Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002660.1 Kokia drynarioides strain JFW-HI SEQ_114909, 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: 31126
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:418 original size:59 final size:60
Alignment explanation
Indices: 341--1015 Score: 326
Period size: 59 Copynumber: 11.3 Consensus size: 60
331 GTAAAAAATC
* * * *
341 TGGTGTTGGCCATCCCATGGCCGACACCCCCTTTTT-TCAGATAAAAAATTTGATTTTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTTAAATTTTT
** * ** * * ** * * *
400 TTATATTGGTCATGCCATGATCGATACTTCATTTTTTATCTGGTAAAAAA-TTAATTTTTT
1 TGGTGTTGGTCATGCCATGGCCGACAC-CCCCTTTTTATCAGATAAAAAATTTAAATTTTT
* * * * * * * **
460 TGGTGTTAGTCATGCAATGGTCGACACTCCCTTTTTGTCATATGAAAAATTCGAATTTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTTAAATTTTT
* * * * *
520 T-TTGTT-GTCAATTG-TATGGCCGACACCCCTTTTTTTATCTGGTACAAAAATTTCAAAATTTT
1 TGGTGTTGGTC-A-TGCCATGGCCGACACCCC-CTTTTTATCAGATA-AAAAATTT--AAA-TTT
582 TT
59 TT
** * * * * * * *
584 TTATATTGATCATTG-CATGGCCGATA-CTCCTTTTTATTTAAATAAAAAA-TCAAATTTTT
1 TGGTGTTGGTCA-TGCCATGGCCGACACCCCCTTTTTA-TCAGATAAAAAATTTAAATTTTT
** * ** * *
643 AAGTGTTGGCCATGCCATGGTTGACACCCCCTTTTTGTCAGAT-AAAAATTCAAATTTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTTAAATTTTT
* * * * * * * * *
702 TTGTGTTGGCCATGTCATGGTCGACA-TCCCTATTTATCTGATAAAAAAAATCAAATTTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGAT-AAAAAATTTAAATTTTT
* * * * * * * *
762 TGGTATTTGCCATGCAATGACC-A-A-CACATTTTT-TCAAATAAAAAATTTCAAATTTTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTT-AAA-TTTTT
* * *
820 TGGTGTTGGTCATTG-CATGGCCGACA-CCCTTTTTTATTAAAATAAAAAA-TTAAATTTTT
1 TGGTGTTGGTCA-TGCCATGGCCGACACCCCCTTTTTA-TCAGATAAAAAATTTAAATTTTT
* * * * * * *
879 GGGTGTTGGCCATGTCATGGCCGACACCCCTTTTTTATCTGGTAAAAAA-TTAATTTTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTTAAATTTTT
* ** * * * **
938 TGGTATTGGTCATGTAATGGTCGACACTCCCTTTTTGTCAGATAAAAAATTCGAA-TTTT
1 TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTTAAATTTTT
* * *
997 TGGTGCTGGCCATGTCATG
1 TGGTGTTGGTCATGCCATG
1016 ACAAACACTC
Statistics
Matches: 464, Mismatches: 124, Indels: 56
0.72 0.19 0.09
Matches are distributed among these distances:
56 7 0.02
57 7 0.02
58 49 0.11
59 211 0.45
60 117 0.25
61 19 0.04
62 12 0.03
63 13 0.03
64 11 0.02
65 16 0.03
66 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (60 bp):
TGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTTAAATTTTT
Found at i:913 original size:118 final size:118
Alignment explanation
Indices: 432--1057 Score: 399
Period size: 118 Copynumber: 5.3 Consensus size: 118
422 GATACTTCAT
* * * * *
432 TTTTTATCTGGTAAAAAATT--AATTTTTTTGGTGTTAGTCATG-CAATGGTCGACACTCCCTTT
1 TTTTTATCAGATAAAAAATTCAAATTTTTTTGGTATTGGTCATGTC-ATGGCCGACACT-CCTTT
* * * * * ** * *
494 TT-GTCATATGAAAAATTCGAATTTTTTTTGTTGTCAATTGT-ATGGCCGACACCCC
64 TTATTAAAAT-AAAAAATCAAATTTTTGGTGTTGGCCA-TGTCATGGCCGACACCCC
* * ** * *
549 TTTTTTTATCTGGTACAAAAATTTCAAAATTTTTTTTATATTGATCAT-TGCATGGCCGATACTC
1 --TTTTTATCAGATA-AAAAA-TTC-AAATTTTTTTGGTATTGGTCATGT-CATGGCCGACACTC
* * * **
