Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004423.1 Hibiscus syriacus cultivar Beakdansim tig00009700_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: 50723
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7119 original size:17 final size:18
Alignment explanation
Indices: 7099--7150 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
7089 ATTAATTATA
7099 TAAAATATTAAA-AAATT
1 TAAAATATTAAATAAATT
7116 T-AAATACTTAAATAAATT
1 TAAAATA-TTAAATAAATT
*
7134 AAAAATA-TAATATAAAT
1 TAAAATATTAA-ATAAAT
7151 ATAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.17
17 9 0.30
18 11 0.37
19 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATTAAATAAATT
Found at i:14670 original size:19 final size:20
Alignment explanation
Indices: 14627--14711 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 20
14617 TGCGATATTC
* **
14627 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACACGAATTT
*
14647 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
14666 CAAA-TCG-----CGAATTT
1 CAAATTCGCAACACGAATTT
14680 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
14700 -AATTTCGCAACA
1 CAAATTCGCAACA
14712 GGTTTTAGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
18 3 0.06
19 19 0.35
20 19 0.35
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:14698 original size:20 final size:19
Alignment explanation
Indices: 14627--14710 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 19
14617 TGCGATATTC
**
14627 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAAC-CGAATTT
*
14647 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACCGAATTT
14666 CAAA-TCG----CGAATTT
1 CAAATTCGCAACCGAATTT
14680 CAAATTCGCAACACGAATTT
1 CAAATTCGCAAC-CGAATTT
*
14700 -AATTTCGCAAC
1 CAAATTCGCAAC
14711 AGGTTTTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
18 3 0.06
19 18 0.34
20 19 0.36
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (19 bp):
CAAATTCGCAACCGAATTT
Found at i:14795 original size:27 final size:27
Alignment explanation
Indices: 14764--14825 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
14754 GCAGCAGCAT
14764 CAACTCATAACCTAAATCCCTAAATCG
1 CAACTCATAACCTAAATCCCTAAATCG
14791 CAACTCATAACCTAAATCCCTAAATCG
1 CAACTCATAACCTAAATCCCTAAATCG
*
14818 TAACTCAT
1 CAACTCAT
14826 TGCATCTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.24
Consensus pattern (27 bp):
CAACTCATAACCTAAATCCCTAAATCG
Found at i:18307 original size:34 final size:34
Alignment explanation
Indices: 18259--18352 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 34
18249 TGCGATCAAC
* *
18259 ACGAAAGTCAAATTCGCAATGCGAAATAAGCGTT
1 ACGATAGTCAAATTCGCAACGCGAAATAAGCGTT
*
18293 ACGGTAGTCAAATTCGCAACGCGAAATAAGCGTT
1 ACGATAGTCAAATTCGCAACGCGAAATAAGCGTT
* * *
18327 GCGATAGTCAAATTCGAAACACGAAA
1 ACGATAGTCAAATTCGCAACGCGAAA
18353 GTCAAATTCG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (34 bp):
ACGATAGTCAAATTCGCAACGCGAAATAAGCGTT
Found at i:18355 original size:20 final size:20
Alignment explanation
Indices: 18332--18372 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18322 GCGTTGCGAT
18332 AGTCAAATTCGAAACACGAA
1 AGTCAAATTCGAAACACGAA
* *
18352 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGAAACACGAA
18372 A
1 A
18373 TAAGCGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
AGTCAAATTCGAAACACGAA
Found at i:18526 original size:25 final size:25
Alignment explanation
Indices: 18488--18537 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
18478 AAATCAATTA
*
18488 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
18513 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
18538 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:19308 original size:39 final size:39
