACTCAGAGAAATGAAAGC
41600 ATCCTCGGTGCACATCAAGGGTAATTCATTATTGGTGATAAACCAACTCACACAAGAGTATAATT
131 ATCCTCGGTGCACATCAAGGGTAATTCATTATTGGTGATAAACCAACTCACACAAGAGTATAATT
*
41665 GCACTAGTCCATCATTGTTGCCATACTATGCAATGACTGTACAATTGTTGGACAAGTTTGACAAT
196 GCACTAGTCCATCATTGTTGCCATACTATGCAATGACAGTACAATTGTTGGACAAGTTTGACAAT
*
41730 GTGAGCATTGAGCACGTGCCTAGACATCAAAATGAAAGTGCAAATGTCACCGCACAACTTGCATC
261 GTGAACATTGAGCACGTGCCTAGACATCAAAATGAAAGTGCAAATGTCACCGCACAACTTGCATC
* * * *
41795 TGGCATTACTTTTCAAGACGATATTTGGAAAAAAGTGGTGAATGTCGAAAGACGCCCTTTACCAT
326 TGGCATTACTTTTCAAGACGATATCTAGAAAAAAGTGGTAAATGTCGAAAGACGCACTTTACCAT
*
41860 CTACTTTGACGAGAGATAACATGTTCGAAGTTTGCAACATTGTTCATAAACATTCCAATTGGCGA
391 ATACTTTGACGAGAGATAACATGTTCGAAGTTTGCAACATTGTTCATAAACATTCCAATTGGCGA
41925 GAACCTTTCCTGGAATACTTAAAAGATCCAACTAAGAGGTTTAATCGAC
456 GAACCTTTCCTGGAATACTTAAAAGATCCAACTAAGAGGTTTAATCGAC
* *
41974 GAATCATCATCACATCACCTGATGATGATTGTACCATGATGGCTTTTCACTTAGACATTGATTGT
1 GAATCATCATCACATCACCTAATGATGAATGTACCATGATGGCTTTTCACTTAGACATTGATTGT
** * *
42039 ACTAATGATCAAGCTGAGTATGAGGCACTCATCACTGTTTTAGAATTACTCAGAGAAATGCAAGC
66 ACTAACAATCAAGCTGAGTATGAGGCACTCATCACTGGTTTAGAATTACTCAGAGAAATGAAAGC
* *
42104 ATCCTCGGTGCACATCAAGGGTGATTCATTATTGGTGATAAACCAACTCACGCAAGAGTATAATT
131 ATCCTCGGTGCACATCAAGGGTAATTCATTATTGGTGATAAACCAACTCACACAAGAGTATAATT
*
42169 GCACTAGTCCATCATTGTTGCCATACTATGCAATGGCAGTACAATTGTTGGACAAGTTTGACAAT
196 GCACTAGTCCATCATTGTTGCCATACTATGCAATGACAGTACAATTGTTGGACAAGTTTGACAAT
* * * *
42234 GTGAACATTGAGCACGTGCCTAGACATCAAATTGAAAGTGCAAATGTCGCCGTACAATTTGCATC
261 GTGAACATTGAGCACGTGCCTAGACATCAAAATGAAAGTGCAAATGTCACCGCACAACTTGCATC
* *
42299 TGGCCTTACTTTTCAAGATGATATCTAGAAAAAAGTGGTAAATGTCGAAAGACGCACTTTACCAT
326 TGGCATTACTTTTCAAGACGATATCTAGAAAAAAGTGGTAAATGTCGAAAGACGCACTTTACCAT
* *
42364 ATACTTTGACGAGAGATAACGTGTTCGAAGTTTGCAACATTGTTCATAAACATTCCGATTGGCGA
391 ATACTTTGACGAGAGATAACATGTTCGAAGTTTGCAACATTGTTCATAAACATTCCAATTGGCGA
42429 GAACCTTTCCTGGAATACTTAAAAGATCCAACTAAGAGGTTTAATCGAC
456 GAACCTTTCCTGGAATACTTAAAAGATCCAACTAAGAGGTTTAATCGAC
42478 GAAT
1 GAAT
42482 TAGGACCTTG
Statistics
Matches: 482, Mismatches: 26, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
504 482 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (504 bp):
GAATCATCATCACATCACCTAATGATGAATGTACCATGATGGCTTTTCACTTAGACATTGATTGT
ACTAACAATCAAGCTGAGTATGAGGCACTCATCACTGGTTTAGAATTACTCAGAGAAATGAAAGC
ATCCTCGGTGCACATCAAGGGTAATTCATTATTGGTGATAAACCAACTCACACAAGAGTATAATT
GCACTAGTCCATCATTGTTGCCATACTATGCAATGACAGTACAATTGTTGGACAAGTTTGACAAT
GTGAACATTGAGCACGTGCCTAGACATCAAAATGAAAGTGCAAATGTCACCGCACAACTTGCATC
TGGCATTACTTTTCAAGACGATATCTAGAAAAAAGTGGTAAATGTCGAAAGACGCACTTTACCAT
ATACTTTGACGAGAGATAACATGTTCGAAGTTTGCAACATTGTTCATAAACATTCCAATTGGCGA
GAACCTTTCCTGGAATACTTAAAAGATCCAACTAAGAGGTTTAATCGAC
Found at i:47259 original size:16 final size:16
Alignment explanation
Indices: 47238--47270 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47228 CAATGGAAAG
*
47238 TTGTATATATATTTTT
1 TTGTATACATATTTTT
