Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015085.1 Kokia drynarioides strain JFW-HI SEQ_130129, 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: 897486
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 584 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:778586 original size:26 final size:25
Alignment explanation
Indices: 778533--778594 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
778523 TTAGGATAAG
* * *
778533 ATTCAGAGATTTTTTTTTTATACAAC
1 ATTCAGAGA-ATTTTTTTGAAACAAC
778559 ATTCAGAGAATTTTTTTGAAACATAC
1 ATTCAGAGAATTTTTTTGAAACA-AC
*
778585 ATTCAAAGAA
1 ATTCAGAGAA
778595 AATTTAAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (25 bp):
ATTCAGAGAATTTTTTTGAAACAAC
Found at i:781868 original size:33 final size:33
Alignment explanation
Indices: 781831--781897 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
781821 CAAAATGTGT
781831 AATAAAAGTAAACTTAAACAGATTTATAAACAA
1 AATAAAAGTAAACTTAAACAGATTTATAAACAA
781864 AATAAAAGTAAACTTAAACAGATTTATAAACAA
1 AATAAAAGTAAACTTAAACAGATTTATAAACAA
781897 A
1 A
781898 CCAATTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (33 bp):
AATAAAAGTAAACTTAAACAGATTTATAAACAA
Found at i:783449 original size:17 final size:17
Alignment explanation
Indices: 783417--783450 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
783407 CATAAGAGGG
**
783417 AAACCTTTTTCTTTAAA
1 AAACCTTTTTAATTAAA
783434 AAACCTTTTTAATTAAA
1 AAACCTTTTTAATTAAA
783451 TCAAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
AAACCTTTTTAATTAAA
Found at i:789910 original size:11 final size:13
Alignment explanation
Indices: 789894--789928 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
789884 TTGTAGATCC
789894 TTTTCTTTTT-A-
1 TTTTCTTTTTCAT
789905 TTTTCTTTTTCAT
1 TTTTCTTTTTCAT
789918 TTTTCTTTTTC
1 TTTTCTTTTTC
789929 CTATCCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.45
12 1 0.05
13 11 0.50
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTCAT
Found at i:800756 original size:18 final size:18
Alignment explanation
Indices: 800733--800771 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
800723 AATTTAAATG
* *
800733 ATAAATTTATTTTTAAAA
1 ATAAATTTAATTATAAAA
800751 ATAAATTTAATTATAAAA
1 ATAAATTTAATTATAAAA
800769 ATA
1 ATA
800772 TATAAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATTTAATTATAAAA
Found at i:802807 original size:36 final size:36
Alignment explanation
Indices: 802755--802858 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
802745 TGGTAAAAGA
* * *
802755 CATGACCTTTGGGTCAATAGGGAATAAAACGAGCAT
1 CATGACCTCTAGGTCAATAGGGAGTAAAACGAGCAT
* *
802791 CATGACCTCTATGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTCTAGGTCAATAGGGAGTAAAACGAGCAT
*
802827 TATGACCTCTAGGTCAATAGGGAGTAAAACGA
1 CATGACCTCTAGGTCAATAGGGAGTAAAACGA
802859 AATAACGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (36 bp):
CATGACCTCTAGGTCAATAGGGAGTAAAACGAGCAT
Found at i:808438 original size:7 final size:7
Alignment explanation
Indices: 808425--808478 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
808415 TTCGAAAAAA
808425 GTCAACG
1 GTCAACG
*
808432 ATCAACG
1 GTCAACG
808439 GTCAACG
1 GTCAACG
808446 GTCAACG
1 GTCAACG
*
808453 GTCAA-A
1 GTCAACG
*
808459 GTCGACG
1 GTCAACG
808466 GTCAACG
1 GTCAACG
*
808473 ATCAAC
1 GTCAAC
808479 TGTCGATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 4 0.10
7 35 0.90
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:808444 original size:14 final size:14
Alignment explanation
Indices: 808425--808478 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
808415 TTCGAAAAAA
808425 GTCAACGATCAACG
1 GTCAACGATCAACG
*
808439 GTCAACGGTCAACG
1 GTCAACGATCAACG
* *
808453 GTCAAAG-TCGACG
1 GTCAACGATCAACG
808466 GTCAACGATCAAC
1 GTCAACGATCAAC
808479 TGTCGATCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 11 0.32
14 23 0.68
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (14 bp):
