Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007099.1 Hibiscus syriacus cultivar Beakdansim tig00018548_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: 93637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:434 original size:22 final size:23
Alignment explanation
Indices: 406--453 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
396 GGACGGTGAT
406 GGAGGCGG-CACCGCCTC-GCGAA
1 GGAGGCGGCCACCGCCTCTG-GAA
428 GGAGGCGGCCACCGCCTCTGGAA
1 GGAGGCGGCCACCGCCTCTGGAA
451 GGA
1 GGA
454 AACTTCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 15 0.62
24 1 0.04
ACGTcount: A:0.19, C:0.33, G:0.42, T:0.06
Consensus pattern (23 bp):
GGAGGCGGCCACCGCCTCTGGAA
Found at i:10246 original size:20 final size:20
Alignment explanation
Indices: 10221--10264 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
10211 TCCACTGAGA
10221 CACCTTAAGAAATACCTTGT
1 CACCTTAAGAAATACCTTGT
10241 CACCTTAAGAAATACCTTGT
1 CACCTTAAGAAATACCTTGT
10261 CACC
1 CACC
10265 CATGACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.27
Consensus pattern (20 bp):
CACCTTAAGAAATACCTTGT
Found at i:18142 original size:23 final size:22
Alignment explanation
Indices: 18103--18179 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
18093 CAGAGATAAT
*
18103 CGATACCCCCTTGAAGGGGAAC
1 CGATACCCCCTTAAAGGGGAAC
*
18125 CGATTCCCCCTTTAAAGGGGAAC
1 CGATACCCCC-TTAAAGGGGAAC
* * *
18148 CGATTCCCCC-TACAGGGGAAT
1 CGATACCCCCTTAAAGGGGAAC
18169 CGATACCCCCT
1 CGATACCCCCT
18180 GAGGGTTCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 18 0.38
22 9 0.19
23 21 0.44
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.18
Consensus pattern (22 bp):
CGATACCCCCTTAAAGGGGAAC
Found at i:18166 original size:21 final size:21
Alignment explanation
Indices: 18116--18179 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
18106 TACCCCCTTG
18116 AAGGGGAACCGATTCCCCCTTTA
1 AAGGGGAACCGATTCCCCC--TA
18139 AAGGGGAACCGATTCCCCCTA
1 AAGGGGAACCGATTCCCCCTA
* * *
18160 CAGGGGAATCGATACCCCCT
1 AAGGGGAACCGATTCCCCCT
18180 GAGGGTTCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.50
23 19 0.50
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (21 bp):
AAGGGGAACCGATTCCCCCTA
Found at i:18552 original size:16 final size:16
Alignment explanation
Indices: 18531--18563 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18521 TAATTTCATC
18531 AAAAACATTTTTTTAA
1 AAAAACATTTTTTTAA
18547 AAAAACATTTTTTTAA
1 AAAAACATTTTTTTAA
18563 A
1 A
18564 TTATTGTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAACATTTTTTTAA
Found at i:24281 original size:17 final size:18
Alignment explanation
Indices: 24245--24283 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24235 TGATTGTTTG
*
24245 AAAAAAACAAAATGTGAA
1 AAAAAAACAAAATATGAA
*
24263 AAAAAAAGAAAATAT-AA
1 AAAAAAACAAAATATGAA
24280 AAAA
1 AAAA
24284 GAAAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAAAAACAAAATATGAA
Found at i:24288 original size:21 final size:22
Alignment explanation
Indices: 24264--24312 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
24254 AAATGTGAAA
24264 AAAAAAGAAAATATAAAAAA-G
1 AAAAAAGAAAATATAAAAAAGG
*
24285 AAAAAAGAAAATGTAAAAAAGG
1 AAAAAAGAAAATATAAAAAAGG
24307 AAAAAA
1 AAAAAA
24313 AAGAACGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (22 bp):
AAAAAAGAAAATATAAAAAAGG
Found at i:27259 original size:17 final size:16
Alignment explanation
