Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014841.1 Kokia drynarioides strain JFW-HI SEQ_129884, 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: 96636
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:1010 original size:6 final size:6
Alignment explanation
Indices: 999--1027 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
989 TGATCAAAAT
999 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1028 TTGGAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:3082 original size:13 final size:11
Alignment explanation
Indices: 3051--3075 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3041 AATTCAACAC
3051 TATTATTTTTT
1 TATTATTTTTT
3062 TATTATTTTTT
1 TATTATTTTTT
3073 TAT
1 TAT
3076 AATATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTATTTTTT
Found at i:6167 original size:19 final size:21
Alignment explanation
Indices: 6145--6183 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6135 TTTAAAAAAT
6145 TAAA-TAAAAATT-TATTTTA
1 TAAATTAAAAATTATATTTTA
*
6164 TAAATTATAAATTATATTTT
1 TAAATTAAAAATTATATTTT
6184 TTATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATTAAAAATTATATTTTA
Found at i:16373 original size:23 final size:23
Alignment explanation
Indices: 16314--16487 Score: 132
Period size: 23 Copynumber: 7.8 Consensus size: 23
16304 GAGAGTACCG
* *
16314 AAGTACTAAACAGAGAGCACA-T
1 AAGTGCTAAACAGAGAGCACACA
*
16336 AAGTGCTGGGCAACAGAGAGCACACA
1 AAGTGCT---AAACAGAGAGCACACA
* * *
16362 AAATACTAAACAGAGAGTACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
16385 AA--G-T--AC--TGAGCATACA
1 AAGTGCTAAACAGAGAGCACACA
* *
16401 AAGTGCTAATCAGAGAGCACACG
1 AAGTGCTAAACAGAGAGCACACA
*
16424 AAGTGCTAATCAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
16447 TAA-TGCTAAACAGAGAGCACACA
1 -AAGTGCTAAACAGAGAGCACACA
* *
16470 CAGTGCTAATCAGAGAGC
1 AAGTGCTAAACAGAGAGC
16488 GCGCTAGTGT
Statistics
Matches: 120, Mismatches: 19, Indels: 25
0.73 0.12 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 1 0.01
22 7 0.06
23 78 0.65
24 2 0.02
25 13 0.11
26 5 0.04
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACA
Found at i:16415 original size:39 final size:39
Alignment explanation
Indices: 16353--16427 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
16343 GGGCAACAGA
*
16353 GAGCACACAAAATACTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAATACTAAACAGAGAGCACACAAAGTACT
* * * * *
16392 GAGCATACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAATACTAAACAGAGAGCACACAAAGT
16428 GCTAATCAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAATACTAAACAGAGAGCACACAAAGTACT
Found at i:19403 original size:18 final size:19
Alignment explanation
Indices: 19371--19409 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19361 TTTTTTTATT
**
19371 AATTTAAAATTTTAAA-AA
1 AATTTAAAAACTTAAATAA
19389 AATTTAAAAACTTAAATAA
1 AATTTAAAAACTTAAATAA
19408 AA
1 AA
19410 AAAATCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTTAAAAACTTAAATAA
Found at i:23149 original size:3 final size:3
Alignment explanation
Indices: 23141--23165 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23131 TAGAGAGGAA
23141 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
23166 AGCATTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:23573 original size:22 final size:22
Alignment explanation
Indices: 23548--23590 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23538 ATTTTAAATT
* *
23548 TTAAAATGTTTAAATTATATTC
1 TTAAAATATTAAAATTATATTC
*
23570 TTAAATTATTAAAATTATATT
1 TTAAAATATTAAAATTATATT
23591 AATCAGACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAAATATTAAAATTATATTC
Found at i:29493 original size:29 final size:27
Alignment explanation
Indices: 29440--29499 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
29430 ATTATTAATG
* *
29440 ATTATTATTTTTTTAAAAGATATTATT
1 ATTATTATTTTTTTAAAAAAAATTATT
29467 ATTATTATTATTGTTTAAAAAAAATTATT
1 ATTATTATT-TT-TTTAAAAAAAATTATT
29496 ATTA
1 ATTA
