Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013150.1 Kokia drynarioides strain JFW-HI SEQ_128169, 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: 32169
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:3496 original size:58 final size:59
Alignment explanation
Indices: 3291--3692 Score: 338
Period size: 58 Copynumber: 7.0 Consensus size: 59
3281 AGAAAGTTTA
* * * *
3291 TGTCGGTCAATGCATGACCAACAC---CAAAATTTTTTTTTATCTGATAAAAAAGGTGA
1 TGTCGGCCAATGCATGACCAACACAAAAAAAAATTTTTTTTATCTGATAAAAAAGGTGG
* * *
3347 TGTAGGCTAATGCATGACCAACACAAAAAAAAAATTGTTCTTTTATTTGATAAAAAAGGTGG
1 TGTCGGCCAATGCATGACCAACAC-AAAAAAAAATT-TT-TTTTATCTGATAAAAAAGGTGG
* * * * * * *
3409 TATCAGCCAA-GCATTGACTAACAC-CAAAAAAATTATTTTTATCTGAT-AAAAAGATAG
1 TGTCGGCCAATGCA-TGACCAACACAAAAAAAAATTTTTTTTATCTGATAAAAAAGGTGG
* *
3466 TGTCGGTCAATGCATGGCCAACACAAAAAAAAATTGTTTTTTTAT-TAGATAAAAAAGGTGG
1 TGTCGGCCAATGCATGACCAACACAAAAAAAAA-T-TTTTTTTATCT-GATAAAAAAGGTGG
** * * *
3527 TGTCGGCCAA-GCATTGACCAACA-TGAAAAAAATATTTTTTATTTGATAAAAAAAGTGG
1 TGTCGGCCAATGCA-TGACCAACACAAAAAAAAATTTTTTTTATCTGATAAAAAAGGTGG
* * *
3585 TGTCGACCAATGCATGACCAACAC------AAATTTTTTTTATCAGATAAAAAAGGTTG
1 TGTCGGCCAATGCATGACCAACACAAAAAAAAATTTTTTTTATCTGATAAAAAAGGTGG
* * **
3638 TGTCGGCCAA-GCATTGGCCAACAC--CAAAATTTTTTTTTTATCTGAT-AAAAAGGTG
1 TGTCGGCCAATGCA-TGACCAACACAAAAAAAAATTTTTTTTATCTGATAAAAAAGGTG
3693 TTGGCCAACA
Statistics
Matches: 280, Mismatches: 44, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
52 3 0.01
53 42 0.15
56 29 0.10
57 38 0.14
58 59 0.21
59 8 0.03
60 36 0.13
61 30 0.11
62 35 0.12
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (59 bp):
TGTCGGCCAATGCATGACCAACACAAAAAAAAATTTTTTTTATCTGATAAAAAAGGTGG
Found at i:3518 original size:118 final size:116
Alignment explanation
Indices: 3291--3689 Score: 410
Period size: 118 Copynumber: 3.5 Consensus size: 116
3281 AGAAAGTTTA
* * * * *
3291 TGTCGGTCAATGCA-TGACCAACACC--AAAATTTTTTTTTATCTGATAAAAAAGGTGATGTAGG
1 TGTCGGCCAA-GCATTGACCAACACCAAAAAAATTATTTTTATCTGAT-AAAAAGATG-TGTCGG
* *
3353 CTAATGCATGACCAACACAAAAAAAAAATTGTTCTTTTATTTGATAAAAAAGGTGG
63 C-AATGCATGACCAACAC-AAAAAAAAATTGTTTTTTTATTAGATAAAAAAGGTGG
* * *
3409 TATCAGCCAAGCATTGACTAACACCAAAAAAATTATTTTTATCTGATAAAAAGATAGTGTCGGTC
1 TGTCGGCCAAGCATTGACCAACACCAAAAAAATTATTTTTATCTGATAAAAAGAT-GTGTCGG-C
*
3474 AATGCATGGCCAACACAAAAAAAAATTGTTTTTTTATTAGATAAAAAAGGTGG
64 AATGCATGACCAACACAAAAAAAAATTGTTTTTTTATTAGATAAAAAAGGTGG
** * *
3527 TGTCGGCCAAGCATTGACCAACATGAAAAAAA-TATTTTTTATTTGATAAAAAAAGTGGTGTCGA
1 TGTCGGCCAAGCATTGACCAACACCAAAAAAATTA-TTTTTATCTGATAAAAAGA-T-GTGTCG-
* * *
3591 CCAATGCATGACCAACAC------AAA-T-TTTTTTTATCAGATAAAAAAGGTTG
62 GCAATGCATGACCAACACAAAAAAAAATTGTTTTTTTATTAGATAAAAAAGGTGG
* ** *
3638 TGTCGGCCAAGCATTGGCCAACACC-AAAATTTTTTTTTTATCTGATAAAAAG
1 TGTCGGCCAAGCATTGACCAACACCAAAAAAATTATTTTTATCTGATAAAAAG
3690 GTGTTGGCCA
Statistics
Matches: 241, Mismatches: 31, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