Indices: 27237--27277 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
27227 ATAAATACCC
27237 TTTTCTTCTTTGTTT-TT
1 TTTTCTT-TTT-TTTCTT
27254 TTTTCTTTTTTTTCTT
1 TTTTCTTTTTTTTCTT
27270 TTTT-TTTT
1 TTTTCTTTT
27278 AATGTTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (16 bp):
TTTTCTTTTTTTTCTT
Found at i:27264 original size:9 final size:9
Alignment explanation
Indices: 27237--27275 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
27227 ATAAATACCC
*
27237 TTTTCTTCT
1 TTTTCTTTT
*
27246 TTGT-TTTT
1 TTTTCTTTT
27254 TTTTCTTTT
1 TTTTCTTTT
27263 TTTTCTTTT
1 TTTTCTTTT
27272 TTTT
1 TTTT
27276 TTAATGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:33914 original size:2 final size:2
Alignment explanation
Indices: 33907--33932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33897 ATAAGTAGTA
33907 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
33933 GTTACTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37086 original size:24 final size:24
Alignment explanation
Indices: 37006--37088 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 24
36996 GAAATCAAAA
* * * *
37006 CAGAATTCAGAACAGAATCCAAAT
1 CAGAAATCAGAACAAAATTCAAGT
* * *
37030 TAGAAATCAGAACAAAATTTAGGT
1 CAGAAATCAGAACAAAATTCAAGT
* * *
37054 CATATATCAGAACATAATTCAAGT
1 CAGAAATCAGAACAAAATTCAAGT
*
37078 CGGAAATCAGA
1 CAGAAATCAGA
37089 TAAAATATTT
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
CAGAAATCAGAACAAAATTCAAGT
Found at i:38836 original size:13 final size:13
Alignment explanation
Indices: 38818--38878 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
38808 TTTAACATAC
38818 GGTCAACGGGTCG
1 GGTCAACGGGTCG
38831 GGTCAACGGATCGGGTCG
1 GGTC-A---A-CGGGTCG
*
38849 GGTCACCGGGTCG
1 GGTCAACGGGTCG
*
38862 AGTCAACGGGTCG
1 GGTCAACGGGTCG
38875 GGTC
1 GGTC
38879 GGGTCGGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 25 0.64
14 1 0.03
17 2 0.05
18 11 0.28
ACGTcount: A:0.15, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:38847 original size:18 final size:17
Alignment explanation
Indices: 38824--38883 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
38814 ATACGGTCAA
38824 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAACGG-T
38842 CGGGTCGGGTC-AC---
1 CGGGTCGGGTCAACGGT
*
38855 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAAC-GGT
38873 CGGGTCGGGTC
1 CGGGTCGGGTC
38884 GGGTTCGGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
13 10 0.29
14 2 0.06
17 2 0.06
18 21 0.60
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:38859 original size:31 final size:31
Alignment explanation
Indices: 38818--38883 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
38808 TTTAACATAC
*
38818 GGTCAACGGGTCGGGTCAACGGATCGGGTCG
1 GGTCAACGGGTCGAGTCAACGGATCGGGTCG
* *
38849 GGTCACCGGGTCGAGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGAGTCAACGGATCGGGTCG
38880 GGTC
1 GGTC
38884 GGGTTCGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTCAACGGATCGGGTCG
Found at i:39900 original size:14 final size:15
Alignment explanation
Indices: 39873--39905 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39863 CTTTTTATGA
39873 AATAAAACAGAAAAG
1 AATAAAACAGAAAAG
*
39888 AATAAAA-AGAAAAT
1 AATAAAACAGAAAAG
39902 AATA
1 AATA
39906 GACTCGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (15 bp):
AATAAAACAGAAAAG
Found at i:40828 original size:23 final size:23
Alignment explanation
