Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012572.1 Kokia drynarioides strain JFW-HI SEQ_127581, 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: 420729
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 120 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:218816 original size:30 final size:30
Alignment explanation
Indices: 218755--219040 Score: 319
Period size: 30 Copynumber: 9.7 Consensus size: 30
218745 CAGGCTCACA
* * *
218755 CTTTGACAGACTCGCACTTT-GCTTGCTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* *
218784 CTTCAACAGGCTCACACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* * *
218814 CTTTGACAGGCTCACACTTT-GCTTGCTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* *
218843 CTTCAACAGGTTCGCACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* *
218873 CTTTAATAGGCTTGCACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* * * * *
218903 CTTTGATAGGCTCACACTTT-ACTTGCTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
*
218932 CTTCAACAGGCTCGCACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
218962 CTTTAACAGGCTCGCACTTTGGCTTACTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* * **
218992 CTTTGACAGGCTCACACTTT-GCTTGTTGT
1 CTTTAACAGGCTCGCACTTTGGCTTACTGT
* * *
219021 CTTCAATAGGATCGCACTTT
1 CTTTAACAGGCTCGCACTTT
219041 TGATGGCTCG
Statistics
Matches: 216, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
29 85 0.39
30 131 0.61
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (30 bp):
CTTTAACAGGCTCGCACTTTGGCTTACTGT
Found at i:218847 original size:59 final size:59
Alignment explanation
Indices: 218755--219040 Score: 349
Period size: 59 Copynumber: 4.8 Consensus size: 59
218745 CAGGCTCACA
* *
218755 CTTTGACAGACTCGCACTTTGCTTGCTGTCTTCAACAGGCTCACACTTTGGCTTACTGT
1 CTTTGACAGGCTCGCACTTTGCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGT
* *
218814 CTTTGACAGGCTCACACTTTGCTTGCTGTCTTCAACAGGTTCGCACTTTGGCTTACTGT
1 CTTTGACAGGCTCGCACTTTGCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGT
* * * * ** * * * *
218873 CTTTAATAGGCTTGCACTTTGGCTTACTGTCTTTGATAGGCTCACACTTT-ACTTGCTGT
1 CTTTGACAGGCTCGCACTTT-GCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGT
** * *
218932 CTTCAACAGGCTCGCACTTTGGCTTACTGTCTTTAACAGGCTCGCACTTTGGCTTACTGT
1 CTTTGACAGGCTCGCACTTT-GCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGT
* * * *
218992 CTTTGACAGGCTCACACTTTGCTTGTTGTCTTCAATAGGATCGCACTTT
1 CTTTGACAGGCTCGCACTTTGCTTGCTGTCTTCAACAGGCTCGCACTTT
219041 TGATGGCTCG
Statistics
Matches: 193, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
59 146 0.76
60 47 0.24
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (59 bp):
CTTTGACAGGCTCGCACTTTGCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGT
Found at i:218931 original size:89 final size:89
Alignment explanation
Indices: 218766--219040 Score: 444
Period size: 89 Copynumber: 3.1 Consensus size: 89
218756 TTTGACAGAC
* * *
218766 TCGCACTTT-GCTTGCTGTCTTCAACAGGCTCACACTTTGGCTTACTGTCTTTGACAGGCTCACA
1 TCGCACTTTGGCTTACTGTCTTTAACAGGCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCACA
*
218830 CTTTGCTTGCTGTCTTCAACAGGT
66 CTTTGCTTGCTGTCTTCAACAGGA
* * *
218854 TCGCACTTTGGCTTACTGTCTTTAATAGGCTTGCACTTTGGCTTACTGTCTTTGATAGGCTCACA
1 TCGCACTTTGGCTTACTGTCTTTAACAGGCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCACA
* *
218919 CTTTACTTGCTGTCTTCAACAGGC
66 CTTTGCTTGCTGTCTTCAACAGGA
218943 TCGCACTTTGGCTTACTGTCTTTAACAGGCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCACA
