Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007485.1 Hibiscus syriacus cultivar Beakdansim tig00020664_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: 61441
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2053 original size:66 final size:65
Alignment explanation
Indices: 1910--2046 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 65
1900 TGCACTAAGT
* *
1910 GTGCATC-AATGCATAAAATGCATTCGATATTTTGAAAAAGCCTGAGTGCATCGAGGCATGGCTG
1 GTGCATCGAATGCATAAAATGCATTCGATATTTTGAAAAACCCTGAGTGCATCGAGGCATGGATG
* * * *
1974 GTGCATCG-ATGCATCAAATGCATTCGATGTTTTCATAAAAACCCTGAGTGCATC-ATGCAT-GA
1 GTGCATCGAATGCATAAAATGCATTCGATATTTT--GAAAAACCCTGAGTGCATCGAGGCATGGA
2036 T-
64 TG
2037 GTGCATCGAA
1 GTGCATCGAA
2047 AATGCATTCG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
63 8 0.13
64 33 0.52
65 5 0.08
66 17 0.27
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (65 bp):
GTGCATCGAATGCATAAAATGCATTCGATATTTTGAAAAACCCTGAGTGCATCGAGGCATGGATG
Found at i:3560 original size:21 final size:24
Alignment explanation
Indices: 3517--3560 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3507 GTAATAAAGT
*
3517 TTTTAATAATATAGTTTGATTTAA
1 TTTTAATAAGATAGTTTGATTTAA
3541 TTTTAAT-AGATA-TTTG-TTTA
1 TTTTAATAAGATAGTTTGATTTA
3561 TTTCTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 4 0.21
24 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTAATAAGATAGTTTGATTTAA
Found at i:3916 original size:15 final size:16
Alignment explanation
Indices: 3889--3920 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3879 TTATTATCAC
3889 TAATTTATTTTAATAT
1 TAATTTATTTTAATAT
3905 TAATTT-TTTTAATAT
1 TAATTTATTTTAATAT
3920 T
1 T
3921 GTTTTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTATTTTAATAT
Found at i:33647 original size:11 final size:11
Alignment explanation
Indices: 33631--33656 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33621 AATTAGTGGC
33631 ATGTAATTATT
1 ATGTAATTATT
33642 ATGTAATTATT
1 ATGTAATTATT
33653 ATGT
1 ATGT
33657 TTTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:33661 original size:832 final size:832
Alignment explanation
Indices: 32053--33722 Score: 3250
Period size: 832 Copynumber: 2.0 Consensus size: 832
32043 GAAAATGTGA
32053 TATTTTACCATGAATGTTATTTCGGGTATGAACTGCCCAATGTTAAATTATAATAATATACTTTG
1 TATTTTACCATGAATGTTATTTCGGGTATGAACTGCCCAATGTTAAATTATAATAATATACTTTG
32118 CCATGAATGAATTGAATAAAGTAGACTATATGCCCGAATAAGTCATTGAGAGACAGGATATAGTT
66 CCATGAATGAATTGAATAAAGTAGACTATATGCCCGAATAAGTCATTGAGAGACAGGATATAGTT
*
32183 GGCACGCCATAGAGTATAGCAGCTGCAGGTTTATATTAGCACTATAGTGTGTAAGGACACTAAGT
131 GGCACGCCATAGAGTACAGCAGCTGCAGGTTTATATTAGCACTATAGTGTGTAAGGACACTAAGT
* *
32248 GCAGGTTTATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGTACGACCTTTTG
196 GCAGGTTTATGTCCGGATTAGCACTATAGCGTAAACTTAGTGTAGGTGGTGGGTACGACCTTATG
32313 TGTATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGTTTAGCACTACGGTGCATGTATT
261 TGTATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGTTTAGCACTACGGTGCATGTATT
32378 CTACTCGTATACCCAGGGTCCTAAGGGTTGTATATTGGGCTATTGTCTATGGTTTTATACATTAT