Indices: 40779--40833 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
40769 TGTTATTAAT
* * ** *
40779 TATGGTATATAATGTATATGTAT
1 TATGTTATATAATATATACATAC
40802 TATGTTATATAATATATACATAC
1 TATGTTATATAATATATACATAC
40825 TATGTTATA
1 TATGTTATA
40834 CACTATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (23 bp):
TATGTTATATAATATATACATAC
Found at i:42876 original size:23 final size:21
Alignment explanation
Indices: 42850--42902 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
42840 GATCCTGATA
*
42850 TTTATGTTTATTTTGTTTTATTT
1 TTTATG-TTATGTT-TTTTATTT
*
42873 TTTATGTTATGTTTTTTGTTT
1 TTTATGTTATGTTTTTTATTT
42894 TTTAT-TTAT
1 TTTATGTTAT
42903 TTGATTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 6 0.21
23 6 0.21
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.77
Consensus pattern (21 bp):
TTTATGTTATGTTTTTTATTT
Found at i:47727 original size:16 final size:16
Alignment explanation
Indices: 47706--47737 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
47696 GTCCGACCAT
47706 ATTTTTAATTATTTTA
1 ATTTTTAATTATTTTA
47722 ATTTTTAATTATTTTA
1 ATTTTTAATTATTTTA
47738 TATTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTAATTATTTTA
Found at i:47855 original size:21 final size:21
Alignment explanation
Indices: 47813--47855 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47803 AAACAAGAGC
* * *
47813 AATTAGAAAATTTAATGAATA
1 AATTAAAAAATTAAAAGAATA
*
47834 AATTAAAAAATTAAAAGTATA
1 AATTAAAAAATTAAAAGAATA
47855 A
1 A
47856 TGGGTAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AATTAAAAAATTAAAAGAATA
Found at i:54114 original size:69 final size:69
Alignment explanation
Indices: 53967--54100 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 69
53957 CGGTTGGGTT
* * * *
53967 AGGAAACAATAAGTTTACAGGCACCATCCCGGATTTATCTAATTGCAGAAGCTTGCAAATTTTTG
1 AGGATACAATAAGTTTACAGGCACCATCCCGGATTTAACTAATTGCAGAAGCTTGCAAATATTAG
*
54032 CTTT
66 CTTC
* * *
54036 AGGATACAATCAGTTTACAGGCACCATCCCGGATTTAACTAATTGCA-AACGCTTGCGAGTATTA
1 AGGATACAATAAGTTTACAGGCACCATCCCGGATTTAACTAATTGCAGAA-GCTTGCAAATATTA
54100 G
65 G
54101 AACTCCGGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 2 0.04
69 55 0.96
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (69 bp):
AGGATACAATAAGTTTACAGGCACCATCCCGGATTTAACTAATTGCAGAAGCTTGCAAATATTAG
CTTC
Found at i:61324 original size:17 final size:17
Alignment explanation
Indices: 61302--61340 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
61292 ATAAAAATAA
*
61302 TAAAAAATATTTTTTAT
1 TAAAAAATAATTTTTAT
61319 TAAAAAATAATTTTTAT
1 TAAAAAATAATTTTTAT
*
61336 GAAAA
1 TAAAA
61341 TATTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAAAAATAATTTTTAT
Found at i:72453 original size:20 final size:20
Alignment explanation
Indices: 72425--72472 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
72415 GGATGAACAT
* *
72425 TATCTATATTGTTCTTCGAG
1 TATCAATATTGTTCTTCAAG
72445 TATCAATATTGTTCTTCAAG
1 TATCAATATTGTTCTTCAAG
72465 TATCAATA
1 TATCAATA
72473 CCATAGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
TATCAATATTGTTCTTCAAG
Found at i:75538 original size:20 final size:20
Alignment explanation
Indices: 75510--75661 Score: 99
Period size: 20 Copynumber: 7.5 Consensus size: 20
75500 ATTTTCAACT
75510 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
75530 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
75551 ATCGCGACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
