Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015289.1 Kokia drynarioides strain JFW-HI SEQ_130334, 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: 116736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:4915 original size:16 final size:16
Alignment explanation
Indices: 4894--4943 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
4884 TGATGGGGAT
4894 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
4910 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
4925 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
4940 ATTA
1 ATTA
4944 GCTAGGTTTA
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:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:5597 original size:4 final size:4
Alignment explanation
Indices: 5590--5645 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
5580 TACCTTTTTT
* *
5590 TTTC TTTC TCCTT- TTTC CTTC -TTC TTTC TTTC TTTC TTTC TCTTT TTTC
1 TTTC TTTC T--TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC
5639 TTTC TTT
1 TTTC TTT
5646 TTCCCTTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
3 5 0.11
4 33 0.75
5 4 0.09
6 2 0.05
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:5604 original size:17 final size:16
Alignment explanation
Indices: 5583--5645 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
5573 AACACATTAC
*
5583 CTTTTTTTTTCTTTCT
1 CTTTTTCTTTCTTTCT
*
5599 CCTTTTTCCTTC-TTCT
1 -CTTTTTCTTTCTTTCT
5615 -TTCTTTCTTTCTTTCT
1 CTT-TTTCTTTCTTTCT
5631 CTTTTTTCTTTCTTT
1 C-TTTTTCTTTCTTT
5646 TTCCCTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.05
15 7 0.18
16 8 0.21
17 20 0.51
18 2 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
CTTTTTCTTTCTTTCT
Found at i:5630 original size:32 final size:31
Alignment explanation
Indices: 5583--5648 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 31
5573 AACACATTAC
5583 CTTT-TTTTTTCTTTCTCCTTTTTCCTTCTT
1 CTTTCTTTTTTCTTTCTCCTTTTTCCTTCTT
* *
5613 CTTTCTTTCTTTCTTTCTCTTTTTTCTTTCTT
1 CTTTCTTT-TTTCTTTCTCCTTTTTCCTTCTT
5645 -TTTC
1 CTTTC
5649 CCTTCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 4 0.12
31 7 0.22
32 21 0.66
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (31 bp):
CTTTCTTTTTTCTTTCTCCTTTTTCCTTCTT
Found at i:8443 original size:43 final size:43
Alignment explanation
Indices: 8365--8450 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
8355 ATGTTTAACG
* * * * *
8365 AAATTGGATCAAAATCTTTAAAATTGACTGCAATTGTCACAAA
1 AAATTGAATCAAAATCATTAAAATGGACGGAAATTGTCACAAA
*
8408 AAATTGAATCAAAATCATTGAAATGGACGGAAATTGTCACAAA
1 AAATTGAATCAAAATCATTAAAATGGACGGAAATTGTCACAAA
8451 TTTCAGTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (43 bp):
AAATTGAATCAAAATCATTAAAATGGACGGAAATTGTCACAAA
Found at i:9205 original size:4 final size:4
Alignment explanation
Indices: 9196--9226 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
9186 AAGCAATTAT
9196 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
9227 GTGTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:12427 original size:9 final size:9
Alignment explanation
Indices: 12366--12420 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
12356 TAGTGACGAG
*
12366 GAAGAAGGT
1 GAAGAAGGA
*
12375 GAAGACGGA
1 GAAGAAGGA
*
12384 GAGGAGAAGAA
1 GA--AGAAGGA
*
12395 GAAGAAGAA
1 GAAGAAGGA
12404 GAAGAAGGA
1 GAAGAAGGA
12413 GAAGAAGG
1 GAAGAAGG
