Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008860.1 Hibiscus syriacus cultivar Beakdansim tig00112084_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: 59923
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6232 original size:18 final size:18
Alignment explanation
Indices: 6210--6259 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
6200 AAAGAATAGT
*
6210 AATAATAGAAATAATAAG
1 AATAATAAAAATAATAAG
* * * *
6228 GATAATATAAAGAATAAT
1 AATAATAAAAATAATAAG
6246 AATAATAAAAATAA
1 AATAATAAAAATAA
6260 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AATAATAAAAATAATAAG
Found at i:6318 original size:3 final size:3
Alignment explanation
Indices: 6310--6352 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
6300 GTATATACGT
*
6310 ATA ATA ATA ATA ATA ACA ATA ATA ATA TATA TATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA -ATA ATA A
6353 AACGTATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:7476 original size:18 final size:16
Alignment explanation
Indices: 7445--7485 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
7435 AAAAAAAATG
7445 TAAATATAATTTATAA
1 TAAATATAATTTATAA
7461 TAAATATATATATTAT-A
1 TAAATATA-AT-TTATAA
7478 T-AATATAA
1 TAAATATAA
7486 GGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTTATAA
Found at i:11914 original size:14 final size:14
Alignment explanation
Indices: 11887--11941 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
11877 ATTTTTTAAA
*
11887 TATT-AATATAATT
1 TATTCAATATTATT
11900 TATTCAATATTATT
1 TATTCAATATTATT
*
11914 TATGCCAATATTA-T
1 TAT-TCAATATTATT
*
11928 TATTAAAATATTAT
1 TATT-CAATATTAT
11942 ATCTATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.12
14 22 0.65
15 8 0.24
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (14 bp):
TATTCAATATTATT
Found at i:12084 original size:47 final size:47
Alignment explanation
Indices: 12033--12238 Score: 142
Period size: 40 Copynumber: 4.4 Consensus size: 47
12023 TTGAAAAGAA
*
12033 TAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTAT
1 TAAAAGATTATAAATTATATTAATTATTTATTCAATAATGTTATTAT
* * * * * * * *
12080 TAAAATATTAAAAATTATAAT-ATTATAAATTATATTATTATATTTTCTTAAAA
1 TAAAAGATTATAAATTATATTAATTAT---TTAT-TCAATA-ATGTTATT--AT
* * *
12133 TAAAATAATTATAAATTATATTGATTATTTATTGAA-AA-G--A--A-
1 TAAAA-GATTATAAATTATATTAATTATTTATTCAATAATGTTATTAT
*
12174 TAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTAT
1 TAAAAGATTATAAATTATATTAATTATTTATTCAATAATGTTATTAT
* *
12221 T-AAATATTAAAAATTATA
1 TAAAAGATTATAAATTATA
12239 ATATTAAAAT
Statistics
Matches: 120, Mismatches: 23, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
40 26 0.22
41 7 0.06
42 2 0.02
44 1 0.01
46 20 0.17
47 18 0.15
49 5 0.04
50 5 0.04
51 8 0.07
52 4 0.03
53 6 0.05
54 13 0.11
55 5 0.04
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (47 bp):
TAAAAGATTATAAATTATATTAATTATTTATTCAATAATGTTATTAT
Found at i:12120 original size:15 final size:15
Alignment explanation
Indices: 12078--12121 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12068 TAATGTTATT
* *
12078 ATTAAAATATTAAAA
1 ATTATAATATTATAA
12093 ATTATAATATTATAA
1 ATTATAATATTATAA
*
12108 ATTATATTATTATA
1 ATTATAATATTATA
12122 TTTTCTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAATATTATAA
Found at i:12124 original size:141 final size:139
Alignment explanation
Indices: 11966--12262 Score: 531
Period size: 141 Copynumber: 2.1 Consensus size: 139