110 20 0.08
111 46 0.19
112 1 0.00
113 3 0.01
117 5 0.02
118 96 0.40
119 50 0.21
120 20 0.08
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (116 bp):
TGTCGGCCAAGCATTGACCAACACCAAAAAAATTATTTTTATCTGATAAAAAGATGTGTCGGCAA
TGCATGACCAACACAAAAAAAAATTGTTTTTTTATTAGATAAAAAAGGTGG
Found at i:3919 original size:56 final size:55
Alignment explanation
Indices: 3772--3921 Score: 153
Period size: 56 Copynumber: 2.7 Consensus size: 55
3762 AATAAAAAGG
* * * * *
3772 TGGTGTCGACCAAACATTGGCTAACACCAAAATTTTTTTATTTGATAAAAAATAC
1 TGGTGTCGACCAAGCATTGGCCAACACCAAATTTTTTTTATCTGATAAAAAAGAC
* * *
3827 TGATGTC-AGCCAATGCA-GGGCCAACGCCAAAATTTTTTTTATCTGATTAAAAAAGAC
1 TGGTGTCGA-CCAA-GCATTGGCCAACACC-AAATTTTTTTTATCTGA-TAAAAAAGAC
* *
3884 -GGTGTCGACCAAGCATTGGCGAACACCAATTTTTTTTT
1 TGGTGTCGACCAAGCATTGGCCAACACCAAATTTTTTTT
3922 CAAAATCTCG
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
54 1 0.01
55 31 0.41
56 34 0.45
57 10 0.13
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (55 bp):
TGGTGTCGACCAAGCATTGGCCAACACCAAATTTTTTTTATCTGATAAAAAAGAC
Found at i:8889 original size:151 final size:150
Alignment explanation
Indices: 8602--8875 Score: 386
Period size: 151 Copynumber: 1.8 Consensus size: 150
8592 AACCACGTAA
* ** *
8602 TAATTTTTTCATTCATTTTAAGATGATTTGATAAAAGAGCATTTAAATTTAAAGGTTAAAAAAAC
1 TAATTTTTTCATTCATTTTAAGATGATTTGATAAAAAAAAACTTAAATTTAAAGGTTAAAAAAAC
*** *
8667 GAAAGTTAAATAAAAGATTAAAATAATTTTTTTATAAAATTAAAAGGGCCAAATAAATAATTATA
66 GAAAGTTAAATAAAAGATTAAAATAATTTTTTTATAAAATTAAAAACACCAAAT-AATAATAATA
8732 ATAATAAAATAAGATTAACTT
130 ATAATAAAATAAGATTAACTT
8753 TAATTTTTTCATTCATTTTAAGATGATTTGATAGAAAAAAAACTTAAATTTAAAGGTTAAAATAA
1 TAATTTTTTCATTCATTTTAAGATGATTTGATA-AAAAAAAACTTAAATTTAAAGGTTAAAA-AA
* * * * * *
8818 ATGAAAGTTATATAGAAGATTAAATTAATTTTTTTTATAAAGTTAAAAACATCAAATA
64 ACGAAAGTTAAATAAAAGATTAAAATAA-TTTTTTTATAAAATTAAAAACACCAAATA
8876 TGGTAATAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
151 33 0.31
152 24 0.22
153 27 0.25
154 23 0.21
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.37
Consensus pattern (150 bp):
TAATTTTTTCATTCATTTTAAGATGATTTGATAAAAAAAAACTTAAATTTAAAGGTTAAAAAAAC
GAAAGTTAAATAAAAGATTAAAATAATTTTTTTATAAAATTAAAAACACCAAATAATAATAATAA
TAATAAAATAAGATTAACTT
Found at i:10071 original size:28 final size:28
Alignment explanation
Indices: 10023--10450 Score: 457
Period size: 28 Copynumber: 15.3 Consensus size: 28
10013 GGGGAATAGA
*
10023 CCTATTTCCCTAATTATTTTTAAAATCGG
1 CCTA-TTCCATAATTATTTTTAAAATCGG
* *
10052 CCTATTCCCCTAATTATTTTTAAAATTGG
1 CCTATT-CCATAATTATTTTTAAAATCGG
* *
10081 CTTACTT-CGTAATTATTTTTAAAATCGG
1 CCTA-TTCCATAATTATTTTTAAAATCGG
* ** *
10109 CTTATTCTGTAATTA-TTTTAAAATCGA
1 CCTATTCCATAATTATTTTTAAAATCGG
* *
10136 CCTATTCCATGATTATTTTTAAAATCGA
1 CCTATTCCATAATTATTTTTAAAATCGG
*
10164 CCTATTCCATAATTATTTTTAAAATCAG
1 CCTATTCCATAATTATTTTTAAAATCGG
** *
10192 CCTATTTTATAATTATTTTTAAAATTGG
1 CCTATTCCATAATTATTTTTAAAATCGG
** * *
10220 TGTATT-TAAAATTATTTTTAAAATCGG
