Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1376
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: 56088
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:239 original size:2 final size:2
Alignment explanation
Indices: 232--264 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
222 TTTATGCAAT
232 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
265 AGAGTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:255 original size:15 final size:15
Alignment explanation
Indices: 235--265 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
225 ATGCAATTAT
235 ATATATATATATATA
1 ATATATATATATATA
250 ATATATATATATATA
1 ATATATATATATATA
265 A
1 A
266 GAGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:1081 original size:2 final size:2
Alignment explanation
Indices: 1069--1122 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
1059 GATTTGTTCT
1069 TA TA T- TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1107 TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1123 TAGATTGTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.11
2 42 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1085 original size:11 final size:11
Alignment explanation
Indices: 1069--1122 Score: 80
Period size: 11 Copynumber: 5.3 Consensus size: 11
1059 GATTTGTTCT
1069 TATATTATATA
1 TATATTATATA
1080 TATA-T-TATA
1 TATATTATATA
1089 TATA-TATATA
1 TATATTATATA
1099 T-TATTATATA
1 TATATTATATA
1109 TATATTATATA
1 TATATTATATA
1120 TAT
1 TAT
1123 TAGATTGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
9 11 0.28
10 13 0.32
11 16 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATTATATA
Found at i:3636 original size:2 final size:2
Alignment explanation
Indices: 3631--3660 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3621 TATATGTGTG
*
3631 TA TA TA TA TA CA 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
3661 GTGAAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4217 original size:13 final size:13
Alignment explanation
Indices: 4190--4231 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
4180 CGTTAACGGG
4190 ATATATATA-TAT
1 ATATATATATTAT
4202 ATATATATATTAT
1 ATATATATATTAT
* *
4215 ATATACACATTAT
1 ATATATATATTAT
4228 ATAT
1 ATAT
4232 TAGTCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:4231 original size:2 final size:2
Alignment explanation
Indices: 4190--4219 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4180 CGTTAACGGG
4190 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4220 CACATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5531 original size:17 final size:17
Alignment explanation
Indices: 5509--5542 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5499 TATGTATTCG
*
5509 TATCATATTATTTTTTA
1 TATCATATTATATTTTA
5526 TATCATATTATATTTTA
1 TATCATATTATATTTTA
5543 AATTTTTTCT
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:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
TATCATATTATATTTTA
Found at i:7910 original size:17 final size:17
Alignment explanation
Indices: 7890--7934 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
7880 ACAATTATTT
7890 AAAAATT-TTAAAGATAA
1 AAAAATTATTAAA-ATAA
7907 AAAAATTGATTAAAATAA
1 AAAAATT-ATTAAAATAA
*
7925 AAAATTTATT
1 AAAAATTATT
7935 TTTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 10 0.40
19 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAAATTATTAAAATAA
Found at i:8414 original size:2 final size:2
Alignment explanation
Indices: 8407--8432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8397 AAAATTTTAT
8407 TA 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
8433 ATGTGCCAGC
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):
TA
Found at i:13302 original size:2 final size:2
Alignment explanation
Indices: 13295--13324 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13285 AATTGGAGTA
13295 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
13325 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15483 original size:17 final size:17
Alignment explanation
Indices: 15461--15518 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
15451 ATAAATAATT
15461 AAAATATATTTATATTA
1 AAAATATATTTATATTA
* *
15478 AAAATAAATATATATTA
1 AAAATATATTTATATTA
*
15495 AAATTATATTTATATTA
1 AAAATATATTTATATTA
15512 AATAATA
1 AA-AATA
15519 ATTAAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 31 0.91
18 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATTTATATTA
Found at i:16036 original size:35 final size:38
Alignment explanation
Indices: 15956--16036 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 38
15946 TAAATCTTAG
* * *
15956 TATTATATAATAAATATTATTTTATTTTATATAATAAT
1 TATTATAAAATAAATATCATTTTATTATATATAATAAT
* *
15994 T-TAATAAAATATATA-CATTTTATTAT-TATAA-AAT
1 TATTATAAAATAAATATCATTTTATTATATATAATAAT
16028 TATTATAAA
1 TATTATAAA
16037 TTAATTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
