Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005698.1 Hibiscus syriacus cultivar Beakdansim tig00013328_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: 59685
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2315 original size:31 final size:31
Alignment explanation
Indices: 2279--2337 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2269 CCCATTTTGA
2279 TGCCTCATTGTTTGACAAATGCAATGTGCGG
1 TGCCTCATTGTTTGACAAATGCAATGTGCGG
* *
2310 TGCCTCCTTGTTTGACAAATGCCATGTG
1 TGCCTCATTGTTTGACAAATGCAATGTG
2338 AAGGCATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (31 bp):
TGCCTCATTGTTTGACAAATGCAATGTGCGG
Found at i:6813 original size:31 final size:31
Alignment explanation
Indices: 6767--6828 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
6757 TTCCCCATTT
*
6767 CGGTTCCTCATTGTTTGACAAATGCAATGTG
1 CGGTGCCTCATTGTTTGACAAATGCAATGTG
* *
6798 CGGTGCCTCCTTGTTTGACAAATGCCATGTG
1 CGGTGCCTCATTGTTTGACAAATGCAATGTG
6829 AAGGCATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (31 bp):
CGGTGCCTCATTGTTTGACAAATGCAATGTG
Found at i:6854 original size:31 final size:31
Alignment explanation
Indices: 6819--6877 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
6809 TGTTTGACAA
6819 ATGCCATGTGAAGGCATGACTTTCAACAATT
1 ATGCCATGTGAAGGCATGACTTTCAACAATT
6850 ATGCCATGTGAAGGCATGACTTTCAACA
1 ATGCCATGTGAAGGCATGACTTTCAACA
6878 GGTCCAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
ATGCCATGTGAAGGCATGACTTTCAACAATT
Found at i:17098 original size:21 final size:20
Alignment explanation
Indices: 17058--17108 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
17048 GTGAACTTGG
** *
17058 TATCGATACCCCTCCTACAA
1 TATCGATACCCAACCCACAA
17078 TTATCGATACCCAACCCACAA
1 -TATCGATACCCAACCCACAA
*
17099 TATTGATACC
1 TATCGATACC
17109 TAGTGTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.33, C:0.35, G:0.06, T:0.25
Consensus pattern (20 bp):
TATCGATACCCAACCCACAA
Found at i:28422 original size:2 final size:2
Alignment explanation
Indices: 28415--28489 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
28405 TTTGTCCACA
28415 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
28457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28490 ATAATTAGAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28806 original size:174 final size:174
Alignment explanation
Indices: 28516--28864 Score: 671
Period size: 174 Copynumber: 2.0 Consensus size: 174
28506 CTACTCTGGT
28516 ATACCTAAGTAAAAAAGTATATACTATATCGATCAATATCAATTAATTTAATAATTATTTATTTA
1 ATACCTAAGTAAAAAAGTATATACTATATCGATCAATATCAATTAATTTAATAATTATTTATTTA
* *
28581 TATATTTTGTTAGATAAAATGGTTAATCCGAGATATAAAATAATAATAATAAACAAATATTTATT
66 TAGATTTTGTTAGATAAAATGGTTAATCCGAGACATAAAATAATAATAATAAACAAATATTTATT
28646 ATATAATCAAACGAAGAAAAATAAATAAAGAATTAAAATAGAGA
131 ATATAATCAAACGAAGAAAAATAAATAAAGAATTAAAATAGAGA
28690 ATACCTAAGTAAAAAAGTATATACTATATCGATCAATATCAATTAATTTAATAATTATTTATTTA
1 ATACCTAAGTAAAAAAGTATATACTATATCGATCAATATCAATTAATTTAATAATTATTTATTTA
28755 TAGATTTTGTTAGATAAAATGGTTAATCCGAGACATAAAATAATAATAATAAACAAATATTTATT
66 TAGATTTTGTTAGATAAAATGGTTAATCCGAGACATAAAATAATAATAATAAACAAATATTTATT
*
28820 ATATAATCAAATGAAGAAAAATAAATAAAGAATTAAAATAGAGA
131 ATATAATCAAACGAAGAAAAATAAATAAAGAATTAAAATAGAGA
28864 A
1 A
28865 ATGAGATTGG
Statistics
Matches: 172, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 172 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (174 bp):
ATACCTAAGTAAAAAAGTATATACTATATCGATCAATATCAATTAATTTAATAATTATTTATTTA
TAGATTTTGTTAGATAAAATGGTTAATCCGAGACATAAAATAATAATAATAAACAAATATTTATT
ATATAATCAAACGAAGAAAAATAAATAAAGAATTAAAATAGAGA
Found at i:30601 original size:21 final size:21
Alignment explanation
Indices: 30561--30601 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30551 TCTGGGCTAA
