Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002167.1 Hibiscus syriacus cultivar Beakdansim tig00004423_pilon, 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: 68064
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:26 original size:5 final size:5
Alignment explanation
Indices: 16--48 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6 AATTATTTTT
*
16 TATTA TATTA TATTA TATTA TATTA TTTTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
49 ATGATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:55 original size:15 final size:15
Alignment explanation
Indices: 7--58 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1 GGTAAA
*
7 ATTATTTTTTATTAT
1 ATTATTTTATATTAT
*
22 ATTATATTATATTAT
1 ATTATTTTATATTAT
37 ATTATTTTATA-TAT
1 ATTATTTTATATTAT
51 GATTATTT
1 -ATTATTT
59 GAAGAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 3 0.09
15 30 0.91
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
ATTATTTTATATTAT
Found at i:2773 original size:4 final size:4
Alignment explanation
Indices: 2764--2789 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2754 TCAAGACATC
2764 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
2790 CCTAATTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:3557 original size:23 final size:21
Alignment explanation
Indices: 3526--3584 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
3516 TTTTTTGTAA
3526 TTTAAAAGAAATTATGATTTTT
1 TTTAAAAGAAATTAT-ATTTTT
* *
3548 TTTATAAAGATAGTAATATTTTT
1 TTTA-AAAGA-AATTATATTTTT
3571 TTTAAAA-AAATTAT
1 TTTAAAAGAAATTAT
3585 CCGATTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 7 0.23
23 15 0.48
24 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAAAAGAAATTATATTTTT
Found at i:4451 original size:15 final size:14
Alignment explanation
Indices: 4431--4464 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4421 ATAATTAATG
*
4431 TTTAATAAGTAATTT
1 TTTAATAA-TAATAT
4446 TTTAATAATAATAT
1 TTTAATAATAATAT
4460 TTTAA
1 TTTAA
4465 AATTAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTAATAATAATAT
Found at i:6173 original size:20 final size:18
Alignment explanation
Indices: 6145--6184 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
6135 GGTATTTTGG
6145 TTTAATTGTGATTTTTATTA
1 TTTAATTGT--TTTTTATTA
*
6165 TTTATTTGTTTTTTATTA
1 TTTAATTGTTTTTTATTA
6183 TT
1 TT
6185 AACATGTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (18 bp):
TTTAATTGTTTTTTATTA
Found at i:6587 original size:3 final size:3
Alignment explanation
Indices: 6579--6615 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6569 AAGATCGAGG
6579 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
6616 CAGGGGGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:14068 original size:38 final size:38
Alignment explanation
Indices: 14026--14102 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
14016 CCTATAATAA
*
14026 TATTGGCTGTAAAGCCTACAACATATTTGTATAGGCTT
1 TATTGGCTGTAAAGCCTACAACATATTTGCATAGGCTT
* ** *
14064 TATTGGTTGTATGGCCTACAGCATATTTGCATAGGCTT
1 TATTGGCTGTAAAGCCTACAACATATTTGCATAGGCTT
14102 T
1 T
14103 CTTTCTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (38 bp):
TATTGGCTGTAAAGCCTACAACATATTTGCATAGGCTT
Found at i:16565 original size:23 final size:23
Alignment explanation
Indices: 16519--16579 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
16509 AGCTCGTATC
*
16519 ATTGCACCGAAGTG-CACGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
*
16541 ATTGCACCGTAGTGCCGCGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
16564 ATTGCACCGTAGTGCC
1 ATTGCACCGTAGTGCC
16580 CTATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
ATTGCACCGTAGTGCCACGTAGA
Found at i:19891 original size:14 final size:14
Alignment explanation
Indices: 19872--19905 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
19862 ATGACAACTA
19872 TTCAATAACATCTG
1 TTCAATAACATCTG
19886 TTCAATAACATCTG
1 TTCAATAACATCTG
19900 TTCAAT
1 TTCAAT
19906 CTAGGGCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (14 bp):
