Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold568
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: 84996
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:5941 original size:27 final size:29
Alignment explanation
Indices: 5880--5943 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
5870 TTAAAATTAT
5880 TTTATAATATTTATTATATTTTCCATAAA
1 TTTATAATATTTATTATATTTTCCATAAA
* * *
5909 TATATAATGTTT-TTA-ATTTTGCA-AGAA
1 TTTATAATATTTATTATATTTTCCATA-AA
5936 TTTATAAT
1 TTTATAAT
5944 TTATCTTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 16 0.53
28 3 0.10
29 10 0.33
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTATAATATTTATTATATTTTCCATAAA
Found at i:9263 original size:19 final size:20
Alignment explanation
Indices: 9236--9278 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9226 CTATTTCTTT
9236 ATATAAT-AATGTT-TTTTTA
1 ATATAATAAAT-TTATTTTTA
*
9255 ATATTATAAATTTATTTTTA
1 ATATAATAAATTTATTTTTA
9275 ATAT
1 ATAT
9279 CTTTTTAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATATAATAAATTTATTTTTA
Found at i:19539 original size:20 final size:20
Alignment explanation
Indices: 19492--19566 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
19482 AAAAAAACAT
** *
19492 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
19512 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
** * *
19532 CGTGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
19552 AATGTATCGATACAT
1 AATGTATCGATACAT
19567 CAGGGTATGA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:20608 original size:229 final size:225
Alignment explanation
Indices: 20073--21258 Score: 1581
Period size: 229 Copynumber: 5.2 Consensus size: 225
20063 ACAGCGGTGA
* * *
20073 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTT
1 TTTG-AAAGGG-TGCCACTAACTTG--TGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTT
** * * * *
20137 TGAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
60 TGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
* * *
20202 GCCACTGACTTGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCTACT
125 GCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTT--GTGGGCTTTAAAA-GAGTGCCACT
* *
20267 GACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGC
187 GAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
* * * * * *
20308 TTTGAAAGAGTGCCACTGAA-TTGTGGGCTTCGCAATG-GTGCCACTAACTTGTGGGCTTCGAAA
1 TTTGAAAGGGTGCCACT-AACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * *
20371 GGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGGTGCCAC
65 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
20436 TGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
130 TGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTT-AAAAGAGTGCCACTGACTTG
20501 TGGGCTTTGAAAGAAGTGCCACTGACTTGTGGGC
193 TGGGCTTTGAAAG-AGTGCCACTGACTTGTGGGC
*
20535 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAA
* *
20600 GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAGTTGTGGGCTTTGAAAGGGTGCCAC
65 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
* *
20665 TGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
130 TGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTT-AAAAGAGTGCCACTGACTTG
20730 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
193 TGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC
*
20764 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
20829 GGTGCCACTGACTTATGGG-TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCAC
66 GGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
* *
20893 TGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGGTGCCACTGACTT
130 TGACTTGTGGGCTTTGAAAAGGTGCCACTGACTT--GTGGGCTTTAAAA-GAGTGCCACTGAC-T
* *
20958 GTGTGGGCTTTGAAAGGGCGCCACTGACTTGTGGGC
191 -TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
* * * * * * * *
20994 TTTTAAAGAGTGCCATTAAATTGTGGGCTTCG-CAAGGGTGCCACTGACTTGTGGGCTTCGAAAG
1 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
** *
21058 GGTGCCACTGACTTGTGGGCTCTAAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCC
66 GGTGCCACTGACTTGTGGGCT-TTGAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCC
** *
21123 ACTGACTTGTGGGCTTTGAAATTGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGATTT
128 ACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTT-AAAAGAGTGCCACTGACTT
* *
21188 GTGGCCTTTGAAAAGAGTGCCACTGTCTTGTGGGC
192 GTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGC
*
21223 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAGG-GTGCCACTAACTTGTGGGCTTTGAAA
21259 GGGATGAACA
Statistics
Matches: 850, Mismatches: 78, Indels: 50
0.87 0.08 0.05
Matches are distributed among these distances:
226 16 0.02
227 66 0.08
228 131 0.15
229 406 0.48
230 116 0.14
231 40 0.05
232 56 0.07
233 9 0.01
234 6 0.01
235 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (225 bp):
TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
GACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGG
GCTTTGAAAGAGTGCCACTGACTTGTGGGC
Found at i:21259 original size:29 final size:29
Alignment explanation
Indices: 20085--21260 Score: 1538
Period size: 28 Copynumber: 40.9 Consensus size: 29
20075 TGAAAAGGGT
* *
20085 TGCCATTGACTTGCATGGGCTTTAAAAGG-G
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAG
*
20115 TGCCACTGACTTGCGTGGGCTTTGAAA-GAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
20145 TGCCACTAACTCGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
20173 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20201 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