1 TCGCACTTTGGCTTACTGTCTTTAACAGGCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCACA
* *
219008 CTTTGCTTGTTGTCTTCAATAGGA
66 CTTTGCTTGCTGTCTTCAACAGGA
219032 TCGCACTTT
1 TCGCACTTT
219041 TGATGGCTCG
Statistics
Matches: 171, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 9 0.05
89 162 0.95
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (89 bp):
TCGCACTTTGGCTTACTGTCTTTAACAGGCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCACA
CTTTGCTTGCTGTCTTCAACAGGA
Found at i:220636 original size:6 final size:6
Alignment explanation
Indices: 220625--220682 Score: 116
Period size: 6 Copynumber: 9.7 Consensus size: 6
220615 GAGCACTTCA
220625 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
220673 TATATG TATA
1 TATATG TATA
220683 CTAACATGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:230466 original size:15 final size:15
Alignment explanation
Indices: 230446--230496 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
230436 TGGCTGTGGT
230446 GGTGGTCAGAGTCGC
1 GGTGGTCAGAGTCGC
* * * *
230461 GGTGGT-GGCTGTGGT
1 GGTGGTCAG-AGTCGC
230476 GGTGGTCAGAGTCGC
1 GGTGGTCAGAGTCGC
230491 GGTGGT
1 GGTGGT
230497 GGCTGCGGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.08, C:0.14, G:0.53, T:0.25
Consensus pattern (15 bp):
GGTGGTCAGAGTCGC
Found at i:230466 original size:18 final size:18
Alignment explanation
Indices: 230443--230498 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
230433 TCGTGGCTGT
230443 GGTGGTGGTCAGAGTCGC
1 GGTGGTGGTCAGAGTCGC
*
230461 GGTGGTGG-C----T-GT
1 GGTGGTGGTCAGAGTCGC
230473 GGTGGTGGTCAGAGTCGC
1 GGTGGTGGTCAGAGTCGC
230491 GGTGGTGG
1 GGTGGTGG
230499 CTGCGGTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
17 2 0.07
18 17 0.57
ACGTcount: A:0.07, C:0.12, G:0.55, T:0.25
Consensus pattern (18 bp):
GGTGGTGGTCAGAGTCGC
Found at i:230469 original size:30 final size:30
Alignment explanation
Indices: 230435--230509 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
230425 GATGGGAATC
230435 GTGGCTGTGGTGGTGGTCAGAGTCGCGGTG
1 GTGGCTGTGGTGGTGGTCAGAGTCGCGGTG
230465 GTGGCTGTGGTGGTGGTCAGAGTCGCGGTG
1 GTGGCTGTGGTGGTGGTCAGAGTCGCGGTG
*
230495 GTGGCTGCGGTGGTG
1 GTGGCTGTGGTGGTG
230510 CTTGTCATGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.05, C:0.13, G:0.55, T:0.27
Consensus pattern (30 bp):
GTGGCTGTGGTGGTGGTCAGAGTCGCGGTG
Found at i:234392 original size:12 final size:12
Alignment explanation
Indices: 234370--234398 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
234360 AGCTTACATC
234370 TAAAA-TAATAA
1 TAAAATTAATAA
234381 TAAAATTAATAA
1 TAAAATTAATAA
234393 TAAAAT
1 TAAAAT
234399 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:239261 original size:10 final size:10
Alignment explanation
Indices: 239248--239282 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
239238 CTCACTCTCT
239248 CTCCCCCTCC
1 CTCCCCCTCC
239258 CTCCCCCTCC
1 CTCCCCCTCC
239268 CTCCCTTCCTCC
1 CTCCC--CCTCC
239280 CTC
1 CTC
239283 TCTAGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 15 0.65
12 8 0.35
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (10 bp):
CTCCCCCTCC
Found at i:248075 original size:2 final size:2
Alignment explanation
Indices: 248068--248094 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
248058 GTAATTTCAC
248068 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
248095 TAATTTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:259570 original size:14 final size:13
Alignment explanation
Indices: 259547--259586 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
259537 AATCCAATTA
259547 TTTTGTAATTACT