1 CCTATTCCATAATTATTTTTAAAATCGG
*** * *
10247 CCTATTTTGTAATTATTTTCAAAATCAG
1 CCTATTCCATAATTATTTTTAAAATCGG
* * *
10275 CCTAATCCGTAATTATTTTTAAAATTGG
1 CCTATTCCATAATTATTTTTAAAATCGG
* *
10303 CCTATTCCCTAATTATTTTTAAAATCAG
1 CCTATTCCATAATTATTTTTAAAATCGG
*
10331 CCTATTCCATAATTCTTTTTAAAATCGG
1 CCTATTCCATAATTATTTTTAAAATCGG
* *
10359 CCTATTCCGTAATTATTTTTAAAATTGG
1 CCTATTCCATAATTATTTTTAAAATCGG
* *** **
10387 CTTATTTTGTAATTATTTTTAAAATCAA
1 CCTATTCCATAATTATTTTTAAAATCGG
*
10415 CCTAATCCATAATTATTTTTAAAATCGG
1 CCTATTCCATAATTATTTTTAAAATCGG
10443 CCTATTCC
1 CCTATTCC
10451 CCTAATTTAT
Statistics
Matches: 337, Mismatches: 57, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
27 47 0.14
28 260 0.77
29 28 0.08
30 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.46
Consensus pattern (28 bp):
CCTATTCCATAATTATTTTTAAAATCGG
Found at i:10217 original size:12 final size:12
Alignment explanation
Indices: 10196--10243 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
10186 AATCAGCCTA
*
10196 TTTTATAATTAT
1 TTTTAAAATTAT
*
10208 TTTTAAAATTGGT
1 TTTTAAAATT-AT
10221 GTATTTAAAATTAT
1 -T-TTTAAAATTAT
10235 TTTTAAAAT
1 TTTTAAAAT
10244 CGGCCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 17 0.57
13 2 0.07
14 2 0.07
15 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:12356 original size:23 final size:23
Alignment explanation
Indices: 12282--12447 Score: 98
Period size: 23 Copynumber: 7.5 Consensus size: 23
12272 TAAACGGAAC
* * *
12282 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
12304 AAACAGAGAGCACA-TAAGTGTT
1 AAACAGAGAGCACACAAAGTGCT
* *
12326 GGGCAACAGAGAGCAAACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
12352 AAACAGAGAGTACATAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
12372 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
12391 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
12414 AATCAGAGAGCATACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
12437 AATCAGAGAGC
1 AAACAGAGAGC
12448 GCGCTACTGT
Statistics
Matches: 111, Mismatches: 21, Indels: 23
0.72 0.14 0.15
Matches are distributed among these distances:
16 9 0.08
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 17 0.15
23 60 0.54
25 12 0.11
26 6 0.05
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:12653 original size:26 final size:26
Alignment explanation
Indices: 12617--12666 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
12607 AGAGCACAGC
12617 TGGGCAACAGAGAGCACACAAAGTGT
1 TGGGCAACAGAGAGCACACAAAGTGT
*
12643 TGGGCAACAGAGAGCACATAAAGT
1 TGGGCAACAGAGAGCACACAAAGT
12667 ACTGAGCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.30, T:0.12
Consensus pattern (26 bp):
TGGGCAACAGAGAGCACACAAAGTGT
Found at i:12700 original size:23 final size:23
Alignment explanation
Indices: 12670--12744 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
12660 ATAAAGTACT
12670 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
12693 GAGCACACGAAA-TGCTAATCAGA
