Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013452.1 Kokia drynarioides strain JFW-HI SEQ_128478, 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: 89534
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:5876 original size:30 final size:31
Alignment explanation
Indices: 5836--5897 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
5826 AAACATTTTT
* * *
5836 ACTTTTCCCCCAAAGCTTTTACT-TCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCTCATCCC
5866 ACTTTCCCCCCAAAACTTTTACTCTCATCCC
1 ACTTTCCCCCCAAAACTTTTACTCTCATCCC
5897 A
1 A
5898 TCCCACCCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.35
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCTCATCCC
Found at i:5907 original size:31 final size:30
Alignment explanation
Indices: 5842--5907 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
5832 TTTTACTTTT
* * **
5842 CCCCCAAAGCTTTTACTTCTTCCCACTTTC
1 CCCCCAAAACTTTTACTTCATCCCACTCCC
5872 CCCCCAAAACTTTTACTCTCATCCCA-TCCC
1 CCCCCAAAACTTTTACT-TCATCCCACTCCC
5902 ACCCCC
1 -CCCCC
5908 CATCTACCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.20, C:0.50, G:0.02, T:0.29
Consensus pattern (30 bp):
CCCCCAAAACTTTTACTTCATCCCACTCCC
Found at i:15126 original size:4 final size:4
Alignment explanation
Indices: 15117--15149 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
15107 CATAATTGCA
15117 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
15150 TAGTATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:16984 original size:19 final size:17
Alignment explanation
Indices: 16950--16998 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
16940 TTATTAAACG
16950 TTTTTATAATATCAAATTAAA
1 TTTTTAT-A-ATCAAA-T-AA
16971 TTTTTATAATCAAATAA
1 TTTTTATAATCAAATAA
16988 TATTTTATAAT
1 T-TTTTATAAT
16999 TTAAGCGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
19 6 0.22
20 1 0.04
21 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTATAATCAAATAA
Found at i:17942 original size:21 final size:22
Alignment explanation
Indices: 17905--17946 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17895 AACAAATGAG
*
17905 TTTAAAATTATTAAAATTATTT
1 TTTAAAATTAATAAAATTATTT
17927 TTTAAAA-TAATAAAATTATT
1 TTTAAAATTAATAAAATTATT
17947 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAAATTAATAAAATTATTT
Found at i:18815 original size:31 final size:31
Alignment explanation
Indices: 18777--18851 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
18767 ATTAAAATTA
18777 TTTAATAATTTTATTATT-TCAAAAAAATAAT
1 TTTAATAATTTTA-TATTCTCAAAAAAATAAT
* *
18808 TTTAATAATTTTATATTCTTAAAACAATAAT
1 TTTAATAATTTTATATTCTCAAAAAAATAAT
*
18839 TTTAATTATTTTA
1 TTTAATAATTTTA
18852 AAATCATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATTTTATATTCTCAAAAAAATAAT
Found at i:21919 original size:30 final size:30
Alignment explanation
Indices: 21885--21949 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
21875 GCTTATTTTA
* *
21885 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
*
21915 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
21945 TTGTT
1 TTGTT
21950 TGTTAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGGCAT
Found at i:27378 original size:9 final size:9
Alignment explanation
Indices: 27364--27393 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
27354 TTACTAATCT
27364 AAAATTTTA
1 AAAATTTTA
27373 AAAATTTTA
1 AAAATTTTA
*
27382 AAAGTTTTA
1 AAAATTTTA
27391 AAA
1 AAA
27394 GCCTAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (9 bp):