12421 GCAAGAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
9 32 0.82
11 7 0.18
ACGTcount: A:0.53, C:0.02, G:0.44, T:0.02
Consensus pattern (9 bp):
GAAGAAGGA
Found at i:12433 original size:3 final size:3
Alignment explanation
Indices: 12388--12419 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12378 GACGGAGAGG
*
12388 AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
12420 GGCAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:15195 original size:61 final size:59
Alignment explanation
Indices: 15094--15209 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 59
15084 ATCACTTTAA
* * * *
15094 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAAATAAACATTAAATTAAATTAAACATTAAATCT
* *
15153 TATTAAATTAATAGAATA-TTATCTACAAAATAAACATTAAATTTAATTTAACATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAAATAAACATTAAATTAAATTAAACATTAA
15210 GATAATCACC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 3 0.06
59 17 0.35
60 1 0.02
61 27 0.56
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAAATAAACATTAAATTAAATTAAACATTAAATCT
Found at i:26301 original size:3 final size:3
Alignment explanation
Indices: 26293--26328 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
26283 GCCTATCCAC
26293 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26329 CTTTAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27368 original size:9 final size:9
Alignment explanation
Indices: 27356--27425 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
27346 TAAATTACCC
27356 TTATTATGA
1 TTATTATGA
27365 TTATGATTATGA
1 -T-T-ATTATGA
* *
27377 TGATGATGA
1 TTATTATGA
* *
27386 TGATGATGA
1 TTATTATGA
*
27395 TTATTATTA
1 TTATTATGA
*
27404 TTATTATTA
1 TTATTATGA
*
27413 TTATTATGT
1 TTATTATGA
27422 TTAT
1 TTAT
27426 GTTTATGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 41 0.80
10 1 0.02
11 2 0.04
12 7 0.14
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (9 bp):
TTATTATGA
Found at i:27369 original size:6 final size:6
Alignment explanation
Indices: 27358--27416 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
27348 AATTACCCTT
* * * * *
27358 ATTATG ATTATG ATTATG ATGATG ATGATG ATGATG ATTATT ATTATT
1 ATTATG ATTATG ATTATG ATTATG ATTATG ATTATG ATTATG ATTATG
*
27406 ATTATT ATTAT
1 ATTATG ATTAT
27417 TATGTTTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
ATTATG
Found at i:27379 original size:3 final size:3
Alignment explanation
Indices: 27361--27395 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
27351 TACCCTTATT
* *
27361 ATG ATT ATG ATT ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
27396 TATTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (3 bp):
ATG
Found at i:27400 original size:3 final size:3
Alignment explanation
Indices: 27394--27419 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27384 GATGATGATG
27394 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
27420 GTTTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27425 original size:18 final size:18
Alignment explanation
Indices: 27410--27446 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27400 ATTATTATTA
27410 TTATTATTATGTTTATGT
1 TTATTATTATGTTTATGT
27428 TTATGT-TTATGTTTATGT
1 TTAT-TATTATGTTTATGT
27446 T
1 T
27447 GTTTATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.68
Consensus pattern (18 bp):
TTATTATTATGTTTATGT
Found at i:27451 original size:9 final size:9