613 CTTTTTATTTAAATAAAAAATCAAATTTTTAAGTGTTGGCCATGCCATGGTTGACACCCCC
60 CTTTTTATTAAAATAAAAAATCAAATTTTT-GGTGTTGGCCATGTCATGGCCGACA-CCCC
* * * * *
674 TTTTTGTCAGAT-AAAAATTCAAATTTTTTT-GTGTTGGCCATGTCATGGTCGACA-TCCCTATT
1 TTTTTATCAGATAAAAAATTCAAATTTTTTTGGTATTGGTCATGTCATGGCCGACACT-CCTTTT
* * * * * *
736 TATCTGATAA-AAAAAATCAAATTTTTTGGTATTTGCCATG-CAATGACC-A-ACACA
65 TAT-T-AAAATAAAAAATCAAA-TTTTTGGTGTTGGCCATGTC-ATGGCCGACACCCC
* *
790 TTTTT-TCAAATAAAAAATTTCAAATTTTTTTGGTGTTGGTCAT-TGCATGGCCGACAC-CCTTT
1 TTTTTATCAGATAAAAAA-TTCAAATTTTTTTGGTATTGGTCATGT-CATGGCCGACACTCC-TT
*
852 TTTATTAAAATAAAAAATTAAATTTTTGGGTGTTGGCCATGTCATGGCCGACACCCC
63 TTTATTAAAATAAAAAATCAAATTTTT-GGTGTTGGCCATGTCATGGCCGACACCCC
* * * *
909 TTTTTTATCTGGTAAAAAATT--AATTTTTTTGGTATTGGTCATGTAATGGTCGACACTCCCTTT
1 -TTTTTATCAGATAAAAAATTCAAATTTTTTTGGTATTGGTCATGTCATGGCCGACACT-CCTTT
* * * * * * ** *
972 TT-GTCAGATAAAAAATTCGAATTTTTGGTGCTGGCCATGTCATGACAAACACTCC
64 TTATTAAAATAAAAAA-TCAAATTTTTGGTGTTGGCCATGTCATGGCCGACACCCC
* * *
1027 TATTTATCTGATAAAAAAATCAATATTTTTT
1 TTTTTATCAGATAAAAAATTCAA-ATTTTTT
1058 GTGTTATCCA
Statistics
Matches: 401, Mismatches: 69, Indels: 73
0.74 0.13 0.13
Matches are distributed among these distances:
115 5 0.01
116 20 0.05
117 62 0.15
118 118 0.29
119 67 0.17
120 31 0.08
121 16 0.04
123 32 0.08
124 45 0.11
125 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (118 bp):
TTTTTATCAGATAAAAAATTCAAATTTTTTTGGTATTGGTCATGTCATGGCCGACACTCCTTTTT
ATTAAAATAAAAAATCAAATTTTTGGTGTTGGCCATGTCATGGCCGACACCCC
Found at i:997 original size:236 final size:242
Alignment explanation
Indices: 431--997 Score: 640
Period size: 236 Copynumber: 2.4 Consensus size: 242
421 CGATACTTCA
* *
431 TTTTTTATCTGGTAAAAAATTAATTTTTTTGGTGTTAGTCATGCAATGGTCGACACTCCCTTTTT
1 TTTTTTATCTGGTAAAAAATTAATTTTTTTGGTGTTGGTCATGTAATGGTCGACACTCCCTTTTT
* * * * * * **
496 GTCATATGAAAAATTCGAATTTTTTTTGTTGTCAATTGTATGGCCGACACCCCTTTTTTTATCTG
66 GTCAGATAAAAAATTCGAATTTTTTTTGTTGTCAATTGAATGACCGACACCACTATTTTTATCAA
* * * *
561 GTACAAAAATTTCAAAATTTTTTTTATATTGATCATTGCATGGCCGATACTCCTTTTTATTTAAA
131 ATACAAAAATTTCAAAATTTTTTTGATATTGATCATTGCATGGCCGACACTCCTTTTTATTAAAA
**
626 TAAAAAATCAAATTTTTAAGTGTTGGCCATGCCATGGTTGACACCCC
196 TAAAAAATCAAATTTTTAAGTGTTGGCCATGCCATGGCCGACACCCC
* * * * * * *
673 CTTTTTGTCAGAT-AAAAATTCAAATTTTTTT-GTGTTGGCCATGTCATGGTCGACA-TCCCTAT
1 TTTTTTATCTGGTAAAAAATT--AATTTTTTTGGTGTTGGTCATGTAATGGTCGACACTCCCTTT
* * * * *
735 TTATCTGATAAAAAAAATCAAATTTTTTGGTAT-TTG-CCA-TGCAATGACC-A-A-CAC-ATTT
64 TTGTCAGAT-AAAAAATTCGAATTTTTT--T-TGTTGTCAATTG-AATGACCGACACCACTATTT
* * *
793 TT-TCAAATA-AAAAATTTC-AAATTTTTTTGGTGTTGGTCATTGCATGGCCGACAC-CCTTTTT
124 TTATCAAATACAAAAATTTCAAAATTTTTTTGATATTGATCATTGCATGGCCGACACTCC-TTTT
* ** *
854 TATTAAAATAAAAAATTAAATTTTTGGGTGTTGGCCATGTCATGGCCGACACCCC
188 TATTAAAATAAAAAATCAAATTTTTAAGTGTTGGCCATGCCATGGCCGACACCCC
*
909 TTTTTTATCTGGTAAAAAATTAATTTTTTTGGTATTGGTCATGTAATGGTCGACACTCCCTTTTT
1 TTTTTTATCTGGTAAAAAATTAATTTTTTTGGTGTTGGTCATGTAATGGTCGACACTCCCTTTTT
974 GTCAGATAAAAAATTCGAATTTTT
66 GTCAGATAAAAAATTCGAATTTTT
998 GGTGCTGGCC
Statistics