1 GAGCACAC-AAAGTGCTAATCAGA
*
12716 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
12739 GAGCAC
1 GAGCAC
12745 GCTAGTGTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
22 2 0.04
23 44 0.90
24 3 0.06
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:12883 original size:295 final size:295
Alignment explanation
Indices: 12353--12884 Score: 1010
Period size: 295 Copynumber: 1.8 Consensus size: 295
12343 CAAAGTGCTA
* *
12353 AACAGAGAGTACATAAAGTACTGAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATC
1 AACAGAGAGCACATAAAGTACTGAGCACACAAAGTGCTAATCAGAGAGCACACGAAATGCTAATC
* *
12418 AGAGAGCATACACAGTGCTAATCAGAGAGCGCGCTACTGTTCCTTAATGGCATGTCACTATTATC
66 AGAGAGCACACACAGTGCTAATCAGAGAGCACGCTACTGTTCCTTAATGGCATGTCACTATTATC
*
12483 ACAATGGTTCTAACTTGTCTACATGGGCATAATCTCTCATTTTCATCATTTCTCATAATTTCATA
131 ACAATGGTTCTAACTTGTCTACATGGACATAATCTCTCATTTTCATCATTTCTCATAATTTCATA
12548 TACCACATTTACATTTCTTTTCACATATACATAATCATGTATACCGAAGTACTAAACAGAGAGCA
196 TACCACATTTACATTTCTTTTCACATATACATAATCATGTATACCGAAGTACTAAACAGAGAGCA
12613 CAGCTGGGCAACAGAGAGCACACAAAGTGTTGGGC
261 CAGCTGGGCAACAGAGAGCACACAAAGTGTTGGGC
12648 AACAGAGAGCACATAAAGTACTGAGCACACAAAGTGCTAATCAGAGAGCACACGAAATGCTAATC
1 AACAGAGAGCACATAAAGTACTGAGCACACAAAGTGCTAATCAGAGAGCACACGAAATGCTAATC
*
12713 AGAGAGCACACACAGTGCTAATCAGAGAGCACGCTAGTGTTCCTTAATGGCATGTCACTATTATC
66 AGAGAGCACACACAGTGCTAATCAGAGAGCACGCTACTGTTCCTTAATGGCATGTCACTATTATC
12778 ACAATGGTTCTAACTTGTCTACATGGACATAATCTCTCATTTTCATCATTTCTCATAATTTCATA
131 ACAATGGTTCTAACTTGTCTACATGGACATAATCTCTCATTTTCATCATTTCTCATAATTTCATA
12843 TACCACATTTACATTTCTTTTCACATATACATAATCATGTAT
196 TACCACATTTACATTTCTTTTCACATATACATAATCATGTAT
12885 TTCTCACCTT
Statistics
Matches: 231, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
295 231 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (295 bp):
AACAGAGAGCACATAAAGTACTGAGCACACAAAGTGCTAATCAGAGAGCACACGAAATGCTAATC
AGAGAGCACACACAGTGCTAATCAGAGAGCACGCTACTGTTCCTTAATGGCATGTCACTATTATC
ACAATGGTTCTAACTTGTCTACATGGACATAATCTCTCATTTTCATCATTTCTCATAATTTCATA
TACCACATTTACATTTCTTTTCACATATACATAATCATGTATACCGAAGTACTAAACAGAGAGCA
CAGCTGGGCAACAGAGAGCACACAAAGTGTTGGGC
Found at i:14139 original size:11 final size:11
Alignment explanation
Indices: 14113--14151 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14103 TGGATGCCTT
*
14113 AGAAATGTAAGA
1 AGAAATG-ATGA
*
14125 AGAAATGGTGA
1 AGAAATGATGA
14136 AGAAATGATGA
1 AGAAATGATGA
14147 AGAAA
1 AGAAA
14152 ATGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (11 bp):
AGAAATGATGA
Found at i:19462 original size:18 final size:19
Alignment explanation
Indices: 19425--19462 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19415 ATCCAATTCG
*
19425 ATTAGATAAAATATTAAAA
1 ATTAGATAAAATATAAAAA
19444 ATTA-ATAAAATATAAAAA
1 ATTAGATAAAATATAAAAA
19462 A
1 A
19463 AATATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
ATTAGATAAAATATAAAAA
Found at i:22696 original size:9 final size:9
Alignment explanation