34 4 0.11
35 11 0.31
36 9 0.25
37 11 0.31
38 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (38 bp):
TATTATAAAATAAATATCATTTTATTATATATAATAAT
Found at i:16291 original size:2 final size:2
Alignment explanation
Indices: 16284--16323 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16274 GCACTATAAA
16284 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16324 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19239 original size:20 final size:20
Alignment explanation
Indices: 19208--19282 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
19198 TCATACCCTG
*
19208 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
19228 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
19248 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
19268 ATGTATCGATACATT
1 ATGTATCGATACATT
19283 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:19275 original size:40 final size:39
Alignment explanation
Indices: 19208--19285 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
19198 TCATACCCTG
* *
19208 ATGTATCAATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTACAATATATCGATACAT-TATGA
* * *
19248 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCAATACATTCTACAATATATCGATACATTATG
19286 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCAATACATTCTACAATATATCGATACATTATGA
Found at i:20232 original size:23 final size:23
Alignment explanation
Indices: 20202--20250 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
20192 TGACCATGCA
20202 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
20225 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
20248 TTT
1 TTT
20251 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTTTTATTATGTTTCATGCATT
Found at i:20257 original size:20 final size:21
Alignment explanation
Indices: 20196--20250 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 21
20186 AGCCTTTGAC
20196 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
20217 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTATTATGTTT
20240 CATGCATTTTT
1 CATGCATTTTT
20251 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.34
23 21 0.66
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:33341 original size:27 final size:26
Alignment explanation
Indices: 33316--33392 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 26
33306 CCTTTACACC
*
33316 CAAAAAAAAA-AACACAAAAAAAACA
1 CAAAAAAAAACAAAACAAAAAAAACA
33341 CAAAAAAAAACAAAAC-AAAAAAACA
1 CAAAAAAAAACAAAACAAAAAAAACA
* *
33366 AAAAAAAAGAAAAAATAGCAAAAAAAA
1 CAAAAAAA-AACAAA-A-CAAAAAAAA
33393 TAGAAGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 26 0.59
26 9 0.20
27 1 0.02
28 1 0.02
29 7 0.16
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (26 bp):
CAAAAAAAAACAAAACAAAAAAAACA
Found at i:33349 original size:23 final size:23
Alignment explanation
Indices: 33319--33378 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
33309 TTACACCCAA
*
33319 AAAAAAAAACACAAA-AAAAACAC
1 AAAAAAAAACA-AAACAAAAAAAC
33342 AAAAAAAAACAAAACAAAAAAAC
1 AAAAAAAAACAAAACAAAAAAAC
*
33365 AAAAAAAAAGAAAA
1 AAAAAAAAACAAAA
33379 AATAGCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.87, C:0.12, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAAAAAACAAAACAAAAAAAC
Found at i:33380 original size:11 final size:11
Alignment explanation
Indices: 33318--33373 Score: 76
Period size: 11 Copynumber: 4.8 Consensus size: 11
33308 TTTACACCCA
33318 AAAAAAAAAAC
1 AAAAAAAAAAC
*
33329 ACAAAAAAAAC
1 AAAAAAAAAAC
33340 ACAAAAAAAAAC
1 A-AAAAAAAAAC
33352 AAAACAAAAAAAC
1 -AAA-AAAAAAAC
33365 AAAAAAAAA
1 AAAAAAAAA
33374 GAAAAAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
11 17 0.43
12 14 0.35
13 9 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:33392 original size:1 final size:1
Alignment explanation
Indices: 33317--33380 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
33307 CTTTACACCC
* * * * * * * *
33317 AAAAAAAAAAACACAAAAAAAACACAAAAAAAAACAAAACAAAAAAACAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33381 TAGCAAAAAA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:33392 original size:23 final size:20
Alignment explanation
Indices: 33317--33372 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
33307 CTTTACACCC
*
33317 AAAAAAAAAAACACAAAAAA
1 AAAAAAAAAAAAACAAAAAA
*
33337 AACACAAAAAAAAACAAAACAA
1 AA-AAAAAAAAAAACAAAA-AA
33359 AAAAACAAAAAAAA
1 AAAAA-AAAAAAAA
33373 AGAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 16 0.53
22 12 0.40
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAACAAAAAA
Found at i:33395 original size:12 final size:10
Alignment explanation
Indices: 33320--33392 Score: 74
Period size: 10 Copynumber: 6.8 Consensus size: 10
33310 TACACCCAAA
33320 AAAAAAAACAC
1 AAAAAAAA-AC
33331 AAAAAAAACAC
1 AAAAAAAA-AC
33342 AAAAAAAAAC
1 AAAAAAAAAC
33352 AAAACAAAAAAAC
1 --AA-AAAAAAAC
*
33365 AAAAAAAAAG