Matches: 267, Mismatches: 47, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
235 11 0.04
236 128 0.48
237 29 0.11
238 4 0.01
239 5 0.02
240 2 0.01
241 20 0.07
242 47 0.18
243 16 0.06
244 4 0.01
245 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (242 bp):
TTTTTTATCTGGTAAAAAATTAATTTTTTTGGTGTTGGTCATGTAATGGTCGACACTCCCTTTTT
GTCAGATAAAAAATTCGAATTTTTTTTGTTGTCAATTGAATGACCGACACCACTATTTTTATCAA
ATACAAAAATTTCAAAATTTTTTTGATATTGATCATTGCATGGCCGACACTCCTTTTTATTAAAA
TAAAAAATCAAATTTTTAAGTGTTGGCCATGCCATGGCCGACACCCC
Found at i:1055 original size:59 final size:57
Alignment explanation
Indices: 609--1062 Score: 226
Period size: 59 Copynumber: 7.7 Consensus size: 57
599 CATGGCCGAT
* * * * **
609 ACTCCTTTTTAT-TTAAATAAAAAATCAAATTTTTAAGTGTTGGCCATGCCATGGTTGAC
1 ACTCCTTTTTATCTGATA-AAAAAATCAAATTTTT-GGTGTTGGCCATGTCAT-GACGAC
* * * * * *
668 ACCCCCTTTTTGTCAGAT-AAAAATTCAAATTTTTTTGTGTTGGCCATGTCATGGTCGAC
1 A-CTCCTTTTTATCTGATAAAAAAATCAAA-TTTTTGGTGTTGGCCATGTCAT-GACGAC
* * * *
727 A-TCCCTATTTATCTGATAAAAAAAATCAAATTTTTTGGTATTTGCCATG-CAATGACCA-
1 ACT-CCTTTTTATCTGAT-AAAAAAATCAAA-TTTTTGGTGTTGGCCATGTC-ATGACGAC
* * ** * * *
785 ACACATTTTT-TCAAATAAAAAATTTCAAATTTTTTTGGTGTTGGTCAT-TGCATGGCCGAC
1 ACTCCTTTTTATCTGATAAAAAA-ATCAAA--TTTTTGGTGTTGGCCATGT-CAT-GACGAC
* * * *
845 AC-CCTTTTTTAT-TAAAATAAAAAATTAAATTTTTGGGTGTTGGCCATGTCATGGCCGAC
1 ACTCC-TTTTTATCTGATA-AAAAAATCAAATTTTT-GGTGTTGGCCATGTCAT-GACGAC
* * * * * * * *
904 ACCCCTTTTTTATCTGGT-AAAAAATTAATTTTTTTGGTATTGGTCATGTAATGGTCGAC
1 ACTCC-TTTTTATCTGATAAAAAAATCAA-ATTTTTGGTGTTGGCCATGTCAT-GACGAC
* * * * * *
963 ACTCCCTTTTTGTCAGATAAAAAATTCGAATTTTTGGTGCTGGCCATGTCATGACAAAC
1 ACT-CCTTTTTATCTGATAAAAAAATCAAATTTTTGGTGTTGGCCATGTCATGAC-GAC
* *
1022 ACTCCTATTTATCTGATAAAAAAATCAATATTTTTTGTGTT
1 ACTCCTTTTTATCTGATAAAAAAATCAA-ATTTTTGGTGTT
1063 ATCCATGCAA
Statistics
Matches: 304, Mismatches: 65, Indels: 52
0.72 0.15 0.12
Matches are distributed among these distances:
56 6 0.02
57 9 0.03
58 61 0.20
59 139 0.46
60 81 0.27
61 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (57 bp):
ACTCCTTTTTATCTGATAAAAAAATCAAATTTTTGGTGTTGGCCATGTCATGACGAC
Found at i:1500 original size:59 final size:59
Alignment explanation
Indices: 1388--1513 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 59
1378 TTTTATCTTA
* *
1388 ATAAAAAATCAAATTTTTGAGTGTTGGCCATATCATGGTCAACACTCCTTTTTTGTCAG
1 ATAAAAAATCAAATTTTTGAGTGTTGGCCATATAACGGTCAACACTCCTTTTTTGTCAG
* * * *
1447 ATAAAAAATTCAATTTTTTTAGTGTTGGTCATATAACGGTCGACAC-CTCTTTTTT-TCAG
1 ATAAAAAA-TCAAATTTTTGAGTGTTGGCCATATAACGGTCAACACTC-CTTTTTTGTCAG
1506 ATAAAAAA
1 ATAAAAAA
1514 AATTCATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
59 21 0.36
60 38 0.64
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (59 bp):
ATAAAAAATCAAATTTTTGAGTGTTGGCCATATAACGGTCAACACTCCTTTTTTGTCAG
Found at i:2340 original size:59 final size:60
Alignment explanation
Indices: 2230--2373 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 60
2220 TTGCATAGCC
* * *
2230 AACACCAAAAAAATTTGAAATTTTTTTATCCGATAAAAAAGGGTTTCGACCATTGCATGA-T
1 AACA-CAAAAAAATTT-AATTTTTTTTATCCGATAAAAAAGGGTGTAGACCATTGCATGACT
* * * *