Alignment explanation
Indices: 27437--27461 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27427 TTTATGTTTA
27437 TGTTTATGT
1 TGTTTATGT
27446 TGTTTATGT
1 TGTTTATGT
27455 TGTTTAT
1 TGTTTAT
27462 ATAGTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.20, T:0.68
Consensus pattern (9 bp):
TGTTTATGT
Found at i:27455 original size:6 final size:6
Alignment explanation
Indices: 27416--27446 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
27406 ATTATTATTA
27416 TTATGT TTATGT TTATGT TTATGT TTATGT T
1 TTATGT TTATGT TTATGT TTATGT TTATGT T
27447 GTTTATGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTATGT
Found at i:27646 original size:90 final size:90
Alignment explanation
Indices: 27540--27708 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 90
27530 AAATTAATTT
* *
27540 TTTTTTTTGCACTCAATTAAGTATTTAAACAGTT-AAAATGTATCAAAAAG-ACCTTCA-AATTT
1 TTTTTTTTGCACTCAATTAAGTATTCAAAC-GTTCAAAATGCATCAAAAAGAACC-TCAGAA-TT
*
27602 TTTCAAAAAGAGCAATTAAGCCCCTGCC
63 TTTCAAAAAAAGCAATTAAGCCCCTGCC
* * * * *
27630 TTTTTTTTGCATTCAATTGAGTGTTCGAACTTTCAAAATGCATCAAAAAGAACCTCAGAATTTTT
1 TTTTTTTTGCACTCAATTAAGTATTCAAACGTTCAAAATGCATCAAAAAGAACCTCAGAATTTTT
27695 CAAAAAAAGCAATT
66 CAAAAAAAGCAATT
27709 TAGCACCTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
89 2 0.03
90 61 0.90
91 5 0.07
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (90 bp):
TTTTTTTTGCACTCAATTAAGTATTCAAACGTTCAAAATGCATCAAAAAGAACCTCAGAATTTTT
CAAAAAAAGCAATTAAGCCCCTGCC
Found at i:27724 original size:90 final size:90
Alignment explanation
Indices: 27539--27727 Score: 213
Period size: 90 Copynumber: 2.1 Consensus size: 90
27529 AAAATTAATT
* *
27539 TTTTTTTTTGCACTCAATTAAGTATTTAAACAGTTAAAATGTATCAAAAAGACCTTCAAATTTTT
1 TTTTTTTTTGCACTCAATTAAGTATTCAAACAGTTAAAATGCATCAAAAAGACCTTCAAATTTTT
* * **
27604 TCAAAAAGAGCAATTAAGCCCCTGC
66 TCAAAAAAAGCAATTAAGCACCTAA
* * * * * *
27629 CTTTTTTTTGCATTCAATTGAGTGTTCGAAC-TTTCAAAATGCATCAAAAAGAACC-TCAGAA-T
1 TTTTTTTTTGCACTCAATTAAGTATTCAAACAGTT-AAAATGCATCAAAAAG-ACCTTCA-AATT
*
27691 TTTTCAAAAAAAGCAATTTAGCACCTAA
63 TTTTCAAAAAAAGCAATTAAGCACCTAA
27719 TTTTTTTTT
1 TTTTTTTTT
27728 ACTTAATTGG
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
89 2 0.02
90 75 0.91
91 5 0.06
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (90 bp):
TTTTTTTTTGCACTCAATTAAGTATTCAAACAGTTAAAATGCATCAAAAAGACCTTCAAATTTTT
TCAAAAAAAGCAATTAAGCACCTAA
Found at i:27957 original size:20 final size:20
Alignment explanation
Indices: 27884--27957 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
27874 TTTATAGAAA
*
27884 ATAAAAATTATTAAATTTGA-
1 ATAAAAATTATAAAATTT-AT
* *
27904 ATAAAAAATATATAATTTAT
1 ATAAAAATTATAAAATTTAT
* *
27924 -TAAAAATTAGAAAATTTTT
1 ATAAAAATTATAAAATTTAT
*
27943 ATAAAAATCATAAAA
1 ATAAAAATTATAAAA
27958 AAATTATAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 16 0.37
20 27 0.63
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (20 bp):
ATAAAAATTATAAAATTTAT
Found at i:28209 original size:10 final size:10
Alignment explanation
Indices: 28190--28376 Score: 58
Period size: 10 Copynumber: 19.1 Consensus size: 10
28180 TTTTAGTACG
28190 ATAA-TTTTT
1 ATAATTTTTT
28199 ATAATTTTTT
1 ATAATTTTTT
*
28209 ACGAA--TTTT
1 A-TAATTTTTT
28218 AT-ATTTCTTT
1 ATAATTT-TTT
*
28228 A-CATTTTTT
1 ATAATTTTTT
28237 ATAATTTTCTT
1 ATAATTTT-TT
**
28248 AT--GGTTTT
