Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015158.1 Kokia drynarioides strain JFW-HI SEQ_130202, 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: 45499
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 154 characters in sequence are not A, C, G, or T
Found at i:7400 original size:22 final size:24
Alignment explanation
Indices: 7341--7386 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
7331 AGCATTTTGT
*
7341 TAAAAAATAATAA-TCAAATTAAAC
1 TAAAAAATAAAAACTC-AATTAAAC
7365 TAAAAAATAAAAACTCAATTAA
1 TAAAAAATAAAAACTCAATTAA
7387 CAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAAAAATAAAAACTCAATTAAAC
Found at i:9471 original size:27 final size:27
Alignment explanation
Indices: 9438--9493 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
9428 TAAAGACTTA
9438 AAACCAGTTTGAAAATAATGAAAATGT
1 AAACCAGTTTGAAAATAATGAAAATGT
9465 AAACCAGTTTGAAAATAATGAAAATGT
1 AAACCAGTTTGAAAATAATGAAAATGT
9492 AA
1 AA
9494 TTTTTACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (27 bp):
AAACCAGTTTGAAAATAATGAAAATGT
Found at i:10513 original size:6 final size:6
Alignment explanation
Indices: 10488--10526 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
10478 ACAATTCATA
* * *
10488 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
10527 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:20188 original size:27 final size:27
Alignment explanation
Indices: 20149--20208 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
20139 AACTTTCAAC
* *
20149 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCATCTTCT
*
20177 TAATATTGTTTCTTTTGATCATCTTCT
1 TAATATTGTTTCCTTTGATCATCTTCT
20204 TAATA
1 TAATA
20209 AAATTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.57
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCATCTTCT
Found at i:21310 original size:199 final size:199
Alignment explanation
Indices: 20841--21365 Score: 613
Period size: 201 Copynumber: 2.6 Consensus size: 199
20831 AGTAATAAAG
* * * *
20841 GTTAGCTTCTTGATGAGATACTGAGGAGTCAACCAAATTTGCCTTCCTGATGAGATACA-AAGAA
1 GTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAA-AA
* * *
20905 GCGAGTTGAAACAAATGACG-CGG-TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
65 GCGAATTGAAACAAAAG-CGATGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
*
20968 GGCTCAAAGTGAGCAAAATCTTCGAACCCCAACTTCTTGATGAGACACTGAGAAGCAGATCAAAG
129 GGCTCAAAATGAGCAAAATCTTCGAACCCCAACTTCTTGATGAGA-AC-GAGAA-CAGATCAAAG
21033 AGATAAAAC
191 AGATAAAAC
* **
21042 GTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAG
1 GTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAAG
* * * *
21107 CGAATTGAAACAAACAGCGATGTGATCATCTTCTTGATGAGGCACTGAGAAGAAGTCTCAAACGA
66 CGAATTGAAACAAA-AGCGATG-GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
* * ** *
21172 GGCTCAAAATGAGCAAAAATCTTCGAACCCCAGCTTCTTGATTGAG-A-G-GCA-AG-TTGAGGC
129 GGCTCAAAATGAGC-AAAATCTTCGAACCCCAACTTCTTGA-TGAGAACGAGAACAGATCAAAG-
*
21232 A-ATAAAAT
191 AGATAAAAC
* * * *
21240 GATTAGCTTCTTGAGGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAAAA
1 G-TTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAA
* * *
21305 GCGAATTGAAAC-AAA-CGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAAC
65 GCGAATTGAAACAAAAGCGATGGA-TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAC
21366 AAACCCACGC
Statistics
Matches: 279, Mismatches: 35, Indels: 25
0.82 0.10 0.07
Matches are distributed among these distances:
195 1 0.00
196 37 0.13
197 1 0.00
198 12 0.04
199 71 0.25
201 73 0.26
202 4 0.01
203 1 0.00
204 50 0.18
205 25 0.09
206 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (199 bp):
GTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAAG
CGAATTGAAACAAAAGCGATGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGG
CTCAAAATGAGCAAAATCTTCGAACCCCAACTTCTTGATGAGAACGAGAACAGATCAAAGAGATA
AAAC
Found at i:21393 original size:199 final size:196
