Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011808.1 Kokia drynarioides strain JFW-HI SEQ_126803, 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: 250982
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 147 characters in sequence are not A, C, G, or T
Found at i:187 original size:15 final size:14
Alignment explanation
Indices: 158--193 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
148 ATATTTTTAT
158 ATTAAAAAAAGAAA
1 ATTAAAAAAAGAAA
*
172 ATTAAATAAAATAAA
1 ATTAAA-AAAAGAAA
187 ATTAAAA
1 ATTAAAA
194 TTTGACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
ATTAAAAAAAGAAA
Found at i:244 original size:27 final size:27
Alignment explanation
Indices: 201--253 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
191 AAATTTGACA
*
201 AATGGTGCCTTTAGGGTAGGCGGCACC
1 AATGGTGCCTCTAGGGTAGGCGGCACC
228 AATGGTGCCTACT-GGGTAGGCGGCAC
1 AATGGTGCCT-CTAGGGTAGGCGGCAC
254 TAGTGATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.38, T:0.21
Consensus pattern (27 bp):
AATGGTGCCTCTAGGGTAGGCGGCACC
Found at i:8620 original size:26 final size:26
Alignment explanation
Indices: 8571--8620 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
8561 TCTGTTTAAA
**
8571 TTTGAATTTATTTAATATTTTTTATG
1 TTTGAATTTATTTAATATGGTTTATG
8597 TTTGAATTTATTTAATGA-GGTTTA
1 TTTGAATTTATTTAAT-ATGGTTTA
8621 GCAAATGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (26 bp):
TTTGAATTTATTTAATATGGTTTATG
Found at i:11647 original size:17 final size:17
Alignment explanation
Indices: 11627--11660 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11617 TTTTACATGA
*
11627 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
11644 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
11661 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:12001 original size:27 final size:27
Alignment explanation
Indices: 11958--12009 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
11948 ATTGGGATCA
11958 GGTGCCGCCTGATAGGTAGGCACCATT
1 GGTGCCGCCTGATAGGTAGGCACCATT
*
11985 GGTGCTGCCT-ATCAGGTAGGCACCA
1 GGTGCCGCCTGAT-AGGTAGGCACCA
12010 CCCAAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.19, C:0.27, G:0.33, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTGATAGGTAGGCACCATT
Found at i:12504 original size:21 final size:21
Alignment explanation
Indices: 12480--12519 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12470 CATGCAGTTT
12480 ATTTGCCGTTTAATTGTTATA
1 ATTTGCCGTTTAATTGTTATA
*
12501 ATTTTCCGTTTAATTGTTA
1 ATTTGCCGTTTAATTGTTA
12520 GAATCTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (21 bp):
ATTTGCCGTTTAATTGTTATA
Found at i:12654 original size:48 final size:48
Alignment explanation
Indices: 12583--12677 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
12573 TAACCTAATA
12583 ATCAAGAATATTCGTTATCCCAAATGTGATCTAAATTTAAATCACGTG
1 ATCAAGAATATTCGTTATCCCAAATGTGATCTAAATTTAAATCACGTG
* * * *
12631 ATCAAGAGTATTTGTTATCCCAAATGTGATCTAATTTTAAGTCACGT
1 ATCAAGAATATTCGTTATCCCAAATGTGATCTAAATTTAAATCACGT
12678 CACTCGCGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (48 bp):
ATCAAGAATATTCGTTATCCCAAATGTGATCTAAATTTAAATCACGTG
Found at i:23969 original size:22 final size:22
Alignment explanation
Indices: 23927--23968 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
23917 TATTTCAGTT
*
23927 TTTTTAAATAATTTATTTTTTA
1 TTTTTAAATAATTAATTTTTTA
23949 TTTTTAAA-AATTAATTTTTT
1 TTTTTAAATAATTAATTTTTT
23969 TGAGTGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTAAATAATTAATTTTTTA
Found at i:24197 original size:4 final size:4
Alignment explanation
Indices: 24188--24228 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
24178 CCCTAAAATT
*
24188 TTTA TTTA TTTA TTT- GTTA TTTA TTTA -TTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
24229 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 8 0.25
4 24 0.75
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:24209 original size:11 final size:11
Alignment explanation
Indices: 24188--24224 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
24178 CCCTAAAATT
24188 TTTATTTATTTA
1 TTTA-TTATTTA
*
24200 TTTGTTATTTA
1 TTTATTATTTA
24211 TTTATTATTTA
1 TTTATTATTTA
24222 TTT
1 TTT
24225 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 20 0.87
12 3 0.13