1 AAAAAAAAAC
* *
33375 AAAAAATAGC
1 AAAAAAAAAC
33385 AAAAAAAA
1 AAAAAAAA
33393 TAGAAGGGTC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
10 23 0.43
11 21 0.39
12 2 0.04
13 8 0.15
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:34722 original size:28 final size:28
Alignment explanation
Indices: 34614--35964 Score: 1638
Period size: 28 Copynumber: 47.4 Consensus size: 28
34604 GAATGTTCAT
34614 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
34642 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
34671 CTCTTTTCAAAGCCCACAACTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
34700 CCCTTTCAAAGCCCATAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
34728 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
34757 CTCTTTTTAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
34786 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
34815 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
34843 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
34871 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
34900 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
34928 CTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
34957 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
34985 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
35014 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35042 CTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35071 CCCTTTCAAAGCCGACAACTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
35099 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35127 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35156 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35185 CTCTTTTC-AAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
35213 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35241 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35269 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35297 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35325 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
35354 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35382 CTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
35411 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
35439 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
35468 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35496 CTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
35525 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* ** * *
35553 --C--T--AAGCCAAGTAGTGCACTAAGC-
1 CCCTTTCAAAGCCCACAAGT-CAGT-GGCA
* ** * * **
35576 CCACAAGTT-AGTGGCACTCTTTTCAAAGCCCACAAGGCA
1 CC-C--TTTCA-AAGC-C-C---AC-AAG-TCA-GTGGCA
35615 -CC-TTC-AAG----CAAGT-AGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35635 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
35664 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
35692 CCATTGCGAAGCTCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35720 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35748 CCCTTTTAAAGCTCACACAAGTCAGTGGCA
1 CCCTTTCAAAGC-C-CACAAGTCAGTGGCA
* * *
35778 CTCCTTTTAAAGCTCACGCAAGTCAGTGGTA
1 C-CCTTTCAAAGC-C-CACAAGTCAGTGGCA
*
35809 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35837 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
35865 TCCTTTCAAAGCCCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
35893 TTCTTTCAAAGCCCACGCACGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
35923 CCCTTTTAAAGCCCATGCAAGTCAATGGCAA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGC-A
35954 CCCTTTTCAAA
1 CCC-TTTCAAA
35965 TCACCACTGT
Statistics
Matches: 1175, Mismatches: 99, Indels: 94
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.00
21 1 0.00
22 10 0.01
23 9 0.01
24 7 0.01
26 2 0.00
27 5 0.00
28 604 0.51
29 422 0.36
30 59 0.05
31 32 0.03
32 8 0.01
33 2 0.00
34 2 0.00
37 1 0.00
38 7 0.01
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:34736 original size:57 final size:57
Alignment explanation
Indices: 34614--35554 Score: 1525
Period size: 57 Copynumber: 16.5 Consensus size: 57
34604 GAATGTTCAT
* *
34614 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
34671 CTCTTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAAGCCCATAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
34728 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
34786 CTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
34843 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
34900 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
34957 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35014 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35071 CCCTTTCAAAGCCGACAACTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
