Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005492.1 Kokia drynarioides strain JFW-HI SEQ_119553, 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: 102332
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:10005 original size:95 final size:95
Alignment explanation
Indices: 9842--10032 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
9832 GTTATTTAGA
*
9842 TCTGAAACCCATTTTTGTGTAAAAAACAAGAAAATTTCTCAAGGAAGCATGAACAAGATGCAAAG
1 TCTGAAACCCATTTTTGTGTAAAAAACAAGAAAATTTCTCAAGAAAGCATGAACAAGATGCAAAG
9907 TTTCAGAGATTCATGCTCACATTGAAGGGC
66 TTTCAGAGATTCATGCTCACATTGAAGGGC
9937 TCTGAAACCCATTTTTGTGTAAAAAACAAGAAAATTTCTCAAGAAAGCATGAACAAGATGCAAAG
1 TCTGAAACCCATTTTTGTGTAAAAAACAAGAAAATTTCTCAAGAAAGCATGAACAAGATGCAAAG
10002 TTTCAGAGATTCATGCTCACATTGAAGGGC
66 TTTCAGAGATTCATGCTCACATTGAAGGGC
10032 T
1 T
10033 TCCAAGCATA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (95 bp):
TCTGAAACCCATTTTTGTGTAAAAAACAAGAAAATTTCTCAAGAAAGCATGAACAAGATGCAAAG
TTTCAGAGATTCATGCTCACATTGAAGGGC
Found at i:29485 original size:19 final size:19
Alignment explanation
Indices: 29461--29517 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
29451 TTTTTTTCAC
29461 TTTAATAATATATAATTAT
1 TTTAATAATATATAATTAT
29480 TTTAAT--TATAT-ATTAT
1 TTTAATAATATATAATTAT
* * *
29496 ATTATATAACATATAAATAT
1 TTTA-ATAATATATAATTAT
29516 TT
1 TT
29518 CAAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
19 10 0.33
20 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATAATATATAATTAT
Found at i:29726 original size:14 final size:16
Alignment explanation
Indices: 29708--29740 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29698 CAAAAAAGTT
*
29708 AAAAA-GAAAAGGGAG
1 AAAAATGAAAAGAGAG
29723 AAAAATGAAAAGAGAG
1 AAAAATGAAAAGAGAG
29739 AA
1 AA
29741 GAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (16 bp):
AAAAATGAAAAGAGAG
Found at i:34612 original size:4 final size:4
Alignment explanation
Indices: 34605--34690 Score: 55
Period size: 4 Copynumber: 21.5 Consensus size: 4
34595 GACACTTTCT
* * * * * * *
34605 TACA TACA TACG TACA TGCA TATA TACA TACA CACA TTCT TACA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
34653 TACA TACT TATA CACA TTCT TACC TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
34691 TATATATGTT
Statistics
Matches: 57, Mismatches: 25, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (4 bp):
TACA
Found at i:34648 original size:28 final size:28
Alignment explanation
Indices: 34617--34690 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
34607 CATACATACG
*
34617 TACATGCATATATACATACACACATTCT
1 TACATGCATACATACATACACACATTCT
* *
34645 TACATGCATACATACTTATACACATTCT
1 TACATGCATACATACATACACACATTCT
* *
34673 TACCTACATACATACATA
1 TACATGCATACATACATA
34691 TATATATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (28 bp):
TACATGCATACATACATACACACATTCT
Found at i:36379 original size:14 final size:15
Alignment explanation
Indices: 36350--36380 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36340 TTAATAATGT
36350 AATTTTATTATTTTC
1 AATTTTATTATTTTC
36365 AATTTTATT-TTTTC
1 AATTTTATTATTTTC
36379 AA
1 AA
36381 CAACAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTATTATTTTC
Found at i:44684 original size:33 final size:33
Alignment explanation
Indices: 44637--44728 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
44627 AGGGTGCTGT
* *