75571 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
75592 ATCGCGACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
75612 ATCGCAACGCG-ATTGTCAACT
1 ATCGCAACGCGAAATG-GAA-A
*
75633 ATCGCATCGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
75653 ATCACAACG
1 ATCGCAACG
75662 TGATTTTCAA
Statistics
Matches: 92, Mismatches: 35, Indels: 10
0.67 0.26 0.07
Matches are distributed among these distances:
19 3 0.03
20 47 0.51
21 39 0.42
22 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:75545 original size:41 final size:41
Alignment explanation
Indices: 75500--75697 Score: 326
Period size: 41 Copynumber: 4.8 Consensus size: 41
75490 TCTCAAATAT
* *
75500 ATTTTCAACTATCGCAACGCGAAATGGAAAATCGTAACGCG
1 ATTTTCAACTATCGCGACGCGAAATGGAAAATCGCAACGCG
75541 ATTTTCAACTATCGCGACGCGAAATGGAAAATCGCAACGCG
1 ATTTTCAACTATCGCGACGCGAAATGGAAAATCGCAACGCG
75582 ATTTTCAACTATCGCGACGCGAAATGGAAAATCGCAACGCG
1 ATTTTCAACTATCGCGACGCGAAATGGAAAATCGCAACGCG
* * *
75623 ATTGTCAACTATCGC-ATCGCGAAATGGAAAATCACAACGTG
1 ATTTTCAACTATCGCGA-CGCGAAATGGAAAATCGCAACGCG
*
75664 ATTTTCAACTATCGTGACGCGAAATGGAAAATCG
1 ATTTTCAACTATCGCGACGCGAAATGGAAAATCG
75698 AATTTGCGAT
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 145 0.99
42 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
ATTTTCAACTATCGCGACGCGAAATGGAAAATCGCAACGCG
Found at i:75560 original size:21 final size:21
Alignment explanation
Indices: 75536--75603 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
75526 GAAAATCGTA
75536 ACGCGATTTTCAACTATCGCG
1 ACGCGATTTTCAACTATCGCG
** ** * *
75557 ACGCGAAATGGAA-AATCGCA
1 ACGCGATTTTCAACTATCGCG
75577 ACGCGATTTTCAACTATCGCG
1 ACGCGATTTTCAACTATCGCG
75598 ACGCGA
1 ACGCGA
75604 AATGGAAAAT
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (21 bp):
ACGCGATTTTCAACTATCGCG
Found at i:76694 original size:9 final size:9
Alignment explanation
Indices: 76675--76724 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
76665 ATAATTTTTC
76675 ATTTA-AAA
1 ATTTATAAA
76683 ATTTATAAA
1 ATTTATAAA
76692 ATTTATAAA
1 ATTTATAAA
*
76701 ATATATAATA
1 ATTTATAA-A
76711 ATTT-TAAA
1 ATTTATAAA
*
76719 TTTTAT
1 ATTTAT
76725 GAGAGTTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 9 0.25
9 23 0.64
10 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTTATAAA
Found at i:82756 original size:16 final size:16
Alignment explanation
Indices: 82735--82770 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
82725 GCAATAGGTC
82735 ATCAGGTATATGGTAA
1 ATCAGGTATATGGTAA
82751 ATCAGGTATATGGTAA
1 ATCAGGTATATGGTAA
82767 ATCA
1 ATCA
82771 TAGATTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (16 bp):
ATCAGGTATATGGTAA
Found at i:88683 original size:391 final size:390
Alignment explanation
Indices: 87959--88744 Score: 1193
Period size: 391 Copynumber: 2.0 Consensus size: 390
87949 TACCAGTTTG
* * * * * *
87959 ATCA-GAGCTGAACCTCTGTACTCCAGACTCCTACCCATATAGTATCTAGTATAAATCAGATTGA
1 ATCATGAGCTGAACCTCCGTACTCCAGACTCCTAACCATACAATATCCAGTAGAAATCAGATTGA
* * * *
88023 GTAGTAACTTTAATATTAAAATCATGATCTAGTAAAATGTTTTAATAATGAAAATTTAGTTTTTT
66 GTAGTAACTTTAATATTAAAATCATAATATAATAAAATGTTTTAATAATGAAAATTTAGTTATTT
* * * * * * *
88088 AAATCATATAAACACCCTTCGTTCATATAACAAAATACAGTCCCATACTAAGGGAGTGCCTTGGG
131 AAATCACATAAACACCCTCCATCCATACAACAAAATACAATCCCATACTAAGGGAGTACCTTGGG
* * * * *
88153 GCCTTTGAGCCTACCCAAGGAATACCTTAGGTCCTTAAGGAATTGTCAGCTTGATCAGAGCCTAA
