Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010964.1 Kokia drynarioides strain JFW-HI SEQ_125932, 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: 47682
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:100 original size:63 final size:63
Alignment explanation
Indices: 1--123 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
1 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCACTTG
1 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCACTTG
64 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCAC
1 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCAC
124 CTGAACTTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (63 bp):
CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCACTTG
Found at i:6289 original size:30 final size:29
Alignment explanation
Indices: 6252--6338 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
6242 GCAACAGGAG
6252 GTGGGTTTGCTGGTTTGGCTTCAGGTGGT
1 GTGGGTTTGCTGGTTTGGCTTCAGGTGGT
*
6281 GTTGGGTTTTCTGGTGTT-GCTTCAGGT-G-
1 G-TGGGTTTGCTGGT-TTGGCTTCAGGTGGT
* * *
6309 GTGGATTTGGTGGTCTGGCTTCAGGTGGT
1 GTGGGTTTGCTGGTTTGGCTTCAGGTGGT
6338 G
1 G
6339 GGAGATTTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.02
27 19 0.40
28 2 0.04
29 3 0.06
30 21 0.44
31 2 0.04
ACGTcount: A:0.05, C:0.10, G:0.44, T:0.41
Consensus pattern (29 bp):
GTGGGTTTGCTGGTTTGGCTTCAGGTGGT
Found at i:6291 original size:57 final size:57
Alignment explanation
Indices: 6230--6338 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
6220 TGCTGCTGGA
* *
6230 TTTTCTAATGCTGCAACAGGAGGTGGGTTTGCTGGTTTGGCTTCAGGTGGTGTTGGG
1 TTTTCTAATGCTGCAACAGGAGGTGGATTTGCTGGTCTGGCTTCAGGTGGTGTTGGG
** * ** * *
6287 TTTTCTGGTGTTGCTTCAGGTGGTGGATTTGGTGGTCTGGCTTCAGGTGGTG
1 TTTTCTAATGCTGCAACAGGAGGTGGATTTGCTGGTCTGGCTTCAGGTGGTG
6339 GGAGATTTGG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.09, C:0.12, G:0.39, T:0.39
Consensus pattern (57 bp):
TTTTCTAATGCTGCAACAGGAGGTGGATTTGCTGGTCTGGCTTCAGGTGGTGTTGGG
Found at i:6339 original size:30 final size:30
Alignment explanation
Indices: 6251--6347 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
6241 TGCAACAGGA
* *
6251 GGTGGGTTTGCTGGTTTGGCTTCAGGTGGT
1 GGTGGATTTGCTGGTCTGGCTTCAGGTGGT
* * * * *
6281 GTTGGGTTTTCTGGTGTTGCTTCA---GGT
1 GGTGGATTTGCTGGTCTGGCTTCAGGTGGT
*
6308 GGTGGATTTGGTGGTCTGGCTTCAGGTGGT
1 GGTGGATTTGCTGGTCTGGCTTCAGGTGGT
6338 GG-GAGATTTG
1 GGTG-GATTTG
6348 GTAGCTTAGC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
27 21 0.40
29 1 0.02
30 31 0.58
ACGTcount: A:0.06, C:0.09, G:0.44, T:0.40
Consensus pattern (30 bp):
GGTGGATTTGCTGGTCTGGCTTCAGGTGGT
Found at i:14239 original size:28 final size:27
Alignment explanation
Indices: 14206--14312 Score: 124
Period size: 28 Copynumber: 3.9 Consensus size: 27
14196 TAGTTTCTAA
14206 AAAGTGAGCCTTTGTGGCTGATTCTATT
1 AAAGTGAGCCTTTGTGGCTGATT-TATT
* * **
14234 AAAGTGAGCCTCTATGGCCAAATTTATT
1 AAAGTGAGCCTTTGTGG-CTGATTTATT
* *
14262 AAAGTAAGCCTTTGTGGCTGAATTTGTT
1 AAAGTGAGCCTTTGTGGCTG-ATTTATT
*