44637 TGAGCAGGTAGTGGGTACTGCGGAT-GCTGCAGC
1 TGAGCAGGTGGTGGGTATTGCGG-TGGCTGCAGC
** **
44670 TGAGTTGGTGGTGGGTATTGCGGTGGCTGTTGC
1 TGAGCAGGTGGTGGGTATTGCGGTGGCTGCAGC
44703 TGAGCAGGTGGTGGGTATTGCGGTGG
1 TGAGCAGGTGGTGGGTATTGCGGTGG
44729 TTGCTGCGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
32 1 0.02
33 49 0.98
ACGTcount: A:0.12, C:0.12, G:0.48, T:0.28
Consensus pattern (33 bp):
TGAGCAGGTGGTGGGTATTGCGGTGGCTGCAGC
Found at i:46607 original size:19 final size:19
Alignment explanation
Indices: 46575--46613 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
46565 GGTATAATGA
* *
46575 TAAATTTAATTTTTGTTTT
1 TAAATTTAACTTTTATTTT
*
46594 TAAATTTGACTTTTATTTT
1 TAAATTTAACTTTTATTTT
46613 T
1 T
46614 TCAAATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (19 bp):
TAAATTTAACTTTTATTTT
Found at i:46652 original size:29 final size:31
Alignment explanation
Indices: 46616--46686 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
46606 TTATTTTTTC
*
46616 AAATCAAATTTTAC-TCAACGTTTT-AAAAA-
1 AAATCAAATTTGACATCAAC-TTTTCAAAAAG
46645 AAATCAAATTTGACTATCAACTTTTCAAAAAG
1 AAATCAAATTTGAC-ATCAACTTTTCAAAAAG
*
46677 ATATCAAATT
1 AAATCAAATT
46687 GATATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 13 0.36
30 4 0.11
31 10 0.28
32 9 0.25
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (31 bp):
AAATCAAATTTGACATCAACTTTTCAAAAAG
Found at i:47833 original size:31 final size:31
Alignment explanation
Indices: 47798--47858 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
47788 TATAAAATGA
*
47798 TTATTAAATTATTCAAAAGCTTTTGTTTAAG
1 TTATTAAATTATTCAAAAGCTTTTATTTAAG
* *
47829 TTATTAAATTATTCCAAAGTTTTTATTTAA
1 TTATTAAATTATTCAAAAGCTTTTATTTAA
47859 ATCACTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (31 bp):
TTATTAAATTATTCAAAAGCTTTTATTTAAG
Found at i:54758 original size:2 final size:2
Alignment explanation
Indices: 54751--54812 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
54741 AAAATAATAC
54751 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
54793 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
54813 TAAAATAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55694 original size:55 final size:55
Alignment explanation
Indices: 55609--55718 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
55599 ATCTATATTC
*
55609 AAAGGAAAAGTAATTCCTAGTCTTCGTATTTTTTGATAAATAATTCCAAAGTCAA
1 AAAGGAAAAGTAATTCCTAGTCTACGTATTTTTTGATAAATAATTCCAAAGTCAA
*
55664 AAAGGAAAAGTAATTCCTAGTCTACTTATTTTTTGATAAATAATTCCAAAGTCAA
1 AAAGGAAAAGTAATTCCTAGTCTACGTATTTTTTGATAAATAATTCCAAAGTCAA
55719 TAATAACTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (55 bp):
AAAGGAAAAGTAATTCCTAGTCTACGTATTTTTTGATAAATAATTCCAAAGTCAA
Found at i:65353 original size:243 final size:242
Alignment explanation
Indices: 64910--65360 Score: 689
Period size: 243 Copynumber: 1.9 Consensus size: 242
64900 AATTCTCACC
*
64910 AAAAAAGTCAATCAAATTCTTCAATTATAGATTTAAAATCAAAAGAGACAATGAGACAATAAAAT
1 AAAAAAGTCAATCAAATTCCTCAATTATAGATTTAAAATCAAAAGAGACAATGAGACAATAAAAT
***
64975 TACCCAAAAAAATGTAGAAATTCAAGCAATGAACAATAAAAAAACTCTAAAAACAAATAACAGTA
66 TAAAAAAAAAAATGTAGAAATTCAAGCAATGAACAATAAAAAAACTCTAAAAACAAATAACAGTA
* * *
65040 TAATAAAGTCCATCTCAAGTTTATAAAGTAAAAAAAAAGCTCACCTTTTGTTTTTCTAAAGAGAA
131 TAATAAAATCCATCTCAAGTTTATAAAGTAAAAAAAAAGCTCACCTCTTGTTTTTCCAAAGAGAA
65105 AAAAATTCAAAGAGGCAATAAGCTCTCCACGACAACAAAGTAATTCTT