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:24209 original size:15 final size:14
Alignment explanation
Indices: 24185--24228 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
24175 CTTCCCTAAA
24185 ATTTTTATTTATTT
1 ATTTTTATTTATTT
24199 ATTTGTTATTTATTT
1 ATTT-TTATTTATTT
24214 ATTATTTATTT-TTT
1 ATT-TTTATTTATTT
24228 A
1 A
24229 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.29
15 19 0.68
16 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (14 bp):
ATTTTTATTTATTT
Found at i:24325 original size:18 final size:18
Alignment explanation
Indices: 24304--24339 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24294 ATTATATAAT
24304 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
24322 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
24340 TTTTTGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:25364 original size:24 final size:25
Alignment explanation
Indices: 25332--25382 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
25322 TTTCCACTTG
*
25332 ATTTG-AAAACATTATTTTGTTTTA
1 ATTTGAAAAACATTATTTTATTTTA
* *
25356 ATTTTAAAAATATTATTTTATTTTA
1 ATTTGAAAAACATTATTTTATTTTA
25381 AT
1 AT
25383 ATATTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTTGAAAAACATTATTTTATTTTA
Found at i:28877 original size:2 final size:2
Alignment explanation
Indices: 28866--28894 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28856 ATCTATATTT
28866 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28895 AAAGCACGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:46457 original size:16 final size:16
Alignment explanation
Indices: 46432--46462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46422 TAATTTTATC
*
46432 TTTATTAATTTTAAAT
1 TTTATAAATTTTAAAT
46448 TTTATAAATTTTAAA
1 TTTATAAATTTTAAA
46463 AAACCTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATAAATTTTAAAT
Found at i:47465 original size:13 final size:13
Alignment explanation
Indices: 47447--47471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47437 AAAATAAATT
47447 AAATATATATTTG
1 AAATATATATTTG
47460 AAATATATATTT
1 AAATATATATTT
47472 TATTGTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AAATATATATTTG
Found at i:48623 original size:18 final size:18
Alignment explanation
Indices: 48597--48638 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
48587 GAGAGGTGGA
*
48597 TTTAAATAATGTTATTTT
1 TTTAAATAATATTATTTT
*
48615 TTTAGATAATATTATTTT
1 TTTAAATAATATTATTTT
*
48633 TCTAAA
1 TTTAAA
48639 ATATATAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTAAATAATATTATTTT
Found at i:55569 original size:14 final size:15
Alignment explanation
Indices: 55545--55574 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55535 AGATTTGGAT
55545 AATTGTAATTATTAA
1 AATTGTAATTATTAA
55560 AATT-TAATTATTAA
1 AATTGTAATTATTAA
55574 A
1 A
55575 CTATTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTGTAATTATTAA
Found at i:67874 original size:2 final size:2
Alignment explanation
Indices: 67867--67918 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
67857 CACTAATGGA
67867 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
67909 AT AT AT AT AT
1 AT AT AT AT AT
67919 TTATTTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89041 original size:19 final size:18
Alignment explanation
Indices: 89019--89058 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
89009 TTTTTTTAAA
89019 TTATTTTCATACATAATTT
1 TTATTTTCATA-ATAATTT
* *
89038 TTATTTTTATATTAATTT
1 TTATTTTCATAATAATTT
89056 TTA
1 TTA
89059 ATAATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTCATAATAATTT
Found at i:89227 original size:11 final size:11
Alignment explanation
Indices: 89206--89252 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
89196 TTTAAAATAT
*
89206 AATTTTTTTAA
1 AATTATTTTAA
*
89217 AAATATTTTAA
1 AATTATTTTAA
*
89228 AATTAATTTAA
1 AATTATTTTAA
*
89239 AATTATTTTTA
1 AATTATTTTAA
89250 AAT
1 AAT
89253 ATAAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:89454 original size:24 final size:24
Alignment explanation
Indices: 89427--89482 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
89417 GAAGCCTGTG
*
89427 AAGGAGAAGAAACCCAAA-GCTCCT
1 AAGGAGAAGAAA-CCAAAGGCTCCA
* *
89451 AAGGAGAAGGAACCAAAGGTTCCA
1 AAGGAGAAGAAACCAAAGGCTCCA
89475 AAGGAGAA
1 AAGGAGAA