326 CTACTCGTATACCCAGGGTCCTAAGGGTTGTATATTGGGCTATTGTCTATGGTTTTATACATTAT
*
32443 TGGTTAATAAATGGTAAGCACGAAATTAAGCTTACGAGCTTAAGAAATTAATGGCAAGTATATTG
391 TGGTTAATAAATGGTAAGCACGAAATTAAGCTTACGAGCTTAAGAAATTAAGGGCAAGTATATTG
32508 GTAAGGAATTTTATATTCAGTTATATTATTTTTGATCATGGTAAAATATTGGATATGCTGATAAT
456 GTAAGGAATTTTATATTCAGTTATATTATTTTTGATCATGGTAAAATATTGGATATGCTGATAAT
*
32573 ATGATTGTAAGGTATTTGGTTTTTATAATAAAATTATGCATGAATTGTATTGCACTGTAAAATGT
521 ATGATTGTAAGGTATTTGGTTTTTATAATAAAATTATGCATGAATTGTATTACACTGTAAAATGT
32638 TTTAATTGCCTCACTAAGTATATACTTAGCGTGTGATGATTTTTACGCGTAGGTAAAAAGCTCGT
586 TTTAATTGCCTCACTAAGTATATACTTAGCGTGTGATGATTTTTACGCGTAGGTAAAAAGCTCGT
*
32703 AGAAGAATAGAGAGTTCAAGGCAACATCAAGCATCAAGAAGTATATTTCTTTATCAGTAAGACAT
651 AGAAGAATAGAGAGTTCAAGGCAACATCAAACATCAAGAAGTATATTTCTTTATCAGTAAGACAT
32768 CCTAAAATGTAATGTAGATTTAATTAGTGGCATGTAATTATTATGTAATTATTACGTTTTATTTG
716 CCTAAAATGTAATGTAGATTTAATTAGTGGCATGTAATTATTATGTAATTATTACGTTTTATTTG
32833 CTTTGTTGAACAAAATTGGAAACAAGAAAATGGAATTTTATGAATGTATATG
781 CTTTGTTGAACAAAATTGGAAACAAGAAAATGGAATTTTATGAATGTATATG
32885 TATTTTACCATGAATGTTATTTCGGGTATGAACTGCCCAATGTTAAATTATAATAATATACTTTG
1 TATTTTACCATGAATGTTATTTCGGGTATGAACTGCCCAATGTTAAATTATAATAATATACTTTG
*
32950 CCATGAATGAATTGAATAAAGTAGACTATATGCCCGAATAAGTCATTGAGGGACAGGATATAGTT
66 CCATGAATGAATTGAATAAAGTAGACTATATGCCCGAATAAGTCATTGAGAGACAGGATATAGTT
* *
33015 GGCATGTCATAGAGTACAGCAGCTGCAGGTTTATATTAGCACTATAGTGTGTAAGGACACTAAGT
131 GGCACGCCATAGAGTACAGCAGCTGCAGGTTTATATTAGCACTATAGTGTGTAAGGACACTAAGT
33080 GCAGGTTTATGTCCGGATTAGCACTATAGCGTAAACTTAGTGTAGGTGGTGGGTACGACCTTATG
196 GCAGGTTTATGTCCGGATTAGCACTATAGCGTAAACTTAGTGTAGGTGGTGGGTACGACCTTATG
33145 TGTATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGTTTAGCACTACGGTGCATGTATT
261 TGTATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGTTTAGCACTACGGTGCATGTATT
33210 CTACTCGTATACCCAGGGTCCTAAGGGTTGTATATTGGGCTATTGTCTATGGTTTTATACATTAT
326 CTACTCGTATACCCAGGGTCCTAAGGGTTGTATATTGGGCTATTGTCTATGGTTTTATACATTAT
33275 TGGTTAATAAATGGTAAGCACGAAATTAAGCTTACGAGCTTAAGAAATTAAGGGCAAGTATATTG
391 TGGTTAATAAATGGTAAGCACGAAATTAAGCTTACGAGCTTAAGAAATTAAGGGCAAGTATATTG
33340 GTAAGGAATTTTATATTCAGTTATATTATTTTTGATCATGGTAAAATATTGGATATGCTGATAAT
456 GTAAGGAATTTTATATTCAGTTATATTATTTTTGATCATGGTAAAATATTGGATATGCTGATAAT
33405 ATGATTGTAAGGTATTTGGTTTTTATAATAAAATTATGCATGAATTGTATTACACTGTAAAATGT
521 ATGATTGTAAGGTATTTGGTTTTTATAATAAAATTATGCATGAATTGTATTACACTGTAAAATGT
33470 TTTAATTGCCTCACTAAGTATATACTTAGCGTGTGATGATTTTTACGCGTAGGTAAAAAGCTCGT
586 TTTAATTGCCTCACTAAGTATATACTTAGCGTGTGATGATTTTTACGCGTAGGTAAAAAGCTCGT
33535 AGAAGAATAGAGAGTTCAAGGCAACATCAAACATCAAGAAGTATATTTCTTTATCAGTAAGACAT
651 AGAAGAATAGAGAGTTCAAGGCAACATCAAACATCAAGAAGTATATTTCTTTATCAGTAAGACAT
*
33600 CCTAAAATGTAATGTAGATTTAATTAGTGGCATGTAATTATTATGTAATTATTATGTTTTATTTG
716 CCTAAAATGTAATGTAGATTTAATTAGTGGCATGTAATTATTATGTAATTATTACGTTTTATTTG
33665 CTTTGTTGAACAAAATTGGAAACAAGAAAATGGAATTTTATGAATGTATATG
781 CTTTGTTGAACAAAATTGGAAACAAGAAAATGGAATTTTATGAATGTATATG
33717 TATTTT
1 TATTTT
33723 CGCTGTTACT
Statistics
Matches: 828, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