Alignment explanation
Indices: 19262--19348 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
19252 TCTGATGCTC
19262 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* * * *
19301 ATTAAAATTCAAATCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
19340 ATCAAAATC
1 ATCAAAATC
19349 TACAACTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:19576 original size:20 final size:20
Alignment explanation
Indices: 19551--19588 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19541 GCAACCCTTA
19551 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
19571 TTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
19589 TACCTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:21172 original size:21 final size:21
Alignment explanation
Indices: 21148--21224 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
21138 AAACGATGAT
*
21148 AGGGGCCTCTTGAACGGTAGG
1 AGGGGCCTCTTGAACGATAGG
* * *
21169 AGGGGCTTCTTCG-ATGAT-GAT
1 AGGGGCCTCTT-GAACGATAG-G
21190 AGGGGCCTCTTGAACGATAGG
1 AGGGGCCTCTTGAACGATAGG
*
21211 AGGCGCCTCTTGAA
1 AGGGGCCTCTTGAA
21225 TGATGATAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATAGG
Found at i:21188 original size:42 final size:42
Alignment explanation
Indices: 21142--21234 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
21132 CCACTTAAAC
* * *
21142 GATGATAGGGGCCTCTTGAACGGTAGGAGGGGCTTCTTCG-AT
1 GATGATAGGGGCCTCTTGAACGATAGGAGGCGCCTCTT-GAAT
21184 GATGATAGGGGCCTCTTGAACGATAGGAGGCGCCTCTTGAAT
1 GATGATAGGGGCCTCTTGAACGATAGGAGGCGCCTCTTGAAT
21226 GATGATAGG
1 GATGATAGG
21235 TGCATCGGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.25
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGATAGGAGGCGCCTCTTGAAT
Found at i:21666 original size:21 final size:21
Alignment explanation
Indices: 21640--21687 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
21630 CATTATCTTC
*
21640 ACGTAAAGTACCGACCTCATG
1 ACGTAAAGCACCGACCTCATG
21661 ACGTAAAGCACCGACCTCATG
1 ACGTAAAGCACCGACCTCATG
21682 ACGTAA
1 ACGTAA
21688 TTCCCCTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (21 bp):
ACGTAAAGCACCGACCTCATG
Found at i:23460 original size:13 final size:13
Alignment explanation
Indices: 23442--23473 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
23432 GGGTTTCTTC
23442 AACAAAAAGACAA
1 AACAAAAAGACAA
*
23455 AACAAAAAGATAA
1 AACAAAAAGACAA
23468 AACAAA
1 AACAAA
23474 GACAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.03
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:23723 original size:22 final size:22
Alignment explanation
Indices: 23691--23733 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23681 GAGATAGAAG
*
23691 GATTTCGTCGGAAATGGGGACA
1 GATTTCATCGGAAATGGGGACA
*
23713 GATTTCATCGGAGATGGGGAC
1 GATTTCATCGGAAATGGGGAC
23734 GGATGTCGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (22 bp):
GATTTCATCGGAAATGGGGACA
Found at i:23904 original size:19 final size:20
Alignment explanation
Indices: 23865--23928 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
23855 GCGTAAAAAC
23865 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
23885 ATTTGACTTTCGCG-TGCGA
1 ATTTGACTTTCGCGTTGCGA
** *
23904 ATTTGACTACCGCGTTGAGA
1 ATTTGACTTTCGCGTTGCGA
23924 ATTTG
1 ATTTG
23929 GAAAATCGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:24001 original size:20 final size:19
Alignment explanation
Indices: 23956--24024 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
23946 TTATATATTT
*
23956 GCGTTGCGAAATTGGAAAC
1 GCGTTGCGAAATTGGAATC
*
23975 TGGGTTGCGAAATTGGAATTC
1 -GCGTTGCGAAATTGGAA-TC
*
23996 GCGTTGCG-AATTTGAGATC
1 GCGTTGCGAAATTGGA-ATC
24015 GCGTTGCGAA
1 GCGTTGCGAA
24025 TTTGTTGGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 16 0.38