89483 AAAGCCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.48, C:0.18, G:0.27, T:0.07
Consensus pattern (24 bp):
AAGGAGAAGAAACCAAAGGCTCCA
Found at i:113695 original size:20 final size:19
Alignment explanation
Indices: 113672--113713 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
113662 GGTTAAAAAG
*
113672 TAATTTTATTTTTATTAATT
1 TAATTTT-TTTTTATTAAAT
*
113692 TAATTTTTTTTTTTTAAAT
1 TAATTTTTTTTTATTAAAT
113711 TAA
1 TAA
113714 GAGTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TAATTTTTTTTTATTAAAT
Found at i:121513 original size:2 final size:2
Alignment explanation
Indices: 121506--121537 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
121496 TTTTACATAC
121506 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
121538 TCAAACCCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123105 original size:2 final size:2
Alignment explanation
Indices: 123100--123138 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
123090 TCTCTCTCTC
*
123100 TA TA TA TT TA TA 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 TA TA TA TA TA TA T
123139 CCCACTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:129255 original size:3 final size:3
Alignment explanation
Indices: 129247--129275 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
129237 ATTCCATGTT
129247 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
129276 CTCAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:129527 original size:20 final size:20
Alignment explanation
Indices: 129489--129525 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
129479 AACCCCCTTT
129489 ATATTTATCATTCTTTTTCC
1 ATATTTATCATTCTTTTTCC
*
129509 ATATTTATGA-TCTTTTT
1 ATATTTATCATTCTTTTT
129526 TCTTTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.62
Consensus pattern (20 bp):
ATATTTATCATTCTTTTTCC
Found at i:135132 original size:13 final size:14
Alignment explanation
Indices: 135110--135139 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
135100 GTCTTAATTT
135110 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
135124 TTTTT-TTTTTTTG
1 TTTTTGTTTTTTTG
135137 TTT
1 TTT
135140 ATAATCGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:138345 original size:2 final size:2
Alignment explanation
Indices: 138338--138362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
138328 TGAAAGAAAA
138338 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
138363 AGGGGGTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:141750 original size:2 final size:2
Alignment explanation
Indices: 141743--141767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
141733 GAGACTACAC
141743 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
141768 CACTTATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:149905 original size:21 final size:21
Alignment explanation
Indices: 149866--149926 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
149856 GTTTTGATTG
149866 CTGTTTTGATG-TTTTTTTTA
1 CTGTTTTGATGCTTTTTTTTA
* *
149886 CTGTTTTGGTGCTCTTTTTTA
1 CTGTTTTGATGCTTTTTTTTA
* *
149907 CTATTTTGTTGCTTTTTTTT
1 CTGTTTTGATGCTTTTTTTT
149927 TTGTTGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.07, C:0.10, G:0.15, T:0.69
Consensus pattern (21 bp):
CTGTTTTGATGCTTTTTTTTA
Found at i:149998 original size:20 final size:23
Alignment explanation
Indices: 149952--150003 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
149942 TTGTTTTGCC
*
149952 GTTATTTTAACTGCTGTTTTGATT
1 GTTATTTTAACT-CTGTTTGGATT
149976 GTTATTTTAA-T-TGTTTGGA-T
1 GTTATTTTAACTCTGTTTGGATT
149996 GTTATTTT
1 GTTATTTT
150004 TATGCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
23 1 0.04
24 10 0.37
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (23 bp):
GTTATTTTAACTCTGTTTGGATT
Found at i:155383 original size:21 final size:21
Alignment explanation
Indices: 155359--155399 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
155349 TGTCACCAAT
*
155359 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
155380 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
155400 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Found at i:159788 original size:71 final size:70
Alignment explanation
Indices: 159669--159804 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 70
159659 CACAAACGTT
* *
