Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009668.1 Kokia drynarioides strain JFW-HI SEQ_124386, 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: 84402
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:128 original size:4 final size:4
Alignment explanation
Indices: 110--142 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
100 CTTCTCCTCG
*
110 TTCT TTC- TTCC TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
143 ATTTTTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:150 original size:19 final size:19
Alignment explanation
Indices: 83--137 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
73 AACACATTAA
* *
83 TTCTTTTTTTCCTTC-TCC
1 TTCTTTCTTTCTTTCTTCC
* *
101 TTCTCCTCGTTCTTTCTTCC
1 TTCT-TTCTTTCTTTCTTCC
121 TTCTTTCTTTCTTTCTT
1 TTCTTTCTTTCTTTCTT
138 TCTTTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 4 0.14
19 18 0.62
20 7 0.24
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (19 bp):
TTCTTTCTTTCTTTCTTCC
Found at i:277 original size:2 final size:2
Alignment explanation
Indices: 272--299 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
262 TTTTAAAAAA
272 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
300 GGCACAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1073 original size:9 final size:8
Alignment explanation
Indices: 1041--1069 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1031 TTGCTCTATA
1041 TTTAATTT
1 TTTAATTT
1049 TTTAATTT
1 TTTAATTT
1057 TTTAATTT
1 TTTAATTT
1065 TTTAA
1 TTTAA
1070 ATTTACGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTAATTT
Found at i:1242 original size:38 final size:39
Alignment explanation
Indices: 1177--1260 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
1167 ATTAATTCTT
1177 AAAATTTAAAAATTTAAAAATTATATAAAAA-ATATTTTA
1 AAAATTTAAAAATTTAAAAATTATATAAAAATAT-TTTTA
1216 AAAATTTAAACTAA-TT-AAAATT-TATAAAAATATTTTTA
1 AAAATTTAAA--AATTTAAAAATTATATAAAAATATTTTTA
*
1254 AATATTT
1 AAAATTT
1261 TTAAAATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
38 19 0.46
39 18 0.44
40 2 0.05
41 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (39 bp):
AAAATTTAAAAATTTAAAAATTATATAAAAATATTTTTA
Found at i:2718 original size:21 final size:22
Alignment explanation
Indices: 2694--2735 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2684 TTATAATTAT
2694 AATAA-ATGTTTTAATTTTTTA
1 AATAATATGTTTTAATTTTTTA
*
2715 AATAATTTGTTTTAATTTTTT
1 AATAATATGTTTTAATTTTTT
2736 TAGAAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
AATAATATGTTTTAATTTTTTA
Found at i:2817 original size:34 final size:34
Alignment explanation
Indices: 2757--2821 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2747 TCCTATAAAT
* *
2757 AATCCTTATTATACTAAAATCCAATTAGCATTAA
1 AATCCTTATAATACAAAAATCCAATTAGCATTAA
*
2791 AATCCTTATAATA-AAAAACTCTAATTAGCAT
1 AATCCTTATAATACAAAAA-TCCAATTAGCAT
2822 AAATTATACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (34 bp):
AATCCTTATAATACAAAAATCCAATTAGCATTAA
Found at i:2928 original size:29 final size:30
Alignment explanation
Indices: 2895--2963 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
2885 GTAATTATGG
*
2895 ATTTTTTATTGATAATGAATTAG-AAT-AAA-
1 ATTTTTTATTAAT-ATGAATT-GTAATGAAAT
*
2924 ATTTTTTTTTAATATGAATTGTAATGAAAT
1 ATTTTTTATTAATATGAATTGTAATGAAAT
2954 ATTTTTTATT
1 ATTTTTTATT
2964 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.03
28 10 0.29
29 14 0.41
30 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (30 bp):
ATTTTTTATTAATATGAATTGTAATGAAAT
Found at i:4593 original size:18 final size:20
Alignment explanation
Indices: 4570--4609 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4560 AATTTAAAAG
*
4570 AAATTAA-AG-TTAGTGGTA
1 AAATTAATAGTTTAGCGGTA
4588 AAATTAATAGTTTAGCGGTA
1 AAATTAATAGTTTAGCGGTA
4608 AA
1 AA
4610 TTCCAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (20 bp):
AAATTAATAGTTTAGCGGTA
Found at i:5824 original size:39 final size:39