TTCAATAACATCTG
Found at i:21525 original size:23 final size:23
Alignment explanation
Indices: 21479--21539 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
21469 AGCTCGTATC
*
21479 ATTGCACCGAAGTG-CACGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
*
21501 ATTGCACCGTAGTGCCGCGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
21524 ATTGCACCGTAGTGCC
1 ATTGCACCGTAGTGCC
21540 TTATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
ATTGCACCGTAGTGCCACGTAGA
Found at i:24845 original size:14 final size:14
Alignment explanation
Indices: 24826--24859 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
24816 ATGACAACTA
24826 TTCAATAACATCTG
1 TTCAATAACATCTG
24840 TTCAATAACATCTG
1 TTCAATAACATCTG
24854 TTCAAT
1 TTCAAT
24860 CTAGGGCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (14 bp):
TTCAATAACATCTG
Found at i:26210 original size:18 final size:18
Alignment explanation
Indices: 26187--26225 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
26177 ACTTTCTTAG
26187 CATTATCATATAT-ATTAT
1 CATTATC-TATATCATTAT
*
26205 CATTATCTCTATCATTAT
1 CATTATCTATATCATTAT
26223 CAT
1 CAT
26226 CGAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (18 bp):
CATTATCTATATCATTAT
Found at i:26469 original size:23 final size:23
Alignment explanation
Indices: 26423--26483 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
26413 AGCTCGTATC
*
26423 ATTGCACCGAAGTG-CACGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
*
26445 ATTGCACCGTAGTGCCGCGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
26468 ATTGCACCGTAGTGCC
1 ATTGCACCGTAGTGCC
26484 CTATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
ATTGCACCGTAGTGCCACGTAGA
Found at i:32502 original size:12 final size:12
Alignment explanation
Indices: 32487--32524 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
32477 GTTATTTAAA
32487 CGGGTATTGGGC
1 CGGGTATTGGGC
*
32499 CGGGTATTGGGT
1 CGGGTATTGGGC
32511 CGGGTATTGGGC
1 CGGGTATTGGGC
32523 CG
1 CG
32525 AGAATCGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:32541 original size:24 final size:24
Alignment explanation
Indices: 32490--32541 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
32480 ATTTAAACGG
* * * * *
32490 GTATTGGGCCGGGTATTGGGTCGG
1 GTATTGGGCCGAGAATCGGGCCGA
32514 GTATTGGGCCGAGAATCGGGCCGA
1 GTATTGGGCCGAGAATCGGGCCGA
32538 GTAT
1 GTAT
32542 ATATATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.44, T:0.25
Consensus pattern (24 bp):
GTATTGGGCCGAGAATCGGGCCGA
Found at i:32546 original size:2 final size:2
Alignment explanation
Indices: 32539--32631 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
32529 TCGGGCCGAG
* * * *
32539 TA TA TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
32580 TA TA TT TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32618 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
32632 ATTATTTTTA
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
1 5 0.07
2 63 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:32594 original size:33 final size:33
Alignment explanation
Indices: 32539--32635 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
32529 TCGGGCCGAG
*
32539 TATATATATATATATATATATTTAAATTAAATA
1 TATAAATATATATATATATATTTAAATTAAATA
* * * *
32572 TATAAATATATATTTTTTTATTTAAATTAAATT
1 TATAAATATATATATATATATTTAAATTAAATA
* *
32605 TATTAATATTATATATATATATATATAATTA
1 TATAAATA-TATATATATATATTTA-AATTA
32636 TTTTTAATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 35 0.67
34 12 0.23
35 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TATAAATATATATATATATATTTAAATTAAATA
Found at i:32664 original size:12 final size:13
Alignment explanation
Indices: 32648--32691 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
32638 TTTAATATTT
32648 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
32660 ATCGGG-CGGGTA
1 ATCGGGTCGGGTA
*
32672 ATCGGGGCGGGTA
1 ATCGGGTCGGGTA
32685 ATCGGGT
1 ATCGGGT
32692 AATCGGGGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 5 0.17
