Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010943.1 Kokia drynarioides strain JFW-HI SEQ_125911, 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: 71922
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:352 original size:17 final size:17
Alignment explanation
Indices: 332--409 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
322 TAAATCTTAA
*
332 ATTTAAATTTATAATAT
1 ATTTAAATTTAAAATAT
**
349 ATTTAAATTTCCAATGA-
1 ATTTAAATTTAAAAT-AT
*
366 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAT
* *
383 ACTTAATTTTAAAAT-T
1 ATTTAAATTTAAAATAT
399 AATTTAAATTT
1 -ATTTAAATTT
410 TGTTGGGCTC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
16 1 0.02
17 47 0.96
18 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (17 bp):
ATTTAAATTTAAAATAT
Found at i:354 original size:23 final size:23
Alignment explanation
Indices: 315--358 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
305 TATGGACATT
315 ATTTAAATAAATCTTAAATTTAA
1 ATTTAAATAAATCTTAAATTTAA
*
338 ATTTATAATATAT-TTAAATTT
1 ATTTA-AATAAATCTTAAATTT
359 CCAATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTAAATAAATCTTAAATTTAA
Found at i:369 original size:34 final size:34
Alignment explanation
Indices: 331--409 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
321 ATAAATCTTA
* * * **
331 AATTTAAATTTATAATATATTTAAATTTCCAATG
1 AATTTAAATTTAAAATAAACTTAAATTTAAAATG
* *
365 AATTTAAATTTAAAATAAACTTAATTTTAAAATT
1 AATTTAAATTTAAAATAAACTTAAATTTAAAATG
399 AATTTAAATTT
1 AATTTAAATTT
410 TGTTGGGCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (34 bp):
AATTTAAATTTAAAATAAACTTAAATTTAAAATG
Found at i:1321 original size:49 final size:48
Alignment explanation
Indices: 1257--1688 Score: 200
Period size: 49 Copynumber: 8.6 Consensus size: 48
1247 CTAAGGTATA
*
1257 AGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTGTATCTTCATGGTAC
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCATGGTAC
* * *
1305 TGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-CATGCTTC-TGAGGTAC
1 AGG-TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTAT-CTTCAT--GGTAC
* ** * * * *
1354 AAGGTTCACCGTTAAGACTTAAACCTTCCCTTTCATATCTTCGTGTCTTCATGGTAT
1 -AGGTTCGCCGTTGCGGCTTAAACCTTTCC---C---T-TT-GTATCTTCATGGTAC
* * * *
1411 TGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-CATGCTTC-TGAGGTAGA
1 AGG-TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTAT-CTTCAT--GGTA-C
* * * * ** *
1461 AGGTTCGCTGTTGCGACTTAAACCTTTCCCTTTTGTGTCCTCGCGATAC
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCC-TTTGTATCTTCATGGTAC
* * * * * *
1510 TGGATTTGCCGTTGCGGTTTAAATCTTTCCCTTCATGTTTC-TGA-GGTAC
1 AGG-TTCGCCGTTGCGGCTTAAACCTTTCCCTT--TGTATCTTCATGGTAC
* * ** *
1559 AAGGTTCGCCGTTGCGACTTAAACTTTTCCCTTCATATCTTCGTGGTAC
1 -AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCATGGTAC
* * * * *
1608 TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCACGTCTC-TGA-GGTAC
1 AGG-TTCGCCGTTGCGGCTTAAACCTTTCCCTT--TGTATCTTCATGGTAC
*
1657 AAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
1 -AGGTTCGCCGTTGCGGCTTAAACCTTTCCCT
1689 CCATGTTTCG
Statistics
Matches: 283, Mismatches: 66, Indels: 69
0.68 0.16 0.17
Matches are distributed among these distances:
47 8 0.03
48 15 0.05
49 174 0.61
50 35 0.12
51 14 0.05
52 2 0.01
54 1 0.00
56 2 0.01
57 26 0.09
58 4 0.01
59 2 0.01
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (48 bp):
AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCATGGTAC
Found at i:1393 original size:98 final size:99
Alignment explanation
Indices: 1201--1688 Score: 601
Period size: 98 Copynumber: 4.9 Consensus size: 99
1191 CTTCAATCCG
** * * * *
1201 CATGGTACTAAATTCGCCGTTGCGGCTTAAAT-TTT-CTTTCGTGCTTCTAAGGTATAAGGTTCG
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCG
* * *
1264 CCATTGCGGCTTAAACCTTTCCCTTT-GTATCTT
66 CCGTTGCGACTTAAACCTTTCCCTTTCATATCTT
*
1297 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCA
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCG
**
1362 CCGTTAAGACTTAAACC-TTCCCTTTCATATCTTCGTGTCTT
66 CCGTTGCGACTTAAACCTTTCCCTTTCATA--------TCTT
* *
1403 CATGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTAGAAGGTTCG
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCG
* ** * *
1468 CTGTTGCGACTTAAACCTTTCCCTTTTGTGTCCT
66 CCGTTGCGACTTAAACCTTTCCCTTTCATATCTT
** * * * *
1502 CGCGATACTGGATTTGCCGTTGCGGTTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCG
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCG
*
1567 CCGTTGCGACTTAAACTTTTCCC-TTCATATCTT
66 CCGTTGCGACTTAAACCTTTCCCTTTCATATCTT
* *
1600 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCACG-TCTCTGAGGTACAAGGTTC
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTC
1664 GCCGTTGCGACTTAAACCTTTCCCT
65 GCCGTTGCGACTTAAACCTTTCCCT
1689 CCATGTTTCG
Statistics
Matches: 336, Mismatches: 42, Indels: 25
0.83 0.10 0.06
Matches are distributed among these distances:
96 30 0.09
97 12 0.04
98 124 0.37
99 81 0.24
106 80 0.24
107 9 0.03
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.37
Consensus pattern (99 bp):
CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCG
CCGTTGCGACTTAAACCTTTCCCTTTCATATCTT
Found at i:7036 original size:24 final size:24
Alignment explanation
Indices: 7009--7057 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6999 AAGCTGAGTC
*
7009 ATTATCAATGAGCACTTCGGGCAA
1 ATTATCAATGAGCACTTCGAGCAA
7033 ATTATCAATGAGCACTTCGAGCAA
1 ATTATCAATGAGCACTTCGAGCAA
7057 A
1 A
7058 GTATACCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
ATTATCAATGAGCACTTCGAGCAA
Found at i:13537 original size:59 final size:58
Alignment explanation
Indices: 13387--13660 Score: 245
Period size: 59 Copynumber: 4.7 Consensus size: 58
13377 GGATGCGCGG
* * **
13387 GGGTAAAAATGGTAATTTTGGAAAGTTCAGAGTTAAAAATAAAG-TTTTAGATGTCCGA
1 GGGT-AAAATGGTAATTTTGGAAAGTTCAGGGTTAAAAATAGAGTTTTTAGACATCCGA
* * *
13445 GGGTATAATGGTGATTTTTGGAAAGTTCAGGGTTAAAAATGGAGTTTTTAGACATCCGA
1 GGGTAAAATGGT-AATTTTGGAAAGTTCAGGGTTAAAAATAGAGTTTTTAGACATCCGA
* * ** * * *
13504 GGGTAAAATGGTAATTTTAGAAGGATTGGGGGTTAAAAATAGAATTTTTAGACATTCGG
1 GGGTAAAATGGTAATTTTGGAAAG-TTCAGGGTTAAAAATAGAGTTTTTAGACATCCGA
* * * * * *
13563 GGGTAAAATGATAATTTTTGGAAAGTTCGGGGGTAAAAAT-GTAG-TTTTGGAAAATTCGA
1 GGGTAAAATGGTAA-TTTTGGAAAGTTCAGGGTTAAAAATAG-AGTTTTTAG-ACATCCGA
13622 -GGTAAAAAAT-GTAATTTTGGAAAGTTCGAGGG-TAAAAAT
1 GGGT--AAAATGGTAATTTTGGAAAGTTC-AGGGTTAAAAAT
13661 GTAATTTTTG
Statistics
Matches: 179, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
57 7 0.04
58 69 0.39
59 90 0.50
60 13 0.07
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCAGGGTTAAAAATAGAGTTTTTAGACATCCGA
Found at i:13658 original size:30 final size:29
Alignment explanation
Indices: 13387--13778 Score: 200
Period size: 29 Copynumber: 13.3 Consensus size: 29
13377 GGATGCGCGG
13387 GGGTAAAAATGGTAATTTTGGAAAGTTC-A
1 GGGTAAAAAT-GTAATTTTGGAAAGTTCGA
* * * * *
13416 GAGTTAAAAAT-AAAGTTTTAG-ATGTCCGA