Alignment explanation
Indices: 5770--5926 Score: 314
Period size: 39 Copynumber: 4.0 Consensus size: 39
5760 TTTTTAAGTA
5770 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
1 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
5809 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
1 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
5848 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
1 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
5887 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
1 AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
5926 A
1 A
5927 TTTATTCATA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (39 bp):
AATAAATGACGTCAAAATAAATTGATAAATTATAATTAT
Found at i:16002 original size:24 final size:24
Alignment explanation
Indices: 15967--16038 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
15957 AATCATGTTC
15967 AACCTT-TCATCTCCCTTGACTTTT
1 AACCTTCT-ATCTCCCTTGACTTTT
*
15991 AACCTTCTATCTCCCTTGACCTTT
1 AACCTTCTATCTCCCTTGACTTTT
* * * *
16015 AACTTTCCATCTTCCTTAACTTTT
1 AACCTTCTATCTCCCTTGACTTTT
16039 CATATTCTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.18, C:0.33, G:0.03, T:0.46
Consensus pattern (24 bp):
AACCTTCTATCTCCCTTGACTTTT
Found at i:18182 original size:34 final size:34
Alignment explanation
Indices: 18139--18242 Score: 172
Period size: 34 Copynumber: 3.1 Consensus size: 34
18129 AACCTTCATT
*
18139 TCCCTTGACTTTTAACCTTCCATCTTTCTTAACC
1 TCCCTTGACTTTTAACCTTCCATCTTCCTTAACC
* *
18173 TCCCTTGACTTTTAACCTTCTATCTTCCTTGACC
1 TCCCTTGACTTTTAACCTTCCATCTTCCTTAACC
*
18207 TCCCTTGACCTTTAACCTTCCATCTTCCTTAACC
1 TCCCTTGACTTTTAACCTTCCATCTTCCTTAACC
18241 TC
1 TC
18243 TCATATTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.16, C:0.38, G:0.04, T:0.42
Consensus pattern (34 bp):
TCCCTTGACTTTTAACCTTCCATCTTCCTTAACC
Found at i:18187 original size:17 final size:17
Alignment explanation
Indices: 18139--18190 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
18129 AACCTTCATT
18139 TCCCTTGACTTTTAACC
1 TCCCTTGACTTTTAACC
* *
18156 TTCCAT--CTTTCTTAACC
1 TCCCTTGAC-TT-TTAACC
18173 TCCCTTGACTTTTAACC
1 TCCCTTGACTTTTAACC
18190 T
1 T
18191 TCTATCTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
15 1 0.04
16 2 0.07
17 21 0.78
18 2 0.07
19 1 0.04
ACGTcount: A:0.17, C:0.35, G:0.04, T:0.44
Consensus pattern (17 bp):
TCCCTTGACTTTTAACC
Found at i:18238 original size:17 final size:17
Alignment explanation
Indices: 18150--18241 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
18140 CCCTTGACTT
*
18150 TTAACCTTCCATCTTTC
1 TTAACCTTCCATCTTCC
* *
18167 TTAACCTCCCTTGACTT--
1 TTAACCTTCCAT--CTTCC
*
18184 TTAACCTTCTATCTTCC
1 TTAACCTTCCATCTTCC
*
18201 TTGACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
18217 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
18235 TTAACCT
1 TTAACCT
18242 CTCATATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 4 0.07
17 36 0.63
18 5 0.09
19 3 0.05
20 3 0.05
ACGTcount: A:0.17, C:0.37, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:18448 original size:28 final size:28
Alignment explanation
Indices: 18417--18470 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
18407 CATTATTATT
18417 TTATAACA-AATTTTTAAAAAATAAAACA
1 TTATAACATAATTTTT-AAAAATAAAACA
**
18445 TTATTGCATAATTTTTAAAAATAAAA
1 TTATAACATAATTTTTAAAAATAAAA
18471 ACTAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (28 bp):
TTATAACATAATTTTTAAAAATAAAACA
Found at i:20445 original size:31 final size:32
Alignment explanation
Indices: 20391--20459 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
20381 CAGAAGAGTG
* * *
20391 ACTAAAATAAAAAATGATTTAAAACGTGAATA
1 ACTAAAATAAAAAATAATCTAAAACGTAAATA
* *
20423 ACTAAAAT-AAAAATAATCTAAAATGTAAATG
1 ACTAAAATAAAAAATAATCTAAAACGTAAATA
20454 ACTAAA
1 ACTAAA
20460 TTGAGTGCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (32 bp):
ACTAAAATAAAAAATAATCTAAAACGTAAATA