*
30561 GGGAATCGATACCCATTCAAG
1 GGGAATCGATACCCACTCAAG
*
30582 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
30602 ACGAACATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCACTCAAG
Found at i:30674 original size:23 final size:22
Alignment explanation
Indices: 30630--30674 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
30620 AATGACAGAG
* *
30630 GGGAATCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
30652 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
30675 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:32464 original size:103 final size:103
Alignment explanation
Indices: 32137--32456 Score: 561
Period size: 103 Copynumber: 3.1 Consensus size: 103
32127 GTCGAGGGTC
*
32137 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
32202 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
32240 TATGTAGTCCTTCGGGATATATATGTATTCTTTGGAACATGTATG-AGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
32304 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
32342 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * *
32407 TTGATCCCTAGTATATGTATATGATTCTTAAAGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
32445 TATGTGGTCCTT
1 TATGTGGTCCTT
32457 ATGGACATTA
Statistics
Matches: 205, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
102 99 0.48
103 106 0.52
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:32529 original size:23 final size:23
Alignment explanation
Indices: 32473--32529 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
32463 ATTATTATAT
* *
32473 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTACAATTCTACGC
* *
32496 GGCACTACGGTACAATTCTATGT
1 GGCACTACGGTACAATTCTACGC
*
32519 GGCACTTCGGT
1 GGCACTACGGT
32530 GCATTTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTACAATTCTACGC
Found at i:32540 original size:23 final size:23
Alignment explanation
Indices: 32463--32540 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
32453 CCTTATGGAC
* * *
32463 ATTATTATATGGCACTACAGTGCA
1 ATTA-TATGTGGCACTACGGTACA
* * *
32487 ATTCTACGCGGCACTACGGTACA
1 ATTATATGTGGCACTACGGTACA
* * *
32510 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTACA
*
32533 TTTATATG
1 ATTATATG
32541 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTACA
Found at i:35865 original size:23 final size:22
Alignment explanation
Indices: 35823--35865 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35813 TGCCAGAGGG
*
35823 GAACCGATACCCCCACAGGAGA
1 GAACCGATACCCCCAAAGGAGA
*
35845 GAACCGATTCCCCCTAAAGGA
1 GAACCGATACCCCC-AAAGGA
35866 AAATTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.35, C:0.35, G:0.21, T:0.09
Consensus pattern (22 bp):
GAACCGATACCCCCAAAGGAGA
Found at i:37507 original size:103 final size:103
Alignment explanation
Indices: 37328--37656 Score: 570
Period size: 103 Copynumber: 3.2 Consensus size: 103
37318 GTCGAGGGTC
* * *
37328 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAAGTGTGAAGTCTGGTGAGAAACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
37393 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
37431 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
37496 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
37534 TATGTGGTCGTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
37599 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
37637 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
37657 TATTATATGG
Statistics
Matches: 215, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:37732 original size:23 final size:23
Alignment explanation
Indices: 37664--37724 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
37654 CATTATTATA
*
37664 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