Indices: 22525--22673 Score: 79
Period size: 9 Copynumber: 16.1 Consensus size: 9
22515 ACTTTATTAT
22525 AATTATAAA
1 AATTATAAA
22534 AA-TATAAA
1 AATTATAAA
** *
22542 AAAAATTAA
1 AATTATAAA
*
22551 AATCAATAAA
1 AAT-TATAAA
*
22561 AGTTATAAA
1 AATTATAAA
* *
22570 TATTATTAA
1 AATTATAAA
*
22579 ATTTA-AAA
1 AATTATAAA
22587 AATATATTTAAA
1 AAT-TA--TAAA
22599 AATTATTAAA
1 AATTA-TAAA
*
22609 AATTAGAAAA
1 AATTA-TAAA
**
22619 AATCGTAAA
1 AATTATAAA
22628 AA-TATAAA
1 AATTATAAA
*
22636 AATTGTAAA
1 AATTATAAA
**
22645 TTTTTATAAA
1 -AATTATAAA
*
22655 AATCATAAA
1 AATTATAAA
22664 AATTATAAA
1 AATTATAAA
22673 A
1 A
22674 TATATAGACA
Statistics
Matches: 104, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
8 18 0.17
9 49 0.47
10 29 0.28
11 2 0.02
12 6 0.06
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:22951 original size:21 final size:20
Alignment explanation
Indices: 22925--23003 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 20
22915 TGTTGAAGGG
22925 ATTTTTTGATGCA-TTTTATAA
1 ATTTTTT-ATG-ATTTTTATAA
22946 ATTTTTTATGATTTTTATAA
1 ATTTTTTATGATTTTTATAA
* *
22966 A-ATTTTATAATTTTT-T-A
1 ATTTTTTATGATTTTTATAA
* *
22983 TTTTTTTACGATTTTTATAA
1 ATTTTTTATGATTTTTATAA
23003 A
1 A
23004 CAAAATTCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.02
18 12 0.26
19 14 0.30
20 13 0.28
21 7 0.15
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
ATTTTTTATGATTTTTATAA
Found at i:23032 original size:17 final size:17
Alignment explanation
Indices: 23006--23066 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 17
22996 TTTATAAACA
* *
23006 AAATTCTAATTTTTCAT
1 AAATTTTAATTTTTAAT
*
23023 AAATTTTAA-TTTAAAT
1 AAATTTTAATTTTTAAT
* *
23039 AATTTTTATATTTTTTAT
1 AAATTTTA-ATTTTTAAT
*
23057 AATTTTTAAT
1 AAATTTTAAT
23067 AAGAGCAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 12 0.33
17 11 0.31
18 13 0.36
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATTTTAATTTTTAAT
Found at i:25940 original size:2 final size:2
Alignment explanation
Indices: 25933--25959 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25923 GAAAGATAGG
25933 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
25960 GAATGTTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26562 original size:6 final size:6
Alignment explanation
Indices: 26551--26578 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
26541 ATTCGTTCTC
26551 TTCTGT TTCTGT TTCTGT TTCTGT TTCT
1 TTCTGT TTCTGT TTCTGT TTCTGT TTCT
26579 TTCATTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.14, T:0.68
Consensus pattern (6 bp):
TTCTGT
Found at i:27656 original size:13 final size:13
Alignment explanation
Indices: 27618--27657 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
27608 CTAATACGGG
27618 ACTTGATTAAACT
1 ACTTGATTAAACT
* * *
27631 AATTTATTTAACT
1 ACTTGATTAAACT
27644 ACTTGATTAAACT
1 ACTTGATTAAACT
27657 A
1 A
27658 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (13 bp):
ACTTGATTAAACT
Done.