Alignment explanation
Indices: 20841--21416 Score: 621
Period size: 199 Copynumber: 2.9 Consensus size: 196
20831 AGTAATAAAG
* * * *
20841 GTTAGCTTCTTGATGAGATACTGAGGAGTCAACCAAATTTGCCTTCCTGATGAGATACA-AAGAA
1 GTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAA-AA
* * * *
20905 GCGAGTTGAAACAAATGACGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGG
65 GCGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGG
*
20970 CTCAAAGTGAGCAAAATCTTCGAACCCCAACTTCTTGATGAGACACTGAGAAGCAGATCAAAGAG
130 CTCAAA-TGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAG--AC-GAGAA-CAGATCAAAGAG
21035 ATAAAAC
190 ATAAAAC
* **
21042 GTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAG
1 GTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAAG
* * * * *
21107 CGAATTGAAACAAACAGCGATG-TGATCATCTTCTTGATGAGGCACTGAGAAGAAGTCTCAAACG
66 CGAATTGAAAC-AA-A-CGATGCAG-TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACG
* ** *
21171 AGGCTCAAAATGAGCAAAAATCTTCGAACCCCAGCTTCTTGATTGAGA-G-GCA-AG-TTGAGGC
127 AGGCTC-AAATGAGC-AAAATCTTCGAACCCCAGCTTCTTGA-TGAGACGAGAACAGATCAAAG-
*
21232 A-ATAAAAT
188 AGATAAAAC
* * * *
21240 GATTAGCTTCTTGAGGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAAAA
1 G-TTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAA
*
21305 GCGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAACAAAC
65 GCGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACC----CAAA-
* * *
21370 CCACGCTCGATATGAGC-AAATCTTCGAACCCCAG-TATCTTGATGAGA
125 CGAGGCTC-AAATGAGCAAAATCTTCGAACCCCAGCT-TCTTGATGAGA
21417 TATTGGGAAG
Statistics
Matches: 320, Mismatches: 38, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
196 33 0.10
197 2 0.01
198 18 0.06
199 94 0.29
200 4 0.01
201 81 0.25
202 4 0.01
203 2 0.01
204 50 0.16
205 28 0.09
206 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (196 bp):
GTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAAG
CGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGC
TCAAATGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGACGAGAACAGATCAAAGAGATAAAA
C
Found at i:21836 original size:17 final size:17
Alignment explanation
Indices: 21805--21880 Score: 109
Period size: 17 Copynumber: 4.5 Consensus size: 17
21795 CTATTGGAAA
21805 TTAAATTTA-TTTAAAT
1 TTAAATTTATTTTAAAT
*
21821 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
21838 TTAAATTTATTTGAAAT
1 TTAAATTTATTTTAAAT
* *
21855 TTAAATTTATTATAAAA
1 TTAAATTTATTTTAAAT
21872 TTAAATTTA
1 TTAAATTTA
21881 GAAAGTCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 8 0.15
17 45 0.85
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:21856 original size:7 final size:6
Alignment explanation
Indices: 21805--21880 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
21795 CTATTGGAAA
* *
21805 TTAAAT TT--AT TTAAAT TTAAGT TT-ATT TTAAAT TTAAAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
21848 TTGAAAT TTAAAT TT--AT TATAAAA TTAAAT TTA
1 TT-AAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTA
21881 GAAAGTCCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
4 11 0.20
5 5 0.09
6 34 0.61
7 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:21864 original size:34 final size:33
Alignment explanation
Indices: 21802--21880 Score: 122
Period size: 34 Copynumber: 2.4 Consensus size: 33
21792 GACCTATTGG
* *
21802 AAATTAAATTTATTTAAATTTAAGTTTATTTTA
1 AAATTAAATTTATTTAAATTTAAATTTATTATA
*
21835 AATTTAAATTTATTTGAAATTTAAATTTATTATA
1 AAATTAAATTTATTT-AAATTTAAATTTATTATA
21869 AAATTAAATTTA
1 AAATTAAATTTA
21881 GAAAGTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 14 0.34
34 27 0.66
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (33 bp):
AAATTAAATTTATTTAAATTTAAATTTATTATA
Found at i:21934 original size:15 final size:15
Alignment explanation
Indices: 21914--21992 Score: 122
Period size: 15 Copynumber: 5.3 Consensus size: 15
21904 AAACAAAGTA
21914 CAATTACAAATGGCC
