Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004748.1 Hibiscus syriacus cultivar Beakdansim tig00010719_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: 120464
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1517 original size:19 final size:20
Alignment explanation
Indices: 1437--1523 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
1427 AAACTTAAAT
**
1437 TCGCAACGTAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* * *
1457 TCACAATGGGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1477 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1497 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1516 TCGCAACG
1 TCGCAACG
1524 TGATTTTCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:2127 original size:19 final size:20
Alignment explanation
Indices: 2014--2139 Score: 118
Period size: 20 Copynumber: 6.4 Consensus size: 20
2004 CGCGTAAAAT
*
2014 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
2034 ATTTGACTTAT-GTGTTGCG-
1 ATTTGAC-TATCGCGTTGCGA
* *
2053 ATTT-A-TAAATTGCGTCGCGA
1 ATTTGACT--ATCGCGTTGCGA
* * *
2073 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
2093 ATTTGACTATCGCGTTGTGA
1 ATTTGACTATCGCGTTGCGA
2113 ATTTGACTA-CGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
2132 ATTTGACT
1 ATTTGACT
2140 TCTGTGTTGC
Statistics
Matches: 87, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
16 1 0.01
18 3 0.03
19 27 0.31
20 52 0.60
21 3 0.03
22 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:2756 original size:31 final size:33
Alignment explanation
Indices: 2702--2763 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
2692 AATTATATAA
** *
2702 TTTTTAAATTTGACACATTAAAATAACTTTTTT
1 TTTTTAAATTTGACACACCAAAATAAATTTTTT
2735 TTTTTAAA-TTGACAC-CCAAAATAAATTTT
1 TTTTTAAATTTGACACACCAAAATAAATTTT
2764 ATAGCCCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 11 0.42
32 7 0.27
33 8 0.31
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (33 bp):
TTTTTAAATTTGACACACCAAAATAAATTTTTT
Found at i:6005 original size:31 final size:31
Alignment explanation
Indices: 5967--6025 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
5957 ATACAATCAA
*
5967 TTTCGTTTTTATTTAATTAAGGTATGATTAT
1 TTTCGTTTTTATTTAATTAAGATATGATTAT
5998 TTTCGTTTTTATTTAATTAAGATATGAT
1 TTTCGTTTTTATTTAATTAAGATATGAT
6026 CACCACCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (31 bp):
TTTCGTTTTTATTTAATTAAGATATGATTAT
Found at i:7193 original size:18 final size:19
Alignment explanation
Indices: 7170--7215 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
7160 ATATATATTT
*
7170 TTTCTTA-TTGAAAGCATG
1 TTTCTTATTTAAAAGCATG
7188 TTTCTTAATTTTAAAAGCATG
1 TTTCTT-A-TTTAAAAGCATG
7209 TTTCTTA
1 TTTCTTA
7216 CTATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 1 0.04
21 16 0.67
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTCTTATTTAAAAGCATG
Found at i:7206 original size:21 final size:21
Alignment explanation
Indices: 7175--7224 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
7165 TATTTTTTCT
*
7175 TATTGAAAGCATGTTTCTTAA
1 TATTAAAAGCATGTTTCTTAA
* *
7196 TTTTAAAAGCATGTTTCTTAC
1 TATTAAAAGCATGTTTCTTAA
7217 TATTAAAA
1 TATTAAAA
7225 TTTTTGTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
TATTAAAAGCATGTTTCTTAA
Found at i:11496 original size:34 final size:34
Alignment explanation
Indices: 11431--11496 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
11421 TTACATATAT
**
11431 AAATAATTTTTTATTTGATATATGGGTATACAAA
1 AAATAATTTTTTATTTGATATATGGAAATACAAA
*
11465 AAATAATTTTTTATTTGTTTATAT-GAAATACA
1 AAATAATTTTTTATTTG-ATATATGGAAATACA
11497 GATAAATCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (34 bp):
AAATAATTTTTTATTTGATATATGGAAATACAAA
Found at i:15643 original size:26 final size:26
Alignment explanation
Indices: 15613--15699 Score: 174
Period size: 26 Copynumber: 3.3 Consensus size: 26