12 12 0.41
13 12 0.41
ACGTcount: A:0.14, C:0.16, G:0.50, T:0.20
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:32703 original size:13 final size:13
Alignment explanation
Indices: 32648--32690 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
32638 TTTAATATTT
*
32648 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
32660 ATC-GGGCGGGTA
1 ATCGGGGCGGGTA
32672 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
32685 ATCGGG
1 ATCGGG
32691 TAATCGGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 7 0.25
12 6 0.21
13 15 0.54
ACGTcount: A:0.14, C:0.16, G:0.51, T:0.19
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:34945 original size:73 final size:74
Alignment explanation
Indices: 34826--34972 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 74
34816 TATCTCGCAT
34826 CCCTCCTGCATGTTGGGTCGATTTTAGAATCGGGTTTTAAAGTTGAAGATGATTGCTTTGAAGAA
1 CCCTCCTGCATGTTGGGTCGATTTTAGAATCGGGTTTTAAAGTTGAAGATGATTGCTTTGAAGAA
34891 TAA-AAAAA
66 TAAGAAAAA
* *
34899 CCCTCCTGCATGTTGGGTCGATTTTGGAGTCGGGTTTTAAAGTTGAAGATGATTGCTTTGAAGAA
1 CCCTCCTGCATGTTGGGTCGATTTTAGAATCGGGTTTTAAAGTTGAAGATGATTGCTTTGAAGAA
34964 TAAGAAAAA
66 TAAGAAAAA
34973 AGAAGGAAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 66 0.93
74 5 0.07
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (74 bp):
CCCTCCTGCATGTTGGGTCGATTTTAGAATCGGGTTTTAAAGTTGAAGATGATTGCTTTGAAGAA
TAAGAAAAA
Found at i:35349 original size:2 final size:2
Alignment explanation
Indices: 35344--35393 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
35334 ACACACACAC
35344 AT AT AT AT AT 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 AT AT AT AT AT
35386 AT AT AT AT
1 AT AT AT AT
35394 CTCACCTCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37181 original size:16 final size:16
Alignment explanation
Indices: 37160--37200 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
37150 CATTTAATAA
37160 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
37176 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
37192 ATAAACGAA
1 ATAAACGAA
37201 TAAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:38387 original size:14 final size:14
Alignment explanation
Indices: 38370--38420 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
38360 GATTGGATTA
38370 AACATAAATGAACG
1 AACATAAATGAACG
38384 AACAT--A--AACG
1 AACATAAATGAACG
**
38394 AACATAACCGAACG
1 AACATAAATGAACG
38408 AACATAAATGAAC
1 AACATAAATGAAC
38421 ATAACCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 9 0.30
12 1 0.03
14 20 0.67
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:38406 original size:24 final size:24
Alignment explanation
Indices: 38370--38431 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
38360 GATTGGATTA
**
38370 AACATAAATGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
*
38394 AACATAACCGAACGAACATAAATG
1 AACATAACCGAACGAACATAAACG
*
38418 AACATAACCAAACG
1 AACATAACCGAACG
38432 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:40028 original size:39 final size:39
Alignment explanation
Indices: 39984--40074 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
39974 AATTAGGGTT
39984 TGACATGTGTCAATAAAAGACTAAAACACGTGTCATTAA
1 TGACATGTGTCAATAAAAGACTAAAACACGTGTCATTAA
* *
40023 TGACATGTGTCAGTAAAAGACTATAACACGTGTCATTAA
1 TGACATGTGTCAATAAAAGACTAAAACACGTGTCATTAA
*
40062 TGACATGTATCAA
1 TGACATGTGTCAA
40075 GACATGATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.27
Consensus pattern (39 bp):
TGACATGTGTCAATAAAAGACTAAAACACGTGTCATTAA
Found at i:53303 original size:2 final size:2
Alignment explanation
Indices: 53296--53335 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53286 TCATAATTGA
53296 AT AT AT AT 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 AT AT AT AT
53336 TAAAATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55018 original size:261 final size:254
Alignment explanation
Indices: 54545--55159 Score: 851