35127 CTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35185 CTCTTTTC-AAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35241 CCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35297 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35354 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35411 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
35468 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
35525 CCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACT
35555 AAGCCAAGTA
Statistics
Matches: 829, Mismatches: 48, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
55 6 0.01
56 155 0.19
57 559 0.67
58 109 0.13
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (57 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:34934 original size:114 final size:114
Alignment explanation
Indices: 34614--35964 Score: 1779
Period size: 114 Copynumber: 11.6 Consensus size: 114
34604 GAATGTTCAT
* *
34614 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
* *
34679 AAAGCCCACAACTCAGTGGCAC-CCTTTCAAAGCCCATAAGTCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
34728 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAATCAGTGGCACTCTTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTT
*
34793 CAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
64 CAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
34843 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
34908 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
66 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
34957 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
35022 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
66 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
35071 CCCTTTCAAAGCCGACAACTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
* * *
35135 AAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
35185 CTCTTTTC-AAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTC
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
*
35248 AAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
35297 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
35362 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
66 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
35411 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
35476 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
66 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
35525 CCCTTTCAAAGCCCACAAGTCAGTGGCACTAAGCCAAGTAGTGCACTAAGCCCACAAGTTAGTGG
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACT----C---T-TTTCA--AAGCCCACAAGTCAGTGG
* *
35590 CACTCTTTTCAAAGCCCACAAGGCACCTTCAAGCAAGTAGTGGCACTCTTTTCAAAGCCCACAAG
56 CAC-CCTTTCAAAGCCCACAA-G-----T----C----AGTGGCACTCCTTTCAAAGCCCACAAG
35655 TCAGTGGCA
106 TCAGTGGCA
* * * * * *
35664 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CATTGCGAAGCTCACAATTCAGTGGCACTCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
35728 AAGCCCACAAGTCAGTGGCAC-CCTTTTAAAGCTCACACAAGTCAGTGGCA
66 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC-C-CACAAGTCAGTGGCA
* * * *
35778 CTCCTTTTAAAGCTCACGCAAGTCAGTGGTAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 C-CCTTTCAAAGC-C-CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
35842 TCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCA
63 TCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
** * * *
35893 TTCTTTCAAAGCCCACGCACGTCAGTGGCACCCTTTT-AAAGCCCATGCAAGTCAATGGCAACCC
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAGTGGC-ACCC
35957 TTTTCAAA
61 -TTTCAAA
35965 TCACCACTGT
Statistics
Matches: 1120, Mismatches: 72, Indels: 86
0.88 0.06 0.07
Matches are distributed among these distances:
111 6 0.01
112 57 0.05
113 144 0.13
114 526 0.47
115 143 0.13
116 13 0.01
117 78 0.07
118 8 0.01
121 1 0.00
122 3 0.00
124 20 0.02
125 17 0.02
126 2 0.00
127 15 0.01
128 18 0.02
130 3 0.00
131 1 0.00
134 1 0.00
135 1 0.00
139 63 0.06
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (114 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:35572 original size:17 final size:19
Alignment explanation
Indices: 35540--35576 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
35530 TCAAAGCCCA
35540 CAAGTCAGTGGCACTAAGC
1 CAAGTCAGTGGCACTAAGC
35559 CAAGT-AGT-GCACTAAGC
1 CAAGTCAGTGGCACTAAGC
35576 C
1 C
35577 CACAAGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.16
Consensus pattern (19 bp):
CAAGTCAGTGGCACTAAGC
Found at i:35917 original size:145 final size:144
Alignment explanation
Indices: 35623--35964 Score: 417
Period size: 145 Copynumber: 2.4 Consensus size: 144
35613 CACCTTCAAG
* * *
35623 CAAGT-AGTGGCACT-CTTTTCAAAGCC-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
1 CAAGTCAGTGGCACTCCTTTT-AAAGCCACGCAAGTCAGTGGAACCTTTTCAAAGCCCACAAGTC
* * *
35685 AGTGGCACCATTGCGAAGCTCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACC
65 AGTGGCACCATTGCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACC
* *