15603 CCTGAGACAT
15613 TACTTAAACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
15639 TACTTAAACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
15665 TACTTAAACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
15691 TACTTAAAC
1 TACTTAAAC
15700 CAACCCGTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (26 bp):
TACTTAAACGATATCAAGATGTTTAC
Found at i:17040 original size:18 final size:18
Alignment explanation
Indices: 17017--17127 Score: 114
Period size: 18 Copynumber: 5.9 Consensus size: 18
17007 GTTCAGTATT
*
17017 TGTCCCGGAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
17035 TGTCCCGGAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
17054 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
17073 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
* * *
17093 TGTTCCGAAGAACCATTA
1 TGTCCCGAAGGACCACTA
17111 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
17128 GTTCATCCCT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
18 46 0.61
19 2 0.03
20 28 0.37
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:17129 original size:38 final size:38
Alignment explanation
Indices: 17028--17130 Score: 179
Period size: 38 Copynumber: 2.7 Consensus size: 38
17018 GTCCCGGAGG
* *
17028 ACCACTATGTCCCGGAGGACCACTGATTGTTCCGAAGA
1 ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
17066 ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
1 ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
*
17104 ACCATTATGTCCCGAAGGACCACTGTT
1 ACCACTATGTCCCGAAGGACCACTGTT
17131 CATCCCTCTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (38 bp):
ACCACTATGTCCCGAAGGACCACTGTTTGTTCCGAAGA
Found at i:18391 original size:19 final size:19
Alignment explanation
Indices: 18353--18391 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
18343 CCTTAACATG
**
18353 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTAATTA
*
18372 TGCATCGATGCATTAATTA
1 TGCATCGATGCACTAATTA
18391 T
1 T
18392 ATTCGATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (19 bp):
TGCATCGATGCACTAATTA
Found at i:22261 original size:20 final size:20
Alignment explanation
Indices: 22238--22302 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
22228 GTCCCGGAGG
22238 ACCACTGATTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
*
22258 ACCACTGTTTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
* * *
22278 ACCA-TTA-TGTCCCGAAGG
1 ACCACTGATTGTTCCGAAGA
22296 ACCACTG
1 ACCACTG
22303 TTCATCCCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 13 0.34
19 2 0.05
20 23 0.61
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (20 bp):
ACCACTGATTGTTCCGAAGA
Found at i:22294 original size:18 final size:20
Alignment explanation
Indices: 22227--22303 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
22217 GTTCAGTATT
* *
22227 TGTCCCGGAGGACCACTG-A
1 TGTCCCGAAGAACCACTGTA
* *
22246 TTGTTCCGAAGAACCACTGTT
1 -TGTCCCGAAGAACCACTGTA
*
22267 TGTTCCGAAGAACCA-T-TA
1 TGTCCCGAAGAACCACTGTA
*
22285 TGTCCCGAAGGACCACTGT
1 TGTCCCGAAGAACCACTGT
22304 TCATCCCTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.30
19 2 0.04
20 31 0.66
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGAACCACTGTA
Found at i:25659 original size:17 final size:16
Alignment explanation
Indices: 25639--25673 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
25629 TAAATTCAAC
25639 AAAATAATATTTATCTA
1 AAAATAA-ATTTATCTA
25656 AAAATAAATTTATCTA
1 AAAATAAATTTATCTA
25672 AA
1 AA
25674 TTTTCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAAATTTATCTA
Found at i:27040 original size:22 final size:22
Alignment explanation
Indices: 27015--27063 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
27005 CTTACTTTCA
27015 CCCAAAATCCTAAATCT-AAATT
1 CCCAAAATCC-AAATCTCAAATT
* *
27037 CCCAATATCCAAATCTCTAATT
1 CCCAAAATCCAAATCTCAAATT
27059 CCCAA
1 CCCAA