1 TTTTGTAATTACT
259560 TTTTGGTAATT--T
1 TTTT-GTAATTACT
259572 TTTTGTAATTACT
1 TTTTGTAATTACT
259585 TT
1 TT
259587 AATCTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.25
12 5 0.21
13 7 0.29
14 6 0.25
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.65
Consensus pattern (13 bp):
TTTTGTAATTACT
Found at i:260116 original size:21 final size:22
Alignment explanation
Indices: 260074--260118 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
260064 TTAAAATACA
* *
260074 TTAAAATAATTTTTATTTTATT
1 TTAAAATAATATTTATTATATT
*
260096 TTAAATTAATATTT-TTATATT
1 TTAAAATAATATTTATTATATT
260117 TT
1 TT
260119 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTAAAATAATATTTATTATATT
Found at i:260130 original size:24 final size:23
Alignment explanation
Indices: 260076--260132 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
260066 AAAATACATT
*
260076 AAAATAATTTTTATTTTATTTTA
1 AAAATATTTTTTATTTTATTTTA
260099 AATTAATATTTTTATATTTT-TATTTA
1 AA--AATATTTTT-TATTTTAT-TTTA
260125 AAAATATT
1 AAAATATT
260133 ATCCCAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 9 0.31
26 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AAAATATTTTTTATTTTATTTTA
Found at i:261041 original size:6 final size:6
Alignment explanation
Indices: 261024--261054 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
261014 TTTTACTATT
261024 AAATCC -AATCC AAATCC AAATCC AAATCC AA
1 AAATCC AAATCC AAATCC AAATCC AAATCC AA
261055 CTAGATGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATCC
Found at i:262214 original size:23 final size:20
Alignment explanation
Indices: 262169--262206 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
262159 AAATTTATTT
262169 ATAAAATAATAATTTTATAA
1 ATAAAATAATAATTTTATAA
*
262189 ATAAAATAATAATATTAT
1 ATAAAATAATAATTTTAT
262207 TATAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAATAATAATTTTATAA
Found at i:262217 original size:20 final size:19
Alignment explanation
Indices: 262167--262217 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
262157 GGAAATTTAT
*
262167 TTATAAAATAATAATTTTA
1 TTATAAAATAATAATATTA
*
262186 TAAATAAAATAATAATATTA
1 T-TATAAAATAATAATATTA
262206 TTATAAATATAA
1 TTATAAA-ATAA
262218 CAATTTAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTATAAAATAATAATATTA
Found at i:268350 original size:19 final size:19
Alignment explanation
Indices: 268296--268353 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
268286 CAACAAAAAA
*
268296 AAAATAGTTTTCAAAAATTC
1 AAAATAATTTT-AAAAATTC
* *
268316 AAAATAATTTTTAAAATTT
1 AAAATAATTTTAAAAATTC
268335 AAAAT-ATTTATAAAAATTC
1 AAAATAATTT-TAAAAATTC
268354 CAATAACTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.12
19 18 0.56
20 10 0.31
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTC
Found at i:268398 original size:20 final size:23
Alignment explanation
Indices: 268373--268423 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
268363 ATATATTTTT
268373 AAAAATTATTAAA-AA-AT-TAA
1 AAAAATTATTAAAGAATATATAA
*
268393 AAAAATT-CTAAAGAATATATAA
1 AAAAATTATTAAAGAATATATAA
268415 AAAAATTAT
1 AAAAATTAT
268424 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 2 0.08
22 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAATTATTAAAGAATATATAA
Found at i:272227 original size:8 final size:8
Alignment explanation
Indices: 272210--272242 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
272200 TAATAATAAA
272210 TATT-TTT
1 TATTATTT
272217 TATTATTT
1 TATTATTT
272225 TATTATTT
1 TATTATTT
272233 TATTATTT
1 TATTATTT
272241 TA
1 TA