35750 CTTTTAAAGCTCACA
130 CTTTCAAAGCCCACA
*
35765 CAAGTCAGTGGCACTCCTTTTAAAGCTCACGCAAGTCAGTGGTACCTTTTCAAAGCCCACAAGTC
1 CAAGTCAGTGGCACTCCTTTTAAAGC-CACGCAAGTCAGTGGAACCTTTTCAAAGCCCACAAGTC
* * *
35830 AGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCA
65 AGTGGCAC-CATTGCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCA
** *
35893 TTCTTTCAAAGCCCACG
128 CCCTTTCAAAGCCCACA
* * *
35910 CACGTCAGTGGCAC-CCTTTTAAAGCCCATGCAAGTCAATGGCAACCCTTTTCAAA
1 CAAGTCAGTGGCACTCCTTTTAAAG-CCACGCAAGTCAGTGG-AA-CCTTTTCAAA
35965 TCACCACTGT
Statistics
Matches: 173, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
142 5 0.03
143 14 0.08
144 30 0.17
145 113 0.65
146 11 0.06
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (144 bp):
CAAGTCAGTGGCACTCCTTTTAAAGCCACGCAAGTCAGTGGAACCTTTTCAAAGCCCACAAGTCA
GTGGCACCATTGCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCC
TTTCAAAGCCCACA
Found at i:36487 original size:20 final size:19
Alignment explanation
Indices: 36441--36517 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
36431 TCATACCCTG
* *
36441 ATGTATCGATGCATTTTTCA
1 ATGTATCGATACA-TTATCA
* *
36461 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
36481 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
36501 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
36518 GTCTTTTTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:36508 original size:40 final size:39
Alignment explanation
Indices: 36441--36518 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
36431 TCATACCCTG
* * *
36441 ATGTATCGATGCATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
36481 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
36519 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:37452 original size:22 final size:22
Alignment explanation
Indices: 37426--37479 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
37416 AGCCTTTGAC
37426 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
37448 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
37469 CATGCATTTTT
1 CATGCATTTTT
37480 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:37486 original size:20 final size:21
Alignment explanation
Indices: 37426--37486 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
37416 AGCCTTTGAC
**
37426 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
37448 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAACATGTTT
37469 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
37487 CCAGCATCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.27
21 21 0.57
22 6 0.16
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.57
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:42893 original size:42 final size:42
Alignment explanation
Indices: 42838--42956 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
42828 TTCTTCTCTC
* *
42838 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
42880 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* * * *
42922 TTCCTCCTATCATCCCTCATCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
42957 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.09, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:46161 original size:19 final size:18
Alignment explanation
Indices: 46120--46162 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
46110 AATAAAATAG
46120 GAAAAAAAAATATTTTGA
1 GAAAAAAAAATATTTTGA
* * *
46138 TAAAAAATAAATTTTTTTA
1 GAAAAAA-AAATATTTTGA
46157 GAAAAA
1 GAAAAA
46163 TCAATTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
GAAAAAAAAATATTTTGA
Found at i:46248 original size:20 final size:21
Alignment explanation
Indices: 46208--46245 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
46198 AACAATAAAA
46208 TTATTATAAAATAAATATTAT
1 TTATTATAAAATAAATATTAT
46229 TTATT-TAAAAT-AATATT
1 TTATTATAAAATAAATATT
46246 TATACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATTATAAAATAAATATTAT
Found at i:46986 original size:2 final size:2
Alignment explanation
Indices: 46981--47008 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46971 ATTGCGTGTG
46981 TA TA 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
47009 CTAACTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50850 original size:8 final size:8
Alignment explanation
Indices: 50839--51006 Score: 59
Period size: 8 Copynumber: 20.9 Consensus size: 8
50829 TTAATATGGT
50839 TATATAAA
1 TATATAAA
*
50847 TATA-ATA
1 TATATAAA
*
50854 TATAAAAA
1 TATATAAA
50862 TA-ATATAA
1 TATATA-AA
*
50870 TATA-AGA
1 TATATAAA
*
50877 TAATATGAA
1 T-ATATAAA
*
50886 TATTTAAA
1 TATATAAA
* *
50894 TTTTTAAA
1 TATATAAA
* * *
50902 AATTTATA
1 TATATAAA
50910 TAATATAAA
1 T-ATATAAA
50919 T-TATTAAA
1 TATA-TAAA
50927 -ATATTAAAA
1 TATA-T-AAA
50936 TTTATATAAA
1 --TATATAAA
50946 TATA-AAA
1 TATATAAA
* *
50953 TATTTTAA
1 TATATAAA
50961 -ATATAAA
1 TATATAAA
50968 TATAGTAAA
1 TATA-TAAA
50977 -ATA-AAA
1 TATATAAA
50983 TATATAAA