27064 CTTCAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.27
Consensus pattern (22 bp):
CCCAAAATCCAAATCTCAAATT
Found at i:27352 original size:18 final size:18
Alignment explanation
Indices: 27329--27371 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
27319 TTGGAAGGAG
27329 GAAAGGGAAAGGGAAAGA
1 GAAAGGGAAAGGGAAAGA
* *
27347 GAAAGGGGAAGGGGAAGA
1 GAAAGGGAAAGGGAAAGA
*
27365 GCAAGGG
1 GAAAGGG
27372 TGGGGTCGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (18 bp):
GAAAGGGAAAGGGAAAGA
Found at i:27703 original size:23 final size:22
Alignment explanation
Indices: 27677--27723 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
27667 TTTTTAACAG
* *
27677 TAAATTAAATAAAAATCAACTTT
1 TAAATCAAAT-AAAATCAAATTT
*
27700 TAAATCAAATCAAATCAAATTT
1 TAAATCAAATAAAATCAAATTT
27722 TA
1 TA
27724 TTCACCTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATCAAATAAAATCAAATTT
Found at i:28985 original size:267 final size:272
Alignment explanation
Indices: 28690--29234 Score: 746
Period size: 276 Copynumber: 2.0 Consensus size: 272
28680 GAAATATTTT
*
28690 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTTTTATAATATTATATAATCAAA-T-T
1 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
* * *
28753 ATTTTTATAC-ATGACCCTCAAACTCATAAAAAA-TTAATATGATAC-CTTGATCAAC-TGTTTC
66 ATTTTTATACTATGACCCTCAAACTCAGAAAAAACTCAATATGAT-CTCTTAATCAACAT-TTTC
* * ** ** * *
28814 TATCATTAG-CATTACAATACCAACACGACATTTCATGATGCTGACGTGA-TGATTCACGATAAC
129 TATCATTAGTCAATACAATACCAACACGACAATTCACAACACTAACGTGATTG-TTCAAGATAAC
* * *
28877 TAATGACATATTCACATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAGTTTATAATT
193 TAATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAATT
*
28942 AATATACTTTTATTG
258 AATACACTTTTATTG
28957 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
1 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
* **
29022 TTTTTTATACTTAATATGGTCCTCAAACTCAGAAAAAACTCAATATGATCTCTTAATCAACATTT
66 ATTTTTATAC----TATGACCCTCAAACTCAGAAAAAACTCAATATGATCTCTTAATCAACATTT
* * * * *
29087 TCTATCATTAGTCAATACAATATCAGCATGATAATTCACAACACTAACGTGATTGTTCAAGATGA
127 TCTATCATTAGTCAATACAATACCAACACGACAATTCACAACACTAACGTGATTGTTCAAGATAA
*
29152 CTAATAACATATTCAAATTATCTTTTTAATTAATTAATAAAAACATATTCCCTTGAATTTATAAT
192 CTAATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAAT
29217 TAATACACTTTTATTG
257 TAATACACTTTTATTG
29233 TT
1 TT
29235 TTTCCTCTAC
Statistics
Matches: 241, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
267 60 0.25
268 1 0.00
269 10 0.04
274 21 0.09
275 31 0.13
276 116 0.48
277 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (272 bp):
TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
ATTTTTATACTATGACCCTCAAACTCAGAAAAAACTCAATATGATCTCTTAATCAACATTTTCTA
TCATTAGTCAATACAATACCAACACGACAATTCACAACACTAACGTGATTGTTCAAGATAACTAA
TAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAATTAAT
ACACTTTTATTG
Found at i:34276 original size:14 final size:14
Alignment explanation
Indices: 34236--34278 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
34226 AAGGAATATC
*
34236 AGATGAAAGAAAAA
1 AGATGAAAGATAAA
* *
34250 AGGTGAAAAATAAA
1 AGATGAAAGATAAA
*
34264 AGATTAAAGATAAA
1 AGATGAAAGATAAA
34278 A
1 A
34279 TAAATCAGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (14 bp):
AGATGAAAGATAAA
Found at i:39190 original size:49 final size:49
Alignment explanation
Indices: 39137--39245 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
39127 GGAATATGTA
* *
39137 AAAATATTTATAGTTTTATCC-ATGTAAGTATACATATGAGAAATCTGTG
1 AAAATATTTATAATATTA-CCAATGTAAGTATACATATGAGAAATCTGTG
* ** * * *
39186 AAAATATTCATAATATTACCAATGTAAGTATATGTATGTGACATTTGTG
1 AAAATATTTATAATATTACCAATGTAAGTATACATATGAGAAATCTGTG
39235 -AAATATTTATA
1 AAAATATTTATA
39246 TCTACATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
48 12 0.24
49 38 0.76
