Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002031.1 Hibiscus syriacus cultivar Beakdansim tig00004143_pilon, 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: 51250
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:11446 original size:3 final size:3
Alignment explanation
Indices: 11438--11495 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
11428 TTTGTCTCAT
11438 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11484 TTA TTA TTA TTA
1 TTA TTA TTA TTA
11496 AATGGTAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 49 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11474 original size:26 final size:26
Alignment explanation
Indices: 11438--11495 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
11428 TTTGTCTCAT
11438 TTATTATTATTATTATATTATTATTA
1 TTATTATTATTATTATATTATTATTA
*
11464 TTATTATTATTATTATTTTATTATTA
1 TTATTATTATTATTATATTATTATTA
11490 TTATTA
1 TTATTA
11496 AATGGTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATTATTATTATTATATTATTATTA
Found at i:12494 original size:14 final size:15
Alignment explanation
Indices: 12475--12512 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
12465 AAATATTTGA
12475 TATTTTAATCTT-AT
1 TATTTTAATCTTCAT
*
12489 TATTTTAATCTTCTT
1 TATTTTAATCTTCAT
12504 TATTTTAAT
1 TATTTTAAT
12513 TACTAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTAATCTTCAT
Found at i:12550 original size:13 final size:13
Alignment explanation
Indices: 12527--12562 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12517 AAAATCATAT
12527 TTTACGATTTTTAA
1 TTTA-GATTTTTAA
12541 TTTAGATTTTTAA
1 TTTAGATTTTTAA
12554 TTTA-ATTTT
1 TTTAGATTTT
12563 ATTTTAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (13 bp):
TTTAGATTTTTAA
Found at i:12563 original size:24 final size:24
Alignment explanation
Indices: 12535--12583 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12525 ATTTTACGAT
*
12535 TTTTAATTTAGAT-TTTTAATTTAA
1 TTTTAATTTA-ATCATTTAATTTAA
*
12559 TTTTATTTTAATCATTTAATTTAA
1 TTTTAATTTAATCATTTAATTTAA
12583 T
1 T
12584 GTAATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAATTTAATCATTTAATTTAA
Found at i:12568 original size:11 final size:11
Alignment explanation
Indices: 12535--12583 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 11
12525 ATTTTACGAT
12535 TTTTAATTTAGA
1 TTTTAATTTA-A
12547 TTTTTAATTTAA
1 -TTTTAATTTAA
*
12559 TTTTATTTTAA
1 TTTTAATTTAA
12570 TCATTTAATTTAA
1 T--TTTAATTTAA
12583 T
1 T
12584 GTAATTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.34
12 1 0.03
13 20 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:14178 original size:30 final size:29
Alignment explanation
Indices: 14140--14209 Score: 113
Period size: 30 Copynumber: 2.4 Consensus size: 29
14130 AACTAAATTA
14140 AACGGGGACGGGAAAAAATCGTTTATGCT
1 AACGGGGACGGGAAAAAATCGTTTATGCT
*
14169 AACCGGGGACGGGAAAAAATCGTTTATGTT
1 AA-CGGGGACGGGAAAAAATCGTTTATGCT
*
14199 AAAGGGGACGG
1 AACGGGGACGG
14210 AGACGGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (29 bp):
AACGGGGACGGGAAAAAATCGTTTATGCT
Found at i:14514 original size:24 final size:25
Alignment explanation
Indices: 14465--14514 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
14455 TAAATCCGGC
*
14465 GATTTTTTAAACAGAGACGGATACG
1 GATTTTTTAAACAGAGACGGAGACG
*
14490 GATTTTTTAAACGGAGAC-GAGACG
1 GATTTTTTAAACAGAGACGGAGACG
14514 G
1 G
14515 GAGACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (25 bp):
GATTTTTTAAACAGAGACGGAGACG
Found at i:17958 original size:210 final size:211
Alignment explanation
Indices: 17595--18017 Score: 776
Period size: 210 Copynumber: 2.0 Consensus size: 211
17585 TTCGTTTGGG
* *
17595 TCCAAAATTTCCACCACAAGCATAATTATGGCAAAAAGGCTAAAATAGAATGTAATTCATTTTCT
1 TCCAAAATTTCCACCACAAGCATAATCATGGCAAAAAGGCTAAAATAGAATGGAATTCATTTTCT
17660 GGCACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATA
66 GGCACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATA
* *
17725 ATACTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGGTAGATTTTCTGTAAC
131 ATACTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAAC
17790 TAAATAATTTACCATA
196 TAAATAATTTACCATA
* *
17806 TCCAAAATTTCCACCTCAAGCATAATCATGGC-AAAAGGCTAAAATAGAATGGAATTCGTTTTCT
1 TCCAAAATTTCCACCACAAGCATAATCATGGCAAAAAGGCTAAAATAGAATGGAATTCATTTTCT
*
17870 GGTACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATA
66 GGCACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATA
17935 ATACTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAAC
131 ATACTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAAC
18000 TAAATAATTTACCATA
196 TAAATAATTTACCATA
18016 TC
1 TC
18018 TGCGTACCAA
Statistics
Matches: 205, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
210 175 0.85
211 30 0.15
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (211 bp):
TCCAAAATTTCCACCACAAGCATAATCATGGCAAAAAGGCTAAAATAGAATGGAATTCATTTTCT
GGCACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATA
ATACTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAAC
TAAATAATTTACCATA
Found at i:18356 original size:13 final size:13
Alignment explanation
Indices: 18318--18356 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
18308 GGTAGAGTTG
*
18318 TTGCATTGAGCAG
1 TTGCATTGAGCAA
18331 TTGCATTGAGCAA
1 TTGCATTGAGCAA
18344 TTGCATTGAGCAA
1 TTGCATTGAGCAA
18357 CATTCAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (13 bp):
TTGCATTGAGCAA
Found at i:24049 original size:26 final size:25
Alignment explanation
Indices: 24001--24064 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
23991 ATTTTCTTGT
*
24001 TTCATATCATTTTAAATAGTTCATG
1 TTCATATCATTTAAAATAGTTCATG
24026 TTCATATCATTTAAAATTTA-TTCATG
1 TTCATATCATTTAAAA--TAGTTCATG
24052 TTCATATCATTTA
1 TTCATATCATTTA
24065 CACGTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 15 0.42
26 19 0.53
27 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (25 bp):
TTCATATCATTTAAAATAGTTCATG
Found at i:26822 original size:21 final size:21
Alignment explanation
Indices: 26796--26836 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
26786 GACGTACTTG
26796 GGTTATCGT-CATAACCTTTAA
1 GGTTATC-TCCATAACCTTTAA
26817 GGTTATCTCCATAACCTTTA
1 GGTTATCTCCATAACCTTTA
26837 GGGGTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (21 bp):
GGTTATCTCCATAACCTTTAA
Found at i:29116 original size:21 final size:20
Alignment explanation
Indices: 29030--29228 Score: 114
Period size: 21 Copynumber: 9.8 Consensus size: 20
29020 AAATGACCAA
**
29030 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