832 828 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (832 bp):
TATTTTACCATGAATGTTATTTCGGGTATGAACTGCCCAATGTTAAATTATAATAATATACTTTG
CCATGAATGAATTGAATAAAGTAGACTATATGCCCGAATAAGTCATTGAGAGACAGGATATAGTT
GGCACGCCATAGAGTACAGCAGCTGCAGGTTTATATTAGCACTATAGTGTGTAAGGACACTAAGT
GCAGGTTTATGTCCGGATTAGCACTATAGCGTAAACTTAGTGTAGGTGGTGGGTACGACCTTATG
TGTATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGTTTAGCACTACGGTGCATGTATT
CTACTCGTATACCCAGGGTCCTAAGGGTTGTATATTGGGCTATTGTCTATGGTTTTATACATTAT
TGGTTAATAAATGGTAAGCACGAAATTAAGCTTACGAGCTTAAGAAATTAAGGGCAAGTATATTG
GTAAGGAATTTTATATTCAGTTATATTATTTTTGATCATGGTAAAATATTGGATATGCTGATAAT
ATGATTGTAAGGTATTTGGTTTTTATAATAAAATTATGCATGAATTGTATTACACTGTAAAATGT
TTTAATTGCCTCACTAAGTATATACTTAGCGTGTGATGATTTTTACGCGTAGGTAAAAAGCTCGT
AGAAGAATAGAGAGTTCAAGGCAACATCAAACATCAAGAAGTATATTTCTTTATCAGTAAGACAT
CCTAAAATGTAATGTAGATTTAATTAGTGGCATGTAATTATTATGTAATTATTACGTTTTATTTG
CTTTGTTGAACAAAATTGGAAACAAGAAAATGGAATTTTATGAATGTATATG
Found at i:36938 original size:20 final size:20
Alignment explanation
Indices: 36913--36955 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
36903 TTCCAAATTG
36913 TATTCAAGAA-ATATTTTAAT
1 TATTCAAGAATATA-TTTAAT
*
36933 TATTCATGAATATATTTAAT
1 TATTCAAGAATATATTTAAT
36953 TAT
1 TAT
36956 ATATTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TATTCAAGAATATATTTAAT
Found at i:37779 original size:24 final size:24
Alignment explanation
Indices: 37695--37779 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
37685 TATATCAAAA
* * * * *
37695 ATCAAAACATAATTCATGTCCGAT
1 ATCATAACAGAATCCATGTCAGGT
* *
37719 ATCATAATAGAATCCAGGTCAGGT
1 ATCATAACAGAATCCATGTCAGGT
* *
37743 ATTAGAACAGAATCCATGTCAGGT
1 ATCATAACAGAATCCATGTCAGGT
*
37767 ATCATAACCGAAT
1 ATCATAACAGAAT
37780 TCAAATCGAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCATAACAGAATCCATGTCAGGT
Found at i:39321 original size:31 final size:31
Alignment explanation
Indices: 39244--39305 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39234 CAGTTACGTC
* *
39244 AGGGACCATATTGCAAACAGGCTAAATGTTG
1 AGGGACCATATTGTAAACAGACTAAATGTTG
39275 AGGGACCATATTGTAAACAGACTAAATGTTG
1 AGGGACCATATTGTAAACAGACTAAATGTTG
39306 GGAGATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (31 bp):
AGGGACCATATTGTAAACAGACTAAATGTTG
Found at i:41099 original size:18 final size:20
Alignment explanation
Indices: 41076--41114 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41066 GTTATTGTAC
*
41076 GACTGCA-A-TACCTGTAAT
1 GACTGCATAGTACCTGCAAT
41094 GACTGCATAGTACCTGCAAT
1 GACTGCATAGTACCTGCAAT
41114 G
1 G
41115 TCCACATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (20 bp):
GACTGCATAGTACCTGCAAT
Found at i:42590 original size:19 final size:19
Alignment explanation
Indices: 42566--42628 Score: 126
Period size: 19 Copynumber: 3.3 Consensus size: 19
42556 TACACCTCCA
42566 GCAAAAAGAACAAAACAAC
1 GCAAAAAGAACAAAACAAC
42585 GCAAAAAGAACAAAACAAC
1 GCAAAAAGAACAAAACAAC
42604 GCAAAAAGAACAAAACAAC
1 GCAAAAAGAACAAAACAAC
42623 GCAAAA
1 GCAAAA
42629 GAGCAAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.68, C:0.21, G:0.11, T:0.00