GTCAACGATCAACG
Found at i:808468 original size:13 final size:14
Alignment explanation
Indices: 808433--808471 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
808423 AAGTCAACGA
*
808433 TCAACGGTCAACGG
1 TCAACGGTCAACAG
808447 TCAACGGTCAA-AG
1 TCAACGGTCAACAG
*
808460 TCGACGGTCAAC
1 TCAACGGTCAAC
808472 GATCAACTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (14 bp):
TCAACGGTCAACAG
Found at i:808564 original size:23 final size:23
Alignment explanation
Indices: 808538--808581 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
808528 GTCCAATTGG
808538 GTTATTGGGTCAAATGGGTTTGA
1 GTTATTGGGTCAAATGGGTTTGA
*
808561 GTTATTGGGTCAATTGGGTTT
1 GTTATTGGGTCAAATGGGTTT
808582 AAAGGGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.34, T:0.43
Consensus pattern (23 bp):
GTTATTGGGTCAAATGGGTTTGA
Found at i:808621 original size:22 final size:23
Alignment explanation
Indices: 808591--808645 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
808581 TAAAGGGTTA
* *
808591 TTGGATTTA-ATTTTTAAAGGAT
1 TTGGGTTTAGATTTTAAAAGGAT
* *
808613 TTGGGTTTAGGTTTTAAAAGGGT
1 TTGGGTTTAGATTTTAAAAGGAT
*
808636 TTGGGCTTAG
1 TTGGGTTTAG
808646 GCACAAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (23 bp):
TTGGGTTTAGATTTTAAAAGGAT
Found at i:808632 original size:23 final size:23
Alignment explanation
Indices: 808601--808646 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
808591 TTGGATTTAA
* *
808601 TTTTTAAAGGATTTGGGTTTAGG
1 TTTTAAAAGGATTTGGGCTTAGG
*
808624 TTTTAAAAGGGTTTGGGCTTAGG
1 TTTTAAAAGGATTTGGGCTTAGG
808647 CACAAGTTTA
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:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (23 bp):
TTTTAAAAGGATTTGGGCTTAGG
Found at i:812373 original size:36 final size:36
Alignment explanation
Indices: 812331--812433 Score: 143
Period size: 36 Copynumber: 2.9 Consensus size: 36
812321 GGTAACAGGC
* *
812331 ATGACCTTTAGGTCAATAGGGAGTAAAATGAGCATG
1 ATGACCTCTAGGTCAATAGGGAGTAAAACGAGCATG
** *
812367 ATGACCTCTAGGTCAATATAGAGTAAAACGAGCATT
1 ATGACCTCTAGGTCAATAGGGAGTAAAACGAGCATG
* *
812403 ATGACCTCTAGGTCAACAGGGAGTGAAACGA
1 ATGACCTCTAGGTCAATAGGGAGTAAAACGA
812434 ATAACAAACT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (36 bp):
ATGACCTCTAGGTCAATAGGGAGTAAAACGAGCATG
Found at i:814860 original size:22 final size:23
Alignment explanation
Indices: 814821--814873 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
814811 ATGAATACAA
* *
814821 ATAATTAAATGAAGACAATCAAAT
1 ATAATT-AATGAACACAATAAAAT
814845 ATAATTAAT-AACACAATAAAAT
1 ATAATTAATGAACACAATAAAAT
814867 ATAATTA
1 ATAATTA
814874 TAGTTATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 18 0.67
23 3 0.11
24 6 0.22
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (23 bp):
ATAATTAATGAACACAATAAAAT
Found at i:815214 original size:20 final size:20
Alignment explanation
Indices: 815191--815238 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
815181 AACAAATAAG
* * *
815191 ATAATAAATTAAATGTCAAA
1 ATAATAAACTAAATATAAAA
815211 ATAA-ACAACTAAATATAAAA
1 ATAATA-AACTAAATATAAAA
815231 ATAATAAA
1 ATAATAAA
815239 AAAAAAGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (20 bp):
ATAATAAACTAAATATAAAA
Found at i:817242 original size:34 final size:34
Alignment explanation
Indices: 817195--817261 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
817185 TTTTTTGTGC
*
817195 TGTAATACACAAAGCTGAATTTTAGTATTTGAAT
1 TGTAAAACACAAAGCTGAATTTTAGTATTTGAAT
*
817229 TGTAAAACCCAAAGCTGAATTTTAGTATTTGAA
1 TGTAAAACACAAAGCTGAATTTTAGTATTTGAA
817262 CTAGCAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (34 bp):
TGTAAAACACAAAGCTGAATTTTAGTATTTGAAT
Found at i:831848 original size:3 final size:3
Alignment explanation
Indices: 831840--831880 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
831830 ACCTACTTCT
831840 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