29049 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
29069 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
29089 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
29110 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
29131 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
29151 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
29172 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
29192 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
29213 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
29229 ACACATAAAT
Statistics
Matches: 134, Mismatches: 39, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
19 16 0.12
20 56 0.42
21 62 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:29178 original size:20 final size:20
Alignment explanation
Indices: 29030--29247 Score: 113
Period size: 20 Copynumber: 10.8 Consensus size: 20
29020 AAATGACCAA
29030 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
29049 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
29069 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
29088 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
29110 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
29130 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
29151 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* ** * *
29172 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
29192 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
29213 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
29232 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
29248 TATCCGTAAA
Statistics
Matches: 146, Mismatches: 42, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 69 0.47
21 58 0.40
22 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:29190 original size:41 final size:41
Alignment explanation
Indices: 29111--29222 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
29101 GCGATTCTTG
*
29111 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
29153 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
29194 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
29223 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:29257 original size:20 final size:20
Alignment explanation
Indices: 29195--29387 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
29185 CGATTTTCCA
* ** *
29195 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
29215 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
29235 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
29255 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
29275 AAATCGCAACGCGTAT-GGT
1 AAATCGCAACGCGTATCCGT
*
29294 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
29314 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
29334 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
29354 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
29375 AAATCGCAACGCG
1 AAATCGCAACGCG
29388 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
19 19 0.13
20 109 0.75
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:29320 original size:59 final size:60
Alignment explanation
Indices: 29195--29387 Score: 237
Period size: 59 Copynumber: 3.2 Consensus size: 60
29185 CGATTTTCCA
* ** * ** *
29195 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAATCGCAACGCGTATCCGT
* * ** *
29255 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-AT-GGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACATAAATCGCAACGCGTATCCGT
*
29314 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT-AAATCGCAACGCGTATCCGT
29375 AAATCGCAACGCG
1 AAATCGCAACGCG
29388 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
58 1 0.01
59 51 0.46
60 28 0.25
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAATCGCAACGCGTATCCGT
Found at i:29807 original size:33 final size:33
Alignment explanation
Indices: 29768--29838 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
29758 TTCACTTAGA
* *
29768 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
29801 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
29834 TTTCA
1 TTTCA
29839 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:29944 original size:21 final size:20
Alignment explanation
Indices: 29918--30023 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
29908 TGCAGAAGAG
29918 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
29939 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
29959 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
29980 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
29994 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
30013 TCGCAACGAGA
1 TCGCAACGAGA
30024 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:29962 original size:20 final size:21
Alignment explanation
Indices: 29916--29994 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
29906 TTTGCAGAAG
*
29916 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
29938 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
29957 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
29979 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
29995 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:29975 original size:41 final size:38
Alignment explanation
Indices: 29911--30027 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
29901 TTCAATTTGC
* *
29911 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
29949 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
29990 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
30023 AGAAT
1 AGAAT
30028 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:30000 original size:14 final size:14
Alignment explanation
Indices: 29981--30034 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
29971 AAATGAAAAG
29981 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
29995 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
30014 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
30028 CGCAACG
1 CGCAACG
30035 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:30010 original size:33 final size:33
Alignment explanation
Indices: 29970--30039 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
29960 CGCAACGAGA
29970 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
30003 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
30036 GAAA
1 GAAA
30040 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:30046 original size:33 final size:33
Alignment explanation
Indices: 29976--30050 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