1 ATAATTTTTT
**
28256 ATAAAATTTT
1 ATAATTTTTT
28266 ATAATTTTTCT
1 ATAATTTTT-T
*
28277 AT-A-TTTCT
1 ATAATTTTTT
*
28285 AT-ATATTTT
1 ATAATTTTTT
*
28294 A-AAATTTTT
1 ATAATTTTTT
*
28303 ATAATTTTTA
1 ATAATTTTTT
**
28313 ATAA-AATTT
1 ATAATTTTTT
*
28322 AAATATTTTTT
1 ATA-ATTTTTT
*
28333 ATATATATATTT
1 ATA-AT-TTTTT
*
28345 A-AAATTTTT
1 ATAATTTTTT
28354 ATAACTTTTTTT
1 ATAA--TTTTTT
*
28366 ATCATTTTTT
1 ATAATTTTTT
28376 A
1 A
28377 CCACATGTCA
Statistics
Matches: 130, Mismatches: 28, Indels: 39
0.66 0.14 0.20
Matches are distributed among these distances:
7 1 0.01
8 8 0.06
9 38 0.29
10 52 0.40
11 18 0.14
12 13 0.10
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:28219 original size:19 final size:19
Alignment explanation
Indices: 28195--28244 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
28185 GTACGATAAT
28195 TTTTATAATTTTTTACGA-A
1 TTTTATAATTTTTTAC-ATA
*
28214 TTTTAT-ATTTCTTTACATT
1 TTTTATAATTT-TTTACATA
28233 TTTTATAATTTT
1 TTTTATAATTTT
28245 CTTATGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTACATA
Found at i:28287 original size:29 final size:29
Alignment explanation
Indices: 28233--28374 Score: 103
Period size: 29 Copynumber: 4.8 Consensus size: 29
28223 TCTTTACATT
**
28233 TTTTATAATTTTCT-TATGGTTTTATAAAA
1 TTTTATAATTTT-TATATATTTTTATAAAA
* * *
28262 TTTTATAATTTTTCTATATTTCTAT-ATA
1 TTTTATAATTTTTATATATTTTTATAAAA
*
28290 TTTTAAAATTTTTATA-ATTTTTAATAAAA
1 TTTTATAATTTTTATATATTTTT-ATAAAA
* * *
28319 TTTAAATATTTTTTATATATATATTTA-AAAT
1 TTT-TATAATTTTTATATAT-T-TTTATAAAA
*
28350 TTTTATAACTTTTTTTATCATTTTT
1 TTTTATAA-TTTTTATAT-ATTTTT
28375 TACCACATGT
Statistics
Matches: 89, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.06
28 19 0.21
29 25 0.28
30 16 0.18
31 17 0.19
32 4 0.04
33 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (29 bp):
TTTTATAATTTTTATATATTTTTATAAAA
Found at i:28301 original size:28 final size:28
Alignment explanation
Indices: 28259--28336 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
28249 TGGTTTTATA
*
28259 AAATTTTATAATTTTTCTATATTTCT-AT
1 AAATTTTAAAATTTTT-TATATTTCTAAT
* *
28287 ATATTTTAAAA-TTTTTATAATTTTTAAT
1 AAATTTTAAAATTTTTTAT-ATTTCTAAT
*
28315 AAAATTTAAATATTTTTTATAT
1 AAATTTTAAA-ATTTTTTATAT
28337 ATATATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 3 0.07
27 9 0.22
28 19 0.46
29 3 0.07
30 7 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
AAATTTTAAAATTTTTTATATTTCTAAT
Found at i:28328 original size:37 final size:36
Alignment explanation
Indices: 28257--28330 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
28247 TATGGTTTTA
* * * *
28257 TAAAATTTTATAATTTTTCTATATTTCTATATATTT
1 TAAAATTTTATAATTTTTATAAAATTCTAAATATTT
28293 TAAAATTTTTATAATTTTTAATAAAATT-TAAATATTT
1 TAAAA-TTTTATAATTTTT-ATAAAATTCTAAATATTT
28330 T
1 T
28331 TTATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 5 0.16
37 22 0.69
38 5 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (36 bp):
TAAAATTTTATAATTTTTATAAAATTCTAAATATTT
Found at i:28331 original size:21 final size:22
Alignment explanation
Indices: 28293--28353 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
28283 CTATATATTT
** *
28293 TAAAATTTTTATAATTTTTA-A
1 TAAAATTTAAATATTTTTTATA
28314 TAAAATTTAAATATTTTTTATA
1 TAAAATTTAAATATTTTTTATA
*
28336 TATATATTTAAA-ATTTTT
1 TA-AAATTTAAATATTTTT
28354 ATAACTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.50