20229 TACCACTGACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
20260 TGCTACTGACTTGTGTGGGCTTTAAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
20290 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
20318 TGCCACTGAATTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20346 TGCCACTAACTTGTGGGCTTCGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20374 TGCCACTGACTTGTGGGCTCTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20402 TGCCACTAACTCGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20430 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20459 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20488 TGCCACTGACTTGTGGGCTTTGAAAGAAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
20517 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20545 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20574 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
20603 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20631 TGCCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20659 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20688 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
20717 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
20746 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20774 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
20803 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20831 TGCCACTGACTTATGGG-TTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
20859 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20887 TGCCACTGACTCGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
20915 TGCCACTGACTTGCGTGGGCTTTAAAAGGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
20946 TGCCACTGACTTGTGTGGGCTTTGAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
* *
20976 CGCCACTGACTTGTGGGCTTTTAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * * *
21004 TGCCATTAAATTGTGGGCTTCGCAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
21032 TGCCACTGACTTGTGGGCTTCGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
21060 TGCCACTGACTTGTGGGCTCTAAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
21089 TGCCACTGACTTGTGTGGGCTTTGAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
**
21119 TGCCACTGACTTGTGGGCTTTGAAA-TTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
21147 TGCCACTGACTTGTGGGCTTTAAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
21176 TGCCACTGATTTGTGGCCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
21205 TGCCACTGTCTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
21234 TGCCACTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
21261 GATGAACATT
Statistics
Matches: 1026, Mismatches: 89, Indels: 63
0.87 0.08 0.05
Matches are distributed among these distances:
27 12 0.01
28 506 0.49
29 353 0.34
30 89 0.09
31 61 0.06
32 3 0.00
33 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:22492 original size:1 final size:1
Alignment explanation
Indices: 22488--22548 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
22478 TTTTTTGCTA
* * * * * * *
22488 TTTTTTTCTCTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22549 GGGTGTAAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:22504 original size:10 final size:10
Alignment explanation
Indices: 22472--22514 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
22462 CATCTAGACC
22472 TTTCTATTTT
1 TTTCTATTTT
*
22482 TTGCTATTTT
1 TTTCTATTTT
*
22492 TTTCTCTTTT
1 TTTCTATTTT
* *
22502 TTTTTGTTTT
1 TTTCTATTTT
22512 TTT
1 TTT
22515 TGTTTTGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.81
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:22511 original size:9 final size:9
Alignment explanation
Indices: 22499--22549 Score: 72
Period size: 9 Copynumber: 6.0 Consensus size: 9
22489 TTTTTTCTCT
22499 TTTTTTTTG
1 TTTTTTTTG
22508 TTTTTTTTG
1 TTTTTTTTG
*
22517 --TTTTGT-
1 TTTTTTTTG
22523 TTTTTTTTG
1 TTTTTTTTG
22532 TTTTTTTTG
1 TTTTTTTTG
22541 TTTTTTTTG
1 TTTTTTTTG
22550 GGTGTAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 5 0.14
8 5 0.14
9 27 0.73
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:22515 original size:24 final size:24
Alignment explanation
Indices: 22478--22548 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
22468 GACCTTTCTA
* * *
22478 TTTTTTGCTATTTTT-TTCTCTTT
1 TTTTTTGTTTTTTTTGTTTTCTTT
*
22501 TTTTTTGTTTTTTTTGTTTTGTTT
1 TTTTTTGTTTTTTTTGTTTTCTTT
22525 TTTTTTGTTTTTTTTGTTTT-TTT
1 TTTTTTGTTTTTTTTGTTTTCTTT
22548 T
1 T
22549 GGGTGTAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.40
24 26 0.60
ACGTcount: A:0.01, C:0.04, G:0.08, T:0.86
Consensus pattern (24 bp):
TTTTTTGTTTTTTTTGTTTTCTTT
Found at i:29167 original size:52 final size:52
Alignment explanation
Indices: 29089--29289 Score: 323
Period size: 52 Copynumber: 3.9 Consensus size: 52
29079 CGAAATATGA
* *
29089 AAATTTGCTTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
29141 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
29193 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
29245 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
29290 ATGTATCGAT
Statistics
Matches: 140, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
51 2 0.01
52 138 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:29296 original size:13 final size:13
Alignment explanation
Indices: 29278--29302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29268 CAAAGATCAG
29278 TGTATCGATACAA
1 TGTATCGATACAA
29291 TGTATCGATACA
1 TGTATCGATACA
29303 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:29380 original size:33 final size:33
Alignment explanation
