Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015372.1 Kokia drynarioides strain JFW-HI SEQ_130419, 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: 487716
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 308 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:397099 original size:18 final size:19
Alignment explanation
Indices: 397059--397099 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
397049 AAAACAAATG
*
397059 GGAGAAGGGAGAGGGAGAG
1 GGAGAAGGGAGAGGGAGAC
397078 GGAG-AGGGAGAGTGGA-AC
1 GGAGAAGGGAGAG-GGAGAC
397096 GGAG
1 GGAG
397100 GAGATGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.61, T:0.02
Consensus pattern (19 bp):
GGAGAAGGGAGAGGGAGAC
Found at i:397783 original size:21 final size:20
Alignment explanation
Indices: 397736--397784 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
397726 TAAAATAGTG
*
397736 ACAAAACAACAACAAATACA
1 ACAAAACAACAACAAAAACA
* *
397756 ATAAAAATAACAACAAAAAGCA
1 A-CAAAACAACAACAAAAA-CA
397778 ACAAAAC
1 ACAAAAC
397785 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.82
22 3 0.14
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.06
Consensus pattern (20 bp):
ACAAAACAACAACAAAAACA
Found at i:401209 original size:6 final size:6
Alignment explanation
Indices: 401172--401206 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
401162 ACTTTCATCT
*
401172 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCA CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
401207 ACTTGTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.63, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:403002 original size:22 final size:23
Alignment explanation
Indices: 402970--403014 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
402960 TCCCATTGGC
* *
402970 ATATATTTAAAAA-TCCTAAAAA
1 ATATATATAAAAATTACTAAAAA
402992 ATATATATAAAAATTACTAAAAA
1 ATATATATAAAAATTACTAAAAA
403015 TCATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATATATAAAAATTACTAAAAA
Found at i:403032 original size:16 final size:18
Alignment explanation
Indices: 403001--403034 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
402991 AATATATATA
403001 AAAATTACTAAAAATCAT
1 AAAATTACTAAAAATCAT
403019 AAAATTA-T-AAAATCAT
1 AAAATTACTAAAAATCAT
403035 TTTGAAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTACTAAAAATCAT
Found at i:407902 original size:18 final size:19
Alignment explanation
Indices: 407881--407921 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
407871 TAGATTTTTC
407881 AAAAA-AAAAAACAATTTA
1 AAAAATAAAAAACAATTTA
* *
407899 AAAAATATAAAACATTTTA
1 AAAAATAAAAAACAATTTA
407918 AAAA
1 AAAA
407922 TATGAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATAAAAAACAATTTA
Found at i:407962 original size:2 final size:2
Alignment explanation
Indices: 407957--407982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
407947 AAAAAAAAAA
407957 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
407983 TTGTAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:413828 original size:15 final size:15
Alignment explanation
Indices: 413810--413843 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
413800 TATTTAAAAA
* *
413810 TAATTTATTTCTAAT
1 TAATTAATTTCAAAT
413825 TAATTAATTTCAAAT
1 TAATTAATTTCAAAT
413840 TAAT
1 TAAT
413844 GAAATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTAATTTCAAAT
Found at i:414344 original size:24 final size:24
Alignment explanation
Indices: 414208--414553 Score: 151
Period size: 24 Copynumber: 13.8 Consensus size: 24
414198 GTACATATAT
* *
414208 AAGCTGACGAGTGTAAACTTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* ****
414232 AAGCTGGA-GAGCGTAACAGCATAAAT
1 AAGCT-GACGAGCGTAA-A-CGTGTGC
* *
414258 AAGCTGACTAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* **
414282 AAGCTGGA-GAGCGTAAACGTTTAAAT
1 AAGCT-GACGAGCGTAAACGTGT--GC
414308 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* **
414332 AAGCTGACAAGCGTAAACGTGATAAAT
1 AAGCTGACGAGCGTAAACGTG-T--GC
* **
414359 AAGTTGACGAGCGTAAACACGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * * ****
414383 AAACTGGCGAGCATAAACGCATAAAT
1 AAGCTGACGAGCGTAAACG--TGTGC
*
414409 AACCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
414433 AAGTTGGCGGACGAGCGTAAACGTGTAC
1 AA----GCTGACGAGCGTAAACGTGTGC
* **
414461 AAGCTGACGAGCATAAACACGAT-TAAT
1 AAGCTGACGAGCGT-AA-ACG-TGT-GC
* * *
414488 AAGCAGATGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
414512 AAGCTGGCAAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
414536 -AGACTGGCGAGCGTAAAC
1 AAG-CTGACGAGCGTAAAC
414554 ACAATAAATA
Statistics
Matches: 236, Mismatches: 63, Indels: 46
0.68 0.18 0.13
Matches are distributed among these distances:
23 2 0.01
24 112 0.47
25 17 0.07
26 55 0.23
27 29 0.12
28 21 0.09
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:414409 original size:101 final size:100
Alignment explanation
Indices: 414201--414435 Score: 303
Period size: 101 Copynumber: 2.3 Consensus size: 100
414191 TTTATATGTA
* * * *
414201 CATATATAAGCTGACGAGTGTAAACTTGTGCAAGCTGGAGAGCGTAACAGCATAAATAAGCTGAC
1 CATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGAAAGCGTAACAGCATAAATAAGCTGAC
* * * *
414266 TAGCGTAAACATGTGCAAGCTGGAGAGCGTAAACG
66 GAGCGTAAACACGTGCAAACTGGAGAGCATAAACG
** * *
414301 TTTAAATAAGCTGACGAGCGTAAACGTGTGCAAGCT-GACAAGCGTAA-ACGTGATAAATAAGTT
1 CATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGA-AAGCGTAACA-G-CATAAATAAGCT
*
414364 GACGAGCGTAAACACGTGCAAACTGGCGAGCATAAACG
63 GACGAGCGTAAACACGTGCAAACTGGAGAGCATAAACG
*
414402 CATAAATAACCTGACGAGCGTAAACGTGTGCAAG
1 CATAAATAAGCTGACGAGCGTAAACGTGTGCAAG
414436 TTGGCGGACG
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
99 3 0.03
100 39 0.34
101 74 0.64
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (100 bp):
CATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGAAAGCGTAACAGCATAAATAAGCTGAC
GAGCGTAAACACGTGCAAACTGGAGAGCATAAACG
Found at i:414441 original size:50 final size:50
Alignment explanation
Indices: 414201--414441 Score: 286
Period size: 50 Copynumber: 4.8 Consensus size: 50
414191 TTTATATGTA
* * * *
414201 CATATATAAGCTGACGAGTGTAAACTTGTGCAAGCTGGAGAGCGT-AACAG
1 CATAAATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGCGTAAAC-G
* *
414251 CATAAATAAGCTGACTAGCGTAAACATGTGCAAGCTGGAGAGCGTAAACG
1 CATAAATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGCGTAAACG
** * * *
414301 TTTAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACAAGCGTAAACG
1 CATAAATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGCGTAAACG
* * * * *
414351 TGATAAATAAGTTGACGAGCGTAAACACGTGCAAACTGGCGAGCATAAACG
1 -CATAAATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGCGTAAACG
* * *
414402 CATAAATAACCTGACGAGCGTAAACGTGTGCAAGTTGGCG
1 CATAAATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCG
414442 GACGAGCGTA
Statistics
Matches: 162, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
50 118 0.73
51 44 0.27
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.20
Consensus pattern (50 bp):
CATAAATAAGCTGACGAGCGTAAACATGTGCAAGCTGGCGAGCGTAAACG
Found at i:414472 original size:78 final size:78
Alignment explanation
Indices: 414364--414563 Score: 210