22 9 0.26
23 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAAAATTTAAATATTTTTTATA
Found at i:28568 original size:89 final size:88
Alignment explanation
Indices: 28438--28676 Score: 230
Period size: 89 Copynumber: 2.7 Consensus size: 88
28428 ATAGGGATGA
* * * * **** *
28438 TTCAAGTATCCAATTAAGTGCAAAAAAATCAGGGGCTTAATTG-TTTCTTTTTTTAAAGTTTTAG
1 TTCAAGGACCCAATTGAGTGCAAAAAAATTAGGGGCTTAATTGCTTT-TTTGGAAAAAGTTTGAG
* * *
28502 GGCTTTTTTGATTCATTTTGAAAG
65 GGCCTTTTTAATGCATTTTGAAAG
* *
28526 TTTAAGGACTCAATTGAGTGCAAAAAAATGTAGGGGCTTAATTGCTTTTTTGGAAAAAGTTTGAG
1 TTCAAGGACCCAATTGAGTGCAAAAAAAT-TAGGGGCTTAATTGCTTTTTTGGAAAAAGTTTGAG
* *
28591 GGCCTTTTTAATGCTTTTTGATAG
65 GGCCTTTTTAATGCATTTTGAAAG
* * * * * *
28615 TTCAAGTACCCAATTGAATGGAAAAAATTATAGGGGTTTAATTGCTCCTTTT-GAAAAAGTTT
1 TTCAAGGACCCAATTGAGTGCAAAAAAAT-TAGGGGCTTAATTGCT-TTTTTGGAAAAAGTTT
28677 ATATTTTTTT
Statistics
Matches: 123, Mismatches: 25, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
88 24 0.20
89 92 0.75
90 7 0.06
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (88 bp):
TTCAAGGACCCAATTGAGTGCAAAAAAATTAGGGGCTTAATTGCTTTTTTGGAAAAAGTTTGAGG
GCCTTTTTAATGCATTTTGAAAG
Found at i:31136 original size:7 final size:7
Alignment explanation
Indices: 31124--31176 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
31114 CTTCTTCTCC
31124 TTCTTCT
1 TTCTTCT
31131 TTCTTCT
1 TTCTTCT
*
31138 TCCTTTCT
1 TTC-TTCT
31146 TTCTTTCT
1 TTC-TTCT
31154 TTC-TCT
1 TTCTTCT
*
31160 TTTTTCT
1 TTCTTCT
*
31167 TTCTTTT
1 TTCTTCT
31174 TTC
1 TTC
31177 CTTCAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 5 0.13
7 20 0.51
8 14 0.36
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCTTCT
Found at i:31147 original size:4 final size:4
Alignment explanation
Indices: 31127--31176 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
31117 CTTCTCCTTC
* *
31127 TTCT TTC- TTCT TCCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT
31174 TTC
1 TTC
31177 CTTCAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 6 0.15
4 30 0.77
5 3 0.08
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:51922 original size:17 final size:17
Alignment explanation
Indices: 51900--51934 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
51890 CCTTTCTACG
51900 TGCACCCAAAACAACTT
1 TGCACCCAAAACAACTT
51917 TGCACCCAAAACAACTT
1 TGCACCCAAAACAACTT
51934 T
1 T
51935 TCGGCATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.34, G:0.06, T:0.20
Consensus pattern (17 bp):
TGCACCCAAAACAACTT
Found at i:55392 original size:23 final size:24
Alignment explanation
Indices: 55347--55399 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
55337 CATAAATATA
55347 TATAATTTTAAAATATTAAAAAAT
1 TATAATTTTAAAATATTAAAAAAT
*
55371 TATAATTTTTAAAT-TTAAAAAAT
1 TATAATTTTAAAATATTAAAAAAT
*
55394 AATAAT
1 TATAAT
55400 GAATTGCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAATTTTAAAATATTAAAAAAT
Found at i:56066 original size:17 final size:18
Alignment explanation
Indices: 56033--56066 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56023 GGAACGGCAC
*
56033 AAATATAAAGACTAAAAA
1 AAATAAAAAGACTAAAAA
56051 AAATAAAAAG-CTAAAA
1 AAATAAAAAGACTAAAA
56067 CATCTTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (18 bp):
AAATAAAAAGACTAAAAA
Found at i:70686 original size:64 final size:64
Alignment explanation