Found at i:22355 original size:36 final size:36
Alignment explanation
Indices: 22314--22384 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
22304 GGAAAAAAGA
*
22314 AAGTATAATTTATAAAATGATAGTCACACAGGACTT
1 AAGTATAATTTATAAAACGATAGTCACACAGGACTT
22350 AAGTATAATTTATAAAACGATAGTCACACAGGACT
1 AAGTATAATTTATAAAACGATAGTCACACAGGACT
22385 CAACTAAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (36 bp):
AAGTATAATTTATAAAACGATAGTCACACAGGACTT
Found at i:26440 original size:20 final size:19
Alignment explanation
Indices: 26411--26450 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
26401 AATTGATTGC
*
26411 ACAAAAAATTATTTTATAAA
1 ACAAAAAATT-TTATATAAA
*
26431 ACAAATAATTTTATATAAA
1 ACAAAAAATTTTATATAAA
26450 A
1 A
26451 ATAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ACAAAAAATTTTATATAAA
Found at i:26441 original size:17 final size:16
Alignment explanation
Indices: 26413--26454 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
26403 TTGATTGCAC
*
26413 AAAAAATTATTTTATA
1 AAAAAATAATTTTATA
26429 AAACAAATAATTTTATA
1 AAA-AAATAATTTTATA
*
26446 TAAAAATAA
1 AAAAAATAA
26455 ATTAATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAAATAATTTTATA
Found at i:27165 original size:22 final size:24
Alignment explanation
Indices: 27132--27175 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
27122 TTTTTTCCTG
27132 TTTTAAAATATT-ATTTATTCAAC
1 TTTTAAAATATTAATTTATTCAAC
*
27155 TTTT-AAATATTAATTTTTTCA
1 TTTTAAAATATTAATTTATTCA
27176 CTCTAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAAAATATTAATTTATTCAAC
Found at i:36106 original size:30 final size:30
Alignment explanation
Indices: 36034--36116 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
36024 CTTAACAGCC
*
36034 CAATGATTTAAATAAAACTTTTGAATAGTT
1 CAATGACTTAAATAAAACTTTTGAATAGTT
* * * *
36064 TATTTACTTAAATAAAAACTTTTGGATAGTT
1 CAATGACTTAAAT-AAAACTTTTGAATAGTT
*
36095 CAATGAC-TAAATTATAACTTTT
1 CAATGACTTAAA-TAAAACTTTT
36117 TTAGTTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
30 21 0.50
31 21 0.50
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (30 bp):
CAATGACTTAAATAAAACTTTTGAATAGTT
Found at i:47975 original size:3 final size:3
Alignment explanation
Indices: 47960--47991 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
47950 TAATCACCTT
*
47960 TCA TCA TCG TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
47992 TTCTTCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.03, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:48512 original size:3 final size:3
Alignment explanation
Indices: 48506--48552 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
48496 TTATTATTAT
48506 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
48553 TTGTTTAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:56844 original size:6 final size:6
Alignment explanation
Indices: 56833--56869 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
56823 AGTTTTGTAA
56833 GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT G
1 GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT G
56870 CTTAGTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.32
Consensus pattern (6 bp):
GGAGTT
Found at i:57618 original size:29 final size:30
Alignment explanation
Indices: 57553--57620 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
57543 TTAAAATTAT
* * * *
57553 ACATGAACTTTGATTTAATGTGCAATTGTAT
1 ACATGAAATTTAATTT-ATGTGCAATTATAC
*
57584 AAATGAAATTTAATTT-TGTGCAATTATAC
1 ACATGAAATTTAATTTATGTGCAATTATAC
57613 ACATGAAA
1 ACATGAAA
57621 CTCTAATTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 18 0.58
31 13 0.42
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (30 bp):
ACATGAAATTTAATTTATGTGCAATTATAC
Found at i:58282 original size:38 final size:38
Alignment explanation
Indices: 58239--58311 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
58229 TTACAAACAT
* * * *
58239 GGAGTTTTAGAAATTATCTTTTCCACATAAAATTAAAA