1 CAATTACAAATGGCC
*
21929 CAATTACAAACGGCC
1 CAATTACAAATGGCC
*
21944 CAATTACAAATGGAC
1 CAATTACAAATGGCC
*
21959 CAAGTACAAATGGCC
1 CAATTACAAATGGCC
*
21974 CAATTACAAACGGCC
1 CAATTACAAATGGCC
21989 CAAT
1 CAAT
21993 GGCCCAAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (15 bp):
CAATTACAAATGGCC
Found at i:22621 original size:16 final size:15
Alignment explanation
Indices: 22600--22653 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
22590 TTAATGACTA
22600 TTAATAATAAATGTTT
1 TTAATAATAAAT-TTT
*
22616 TTAATAAT--A-TTA
1 TTAATAATAAATTTT
*
22628 ATAATAATAAATATTT
1 TTAATAATAAAT-TTT
22644 TTAATAATAA
1 TTAATAATAA
22654 TAAATAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 9 0.30
14 2 0.07
16 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAATAATAAATTTT
Found at i:22640 original size:19 final size:19
Alignment explanation
Indices: 22618--22675 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
22608 AAATGTTTTT
22618 AATAATATTAATAATAATA
1 AATAATATTAATAATAATA
* *
22637 AATATTTTTAATAATAATA
1 AATAATATTAATAATAATA
* *
22656 AATAACATT-TTAATAATA
1 AATAATATTAATAATAATA
22674 AA
1 AA
22676 AAAAAAGGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATATTAATAATAATA
Found at i:22651 original size:22 final size:21
Alignment explanation
Indices: 22625--22674 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
22615 TTTAATAATA
*
22625 TTAATAATAATAAAT-A-TTT
1 TTAATAATAATAAATAACATT
22644 TTAATAATAATAAATAACATT
1 TTAATAATAATAAATAACATT
22665 TTAATAATAA
1 TTAATAATAA
22675 AAAAAAAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 15 0.54
20 1 0.04
21 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATAATAATAAATAACATT
Found at i:23761 original size:59 final size:59
Alignment explanation
Indices: 23686--23925 Score: 292
Period size: 59 Copynumber: 4.1 Consensus size: 59
23676 CGTGTCATCT
* * * *
23686 TTTTTACCCTTCAACTTCTAAAAATCCTATTTTTTACCCTGAAACTTCCAAAAATTCCA
1 TTTTTACCCCTAAACTTCCAAAAATCCTATTTTTTACCCCGAAACTTCCAAAAATTCCA
* *
23745 TTTTTACCCCTAAACTTCCAAAAATCCTATTTTTTACCTCGAAACTTTCAAAAA-TCCTA
1 TTTTTACCCCTAAACTTCCAAAAATCCTATTTTTTACCCCGAAACTTCCAAAAATTCC-A
* * *
23804 TTTTTGACCCCAAAACTTCCAAAAATTCC-A-TTTATACCCCCG-AACTTCCAAAAATCCCA
1 TTTTT-ACCCCTAAACTTCCAAAAA-TCCTATTTTTTA-CCCCGAAACTTCCAAAAATTCCA
* * *
23863 TTTTGACCTCGAAACTTCCAAAAAT-CTCATTTTTTACCCCGAAACTTCCAAAAATTCCA
1 TTTTTACCCCTAAACTTCCAAAAATCCT-ATTTTTTACCCCGAAACTTCCAAAAATTCCA
23922 TTTT
1 TTTT
23926 ATCCCCGAAT
Statistics
Matches: 156, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
56 1 0.01
57 1 0.01
58 26 0.17
59 100 0.64
60 25 0.16
61 3 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
TTTTTACCCCTAAACTTCCAAAAATCCTATTTTTTACCCCGAAACTTCCAAAAATTCCA
Found at i:23931 original size:29 final size:29
Alignment explanation
Indices: 23698--23953 Score: 249
Period size: 30 Copynumber: 8.7 Consensus size: 29
23688 TTTACCCTTC
* * *
23698 AACTTCTAAAAATCCTATTTTTTACCCTGA
1 AACTTCCAAAAATCC-ATTTTATACCCCGA
*
23728 AACTTCCAAAAATTCCATTTT-TACCCCTA
1 AACTTCCAAAAA-TCCATTTTATACCCCGA
* *
23757 AACTTCCAAAAATCCTATTTTTTACCTCGA
1 AACTTCCAAAAATCC-ATTTTATACCCCGA
* *
23787 AACTTTCAAAAATCCTATTTT-TGACCCCAA
1 AACTTCCAAAAATCC-ATTTTAT-ACCCCGA
23817 AACTTCCAAAAATTCCA-TTTATACCCCCG-
1 AACTTCCAAAAA-TCCATTTTATA-CCCCGA
* *
23846 AACTTCCAAAAATCCCATTTT-GACCTCGA
1 AACTTCCAAAAAT-CCATTTTATACCCCGA
*
23875 AACTTCCAAAAATCTCATTTTTTACCCCGA
1 AACTTCCAAAAATC-CATTTTATACCCCGA
23905 AACTTCCAAAAATTCCATTTTAT-CCCCG-
1 AACTTCCAAAAA-TCCATTTTATACCCCGA
23933 AA-TGTCCAAAAACTCCATTTT
1 AACT-TCCAAAAA-TCCATTTT
23954 TGACCTCAAA
Statistics
Matches: 196, Mismatches: 16, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.01
28 27 0.14
29 68 0.35
30 92 0.47
31 8 0.04
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATCCATTTTATACCCCGA
Found at i:23984 original size:58 final size:57
Alignment explanation
Indices: 23705--23988 Score: 167