Period size: 75 Copynumber: 2.6 Consensus size: 78
414354 TAAATAAGTT
** * * * *
414364 GACGAGCGTAAACACGTGCAAACTGGCGAGCATAAACGC-ATAAATAACCTGACGAGCGTAAACG
1 GACGAGCGTAAACGTGTACAAACTGACGAGCATAAACACGATAAATAACCAGACGAGCGTAAACG
*
414428 TGTGCAAGTTGGC
66 TGTGCAAGCTGGC
* * * * *
414441 GGACGAGCGTAAACGTGTACAAGCTGACGAGCATAAACACGATTAATAAGCAGATGAGTGTAAAC
1 -GACGAGCGTAAACGTGTACAAACTGACGAGCATAAACACGATAAATAACCAGACGAGCGTAAAC
414506 GTGTGCAAGCTGGC
65 GTGTGCAAGCTGGC
* * * * *
414520 -A--AGCGTAAACGTGTGCAGACTGGCGAGCGTAAACACAATAAATA
1 GACGAGCGTAAACGTGTACAAACTGACGAGCATAAACACGATAAATA
414564 TCTTGATATG
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
75 36 0.35
77 1 0.01
78 33 0.32
79 32 0.31
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.17
Consensus pattern (78 bp):
GACGAGCGTAAACGTGTACAAACTGACGAGCATAAACACGATAAATAACCAGACGAGCGTAAACG
TGTGCAAGCTGGC
Found at i:415853 original size:30 final size:31
Alignment explanation
Indices: 415819--415891 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
415809 CATTTAACAC
415819 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACATTATCGAAAA-GTGACAA
415849 AACAGTCACTAACATTATCGAAAAGTGACAA
1 AACAGTCACTAACATTATCGAAAAGTGACAA
415880 AACAGTCACTAA
1 AACAGTCACTAA
415892 TTAACAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 3 0.08
30 12 0.30
31 20 0.50
32 5 0.12
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACATTATCGAAAAGTGACAA
Found at i:416087 original size:12 final size:12
Alignment explanation
Indices: 416033--416094 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
416023 TAACAAACAG
416033 AATCC-AATCAA
1 AATCCAAATCAA
*
416044 AATCGAAAT---
1 AATCCAAATCAA
416053 AATCCTAAATCGAA
1 AATCC-AAATC-AA
**
416067 AATGAAAATCAA
1 AATCCAAATCAA
416079 AATCCAAATCAA
1 AATCCAAATCAA
416091 AATC
1 AATC
416095 GAATAAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
9 4 0.10
10 4 0.10
11 4 0.10
12 19 0.49
13 5 0.13
14 3 0.08
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.19
Consensus pattern (12 bp):
AATCCAAATCAA
Found at i:416514 original size:35 final size:35
Alignment explanation
Indices: 416468--416551 Score: 118
Period size: 35 Copynumber: 2.4 Consensus size: 35
416458 GATGTTGATA
*
416468 TTGATTGTGATTTTTGGTTTAGGGTT-TATTCGATT
1 TTGATTGTGATTTTTGATTTAGGGTTAT-TTCGATT
*
416503 TTGATTTTGATTTTTGATTTAGGGTTATTTCGATT
1 TTGATTGTGATTTTTGATTTAGGGTTATTTCGATT
*
416538 TTAATTG-GATTTTT
1 TTGATTGTGATTTTT
416552 ATTGCTATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 7 0.16
35 36 0.82
36 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.21, T:0.60
Consensus pattern (35 bp):
TTGATTGTGATTTTTGATTTAGGGTTATTTCGATT
Found at i:416732 original size:30 final size:29
Alignment explanation
Indices: 416692--416761 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 29
416682 ACTGTTAATC
*
416692 AATGATTGTTTTGT-CATTTTCGATAACGTT-
1 AATGACTGTTTTGTACATTTTC-A-AA-GTTG
416722 AATGACTGTTTTGTCACATTTTCAAAGTTG
1 AATGACTGTTTTGT-ACATTTTCAAAGTTG
416752 AATGACTGTT
1 AATGACTGTT
416762 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 3 0.08
30 25 0.69
31 1 0.03
32 7 0.19
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (29 bp):
AATGACTGTTTTGTACATTTTCAAAGTTG
Found at i:417027 original size:31 final size:31
Alignment explanation
Indices: 416980--417043 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
416970 TAAATGTCCA
*
416980 AAGGATTGAACCGAAAATATCTAATAATATT
1 AAGGATTAAACCGAAAATATCTAATAATATT
* * *
417011 AAGGATTAAACTGAAAATATTTGATAATATT
1 AAGGATTAAACCGAAAATATCTAATAATATT
417042 AA
1 AA
417044 AAATTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (31 bp):