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (49 bp):
AAAATATTTATAATATTACCAATGTAAGTATACATATGAGAAATCTGTG
Found at i:39370 original size:50 final size:50
Alignment explanation
Indices: 39311--39451 Score: 140
Period size: 50 Copynumber: 2.8 Consensus size: 50
39301 TCAATGTAGT
* * *
39311 TATAGATTATATGAAATCTGTGAAATTAATCATGTTTATAATAGTGT-AAT
1 TATA-ATTATATGAAATATGTGAAATTAATCATGTTTACAATAGTGTAAAA
* * * * * *
39361 TATGAATTATATAAAATATGTAAAATTAATCACGATAACACTAGTGTAAAA
1 TAT-AATTATATGAAATATGTGAAATTAATCATGTTTACAATAGTGTAAAA
* ** *
39412 TATAATTATATGAAATTTGTGATGTTGATCATGTTTACAA
1 TATAATTATATGAAATATGTGAAATTAATCATGTTTACAA
39452 CAATATAAGT
Statistics
Matches: 70, Mismatches: 19, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
50 64 0.91
51 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (50 bp):
TATAATTATATGAAATATGTGAAATTAATCATGTTTACAATAGTGTAAAA
Found at i:39742 original size:21 final size:21
Alignment explanation
Indices: 39716--39767 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
39706 CAAGTTTAAT
39716 ATTTCGTGTGCACCAGGT-GA
1 ATTTCGTGTGCACCAGGTGGA
* * *
39736 CATTTCGTGTACATCATGTGGA
1 -ATTTCGTGTGCACCAGGTGGA
39758 ATTTCGTGTG
1 ATTTCGTGTG
39768 TTCGTGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
ATTTCGTGTGCACCAGGTGGA
Found at i:41426 original size:54 final size:54
Alignment explanation
Indices: 41362--41798 Score: 377
Period size: 54 Copynumber: 8.1 Consensus size: 54
41352 CAACTACAAT
41362 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
41416 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** * * * *
41470 AATAAATCAA-TCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 AATAAATCAATTC-AT---ATTTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAA
* * * * ** * ** *
41533 ACT-AAT-AAAT--TA-TTTAAAATAAATCAATCTA-AATTTTAAAATAAAT-C
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** ** * *
41580 AATCCATACTAATAAAT-TATTTAAAATAAATTAATCCATAC-AACTACA--A--T--
1 AATAAAT-C-AATTCATAT-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
41630 AATAAATCAA-TCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
41684 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
41738 AATAAATCAATCCATAATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
41792 AATAAAT
1 AATAAAT
41799 TATTTTAAAA
Statistics
Matches: 313, Mismatches: 39, Indels: 62
0.76 0.09 0.15
Matches are distributed among these distances:
47 2 0.01
48 32 0.10
49 8 0.03
50 6 0.02
51 4 0.01
52 1 0.00
53 4 0.01
54 206 0.66
55 8 0.03
56 1 0.00
57 4 0.01
58 16 0.05
59 1 0.00
60 1 0.00
61 2 0.01
62 11 0.04
63 6 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:41437 original size:22 final size:22
Alignment explanation
Indices: 41411--41453 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41401 TAATAAATTA
41411 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
41433 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
41454 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:41453 original size:134 final size:134
Alignment explanation
Indices: 41299--41753 Score: 822
Period size: 134 Copynumber: 3.4 Consensus size: 134
41289 TAATAAATTA
* *
41299 TTTAAAATAAATCAATCCATACTAATATATTATTTAAAATAAATCAATCCGTACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
41364 TAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
66 TAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
41429 ATAT
131 ATAT
*
41433 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
* * *
41498 TAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCT
66 TAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
*
41563 AAAT
131 ATAT
*
41567 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
41632 TAAATCAA-TCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
66 TAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
41696 CATAT
130 CATAT