47254 TTGTATACATATTTTT
1 TTGTATACATATTTTT
47270 T
1 T
47271 ATAATTGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (16 bp):
TTGTATACATATTTTT
Found at i:47332 original size:2 final size:2
Alignment explanation
Indices: 47325--47361 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
47315 TACTAAGTGC
* *
47325 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47362 AACAATAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48973 original size:28 final size:28
Alignment explanation
Indices: 48941--49009 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
48931 AGTGCACTTG
* *
48941 AAATGATCAAAATGCCCCTGGACATGTA
1 AAATGACCAAAATGCCCCTGGACATGCA
*
48969 AAATGACCAAAATGCCCCTGGACTTGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
*
48997 AAATGACCGAAAT
1 AAATGACCAAAAT
49010 AAGAAGTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:60321 original size:36 final size:36
Alignment explanation
Indices: 60239--60327 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
60229 AGCCAATCAT
*
60239 GTATTAGGCGACTTAGGCCAGCGAAGTTATAGCCAA
1 GTATTAGGCGACTAAGGCCAGCGAAGTTATAGCCAA
** * ***
60275 ACATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAA
1 GTATTAGGCGACTAAGGCCAGCGAAGTTATAGCCAA
*
60311 GTATTAGGCGACCAAGG
1 GTATTAGGCGACTAAGG
60328 TCAGGGGTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.20
Consensus pattern (36 bp):
GTATTAGGCGACTAAGGCCAGCGAAGTTATAGCCAA
Found at i:62922 original size:27 final size:26
Alignment explanation
Indices: 62892--62977 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 26
62882 GCTTTTGAAA
62892 TGGATGATAGGTTTGGTAGCAACATTG
1 TGGATGA-AGGTTTGGTAGCAACATTG
* * * *
62919 TGGATGAAGCTTTGTTA-CAGCTTTTG
1 TGGATGAAGGTTTGGTAGCAAC-ATTG
62945 AAATGGATGACAGGTTTGGTAGCAACATTG
1 ---TGGATGA-AGGTTTGGTAGCAACATTG
62975 TGG
1 TGG
62978 TGGAACTAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
25 3 0.07
26 11 0.24
27 10 0.22
29 7 0.16
30 11 0.24
31 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.34
Consensus pattern (26 bp):
TGGATGAAGGTTTGGTAGCAACATTG
Found at i:62933 original size:56 final size:56
Alignment explanation
Indices: 62866--62977 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
62856 TTGCTATTAT
* *
62866 ATGAAGCTTTGTTGCAGCTTTTGAAATGGATGATAGGTTTGGTAGCAACATTGTGG
1 ATGAAGCTTTGTTACAGCTTTTGAAATGGATGACAGGTTTGGTAGCAACATTGTGG
62922 ATGAAGCTTTGTTACAGCTTTTGAAATGGATGACAGGTTTGGTAGCAACATTGTGG
1 ATGAAGCTTTGTTACAGCTTTTGAAATGGATGACAGGTTTGGTAGCAACATTGTGG
62978 TGGAACTAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (56 bp):
ATGAAGCTTTGTTACAGCTTTTGAAATGGATGACAGGTTTGGTAGCAACATTGTGG
Found at i:62952 original size:29 final size:29
Alignment explanation
Indices: 62866--62954 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 29
62856 TTGCTATTAT
*
62866 ATGAAGCTTTGTTGCAGCTTTTGAAATGG
1 ATGAAGCTTTGTTACAGCTTTTGAAATGG
* * * *
62895 ATGATAGGTTTGGTAGCAAC-ATTG---TGG
1 ATGA-AGCTTTGTTA-CAGCTTTTGAAATGG
62922 ATGAAGCTTTGTTACAGCTTTTGAAATGG