29500 ATAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.31
28 2 0.07
29 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
ATTATTATTTTTTTAAAAAAAATTATT
Found at i:29515 original size:29 final size:29
Alignment explanation
Indices: 29461--29516 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
29451 TTTAAAAGAT
* * *
29461 ATTATTATTATTATTATTGTTTAAAAAAA
1 ATTATTATTATAAATATTGTTGAAAAAAA
29490 ATTATTATTAATAAATATT-TTGAAAAA
1 ATTATTATT-ATAAATATTGTTGAAAAA
29517 CCGCCCACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTATTATTATAAATATTGTTGAAAAAAA
Found at i:29557 original size:24 final size:23
Alignment explanation
Indices: 29524--29570 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29514 AAACCGCCCA
29524 CTTGTCATTAATGCC-ATTATTATT
1 CTTGTCATTAA--CCAATTATTATT
*
29548 CTTGTTATTAACCAATTATTATT
1 CTTGTCATTAACCAATTATTATT
29571 AATGATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 9 0.43
24 10 0.48
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (23 bp):
CTTGTCATTAACCAATTATTATT
Found at i:30194 original size:17 final size:17
Alignment explanation
Indices: 30172--30228 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
30162 TGGACTTTTC
* *
30172 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
30189 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
30206 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
30223 TAAATT
1 TAAATT
30229 CAATTTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:36809 original size:13 final size:13
Alignment explanation
Indices: 36762--36823 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
36752 TTTTTTATTA
36762 TTATT-ATTTATAT
1 TTATTGATTTA-AT
36775 TTAGTTG-TTT-AT
1 TTA-TTGATTTAAT
* *
36787 TTTTTCATTTAAT
1 TTATTGATTTAAT
36800 TTATTGATTTAAT
1 TTATTGATTTAAT
*
36813 TTATTTATTTA
1 TTATTGATTTA
36824 TCATTTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 2 0.05
12 7 0.17
13 26 0.65
14 5 0.12
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (13 bp):
TTATTGATTTAAT
Found at i:44960 original size:18 final size:18
Alignment explanation
Indices: 44937--44980 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
44927 AAAACTTTAT
*
44937 TCCTCCTCGTCCATC-TCA
1 TCCTCCTCAT-CATCATCA
44955 TCCTCCTCATCATCATCA
1 TCCTCCTCATCATCATCA
*
44973 TCGTCCTC
1 TCCTCCTC
44981 TCCTTCTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.14, C:0.48, G:0.05, T:0.34
Consensus pattern (18 bp):
TCCTCCTCATCATCATCA
Found at i:49382 original size:3 final size:3
Alignment explanation
Indices: 49374--49417 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
49364 TTCCTTAGGG
* ***
49374 TCT TCT TCT TCT TCT TCT TCT TCA GGA TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
49418 AGGATCTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.05, C:0.32, G:0.05, T:0.59
Consensus pattern (3 bp):
TCT
Found at i:49404 original size:21 final size:21
Alignment explanation
Indices: 49380--49425 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
49370 AGGGTCTTCT
49380 TCTTCTTCTTCTTCTTCAGGA
1 TCTTCTTCTTCTTCTTCAGGA
49401 TCTTCTTCTTCTTCTTCAGGA
1 TCTTCTTCTTCTTCTTCAGGA
49422 TCTT
1 TCTT
49426 GTTGTTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.54
Consensus pattern (21 bp):
TCTTCTTCTTCTTCTTCAGGA
Found at i:58487 original size:14 final size:13
Alignment explanation
Indices: 58464--58522 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 13
58454 GCAATATATA
*
58464 CTTTT-TTTTTTG
1 CTTTTCTTTTTTT
58476 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
*
58489 CTTTGCTTTCTTTTT
1 CTTTTC-TT-TTTTT
58504 CTTCTTCTCTTTTTT
1 CTT-TTCT-TTTTTT
58519 -TTTT
1 CTTTT
58523 ATACGTGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.13
13 13 0.33
14 4 0.10
15 14 0.36
16 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:58488 original size:18 final size:17
Alignment explanation
Indices: 58464--58522 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
58454 GCAATATATA