41701 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
41754 ATTTAAAATA
Statistics
Matches: 306, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
133 1 0.00
134 305 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (134 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
ATAT
Found at i:41462 original size:22 final size:22
Alignment explanation
Indices: 41413--41461 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
41403 ATAAATTATT
**
41413 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
41435 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
41458 TAAA
1 TAAA
41462 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:41500 original size:80 final size:80
Alignment explanation
Indices: 41416--41563 Score: 287
Period size: 80 Copynumber: 1.9 Consensus size: 80
41406 AATTATTTAA
41416 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
41481 CTATACAACTACAAT
66 CTATACAACTACAAT
*
41496 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
41561 CTA
66 CTA
41564 AATTTTAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CTATACAACTACAAT
Found at i:41542 original size:22 final size:23
Alignment explanation
Indices: 41467--41541 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
41457 ATAAATTATT
41467 TAAAATAAATCAATCTATAC-AA
1 TAAAATAAATCAATCTATACTAA
* **
41489 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCTATACTAA
41515 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATACTAA
41538 TAAA
1 TAAA
41542 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAATAAATCAATCTATACTAA
Found at i:41634 original size:80 final size:80
Alignment explanation
Indices: 41550--41699 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
41540 AATTATTTAA
*
41550 AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAAT
1 AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
41615 CCATACAACTACAAT
66 CCATACAACTACAAT
*
41630 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
41695 CCATA
66 CCATA
41700 TTTTAAAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:41690 original size:188 final size:187
Alignment explanation
Indices: 41362--41800 Score: 608
Period size: 188 Copynumber: 2.3 Consensus size: 187
41352 CAACTACAAT
* *
41362 AATAAATCAAT-TCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCT-AAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAA
*** * * *
41426 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACT
65 TCCATAAACTAAAATAAATAAATCAATACTAAT-AATTATTTAAAATAAATCAATCCATACAACT
* *
41491 ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
129 AAAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
41550 AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAAT
1 AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAAT
*
41615 CCATACAACTACAAT-AATAAATCAAT-CT-AT-A-T-TTTAAAATAAATCAATCCATACTAA-T
66 CCATA-AACTAAAATAAATAAATCAATACTAATAATTATTTAAAATAAATCAATCCATAC-AACT
41673 AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
129 AAA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
41738 AATAAATCAATCCATAA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTA
1 AATAAATCAATCTA-AATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTA
41801 TTTTAAAATA
Statistics
Matches: 229, Mismatches: 12, Indels: 20
0.88 0.05 0.08
Matches are distributed among these distances:
182 24 0.10
183 3 0.01
184 2 0.01
186 3 0.01
187 2 0.01
188 187 0.82
189 8 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (187 bp):
AATAAATCAATCTAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAAT
CCATAAACTAAAATAAATAAATCAATACTAATAATTATTTAAAATAAATCAATCCATACAACTAA
AATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:41705 original size:22 final size:22
Alignment explanation
Indices: 41679--41721 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41669 TAATAAATTA