11956 AAATAAAAAT
*
11966 ATTATGATTATTATATTTTCTTAAAATAAAATTATTATAAATTATATTGATTATTTATTGAAAAG
1 ATTAT-ATTATTATATTTTCTTAAAATAAAATAATTATAAATTATATTGATTATTTATTGAAAAG
12031 AATAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTATTAAAATATTAAAAATT
65 AATAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTATT-AAATATTAAAAATT
12096 ATAATATTATAA
129 ATAATATTA-AA
12108 ATTATATTATTATATTTTCTTAAAATAAAATAATTATAAATTATATTGATTATTTATTGAAAAGA
1 ATTATATTATTATATTTTCTTAAAATAAAATAATTATAAATTATATTGATTATTTATTGAAAAGA
12173 ATAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTATTAAATATTAAAAATTAT
66 ATAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTATTAAATATTAAAAATTAT
12238 AATATTAAA
131 AATATTAAA
* * *
12247 ATAAGAATATTATATT
1 ATTATATTATTATATT
12263 ATATTTTAAG
Statistics
Matches: 151, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
139 15 0.10
140 23 0.15
141 108 0.72
142 5 0.03
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (139 bp):
ATTATATTATTATATTTTCTTAAAATAAAATAATTATAAATTATATTGATTATTTATTGAAAAGA
ATAAAAGATTATTAATTATATTAATTATTTATTCAATAATGTTATTATTAAATATTAAAAATTAT
AATATTAAA
Found at i:12325 original size:27 final size:28
Alignment explanation
Indices: 12295--12349 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
12285 AATATTCAAC
*
12295 AATAAATAATATTATTTTTATAA-AATT
1 AATAAATAATATTAATTTTATAATAATT
12322 AATAAATAATATTAATTTTATAATAATT
1 AATAAATAATATTAATTTTATAATAATT
12350 TATTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATAAATAATATTAATTTTATAATAATT
Found at i:12459 original size:40 final size:39
Alignment explanation
Indices: 12402--12519 Score: 100
Period size: 38 Copynumber: 3.1 Consensus size: 39
12392 TAATATAGTT
* *
12402 ATAACAATAAAAT-ATAATATTATATTAT-TAAAATTATCA
1 ATAA-AATAATATAATAATATTATATTATATAAAATGAT-A
* * *
12441 ATAAATATAATTTAATAAT-TAATATTTTATAAAATGATA
1 ATAAA-ATAATATAATAATATTATATTATATAAAATGATA
* * * *
12480 CTAAAATAATATATTAATATTA-AATATATAAAATAATA
1 ATAAAATAATATAATAATATTATATTATATAAAATGATA
12518 AT
1 AT
12520 GTTTTGATTG
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
38 26 0.42
39 23 0.37
40 13 0.21
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (39 bp):
ATAAAATAATATAATAATATTATATTATATAAAATGATA
Found at i:16931 original size:49 final size:49
Alignment explanation
Indices: 16871--16986 Score: 214
Period size: 49 Copynumber: 2.4 Consensus size: 49
16861 TACATCTGTA
*
16871 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACAGTCACAAAG
*
16920 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCATAGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACAGTCACAAAG
16969 ACGTCAGACGTGCTAAAT
1 ACGTCAGACGTGCTAAAT
16987 GCTCCCCTCT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (49 bp):
ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACAGTCACAAAG
Found at i:20366 original size:20 final size:19
Alignment explanation
Indices: 20341--20380 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
20331 TGAATCAGAA
*
20341 GAATAGTATCGATACCGAAG
1 GAATAGCATCGATACC-AAG
20361 GAATAGCATCGATACCAAG
1 GAATAGCATCGATACCAAG
20380 G
1 G
20381 GTATCGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (19 bp):
GAATAGCATCGATACCAAG
Found at i:20896 original size:16 final size:16
Alignment explanation
Indices: 20875--20940 Score: 71
Period size: 16 Copynumber: 3.9 Consensus size: 16
20865 TGCATTGTTC
20875 TACATGATCTATGTGT
1 TACATGATCTATGTGT