2291 CAACACTAAAAAATTTAATTTTTTTTATCTGA-AAAAAGGGGTGTAGACCATTGTATGACT
1 -AACACAAAAAAATTTAATTTTTTTTATCCGATAAAAAAGGGTGTAGACCATTGCATGACT
2351 AACACAAAAAAATTGT-ATTTTTT
1 AACACAAAAAAATT-TAATTTTTT
2374 ATCTAACAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
59 42 0.58
60 16 0.22
61 10 0.14
62 4 0.06
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (60 bp):
AACACAAAAAAATTTAATTTTTTTTATCCGATAAAAAAGGGTGTAGACCATTGCATGACT
Found at i:2385 original size:59 final size:58
Alignment explanation
Indices: 2229--2393 Score: 158
Period size: 59 Copynumber: 2.7 Consensus size: 58
2219 ATTGCATAGC
* * *
2229 CAACACCAAAAAAATTTGAAATTTTTTTATC-CGATAAAAAAGGGTTTCGACCATTGCATGAT
1 CAACA-CAAAAAAATTT--AATTTTTTTATCTC-A-AAAAAGGGGTGTAGACCATTGCATGAT
* * *
2291 CAACACTAAAAAATTTAATTTTTTTTATCTGAAAAAAGGGGTGTAGACCATTGTATGA-
1 CAACACAAAAAAATTTAA-TTTTTTTATCTCAAAAAAGGGGTGTAGACCATTGCATGAT
2349 CTAACACAAAAAAATTGT-A-TTTTTTATCTAACAAAAAAGGGGTGT
1 C-AACACAAAAAAATT-TAATTTTTTTATCT--CAAAAAAGGGGTGT
2394 CGGCCATGCA
Statistics
Matches: 89, Mismatches: 8, Indels: 15
0.79 0.07 0.13
Matches are distributed among these distances:
57 10 0.11
58 1 0.01
59 51 0.57
60 12 0.13
61 10 0.11
62 5 0.06
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (58 bp):
CAACACAAAAAAATTTAATTTTTTTATCTCAAAAAAGGGGTGTAGACCATTGCATGAT
Found at i:5409 original size:2 final size:2
Alignment explanation
Indices: 5402--5465 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
5392 TATAAAACAA
5402 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5444 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5466 TAATTTTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5544 original size:19 final size:20
Alignment explanation
Indices: 5507--5544 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5497 ATAATTTCAT
*
5507 TTTAAATTTTAAGATTTTTA
1 TTTAAATTTTAAGACTTTTA
*
5527 TTTAAA-TTTAATACTTTT
1 TTTAAATTTTAAGACTTTT
5545 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTAAGACTTTTA
Found at i:7450 original size:4 final size:4
Alignment explanation
Indices: 7443--7485 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
7433 CGGGCAGAAG
* *
7443 AAGA AAGA AAGA AAGA AAGAA AATA AATAA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAG-A AAGA AA-GA AAGA AAGA AAGA A
7486 GGAAGAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
4 28 0.82
5 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (4 bp):
AAGA
Found at i:9184 original size:15 final size:15
Alignment explanation
Indices: 9164--9194 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9154 CTTCGATAGA
9164 GGGAAGGGTATTATT
1 GGGAAGGGTATTATT
9179 GGGAAGGGTATTATT
1 GGGAAGGGTATTATT
9194 G
1 G
9195 CAACCATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32
Consensus pattern (15 bp):
GGGAAGGGTATTATT
Found at i:10397 original size:15 final size:15
Alignment explanation
Indices: 10385--10421 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
10375 ATGGTTTAGT
*
10385 GTTTTGAATTTTAAG
1 GTTTTAAATTTTAAG
10400 GTTTTAAA-TTTAAG
1 GTTTTAAATTTTAAG
10414 GTTTTAAA
1 GTTTTAAA