196 AAAAA-TCAAAGAGGCAATAAGCTCTCCACGACAACAAAGTAATTCTT
65153 AAAAAAG-CTAATCAAATTCCTCAATTATAGATTTAAAATCAAAAGAGACAATGAGACAATAAAA
1 AAAAAAGTC-AATCAAATTCCTCAATTATAGATTTAAAATCAAAAGAGACAATGAGACAAT-AAA
*
65217 CTATCTAAAAAAAAAAATGTAGAAATTCAAGCAATGAACAATAAAAAAACT-TTAAAA-AAATGA
64 --AT-TAAAAAAAAAAATGTAGAAATTCAAGCAATGAACAATAAAAAAACTCTAAAAACAAAT-A
** * *
65280 A-AGTATAATAAAATCCATCTCAAGTTTATACGGT-ATAAAAAAGTTCACCTCTTGTTTTTCCAA
125 ACAGTATAATAAAATCCATCTCAAGTTTATAAAGTAAAAAAAAAGCTCACCTCTTGTTTTTCCAA
65343 AGAG-AAAAAATCAAAGAG
190 AGAGAAAAAAATCAAAGAG
65361 ACAACAAGTT
Statistics
Matches: 190, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
242 9 0.05
243 63 0.33
244 32 0.17
245 34 0.18
246 9 0.05
247 43 0.23
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (242 bp):
AAAAAAGTCAATCAAATTCCTCAATTATAGATTTAAAATCAAAAGAGACAATGAGACAATAAAAT
TAAAAAAAAAAATGTAGAAATTCAAGCAATGAACAATAAAAAAACTCTAAAAACAAATAACAGTA
TAATAAAATCCATCTCAAGTTTATAAAGTAAAAAAAAAGCTCACCTCTTGTTTTTCCAAAGAGAA
AAAAATCAAAGAGGCAATAAGCTCTCCACGACAACAAAGTAATTCTT
Found at i:73226 original size:4 final size:4
Alignment explanation
Indices: 73217--73247 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
73207 TTTTCATTAT
*
73217 ATAC ATAC ATAC ATAC ATAC ATAC ATCC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
73248 TGAAGCGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:74929 original size:39 final size:38
Alignment explanation
Indices: 74852--74968 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 38
74842 TTTTGGTACG
* ** **
74852 ATATTTTTATAATTTTTTGAACGAATTTTAT-ATTTTTT
1 ATATTTTCATAATTTTTTTTACG-ATTTTATAAAATTTT
74890 ATATTTTGCATAATTTTTTTTACGATTTTATAAAATTTT
1 ATATTTT-CATAATTTTTTTTACGATTTTATAAAATTTT
* *
74929 ATA-TTTCTATTATGATTTTTTACGATTTTTATTAAAATTT
1 ATATTTTC-ATAAT-TTTTTTTACGA-TTTTA-TAAAATTT
74969 AGTAATTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
37 1 0.02
38 21 0.32
39 31 0.47
40 5 0.08
41 8 0.12
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (38 bp):
ATATTTTCATAATTTTTTTTACGATTTTATAAAATTTT
Found at i:84954 original size:18 final size:18
Alignment explanation
Indices: 84919--84957 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
84909 AACTTAAACC
*
84919 ATAAAAAAAATATGAAAA
1 ATAAAAAAAAAATGAAAA
84937 ATAAAAAAATAAAT-AAAA
1 ATAAAAAAA-AAATGAAAA
84955 ATA
1 ATA
84958 TCTCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
ATAAAAAAAAAATGAAAA
Found at i:85443 original size:19 final size:20
Alignment explanation
Indices: 85411--85454 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
85401 ATCTACGTGT
* *
85411 ACTTTATATTATTT-TTTTA
1 ACTTTTTATAATTTGTTTTA
85430 ACTTTTTATAATTTGTTTTA
1 ACTTTTTATAATTTGTTTTA
85450 A-TTTT
1 ACTTTT
85455 GAATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (20 bp):
ACTTTTTATAATTTGTTTTA
Found at i:87519 original size:126 final size:127
Alignment explanation
Indices: 87294--87546 Score: 445
Period size: 126 Copynumber: 2.0 Consensus size: 127
87284 TCACATATAA
* * *
87294 TTGTCTTGTTATTTCATCAACAATGCCAATTTTTAATAGTAGAAATAAATGAATTTTTTAATAGA
1 TTGTCTTGTTATTTCATCAACAATGCCAAATTTTAATAGTAAAAATAAATGAAATTTTTAATAGA
* *
87359 AATGATCAATTTGCTATTTGATCCAAAATATAAAAACTAATTTACCCA-TTTTTAAGTAAAT
66 AATGATAAATTTGCTATTTAATCCAAAATATAAAAACTAATTTACCCATTTTTTAAGTAAAT
*
87420 TTGTCTTGTTATTTCATCAACAATGCCAAATTTTAATAGTAAAAATGAATGAAATTTTTAATAGA