272243 AATAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.16
8 21 0.84
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:277710 original size:14 final size:13
Alignment explanation
Indices: 277690--277723 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
277680 GTGCAAGGTA
277690 AATTTTATTTTCTT
1 AATTTTATTTT-TT
*
277704 TATTTTATTTTTT
1 AATTTTATTTTTT
277717 AATTTTA
1 AATTTTA
277724 AATTCATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTATTTTTT
Found at i:278044 original size:3 final size:3
Alignment explanation
Indices: 278038--278076 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
278028 AGGTGTTGTT
*
278038 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
278077 TACCTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:284661 original size:21 final size:22
Alignment explanation
Indices: 284607--284669 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
284597 TAGGTACATA
* *
284607 TTTTA-TTATACTAAGATAATT
1 TTTTATTTATATTAAGATTATT
284628 TTTT-TTTAAATATTAA-ATTATT
1 TTTTATTT--ATATTAAGATTATT
*
284650 TTTTATTTATATTAATATTA
1 TTTTATTTATATTAAGATTA
284670 AACTAAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 13 0.37
22 13 0.37
23 9 0.26
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATTTATATTAAGATTATT
Found at i:296956 original size:12 final size:12
Alignment explanation
Indices: 296941--296991 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
296931 ATATAAATAT
296941 AAAATAAAATTA
1 AAAATAAAATTA
*
296953 AAAAT--ATTTA
1 AAAATAAAATTA
* *
296963 AAAAT-TAATCA
1 AAAATAAAATTA
296974 AAAATAAAATTA
1 AAAATAAAATTA
296986 AAAATA
1 AAAATA
296992 TTTAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 9 0.28
11 8 0.25
12 15 0.47
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATAAAATTA
Found at i:296964 original size:33 final size:33
Alignment explanation
Indices: 296925--297005 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
296915 ACGTACTCGA
*
296925 ATTTAAATATAAAT-ATAAAATAAAATTAAAAAT
1 ATTTAAAAATAAATCA-AAAATAAAATTAAAAAT
*
296958 ATTTAAAAATTAATCAAAAATAAAATTAAAAAT
1 ATTTAAAAATAAATCAAAAATAAAATTAAAAAT
*
296991 ATTTAAAAATTAATC
1 ATTTAAAAATAAATC
297006 GAACATATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 44 0.98
34 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (33 bp):
ATTTAAAAATAAATCAAAAATAAAATTAAAAAT
Found at i:296965 original size:10 final size:10
Alignment explanation
Indices: 296948--297000 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
296938 TATAAAATAA
296948 AATTAAAAAT
1 AATTAAAAAT
*
296958 ATTTAAAAATT
1 AATTAAAAA-T
*
296969 AATCAAAAAT
1 AATTAAAAAT
296979 AAAATTAAAAAT
1 --AATTAAAAAT
*
296991 ATTTAAAAAT
1 AATTAAAAAT
297001 TAATCGAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 18 0.51
11 8 0.23
12 9 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAAAAAT
Found at i:296966 original size:17 final size:17
Alignment explanation
Indices: 296946--297003 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
296936 AATATAAAAT
296946 AAAATTAAAAATATTTA
1 AAAATTAAAAATATTTA
*
296963 AAAATTAATCAAA-A-AT-
1 AAAATTAA--AAATATTTA
296979 AAAATTAAAAATATTTA
1 AAAATTAAAAATATTTA
296996 AAAATTAA
1 AAAATTAA
297004 TCGAACATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 9 0.26
17 17 0.50
18 1 0.03
19 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTAAAAATATTTA
Found at i:298682 original size:62 final size:62
Alignment explanation
Indices: 298585--298712 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
298575 GTCATTAATG