14290 AAAGTGAGCTTTTGTGGCTGATT
1 AAAGTGAGCCTTTGTGGCTGATT
14313 CTGTAAAGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
27 4 0.06
28 57 0.88
29 4 0.06
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (27 bp):
AAAGTGAGCCTTTGTGGCTGATTTATT
Found at i:14330 original size:27 final size:28
Alignment explanation
Indices: 14206--14335 Score: 99
Period size: 28 Copynumber: 4.7 Consensus size: 28
14196 TAGTTTCTAA
* *
14206 AAAGTGAGCCTTTGTGGCTG-ATTCTATT
1 AAAGTGAACCTTTGTGGCTGAATT-TGTT
* * * ** *
14234 AAAGTGAGCCTCTATGGCCAAATTTATT
1 AAAGTGAACCTTTGTGGCTGAATTTGTT
14262 AAAGT-AAGCCTTTGTGGCTGAATTTGTT
1 AAAGTGAA-CCTTTGTGGCTGAATTTGTT
* *
14290 AAAGTGAGCTTTTGTGGCTG-ATTCTG-T
1 AAAGTGAACCTTTGTGGCTGAATT-TGTT
14317 AAAG-GACACCTTTGTGGCT
1 AAAGTGA-ACCTTTGTGGCT
14336 ATCTCTGAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.02
27 19 0.23
28 58 0.70
29 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAGTGAACCTTTGTGGCTGAATTTGTT
Found at i:14342 original size:27 final size:26
Alignment explanation
Indices: 14300--14367 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
14290 AAAGTGAGCT
14300 TTTGTGGCTGAT-TCTGTAAAGGACACC
1 TTTGTGGCT-ATCTCTG-AAAGGACACC
* **
14327 TTTGTGGCTATCTCTGAATGGATGCC
1 TTTGTGGCTATCTCTGAAAGGACACC
*
14353 TTTGTCGCTATCTCT
1 TTTGTGGCTATCTCT
14368 AATAAAGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 23 0.64
27 13 0.36
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (26 bp):
TTTGTGGCTATCTCTGAAAGGACACC
Found at i:15280 original size:23 final size:23
Alignment explanation
Indices: 15237--15280 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
15227 AAATTATTTA
* *
15237 ATGTCATGTTAGCATCTTTTTCC
1 ATGTCATGATAGCATCATTTTCC
15260 ATGTCATTGATAG-ATCATTTT
1 ATGTCA-TGATAGCATCATTTT
15281 GGTAACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.48
Consensus pattern (23 bp):
ATGTCATGATAGCATCATTTTCC
Found at i:15534 original size:7 final size:7
Alignment explanation
Indices: 15465--15745 Score: 83
Period size: 7 Copynumber: 39.9 Consensus size: 7
15455 GTTTATCTAG
15465 GGTTT-A
1 GGTTTAA
15471 GGATTTCAA
1 GG-TTT-AA
*
15480 GGTTCAA
1 GGTTTAA
*
15487 GGTCTAA
1 GGTTTAA
*
15494 GATTTAA
1 GGTTTAA
* *
15501 GATTCAA
1 GGTTTAA
*
15508 TGTTTAA
1 GGTTTAA
15515 GGTTTAA
1 GGTTTAA
* *
15522 GATTTAG
1 GGTTTAA
15529 GGTTTAA
1 GGTTTAA
*
15536 TGTCTT-A
1 GGT-TTAA
15543 GGTTT-A
1 GGTTTAA
*
15549 GGTTTAG
1 GGTTTAA
15556 GGTTTATTCA
1 GGTTTA---A
15566 GGGTTTAA
1 -GGTTTAA
*
15574 GATTTAA
1 GGTTTAA
15581 GGTTTAA
1 GGTTTAA
*
15588 GGTATAA
1 GGTTTAA
* *
15595 GATTTAG
1 GGTTTAA
**
15602 GGTCCAA
1 GGTTTAA
*
15609 CGTTTAA
1 GGTTTAA
*
15616 GGTCT-A
1 GGTTTAA
15622 GGATTTAA
1 GG-TTTAA
**
15630 GGTCCAA
1 GGTTTAA
* *
15637 GGTCTAG
1 GGTTTAA
*
15644 GGTCTAA
1 GGTTTAA
15651 GGTCTTAA
1 GGT-TTAA
* **
15659 -GTCTCG
1 GGTTTAA
*
15665 GGTCT-A
1 GGTTTAA
*
15671 GGTTTTA
1 GGTTTAA
* *
15678 GGGTTCA
1 GGTTTAA
* *
15685 --TCTAG
1 GGTTTAA
*
15690 GGTTTAT
1 GGTTTAA
*
15697 GAATTTAA
1 G-GTTTAA
15705 GGTTTAA