Indices: 70585--70711 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 64
70575 TAATCAATTG
* *
70585 AGAAGAAACAGTATTTCAACATAGCAATTGATTTAAACAAATAAACAATCAATTCAAAAGAAAA
1 AGAAGAAACAGTATTTCAACATAACAATCGATTTAAACAAATAAACAATCAATTCAAAAGAAAA
* * * * *
70649 AGAAGAAGCAGTATTTCACCATAACAATCGATTTAAACATATAAATAATCTATTCAAAAGAAA
1 AGAAGAAACAGTATTTCAACATAACAATCGATTTAAACAAATAAACAATCAATTCAAAAGAAA
70712 CAATATTCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (64 bp):
AGAAGAAACAGTATTTCAACATAACAATCGATTTAAACAAATAAACAATCAATTCAAAAGAAAA
Found at i:70738 original size:34 final size:34
Alignment explanation
Indices: 70695--70766 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
70685 ACATATAAAT
*
70695 AATCTATTCAAAAGAAACAATATTCCAACATGAC
1 AATCAATTCAAAAGAAACAATATTCCAACATGAC
* *
70729 AATCAATTCAAAAGAAACAGTATTCTAACATGAC
1 AATCAATTCAAAAGAAACAATATTCCAACATGAC
70763 AATC
1 AATC
70767 GATAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (34 bp):
AATCAATTCAAAAGAAACAATATTCCAACATGAC
Found at i:86860 original size:4 final size:4
Alignment explanation
Indices: 86851--86875 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
86841 TGTGCACAAT
86851 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
86876 TCCTTCTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:88084 original size:21 final size:20
Alignment explanation
Indices: 88060--88123 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
88050 AGAGATTACC
88060 AAAAATTTTGAAGAAGTATAA
1 AAAAATTTTGAAGAA-TATAA
**
88081 AAAAATTAAG-AGAATAT-A
1 AAAAATTTTGAAGAATATAA
*
88099 AAAAATTATT-AAAAATATAA
1 AAAAATT-TTGAAGAATATAA
88119 AAAAA
1 AAAAA
88124 AATGAGGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 8 0.23
19 9 0.26
20 10 0.29
21 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (20 bp):
AAAAATTTTGAAGAATATAA
Found at i:88098 original size:19 final size:18
Alignment explanation
Indices: 88070--88123 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 18
88060 AAAAATTTTG
88070 AAGAAGTATAAAAAAATTA
1 AAGAA-TATAAAAAAATTA
88089 AGAGAATATAAAAAATTATTA
1 A-AGAATATAAAAAA--ATTA
88110 AA-AATATAAAAAAA
1 AAGAATATAAAAAAA
88124 AATGAGGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.03
19 21 0.66
20 5 0.16
21 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (18 bp):
AAGAATATAAAAAAATTA
Found at i:96619 original size:19 final size:19
Alignment explanation
Indices: 96588--96646 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
96578 CTTTTTAAGT
*
96588 AATTAAATT-TTTATATGA
1 AATTTAATTATTTATATGA
* *
96606 AATTTAATTATTTAAATAA
1 AATTTAATTATTTATATGA
* *
96625 TAAATT-ATTAATTATATGA
1 -AATTTAATTATTTATATGA
96644 AAT
1 AAT
96647 AAAAAAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 10 0.32
19 17 0.55
20 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AATTTAATTATTTATATGA
Found at i:110819 original size:4 final size:4
Alignment explanation
Indices: 110806--110855 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
110796 AAAATTGAAG
* * *
110806 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GGAA GGAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
110853 GAA
1 GAA
110856 GAAGGAGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
3 6 0.15
4 31 0.77
5 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:110852 original size:19 final size:16
Alignment explanation
Indices: 110811--110883 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 16