1 TTGTCTTGTTATTTCATCAACAATGCCAAATTTTAATAGTAAAAATAAATGAAATTTTTAATAGA
87485 AATGATAAATTTGCTATTTAATCCAAAATATAAAAACTAATTTACCCATTTTTTAAGTAAAT
66 AATGATAAATTTGCTATTTAATCCAAAATATAAAAACTAATTTACCCATTTTTTAAGTAAAT
87547 AAGACAAAAC
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
126 107 0.89
127 13 0.11
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (127 bp):
TTGTCTTGTTATTTCATCAACAATGCCAAATTTTAATAGTAAAAATAAATGAAATTTTTAATAGA
AATGATAAATTTGCTATTTAATCCAAAATATAAAAACTAATTTACCCATTTTTTAAGTAAAT
Found at i:92848 original size:13 final size:13
Alignment explanation
Indices: 92830--92893 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 13
92820 CTTGTGTTTT
92830 ATTTTTTTATAAA
1 ATTTTTTTATAAA
*
92843 A-TTTTTAATAAA
1 ATTTTTTTATAAA
*
92855 TATTTTTTTA-ATA
1 -ATTTTTTTATAAA
* *
92868 ATTTTATTAT-AG
1 ATTTTTTTATAAA
92880 ATTTTTATTATAAA
1 ATTTTT-TTATAAA
92894 TGCTTTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
12 23 0.61
13 8 0.21
14 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTTTTTTATAAA
Found at i:100487 original size:3 final size:3
Alignment explanation
Indices: 100461--100502 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
100451 CTTAAAAGTG
* * *
100461 CTT CTG CTT CTG CTT CTG CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
100503 GTATTTAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:100502 original size:12 final size:12
Alignment explanation
Indices: 100461--100501 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
100451 CTTAAAAGTG
*
100461 CTTCTGCTTCTG
1 CTTCTGCTTCTT
100473 CTTCTGCTTCTT
1 CTTCTGCTTCTT
*
100485 CTTCTTCTTCTT
1 CTTCTGCTTCTT
100497 CTTCT
1 CTTCT
100502 TGTATTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.59
Consensus pattern (12 bp):
CTTCTGCTTCTT
Found at i:101094 original size:12 final size:12
Alignment explanation
Indices: 101076--101105 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
101066 GAATACCCAA
101076 AGAGAGGGAGAG
1 AGAGAGGGAGAG
*
101088 GGAGAGGGAGAG
1 AGAGAGGGAGAG
101100 AGAGAG
1 AGAGAG
101106 AGAAGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
AGAGAGGGAGAG
Found at i:101962 original size:4 final size:4
Alignment explanation
Indices: 101953--102004 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
101943 AAATAAACGG
* * * *
101953 GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
102001 GAAA
1 GAAA
102005 AGTAATGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 3 0.08
4 33 0.82
5 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:101985 original size:17 final size:15
Alignment explanation
Indices: 101953--102004 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
101943 AAATAAACGG
*
101953 GAAAGAAAGAAAGAAA
1 GAAAG-AAGAAGGAAA
*
101969 GGAAGAAGGAGAGGAAA
1 GAAAGAA-GA-AGGAAA
101986 GAAAGAAGAAGGAAA
1 GAAAGAAGAAGGAAA
102001 GAAA
1 GAAA
102005 AGTAATGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 12 0.39
16 8 0.26
17 11 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAGAAGGAAA
Found at i:102006 original size:20 final size:20
Alignment explanation
Indices: 101957--102004 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
101947 AAACGGGAAA
101957 GAAAGAAAGAAAGGAAGAAG
1 GAAAGAAAGAAAGGAAGAAG
*
101977 GAGAGGAAAGAAA-GAAGAAG
1 GA-AAGAAAGAAAGGAAGAAG
101997 GAAAGAAA
1 GAAAGAAA
102005 AGTAATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAGGAAGAAG
Done.