298585 GTGGTTCATGGTTTCAACTATTTTTAGCAAATTATATACTGTGTGATAGCTAAAATTTAAGT
1 GTGGTTCATGGTTTCAACTATTTTTAGCAAATTATATACTGTGTGATAGCTAAAATTTAAGT
298647 GTGGTTCATGGTTTCAACTATTTTTAGCAAATTATATACTGTGTGATAGCTAAAATTTAAGT
1 GTGGTTCATGGTTTCAACTATTTTTAGCAAATTATATACTGTGTGATAGCTAAAATTTAAGT
298709 GTGG
1 GTGG
298713 ATTTTATATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (62 bp):
GTGGTTCATGGTTTCAACTATTTTTAGCAAATTATATACTGTGTGATAGCTAAAATTTAAGT
Found at i:306829 original size:11 final size:11
Alignment explanation
Indices: 306815--306842 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
306805 TATTCAAACA
306815 ATAATAATAAT
1 ATAATAATAAT
306826 ATAATAATAAT
1 ATAATAATAAT
306837 ATAATA
1 ATAATA
306843 GTGAAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:311038 original size:16 final size:17
Alignment explanation
Indices: 311007--311049 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
310997 CTGGGTTTTC
*
311007 TTTTCTCTTTCTTGGGT
1 TTTTCTTTTTCTTGGGT
*
311024 TTTTGTTTTTC-TGGGT
1 TTTTCTTTTTCTTGGGT
311040 TTTTCTTTTT
1 TTTTCTTTTT
311050 ACTATTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (17 bp):
TTTTCTTTTTCTTGGGT
Found at i:315826 original size:57 final size:58
Alignment explanation
Indices: 315719--315853 Score: 191
Period size: 57 Copynumber: 2.3 Consensus size: 58
315709 ACTGGAGCCA
*
315719 CTGTTGGCAACCCTGGTGTGGGTGCAGGTGCAGCCACTGGTCCCATTCCCACAGGAACCG
1 CTGTTGGCAACCCTGGTGTAGGTGC--GTGCAGCCACTGGTCCCATTCCCACAGGAACCG
* * *
315779 CTGTTGGGAACCCTGGTGTAGGTGC-TGCAGCCACTGGTCCCATTCCCACAGGACCCA
1 CTGTTGGCAACCCTGGTGTAGGTGCGTGCAGCCACTGGTCCCATTCCCACAGGAACCG
* *
315836 ATGTTGCCAACCCTGGTG
1 CTGTTGGCAACCCTGGTG
315854 CTGGTGCAGC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 45 0.66
60 23 0.34
ACGTcount: A:0.17, C:0.32, G:0.30, T:0.21
Consensus pattern (58 bp):
CTGTTGGCAACCCTGGTGTAGGTGCGTGCAGCCACTGGTCCCATTCCCACAGGAACCG
Found at i:319630 original size:47 final size:47
Alignment explanation
Indices: 319528--319618 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
319518 ATTGTTTTCC
*
319528 ATACTAAATCTATTTTTATATAAATTATAAATAAACCGTCCATATCA
1 ATACTAAATCTATTTTTATATAAATTATAAATAAACCGTCCATAACA
*
319575 ATACTAAATCTATTTTTATAT-AATTATAAATAAACCTTCC-TAAC
1 ATACTAAATCTATTTTTATATAAATTATAAATAAACCGTCCATAAC
319619 GTTCATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 3 0.07
46 18 0.43
47 21 0.50
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (47 bp):
ATACTAAATCTATTTTTATATAAATTATAAATAAACCGTCCATAACA
Found at i:328599 original size:35 final size:34
Alignment explanation
Indices: 328553--328623 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
328543 CTAAATTTTA
328553 AAAATAAAATTTTATAAAAATTTAACATCTAACTC
1 AAAATAAAATTTTATAAAAATTTAACATC-AACTC
* *
328588 AAAATGAAATTTTATAAAAGTTTAACATCAACTC
1 AAAATAAAATTTTATAAAAATTTAACATCAACTC
328622 AA
1 AA
328624 CTAACTCGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 7 0.21
35 27 0.79
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (34 bp):
AAAATAAAATTTTATAAAAATTTAACATCAACTC
Found at i:331822 original size:17 final size:18
Alignment explanation
Indices: 331800--331833 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
331790 GTTAAATATT
331800 TTTTATAAT-TTTATTAA
1 TTTTATAATATTTATTAA
331817 TTTTATAATATTTATTA
1 TTTTATAATATTTATTA
331834 TTATTAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATAATATTTATTAA
Found at i:340064 original size:53 final size:53
Alignment explanation
Indices: 340006--340111 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