Indices: 29343--29409 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
29333 AGTAGCTTAA
29343 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
29376 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
29409 A
1 A
29410 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:29383 original size:13 final size:13
Alignment explanation
Indices: 29365--29389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29355 CAAAAAAATA
29365 TGTATCGATACAT
1 TGTATCGATACAT
29378 TGTATCGATACA
1 TGTATCGATACA
29390 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:37963 original size:52 final size:52
Alignment explanation
Indices: 37894--38013 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
37884 AAAATTTATT
*
37894 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
37946 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGTC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
37998 TGCATGTATCGATACA
1 TGCATGTATCGATACA
38014 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:38026 original size:52 final size:51
Alignment explanation
Indices: 37885--38033 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
37875 CGAAATATGA
* *
37885 AAATTTATTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
37937 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
37989 AAATTTGTCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGTCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
38034 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATTTGTCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:38040 original size:13 final size:13
Alignment explanation
Indices: 38022--38046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38012 CAAAGATCAG
38022 TGTATCGATACAA
1 TGTATCGATACAA
38035 TGTATCGATACA
1 TGTATCGATACA
38047 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:38127 original size:33 final size:33
Alignment explanation
Indices: 38085--38154 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
38075 GGCAGTAGCT
38085 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
38118 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
38151 TACA
1 TACA
38155 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:38128 original size:13 final size:13
Alignment explanation
Indices: 38110--38134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38100 CAAAAAAATA
38110 TGTATCGATACAT
1 TGTATCGATACAT
38123 TGTATCGATACA
1 TGTATCGATACA
38135 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:39119 original size:115 final size:112
Alignment explanation
Indices: 38968--40192 Score: 541
Period size: 98 Copynumber: 11.8 Consensus size: 112
38958 AGGTGCCAAT
* *
38968 ATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAAAAGTGATAAAGATGCCAATATGTT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AAAA-TGA-AAAGATGCCAATATGCT
* * *
39033 GATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAAC
63 GATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * *
39083 GTGCTGATTCAAGGCCAGCTACATTGAACTT-AA-A-G---ATG--AAGATGCCAATATGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* *
39140 TCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAGTGATAAAGATGCCAAT
66 TCAAGGCCAACGATATTGGACTT-AAA-GATGA-GA-AAAAG-GAT---G-T--CAAC
* * * * * * * **
39198 ATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAA--AAAGGATGTCAACGTGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * * * * *
39261 TCAAGGCCAGCTACATTGAACTTAAAGAT--G---AA-GATGCCAAT
66 TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
39302 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAGTGATAAAGATGCCAA
1 ATGCTGATTCAAGGCCAGCGATATTGGACTT--AA--A-GAT--GAAAA-TGA-AAAGATGCCAA
* * *
39367 TATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAAC
57 TATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * *
39423 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-----GAAAATG-TGCCAATATGCTGA
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAA-GATGCCAATATGCTGA
* * * *
39482 TTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TGCCAAT
65 TTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * * *
39524 ATGCTGATTCAAGGCCAGCTATATTGGACTT--A-ATG---GTG--AAGGTGCCAATGTGCTGAG
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * * *
39581 TCAAGGCCAACTACATTGGACTTAAAGAT-----AAAGG-TGCCAAT
66 TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* *
39622 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-A-G----TGGAAAAGGTGCCAATATGCTGA
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAT-GAAAAGATGCCAATATGCTGA
* * * * * *
39681 TTCAAGGCCAGCTATATTGGGCTT----A-GAGATAAAGG-TGCCAAT
65 TTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
*
39723 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG--AA-G----G-TGCCAATATGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * ** * *
39780 TCAAGGCCAGCTATATTGGACTT--A-ATG-G-TGAAGG-TGCCAAT
66 TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * * *
39821 GTGCTGAGTCAAGGCCAACTACATTGGACTTAAAGAT--AAA-G----G-TGCCAATATGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * * *
39878 TCAAGGCCAGCTATATTGGAC-T-----T----AAAA-G-TGCCAAT
66 TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * * *
39913 GTGCTGAGTCAAGGCCAGCTACATTGGACTT-CA-A-G---ATG--AAGATGCCAATATGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * *
39970 TCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TGCCAAT
66 TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * *
40011 GTGCTGAGTCAAGGCCAGCTACATTGGACTT-AA-A-G---ATG--AAGATGCCAATATGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * *
40068 TCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TGCCAAT
66 TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
* * * * *
40109 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-----GAAAAGGTGCCAATATGCTGAT
1 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
* * *
40169 TCAAGGCCAGCTATATTGGGCTTA
66 TCAAGGCCAACGATATTGGACTTA
40193 GAAGGGTTGC
Statistics
Matches: 952, Mismatches: 82, Indels: 166
0.79 0.07 0.14
Matches are distributed among these distances:
88 1 0.00
89 1 0.00
90 1 0.00
91 2 0.00
92 73 0.08
93 3 0.00
95 1 0.00
97 5 0.01
98 347 0.36
99 9 0.01
100 5 0.01
101 157 0.16
102 5 0.01
103 2 0.00
104 68 0.07
105 4 0.00
106 7 0.01
107 47 0.05
108 10 0.01
109 6 0.01
110 3 0.00
111 4 0.00
112 4 0.00
113 2 0.00
114 4 0.00
115 91 0.10
116 6 0.01
117 3 0.00
118 1 0.00
119 5 0.01
120 5 0.01
121 70 0.07
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (112 bp):
ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATGAAAAGATGCCAATATGCTGAT
TCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAAC
Found at i:39163 original size:49 final size:49
Alignment explanation
Indices: 39017--39174 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
39007 AAAAGTGATA
* * * * *
39017 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
39068 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
39121 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
39169 ATGATG
1 AAGATG
39175 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
48 8 0.09
49 37 0.44
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:39234 original size:170 final size:170
Alignment explanation
Indices: 38953--39513 Score: 999
Period size: 170 Copynumber: 3.3 Consensus size: 170
38943 TTTTAGAGAT
* *
38953 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT--AA--A-GATGA-AAAAG
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
*
39012 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGAT
66 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
39077 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
39117 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
39182 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
66 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
39247 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
39287 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
39352 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
66 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
39417 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
39457 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGA
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATGA
39514 AGGTGCCAAT
Statistics
Matches: 382, Mismatches: 5, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
164 44 0.12
166 2 0.01
168 1 0.00
169 5 0.01
170 282 0.74
171 4 0.01
173 40 0.10
174 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (170 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:39333 original size:49 final size:49
Alignment explanation
Indices: 39187--39344 Score: 156
Period size: 49 Copynumber: 3.1 Consensus size: 49
39177 AAAAGTGATA
* * * *
39187 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
39238 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
39291 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
39339 ATGATG
1 AAGATG
39345 AGAAAAGTGA
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
48 8 0.09
49 37 0.43
50 2 0.02
53 1 0.01
54 2 0.02
55 36 0.42
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:39539 original size:49 final size:49
Alignment explanation
Indices: 39361--40192 Score: 1084
Period size: 49 Copynumber: 16.8 Consensus size: 49
39351 GTGATAAAGA
* * * * *
39361 TGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
* ** * * *
39415 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGG
39468 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
39517 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * * * *
39566 TGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
39615 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-AGTGGAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA-T-G--AAGG
* * *
39667 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
39716 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
39765 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * * * *
39814 TGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
39863 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-A--AA-G
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * * * *
39906 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTCAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
39955 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * * *
40004 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
40053 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * *
40102 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGG
*
40154 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
40193 GAAGGGTTGC
Statistics
Matches: 684, Mismatches: 79, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
43 36 0.05
44 2 0.00
45 1 0.00
46 2 0.00
47 1 0.00
48 3 0.00
49 474 0.69
50 1 0.00
51 1 0.00
52 122 0.18
53 6 0.01
54 1 0.00
55 34 0.05
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:39793 original size:248 final size:248
Alignment explanation
Indices: 39353--40194 Score: 1211
Period size: 248 Copynumber: 3.4 Consensus size: 248
39343 TGAGAAAAGT
* * * * * *
39353 GATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-AAAAGG-TG