AAGGATTAAACCGAAAATATCTAATAATATT
Found at i:418207 original size:24 final size:24
Alignment explanation
Indices: 418180--418226 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
418170 AACCTAAATT
418180 TTAAAATCTAAAAAATAAAAATAA
1 TTAAAATCTAAAAAATAAAAATAA
* * *
418204 TTAAATTCTTAAAATTAAAAATA
1 TTAAAATCTAAAAAATAAAAATA
418227 TATGGATTAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
TTAAAATCTAAAAAATAAAAATAA
Found at i:426527 original size:25 final size:23
Alignment explanation
Indices: 426499--426544 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
426489 GTTGGATCCA
426499 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
426524 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
426545 CTCTAACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:429931 original size:6 final size:6
Alignment explanation
Indices: 429920--429958 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
429910 TGATCAAAAT
* * *
429920 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
429959 NNNNNNNNNN
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:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:431704 original size:17 final size:17
Alignment explanation
Indices: 431669--431706 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
431659 GTTTTTAAAG
*
431669 TTTAATTTTTTTTTCAA
1 TTTAATTTTTTTATCAA
*
431686 TTTAATTTTTTTATGAA
1 TTTAATTTTTTTATCAA
431703 TTTA
1 TTTA
431707 CATTACGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTAATTTTTTTATCAA
Found at i:432691 original size:17 final size:17
Alignment explanation
Indices: 432661--432694 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
432651 GAATTATGAT
432661 TTGAATATGAAATGAAA
1 TTGAATATGAAATGAAA
432678 TTGAA-ATGAGAATGAAA
1 TTGAATATGA-AATGAAA
432695 ATGGAGGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (17 bp):
TTGAATATGAAATGAAA
Found at i:433111 original size:13 final size:12
Alignment explanation
Indices: 433093--433126 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
433083 ATTCTATTTT
433093 TATTAGGATTAA
1 TATTAGGATTAA
*
433105 TATTTAGGATTAT
1 TA-TTAGGATTAA
433118 TATTAGGAT
1 TATTAGGAT
433127 ATTATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (12 bp):
TATTAGGATTAA
Found at i:435793 original size:23 final size:23
Alignment explanation
Indices: 435767--435813 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
435757 TTTTCTTCTA
435767 GTTTTT-CTCTGCCTTTGTGGCAC
1 GTTTTTCCTCTGCC-TTGTGGCAC
*
435790 GTTTTTCCTCTGTCTTGTGGCAC
1 GTTTTTCCTCTGCCTTGTGGCAC
435813 G
1 G
435814 CTTCTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.04, C:0.26, G:0.23, T:0.47
Consensus pattern (23 bp):
GTTTTTCCTCTGCCTTGTGGCAC
Found at i:438209 original size:18 final size:17
Alignment explanation
Indices: 438186--438230 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
438176 TTATAAAAAA
438186 ATATATTATATTAA-TT
1 ATATATTATATTAATTT
438202 ATATA-TAT-TTATATTT
1 ATATATTATATTA-ATTT
438218 ATAT-TTATATTAA
1 ATATATTATATTAA
438231 ATCTTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 4 0.16
16 15 0.60
17 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTATATTAATTT
Found at i:438216 original size:6 final size:6
Alignment explanation
Indices: 438186--438228 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
438176 TTATAAAAAA
* *
438186 ATATATT ATATTA ATTATAT ATATTT ATATTT ATATTT ATATT
1 ATAT-TT ATATTT A-TATTT ATATTT ATATTT ATATTT ATATT
438229 AAATCTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 23 0.74