339996 CAAAATATTT
340006 TTTTTTAACTTTCTTATTATTTCCAACATGGCTAAATCAATTTTTATAATCTG
1 TTTTTTAACTTTCTTATTATTTCCAACATGGCTAAATCAATTTTTATAATCTG
340059 TTTTTTAACTTTCTTATTATTTCCAACATGGCTAAATCAATTTTTATAATCTG
1 TTTTTTAACTTTCTTATTATTTCCAACATGGCTAAATCAATTTTTATAATCTG
340112 GTTACATGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (53 bp):
TTTTTTAACTTTCTTATTATTTCCAACATGGCTAAATCAATTTTTATAATCTG
Found at i:340635 original size:16 final size:16
Alignment explanation
Indices: 340614--340651 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
340604 AATGCTTTTT
340614 AAAAGTATTTTTGAGA
1 AAAAGTATTTTTGAGA
340630 AAAAGTATTTTTGAGA
1 AAAAGTATTTTTGAGA
340646 AAAAGT
1 AAAAGT
340652 TTAAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (16 bp):
AAAAGTATTTTTGAGA
Found at i:342636 original size:30 final size:31
Alignment explanation
Indices: 342578--342640 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
342568 ATTTGATCAC
*
342578 TGAATTATTCAAAAGTTTTCATTTAAGTCAT
1 TGAATTATTCAAAAATTTTCATTTAAGTCAT
342609 TGAATTATTCAAAAAATTTT-A-TTAAGTCAT
1 TGAATTATTC-AAAAATTTTCATTTAAGTCAT
342639 TG
1 TG
342641 GGTTGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.37
31 11 0.37
32 8 0.27
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (31 bp):
TGAATTATTCAAAAATTTTCATTTAAGTCAT
Found at i:349119 original size:21 final size:22
Alignment explanation
Indices: 349090--349138 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
349080 CACTTAGAAA
*
349090 AATTATTTTAGT-TT-TTTATTT
1 AATTTTTTTAGTCTTATTT-TTT
*
349111 AATTTTTTTTGTCTTATTTTTT
1 AATTTTTTTAGTCTTATTTTTT
349133 AATTTT
1 AATTTT
349139 ATGCTTGCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
22 11 0.46
23 3 0.12
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (22 bp):
AATTTTTTTAGTCTTATTTTTT
Found at i:352466 original size:2 final size:2
Alignment explanation
Indices: 352453--352501 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
352443 AATTACATAC
*
352453 AT AT AC 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
352495 AT AT AT A
1 AT AT AT A
352502 ATTTTTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:353921 original size:3 final size:3
Alignment explanation
Indices: 353913--353945 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
353903 CAAATTTAAC
*
353913 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
353946 CTAAATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:371979 original size:42 final size:42
Alignment explanation
Indices: 371916--372001 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
371906 TTTTTCTCTT
371916 GTACCAGAAGTAAAAAAAGGCAAGCTTGATAAAAGGGCTGAA
1 GTACCAGAAGTAAAAAAAGGCAAGCTTGATAAAAGGGCTGAA
*
371958 GTACCAGAAGTAAAAAGAGGCAAGCTTGATAAAAGGGCTGAA
1 GTACCAGAAGTAAAAAAAGGCAAGCTTGATAAAAGGGCTGAA
372000 GT
1 GT
372002 TACAGTATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.12, G:0.28, T:0.15
Consensus pattern (42 bp):
GTACCAGAAGTAAAAAAAGGCAAGCTTGATAAAAGGGCTGAA
Found at i:376223 original size:116 final size:115
Alignment explanation
Indices: 376020--376247 Score: 413
Period size: 116 Copynumber: 2.0 Consensus size: 115
376010 AAAAAAAATT
376020 TATCAATTAAGATTATTTTTATCTGACACGTGTAACATAACTGTGCAACAGGCACCAAAATATTT
1 TATCAATTAAGATTATTTTTATCTGACACGTGTAACATAACTGTGCAACAGGCACCAAAATATTT
376085 CCATGCAATTGGCGGATATAATCCGCATGTCTTCAAGCCGCCAAATAATC
66 CCATGCAATTGGCGGATATAATCCGCATGTCTTCAAGCCGCCAAATAATC
376135 TATCAATTAAGATTGA-TTTTATCTGACACGTGTAACATAACTTGTGCAACAGGCACCAAAATAT
1 TATCAATTAAGATT-ATTTTTATCTGACACGTGTAACATAAC-TGTGCAACAGGCACCAAAATAT