* ** * * *
39418 TCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGAT
63 CCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAGAGAT---AAAGGTGCCAATATGCTGAT
39483 TCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATAT
125 TCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATAT
39548 TGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAA
190 TGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAA
39607 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-AGTGGAAAAGGTGCC
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA-TGGAAAAGGTGCC
* *
39671 AATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAGATAAAGGTGCCAATATGCTGATTCAAG
65 AATATGCTGATTCAAGGCCAGCTACATTGGACTTAGAGATAAAGGTGCCAATATGCTGATTCAAG
39736 GCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
130 GCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
39801 TTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAA
195 TTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAA
39855 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--AAAA-GTGCCA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGCCA
* * * *
39911 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTCA-AGATGAAGATGCCAATATGCTGATTCAAG
66 ATATGCTGATTCAAGGCCAGCTACATTGGACTT-AGAGATAAAGGTGCCAATATGCTGATTCAAG
* * * *
39975 GCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
130 GCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * * * * * *
40040 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
195 TTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAA
* * * *
40094 GATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGCCA
* *
40159 ATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGA
66 ATATGCTGATTCAAGGCCAGCTACATTGGACTTAGA
40195 AGGGTTGCCA
Statistics
Matches: 536, Mismatches: 40, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
239 209 0.39
240 6 0.01
242 1 0.00
245 1 0.00
247 6 0.01
248 223 0.42
251 37 0.07
252 6 0.01
253 2 0.00
254 45 0.08
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (248 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGCCA
ATATGCTGATTCAAGGCCAGCTACATTGGACTTAGAGATAAAGGTGCCAATATGCTGATTCAAGG
CCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT
TAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAA
Found at i:40236 original size:33 final size:33
Alignment explanation
Indices: 40192--40289 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
40182 TATTGGGCTT
40192 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGA
1 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTGGA
40226 AGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGTTGCCACCGACTTGTGTGGGCTTT-GGA
40260 AG-A-GTTGCCACCGACTTGTGTGGGCTTTGG
1 AGAAGGTTGCCACCGACTTGTGTGGGCTTTGG
40290 GAAGGGAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
31 2 0.03
32 25 0.40
33 27 0.43
34 9 0.14
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (33 bp):
AGAAGGTTGCCACCGACTTGTGTGGGCTTTGGA
Found at i:40272 original size:32 final size:32
Alignment explanation
Indices: 40185--40293 Score: 161
Period size: 32 Copynumber: 3.4 Consensus size: 32
40175 CCAGCTATAT
*
40185 TGGGC-TTA-GAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
40215 TGGGCTTT-GGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGGAAG-A-GTTGCCACCGACTTGTG
40248 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
1 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
*
40280 TGGGCTTTGGGAAG
1 TGGGCTTTAGGAAG
40294 GGAAAAAGAT
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
30 5 0.07
31 6 0.08
32 30 0.42
33 26 0.36
34 5 0.07
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
Found at i:40350 original size:35 final size:33
Alignment explanation
Indices: 40295--40656 Score: 360
Period size: 34 Copynumber: 10.7 Consensus size: 33
40285 TTTGGGAAGG
* * *
40295 GAAAAAGATGCCACGAAGTTGTGGACTTAAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAA
* *
40328 GGTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 -GAAAAAG-GTGCCACGGAGTTGTGGGCTTAAAAA
* *
40363 GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAG
1 GAAAAAGGTGCCACGGAGTTGTGGGC-TT-AAAAA
* *
40398 GAAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAA
1 G-AAAAAG-GTGCCACGGAGTTGTGGGCTTAAAAA
*
40433 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 GAAAAAGGTGCCACGGAGTTGTGGGC-TT-AAAA-A
*
40469 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAA
1 GAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAAAA
*
40504 GAAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 G-AAAAAGGTGCCACGGAGTTGTGGGC-TTAAAAA
* *
40539 GAAGAAGGTGCCACGGAGTTGTGGGCTT-AAAC
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAA
* *
40571 G-----GGTGCCACGGAGTTGTGGACTTAAAGAC
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTAAA-AA
* * *
40600 GAATTAA-GTGCCACGGAATTGTGGGCTTTAAAA
1 GAA-AAAGGTGCCACGGAGTTGTGGGCTTAAAAA
*
40633 GAAAAAGGTGCCACAGAGTTGTGG
1 GAAAAAGGTGCCACGGAGTTGTGG
40657 ACTTTGAGAA
Statistics
Matches: 281, Mismatches: 28, Indels: 39
0.81 0.08 0.11
Matches are distributed among these distances:
27 21 0.07
28 2 0.01
29 3 0.01
32 6 0.02
33 57 0.20
34 67 0.24
35 60 0.21
36 25 0.09
37 40 0.14
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (33 bp):
GAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAA
Found at i:40369 original size:34 final size:34
Alignment explanation
Indices: 40295--40661 Score: 386
Period size: 33 Copynumber: 10.9 Consensus size: 34
40285 TTTGGGAAGG
* * *
40295 GAAAAAGA-TGCCACGAAGTTGTGGACTTAAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