Period size: 59 Copynumber: 4.9 Consensus size: 57
23695 TTCAACTTCT
* ** *
23705 AAAAATC-CTATTTTTTACCCTGAAACTTCCAAAAATTCCATTTTTACCCCTAAACT-TCC
1 AAAAATCTC-ATTTTTGACCCCAAAACTTCCAAAAATTCCA-TTTTACCCC-GAA-TGTCC
* * * * *
23764 AAAAATC-CTATTTTTTACCTCGAAACTTTCAAAAA-TCCTATTTTTGACCCCAAAACT-TCC
1 AAAAATCTC-ATTTTTGACCCCAAAACTTCCAAAAATTCC-A-TTTT-ACCCC-GAA-TGTCC
* ** * *
23824 AAAAAT-TCCATTTAT-ACCCCCGAACTTCCAAAAATCCCATTTTGACCTCGAAACT-TCC
1 AAAAATCT-CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTT-ACCCCG-AA-TGTCC
* *
23882 AAAAATCTCATTTTTTACCCCGAAACTTCCAAAAATTCCATTTTATCCCCGAATGTCC
1 AAAAATCTCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTA-CCCCGAATGTCC
* *
23940 AAAAA-CTCCATTTTTGACCTCAAAAC-TCTC-AAAATTACCCTTTTACCCC
1 AAAAATCT-CATTTTTGACCCCAAAACTTC-CAAAAATT-CCATTTTACCCC
23989 TAAATGTTTA
Statistics
Matches: 191, Mismatches: 21, Indels: 28
0.80 0.09 0.12
Matches are distributed among these distances:
57 15 0.08
58 65 0.34
59 84 0.44
60 26 0.14
61 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (57 bp):
AAAAATCTCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTACCCCGAATGTCC
Found at i:27581 original size:20 final size:20
Alignment explanation
Indices: 27541--27577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27531 ACATATTCCA
*
27541 TTTATGCTTGTTGTTATTAT
1 TTTATACTTGTTGTTATTAT
27561 TTTATACTTGTT-TTATT
1 TTTATACTTGTTGTTATT
27578 TATTATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (20 bp):
TTTATACTTGTTGTTATTAT
Found at i:36285 original size:14 final size:13
Alignment explanation
Indices: 36265--36299 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
36255 TTTTTAAATA
36265 ATAATATATTGTTT
1 ATAATATATT-TTT
*
36279 TTAATATATTTTT
1 ATAATATATTTTT
36292 ATAATATA
1 ATAATATA
36300 ATTACATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
ATAATATATTTTT
Found at i:39407 original size:62 final size:62
Alignment explanation
Indices: 39305--39451 Score: 215
Period size: 62 Copynumber: 2.4 Consensus size: 62
39295 ACATCTGATA
* * *
39305 ACTCACGATGACATAGAGTCATCGGACCTTAAATTCGTAATAGGATTCATTTCTCATTTACT
1 ACTCACGATGACATAAAGTCATCGGACCTTAAATTCGTAATAGGATCCATTTCTCATTTAAT
* *
39367 ACTCACGATGACATAAAGTCATCTGACCTTTAA-TCTGTAATAGGATCCATTTCTCATTTAAT
1 ACTCACGATGACATAAAGTCATCGGACCTTAAATTC-GTAATAGGATCCATTTCTCATTTAAT
* *
39429 ACTCACGATGACACATAGTCATC
1 ACTCACGATGACATAAAGTCATC
39452 AGATCTCAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
61 2 0.03
62 75 0.97
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (62 bp):
ACTCACGATGACATAAAGTCATCGGACCTTAAATTCGTAATAGGATCCATTTCTCATTTAAT
Found at i:39540 original size:52 final size:51
Alignment explanation
Indices: 39462--39655 Score: 280
Period size: 52 Copynumber: 3.7 Consensus size: 51
39452 AGATCTCAAG
* * * *
39462 GATTCATATACTCACGATAACACATAGTCATCAGACCTCATAATATGTAAAT
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAAT-TATAAAA
*
39514 GATTCATATACTCACGATGACACATAGTCAACGGACCTCATAATTCATAAAA
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATT-ATAAAA
* * *
39566 GATTCATACACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAG
1 GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAAT-TATAAAA
*
39618 GATTCATATACTCACGATGACACATAGTCATCGAACCT
1 GATTCATATACTCACGATGACACATAGTCATCGGACCT
39656 TTGTCATTTA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
51 1 0.01
52 128 0.99
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (51 bp):
GATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATTATAAAA
Found at i:40146 original size:19 final size:19
Alignment explanation
Indices: 40122--40170 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
40112 ACAAATTTAT
40122 TCCTTTAACATCATATTAG
1 TCCTTTAACATCATATTAG
40141 TCCTTTAACATCATATTAG
1 TCCTTTAACATCATATTAG
40160 TCCTTTAACAT
1 TCCTTTAACAT
40171 AAAAATTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (19 bp):
TCCTTTAACATCATATTAG
Done.