196 GCCTTAGAGCCTACCCAAGGAATAACTTAGGTCCATAAGGAATTATCAGCTTGATCAGAGACTAA
* * *
88218 CCTCTATACTCCAAAATCCTACTCAAACAGTATCCCGATAATCAATTCATATAGTAAATAGTAGA
261 CCTCTATACTCCAAAATCCTACCCAAACAGTATCCCAATAATCAATTCATACAGTAAATAGTAGA
88283 TTTCATGATCCATAAAT-AAGTAACGATTATATTTTCCAATGAAAACATATAACCAAAGAACACA
326 TTTCATGATCCATAAATCAAG-AACGATTATATTTTCCAATGAAAACATATAACCAAAGAACACA
88347 C
390 C
88348 ATCATGAGCTGAACCTCCGTACTCCAGACTCCTAACCATACAATATCCAGTAGAAATCAGATTGA
1 ATCATGAGCTGAACCTCCGTACTCCAGACTCCTAACCATACAATATCCAGTAGAAATCAGATTGA
* *
88413 GTAGTAACTTTAATATTAAAATCATAATATAATATAATGTTTTAATAATGACAATTTAGTTATTT
66 GTAGTAACTTTAATATTAAAATCATAATATAATAAAATGTTTTAATAATGAAAATTTAGTTATTT
* * *
88478 AAATCACATAAACGCCCTCCATCCGTACAACAAAATACAATCCCCATACTAAGGGAGTACTTTGG
131 AAATCACATAAACACCCTCCATCCATACAACAAAATACAAT-CCCATACTAAGGGAGTACCTTGG
*
88543 GGCCTTAGAGCCTACCCAATGAATAACTTAGGTCCATAAGGAATTATCAGCTTGATCAGA-ACTG
195 GGCCTTAGAGCCTACCCAAGGAATAACTTAGGTCCATAAGGAATTATCAGCTTGATCAGAGACT-
* * *
88607 AACCT-TCATACTCCAGAATCCTACCCAGACAGTATCCCAATAATTAATTCATACAGTAAATAGT
259 AACCTCT-ATACTCCAAAATCCTACCCAAACAGTATCCCAATAATCAATTCATACAGTAAATAGT
*
88671 AGATTTCATGATCCATAAATCAAGAACGATTATATTTTCCAATGAAAACATGTAACCAAAGAACA
323 AGATTTCATGATCCATAAATCAAGAACGATTATATTTTCCAATGAAAACATATAACCAAAGAACA
88736 CAC
388 CAC
88739 ATCATG
1 ATCATG
88745 TAGCCATAGT
Statistics
Matches: 357, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
389 4 0.01
390 149 0.42
391 201 0.56
392 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (390 bp):
ATCATGAGCTGAACCTCCGTACTCCAGACTCCTAACCATACAATATCCAGTAGAAATCAGATTGA
GTAGTAACTTTAATATTAAAATCATAATATAATAAAATGTTTTAATAATGAAAATTTAGTTATTT
AAATCACATAAACACCCTCCATCCATACAACAAAATACAATCCCATACTAAGGGAGTACCTTGGG
GCCTTAGAGCCTACCCAAGGAATAACTTAGGTCCATAAGGAATTATCAGCTTGATCAGAGACTAA
CCTCTATACTCCAAAATCCTACCCAAACAGTATCCCAATAATCAATTCATACAGTAAATAGTAGA
TTTCATGATCCATAAATCAAGAACGATTATATTTTCCAATGAAAACATATAACCAAAGAACACAC
Found at i:93137 original size:23 final size:23
Alignment explanation
Indices: 93086--93217 Score: 143
Period size: 23 Copynumber: 5.9 Consensus size: 23
93076 TCCGGATAAT
*
93086 TATGTGGTACTTCGG-GACAAA--
1 TATGTGGCACTTCGGTG-CAAACC
*
93107 TATGTGGCACTTCGATGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
93130 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
93153 TATGTGGCACTTTGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
93176 TATGTGGTCA-TTCGG-G-ACAA-T
1 TATGTGG-CACTTCGGTGCA-AACC
*
93197 TATGTGACACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
93218 TTACGAGCTG
Statistics
Matches: 96, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.02
21 29 0.30
22 7 0.07
23 56 0.58
24 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:93172 original size:46 final size:44
Alignment explanation
Indices: 93086--93217 Score: 160
Period size: 44 Copynumber: 3.0 Consensus size: 44
93076 TCCGGATAAT
*
93086 TATGTGGTACTTCGGGACAAATATGTGGCACTTCGATGCAAACC
1 TATGTGGCACTTCGGGACAAATATGTGGCACTTCGATGCAAACC
* *
93130 TATGTGGCACTTCGGTG-CAAACCTATGTGGCACTTTGGTGCAAACC
1 TATGTGGCACTTCGG-GACAAA--TATGTGGCACTTCGATGCAAACC
* * *
93176 TATGTGGTCA-TTCGGGACAATTATGTGACACTTCGGTGCAAA
1 TATGTGG-CACTTCGGGACAAATATGTGGCACTTCGATGCAAA
93218 TTACGAGCTG
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
44 37 0.48
45 2 0.03
46 36 0.47
47 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (44 bp):
TATGTGGCACTTCGGGACAAATATGTGGCACTTCGATGCAAACC
Done.