AAAATTTTA
Found at i:28712 original size:20 final size:21
Alignment explanation
Indices: 28689--28727 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28679 TTTTTTTAAT
*
28689 ATTTTTATA-AGTTTATATCA
1 ATTTTAATACAGTTTATATCA
*
28709 ATTTTAATACATTTTATAT
1 ATTTTAATACAGTTTATAT
28728 TTTTTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTTTAATACAGTTTATATCA
Found at i:28812 original size:50 final size:49
Alignment explanation
Indices: 28671--28813 Score: 177
Period size: 50 Copynumber: 2.9 Consensus size: 49
28661 CAATTCAAGT
28671 TTTTATTATTTTTTTAATATTTTTATAAGTTTATATC-AATTTTAATACA
1 TTTTA-TATTTTTTTAATATTTTTATAAGTTTATATCAAATTTTAATACA
** *
28720 TTTTATATTTTTTATGTTTTTTTTTATGAA-TTT-TAT-AGAATTTTAATACA
1 TTTTATATTTTTT-T-AATATTTTTAT-AAGTTTATATCA-AATTTTAATACA
28770 TTTTATATTTTTTTAATATTTTTATAAGTTTATATCAAAATTTT
1 TTTTATATTTTTTTAATATTTTTATAAGTTTATATC-AAATTTT
28814 TTTTTTTTGG
Statistics
Matches: 79, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
47 2 0.03
48 19 0.24
49 13 0.16
50 42 0.53
51 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (49 bp):
TTTTATATTTTTTTAATATTTTTATAAGTTTATATCAAATTTTAATACA
Found at i:29462 original size:22 final size:22
Alignment explanation
Indices: 29437--29505 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
29427 TAGTGCCTTT
*
29437 TTTTTTACTATTTTGGTTGTTG
1 TTTTTTACTGTTTTGGTTGTTG
* *
29459 TTTTTTATTGTTTTTG-TGTTG
1 TTTTTTACTGTTTTGGTTGTTG
29480 TTTTTTACTGTTTTGGTTGTTG
1 TTTTTTACTGTTTTGGTTGTTG
29502 TTTT
1 TTTT
29506 CGTGTTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 19 0.46
22 22 0.54
ACGTcount: A:0.06, C:0.03, G:0.19, T:0.72
Consensus pattern (22 bp):
TTTTTTACTGTTTTGGTTGTTG
Found at i:29479 original size:24 final size:23
Alignment explanation
Indices: 29437--29545 Score: 95
Period size: 21 Copynumber: 4.9 Consensus size: 23
29427 TAGTGCCTTT
*
29437 TTTTTTACTATTTTG-GTTGTTG
1 TTTTTTACTGTTTTGTGTTGTTG
*
29459 TTTTTTATTGTTTT-TG-TGTTG
1 TTTTTTACTGTTTTGTGTTGTTG
29480 TTTTTTACTGTTTTG-GTTGTTG
1 TTTTTTACTGTTTTGTGTTGTTG
* ** *
29502 TTTTCGTGTTGTTTTTGCTGTTATT-
1 TTTT-TTACTG-TTTTG-TGTTGTTG
29527 TTTTTTACTGTTTT-TGTTG
1 TTTTTTACTGTTTTGTGTTG
29546 CTATTTTGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
21 23 0.33
22 22 0.32
23 7 0.10
24 8 0.12
25 4 0.06
26 5 0.07
ACGTcount: A:0.06, C:0.05, G:0.19, T:0.71
Consensus pattern (23 bp):
TTTTTTACTGTTTTGTGTTGTTG
Found at i:29480 original size:11 final size:11
Alignment explanation
Indices: 29454--29529 Score: 66
Period size: 11 Copynumber: 6.9 Consensus size: 11
29444 CTATTTTGGT
29454 TGTTGTTTTT-
1 TGTTGTTTTTG
*
29464 TATTGTTTTTG
1 TGTTGTTTTTG
29475 TGTTGTTTTT-
1 TGTTGTTTTTG
** *
29485 TACTGTTTTGG
1 TGTTGTTTTTG
*
29496 TTGTTGTTTTCG
1 -TGTTGTTTTTG
29508 TGTTGTTTTTG
1 TGTTGTTTTTG
*
29519 CTGTTATTTTT
1 -TGTTGTTTTT
29530 TTTACTGTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
10 16 0.31
11 19 0.37
12 17 0.33
ACGTcount: A:0.04, C:0.04, G:0.21, T:0.71
Consensus pattern (11 bp):
TGTTGTTTTTG
Found at i:29494 original size:43 final size:47
Alignment explanation
Indices: 29437--29545 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 47
29427 TAGTGCCTTT
* *
29437 TTTTTTACTATTTTGGTTGTTGTTTT-TTATTGTTTTTG-TG-T-TG
1 TTTTTTACTGTTTTGGTTGTTGTTTTCGTATTGTTTTTGCTGTTATG
* *
29480 TTTTTTACTGTTTTGGTTGTTGTTTTCGTGTTGTTTTTGCTGTTATT
1 TTTTTTACTGTTTTGGTTGTTGTTTTCGTATTGTTTTTGCTGTTATG
*
29527 TTTTTTACTGTTTTTGTTG
1 TTTTTTACTGTTTTGGTTG