831881 TTACACTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:839753 original size:30 final size:30
Alignment explanation
Indices: 839719--839779 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
839709 AATTTTATCG
839719 ATTGAATAGTGAATTGAGTAGGAAGGATTA
1 ATTGAATAGTGAATTGAGTAGGAAGGATTA
839749 ATTGAATAGTGAATTGAGTAGGAAGGATTA
1 ATTGAATAGTGAATTGAGTAGGAAGGATTA
839779 A
1 A
839780 ATCGTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (30 bp):
ATTGAATAGTGAATTGAGTAGGAAGGATTA
Found at i:840828 original size:42 final size:42
Alignment explanation
Indices: 840717--840938 Score: 239
Period size: 42 Copynumber: 5.3 Consensus size: 42
840707 TGATGTATAA
* * * *
840717 AAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAATTTG-TAT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGAT-T
* * * * *
840759 AAATGAAAGACTCGTGACTCGGAATGAGCATGAGAATATGATT
1 AAA-GGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
* * * *
840802 AGAGGAAGACTCATGTTTCGGGATGAGAATGAGATTATGGTT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
** * *
840844 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGATTATGGTT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
** *
840886 AAAGGAAGACTCATGTCTTAGTATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
840928 AAAGGAAGACT
1 AAAGGAAGACT
840939 TATAACTCAA
Statistics
Matches: 153, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 120 0.78
43 32 0.21
44 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
Found at i:843196 original size:20 final size:20
Alignment explanation
Indices: 843171--843216 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
843161 TTTTCTCCCG
* *
843171 AAAAAATTTAAATTTAATTAA
1 AAAAAATTTAAA-ATAAATAA
*
843192 AAAAAAGTTAAAATAAATAA
1 AAAAAATTTAAAATAAATAA
843212 AAAAA
1 AAAAA
843217 TTTTGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAATTTAAAATAAATAA
Found at i:843626 original size:13 final size:13
Alignment explanation
Indices: 843589--843618 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
843579 TTTTTCTTGA
843589 AATTTCATTTTTT
1 AATTTCATTTTTT
*
843602 AATTTCCTTTTTT
1 AATTTCATTTTTT
843615 AATT
1 AATT
843619 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTCATTTTTT
Found at i:849476 original size:14 final size:15
Alignment explanation
Indices: 849448--849476 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
849438 GAAGGTATTG
849448 TTTAATTTATGTTTT
1 TTTAATTTATGTTTT
849463 TTTAATTT-TGTTTT
1 TTTAATTTATGTTTT
849477 AAAATAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTAATTTATGTTTT
Found at i:852857 original size:25 final size:24
Alignment explanation
Indices: 852803--852857 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
852793 TTGAATTATG
* * *
852803 TTTTATTTGATGTTTATACCTTTC
1 TTTTATTTGATGTATATACATTTA
*
852827 TCTTTATTTGATGTATATATATATTA
1 T-TTTATTTGATGTATATACAT-TTA
852853 TTTTA
1 TTTTA
852858 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.84
26 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (24 bp):
TTTTATTTGATGTATATACATTTA
Found at i:870968 original size:82 final size:82
Alignment explanation
Indices: 870831--870996 Score: 296
Period size: 82 Copynumber: 2.0 Consensus size: 82
870821 CATTTTTTTC
* * *
870831 ATGTCAGAACCTATGTGGTATTTTAAAGATTTATAGGGCTGTAAATCAAGTTTGAAAGAACGAAT
1 ATGTCAAAACCTATGTGGTATTTTAAAGATTTATAGGGCTGTAAATCAAGTTTGAAAAAACGAAC
870896 TTCTGTTCATATCGTTT
66 TTCTGTTCATATCGTTT
*
870913 ATGTCAAAACCTATGTGGTATTTTAAAGATTTATAGGGCTGTAAATCAAGTTTGAAAAAAGGAAC
1 ATGTCAAAACCTATGTGGTATTTTAAAGATTTATAGGGCTGTAAATCAAGTTTGAAAAAACGAAC
870978 TTCTGTTCATATCGTTT
66 TTCTGTTCATATCGTTT
870995 AT
1 AT
870997 TTATTTTTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (82 bp):
ATGTCAAAACCTATGTGGTATTTTAAAGATTTATAGGGCTGTAAATCAAGTTTGAAAAAACGAAC
TTCTGTTCATATCGTTT
Found at i:873602 original size:10 final size:12
Alignment explanation
Indices: 873585--873616 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