1 G-GGTAAAAATGTAA-TTTTGGAAAGTTCGA
* *
13445 GGGT-ATAATGGTGATTTTTGGAAAGTTC-A
1 GGGTAAAAAT-GT-AATTTTGGAAAGTTCGA
* * * * *
13474 GGGTTAAAAATGGAGTTTTTAGACA-TCCGA
1 GGG-TAAAAATGTA-ATTTTGGAAAGTTCGA
* * *
13504 GGGT-AAAATGGTAATTTTAGAAGGATT-GG
1 GGGTAAAAAT-GTAATTTTGGAAAG-TTCGA
* * *
13533 GGGTTAAAAATAG-AATTTTTAGACA-TTCGG
1 GGG-TAAAAAT-GTAA-TTTTGGAAAGTTCGA
*
13563 GGGT-AAAATGATAATTTTTGGAAAGTTCGG
1 GGGTAAAAATG-TAA-TTTTGGAAAGTTCGA
* *
13593 GGGTAAAAATGTAGTTTTGGAAAATTCGA
1 GGGTAAAAATGTAATTTTGGAAAGTTCGA
13622 -GGTAAAAAATGTAATTTTGGAAAGTTCGA
1 GGGT-AAAAATGTAATTTTGGAAAGTTCGA
* *
13651 GGGTAAAAATGTAATTTTTGAAAAATTC-A
1 GGGTAAAAATGTAA-TTTTGGAAAGTTCGA
* * * *
13680 AGGTCAAAATTGGAATTTTGGAAAGTTTGA
1 GGGT-AAAAATGTAATTTTGGAAAGTTCGA
* * *
13710 GGGTTAAAATGTAATTTTTGGAAAATTTG-
1 GGGTAAAAATGTAA-TTTTGGAAAGTTCGA
** * *
13739 GGGTTAAAAATAAAATTTTAGAAAGTTCAA
1 GGG-TAAAAATGTAATTTTGGAAAGTTCGA
*
13769 GGGTTAAAAT
1 GGGTAAAAAT
13779 ATGATTTTTA
Statistics
Matches: 279, Mismatches: 54, Indels: 60
0.71 0.14 0.15
Matches are distributed among these distances:
27 5 0.02
28 28 0.10
29 126 0.45
30 97 0.35
31 23 0.08
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGGAAAGTTCGA
Found at i:13676 original size:59 final size:59
Alignment explanation
Indices: 13567--13787 Score: 246
Period size: 59 Copynumber: 3.7 Consensus size: 59
13557 ATTCGGGGGT
* *
13567 AAAATGATAATTTTTGGAAAGTTCGGGGGTAAAAATGT-AGTTTTGGAAAATTCGAGGTAA
1 AAAATG-TAA-TTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTCGAGGTAA
* * *
13627 AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAAAAATTCAAGGTCA
1 AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTCGAGGTAA
* * * * * * *
13686 AAATTGGAATTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTTGGAAAATTTGGGGTTA
1 AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTCGAGGTAA
** * * * * *
13745 AAAATAAAATTTTAGAAAGTTCAAGGGTTAAAATATGATTTTT
1 AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTT
13788 AGACAGTTTA
Statistics
Matches: 138, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
58 26 0.19
59 106 0.77
60 6 0.04
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTCGAGGTAA
Found at i:13800 original size:29 final size:29
Alignment explanation
Indices: 13695--13800 Score: 97
Period size: 30 Copynumber: 3.6 Consensus size: 29
13685 AAAATTGGAA
* *
13695 TTTTGGAAAGTTTGAGGGTTAAAATGTAAT
1 TTTTAGAAAGTTT-AGGGTTAAAATATAAT
* * * *
13725 TTTTGGAAAATTTGGGGTTAAAA-ATAAAA
1 TTTTAGAAAGTTTAGGGTTAAAATAT-AAT
* *
13754 TTTTAGAAAGTTCAAGGGTTAAAATATGAT
1 TTTTAGAAAGTT-TAGGGTTAAAATATAAT
*
13784 TTTTAGACAGTTTAGGG
1 TTTTAGAAAGTTTAGGG
13801 ACCTTCAGAG
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.02
29 25 0.41
30 33 0.54
31 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
TTTTAGAAAGTTTAGGGTTAAAATATAAT
Found at i:14850 original size:13 final size:13
Alignment explanation
Indices: 14834--14916 Score: 73
Period size: 13 Copynumber: 6.5 Consensus size: 13
14824 TTTATTTAAA
*
14834 ATTAATATTAATT
1 ATTAATATTTATT
*
14847 ATTAATATTTTTT
1 ATTAATATTTATT
14860 ATTAATATTTATT
1 ATTAATATTTATT
* **
14873 AATGCTATTTATT
1 ATTAATATTTATT
*
14886 ACTT-CTA-TTATT
1 A-TTAATATTTATT
*
14898 ATTATTA-TTATT
1 ATTAATATTTATT
14910 ATTAATA
1 ATTAATA
14917 AATTTATTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
11 2 0.03
12 19 0.32
13 37 0.63
14 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (13 bp):
ATTAATATTTATT
Found at i:15662 original size:12 final size:12