Consensus pattern (19 bp):
GCAAAAAGAACAAAACAAC
Found at i:46412 original size:17 final size:17
Alignment explanation
Indices: 46390--46430 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
46380 AAAATCTGTA
46390 AAACTATCTTCAGGTGC
1 AAACTATCTTCAGGTGC
46407 AAACTATCTTCAGGTGC
1 AAACTATCTTCAGGTGC
*
46424 GAACTAT
1 AAACTAT
46431 GCTCTTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (17 bp):
AAACTATCTTCAGGTGC
Found at i:49528 original size:18 final size:18
Alignment explanation
Indices: 49505--49539 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49495 ACTTAATATT
*
49505 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
49523 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
49540 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:51722 original size:34 final size:32
Alignment explanation
Indices: 51664--51732 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
51654 ACCTTACAAC
* *
51664 TCCCCAGTTTTTCTGGGCTAAACTAGAACATT
1 TCCCCAGTTTTACTGGGATAAACTAGAACATT
*
51696 TCCCCAGCTTTTACATGGGATAAACTAGAACCTT
1 TCCCCAG-TTTTAC-TGGGATAAACTAGAACATT
51730 TCC
1 TCC
51733 TCTTTACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (32 bp):
TCCCCAGTTTTACTGGGATAAACTAGAACATT
Found at i:52082 original size:20 final size:20
Alignment explanation
Indices: 52049--52201 Score: 216
Period size: 20 Copynumber: 7.7 Consensus size: 20
52039 GCAGCCTTCG
* * *
52049 TGCATGGATACACAATAGGA
1 TGCATCGATGCACAACAGGA
*
52069 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAACAGGA
52089 TGCATCGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
*
52109 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAACAGGA
52129 TGCATCGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
* *
52149 TGCATCGATGCACAGCATGA
1 TGCATCGATGCACAACAGGA
* *
52169 TGCATCGATGCACATCAGTA
1 TGCATCGATGCACAACAGGA
*
52189 TGCATTGATGCAC
1 TGCATCGATGCAC
52202 TAAGTGCATT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 120 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:52109 original size:40 final size:40
Alignment explanation
Indices: 52049--52201 Score: 243
Period size: 40 Copynumber: 3.8 Consensus size: 40
52039 GCAGCCTTCG
* * *
52049 TGCATGGATACACAATAGGATGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAACAGGATGCATCGATGCACAGCAGGA
52089 TGCATCGATGCACAACAGGATGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAACAGGATGCATCGATGCACAGCAGGA
*
52129 TGCATCGATGCACAACAGGATGCATCGATGCACAGCATGA
1 TGCATCGATGCACAACAGGATGCATCGATGCACAGCAGGA
* * *
52169 TGCATCGATGCACATCAGTATGCATTGATGCAC
1 TGCATCGATGCACAACAGGATGCATCGATGCAC
52202 TAAGTGCATT
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (40 bp):
TGCATCGATGCACAACAGGATGCATCGATGCACAGCAGGA
Found at i:52268 original size:22 final size:23
Alignment explanation
Indices: 52235--52277 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52225 ATGGATGCAC
*
52235 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATACACTAG
*
52258 TGCA-GGTGCATGGATACACT
1 TGCATGGTGCATCGATACACT