29966 GAGAGAAATG
* **
29976 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
30009 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
30042 AAAATCGCA
1 AAAATCGCA
30051 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:30068 original size:19 final size:19
Alignment explanation
Indices: 30046--30143 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
30036 GAAACCAAAA
*
30046 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
30065 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
30079 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
30098 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
30112 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
30131 TCGCGTTGCGATT
1 TCGCGTTGCGATT
30144 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:30087 original size:14 final size:14
Alignment explanation
Indices: 30068--30157 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
30058 TTTCATTTCG
30068 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
30082 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
30101 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
30115 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
30132 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
30148 CGTTGCGATT
1 CGTTGCGATT
30158 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:30093 original size:33 final size:33
Alignment explanation
Indices: 30051--30165 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
30041 CAAAATCGCA
30051 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
30084 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
30117 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
30150 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
30166 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:32170 original size:184 final size:184
Alignment explanation
Indices: 31861--32240 Score: 708
Period size: 184 Copynumber: 2.1 Consensus size: 184
31851 TAGATTGCTT
*
31861 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
31926 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACT
31991 GTGTATTCTTTAACAC-TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
32045 AGTAAATTTGTTCGGTTGCTGCCAATTCTTCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
32110 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTG
32175 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACAC-GTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
32230 AGTAAATTTAT
1 AGTAAATTTAT
32241 CCATTCAAGT
Statistics
Matches: 190, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
183 20 0.11
184 122 0.64
185 48 0.25
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (184 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTG
TGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32257 original size:93 final size:93
Alignment explanation
Indices: 31861--32238 Score: 708
Period size: 93 Copynumber: 4.1 Consensus size: 93
31851 TAGATTGCTT
*
31861 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31926 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31954 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32017 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
32045 AGTAAATTTGTTCGGTTGCTGCCAATTCTTCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32110 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32138 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32202 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32230 AGTAAATTT
1 AGTAAATTT
32239 ATCCATTCAA
Statistics
Matches: 278, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
91 89 0.32
92 68 0.24
93 121 0.44
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32322 original size:19 final size:19
Alignment explanation
Indices: 32282--32410 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
32272 TAGTTTACTT
* *
32282 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
32302 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
32321 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
32340 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
32354 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
32373 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
32387 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
32406 TCGCA
1 TCGCA
32411 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:32361 original size:33 final size:32
Alignment explanation
Indices: 32318--32410 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
32308 CGCGAAACCA
**
32318 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
32350 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
32383 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
32411 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:32408 original size:52 final size:52
Alignment explanation
Indices: 32282--32410 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
32272 TAGTTTACTT
**
32282 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
32334 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
32387 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
32411 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:32428 original size:19 final size:19
Alignment explanation
Indices: 32406--32540 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
32396 GAAACCAAAA
*
32406 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
32425 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
32441 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
32458 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
32474 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
32491 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
32510 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
32530 TCGTGTTGCGA
1 TCGCGTTGCGA
32541 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32447 original size:14 final size:14
Alignment explanation
Indices: 32428--32484 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32418 TTTCATTTCG
32428 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
32442 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
32459 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
32475 CGTTGCGATT
1 CGTTGCGATT
32485 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:32453 original size:33 final size:33
Alignment explanation
Indices: 32411--32503 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
32401 CAAAATCGCA
*
32411 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