Period size: 261 Copynumber: 2.4 Consensus size: 254
54535 CTTATTCATA
54545 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTCGGTTTTCTAATTCATATATT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTC-G-TTTCTAATTCATATATT
* *
54610 CAGGTCGGGTC-AGTGAAACTTTATTTTGGTCGAGTCGGGTCAGTTTTTTTAAGTGTGATATTCG
64 CGGGTCGGGTCGGGTGAAACTTTA-TTT--T-G-GTCGGGTCAGTTTTTTTAAGTGTGATATTCG
* * * *
54674 GGTCGAGTTCGAGTTTAGGGTGAAAATTACCCAACCGACCTGAAAATATATATAATTTTACCTTA
124 GGCCGAGTTCGAGTTTAGGGTGAAAAATACCCAACCGACCTCAAAAAATATATAATTTTACCTTA
54739 TATATTTAGGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTCAATTAAGTCACTATTT
189 TATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTATTT
54803 T
254 T
54804 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTCAGTTTCTAATTCATATATT
1 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTCGGGTC-GTTTCTAATTCATATATT
* *
54869 TGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAATTTTTTTTAAGTGTGATATTCGAGTC
64 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTC-AGTTTTTTTAAGTGTGATA-T----TC
* * *
54934 GGGCCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACC-CAAAAAATATATAATTTTACCT
123 GGGCCGAGTTCGAGTTTAGGGTGAAAAATACCC-AACCGACCTCAAAAAATATATAATTTTACCT
54998 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTTCAATTAAGTCACT
187 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA--TTTTTTTCAATTAAGTCACT
55063 ATTTT
250 ATTTT
*
55068 TATTGAATAAAAATA-TATTTT-TTA-TT----TCGGGTC-GG--GTTTCTAATTCATATATTCG
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTCGTTTCTAATTCATATATTCG
* *
55123 GGTCGGGTCGGATGAAACTTTATTTTGGTCGGATCAG
66 GGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAG
55160 GTCTCGGATG
Statistics
Matches: 327, Mismatches: 17, Indels: 32
0.87 0.05 0.09
Matches are distributed among these distances:
251 1 0.00
252 52 0.16
255 10 0.03
256 26 0.08
257 2 0.01
259 43 0.13
260 45 0.14
261 97 0.30
262 12 0.04
263 1 0.00
264 38 0.12
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (254 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTCGTTTCTAATTCATATATTCG
GGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGCCGAG
TTCGAGTTTAGGGTGAAAAATACCCAACCGACCTCAAAAAATATATAATTTTACCTTATATATTT
AGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
Found at i:58045 original size:6 final size:6
Alignment explanation
Indices: 58034--58079 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
58024 TAAGGTAGAG
58034 TGATTA TGATTA TGATTA TGATTA TGATTA TGATTA TGATTA TGAT
1 TGATTA TGATTA TGATTA TGATTA TGATTA TGATTA TGATTA TGAT
58080 CTGGTACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGATTA
Found at i:58291 original size:7 final size:7
Alignment explanation
Indices: 58279--58304 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
58269 ATGAAAGAAA
58279 GGAATAT
1 GGAATAT
58286 GGAATAT
1 GGAATAT
58293 GGAATAT
1 GGAATAT
58300 GGAAT
1 GGAAT
58305 TGAAAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (7 bp):
GGAATAT
Found at i:59636 original size:32 final size:31
Alignment explanation
Indices: 59600--59684 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 31
59590 AATAAGATAA
*
59600 ATTATATTTAAATTAGTTTAAA-T-TGATATGTG
1 ATTATATTTAAA--A-TTTAAATTATGATATATG
59632 ATTATATTTAAAATTTAAATTTATGATATATG
1 ATTATATTTAAAATTTAAA-TTATGATATATG
*
59664 ATTATATTTAAAATTTTAATT
1 ATTATATTTAAAATTTAAATT
59685 TTTCATACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
29 6 0.12
30 1 0.02
31 3 0.06
32 38 0.79
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (31 bp):
ATTATATTTAAAATTTAAATTATGATATATG
Found at i:59685 original size:32 final size:32
Alignment explanation
Indices: 59623--59685 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
59613 TAGTTTAAAT
*
59623 TGATATGTGATTATATTTAAAATTTAAATTTA
1 TGATATATGATTATATTTAAAATTTAAATTTA
*
59655 TGATATATGATTATATTTAAAATTTTAATTT
1 TGATATATGATTATATTTAAAATTTAAATTT
59686 TTCATACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (32 bp):
TGATATATGATTATATTTAAAATTTAAATTTA
Done.