40328 GGTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 -GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
40363 GAAAAAG-GTGCCACAGAGTTGTGGGCTTTGAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA
*
40397 GGAAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAA
1 -G-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
40433 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA
*
40467 GGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAA
1 --GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA
40504 GAAAAA-AGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 GAAAAAGA-GTGCCACGGAGTTGTGGGCTTT-AAAA
* *
40539 GAAGAAG-GTGCCACGGAGTTGTGGGC-TTAAAC
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
40571 G-----G-GTGCCACGGAGTTGTGGAC-TTAAAGA
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-A
** *
40599 CGAATTA-AGTGCCACGGAATTGTGGGCTTTAAAA
1 -GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
* *
40633 GAAAAAG-GTGCCACAGAGTTGTGGACTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
40662 GAGAAGAGAT
Statistics
Matches: 290, Mismatches: 22, Indels: 43
0.82 0.06 0.12
Matches are distributed among these distances:
27 24 0.08
29 1 0.00
32 4 0.01
33 67 0.23
34 65 0.22
35 65 0.22
36 17 0.06
37 47 0.16
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (34 bp):
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
Found at i:40422 original size:70 final size:69
Alignment explanation
Indices: 40295--40663 Score: 456
Period size: 70 Copynumber: 5.4 Consensus size: 69
40285 TTTGGGAAGG
* * * *
40295 GAAAAAGATGCCACGAAGTTGTGGAC-TTAAAAAGGTAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
40359 AAAA
66 AAAA
* * *
40363 GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTT
40428 TAAAA
65 TAAAA
* *
40433 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTT
40498 TAAAAA
65 T-AAAA
* *
40504 GAAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGC-T
1 G-AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
40566 TAAAC
65 TAAAA
* ** *
40571 G-----GGTGCCACGGAGTTGTGGAC-TT-AAAGACGAATTA-AGTGCCACGGAATTGTGGGCTT
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
40628 TAAAA
65 TAAAA
*
40633 GAAAAAGGTGCCACAGAGTTGTGGACTTTGA
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGA
40664 GAAGAGATTG
Statistics
Matches: 268, Mismatches: 17, Indels: 31
0.85 0.05 0.10
Matches are distributed among these distances:
59 3 0.01
60 3 0.01
61 41 0.15
62 6 0.02
67 23 0.09
68 26 0.10
69 27 0.10
70 99 0.37
71 7 0.03
72 33 0.12
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (69 bp):
GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
AAAA
Found at i:40580 original size:61 final size:61
Alignment explanation
Indices: 40511--40627 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 61
40501 AAAGAAAAAA
* *
40511 GGTGCCACGGAGTTGTGGGCTTTGAAA-A-GAA-GAAGGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAGACGAATGAA-GTGCCACGGAATTGTGGGCTTAAACG
*
40572 GGTGCCACGGAGTTGTGGACTTAAAGACGAATTAAGTGCCACGGAATTGTGGGCTT
1 GGTGCCACGGAGTTGTGGACTTAAAGACGAATGAAGTGCCACGGAATTGTGGGCTT
40628 TAAAAGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
59 3 0.06
60 3 0.06
61 42 0.84
62 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (61 bp):
GGTGCCACGGAGTTGTGGACTTAAAGACGAATGAAGTGCCACGGAATTGTGGGCTTAAACG
Found at i:40583 original size:27 final size:27
Alignment explanation
Indices: 40545--40596 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40535 AAAAGAAGAA
*
40545 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAACG
40572 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
40597 GACGAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (27 bp):
GGTGCCACGGAGTTGTGGACTTAAACG
Found at i:41677 original size:12 final size:11
Alignment explanation
Indices: 41644--41675 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
41634 GGTTTTTCCC
41644 TTTTTTTTTTG
1 TTTTTTTTTTG
41655 TTTTTTTTTTG
1 TTTTTTTTTTG
41666 TTTTTTTTTT
1 TTTTTTTTTT
41676 TGCATCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:41754 original size:20 final size:18
Alignment explanation
Indices: 41729--41765 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
41719 TCTTATCGAG
41729 CTTTTCTGTTTTGTTTTTTT
1 CTTTTCT-TTTT-TTTTTTT
41749 CTTTTCTTTTTTTTTTT
1 CTTTTCTTTTTTTTTTT
41766 CTTGTGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (18 bp):
CTTTTCTTTTTTTTTTTT
Found at i:42017 original size:1 final size:1
Alignment explanation
Indices: 42011--42045 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
42001 TGCCTTTGCA
*
42011 TTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42046 GTGTTTACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:42057 original size:20 final size:20
Alignment explanation
Indices: 42014--42057 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
42004 CTTTGCATTT
* **
42014 TTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTGTGTTTAC
42034 TTTTTTTTTTTTGTGTTTAC
1 TTTTTTTTTTTTGTGTTTAC
42054 TTTT
1 TTTT
42058 GACTGTTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTTTTGTGTTTAC
Found at i:42057 original size:22 final size:21
Alignment explanation
Indices: 42011--42057 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42001 TGCCTTTGCA
**
42011 TTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTGTTTAC
42032 TTTTTTTTTTTTTTGTGTTTAC
1 TTTTTTTTTTTTTT-TGTTTAC
42054 TTTT
1 TTTT
42058 GACTGTTCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.02, C:0.02, G:0.06, T:0.89
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTGTTTAC
Found at i:49034 original size:52 final size:52
Alignment explanation
Indices: 48965--49084 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
48955 AAAATTTATT
*
48965 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
49017 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGTC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
49069 TGCATGTATCGATACA
1 TGCATGTATCGATACA
49085 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:49097 original size:52 final size:51
Alignment explanation
Indices: 48956--49104 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
48946 CGAAATATGA
* *
48956 AAATTTATTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
49008 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
49060 AAATTTGTCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGTCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
49105 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATTTGTCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:49111 original size:13 final size:13
Alignment explanation
Indices: 49093--49117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49083 CAAAGATCAG
49093 TGTATCGATACAA
1 TGTATCGATACAA
49106 TGTATCGATACA
1 TGTATCGATACA
49118 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:49199 original size:33 final size:33
Alignment explanation
Indices: 49157--49226 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
49147 GGCAGTAGCT
49157 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
49190 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
49223 TACA
1 TACA
49227 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:49200 original size:13 final size:13
Alignment explanation
Indices: 49182--49206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49172 CAAAAAAATA
49182 TGTATCGATACAT
1 TGTATCGATACAT
49195 TGTATCGATACA
1 TGTATCGATACA
49207 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:54994 original size:20 final size:20
Alignment explanation
Indices: 54947--55021 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
54937 AAAAAAACAT
*
54947 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
54966 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
54987 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
55007 AATGTATCGATACAT
1 AATGTATCGATACAT
55022 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:55015 original size:40 final size:39
Alignment explanation
Indices: 54944--55021 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
54934 GGTAAAAAAA
* *
54944 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
54983 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
55022 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:57005 original size:62 final size:62
Alignment explanation
Indices: 56908--57032 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
56898 CTATTTTGGC
* * *
56908 ATCAAGCCAAGTCAGAGTCTGAATACCCAATGATCTCTAACTTATCCAACTTCCTGTATGTG
1 ATCAAGCCAAGTCAGAGTATGAATAACCAATGATCTCTAACTTATCCAACTTCCTATATGTG
*
56970 ATCAAGCCAAGTTAGAGTATGAATAACCAATGATCTCTAACTTATCCAACTTCCTATATGTG
1 ATCAAGCCAAGTCAGAGTATGAATAACCAATGATCTCTAACTTATCCAACTTCCTATATGTG
57032 A
1 A
57033 GGATGTGATG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (62 bp):
ATCAAGCCAAGTCAGAGTATGAATAACCAATGATCTCTAACTTATCCAACTTCCTATATGTG
Found at i:66049 original size:22 final size:22
Alignment explanation
Indices: 66024--66121 Score: 54
Period size: 22 Copynumber: 4.2 Consensus size: 22
66014 AATATTAATA
66024 ATTTAATATTAAAATATAAAAT
1 ATTTAATATTAAAATATAAAAT
*
66046 ATTT-ATGTTTAATAATATTCAAGAAAT
1 ATTTAAT-ATTAA-AATA-T--A-AAAT
* *
66073 ATTTAAAATTAAAATATTAAAT
1 ATTTAATATTAAAATATAAAAT
* * * * *
66095 TTTTTATTTTACAATTTTAAAAT
1 ATTTAATATTA-AAATATAAAAT
66118 ATTT
1 ATTT
66122 TTAATTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 15
0.67 0.14 0.18
Matches are distributed among these distances:
21 2 0.04
22 19 0.34
23 15 0.27
24 1 0.02
25 1 0.02
26 5 0.09
27 12 0.21
28 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTAATATTAAAATATAAAAT
Found at i:66880 original size:21 final size:20
Alignment explanation
Indices: 66846--66886 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
66836 TAGTTATTTT
66846 TATTTAAACAAATTAATTAA
1 TATTTAAACAAATTAATTAA
* *
66866 TATTTGAAATAAATTGATTAA
1 TATTT-AAACAAATTAATTAA
66887 ATGAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
TATTTAAACAAATTAATTAA
Found at i:67128 original size:15 final size:15
Alignment explanation
Indices: 67074--67128 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
67064 ACGCTATAAT
*
67074 ATTATTTTTTTAAAA
1 ATTATATTTTTAAAA
* * *
67089 ATCATATTTATAATA
1 ATTATATTTTTAAAA
67104 ATTATATTTTTAAAA
1 ATTATATTTTTAAAA
*
67119 ATTAAATTTT
1 ATTATATTTT
67129 ATTAAAATCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTTAAAA
Found at i:68805 original size:22 final size:23
Alignment explanation
Indices: 68759--68806 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
68749 TAATTAATCA
68759 TTATTTAATATTTGAAAATTTTT
1 TTATTTAATATTTGAAAATTTTT
**
68782 TTATTTAATATTTGAATTTTTTT
1 TTATTTAATATTTGAAAATTTTT
68805 TT
1 TT
68807 GATAAGTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATTTAATATTTGAAAATTTTT
Found at i:69057 original size:23 final size:23
Alignment explanation
Indices: 69027--69072 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
69017 TTATATTTTG
* *
69027 ATTCTTTGTAATTTGGCATGTTC
1 ATTCTTTGCAACTTGGCATGTTC
69050 ATTCTTTGCAACTTGGCATGTTC
1 ATTCTTTGCAACTTGGCATGTTC
69073 CCCTTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (23 bp):