37687 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
37710 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
37725 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:42227 original size:10 final size:10
Alignment explanation
Indices: 42215--42249 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
42205 TTCGCGTTCG
*
42215 TTCATGTTTG
1 TTCATGTTTA
42225 TTCATGTTTA
1 TTCATGTTTA
42235 TTCATGTTTA
1 TTCATGTTTA
42245 TTCAT
1 TTCAT
42250 TTAAATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.60
Consensus pattern (10 bp):
TTCATGTTTA
Found at i:42326 original size:23 final size:23
Alignment explanation
Indices: 42296--42341 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42286 CGAACGGATG
*
42296 TAAACGAACATAAATGAACACAA
1 TAAACGAACATAAACGAACACAA
* *
42319 TAAACGAACGTTAACGAACACAA
1 TAAACGAACATAAACGAACACAA
42342 GCGAACACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.13
Consensus pattern (23 bp):
TAAACGAACATAAACGAACACAA
Found at i:42470 original size:21 final size:22
Alignment explanation
Indices: 42441--42481 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
42431 TAGAATTTTA
42441 TTTTATTTAATTGT-TTTAAGC
1 TTTTATTTAATTGTATTTAAGC
* *
42462 TTTTTTTTATTTGTATTTAA
1 TTTTATTTAATTGTATTTAA
42482 AATTAATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTATTTAATTGTATTTAAGC
Found at i:42601 original size:10 final size:10
Alignment explanation
Indices: 42588--42626 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
42578 TGAACGCACG
*
42588 TAAACGAACA
1 TAAATGAACA
*
42598 TAAATGAACG
1 TAAATGAACA
42608 TAAATGAACA
1 TAAATGAACA
42618 TAAATGAAC
1 TAAATGAAC
42627 GAACATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (10 bp):
TAAATGAACA
Found at i:42602 original size:24 final size:23
Alignment explanation
Indices: 42570--42628 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 23
42560 GATTGGGCTA
42570 AACATAAATGAACGCACGTAAACG
1 AACATAAATGAACG-ACGTAAACG
*
42594 AACATAAATG-A--ACGTAAATG
1 AACATAAATGAACGACGTAAACG
42614 AACATAAATGAACGA
1 AACATAAATGAACGA
42629 ACATATTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 18 0.58
21 1 0.03
23 2 0.06
24 10 0.32
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (23 bp):
AACATAAATGAACGACGTAAACG
Found at i:54757 original size:22 final size:20
Alignment explanation
Indices: 54732--54779 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
54722 GTAAACTTCA
54732 TTCTTTCTTTTGATCTTCCTCT
1 TTCTTTCTTTTGAT-TTCC-CT
*
54754 TTCTTTCTTTTTATTTCCCT
1 TTCTTTCTTTTGATTTCCCT
54774 TT-TTTC
1 TTCTTTC
54780 ATTTCGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 4 0.16
21 4 0.16
22 13 0.52
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.69
Consensus pattern (20 bp):
TTCTTTCTTTTGATTTCCCT
Found at i:55317 original size:3 final size:3
Alignment explanation
Indices: 55299--55334 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
55289 GGCTGCAAAA
55299 AAT ATAT AATT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
55335 TTTTTAGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:55795 original size:131 final size:131
Alignment explanation
Indices: 55519--56006 Score: 534
Period size: 131 Copynumber: 3.7 Consensus size: 131
55509 GTTTTGATTG
* * * *
55519 TCTAAGGGTGACACGACTCATACGTGATAAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGC
1 TCTAAAGGTGACACGACTCCTACGTGATAAGGAGATCTGGTCAATGGATGACACGGTTCATACGC
* * **
55584 GATGA-GACGGCTA-ACCATCTTTAGAAATGATGATAACACGGTTCCTACACGATGAGGACGGCT
66 GATGAGGATGGC-AGACCATCTTTAG---GGATGATAACACGGTTCCTACGTGATGAGGACGGCT
55647 GGTTA
127 GGTTA
* * * * * *
55652 TCTAGAGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCAATGGATGATACGGTTTATACGT
1 TCTAAAGGTGACACGACTCCTACGTGATAAGGAGATCTGGTCAATGGATGACACGGTTCATACGC
* * * *