29546 CTATTTTGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 25 0.44
44 10 0.18
45 2 0.04
46 1 0.02
47 19 0.33
ACGTcount: A:0.06, C:0.05, G:0.19, T:0.71
Consensus pattern (47 bp):
TTTTTTACTGTTTTGGTTGTTGTTTTCGTATTGTTTTTGCTGTTATG
Found at i:29583 original size:23 final size:24
Alignment explanation
Indices: 29552--29609 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
29542 GTTGCTATTT
* *
29552 TGTTGTTTTTAATGGTGTTTTG-C
1 TGTTATTTTTAATGGTATTTTGAC
* * *
29575 TGTTATTTTTACTGTTATTTTGAT
1 TGTTATTTTTAATGGTATTTTGAC
29599 TGTTATTTTTA
1 TGTTATTTTTA
29610 TTGTTTGGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.14, C:0.03, G:0.17, T:0.66
Consensus pattern (24 bp):
TGTTATTTTTAATGGTATTTTGAC
Found at i:29612 original size:12 final size:12
Alignment explanation
Indices: 29575--29614 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
29565 GGTGTTTTGC
*
29575 TGTTATTTTTAC
1 TGTTATTTTTAT
*
29587 TGTTATTTTGAT
1 TGTTATTTTTAT
29599 TGTTATTTTTAT
1 TGTTATTTTTAT
29611 TGTT
1 TGTT
29615 TGGACGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.03, G:0.12, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTAT
Found at i:33566 original size:17 final size:17
Alignment explanation
Indices: 33544--33577 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
33534 ATTAGCAACA
33544 CCATCATTTCTTTCATT
1 CCATCATTTCTTTCATT
33561 CCATCATTTCTTTCATT
1 CCATCATTTCTTTCATT
33578 TTGGGTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (17 bp):
CCATCATTTCTTTCATT
Found at i:41654 original size:15 final size:15
Alignment explanation
Indices: 41634--41666 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41624 AATCTTTTAA
41634 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
41649 AAATTATTAAAAATT
1 AAATTATTAAAAATT
41664 AAA
1 AAA
41667 ATTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:57428 original size:31 final size:31
Alignment explanation
Indices: 57362--57449 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
57352 AATCATAAAA
* * **
57362 TGATACCTAAACTATAC-TCATTTTTCTAATT
1 TGATACCTAAACTATACTTCA-TTATCCAAAG
*
57393 TGATACCTAAACTATACTTCGTTATCCAAAG
1 TGATACCTAAACTATACTTCATTATCCAAAG
* **
57424 TGATACTTAAGTTATACTTCATTATC
1 TGATACCTAAACTATACTTCATTATC
57450 TAAATTACCC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 45 0.96
32 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (31 bp):
TGATACCTAAACTATACTTCATTATCCAAAG
Found at i:61394 original size:18 final size:18
Alignment explanation
Indices: 61373--61407 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61363 TATCTCACAT
*
61373 TTTAATATTATTATAATA
1 TTTAATATTATCATAATA
*
61391 TTTAATTTTATCATAAT
1 TTTAATATTATCATAAT
61408 CATTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATATTATCATAATA
Found at i:64536 original size:23 final size:24
Alignment explanation
Indices: 64508--64557 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
64498 AGTTTGACTC
64508 AAACAAATAAACAGAG-TTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
64531 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
64555 AAA
1 AAA
64558 GATTATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:69137 original size:19 final size:18
Alignment explanation
Indices: 69088--69139 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
69078 AAATTCACAT
*
69088 ATTTGACCTTTTATCAAC
1 ATTTTACCTTTTATCAAC
*
69106 ATTTTACATTTTTATCCTAA-
1 ATTTTAC-CTTTTAT-C-AAC
69126 ATTTTACCTTTTAT
1 ATTTTACCTTTTAT
69140 TCAATTTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 12 0.43