1 TATATAAA
50991 TATGATATAA
1 TAT-ATA-AA
51001 -ATATAA
1 TATATAA
51007 TAATTGTTTT
Statistics
Matches: 122, Mismatches: 19, Indels: 39
0.68 0.11 0.22
Matches are distributed among these distances:
6 3 0.02
7 27 0.22
8 62 0.51
9 21 0.17
10 5 0.04
11 1 0.01
12 3 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TATATAAA
Found at i:50857 original size:13 final size:13
Alignment explanation
Indices: 50839--50882 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
50829 TTAATATGGT
*
50839 TATATAAATATAA
1 TATATAAAAATAA
50852 TATATAAAAATAA
1 TATATAAAAATAA
*
50865 TATAATATAAGATAA
1 TAT-ATA-AAAATAA
50880 TAT
1 TAT
50883 GAATATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 3 0.11
15 9 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
TATATAAAAATAA
Found at i:50874 original size:16 final size:16
Alignment explanation
Indices: 50840--50888 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
50830 TAATATGGTT
50840 ATATAAATATAATAT--
1 ATATAAA-ATAATATGA
50855 ATA-AAAATAATAT-A
1 ATATAAAATAATATGA
*
50869 ATATAAGATAATATGA
1 ATATAAAATAATATGA
50885 ATAT
1 ATAT
50889 TTAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 12 0.40
16 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
ATATAAAATAATATGA
Found at i:50913 original size:33 final size:32
Alignment explanation
Indices: 50876--50962 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 32
50866 ATAATATAAG
* *
50876 ATAATATGAATATTTAAATTTTTAAAAATTTAT
1 ATAATATAAATATTTAAATTATT-AAAATTTAT
*
50909 ATAATATAAAT-TATTAAAATATTAAAATTTAT
1 ATAATATAAATAT-TTAAATTATTAAAATTTAT
50941 ATAAATATAAAATATTTTAAAT
1 AT-AATAT-AAATA-TTTAAAT
50963 ATAAATATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 12 0.27
33 23 0.51
34 4 0.09
35 5 0.11
36 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
ATAATATAAATATTTAAATTATTAAAATTTAT
Found at i:50946 original size:18 final size:17
Alignment explanation
Indices: 50900--50993 Score: 68
Period size: 15 Copynumber: 6.0 Consensus size: 17
50890 TAAATTTTTA
50900 AAAATTTATAT-AATAT
1 AAAATTTATATAAATAT
50916 -AAA-TTAT-TAAAATATT
1 AAAATTTATAT-AAATA-T
50932 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
50949 AAAATATT-T-TAAATAT
1 AAAAT-TTATATAAATAT
50965 -AAA--TATAGTAAA-AT
1 AAAATTTATA-TAAATAT
50979 AAAA--TATATAAATAT
1 AAAATTTATATAAATAT
50994 GATATAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
12 1 0.02
13 2 0.03
14 10 0.15
15 23 0.35
16 8 0.12
17 10 0.15
18 11 0.17
19 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:50976 original size:25 final size:24
Alignment explanation
Indices: 50898--50979 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 24
50888 TTTAAATTTT
50898 TAAAA-ATTTATATAATATAAAT-TA
1 TAAAATATTT-TA-AATATAAATATA
*
50922 TTAAAATA-TTAAAATTTATATAA-ATA
1 -TAAAATATTTTAAA--TATA-AATATA
50948 TAAAATATTTTAAATATAAATATA
1 TAAAATATTTTAAATATAAATATA
50972 GTAAAATA
1 -TAAAATA
50980 AAATATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
23 4 0.09
24 8 0.17
25 25 0.53
26 10 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (24 bp):
TAAAATATTTTAAATATAAATATA
Found at i:51164 original size:8 final size:10
Alignment explanation
Indices: 51134--51167 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
51124 TGAATATAAA
51134 TAAAATATAT
1 TAAAATATAT
51144 TAAAATATAT
1 TAAAATATAT
51154 TAAAAT-T-T
1 TAAAATATAT
51162 TAAAAT
1 TAAAAT
51168 GAATATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.29
9 1 0.04
10 16 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAAATATAT
Found at i:51204 original size:24 final size:24
Alignment explanation
Indices: 51176--51237 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
51166 ATGAATATGA
51176 TATTTATATTACATATCTCATGTT-
1 TATTTAT-TTACATATCTCATGTTC
* * *
51200 TATTTATTTAAATGTGTCATGTTC
1 TATTTATTTACATATCTCATGTTC
51224 TATTTATTT-CATAT
1 TATTTATTTACATAT
51238 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTTATTTACATATCTCATGTTC
Found at i:51238 original size:7 final size:7
Alignment explanation
Indices: 51228--51267 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
51218 ATGTTCTATT
*
51228 TATTTCA
1 TATTTTA
*
51235 TATTTTT
1 TATTTTA
51242 TATTTTA
1 TATTTTA
51249 TATTTTA
1 TATTTTA
51256 TA-TTTA
1 TATTTTA
51262 TATTTT
1 TATTTT
51268 GTCTTTCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:52795 original size:2 final size:2
Alignment explanation
Indices: 52788--52812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52778 AGTCTCCATA
52788 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52813 AGTATCTTTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54349 original size:3 final size:3
Alignment explanation
Indices: 54343--54368 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54333 ATAATAATTG
54343 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
54369 TATTTATTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.