55717 GTTGAGGATAGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGAATGGCTGGTT
66 GATGAGGATGGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
55782 A
131 A
* ** * * *
55783 TCTAAAGGTGACACGACTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATGGTTCCTACGT
1 TCTAAAGGTGACACGACTCCTACGTGATAAGGAGATCTGGTCAATGGATGACACGGTTCATACGC
* * * * * *
55848 GATGAGGATGG-TGATCATATTTAGGGATGATAACACGATTCTTACGTGATGAGGACGGATGGTT
66 GATGAGGATGGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
55912 A
131 A
* * * * * * * * **
55913 TCTAAGGGT-ATTACGGCTCCTATGTGATGAGGAGGTCTAGTCGATGGATGACGTGGTTCATACG
1 TCTAAAGGTGA-CACGACTCCTACGTGATAAGGAGATCTGGTCAATGGATGACACGGTTCATACG
*
55977 CGATGAGGATGGTAGACCATCTTTAGGGAT
65 CGATGAGGATGGCAGACCATCTTTAGGGAT
56007 AATGGTTTCA
Statistics
Matches: 298, Mismatches: 53, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
129 1 0.00
130 108 0.36
131 114 0.38
133 60 0.20
134 15 0.05
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (131 bp):
TCTAAAGGTGACACGACTCCTACGTGATAAGGAGATCTGGTCAATGGATGACACGGTTCATACGC
GATGAGGATGGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
A
Found at i:55996 original size:261 final size:262
Alignment explanation
Indices: 55519--56006 Score: 642
Period size: 261 Copynumber: 1.9 Consensus size: 262
55509 GTTTTGATTG
* *
55519 TCTAAGGGTGACACGACTCATACGTGATAAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGC
1 TCTAAAGGTGACACGACTCATACGTGATAAAGAGATCTGGTCAGTGGATGACACGGTTCCTACGC
* * * *
55584 GATGAGACGGCTAACCATCTTTAGAAATGATGATAACACGGTTCCTACACGATGAGGACGGCTGG
66 GATGAGACGGCTAACCATATTTAG--AGGATGATAACACGATTCCTACACGATGAGGACGGATGG
* * *
55649 TTATCTAGAGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCAATGGATGATACGGTTTATA
129 TTATCTAGAGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCAATGGATGACACGGTTCATA
* *
55714 CGTGTTGAGGATAGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGAATGGCTG
194 CGCGATGAGGATAGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGAATGGCTG
55779 GTTA
259 GTTA
* * * *
55783 TCTAAAGGTGACACGACTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATGGTTCCTACGT
1 TCTAAAGGTGACACGACTCATACGTGATAAAGAGATCTGGTCAGTGGATGACACGGTTCCTACGC
* * * * **
55848 GATGAGGATGG-TGATCATATTTAG-GGATGATAACACGATTCTTACGTGATGAGGACGGATGGT
66 GATGA-GACGGCTAACCATATTTAGAGGATGATAACACGATTCCTACACGATGAGGACGGATGGT
* * * * **
55911 TATCTA-AGG-GTATTACGGCTCCTATGTGATGAGGAGGTCTAGTCGATGGATGACGTGGTTCAT
130 TATCTAGAGGTG-A-CACGACTCCTACGTGATGAGGAGGTCTAGTCAATGGATGACACGGTTCAT
* *
55974 ACGCGATGAGGATGGTAGACCATCTTTAGGGAT
193 ACGCGATGAGGATAGCAGACCATCTTTAGGGAT
56007 AATGGTTTCA
Statistics
Matches: 192, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
259 1 0.01
260 4 0.02
261 109 0.57
264 74 0.39
265 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (262 bp):
TCTAAAGGTGACACGACTCATACGTGATAAAGAGATCTGGTCAGTGGATGACACGGTTCCTACGC
GATGAGACGGCTAACCATATTTAGAGGATGATAACACGATTCCTACACGATGAGGACGGATGGTT
ATCTAGAGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCAATGGATGACACGGTTCATACG
CGATGAGGATAGCAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGAATGGCTGGT
TA
Found at i:56118 original size:21 final size:20
Alignment explanation
Indices: 56085--56124 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
56075 GTTTCAAGAG
56085 AAATTGTCTCAAGAGAAACA
1 AAATTGTCTCAAGAGAAACA
* *
56105 AAATTCGTTTCAAGGGAAAC
1 AAATT-GTCTCAAGAGAAAC
56125 GATCTCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (20 bp):
AAATTGTCTCAAGAGAAACA
Found at i:56131 original size:36 final size:34
Alignment explanation
Indices: 56091--56198 Score: 82
Period size: 36 Copynumber: 3.2 Consensus size: 34
56081 AGAGAAATTG
56091 TCTCAAGAGAAACAAAATTCGTTTCAAGGGAAACGA
1 TCTCAAGAG--ACAAAATTCGTTTCAAGGGAAACGA