159669 AGAATGTGAAAGGCTTTCTTTTTCAACGGTGAAGCATTTTATCAAACACTTAGGTCGACGAAAAG
1 AGAATGTGAAAGGCTTTCTTTTTCAACAGTGAAGCATTTTATCAAACACTTAGCTCGACGAAAAG
159734 ATGAA
66 ATGAA
* * * * *
159739 AGAATTTGAAAGGCCTTTCTTTTTCATCAGTGAAGCATTTTATCGAACACTTCGCTTGACGAAAA
1 AGAATGTGAAAGG-CTTTCTTTTTCAACAGTGAAGCATTTTATCAAACACTTAGCTCGACGAAAA
159804 G
65 G
159805 TTGGAGGAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
70 12 0.21
71 46 0.79
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (70 bp):
AGAATGTGAAAGGCTTTCTTTTTCAACAGTGAAGCATTTTATCAAACACTTAGCTCGACGAAAAG
ATGAA
Found at i:165595 original size:106 final size:106
Alignment explanation
Indices: 165410--165625 Score: 423
Period size: 106 Copynumber: 2.0 Consensus size: 106
165400 TAAAAACCCA
165410 TAACATAAAGAAGCAAAACCAAAGCTTTGAACTTCATGCAACTTGCAATGATTTTTAAAAGGGTA
1 TAACATAAAGAAGCAAAACCAAAGCTTTGAACTTCATGCAACTTGCAATGATTTTTAAAAGGGTA
165475 ATATAAATTGCTTCCTGATTAGTTTACTAACCTTTTATTAT
66 ATATAAATTGCTTCCTGATTAGTTTACTAACCTTTTATTAT
*
165516 TAACATAAAGAAGCAAAACCAAAGCTTTGAACTTCATGCAACTTGCAGTGATTTTTAAAAGGGTA
1 TAACATAAAGAAGCAAAACCAAAGCTTTGAACTTCATGCAACTTGCAATGATTTTTAAAAGGGTA
165581 ATATAAATTGCTTCCTGATTAGTTTACTAACCTTTTATTAT
66 ATATAAATTGCTTCCTGATTAGTTTACTAACCTTTTATTAT
165622 TAAC
1 TAAC
165626 TTGATAACTT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 109 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (106 bp):
TAACATAAAGAAGCAAAACCAAAGCTTTGAACTTCATGCAACTTGCAATGATTTTTAAAAGGGTA
ATATAAATTGCTTCCTGATTAGTTTACTAACCTTTTATTAT
Found at i:167339 original size:19 final size:19
Alignment explanation
Indices: 167315--167353 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
167305 AATATAAAAC
167315 ATATTTAAACGTTTGTAAA
1 ATATTTAAACGTTTGTAAA
167334 ATATTTAAACGTTTGTAAA
1 ATATTTAAACGTTTGTAAA
167353 A
1 A
167354 AATAAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (19 bp):
ATATTTAAACGTTTGTAAA
Found at i:167357 original size:21 final size:21
Alignment explanation
Indices: 167309--167357 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
167299 TGTAGAAATA
*
167309 TAAAACATATTTAAACGTTTG
1 TAAAAAATATTTAAACGTTTG
167330 T--AAAATATTTAAACGTTTG
1 TAAAAAATATTTAAACGTTTG
167349 TAAAAAATA
1 TAAAAAATA
167358 AAAGGGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 18 0.72
21 7 0.28
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (21 bp):
TAAAAAATATTTAAACGTTTG
Found at i:174914 original size:2 final size:2
Alignment explanation
Indices: 174907--174945 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
174897 GAGTAAGTGA
174907 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
174946 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:180446 original size:2 final size:2
Alignment explanation
Indices: 180439--180464 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
180429 ATGATCATTG
180439 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
180465 TGAACTCTAT
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:186257 original size:7 final size:7
Alignment explanation
Indices: 186245--186277 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
186235 GAAATCTAAC
186245 AAAAGAA
1 AAAAGAA
186252 AAAAGAA
1 AAAAGAA
186259 AAAA-AA
1 AAAAGAA
186265 AAAA-AA
1 AAAAGAA
186271 AAAAGAA
1 AAAAGAA
186278 CTTTAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:188914 original size:18 final size:18
Alignment explanation
Indices: 188879--188917 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
188869 ATATAATATT
188879 ATTTATTAATTTCAGTTA
1 ATTTATTAATTTCAGTTA
*
188897 ATTTGATTAA-TTCGGTTA
1 ATTT-ATTAATTTCAGTTA
188915 ATT
1 ATT
188918 ACCCAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (18 bp):
ATTTATTAATTTCAGTTA
Found at i:189169 original size:76 final size:76
Alignment explanation
Indices: 189043--189195 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
189033 ATTATTTCAA
*
189043 ATTTAACCAAAGTTTGAACACCCCTATAATAATCCCTATAATTAGACGCTAAAAATAATGAATAA
1 ATTTAACCAAAGTTTGAACACCCCTATAATAATCCCTATAATTAAACGCTAAAAATAATGAATAA
189108 ACGTTGACTAT
66 ACGTTGACTAT
189119 ATTTAACCAAAGTTTGAACACCCCTATAATAATCCCTATAATTAAACGCTAAAAATAATGAATAA
1 ATTTAACCAAAGTTTGAACACCCCTATAATAATCCCTATAATTAAACGCTAAAAATAATGAATAA
189184 ACGTTGACTAT
66 ACGTTGACTAT
189195 A
1 A