Alignment explanation
Indices: 15645--15679 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
15635 TATTTAAATA
15645 AATTTTAAATTT
1 AATTTTAAATTT
*
15657 AATTTTAAAATT
1 AATTTTAAATTT
15669 AA-TTTAAATTT
1 AATTTTAAATTT
15680 TATTGAGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTTAAATTT
Found at i:20075 original size:3 final size:3
Alignment explanation
Indices: 20067--20103 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20057 GATTATTCAG
20067 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
20104 CCGTACCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21084 original size:18 final size:18
Alignment explanation
Indices: 21052--21103 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
21042 TTGGGATGAG
21052 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
21068 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
21086 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
21104 CAACTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:21262 original size:29 final size:30
Alignment explanation
Indices: 21220--21292 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
21210 GTGATCACTT
* * *
21220 CATAAGTAATTAAAATGTAACAT-TTCAAA
1 CATAAGTGACTAAAATGTAACATATGCAAA
*
21249 CATAAGTGACTAAAATGTAACCTGATGCAAA
1 CATAAGTGACTAAAATGTAACAT-ATGCAAA
*
21280 CAAAAGTGACTAA
1 CATAAGTGACTAA
21293 TTTGCAGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.54
31 17 0.46
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (30 bp):
CATAAGTGACTAAAATGTAACATATGCAAA
Found at i:48347 original size:87 final size:86
Alignment explanation
Indices: 48194--48353 Score: 207
Period size: 87 Copynumber: 1.8 Consensus size: 86
48184 TTAAATTCGG
* * * *
48194 TGAATTCATCGAGTCCGTTTCAATAAGACCATCCAAACTCTGAGATATGAACTCATTAAGAGTAA
1 TGAATTCATCAAGTCCGTCTCAATAAGACCATCCAAACTCTGAGATATGAACTCATTAAAAAT-A
48259 AAAACTCAATCTCACATGTTGT
65 AAAACTCAATCTCACATGTTGT
* * * *
48281 TGAATTCATCAAGTTCGTCTCAAT-AGAACCA-CTCAAACTTTGGGATATGAAGTCATTAAAAAT
1 TGAATTCATCAAGTCCGTCTCAATAAG-ACCATC-CAAACTCTGAGATATGAACTCATTAAAAAT
48344 AAAAACTCAA
64 AAAAACTCAA
48354 CCTTATGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
86 13 0.21
87 50 0.79
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (86 bp):
TGAATTCATCAAGTCCGTCTCAATAAGACCATCCAAACTCTGAGATATGAACTCATTAAAAATAA
AAACTCAATCTCACATGTTGT
Found at i:49820 original size:34 final size:34
Alignment explanation
Indices: 49777--49857 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
49767 AAACTAAACT
* *
49777 CAAATATTTTTAATTTTTTA-CATTTTATTTTACC
1 CAAATATTTTTAATTTTTTATC-TTCTATCTTACC
49811 CAAATATTTTTAATTTTTTATCTTCTATCTTACC
1 CAAATATTTTTAATTTTTTATCTTCTATCTTACC
49845 CAAATATTGTTTA
1 CAAATATT-TTTA
49858 GTTGGACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 38 0.88
35 5 0.12
ACGTcount: A:0.30, C:0.14, G:0.01, T:0.56
Consensus pattern (34 bp):
CAAATATTTTTAATTTTTTATCTTCTATCTTACC
Found at i:52916 original size:16 final size:17
Alignment explanation
Indices: 52888--52920 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
52878 TATATATGTT
52888 AATTAATAATTTTACAA
1 AATTAATAATTTTACAA
52905 AATTAA-AATTTTACAA
1 AATTAATAATTTTACAA
52921 GTTGGTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATTTTACAA
Found at i:53543 original size:17 final size:17
Alignment explanation
Indices: 53523--53567 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
53513 AATTATTTTT