110801 TGAAGGAAAA
* *
110811 AAGAAAGAAAAAAGAG
1 AAGAAAGAAGAAGGAG
110827 AAAGAAAGAAAGGAAGGAAG
1 -AAGAAAG-AA-GAAGG-AG
110847 AAGAAAGAAGAAGGAG
1 AAGAAAGAAGAAGGAG
*
110863 AAGAAGGGGAAGAAGGAG
1 AAGAA--AGAAGAAGGAG
110881 AAG
1 AAG
110884 GGAAAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 7 0.15
17 12 0.25
18 17 0.35
19 10 0.21
20 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAGAAGGAG
Found at i:110854 original size:7 final size:7
Alignment explanation
Indices: 110806--110858 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
110796 AAAATTGAAG
*
110806 GAAAAAA
1 GAAAGAA
110813 GAAAGAA
1 GAAAGAA
*
110820 AAAAG-A
1 GAAAGAA
110826 GAAAGAAA
1 GAAAG-AA
110834 GAAAGGAA
1 GAAA-GAA
*
110842 GGAAGAA
1 GAAAGAA
110849 GAAAGAA
1 GAAAGAA
110856 GAA
1 GAA
110859 GGAGAAGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 5 0.13
7 22 0.58
8 10 0.26
9 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:110866 original size:9 final size:9
Alignment explanation
Indices: 110839--110883 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
110829 AGAAAGAAAG
110839 GAAGGAAGAA
1 GAAGG-AGAA
110849 GAA--AGAA
1 GAAGGAGAA
110856 GAAGGAGAA
1 GAAGGAGAA
*
110865 GAAGGGGAA
1 GAAGGAGAA
110874 GAAGGAGAA
1 GAAGGAGAA
110883 G
1 G
110884 GGAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 7 0.23
9 21 0.68
10 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GAAGGAGAA
Found at i:111269 original size:20 final size:21
Alignment explanation
Indices: 111228--111270 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
111218 TAATTTACTT
111228 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
111249 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
111269 TA
1 TA
111271 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:111583 original size:16 final size:16
Alignment explanation
Indices: 111535--111585 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
111525 TAAACCTAGC
*
111535 TAATTAATTACCAAAA
1 TAATTAATTAACAAAA
*
111551 T-A-TAATATAAAAAAA
1 TAATTAAT-TAACAAAA
*
111566 TAATTAATTATCAAAA
1 TAATTAATTAACAAAA
111582 TAAT
1 TAAT
111586 ATCTCCATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 12 0.43
17 4 0.14
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTAACAAAA
Found at i:112969 original size:43 final size:43
Alignment explanation
Indices: 112887--112971 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
112877 ATTAACATGT
* * *
112887 TAAATTATATTACTTGACTCGTGTTAATATGGTTTCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
*
112930 TAAATTATATTACTTTG-CTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTAC-TTGACTCGTATTAATATGCTT-ACATGTTA
112972 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 2 0.06
43 31 0.86
44 3 0.08
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
Found at i:113647 original size:45 final size:45
Alignment explanation
Indices: 113540--113634 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
113530 GCATTGCTCA
* * *
113540 TCAAGCTAAAGATATCAACCTCAGTTTAACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAATTTAACGAGCCACCGCAATAC
*
113585 TCAAGCCAAAGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAATTTAACGAGCCACCGCAATAC
113630 TCAAG
1 TCAAG
113635 GGAAGGATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAATTTAACGAGCCACCGCAATAC
Done.