10422 GAAGAGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (15 bp):
GTTTTAAATTTTAAG
Found at i:10455 original size:21 final size:21
Alignment explanation
Indices: 10431--10471 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10421 AGAAGAGGCT
10431 AGGGTTGTGAAATTAAGGTTA
1 AGGGTTGTGAAATTAAGGTTA
* * *
10452 AGGGTTTTTAATTTAAGGTT
1 AGGGTTGTGAAATTAAGGTT
10472 TATGGTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (21 bp):
AGGGTTGTGAAATTAAGGTTA
Found at i:10501 original size:14 final size:14
Alignment explanation
Indices: 10484--10521 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
10474 TGGTTATATG
*
10484 TTTAGGGTTTTGAA
1 TTTAGAGTTTTGAA
10498 TTTA-ATGTTTTGAA
1 TTTAGA-GTTTTGAA
10512 TTTAGAGTTT
1 TTTAGAGTTT
10522 GGAGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (14 bp):
TTTAGAGTTTTGAA
Found at i:10534 original size:21 final size:21
Alignment explanation
Indices: 10504--10549 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
10494 TGAATTTAAT
*
10504 GTTTTGAATTTAGAGTTTGGA
1 GTTTTAAATTTAGAGTTTGGA
* *
10525 GTTTTAAATTTAGGGTTTTGA
1 GTTTTAAATTTAGAGTTTGGA
10546 GTTT
1 GTTT
10550 AAAGCTTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (21 bp):
GTTTTAAATTTAGAGTTTGGA
Found at i:10592 original size:7 final size:7
Alignment explanation
Indices: 10580--10657 Score: 68
Period size: 7 Copynumber: 10.9 Consensus size: 7
10570 TAAGATCTAT
*
10580 GGTTTAG
1 GGTTTAA
10587 GGTTT-A
1 GGTTTAA
10593 GGATTTAA
1 GG-TTTAA
10601 GGTTTAA
1 GGTTTAA
10608 GGTTTAA
1 GGTTTAA
**
10615 AATTTAA
1 GGTTTAA
* *
10622 GGTTCAT
1 GGTTTAA
*
10629 GATTTAA
1 GGTTTAA
10636 GGGTTTAA
1 -GGTTTAA
10644 GGTTTAA
1 GGTTTAA
10651 GGGTTTA
1 -GGTTTA
10658 TGAGTATGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
6 2 0.04
7 39 0.70
8 15 0.27
ACGTcount: A:0.28, C:0.01, G:0.28, T:0.42
Consensus pattern (7 bp):
GGTTTAA
Found at i:10592 original size:21 final size:21
Alignment explanation
Indices: 10568--10657 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
10558 AGGTTTTAAA
* *
10568 TTTAAGATCTATGGTTTAGGG
1 TTTAAGATCTAAGGTTTAAGG
* *
10589 TTTAGGATTTAAGGTTTAAGG
1 TTTAAGATCTAAGGTTTAAGG
* * * * *
10610 TTTAAAATTTAAGGTTCATGA
1 TTTAAGATCTAAGGTTTAAGG
* *
10631 TTTAAGGGTTTAAGGTTTAAGGG
1 TTTAA-GATCTAAGGTTTAA-GG
10654 TTTA
1 TTTA
10658 TGAGTATGAA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
21 38 0.72
22 10 0.19
23 5 0.09
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (21 bp):
TTTAAGATCTAAGGTTTAAGG
Found at i:11021 original size:6 final size:6
Alignment explanation
Indices: 11010--11036 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11000 TCATTCAATG
11010 CCTCTT CCTCTT CCTCTT CCTCTT CCT
1 CCTCTT CCTCTT CCTCTT CCTCTT CCT
11037 TTTGCTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTCTT
Found at i:11573 original size:43 final size:43
Alignment explanation
Indices: 11506--11601 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
11496 GATGAACTGC
* * *
11506 ATAA-TTAATAACATGTCAATATATTAATAAGAGTAAATTAAT
1 ATAATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAAT
* *