20 25 0.60
21 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (19 bp):
GCGTTGCGAAATTGGAATC
Found at i:25366 original size:15 final size:16
Alignment explanation
Indices: 25346--25378 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25336 GAACATCATT
25346 AATTT-AAATTATAAA
1 AATTTAAAATTATAAA
*
25361 AATTTAAAATTCTAAA
1 AATTTAAAATTATAAA
25377 AA
1 AA
25379 ACTTAACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTAAAATTATAAA
Found at i:29294 original size:143 final size:143
Alignment explanation
Indices: 29025--29311 Score: 425
Period size: 143 Copynumber: 2.0 Consensus size: 143
29015 AAATACTCAA
*
29025 TTCAATTTATAAAATAGTTGACTCGAAATTTTTCTATTTGAGTTTATAAAATTTAAATCAAGTCG
1 TTCAATTTATAAAATAGTTGACTCGAAATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC-
* * * *
29090 AATTGAATTGAATTTTCTAGTTTCTGTTTAAATTTAATTATAAATAGTTATCATATTATAATATT
65 -A--GAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATAGTTATAATACTATAATATT
29155 ATTTGATTCTAATTCAG
127 ATTTGATTCTAATTCAG
* *
29172 TTCAGTTTATAAAATAGTTGACT-TAAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAATTTATAAAATAGTTGACTCGAAA--TTTTTCGATTTGAGTTTATAAAATTTAAATCAAGT
* *
29236 C-GAATTGAATTTTCGAGTTTATGTTTAACTTTAATTATAAATATTTATAATACTATAATATTAT
64 CAGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATAGTTATAATACTATAATATTAT
29300 TTGATTCTAATT
129 TTGATTCTAATT
29312 TAAATAGTTT
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
143 69 0.53
146 3 0.02
147 22 0.17
148 35 0.27
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (143 bp):
TTCAATTTATAAAATAGTTGACTCGAAATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCA
GAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATAGTTATAATACTATAATATTATTT
GATTCTAATTCAG
Found at i:30046 original size:18 final size:18
Alignment explanation
Indices: 30023--30147 Score: 196
Period size: 18 Copynumber: 6.9 Consensus size: 18
30013 ACTGAATATT
*
30023 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
*
30041 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
30059 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
30077 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
30095 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
30113 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
30131 TGTCCCAAAGAACCACT
1 TGTCCCGAAGGACCACT
30148 GATAATCCCT
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 98 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:37327 original size:33 final size:34
Alignment explanation
Indices: 37289--37382 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 34
37279 AATGAATTAT
* *
37289 GAATTTGGGGTTGGTCATGTAATTGAA-T-TTTTG
1 GAATTTGGGGTTAG-AATGTAATTGAAGTATTTTG
*
37322 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
1 GAATTTG-GGGTTAGAATGTAATTGAAGTATTTTG
* * *
37357 AAATTTGGAGCTTAAAATGTAATTGA
1 GAATTTGG-GGTTAGAATGTAATTGA
37383 TGATTATGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
33 18 0.35
34 7 0.14
35 26 0.51
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (34 bp):
GAATTTGGGGTTAGAATGTAATTGAAGTATTTTG
Found at i:37363 original size:35 final size:33
Alignment explanation
Indices: 37305--37382 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 33
37295 GGGGTTGGTC
* * *
37305 ATGTAATTGAATTTTTGGAATTT-GAGGTTTAGA
1 ATGTAATTGAATTTTTGAAATTTGGA-GCTTAAA
37338 ATGTAATTGAAGTATTTTGAAATTTGGAGCTTAAA
1 ATGTAATTGAA-T-TTTTGAAATTTGGAGCTTAAA
37373 ATGTAATTGA
1 ATGTAATTGA
37383 TGATTATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 11 0.28
34 1 0.03
35 25 0.64
36 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (33 bp):
ATGTAATTGAATTTTTGAAATTTGGAGCTTAAA
Found at i:42731 original size:31 final size:31