52278 GCAAGGGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATACACTAG
Found at i:52545 original size:21 final size:21
Alignment explanation
Indices: 52521--52560 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52511 ATGTTTAATG
52521 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
52542 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
52561 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:53739 original size:19 final size:20
Alignment explanation
Indices: 53696--53743 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53686 TCTAAATCCT
*
53696 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
53716 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
53735 TTTTCAAAA
1 TTTTCAAAA
53744 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:55011 original size:328 final size:319
Alignment explanation
Indices: 54418--55065 Score: 1152
Period size: 328 Copynumber: 2.0 Consensus size: 319
54408 TTGCAAAGAG
*
54418 GGGTAGAAACGGTTTTTGAGTTTAGGGAGTAAGGAGATTGAAAGATAGAAAATTGTACAGCGATT
1 GGGTAGAAACGGTTTTTGAGTTTAGGGAGTAAGGAGATTGAAAGATAGAAAATTGTACAGAGATT
54483 TCGACTTTCTAAACCAAAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTTCCAACAAAT
66 TCGACTTTCTAAACCAAAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTTCCAACAAAT
*
54548 TCACTAATTTATTCTTTCTTTTGATGACAAATAGATAACCTTACAACTCCCTAGTTTTTCCGGTC
131 TCACTAATTTATTCTTTCTTTTGATGACAAAGAGATAACCTTACAACTCCCTAGTTTTTCCGGTC
54613 TAAACTAGAATCTTTCCCTAGCTTTTACACGAGATAAGCTAGAACCTTTCCTCTTTACAAAATGA
196 TAAACTAGAATCTTTCCCTAGCTTTTACACGAGATAAGCTAGAACCTTTCCTCTTTACAAAATGA
54678 TAAAATAAGTAAACAAGAAAACCTCTCTAAGGTAGGTGTTTACAAGATTGAGCTCACAA
261 TAAAATAAGTAAACAAGAAAACCTCTCTAAGGTAGGTGTTTACAAGATTGAGCTCACAA
*
54737 GGGTCGAAACGGTTTTTGAGTTTAGGGAGTAAGGAGATTGAAAGATAGAAAATTGCATAGCGATT
1 GGGTAGAAACGGTTTTTGAGTTTAGGGAGTAAGGAGATTGAAAGATAGAAAATTG--TA-C-A--
*
54802 TAGAGTGGTTCGACTTTCTAAACCAAAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTT
60 GAGA-T--TTCGACTTTCTAAACCAAAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTT
* *
54867 CCAACAAATTCACTAATTTGTTCTTTCTTTTGATGACAAAGAGATAACCTTACAACTCCCTATTT
122 CCAACAAATTCACTAATTTATTCTTTCTTTTGATGACAAAGAGATAACCTTACAACTCCCTAGTT
*
54932 TTTCCGGTCTAAACTAGAATCTTTCCCTATCTTTTACACGAGATAAGCTAGAACCTTTCCTCTTT
187 TTTCCGGTCTAAACTAGAATCTTTCCCTAGCTTTTACACGAGATAAGCTAGAACCTTTCCTCTTT
54997 ACAAAATGATAAAATAAGTAAACAAGAAAACCTCTCTAAGGTAGGTGTTTACAAGATTGAGCTCA
252 ACAAAATGATAAAATAAGTAAACAAGAAAACCTCTCTAAGGTAGGTGTTTACAAGATTGAGCTCA
55062 CAA
317 CAA
55065 G
1 G
55066 AATAAAATAT
Statistics
Matches: 313, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
319 54 0.17
321 2 0.01
322 1 0.00
323 1 0.00
325 2 0.01
326 1 0.00
328 252 0.81
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (319 bp):
GGGTAGAAACGGTTTTTGAGTTTAGGGAGTAAGGAGATTGAAAGATAGAAAATTGTACAGAGATT
TCGACTTTCTAAACCAAAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTTCCAACAAAT
TCACTAATTTATTCTTTCTTTTGATGACAAAGAGATAACCTTACAACTCCCTAGTTTTTCCGGTC
TAAACTAGAATCTTTCCCTAGCTTTTACACGAGATAAGCTAGAACCTTTCCTCTTTACAAAATGA
TAAAATAAGTAAACAAGAAAACCTCTCTAAGGTAGGTGTTTACAAGATTGAGCTCACAA