189196 ACCCCTAGCC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.29
Consensus pattern (76 bp):
ATTTAACCAAAGTTTGAACACCCCTATAATAATCCCTATAATTAAACGCTAAAAATAATGAATAA
ACGTTGACTAT
Found at i:189825 original size:18 final size:18
Alignment explanation
Indices: 189802--189836 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
189792 GGAACTGAGG
* *
189802 TTTATTTGTTTTTATATA
1 TTTATTTATTTTAATATA
189820 TTTATTTATTTTAATAT
1 TTTATTTATTTTAATAT
189837 TATATATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATTTATTTTAATATA
Found at i:190448 original size:16 final size:17
Alignment explanation
Indices: 190427--190458 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
190417 ACAGAGAAAT
190427 ATAATAA-TAAATAATC
1 ATAATAATTAAATAATC
190443 ATAATAATTAAATAAT
1 ATAATAATTAAATAAT
190459 AATTAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATTAAATAATC
Found at i:217215 original size:19 final size:19
Alignment explanation
Indices: 217191--217233 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
217181 AAACATAAAT
217191 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
217210 TAAATAATATCTTAAATAG
1 TAAATAAAATCTTAAATAA
217229 TAAAT
1 TAAAT
217234 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:218997 original size:4 final size:4
Alignment explanation
Indices: 218988--219034 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
218978 CCTTTCTATT
218988 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
219035 CACAATCAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:223028 original size:22 final size:23
Alignment explanation
Indices: 222990--223042 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
222980 GCAAATCTAT
222990 CACAAAGGTAGACGAAAA-CGTGC
1 CACAAA-GTAGACGAAAAGCGTGC
*
223013 CACAAAGTAGATGAAAAGCGTGC
1 CACAAAGTAGACGAAAAGCGTGC
*
223036 CGCAAAG
1 CACAAAG
223043 ACAGATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.43, C:0.21, G:0.26, T:0.09
Consensus pattern (23 bp):
CACAAAGTAGACGAAAAGCGTGC
Found at i:223052 original size:23 final size:22
Alignment explanation
Indices: 223003--223053 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
222993 AAAGGTAGAC
*
223003 GAAAACGTGCCACAAAGTAGAT
1 GAAAACGTGCCACAAAGCAGAT
*
223025 GAAAAGCGTGCCGCAAAGACAGAT
1 GAAAA-CGTGCCACAAAG-CAGAT
*
223049 AAAAA
1 GAAAA
223054 TCAGAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 11 0.46
24 8 0.33
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.10
Consensus pattern (22 bp):
GAAAACGTGCCACAAAGCAGAT
Found at i:225315 original size:95 final size:95
Alignment explanation
Indices: 225151--225340 Score: 353
Period size: 95 Copynumber: 2.0 Consensus size: 95
225141 TCAAGAGCGG
225151 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
1 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
225216 CTTACCCACAAAATCTCTAGAGGTTTCGTT
66 CTTACCCACAAAATCTCTAGAGGTTTCGTT
* * *
225246 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGATTGCTAAAAGTGGATATATCTATAGTTACT
1 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
225311 CTTACCCACAAAATCTCTAGAGGTTTCGTT
66 CTTACCCACAAAATCTCTAGAGGTTTCGTT
225341 TAGTCGGCCT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (95 bp):
AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
CTTACCCACAAAATCTCTAGAGGTTTCGTT
Found at i:225956 original size:18 final size:15
Alignment explanation
Indices: 225912--225961 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 15
225902 ACACTTTCAT
225912 CAAATCTATCAAAAAAA
1 CAAAT-TAT-AAAAAAA
225929 CAAATTATAAAAAAA
1 CAAATTATAAAAAAA
225944 CAAAAGTTGATAAAAAAA
1 C-AAA-TT-ATAAAAAAA
225962 AAACTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.27
16 6 0.20
17 7 0.23
18 9 0.30
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (15 bp):
CAAATTATAAAAAAA
Found at i:245108 original size:27 final size:27
Alignment explanation
Indices: 245056--245108 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
245046 ATTTTGATAC
* *
245056 TTTTTTTTTAATATGGTACGTGTGTAAT
1 TTTTTTTTTAATATGATACG-ATGTAAT
245084 TTTTTTTTCTAATATGATAC-ATGTA
1 TTTTTTTT-TAATATGATACGATGTA
245109 TTTGACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 4 0.18
28 8 0.36
29 10 0.45
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.57
Consensus pattern (27 bp):
TTTTTTTTTAATATGATACGATGTAAT
Done.