20891 TACATGTCATCCTATGTGT
1 TACATG--AT-CTATGTGT
* *
20910 TACATGATTTATGTGAA
1 TACATGATCTATGTG-T
20927 TACATG-TCTATGTG
1 TACATGATCTATGTG
20941 ATAACCTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
16 19 0.44
17 8 0.19
18 2 0.05
19 14 0.33
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (16 bp):
TACATGATCTATGTGT
Found at i:21102 original size:23 final size:23
Alignment explanation
Indices: 21028--21105 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
21018 GAGTCGAGGG
* * *
21028 TTCTATGCGATCATTCAGGATAA
1 TTCTATGTGGTCATTCGGGATAA
*
21051 TTCTACGTGGTCATTCGGGATAA
1 TTCTATGTGGTCATTCGGGATAA
* *
21074 TACTATGTGGTTC-TTCGGGATAT
1 TTCTATGTGG-TCATTCGGGATAA
21097 TTCTATGTG
1 TTCTATGTG
21106 ACACTTTGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 44 0.96
24 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (23 bp):
TTCTATGTGGTCATTCGGGATAA
Found at i:25652 original size:23 final size:23
Alignment explanation
Indices: 25582--25652 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
25572 GGTTCTACGC
25582 GGTCCTTTGGGACAATTCTATGT
1 GGTCCTTTGGGACAATTCTATGT
* * * **
25605 GATCCTTTGGGATAATACTGCGT
1 GGTCCTTTGGGACAATTCTATGT
* *
25628 GGTCCTTGGGGACATTTCTATGT
1 GGTCCTTTGGGACAATTCTATGT
25651 GG
1 GG
25653 CACTTCAGTG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.37
Consensus pattern (23 bp):
GGTCCTTTGGGACAATTCTATGT
Found at i:25668 original size:24 final size:24
Alignment explanation
Indices: 25641--25697 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
25631 CCTTGGGGAC
*
25641 ATTTCTATGTGGCACTTCAGTGTA
1 ATTTCTACGTGGCACTTCAGTGTA
* *
25665 ATTTCTACGTGGCATTTCGGTGTA
1 ATTTCTACGTGGCACTTCAGTGTA
*
25689 ATTTATACG
1 ATTTCTACG
25698 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (24 bp):
ATTTCTACGTGGCACTTCAGTGTA
Found at i:26743 original size:25 final size:25
Alignment explanation
Indices: 26709--26762 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
26699 ATCATCTTCA
*
26709 ATCTCGTACATAACACACTCCTTTC
1 ATCTCGTACACAACACACTCCTTTC
*
26734 ATCTCTTACACAACACACTCCTTTC
1 ATCTCGTACACAACACACTCCTTTC
26759 ATCT
1 ATCT
26763 TCAAACTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.37, G:0.02, T:0.33
Consensus pattern (25 bp):
ATCTCGTACACAACACACTCCTTTC
Found at i:37871 original size:4 final size:4
Alignment explanation
Indices: 37862--37895 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
37852 GTAAAATAAA
*
37862 AAAG AAAG AAAG AAAT AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
37896 GAATGAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:38218 original size:5 final size:5
Alignment explanation
Indices: 38195--38234 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
38185 ATTTTCCATT
38195 GTTTC GCTTTC GCTTTC GTTTC GTTTC GTTTC GTTTC GTT
1 GTTTC G-TTTC G-TTTC GTTTC GTTTC GTTTC GTTTC GTT
38235 CGGGGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.00, C:0.23, G:0.20, T:0.57
Consensus pattern (5 bp):
GTTTC
Found at i:40961 original size:21 final size:20
Alignment explanation
Indices: 40913--40961 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40903 AATGATTTTC
* * *
40913 TTTT-AAAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
40932 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
40952 TTTTGAAAAA
1 TTTTGAAAAA
40962 TGATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:42520 original size:21 final size:21