1 GGTTTAA
15712 GGTTTAA
1 GGTTTAA
* *
15719 GATTTAG
1 GGTTTAA
*
15726 GGATTAA
1 GGTTTAA
15733 GGTTTAA
1 GGTTTAA
15740 GGTTTA
1 GGTTTA
15746 GGATTTAGGG
Statistics
Matches: 196, Mismatches: 62, Indels: 33
0.67 0.21 0.11
Matches are distributed among these distances:
5 1 0.01
6 18 0.09
7 152 0.78
8 16 0.08
9 3 0.02
11 6 0.03
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.39
Consensus pattern (7 bp):
GGTTTAA
Found at i:15732 original size:28 final size:28
Alignment explanation
Indices: 15701--15755 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
15691 GTTTATGAAT
15701 TTAAGGTTTAAGGTTTAAGATTTAGGGA
1 TTAAGGTTTAAGGTTTAAGATTTAGGGA
*
15729 TTAAGGTTTAAGGTTTAGGATTTAGGG
1 TTAAGGTTTAAGGTTTAAGATTTAGGG
15756 TCGGTCTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (28 bp):
TTAAGGTTTAAGGTTTAAGATTTAGGGA
Found at i:15811 original size:121 final size:122
Alignment explanation
Indices: 15565--15879 Score: 413
Period size: 121 Copynumber: 2.6 Consensus size: 122
15555 GGGTTTATTC
* * * *
15565 AGGGTTTAAG-ATTTAAGGTTTAAGGTATAAGATTTAGGGTCCAACGTTTAAGGTCTAGGATTTA
1 AGGGTTTATGAATTTAAGGTTTAAGGTATAAGATTTAGGGTCTAAGGTTTAAGGTTTAGGATTTA
* * *
15629 AGGTCCAAGGTCTAGGGTCTAAGGTCTTAAGTCTCGGGTCTAGGTTTTAGGGTTCATCT
66 GGGT-C-AGGTCTAGGGTCTAAGGTCTCAAGTCTCGGGTCTAGGTTTTAAGGTTCATCT
*
15688 AGGGTTTATGAATTTAAGGTTTAAGGTTTAAGATTTAGGGAT-TAAGGTTTAAGGTTTAGGATTT
1 AGGGTTTATGAATTTAAGGTTTAAGGTATAAGATTTAGGG-TCTAAGGTTTAAGGTTTAGGATTT
* * *
15752 AGGGTC-GGTCTAGGAT-TCAAGGTCTCGAGTCTTGGGTCTAGGTTTTAAGGTTCATCT
65 AGGGTCAGGTCTAGGGTCT-AAGGTCTCAAGTCTCGGGTCTAGGTTTTAAGGTTCATCT
* * * * * *
15809 AGGGTTTATGATTTTAAAGTTCAATGTCTAAGATTTAGGGTCTAAGATTTAAGGTTTAGGATTTA
1 AGGGTTTATGAATTTAAGGTTTAAGGTATAAGATTTAGGGTCTAAGGTTTAAGGTTTAGGATTTA
15874 GGGTCA
66 GGGTCA
15880 AAGGTTCAAG
Statistics
Matches: 170, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
120 2 0.01
121 106 0.62
123 10 0.06
124 51 0.30
125 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (122 bp):
AGGGTTTATGAATTTAAGGTTTAAGGTATAAGATTTAGGGTCTAAGGTTTAAGGTTTAGGATTTA
GGGTCAGGTCTAGGGTCTAAGGTCTCAAGTCTCGGGTCTAGGTTTTAAGGTTCATCT
Found at i:15853 original size:14 final size:14
Alignment explanation
Indices: 15834--15878 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
15824 AAAGTTCAAT
15834 GTCTAAGATTTAGG
1 GTCTAAGATTTAGG
*
15848 GTCTAAGATTTAAG
1 GTCTAAGATTTAGG
* *
15862 GTTTAGGATTTAGG
1 GTCTAAGATTTAGG
15876 GTC
1 GTC
15879 AAAGGTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.38
Consensus pattern (14 bp):
GTCTAAGATTTAGG
Found at i:19154 original size:20 final size:20
Alignment explanation
Indices: 19125--19162 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19115 TAAAATCCAA
*
19125 AACCTCGAACTTTAAACTCG
1 AACCTCGAACCTTAAACTCG
*
19145 AACCTTGAACCTTAAACT
1 AACCTCGAACCTTAAACT
19163 TCAAACTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (20 bp):
AACCTCGAACCTTAAACTCG
Found at i:22719 original size:26 final size:27
Alignment explanation