1 ATGAAGCTTTGTTACAGCTTTTGAAATGG
62951 ATGA
1 ATGA
62955 CAGGTTTGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
25 3 0.07
26 11 0.24
27 7 0.16
29 11 0.24
30 10 0.22
31 3 0.07
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (29 bp):
ATGAAGCTTTGTTACAGCTTTTGAAATGG
Found at i:70356 original size:6 final size:6
Alignment explanation
Indices: 70347--70379 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
70337 TTTTCGTTAC
*
70347 TTTATT TTTATT TTTACT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTT
70380 CGTTTAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:70370 original size:18 final size:17
Alignment explanation
Indices: 70343--70379 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
70333 TTATTTTTCG
70343 TTACTTTATTTTTATTT
1 TTACTTTATTTTTATTT
70360 TTACTTTTATTTTTATTT
1 TTAC-TTTATTTTTATTT
70378 TT
1 TT
70380 CGTTTAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTACTTTATTTTTATTT
Found at i:77826 original size:33 final size:34
Alignment explanation
Indices: 77769--77835 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
77759 AAAATTGGGC
77769 AAATAAGATCAATAAAAAAACAATCAAATTCTAT
1 AAATAAGATCAATAAAAAAACAATCAAATTCTAT
*
77803 AAATAAGATCAAT-CAAAAACAATCAAATTCTAT
1 AAATAAGATCAATAAAAAAACAATCAAATTCTAT
77836 CCTAGATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 19 0.59
34 13 0.41
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (34 bp):
AAATAAGATCAATAAAAAAACAATCAAATTCTAT
Found at i:79140 original size:18 final size:19
Alignment explanation
Indices: 79113--79157 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
79103 AAATTCAAAG
*
79113 AAAAATTAAT-GTAAAAATT
1 AAAAATTAATAAT-AAAATT
79132 AAAAA-TAATAATAAAATT
1 AAAAATTAATAATAAAATT
79150 -AAAATTAA
1 AAAAATTAA
79158 AATTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATTAATAATAAAATT
Found at i:79152 original size:6 final size:6
Alignment explanation
Indices: 79126--79164 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
79116 AATTAATGTA
*
79126 AAAATT AAAAAT AATAA-T AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AA-AATT AAAATT AAAATT AAAATT AAA
79165 TATGCAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:94048 original size:69 final size:69
Alignment explanation
Indices: 93949--94148 Score: 321
Period size: 69 Copynumber: 2.9 Consensus size: 69
93939 TTGCTTGAAA
*
93949 TGCATCGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTGTCC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTGTCC
94014 TTAG
66 TTAG
*
94018 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTTTCC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTGTCC
*
94083 TTGG
66 TTAG
* * *
94087 TGCATTGTCTTTATATGTAATTTTAGCA-TTGAGATGTATTTAAATGGTGCTCCCACCATTTT
1 TGCATTGTCTTTATATGTAATTTTAGCATTTG-GATGTAATT-AATGGTGTTCCTACCATTTT
94149 TTTTCTTAGT
Statistics
Matches: 123, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
68 3 0.02
69 102 0.83
70 18 0.15