7 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:444562 original size:31 final size:32
Alignment explanation
Indices: 444506--444566 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
444496 AATGATTATT
*
444506 GAATTATTCGAAAAATTATTATTTAAGTCACC
1 GAATTATTAGAAAAATTATTATTTAAGTCACC
* *
444538 GAATTATTAG-AAAGTTTTTATTTAAGTCA
1 GAATTATTAGAAAAATTATTATTTAAGTCA
444567 TCGAGTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (32 bp):
GAATTATTAGAAAAATTATTATTTAAGTCACC
Found at i:445131 original size:15 final size:15
Alignment explanation
Indices: 445111--445175 Score: 62
Period size: 15 Copynumber: 4.2 Consensus size: 15
445101 AAAATATTTG
445111 AAATATTTTAATATA
1 AAATATTTTAATATA
*
445126 AAATATTTT-ATTTCA
1 AAATATTTTAATAT-A
445141 AAATATAATTTAA-ATTA
1 AAATAT--TTTAATA-TA
*
445158 GAATATTTTAATATA
1 AAATATTTTAATATA
445173 AAA
1 AAA
445176 CTAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 3 0.08
15 25 0.62
16 1 0.03
17 9 0.22
18 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:445294 original size:60 final size:62
Alignment explanation
Indices: 445198--445325 Score: 197
Period size: 60 Copynumber: 2.1 Consensus size: 62
445188 TTAATATAAA
* * * *
445198 AATAATTATATTAAGAATGTTATTAAATTATATATTATTATTTTTATTAAGTTATA-TTAAT
1 AATAATTATATTAAGAATATGATTAAATTATATATTATCATTTTTATTAAATTATATTTAAT
*
445259 AATAATTATATTAA-AATATGATTAAATTATTTATTATCATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAGAATATGATTAAATTATATATTATCATTTTTATTAAATTATATTTAAT
445320 AATAAT
1 AATAAT
445326 AATAATAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 36 0.59
61 25 0.41
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.52
Consensus pattern (62 bp):
AATAATTATATTAAGAATATGATTAAATTATATATTATCATTTTTATTAAATTATATTTAAT
Found at i:453642 original size:24 final size:24
Alignment explanation
Indices: 453615--453689 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
453605 GAGAAATAAT
* *
453615 TTTCAGTTAAATTCTGTTTAATTG
1 TTTCAATTAAATTCTGTTTATTTG
*
453639 TTTCAATTAAATTTTGTTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
* *
453663 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
453687 TTT
1 TTT
453690 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAATTCTGTTTATTTG
Found at i:454500 original size:5 final size:5
Alignment explanation
Indices: 454488--454518 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
454478 TATTTTTAAT
454488 AAAT- AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AA
454519 GAGGTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:455773 original size:21 final size:21
Alignment explanation
Indices: 455749--455803 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
455739 AAATATAAAT
* *
455749 ATAAATAATATAATTAAGAAC
1 ATAAATAACATAATTAAGAAA
455770 ATAAATAACATAATTAAGAAA
1 ATAAATAACATAATTAAGAAA
*
455791 ATAAATATCATAA
1 ATAAATAACATAA
455804 ATAATTTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAATAACATAATTAAGAAA
Found at i:459195 original size:31 final size:31
Alignment explanation
Indices: 459148--459259 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
459138 TGAATCTAAA
*
459148 AAAGCTTAGGTACCAAATTAGGAAAAAGTGT
1 AAAGTTTAGGTACCAAATTAGGAAAAAGTGT
* * **
459179 CAAGTTTAGGTGCCAAATTAGGTAAAAAAAAG-
1 AAAGTTTAGGTACCAAATTAGG--AAAAAGTGT
*
459211 AAAGTTTAAGTACCAAATTAGGAAAAAGTGT
1 AAAGTTTAGGTACCAAATTAGGAAAAAGTGT
* * *
459242 TAAGTTCAAGTACCAAAT
1 AAAGTTTAGGTACCAAAT
459260 ATTATATTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
30 6 0.09
31 35 0.53
32 19 0.29
33 6 0.09
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (31 bp):
AAAGTTTAGGTACCAAATTAGGAAAAAGTGT
Done.