41679 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
41701 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
41722 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:41730 original size:22 final size:22
Alignment explanation
Indices: 41681--41783 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 22
41671 ATAAATTATT
**
41681 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
41703 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
* *
41726 TAAATTATTTAAAATAAATCAATCCATAA
1 TAAA--A--T-AAATCAATCCAT--ATAA
41755 TTTAAAATAAATCAATCCATACTAA
1 --TAAAATAAATCAATCCATA-TAA
41780 TAAA
1 TAAA
41784 TTATTTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
22 19 0.30
23 9 0.14
24 1 0.02
25 4 0.06
26 10 0.16
27 2 0.03
28 10 0.16
29 4 0.06
30 1 0.02
31 4 0.06
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:41807 original size:15 final size:15
Alignment explanation
Indices: 41778--41909 Score: 133
Period size: 15 Copynumber: 8.5 Consensus size: 15
41768 AATCCATACT
41778 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
41792 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
41807 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
41829 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
41844 AATAAATTATTTTAT
1 AATAAATTATTTTAA
41859 AATAAATTATTTT-A
1 AATAAATTATTTTAA
* *
41873 AATAATTTATTTTAT
1 AATAAATTATTTTAA
*
41888 AATAATTTATTTTAA
1 AATAAATTATTTTAA
41903 AATAAAT
1 AATAAAT
41910 AACCTTATTA
Statistics
Matches: 99, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
14 21 0.21
15 61 0.62
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:41810 original size:29 final size:30
Alignment explanation
Indices: 41778--41909 Score: 151
Period size: 29 Copynumber: 4.2 Consensus size: 30
41768 AATCCATACT
*
41778 AATAAATTA-TTTAAAATAAATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
*
41807 AATAAATCAATCCATATTTTATAATAATTTATTTTAA
1 AAT--A--AAT---TATTTTATAATAAATTATTTTAA
41844 AATAAATTATTTTATAATAAATTATTTT-A
1 AATAAATTATTTTATAATAAATTATTTTAA
* *
41873 AATAATTTATTTTATAATAATTTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
41903 AATAAAT
1 AATAAAT
41910 AACCTTATTA
Statistics
Matches: 88, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
29 30 0.34
30 27 0.31
31 1 0.01
33 6 0.07
35 1 0.01
36 2 0.02
37 21 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AATAAATTATTTTATAATAAATTATTTTAA
Found at i:41882 original size:44 final size:45
Alignment explanation
Indices: 41777--41909 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 45
41767 CAATCCATAC
*
41777 TAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTA
1 TAATAATTTATTTTAAAATAAATTATTTTAAAAT--A--AAT---TATTTTA
*
41828 TAATAATTTATTTTAAAATAAATTATTTTATAATAAATTATTTTA
1 TAATAATTTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
* *
41873 -AATAATTTATTTTATAATAATTTATTTTAAAATAAAT
1 TAATAATTTATTTTAAAATAAATTATTTTAAAATAAAT
41910 AACCTTATTA
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
44 34 0.45
45 7 0.09
48 3 0.04
50 1 0.01
51 9 0.12
52 22 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (45 bp):
TAATAATTTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
Found at i:41923 original size:29 final size:28
Alignment explanation
Indices: 41821--41932 Score: 102
Period size: 30 Copynumber: 3.9 Consensus size: 28
41811 AATCAATCCA
*
41821 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAT--TAAATTATTTTAAAATAAAT
*
41851 TATTTTATAATAAATTATTTT-AAATAATT
1 TATTTTAT--TAAATTATTTTAAAATAAAT
*
41880 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAT--TAAATTATTTTAAAATAAAT
* **
41910 AACCTTATTAAATTA-TTTAAAAT
1 TATTTTATTAAATTATTTTAAAAT
41933 TATTTTAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.11
28 6 0.08
29 27 0.37
30 32 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTTTATTAAATTATTTTAAAATAAAT