Alignment explanation
Indices: 42664--42775 Score: 127
Period size: 31 Copynumber: 3.6 Consensus size: 31
42654 TGTTAAATTC
* * *
42664 AGATAATGCACAGTAGAATTAGTAT-TGCATTC
1 AGATAATGCACAGCAG-AGTAGTATGT-CATTT
*
42696 AGATAATGCATAGCAGAGTAGTATGTCATTT
1 AGATAATGCACAGCAGAGTAGTATGTCATTT
* *
42727 AGATAATGCACAACAGAGTAGTATGACATTT
1 AGATAATGCACAGCAGAGTAGTATGTCATTT
* *
42758 AGTTAATGCACAGTAGAG
1 AGATAATGCACAGCAGAG
42776 CCAATATCAC
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 54 0.78
32 15 0.22
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (31 bp):
AGATAATGCACAGCAGAGTAGTATGTCATTT
Found at i:45007 original size:15 final size:16
Alignment explanation
Indices: 44989--45018 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44979 ATCGGTTAAA
44989 TTTTAAATTA-GATAG
1 TTTTAAATTATGATAG
45004 TTTTAAATTATGATA
1 TTTTAAATTATGATA
45019 TTAAATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TTTTAAATTATGATAG
Found at i:46524 original size:11 final size:10
Alignment explanation
Indices: 46508--46553 Score: 67
Period size: 11 Copynumber: 4.5 Consensus size: 10
46498 TTGTTAGAGT
46508 TTGTTATTAG
1 TTGTTATTAG
46518 CTTGTTATTAG
1 -TTGTTATTAG
46529 TTGTTATTAG
1 TTGTTATTAG
46539 TTTGTTA-TAG
1 -TTGTTATTAG
46549 TTGTT
1 TTGTT
46554 GGTTACTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:46524 original size:21 final size:21
Alignment explanation
Indices: 46498--46550 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
46488 GAGGTCCAGT
*
46498 TTGTTAGAGTTTGTTATTAGC
1 TTGTTATAGTTTGTTATTAGC
*
46519 TTGTTATTAG-TTGTTATTAGT
1 TTGTTA-TAGTTTGTTATTAGC
46540 TTGTTATAGTT
1 TTGTTATAGTT
46551 GTTGGTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (21 bp):
TTGTTATAGTTTGTTATTAGC
Found at i:46549 original size:10 final size:11
Alignment explanation
Indices: 46495--46550 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 11
46485 CGTGAGGTCC
*
46495 AGTTTGTTA-G
1 AGTTTGTTATT
46505 AGTTTGTTATT
1 AGTTTGTTATT
*
46516 AGCTTGTTATT
1 AGTTTGTTATT
46527 AG-TTGTTATT
1 AGTTTGTTATT
46537 AGTTTGTTA-T
1 AGTTTGTTATT
46547 AGTT
1 AGTT
46551 GTTGGTTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 24 0.57
11 18 0.43
ACGTcount: A:0.20, C:0.02, G:0.21, T:0.57
Consensus pattern (11 bp):
AGTTTGTTATT
Found at i:48113 original size:10 final size:11
Alignment explanation
Indices: 48098--48159 Score: 69
Period size: 10 Copynumber: 6.0 Consensus size: 11
48088 GTAGAGTAAA
48098 TGTTA-TAGTT
1 TGTTATTAGTT
*
48108 TGTTA-TGGTT
1 TGTTATTAGTT
*
48118 TGTTATTAGCT
1 TGTTATTAGTT
*
48129 TGTCATTAG-T
1 TGTTATTAGTT
48139 TGTTATTAGTT
1 TGTTATTAGTT
48150 TGTTA-TAGTT
1 TGTTATTAGTT
48160 GTTGGTTACT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
10 28 0.62
11 17 0.38
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.58
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:48136 original size:11 final size:10
Alignment explanation
Indices: 48117--48162 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
48107 TTGTTATGGT
48117 TTGTTATTAG
1 TTGTTATTAG
*
48127 CTTGTCATTAG
1 -TTGTTATTAG
48138 TTGTTATTAG
1 TTGTTATTAG
48148 TTTGTTA-TAG
1 -TTGTTATTAG
48158 TTGTT
1 TTGTT
48163 GGTTACTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 5 0.16
10 12 0.38
11 15 0.47
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:48141 original size:21 final size:20
Alignment explanation
Indices: 48117--48162 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
48107 TTGTTATGGT
48117 TTGTTATTAGCTTGTCATTAG
1 TTGTTATTAGCTTGTCA-TAG
* *
48138 TTGTTATTAGTTTGTTATAG
1 TTGTTATTAGCTTGTCATAG
48158 TTGTT
1 TTGTT
48163 GGTTACTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (20 bp):
TTGTTATTAGCTTGTCATAG
Done.