32444 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
32477 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
32504 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:34483 original size:14 final size:14
Alignment explanation
Indices: 34464--34499 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34454 ATTGTTTAAT
34464 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34478 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34492 TGATTTGT
1 TGATTTGT
34500 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34630 original size:19 final size:19
Alignment explanation
Indices: 34606--34703 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
34596 AAAATTGACT
34606 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34625 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34644 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
34658 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34677 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
34697 ATTGCAA
1 ATCGCAA
34704 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.56
20 15 0.21
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34735 original size:53 final size:53
Alignment explanation
Indices: 34606--34722 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
34596 AAAATTGACT
34606 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
34658 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
34711 ATCGCAATGCGA
1 ATCGCAATGCGA
34723 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:37057 original size:12 final size:12
Alignment explanation
Indices: 37040--37064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37030 TCTTCGGGGA
37040 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37052 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37064 C
1 C
37065 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37273 original size:24 final size:24
Alignment explanation
Indices: 37239--37285 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37229 CTGAAACATC
37239 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
37263 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
37286 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:37996 original size:20 final size:20
Alignment explanation
Indices: 37968--38217 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
37958 AAATTTCAGT
* *
37968 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
37988 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
38008 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
38028 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
38048 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
38068 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
38088 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
38108 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * * *
38128 ATTACGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
38148 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
38168 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
38188 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
38208 GTTGCGATTT
1 GTTGCGATTT
38218 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:38234 original size:21 final size:21
Alignment explanation
Indices: 38204--38286 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
38194 ATTTTCATAT
*
38204 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
38225 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
38246 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
38267 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
38287 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:38277 original size:42 final size:43
Alignment explanation
Indices: 38184--38282 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
38174 ATTTATGTGT
* *
38184 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
38225 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
38267 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
38283 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:47037 original size:16 final size:16
Alignment explanation
Indices: 47016--47049 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
47006 CCTTTCCACA
47016 GCCTGAATCCATTTGT
1 GCCTGAATCCATTTGT
47032 GCCTGAATCCATTTGT
1 GCCTGAATCCATTTGT
47048 GC
1 GC
47050 AGATGAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (16 bp):
GCCTGAATCCATTTGT
Found at i:47758 original size:43 final size:43
Alignment explanation
Indices: 47703--47937 Score: 256
Period size: 43 Copynumber: 5.4 Consensus size: 43
47693 TTTCAAGAAA
47703 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GACAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGA-AGAC
* *
47746 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* *
47789 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * ***** *
47832 AAACGCCGCAGTAGGTGTCGATTTTTAGCGGCGTTTTTCCCAG
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * ** **
47875 AAACGCCGCAGTAGGTGTTGATGTTTAGTGGCGTTTTTTATTAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTGGAAGAC
*
47919 AAACGCCGCAATAAGTGTT
1 AAACGCCGCAATAGGTGTT
47938 AAGGTTTCGC
Statistics
Matches: 166, Mismatches: 24, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 141 0.85
44 25 0.15
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
Found at i:48443 original size:21 final size:21
Alignment explanation
Indices: 48376--48432 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
48366 ATATGTTGCT
48376 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
48397 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
48418 TCTCTTTGTGCTGCC
1 TCTCTTTGTGCTGCC
48433 ACTGTTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.00, C:0.37, G:0.23, T:0.40
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGCC
Found at i:48460 original size:44 final size:42
Alignment explanation
Indices: 48376--48460 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
48366 ATATGTTGCT
* * * *
48376 TCTCTTTGTGCTGCCGCTGCCTCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTACCGCTGCC
**
48418 TCTCTTTGTGCTGCCACTGTTTCTCTCTCTGCTTACGCGCTGC
1 TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGC-TAC-CGCTGC
48461 TTTGGCTGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 27 0.77
43 2 0.06
44 6 0.17
ACGTcount: A:0.02, C:0.36, G:0.21, T:0.40
Consensus pattern (42 bp):
TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTACCGCTGCC
Done.