11548 ATAATTTAATAACATG-CAACCATATTAACACGAGTCAAGTAAT
1 ATAATTTAATAACATGTCAA-CATATTAACAAGAGTAAAGTAAT
11591 ATAATTTAATA
1 ATAATTTAATA
11602 TGTTAATGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
42 7 0.15
43 40 0.85
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.33
Consensus pattern (43 bp):
ATAATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAAT
Found at i:12500 original size:16 final size:16
Alignment explanation
Indices: 12479--12528 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
12469 TAAAATAAAT
12479 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
12495 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
12510 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
12525 ATTA
1 ATTA
12529 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:14433 original size:12 final size:12
Alignment explanation
Indices: 14410--14452 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
14400 TTCACACATC
*
14410 TATATGTATTTA
1 TATATTTATTTA
*
14422 TATATTTCTTTA
1 TATATTTATTTA
* *
14434 TACATGTATTTA
1 TATATTTATTTA
14446 TATATTT
1 TATATTT
14453 TCAATATTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (12 bp):
TATATTTATTTA
Found at i:21476 original size:17 final size:18
Alignment explanation
Indices: 21456--21490 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21446 TAATGATTTT
21456 TTAAAAA-TATTTTTGAA
1 TTAAAAAGTATTTTTGAA
21473 TTAAAAAGTATTTTTGAA
1 TTAAAAAGTATTTTTGAA
21491 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (18 bp):
TTAAAAAGTATTTTTGAA
Found at i:21496 original size:18 final size:17
Alignment explanation
Indices: 21458--21496 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21448 ATGATTTTTT
*
21458 AAAAATATTTTTGAATTA
1 AAAAATATTTTTGAA-AA
*
21476 AAAAGTATTTTTGAAAA
1 AAAAATATTTTTGAAAA
21493 AAAA
1 AAAA
21497 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
AAAAATATTTTTGAAAA
Found at i:24068 original size:30 final size:30
Alignment explanation
Indices: 24032--24111 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
24022 AAGTAGCAGA
24032 TACTTGACCATAAAAATTAACGTTACTTGT
1 TACTTGACCATAAAAATTAACGTTACTTGT
* * *
24062 TACTTGACCGTAAGAAA-TAGCGTTATTTGT
1 TACTTGACCATAA-AAATTAACGTTACTTGT
*
24092 TACTTGACCATAAGAATTAA
1 TACTTGACCATAAAAATTAA
24112 AATTATAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 2 0.05
30 37 0.88
31 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (30 bp):
TACTTGACCATAAAAATTAACGTTACTTGT
Found at i:28183 original size:42 final size:41
Alignment explanation
Indices: 28137--28241 Score: 97
Period size: 43 Copynumber: 2.5 Consensus size: 41
28127 ACACTTTTAC
* *
28137 CACAAACACCGCTAAAGATTATG-TTTTTAGCGACGG-TTTTCT
1 CACAAACACCGCTAAA-ATTATGATCTTTAACG--GGATTTTCT
** **
28179 CACAAATGCCGCTAAAAAACATGATCTTTAACGGGATTTTTCT
1 CACAAACACCGCT-AAAATTATGATCTTTAACGGGA-TTTTCT
28222 CACAAACACCGCTAAAATTA
1 CACAAACACCGCTAAAATTA
28242 ACAGATTTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
41 2 0.04
42 20 0.41
43 27 0.55
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (41 bp):
CACAAACACCGCTAAAATTATGATCTTTAACGGGATTTTCT
Done.