Found at i:42901 original size:23 final size:23
Alignment explanation
Indices: 42871--42921 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
42861 TGTTTCTGAG
42871 GGAATTGAAATCTGTCAGGAATT
1 GGAATTGAAATCTGTCAGGAATT
42894 GGAATTGAAATCTGTCAGGAATT
1 GGAATTGAAATCTGTCAGGAATT
42917 GGAAT
1 GGAAT
42922 CCAATTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (23 bp):
GGAATTGAAATCTGTCAGGAATT
Found at i:43798 original size:252 final size:249
Alignment explanation
Indices: 43281--43890 Score: 876
Period size: 252 Copynumber: 2.4 Consensus size: 249
43271 CTCCATCCGA
*
43281 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAA--C--C
*
43346 GCGACCCGAAATAATAATAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATA
62 -CGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATA
*
43411 TATAGAGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGT
126 TATAGAGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTT--GT
43476 CGGGTCGGGTCAGGTATTTTTCACCCTAAACCCGAACCCAACCCGAATATCACACTTAAAAAAT
189 CGGGTC-GG--AGGTATTTTTCACCCTAAACCCGAACCCAACCCGAATATCACACTTAAAAAAT
*
43540 --CCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGAC
*
43603 CCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATAT
66 CCGAAATAAT-AAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAA-AATATAT
43668 AGAG-GG-GTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TATTT-TCGGGT
129 AGAGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTGTCGGGT
*
43729 C-G-GGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAATT
194 CGGAGGTATTTTTCACCCTAAACCCG-A----ACCCAACCCGAATATCACACTT-AAAAAA-T
*
43790 GACCCGACCCGACCAAAATAAAGTTTCACCAGACTCGACCCGAATATATGAATTAGAAACCCGAT
1 GACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGA-
*
43855 CCGACCTGAAAAAATAAAAAAATATTTTTATTCAAT
65 -C--CC-GAAATAATAAAAAAATATTTTTATTCAAT
43891 GTATGAATAA
Statistics
Matches: 327, Mismatches: 8, Indels: 35
0.88 0.02 0.09
Matches are distributed among these distances:
243 22 0.07
244 1 0.00
246 1 0.00
248 28 0.09
249 6 0.02
250 1 0.00
251 4 0.01
252 118 0.36
253 48 0.15
254 11 0.03
255 1 0.00
256 23 0.07
257 63 0.19
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (249 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGAC
CCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATATAG
AGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTGTCGGGTCG
GAGGTATTTTTCACCCTAAACCCGAACCCAACCCGAATATCACACTTAAAAAAT
Found at i:47460 original size:20 final size:20
Alignment explanation
Indices: 47431--47468 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47421 CAGAACCCCA
*
47431 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
47451 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
47469 TCAAAGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:47502 original size:20 final size:20
Alignment explanation
Indices: 47450--47510 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
47440 GATTCCCCTG
47450 TGGGGGAATCGGTTCCCCTTCA
1 TGGGGGAATCGGTT-CCC-TCA
**
47472 AAGGGGAATCGGTTCCCTCA
1 TGGGGGAATCGGTTCCCTCA
* *
47492 TGGGGGGATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
47511 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 18 0.55
21 3 0.09
22 12 0.36
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
TGGGGGAATCGGTTCCCTCA
Found at i:55421 original size:19 final size:19
Alignment explanation
Indices: 55397--55437 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
55387 ACTGCAAATG
*
55397 CCCATGCTGGACCATGCTA
1 CCCATGCTGGACCATGCCA
*
55416 CCCATGTTGGACCATGCCA
1 CCCATGCTGGACCATGCCA
55435 CCC
1 CCC
55438 TATTGCAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.20
Consensus pattern (19 bp):
CCCATGCTGGACCATGCCA
Found at i:64013 original size:19 final size:19
Alignment explanation
Indices: 63986--64022 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