1 GGAGTTTCAGAAATGATCTTTTACACAAAAAATTAAAA
58277 GGAGTTTCAGAAATGATCTTTTACACAAAAAATTA
1 GGAGTTTCAGAAATGATCTTTTACACAAAAAATTA
58312 CAAACATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (38 bp):
GGAGTTTCAGAAATGATCTTTTACACAAAAAATTAAAA
Found at i:62158 original size:7 final size:7
Alignment explanation
Indices: 62146--62170 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62136 TTGGGTTACA
62146 AGGGAAG
1 AGGGAAG
62153 AGGGAAG
1 AGGGAAG
62160 AGGGAAG
1 AGGGAAG
62167 AGGG
1 AGGG
62171 GGGGTGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (7 bp):
AGGGAAG
Found at i:62758 original size:2 final size:2
Alignment explanation
Indices: 62751--62782 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62741 ATGTTCTAGC
62751 AT 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 AT
62783 GAGATTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72350 original size:113 final size:113
Alignment explanation
Indices: 72229--72443 Score: 360
Period size: 113 Copynumber: 1.9 Consensus size: 113
72219 AACTTAATGG
72229 GAAGAAGATA-TCGGAACCAAAGATATTGAATCTTTTGGTTAATGAGTTTTAAAGATTCAAGCTT
1 GAAGAAGATACT-GGAACCAAAGATATTGAATCTTTTGGTTAATGAGTTTTAAAGATTCAAGCTT
* * *
72293 TGAGATAGATTTGTAACTAAAGATATTAGAATCAAAAGAAACTTAACAA
65 TGAGACAAATTTGTAACTAAAAATATTAGAATCAAAAGAAACTTAACAA
* *
72342 GAAGAAGATACTGGAACCAAATATATTGAATCTTTTGGTTAATGGGTTTTAAAGATTCAAGCTTT
1 GAAGAAGATACTGGAACCAAAGATATTGAATCTTTTGGTTAATGAGTTTTAAAGATTCAAGCTTT
*
72407 GAGACAAATTTGTAACTAAAAATATTGGAATCAAAAG
66 GAGACAAATTTGTAACTAAAAATATTAGAATCAAAAG
72444 GGAAGAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 94 0.99
114 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (113 bp):
GAAGAAGATACTGGAACCAAAGATATTGAATCTTTTGGTTAATGAGTTTTAAAGATTCAAGCTTT
GAGACAAATTTGTAACTAAAAATATTAGAATCAAAAGAAACTTAACAA
Found at i:72477 original size:20 final size:20
Alignment explanation
Indices: 72452--72491 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
72442 AGGGAAGAAA
*
72452 AAGAAGATGGAGAAGAGAGG
1 AAGAAGATGAAGAAGAGAGG
72472 AAGAAGATGAAGAAGAGAGG
1 AAGAAGATGAAGAAGAGAGG
72492 CATGTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (20 bp):
AAGAAGATGAAGAAGAGAGG
Found at i:79458 original size:14 final size:13
Alignment explanation
Indices: 79433--79457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79423 TATTAGTTCT
79433 ATTAAATTTTTTA
1 ATTAAATTTTTTA
79446 ATTAAATTTTTT
1 ATTAAATTTTTT
79458 TGAAGGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTAAATTTTTTA
Found at i:81161 original size:18 final size:17
Alignment explanation
Indices: 81138--81171 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
81128 TTTAAATATA
81138 TAAAAATAATAAAAAAAT
1 TAAAAA-AATAAAAAAAT
*
81156 TAAAAAATTAAAAAAA
1 TAAAAAAATAAAAAAA
81172 ACACGTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAAATAAAAAAAT
Found at i:83676 original size:18 final size:19
Alignment explanation
Indices: 83639--83684 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
83629 AAAAAAGAGA
83639 AAGAAAGA-AAGAAGAAGG
1 AAGAAAGAGAAGAAGAAGG
*
83657 AAGAAAGAGAAGAAG-GGG
1 AAGAAAGAGAAGAAGAAGG
*
83675 AAGAAGGAGA
1 AAGAAAGAGA
83685 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (19 bp):
AAGAAAGAGAAGAAGAAGG
Found at i:84074 original size:20 final size:21
Alignment explanation
Indices: 84033--84075 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
84023 TAATTTACTT
84033 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
84054 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
84074 TA
1 TA
84076 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:84197 original size:16 final size:16
Alignment explanation
Indices: 84176--84210 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
84166 TAAGATTGTT
84176 TAATGTTTAAATTTAA
1 TAATGTTTAAATTTAA
84192 TAATGTTTAAATTTAA
1 TAATGTTTAAATTTAA
84208 TAA
1 TAA
84211 GATTGTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
TAATGTTTAAATTTAA
Done.