* *
376199 TTCCATGCAATTGGCGGATATAATCCGCATGTCTTCGATCCGCCAAATA
64 TTCCATGCAATTGGCGGATATAATCCGCATGTCTTCAAGCCGCCAAATA
376248 GTTAGCAGCT
Statistics
Matches: 109, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
115 39 0.36
116 70 0.64
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (115 bp):
TATCAATTAAGATTATTTTTATCTGACACGTGTAACATAACTGTGCAACAGGCACCAAAATATTT
CCATGCAATTGGCGGATATAATCCGCATGTCTTCAAGCCGCCAAATAATC
Found at i:384693 original size:28 final size:27
Alignment explanation
Indices: 384658--384711 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
384648 ATAATGCTTA
** *
384658 ATAATAATATTGTTATTAATAATAACC
1 ATAATAATATTAATAATAATAATAACC
384685 ATAATTAATATTAATAATAATAATAAC
1 ATAA-TAATATTAATAATAATAATAAC
384712 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATAATAATATTAATAATAATAATAACC
Found at i:385789 original size:30 final size:30
Alignment explanation
Indices: 385722--385921 Score: 205
Period size: 30 Copynumber: 6.7 Consensus size: 30
385712 GAAGGTCCCT
* *
385722 AAACTATCCAAAAATTCCA-TTTTCA-CCCT
1 AAACT-TCCAAAAATTCCATTTTTAACCCCG
385751 AGAACTTCCAAAAATTCCATTTTTAACCCCG
1 A-AACTTCCAAAAATTCCATTTTTAACCCCG
* *
385782 AAACTTCCAAAAATTCTATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
385812 -AACTTCCAAAAATCCCAATTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
385841 AAATTTCCAAAAATTCCATTTTT-ATCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
385870 AAACTTCCAAAAACTCCATTTTCAACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
385900 AAAC-TCTC-AAAATTACCATTTT
1 AAACTTC-CAAAAATT-CCATTTT
385922 ACCCCCTGAG
Statistics
Matches: 143, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
29 69 0.48
30 70 0.49
31 4 0.03
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCG
Found at i:385795 original size:59 final size:59
Alignment explanation
Indices: 385722--385925 Score: 245
Period size: 59 Copynumber: 3.5 Consensus size: 59
385712 GAAGGTCCCT
*
385722 AAACTATCCAAAAATTCCATTTTCACCCTAGAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTTAACCCCG
* ** * * *
385782 AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCAATTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTTAACCCCG
* * * *
385841 AAATTTCCAAAAATTCCATTTTTATCCCTA-AACTTCCAAAAACTCCATTTTCAACCTCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCTAGAACTTCCAAAAATTCCATTTTTAACCCCG
385900 AAAC-TCTC-AAAATTACCA-TTTTACCC
1 AAACTTC-CAAAAATT-CCATTTTTACCC
385926 CCTGAGTATT
Statistics
Matches: 123, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
57 3 0.02
58 13 0.11
59 99 0.80
60 8 0.07
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTTAACCCCG
Found at i:386324 original size:27 final size:27
Alignment explanation
Indices: 386294--386346 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
386284 ATTCTGAAAT
*
386294 ATTACGCCTTAATTTACTAGGTGCAAA
1 ATTACGCCTTAACTTACTAGGTGCAAA
386321 ATTACGCCTTAACTTACTAGGTGCAA
1 ATTACGCCTTAACTTACTAGGTGCAA
386347 CCTTTCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (27 bp):
ATTACGCCTTAACTTACTAGGTGCAAA
Found at i:416913 original size:23 final size:22
Alignment explanation
Indices: 416862--416915 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
416852 ACATTTAAAG
*
416862 AAATATAATTATTTATATTGGAT
1 AAATATAATTATTTATATT-GAC
416885 AAATATAATTATTTATATAT-AC
1 AAATATAATTATTTATAT-TGAC
416907 AATATATAA
1 AA-ATATAA
416916 ACATAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 24 0.86
24 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
AAATATAATTATTTATATTGAC
Done.