873575 CATGAAACAA
873585 TGAAAAAAAA-G
1 TGAAAAAAAAGG
873596 T-AAAAAAAAGG
1 TGAAAAAAAAGG
873607 TGAAAAAAAA
1 TGAAAAAAAA
873617 ATTTGGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 3 0.16
12 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
TGAAAAAAAAGG
Found at i:873737 original size:68 final size:68
Alignment explanation
Indices: 873660--873800 Score: 246
Period size: 68 Copynumber: 2.1 Consensus size: 68
873650 AACAAGGGAG
* * *
873660 AAAAAAGAGGGGATGAATGCAACAGAGAAATAAGAAGATGATGAAAAGGTGAAGAGGAAAAAAGT
1 AAAAAAGAGGGGATGAATGCAACAGAGAAAGAAGAAGAAGATGAAAAAGTGAAGAGGAAAAAAGT
873725 TAA
66 TAA
873728 AAAAAAGAGGGGATGAATGCAACAGAGAAAGAAGAAGAAGATGAAAAAGTGAAGAGGAAAAAAGT
1 AAAAAAGAGGGGATGAATGCAACAGAGAAAGAAGAAGAAGATGAAAAAGTGAAGAGGAAAAAAGT
*
873793 TCA
66 TAA
873796 AAAAA
1 AAAAA
873801 GGGGAGGAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.58, C:0.04, G:0.28, T:0.10
Consensus pattern (68 bp):
AAAAAAGAGGGGATGAATGCAACAGAGAAAGAAGAAGAAGATGAAAAAGTGAAGAGGAAAAAAGT
TAA
Found at i:877949 original size:2 final size:2
Alignment explanation
Indices: 877944--877970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
877934 TATAAATATA
877944 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
877971 TAAAATGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:881487 original size:21 final size:21
Alignment explanation
Indices: 881462--881520 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
881452 ATAGTGCAGA
881462 CTTCTACCGATACAAGTG-AT
1 CTTCTACCGATACAAGTGAAT
* *
881482 AGTTCTACTGATACAAGTGAAT
1 -CTTCTACCGATACAAGTGAAT
*
881504 CTTCTACCGACACAAGT
1 CTTCTACCGATACAAGT
881521 CTTACTTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (21 bp):
CTTCTACCGATACAAGTGAAT
Found at i:881725 original size:16 final size:18
Alignment explanation
Indices: 881690--881725 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
881680 TTTTAAATGA
881690 AATTAAATATTATGATTT
1 AATTAAATATTATGATTT
881708 AATTAAAT-TTAT-ATTT
1 AATTAAATATTATGATTT
881724 AA
1 AA
881726 ATAATTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTAAATATTATGATTT
Found at i:882278 original size:48 final size:46
Alignment explanation
Indices: 882219--882326 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 46
882209 AACTGCAAAT
*
882219 TATGTGGCTGTTTTCAGCAAATATGTGATGAGTTGT-CCACGATGTGAC
1 TATGTGACTGTTTTCAGCAAATATGTGATG-GTT-TACCACGATGTG-C
* * * *
882267 TATGTGACTGTTATCGGCAATTATGTGGTGGTTTACCCACGATGTGC
1 TATGTGACTGTTTTCAGCAAATATGTGATGGTTTA-CCACGATGTGC
*
882314 TATGTGACCGTTT
1 TATGTGACTGTTT
882327 GTCGATATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
46 1 0.02
47 15 0.29
48 35 0.69
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (46 bp):
TATGTGACTGTTTTCAGCAAATATGTGATGGTTTACCACGATGTGC
Found at i:890411 original size:55 final size:54
Alignment explanation
Indices: 890330--890445 Score: 155
Period size: 55 Copynumber: 2.1 Consensus size: 54
890320 AGTTTAATCA
* *
890330 TGTTTAAGTGCTTTTTATTCTCCTATTCTATTTCATATTTTAATAGAA-CTTAAT
1 TGTTTAAGTGCTTTTTATTCTCCTATTCTAATTCAGATTTTAATA-AAGCTTAAT
*
890384 TGTTCTAAGTG-TGTTTTATTCTTCTATTCTAATTCAGATTTTAATAAAGCTTAAT
1 TGTT-TAAGTGCT-TTTTATTCTCCTATTCTAATTCAGATTTTAATAAAGCTTAAT
*
890439 TATTTAA
1 TGTTTAA
890446 TTTGATTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
54 10 0.18
55 45 0.82
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (54 bp):
TGTTTAAGTGCTTTTTATTCTCCTATTCTAATTCAGATTTTAATAAAGCTTAAT
Found at i:893164 original size:17 final size:16
Alignment explanation
Indices: 893125--893176 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
893115 AACCAAAATA
* *
893125 CCATTAAAACTTATTAT
1 CCATTAAAACTTA-AAC
893142 CC-TTAAAAGCTTAAAC
1 CCATTAAAA-CTTAAAC
*
893158 CCATTAAAATTTAAAC
1 CCATTAAAACTTAAAC
893174 CCA
1 CCA
893177 ATACTCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (16 bp):
CCATTAAAACTTAAAC
Done.