Indices: 22689--22742 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
22679 ATTTTTTTTT
* *
22689 ATTAAATTTTAATAAAAA-TATAAAAA
1 ATTAAACTTTAATAAAAATTAGAAAAA
*
22715 ATTAAACTTTATTAAAAATTAGAAAAA
1 ATTAAACTTTAATAAAAATTAGAAAAA
22742 A
1 A
22743 AATTATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
ATTAAACTTTAATAAAAATTAGAAAAA
Found at i:23285 original size:16 final size:17
Alignment explanation
Indices: 23264--23296 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23254 GTAATTTTAT
*
23264 TTTTAATAA-TTTAAAA
1 TTTTAAAAATTTTAAAA
23280 TTTTAAAAATTTTAAAA
1 TTTTAAAAATTTTAAAA
23297 GGCTTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTTTAAAA
Found at i:25582 original size:5 final size:5
Alignment explanation
Indices: 25572--25599 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
25562 GCAATTTGCA
25572 GTTCT GTTCT GTTCT GTTCT GTTCT GTT
1 GTTCT GTTCT GTTCT GTTCT GTTCT GTT
25600 TTTGTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.61
Consensus pattern (5 bp):
GTTCT
Found at i:27738 original size:21 final size:21
Alignment explanation
Indices: 27714--27777 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
27704 TAATACTTTT
*
27714 AAGGTAAGTCTCGATACTTGC
1 AAGGTAAGTATCGATACTTGC
* * *
27735 AAGGTAGGTATCGGTTCTTGC
1 AAGGTAAGTATCGATACTTGC
**
27756 ACTGTAAGTATCGATACCTTGC
1 AAGGTAAGTATCGATA-CTTGC
27778 CTTCCTTGAT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 28 0.85
22 5 0.15
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (21 bp):
AAGGTAAGTATCGATACTTGC
Found at i:36559 original size:25 final size:25
Alignment explanation
Indices: 36531--36638 Score: 74
Period size: 25 Copynumber: 4.1 Consensus size: 25
36521 CAAAAAGTTG
* *
36531 AAGTAGCAACTTAAAAAAAAATGTC
1 AAGTACCAAATTAAAAAAAAATGTC
**
36556 AAGTACCAAATTAGGAAAAAATGTC
1 AAGTACCAAATTAAAAAAAAATGTC
*
36581 AAGTTTAAGTACCAAATTGAAAAAAAAAT-TT
1 ------AAGTACCAAATT-AAAAAAAAATGTC
* * *
36612 AAATACCAAATTAATAAAAAGTGTC
1 AAGTACCAAATTAAAAAAAAATGTC
36637 AA
1 AA
36639 ATTTAAATAC
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
24 8 0.12
25 35 0.55
31 13 0.20
32 8 0.12
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.23
Consensus pattern (25 bp):
AAGTACCAAATTAAAAAAAAATGTC
Found at i:36591 original size:56 final size:56
Alignment explanation
Indices: 36525--36653 Score: 143
Period size: 56 Copynumber: 2.3 Consensus size: 56
36515 GAACCCCAAA
* * * * *
36525 AAGTTGAAGTAGCAACTT-AAAAAAAAATGTCAAGTACCAAATTAGGAAAAAATGTC
1 AAGTTTAAGTACCAAATTGAAAAAAAAAT-TCAAATACCAAATTAAGAAAAAATGTC
* * *
36581 AAGTTTAAGTACCAAATTGAAAAAAAAATTTAAATACCAAATTAATAAAAAGTGTC
1 AAGTTTAAGTACCAAATTGAAAAAAAAATTCAAATACCAAATTAAGAAAAAATGTC
* * *
36637 AAATTTAAATACTAAAT
1 AAGTTTAAGTACCAAAT
36654 GTTATATTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 51 0.84
57 10 0.16
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (56 bp):
AAGTTTAAGTACCAAATTGAAAAAAAAATTCAAATACCAAATTAAGAAAAAATGTC
Found at i:38184 original size:16 final size:16
Alignment explanation