58464 CTTTTTTT-TTTGCTTTT
1 CTTTTTTTCTTTGC-TTT
58481 CTTTTTTTCTTTGCTTT
1 CTTTTTTTCTTTGCTTT
58498 CTTTTTCTTCTTCT-CTTT
1 CTTTTT-TTCTT-TGCTTT
58516 -TTTTTTT
1 CTTTTTTT
58523 ATACGTGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.05
17 22 0.56
18 14 0.36
19 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
CTTTTTTTCTTTGCTTT
Found at i:59124 original size:17 final size:16
Alignment explanation
Indices: 59104--59147 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
59094 AAATGAACTA
59104 ACAAGTAAAATACAATG
1 ACAA-TAAAATACAATG
*
59121 ACAACTAAAATGCAATG
1 ACAA-TAAAATACAATG
59138 ACAATAAAAT
1 ACAATAAAAT
59148 GAGATGCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (16 bp):
ACAATAAAATACAATG
Found at i:77724 original size:20 final size:21
Alignment explanation
Indices: 77701--77747 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
77691 GACTTAGTTC
77701 AAATTATTTTAACATG-TTTA
1 AAATTATTTTAACATGATTTA
* *
77721 AAATCATTTTAACTTGATTTTA
1 AAATTATTTTAACATGA-TTTA
77743 AAATT
1 AAATT
77748 GTTTCAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 14 0.64
22 8 0.36
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
AAATTATTTTAACATGATTTA
Found at i:77945 original size:14 final size:14
Alignment explanation
Indices: 77920--77954 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
77910 TTTTTGATAT
77920 AATAATTTTTTTTG
1 AATAATTTTTTTTG
77934 AA-AATTTGTTTTTG
1 AATAATTT-TTTTTG
77948 AATAATT
1 AATAATT
77955 GCTCACCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 10 0.53
15 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (14 bp):
AATAATTTTTTTTG
Found at i:79958 original size:20 final size:20
Alignment explanation
Indices: 79917--79970 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
79907 AAGGCCCGTG
**
79917 GTATCGATATTTTT-CACGA
1 GTATCGATATTTTTACAAAA
*
79936 GTATCGATATTTTTATAAAA
1 GTATCGATATTTTTACAAAA
*
79956 GTATCGATAATTTTA
1 GTATCGATATTTTTA
79971 AATTGGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (20 bp):
GTATCGATATTTTTACAAAA
Found at i:86162 original size:20 final size:20
Alignment explanation
Indices: 86094--86168 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
86084 AGTTTCACTC
*
86094 GTTTGAAAAATATTTTGA-A-
1 GTTT-AAAATTATTTTGACAT
* *
86113 GTGTTAAAATGATTTTGACTT
1 GT-TTAAAATTATTTTGACAT
*
86134 AG-TTCAAATTATTTTGACAT
1 -GTTTAAAATTATTTTGACAT
*
86154 GTTTAAAATCATTTT
1 GTTTAAAATTATTTT
86169 AACTTGATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 14 0.33
20 28 0.65
22 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (20 bp):
GTTTAAAATTATTTTGACAT
Found at i:86378 original size:18 final size:19
Alignment explanation
Indices: 86346--86383 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
86336 ACATATACAT
86346 TTAAAAATAATTTTAAAAA
1 TTAAAAATAATTTTAAAAA
*
86365 TTAAAAATTA-TTTAAAAA
1 TTAAAAATAATTTTAAAAA
86383 T
1 T
86384 CATATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAATAATTTTAAAAA
Found at i:86960 original size:17 final size:16
Alignment explanation
Indices: 86921--86960 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
86911 AACTATTGTA
86921 AACATTTTTAAAAATT
1 AACATTTTTAAAAATT
* *
86937 AATATTTTTAAAATTAT
1 AACATTTTTAAAAAT-T
86954 AACATTT
1 AACATTT
86961 GGAATTATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
AACATTTTTAAAAATT
Found at i:87636 original size:12 final size:12
Alignment explanation
Indices: 87619--87643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87609 TAGATAGATG
87619 ATTATTGTTATT
1 ATTATTGTTATT
87631 ATTATTGTTATT
1 ATTATTGTTATT
87643 A
1 A
87644 AATTTTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATTATTGTTATT
Found at i:88644 original size:34 final size:35
Alignment explanation
Indices: 88564--88693 Score: 102
Period size: 35 Copynumber: 3.7 Consensus size: 35
88554 TACCGTCAGG
* * * *
88564 TTATCCAACTAGTGCTGGGCGCA-ACCTTCATCAGT
1 TTATCCAACTAGTGCTGGGCACACAACATCAT-TGT