**** *
56127 TCTCAA-AG--ATGGGT-GTTTCAAGAGAAACTG-
1 TCTCAAGAGACAAAATTCGTTTCAAGGGAAAC-GA
*
56157 TCTCAAGGGAGGCAAAATTCGTTTCAAGGGAAACGA
1 TCTCAA--GAGACAAAATTCGTTTCAAGGGAAACGA
56193 TCTCAA
1 TCTCAA
56199 AGATGGGTGC
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
30 19 0.35
31 3 0.06
33 2 0.04
35 5 0.09
36 25 0.46
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (34 bp):
TCTCAAGAGACAAAATTCGTTTCAAGGGAAACGA
Found at i:56145 original size:30 final size:30
Alignment explanation
Indices: 56111--56212 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 30
56101 AACAAAATTC
56111 GTTTCAAGGGAAACGATCTCAAAGATGGGT
1 GTTTCAAGGGAAACGATCTCAAAGATGGGT
* * *
56141 GTTTCAAGAGAAACTG-TCTCAAGGGA-GGCAAAATT
1 GTTTCAAGGGAAAC-GATCTCAA-AGATGG-----GT
56176 CGTTTCAAGGGAAACGATCTCAAAGATGGGT
1 -GTTTCAAGGGAAACGATCTCAAAGATGGGT
*
56207 GCTTCA
1 GTTTCA
56213 TAAGAAATTG
Statistics
Matches: 55, Mismatches: 7, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
30 26 0.47
31 4 0.07
35 4 0.07
36 21 0.38
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (30 bp):
GTTTCAAGGGAAACGATCTCAAAGATGGGT
Found at i:56163 original size:66 final size:66
Alignment explanation
Indices: 56011--56398 Score: 403
Period size: 66 Copynumber: 5.9 Consensus size: 66
56001 AGGGATAATG
* * * *
56011 GTTTCAAGAGAAACCGACTCAAGAGATAC-AAACTTGTTTCAAGGGAAACAGA-CTCAAAGAT-G
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACA-ATCTCAAAGATGG
56073 GT
65 GT
* * * *
56075 GTTTCAAGAGAAATTGTCTCAAGAGAAACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGGG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGGG
56140 T
66 T
* * * *
56141 GTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGGG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGGG
56206 T
66 T
* * * * * *
56207 GCTTCATA-AGAAATTGTCTCAA-AGTAGAAAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
1 GTTTCA-AGAGAAACTGTCTCAAGAG-AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATG
*
56270 AGT
64 GGT
* * * * * * * **
56273 GTTTCATGAGAATCTATCTTAATG-GAGACAAAATTTGTTTCTAGGGAAATAATCTCAAAGGTTA
1 GTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGG
56337 GT
65 GT
* * *
56339 GTTTCATGAGAAACTGTCTTAAG-GTAGACAAAATTTATTTCAAGGGAAACAATCTCAAAG
1 GTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG
56399 TTTGTCTCAA
Statistics
Matches: 278, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
64 26 0.09
65 30 0.11
66 220 0.79
67 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (66 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGGG
T
Found at i:56557 original size:36 final size:35
Alignment explanation
Indices: 56511--56596 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 35
56501 TATTTCAAAG
* * *
56511 GAAAAATGTCTCAAGCGAGACAATATTTATTTTGA
1 GAAAATTGTCTCAAGCAAGACAATATTTATTTTAA
* * *
56546 GAGAAATTGTCTCAAGTAAGACAATTTTTGTTTTAA
1 GA-AAATTGTCTCAAGCAAGACAATATTTATTTTAA
**
56582 GAAAATAATCTCAAG
1 GAAAATTGTCTCAAG
56597 GTCGATAGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 13 0.31
36 29 0.69
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (35 bp):
GAAAATTGTCTCAAGCAAGACAATATTTATTTTAA
Found at i:56898 original size:16 final size:16
Alignment explanation
Indices: 56871--56901 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56861 TGTATATATG
56871 TGTTGATGTATGTTTA
1 TGTTGATGTATGTTTA
56887 TGTTGATGTATGTTT
1 TGTTGATGTATGTTT
56902 TCTTGGTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (16 bp):
TGTTGATGTATGTTTA
Found at i:57939 original size:2 final size:2
Alignment explanation
Indices: 57932--57962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57922 CAGCTTATTG
57932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57963 TCTGGGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.