Indices: 38153--38195 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
38143 AAAATTAAAT
*
38153 TTTTATAA-ATGTTTA
1 TTTTATAATATGCTTA
38168 TTTTATAATATGCTTA
1 TTTTATAATATGCTTA
* *
38184 TTATATTATATG
1 TTTTATAATATG
38196 AGACGTGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (16 bp):
TTTTATAATATGCTTA
Found at i:41764 original size:32 final size:32
Alignment explanation
Indices: 41701--41764 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
41691 TGTCAATAAT
* *
41701 TAATAATAATAATAAAAGAAATCACATCTTTC
1 TAATAATAATAATAAAAAAAATCACAGCTTTC
**
41733 TAATAA-AATAATAAAATAAAATTTCAGCTTTC
1 TAATAATAATAATAAAA-AAAATCACAGCTTTC
41765 AACATTGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (32 bp):
TAATAATAATAATAAAAAAAATCACAGCTTTC
Found at i:42467 original size:5 final size:5
Alignment explanation
Indices: 42459--42485 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42449 AATGGGCTGG
42459 GGAGA GGAGA GGAGA GGAGA GGAGA GG
1 GGAGA GGAGA GGAGA GGAGA GGAGA GG
42486 TATAAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (5 bp):
GGAGA
Found at i:45361 original size:16 final size:17
Alignment explanation
Indices: 45334--45365 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
45324 TAATATTTAT
45334 ATTTTATTTAAAATATG
1 ATTTTATTTAAAATATG
45351 ATTTT-TTTAAAATAT
1 ATTTTATTTAAAATAT
45366 ATATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTATTTAAAATATG
Found at i:45374 original size:17 final size:17
Alignment explanation
Indices: 45311--45375 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
45301 TTAAAAAATT
*
45311 ATATATATATTTTTAAT
1 ATATATATATTTTTAAA
* *
45328 ATTTATATTTTATTTAAA
1 ATATATATATT-TTTAAA
45346 ATATGAT-T-TTTTTAAA
1 ATAT-ATATATTTTTAAA
45362 ATATATATATTTTT
1 ATATATATATTTTT
45376 TTAAAGGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.05
16 11 0.28
17 16 0.40
18 9 0.22
19 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATATATATATTTTTAAA
Found at i:45576 original size:130 final size:128
Alignment explanation
Indices: 45425--45661 Score: 323
Period size: 130 Copynumber: 1.8 Consensus size: 128
45415 TTGACTGCTA
* * * *
45425 AAAAAATTATTTACCTTTGATACGATTAACTTTAATAGAAAAATTAGATGGAGGGATCAAAATTT
1 AAAAAATTATTTAACTTTGATACCATAAACTTTAATAGAAAAATTAAATGGAGGGATCAAAATTT
45490 TTAAATAAAAAAAAAGTACAAGA-TTCAATGTCTCAAAATTATAAGGATTAAATTTTAAATTTTA
66 TTAAATAAAAAAAAA-TA-AAGACTT-AATGTCTCAAAATTATAAGGATTAAATTTTAAATTTTA
45554 G
128 G
* * * * * *
45555 AAAAAGTTATTTAACTTTGATACCATAAACTTTAGTGGCAAGATTAAATGGAGGGATCAAGATTT
1 AAAAAATTATTTAACTTTGATACCATAAACTTTAATAGAAAAATTAAATGGAGGGATCAAAATTT
** *
45620 TTAAATAAAAAAGTATAAAGACTTAGTGTCTCAAAATTATAA
66 TTAAATAAAAAAAAATAAAGACTTAATGTCTCAAAATTATAA
45662 AAATTAAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
128 21 0.23
129 4 0.04
130 68 0.73
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (128 bp):
AAAAAATTATTTAACTTTGATACCATAAACTTTAATAGAAAAATTAAATGGAGGGATCAAAATTT
TTAAATAAAAAAAAATAAAGACTTAATGTCTCAAAATTATAAGGATTAAATTTTAAATTTTAG
Done.