** *
88599 TTATCTGACTAGTGCTGGGCACACAAC-TCGTTGT
1 TTATCCAACTAGTGCTGGGCACACAACATCATTGT
* * * *
88633 TTATCCAACTAGCGTTAGGCACAAAACATCATTGGT
1 TTATCCAACTAGTGCTGGGCACACAACATCATT-GT
* * *
88669 ATATCCAACTAGAGCTGGGCTCACA
1 TTATCCAACTAGTGCTGGGCACACA
88694 TTTGATATTG
Statistics
Matches: 73, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
34 23 0.32
35 27 0.37
36 23 0.32
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (35 bp):
TTATCCAACTAGTGCTGGGCACACAACATCATTGT
Found at i:93913 original size:41 final size:41
Alignment explanation
Indices: 93867--93951 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
93857 GCGAAGTAAG
93867 ATAAATAAGAAGATAAAATGGTAAAAAATCAAAAATGCAAA
1 ATAAATAAGAAGATAAAATGGTAAAAAATCAAAAATGCAAA
93908 ATAAATAAGAAGATAAAATGGTAAAAAATCAAAAATGCAAA
1 ATAAATAAGAAGATAAAATGGTAAAAAATCAAAAATGCAAA
93949 ATA
1 ATA
93952 CGAGTGCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.18
Consensus pattern (41 bp):
ATAAATAAGAAGATAAAATGGTAAAAAATCAAAAATGCAAA
Found at i:94239 original size:30 final size:30
Alignment explanation
Indices: 94193--94337 Score: 122
Period size: 29 Copynumber: 4.9 Consensus size: 30
94183 ATTAGAGAGC
*
94193 AAAATGGTAATTTTTGAAAGTTTCAGGGTCA
1 AAAATGG-AAATTTTGAAAGTTTCAGGGTCA
* *
94224 AAAATGGAAAATTTGAATG-TTCGAGGGT-A
1 AAAATGGAAATTTTGAAAGTTTC-AGGGTCA
* * *
94253 AAAATGGAATTTTTGGAAGTTTC-GAGGTTA
1 AAAATGGAAATTTTGAAAGTTTCAG-GGTCA
* * *
94283 AAAATGG-AATTTTGGAAGTTTTAGGGTCG
1 AAAATGGAAATTTTGAAAGTTTCAGGGTCA
*
94312 AAAATGG-AATTTTTAGAAGTTT-AGGG
1 AAAATGGAAATTTTGA-AAGTTTCAGGG
94338 GTAAAATGTA
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.01
29 55 0.58
30 32 0.34
31 7 0.07
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGAAATTTTGAAAGTTTCAGGGTCA
Found at i:94264 original size:59 final size:59
Alignment explanation
Indices: 94193--94337 Score: 156
Period size: 59 Copynumber: 2.5 Consensus size: 59
94183 ATTAGAGAGC
94193 AAAATGGTAATTTTTGAAAGTTTCAGGGTCAAAAATGGAAAATTT-GAATGTTCGAGGGT-A
1 AAAATGG-AATTTTTGAAAGTTTCAGGGTCAAAAATGG-AAATTTGGAA-GTTCGAGGGTCA
* * * ** *
94253 AAAATGGAATTTTTGGAAGTTTC-GAGGTTAAAAATGGAATTTTGGAAGTTTTAGGGTCG
1 AAAATGGAATTTTTGAAAGTTTCAG-GGTCAAAAATGGAAATTTGGAAGTTCGAGGGTCA
94312 AAAATGGAATTTTT-AGAAGTTT-AGGG
1 AAAATGGAATTTTTGA-AAGTTTCAGGG
94338 GTAAAATGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
58 16 0.22
59 50 0.68
60 7 0.10
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGAAAGTTTCAGGGTCAAAAATGGAAATTTGGAAGTTCGAGGGTCA
Found at i:94267 original size:29 final size:28
Alignment explanation
Indices: 94193--94354 Score: 132
Period size: 30 Copynumber: 5.5 Consensus size: 28
94183 ATTAGAGAGC
94193 AAAATGGTAATTTTTGAAAGTTTC-AGGGTCA
1 AAAATGG-AATTTTTG-AAG-TTCGAGGGT-A
**
94224 AAAATGGAAAATTTGAATGTTCGAGGGTA
1 AAAATGGAATTTTTGAA-GTTCGAGGGTA
*
94253 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTT-GAAG-TTCGAGGGTA
* ** *
94283 AAAATGGAATTTTGGAAGTTTTAGGGTCG
1 AAAATGGAATTTTTGAAGTTCGAGGGT-A
*
94312 AAAATGGAATTTTTAGAAGTT-TAGGGGT-
1 AAAATGGAATTTTT-GAAGTTCGA-GGGTA
*
94340 AAAATGTAATTTTTG
1 AAAATGGAATTTTTG
94355 GACAATTTAG
Statistics
Matches: 112, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.01
28 19 0.17
29 38 0.34
30 47 0.42
31 7 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGAAGTTCGAGGGTA
Found at i:94363 original size:29 final size:28
Alignment explanation
Indices: 94248--94366 Score: 80
Period size: 29 Copynumber: 4.1 Consensus size: 28
94238 GAATGTTCGA
* * *
94248 GGGTAAAAATGGAATTTTTGGAAGTTTCG
1 GGGT-AAAATGGAATTTTTAGAAATTTAG
* * *
94277 AGGTTAAAAATGGAA-TTTTGGAAGTTTTA-
1 -GGGT-AAAATGGAATTTTTAGAA-ATTTAG
*
94306 GGGTCGAAAATGGAATTTTTAGAAGTTTAG
1 GGGT--AAAATGGAATTTTTAGAAATTTAG
* *
94336 GGGTAAAATGTAATTTTTGGACAATTTAG
1 GGGTAAAATGGAATTTTTAGA-AATTTAG
94365 GG
1 GG
94367 ACCTCTAGGG
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
28 18 0.24
29 29 0.39
30 27 0.36
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGAATTTTTAGAAATTTAG
Done.