Found at i:55389 original size:20 final size:20
Alignment explanation
Indices: 55366--55411 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
55356 TCGTGCATGA
55366 ATGCACATCAGGATGCATCG
1 ATGCACATCAGGATGCATCG
*
55386 ATGCATATCAGGATGCATCG
1 ATGCACATCAGGATGCATCG
55406 ATGCAC
1 ATGCAC
55412 TAAGTGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
ATGCACATCAGGATGCATCG
Found at i:55456 original size:20 final size:20
Alignment explanation
Indices: 55431--55492 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 20
55421 TCGAATTGGA
*
55431 GTGCATGGATGCACTGCATG
1 GTGCATCGATGCACTGCATG
55451 GTGCATCGATGCACTAGTGCA-G
1 GTGCATCGATGCAC---TGCATG
55473 GTGCATCGATGCACTGCATG
1 GTGCATCGATGCACTGCATG
55493 CATGGGTGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 4 0.11
20 14 0.38
22 15 0.41
23 4 0.11
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (20 bp):
GTGCATCGATGCACTGCATG
Found at i:55478 original size:22 final size:23
Alignment explanation
Indices: 55445--55512 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 23
55435 ATGGATGCAC
55445 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
55468 TGCA-GGTGCATCGATGCACT-G
1 TGCATGGTGCATCGATGCACTAG
*
55489 CATGCATGGGTGCATGGATGCACT
1 --TGCAT-GGTGCATCGATGCACT
55513 TTGGCACCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.40
23 8 0.20
25 15 0.38
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:56031 original size:51 final size:51
Alignment explanation
Indices: 55919--56033 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 51
55909 AGTATTAGAT
* * * * * *
55919 TTATTGTTTCATTAGGAATTAAGGTAGATTTAAAATATTATTTTTAATTTA
1 TTATTGTTTTATTAGGAATTAAGATAGAATCAAAACATTATCTTTAATTTA
* * *
55970 TTATTATTTTATTAGGAATTATGATAGAATCAAAACATTATCTTTAGTTTA
1 TTATTGTTTTATTAGGAATTAAGATAGAATCAAAACATTATCTTTAATTTA
56021 TTATTGTTTTATT
1 TTATTGTTTTATT
56034 CAATAGTTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (51 bp):
TTATTGTTTTATTAGGAATTAAGATAGAATCAAAACATTATCTTTAATTTA
Found at i:56456 original size:14 final size:14
Alignment explanation
Indices: 56434--56470 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
56424 TTGTCTTTCT
56434 TTATCTTTATTATC
1 TTATCTTTATTATC
*
56448 TTATTTTTATTATC
1 TTATCTTTATTATC
56462 TTAATCTTT
1 TT-ATCTTT
56471 GTTCTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATCTTTATTATC
Found at i:59162 original size:3 final size:3
Alignment explanation
Indices: 59154--59188 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
59144 GCCCGGGGTT
*
59154 TTA TTA TTA TTA TTA TTA TAA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59189 ATAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:59212 original size:26 final size:26
Alignment explanation
Indices: 59157--59209 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
59147 CGGGGTTTTA
* *
59157 TTATTATTATTATTATAATTATTATT
1 TTATTAATAATATTATAATTATTATT
*
59183 TTATTAATAATATTTTAATTA-TATT
1 TTATTAATAATATTATAATTATTATT
59208 TT
1 TT
59210 TATAGGTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTAATAATATTATAATTATTATT
Done.