53523 AAATTTAAATTTACTTA
1 AAATTTAAATTTACTTA
* *
53540 AAATTTAAATTTAGTTT
1 AAATTTAAATTTACTTA
53557 AAATTTGAAAT
1 AAATTT-AAAT
53568 GATTTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
AAATTTAAATTTACTTA
Found at i:55513 original size:29 final size:29
Alignment explanation
Indices: 55474--55690 Score: 137
Period size: 29 Copynumber: 7.4 Consensus size: 29
55464 CAAAAATAAT
55474 ATTTTGACCCCTGAACTTTCCAAAAATTCC
1 ATTTT-ACCCCTGAACTTTCCAAAAATTCC
* *
55504 ATTTTACCCCCGAAC-TTCCAAAAATTTC
1 ATTTTACCCCTGAACTTTCCAAAAATTCC
*
55532 ATTTTGACCCC--AATTTTTTCCAAAAATTACC
1 ATTTT-ACCCCTGAA--CTTTCCAAAAATT-CC
* * *
55563 ATTTTACCCTTGAAC-TTCCATAAATTTC
1 ATTTTACCCCTGAACTTTCCAAAAATTCC
* *
55591 ATTTTTGACCCC--AATTTTTTC-AAAATTACC
1 A-TTTT-ACCCCTGAA-CTTTCCAAAAATT-CC
* * *
55621 ATTTTATCCC-GAA-TGTCTAAAAATTCC
1 ATTTTACCCCTGAACTTTCCAAAAATTCC
* *
55648 ATTTTTTAACCCTGAACTTTCCCAAAATTACC
1 A--TTTTACCCCTGAACTTTCCAAAAATT-CC
*
55680 ATTTCACCCCT
1 ATTTTACCCCT
55691 CGAGTGTCCA
Statistics
Matches: 145, Mismatches: 23, Indels: 38
0.70 0.11 0.18
Matches are distributed among these distances:
27 7 0.05
28 31 0.21
29 47 0.32
30 40 0.28
31 15 0.10
32 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTACCCCTGAACTTTCCAAAAATTCC
Found at i:55588 original size:59 final size:60
Alignment explanation
Indices: 55490--55653 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 60
55480 ACCCCTGAAC
55490 TTTCCAAAAATT-CCATTTTACCCCCGAACTTCCAAAAATTTCA-TTTTGACCCCAATTT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAATTT
** *
55548 TTTCCAAAAATTACCATTTTACCCTTGAACTTCCATAAATTTCATTTTTGACCCCAATTT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAATTT
* * *
55608 TTT-C-AAAATTACCATTTTA-TCCCGAA-TGTCTAAAAATTCCATTTTT
1 TTTCCAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTTCATTTTT
55654 TAACCCTGAA
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
56 1 0.01
57 19 0.20
58 27 0.29
59 29 0.31
60 18 0.19
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (60 bp):
TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAATTT
Found at i:55728 original size:28 final size:28
Alignment explanation
Indices: 55669--55742 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
55659 CTGAACTTTC
* *
55669 CCAAAATTACCATTTCACCCCTCGAGTGT
1 CCAAAATTACCATTT-TCCCCTCGAGTAT
*
55698 CCAAAATTACCATTTTGCCCTCG-GTTAT
1 CCAAAATTACCATTTTCCCCTCGAG-TAT
55726 CCAAAAATTA-CATTTTC
1 CC-AAAATTACCATTTTC
55743 AAATTCAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 16 0.41
29 22 0.56
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (28 bp):
CCAAAATTACCATTTTCCCCTCGAGTAT
Found at i:68568 original size:22 final size:23
Alignment explanation
Indices: 68528--68577 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
68518 TTCGTGTGCT
*
68528 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCACTATGTGCGCC
* * *
68551 TACTGA-TTGCACTGTGTGTGCT
1 TACTGATTTGCACTATGTGCGCC
68573 TACTG
1 TACTG
68578 TCTCCCCAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (23 bp):
TACTGATTTGCACTATGTGCGCC
Found at i:71136 original size:25 final size:25
Alignment explanation
Indices: 71102--71155 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
71092 TATTATATCC
71102 ATATAAGCCTATGTACATGCCATAA
1 ATATAAGCCTATGTACATGCCATAA
71127 ATATAAGCCTATGTACATGCCATAA
1 ATATAAGCCTATGTACATGCCATAA
71152 ATAT
1 ATAT
71156 TACATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (25 bp):
ATATAAGCCTATGTACATGCCATAA
Done.