ATTCTTTGCAACTTGGCATGTTC
Found at i:73690 original size:9 final size:8
Alignment explanation
Indices: 73689--73794 Score: 62
Period size: 8 Copynumber: 13.0 Consensus size: 8
73679 AATATGATAA
73689 ATATAAA-
1 ATATAAAT
73696 ATAT-AAT
1 ATATAAAT
*
73703 A-AAAAAT
1 ATATAAAT
73710 AATATAAAT
1 -ATATAAAT
73719 ATATAAAT
1 ATATAAAT
* *
73727 TTATTAAT
1 ATATAAAT
73735 ATATTAAATTTT
1 ATA-TAAA---T
73747 ATATAAAT
1 ATATAAAT
73755 ATAT-AAT
1 ATATAAAT
*
73762 ATTTTAAAT
1 A-TATAAAT
73771 ATA-AATAT
1 ATATAA-AT
73779 AATATAAAT
1 -ATATAAAT
73788 A-ATAAAT
1 ATATAAAT
73795 TATTATAATA
Statistics
Matches: 78, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
6 3 0.04
7 20 0.26
8 28 0.36
9 17 0.22
10 2 0.03
11 4 0.05
12 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:73697 original size:16 final size:15
Alignment explanation
Indices: 73653--73705 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
73643 GAGTATAAGA
* *
73653 AATAAATATAACATAA
1 AATAAAT-TAAAATAT
*
73669 AAAAAATTAAAATAT
1 AATAAATTAAAATAT
*
73684 GATAAATATAAAATAT
1 AATAAAT-TAAAATAT
73700 AATAAA
1 AATAAA
73706 AAATAATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AATAAATTAAAATAT
Found at i:73725 original size:36 final size:38
Alignment explanation
Indices: 73656--73726 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
73646 TATAAGAAAT
73656 AAATATAACATAAAAAAAATTAAAATATGATAAATATA
1 AAATATAACATAAAAAAAATTAAAATATGATAAATATA
73694 AAATAT-A-ATAAAAAATAA-TATAAATAT-ATAAAT
1 AAATATAACATAAAAAA-AATTA-AAATATGATAAAT
73727 TTATTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
36 16 0.52
37 9 0.29
38 6 0.19
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (38 bp):
AAATATAACATAAAAAAAATTAAAATATGATAAATATA
Found at i:73735 original size:16 final size:15
Alignment explanation
Indices: 73719--73804 Score: 59
Period size: 16 Copynumber: 5.2 Consensus size: 15
73709 TAATATAAAT
73719 ATATAAATTTATTAA
1 ATATAAATTTATTAA
73734 TATATTAAATTTTATATAA
1 -ATA-TAAA-TTTAT-TAA
73753 ATATATAATATT-TTAA
1 ATATA-AAT-TTATTAA
*
73769 ATATAAATATAATATAA
1 ATATAAAT-TTAT-TAA
73786 ATAATAAA-TTATTATA
1 AT-ATAAATTTATTA-A
73802 ATA
1 ATA
73805 ATTACTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
15 8 0.14
16 18 0.31
17 13 0.22
18 17 0.29
19 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAAATTTATTAA
Found at i:73751 original size:36 final size:34
Alignment explanation
Indices: 73700--73804 Score: 112
Period size: 33 Copynumber: 3.1 Consensus size: 34
73690 TATAAAATAT
*
73700 AATA-AAAAATAATATAAATATATAAATTTATTA
1 AATATAAATATAATATAAATATATAAATTTATTA
* *
73733 ATATATTAAATTTTATATAAATATAT-AATATT-TTA
1 A-ATA-TAAATATAATATAAATATATAAAT-TTATTA
73768 AATATAAATATAATATAAATA-ATAAA-TTATTA
1 AATATAAATATAATATAAATATATAAATTTATTA
73800 TAATA
1 -AATA
73805 ATTACTTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
31 2 0.03
32 5 0.08
33 22 0.37
34 6 0.10
35 7 0.12
36 18 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AATATAAATATAATATAAATATATAAATTTATTA
Found at i:73772 original size:22 final size:20
Alignment explanation
Indices: 73711--73779 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
73701 ATAAAAAATA
73711 ATATAAATATA-TAAA-TTT
1 ATATAAATATATTAAATTTT
73729 AT-T-AATATATTAAATTTT
1 ATATAAATATATTAAATTTT
73747 ATATAAATATA-TAATATTTT
1 ATATAAATATATTAA-ATTTT
73767 AAATATAAATATA
1 --ATATAAATATA
73780 ATATAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.14
17 5 0.11
18 7 0.16
19 4 0.09
20 11 0.25
22 11 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATAAATATATTAAATTTT
Found at i:73805 original size:20 final size:19
Alignment explanation
Indices: 73711--73820 Score: 69
Period size: 18 Copynumber: 6.1 Consensus size: 19
73701 ATAAAAAATA
73711 ATATAAATATATAAA-T-TT
1 ATATAAATA-ATAAATTATT
*
73729 AT-TAATATATTAAATT-TT
1 ATATAA-ATAATAAATTATT
73747 ATATAAAT-ATATAA-TATT
1 ATATAAATAATA-AATTATT
*
73765 -T-TAAAT-ATAAA-TATA
1 ATATAAATAATAAATTATT
73780 ATATAAATAATAAATTATT
1 ATATAAATAATAAATTATT
* * *
73799 ATAATAATTACTTAATTATT
1 AT-ATAAATAATAAATTATT
73819 AT
1 AT
73821 TGTACTTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
15 5 0.07
16 9 0.12
17 16 0.21
18 21 0.28
19 8 0.11
20 16 0.21
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAAATAATAAATTATT
Found at i:74192 original size:23 final size:22
Alignment explanation
Indices: 74151--74205 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
74141 TTTATTTAAT
74151 ATATTTTAA-ATATTAAA-TTC
1 ATATTTTAATATATTAAATTTC
* *
74171 GATTATTTTAATTTATTCAATTTC
1 -A-TATTTTAATATATTAAATTTC
74195 ATATTTTAATA
1 ATATTTTAATA
74206 ACCGAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 17 0.61
23 7 0.25
24 3 0.11
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTTTAATATATTAAATTTC
Found at i:74309 original size:28 final size:28
Alignment explanation
Indices: 74278--74333 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
74268 ATTAATCAAA
* *
74278 TCAATTTAACTAAATTTAATTAATTTTT
1 TCAATTAAACTAAATTTAACTAATTTTT
* *
74306 TCAATTAAATTAATTTTAACTAATTTTT
1 TCAATTAAACTAAATTTAACTAATTTTT
74334 ACTCCTCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (28 bp):
TCAATTAAACTAAATTTAACTAATTTTT
Found at i:75972 original size:14 final size:14
Alignment explanation
Indices: 75953--76007 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
75943 AAGTGCTGTG
*
75953 CCAAAGTATCTCTA
1 CCAAAGTACCTCTA
** * *
75967 CCAAAGTTTCTTTG
1 CCAAAGTACCTCTA
*
75981 CTAAAGTACCTCTA
1 CCAAAGTACCTCTA
75995 CCAAAGTACCTCT
1 CCAAAGTACCTCT
76008 GCCACGGTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (14 bp):
CCAAAGTACCTCTA
Done.