Alignment explanation
Indices: 42494--42570 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
42484 TTATTAGTGC
42494 AGTATCGATACTCCAAGCCTG
1 AGTATCGATACTCCAAGCCTG
42515 AGTATCGATACTCCAAGCCTG
1 AGTATCGATACTCCAAGCCTG
**
42536 AGTATCGATACTCCAAGTATG
1 AGTATCGATACTCCAAGCCTG
42557 AGTATCGATACTCC
1 AGTATCGATACTCC
42571 CTGGTCTCGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (21 bp):
AGTATCGATACTCCAAGCCTG
Found at i:43723 original size:17 final size:19
Alignment explanation
Indices: 43677--43716 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43667 ACTATTGAAT
* *
43677 TTTAAGATTTTATATTCGA
1 TTTAAAATTATATATTCGA
43696 TTTAAAATTATATATTCGA
1 TTTAAAATTATATATTCGA
43715 TT
1 TT
43717 AAATTATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTAAAATTATATATTCGA
Found at i:47341 original size:433 final size:433
Alignment explanation
Indices: 46516--47383 Score: 1630
Period size: 434 Copynumber: 2.0 Consensus size: 433
46506 GAGGAGTGGT
*
46516 AACCTTTGGTGACAACTCAAAAGGTTACATTGAAGGTATAGGTACTATAGGTAATACCTCTTCCA
1 AACCTTTGGTGACAACTCAAAAGGTTACATTGAAGGTATAAGTACTATAGGTAATACCTCTTCCA
46581 TACAAATAGAAAAGTTTTACATGTGAATGGTTTAAAGCATAATCTATTGAGTATTAGTCAATTAT
66 TACAAATAGAAAAGTTTTACATGTGAATGGTTTAAAGCATAATCTATTGAGTATTAGTCAATTAT
46646 GCGATAAAGGATACAATGTCTTATTTGAAACAAATGGTTGTAAAATTGTTGACATTGCATCTAAT
131 GCGATAAAGGATACAATGTCTTATTTGAAACAAATGGTTGTAAAATTGTTGACATTGCATCTAAT
*
46711 CAAATGATGCTTGTTGATCATAAAATAGGAAACATATACATGGTGCATTTAGATTCTATTAATAT
196 CAAATGACGCTTGTTGATCATAAAATAGGAAACATATACATGGTGCATTTAGATTCTATTAATAT
* *
46776 GACTAACTTGTGCCTAGTTGCTAAGGATGAACATGATAGTTAGTTATGGCCATAGAAGACTAGGA
261 GACTAACTTGTGCCTAGTTGCTAAGGATGAACAAGATAGTTAGTTATGGACATAGAAGACTAGGA
* *
46841 CATACTAGCATGAGTGTTTTACAAAGACTAATTCAAGGAGATTTAGTAAGAGGATTGCTAAAGCT
326 CATACTAGCATGAGTGTTTTACAAAGACTAATTCAAGGAGATTTAATAAGAGGATTGCCAAAGCT
*
46906 AAAATTTGATAATGATAAAATCTGTGATGTATGTGCTAAAGGA
391 AAAATTTGATAATGATAAAATATGTGATGTATGTGCTAAAGGA
46949 AACCTTTGGTGACAACTCAAAAGGTTACATTGAAGGTATAAGTACTATAGGTAATACCTCTTCCA
1 AACCTTTGGTGACAACTCAAAAGGTTACATTGAAGGTATAAGTACTATAGGTAATACCTCTTCCA
47014 TACAAATAGAAAACGTTTTACATGTGAATGGTTTAAAGCATAATCTATTGAGTATTAGTCAATTA
66 TACAAATAGAAAA-GTTTTACATGTGAATGGTTTAAAGCATAATCTATTGAGTATTAGTCAATTA
47079 TGCGATAAAGGATACAATGTCTTATTTGAAACAAATGGTTGTAAAATTGTTGACATTGCATCTAA
130 TGCGATAAAGGATACAATGTCTTATTTGAAACAAATGGTTGTAAAATTGTTGACATTGCATCTAA
*
47144 TCAAATGACGCTTGTTGATCATAGAATAGGAAACATATACATGGTGCATTTAGATTCTATTAATA
195 TCAAATGACGCTTGTTGATCATAAAATAGGAAACATATACATGGTGCATTTAGATTCTATTAATA
*
47209 TGACTAACTTGTGCCTAGTTGCTAAGGATGAACAAGATAGTTAGTTAT-GACATAGGAGACTAGG
260 TGACTAACTTGTGCCTAGTTGCTAAGGATGAACAAGATAGTTAGTTATGGACATAGAAGACTAGG
*
47273 ACATACTAGCATGAGTGTTTTACAAAGACTAATTCAAGGAGATTTAATAAGAGGATTTCCAAAGC
325 ACATACTAGCATGAGTGTTTTACAAAGACTAATTCAAGGAGATTTAATAAGAGGATTGCCAAAGC
47338 TAAAATTTGATAATGATAAAATATGTGATGTATGTGCTAAAGGA
390 TAAAATTTGATAATGATAAAATATGTGATGTATGTGCTAAAGGA
47382 AA
1 AA
47384 ACACAAAAGA
Statistics
Matches: 424, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
433 198 0.47
434 226 0.53
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (433 bp):
AACCTTTGGTGACAACTCAAAAGGTTACATTGAAGGTATAAGTACTATAGGTAATACCTCTTCCA
TACAAATAGAAAAGTTTTACATGTGAATGGTTTAAAGCATAATCTATTGAGTATTAGTCAATTAT
GCGATAAAGGATACAATGTCTTATTTGAAACAAATGGTTGTAAAATTGTTGACATTGCATCTAAT
CAAATGACGCTTGTTGATCATAAAATAGGAAACATATACATGGTGCATTTAGATTCTATTAATAT