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (69 bp):
TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTGTCC
TTAG
Found at i:95593 original size:103 final size:103
Alignment explanation
Indices: 95414--95606 Score: 287
Period size: 103 Copynumber: 1.9 Consensus size: 103
95404 GCATTTGTAT
* * * * *
95414 TTGAAATTCATCATAATAAGGTCACAAGATTTTAACAAGAATAAGAATTTGCTTTTTTAAATCAG
1 TTGAAATTCATCAGAATAAGGTCACAAGATTTTAACAAAAAGAAGAATTTGCTTTCTTAAATCAA
* *
95479 TTTACTGCATTTGTATATGAAATTCGTCAGAATGAGGA
66 TTCACTGCATTTGTATATCAAATTCGTCAGAATGAGGA
* * *
95517 TTGAAATTCATCAGAATAAGGTCATAATATTTTAACAAAAAGAAGATTTTGCTTTCTTAAATCAA
1 TTGAAATTCATCAGAATAAGGTCACAAGATTTTAACAAAAAGAAGAATTTGCTTTCTTAAATCAA
*
95582 TTCCCTGCATTTGTATATCAAATTC
66 TTCACTGCATTTGTATATCAAATTC
95607 ATTAGAATAA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (103 bp):
TTGAAATTCATCAGAATAAGGTCACAAGATTTTAACAAAAAGAAGAATTTGCTTTCTTAAATCAA
TTCACTGCATTTGTATATCAAATTCGTCAGAATGAGGA
Found at i:99157 original size:48 final size:49
Alignment explanation
Indices: 99084--99181 Score: 164
Period size: 48 Copynumber: 2.0 Consensus size: 49
99074 CTTGGTGGCA
99084 GTGTGGAGTTGGATGACTCGCCAATATC-ATCGAGGTGGAGCAAAATTG
1 GTGTGGAGTTGGATGACTCGCCAATATCAATCGAGGTGGAGCAAAATTG
*
99132 GTGTGGAGTTGGATGACTCTG-CAATATCAATTGAGGTGGAGCAAAATTG
1 GTGTGGAGTTGGATGACTC-GCCAATATCAATCGAGGTGGAGCAAAATTG
99181 G
1 G
99182 CAATCTTTGG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 26 0.55
49 21 0.45
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.27
Consensus pattern (49 bp):
GTGTGGAGTTGGATGACTCGCCAATATCAATCGAGGTGGAGCAAAATTG
Found at i:99457 original size:13 final size:13
Alignment explanation
Indices: 99435--99496 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
99425 TTTTGCATTG
*
99435 CATTAACATATCA
1 CATTAGCATATCA
*
99448 TATTAGCATATCA
1 CATTAGCATATCA
**
99461 CATTAAAATATCA
1 CATTAGCATATCA
*
99474 GATTAGCATATCA
1 CATTAGCATATCA
*
99487 CATTTGCATA
1 CATTAGCATA
99497 GTATGTTTGC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (13 bp):
CATTAGCATATCA
Found at i:99464 original size:26 final size:26
Alignment explanation
Indices: 99435--99490 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
99425 TTTTGCATTG
* *
99435 CATTAACATATCATATTAGCATATCA
1 CATTAAAATATCAGATTAGCATATCA
99461 CATTAAAATATCAGATTAGCATATCA
1 CATTAAAATATCAGATTAGCATATCA
99487 CATT
1 CATT
99491 TGCATAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (26 bp):
CATTAAAATATCAGATTAGCATATCA
Found at i:100314 original size:48 final size:48
Alignment explanation
Indices: 100262--100357 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
100252 TACTAAAATG
100262 AAACTGCATTTTTAGAACTACATGTCACATGCCAAATCACCACAAGCA
1 AAACTGCATTTTTAGAACTACATGTCACATGCCAAATCACCACAAGCA
*
100310 AAACTGCATTTTTAGAACTACATTTCACATGCCAAATCACCACAAGCA
1 AAACTGCATTTTTAGAACTACATGTCACATGCCAAATCACCACAAGCA
100358 GTCATATGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (48 bp):
AAACTGCATTTTTAGAACTACATGTCACATGCCAAATCACCACAAGCA
Done.