20 8 0.29
21 2 0.07
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTTTACCTTTTATCAAC
Found at i:70796 original size:3 final size:3
Alignment explanation
Indices: 70788--70827 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
70778 TTAAAATAGA
70788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
70828 GAAAAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:77464 original size:24 final size:24
Alignment explanation
Indices: 77418--77464 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
77408 AATAAAATCA
*
77418 TATAATTGAATATATTTACAAACT
1 TATAATTGAATATATTCACAAACT
* *
77442 TATAATTGAATATGTTCATAAAC
1 TATAATTGAATATATTCACAAAC
77465 AAATGTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (24 bp):
TATAATTGAATATATTCACAAACT
Found at i:83967 original size:2 final size:2
Alignment explanation
Indices: 83960--83987 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
83950 AAAGATTCTT
83960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83988 AAGAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85101 original size:31 final size:31
Alignment explanation
Indices: 85025--85119 Score: 86
Period size: 31 Copynumber: 3.0 Consensus size: 31
85015 ATTTAATAAT
* *
85025 ATAATAATTTGTCAATATAATTTATTATTTTA
1 ATAATAATTT-TTAATATAAATTATTATTTTA
*
85057 ATAA-AACTATTTAATATAGAATT-TTATTTTA
1 ATAATAA-TTTTTAATATA-AATTATTATTTTA
* * **
85088 ATAATAATTTTTAACATTAACAATTATTTTA
1 ATAATAATTTTTAATATAAATTATTATTTTA
85119 A
1 A
85120 ATTAAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
30 2 0.04
31 38 0.75
32 11 0.22
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (31 bp):
ATAATAATTTTTAATATAAATTATTATTTTA
Found at i:85129 original size:17 final size:18
Alignment explanation
Indices: 85096--85137 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
85086 TAATAATAAT
*
85096 TTTTAACATTAACAATTA
1 TTTTAACATTAAAAATTA
85114 TTTTAA-ATTAAAAATTA
1 TTTTAACATTAAAAATTA
85131 TTCTTAA
1 TT-TTAA
85138 TATTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTAACATTAAAAATTA
Found at i:87121 original size:16 final size:17
Alignment explanation
Indices: 87100--87131 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
87090 AGTATTGATT
87100 AATAAT-TTTTTTAGAA
1 AATAATATTTTTTAGAA
87116 AATAATATTTTTTAGA
1 AATAATATTTTTTAGA
87132 TAAACAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
AATAATATTTTTTAGAA
Found at i:87140 original size:18 final size:17
Alignment explanation
Indices: 87106--87140 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
87096 GATTAATAAT
*
87106 TTTTTTAGAAAATAATA
1 TTTTTTAGAAAACAATA
87123 TTTTTTAGATAAACAATA
1 TTTTTTAGA-AAACAATA
87141 ATTAAGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (17 bp):
TTTTTTAGAAAACAATA
Found at i:88725 original size:76 final size:76
Alignment explanation
Indices: 88599--88752 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
88589 GTGTGTGTCT
88599 CAGGTCTACATCTTTCAACAAACGCGCTTACAAGTATGGGATCCAATTTACACTCCTTACCTATA
1 CAGGTCTACATCTTTCAACAAACGCGCTTACAAGTATGGGATCCAATTTACACTCCTTACCTATA
88664 TGAGCCACGTG
66 TGAGCCACGTG
88675 CAGGTCTACATCTTTCAACAAACGCGCTTACAAGTATGGGATCCAATTTACACTCCTTACCTATA
1 CAGGTCTACATCTTTCAACAAACGCGCTTACAAGTATGGGATCCAATTTACACTCCTTACCTATA
88740 TGAGCCACGTG
66 TGAGCCACGTG
88751 CA
1 CA
88753 AAAATCTCAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (76 bp):
CAGGTCTACATCTTTCAACAAACGCGCTTACAAGTATGGGATCCAATTTACACTCCTTACCTATA
TGAGCCACGTG
Done.