GACTAACTTGTGCCTAGTTGCTAAGGATGAACAAGATAGTTAGTTATGGACATAGAAGACTAGGA
CATACTAGCATGAGTGTTTTACAAAGACTAATTCAAGGAGATTTAATAAGAGGATTGCCAAAGCT
AAAATTTGATAATGATAAAATATGTGATGTATGTGCTAAAGGA
Found at i:50232 original size:21 final size:20
Alignment explanation
Indices: 50208--50267 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 20
50198 ACCTCCTCGC
50208 TATGTATCGATACACTATGAA
1 TATGTATCGATACACT-TGAA
*
50229 TATGTACCGATACATTCCTTGAA
1 TATGTATCGATACA---CTTGAA
*
50252 TGTGTATCGATACACT
1 TATGTATCGATACACT
50268 CACAAGTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.06
21 13 0.39
23 16 0.48
24 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (20 bp):
TATGTATCGATACACTTGAA
Found at i:54103 original size:19 final size:19
Alignment explanation
Indices: 54076--54113 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54066 TTTATGTTTA
54076 CATTATAATTGTAAATATT
1 CATTATAATTGTAAATATT
* *
54095 CATTGTAATTGTAGATATT
1 CATTATAATTGTAAATATT
54114 TTCTGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (19 bp):
CATTATAATTGTAAATATT
Found at i:54679 original size:30 final size:29
Alignment explanation
Indices: 54604--54689 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
54594 ATGAAAAAAA
* *
54604 ATTATTATGATTAATGAAATGTAAT-AATAT
1 ATTATTATGA-TAATTAAAT-TAATAAATAG
54634 ATTATTATGATAATTAAATTAATAAATAG
1 ATTATTATGATAATTAAATTAATAAATAG
*
54663 ACTTATTAT-ATAAATT-ATTTAATAAAT
1 A-TTATTATGAT-AATTAAATTAATAAAT
54690 TAATAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.08
29 25 0.50
30 21 0.42
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (29 bp):
ATTATTATGATAATTAAATTAATAAATAG
Found at i:54698 original size:21 final size:22
Alignment explanation
Indices: 54674--54720 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
54664 CTTATTATAT
54674 AAATTATTTAA-TAAATTAATA
1 AAATTATTTAAGTAAATTAATA
54695 AAATTATTTAATGTAAATTAATA
1 AAATTATTTAA-GTAAATTAATA
54718 AAA
1 AAA
54721 ATCATGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.46
23 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTATTTAAGTAAATTAATA
Found at i:54801 original size:23 final size:24
Alignment explanation
Indices: 54761--54814 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
54751 CAATGATTAA
54761 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
54785 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
54808 ATGTAAA
1 ATGTAAA
54815 GAAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:56443 original size:54 final size:54
Alignment explanation
Indices: 56371--56612 Score: 333
Period size: 54 Copynumber: 4.5 Consensus size: 54
56361 CCGATACATT
* * * * * * *
56371 AATTCACAAACTCATTATGAATTACGTGGGTTTGCACAAATAGTGTCAATACGG-
1 AATTCATAAACTTATTATGAATTTCTTAGG-TTGCACACATAGTGCCAATACGGA
* * * *
56425 AATTCATAAACTCATTATGAATTTCATGAGGTTGTACATATAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGGA
56480 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
* *
56534 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGTCAATACGAA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
*
56588 AATTCATAAACTTATTATGATTTTC
1 AATTCATAAACTTATTATGAATTTC
56613 CCAAGTAGCC
Statistics
Matches: 171, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
54 145 0.85
55 26 0.15
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (54 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
Done.