63976 GCACTGTAAA
*
63986 TGCCCATGCTGAACCATGC
1 TGCCAATGCTGAACCATGC
*
64005 TGCCAATGCTGGACCATG
1 TGCCAATGCTGAACCATG
64023 TCGCCCTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (19 bp):
TGCCAATGCTGAACCATGC
Found at i:65254 original size:22 final size:20
Alignment explanation
Indices: 65213--65255 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
65203 ACACTACCAC
*
65213 CATTCCATTTTCACATCATT
1 CATTCCATTTTCACAACATT
65233 CATTCCATTTTGCCACAACATT
1 CATTCCATTTT--CACAACATT
65255 C
1 C
65256 TCATTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.40
Consensus pattern (20 bp):
CATTCCATTTTCACAACATT
Found at i:68318 original size:66 final size:66
Alignment explanation
Indices: 68228--68453 Score: 355
Period size: 66 Copynumber: 3.4 Consensus size: 66
68218 GAGAGTTATA
* * * *
68228 GGTGCATT-TTGGCATAAAAGGTGCCACTAATAAAAATTATTGATCGATTTTGATTAATGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAAAGCATAA
68292 C
66 C
* *
68293 GGTGCATTATCGGTATAAAATGTGCCACTAATGAAAATTATCGATCGATTTTGATTAAAGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAAAGCATAA
68358 C
66 C
* *
68359 GGTGCATTATCGGCATAAAAGGTGCTACTAATGAAAATTATCGATCGATTTTGATTAACGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAAAGCATAA
68424 C
66 C
* *
68425 GGTGCATTATCGACATAAAAGATGCCACT
1 GGTGCATTATCGGCATAAAAGGTGCCACT
68454 CATGGTATTA
Statistics
Matches: 147, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 8 0.05
66 139 0.95
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (66 bp):
GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAAAGCATAA
C
Found at i:75449 original size:66 final size:66
Alignment explanation
Indices: 75357--75569 Score: 363
Period size: 66 Copynumber: 3.2 Consensus size: 66
75347 GCATTTTGGT
* *
75357 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAATGGTGCATTATCGG
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGA
75422 C
66 C
* *
75423 ATAAAAGGTGCCACTAATGAAAATTATAGATCGATTTTGATTAATGCATGACGGTGCATTATCGA
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGA
75488 C
66 C
* * *
75489 ATAAAAGGTGCTACTAATGAAAATTATCAATTGATTTTGATTAATGCATAACGGTGCATTATCGA
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGA
75554 C
66 C
75555 ATAAAAGGTGCCACT
1 ATAAAAGGTGCCACT
75570 CATGGTATTC
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 137 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (66 bp):
ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGA
C
Found at i:80870 original size:2 final size:2
Alignment explanation
Indices: 80865--80904 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
80855 CTTTTCTAGG
80865 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
80905 CTAAGTTCAC
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):
TC
Found at i:83008 original size:16 final size:16
Alignment explanation
Indices: 82962--83021 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
82952 AAGATTGTTT
82962 TGATAAAAAA-ATAAAA
1 TGATAAAAAAGA-AAAA
* *
82978 TG-TTAAAAGGTAAAAA
1 TGATAAAAAAG-AAAAA
82994 TGATAAAAAAGAAAAA
1 TGATAAAAAAGAAAAA
*
83010 AGA-AAAAAAGAA
1 TGATAAAAAAGAA
83022 TAGAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 14 0.39
16 15 0.42
17 7 0.19
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (16 bp):
TGATAAAAAAGAAAAA
Found at i:83330 original size:30 final size:30
Alignment explanation
Indices: 83253--83346 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
83243 TATTCATTTG
* * *
83253 TTTATTTTTGAAGGTGTTCATATTCGTTTAA
1 TTTATTTTTTAAGGTGTTTATGTTCGTTT-A
** **
83284 TTT-TTTGGTATTGTGTTTATGTTCGTTTA
1 TTTATTTTTTAAGGTGTTTATGTTCGTTTA
*
83313 TTTATTTTTTAAGGTGTTTGTGTTCGTTTA
1 TTTATTTTTTAAGGTGTTTATGTTCGTTTA
83343 TTTA
1 TTTA
83347 ACGTTCACGA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 4 0.08
30 43 0.86
31 3 0.06
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (30 bp):
TTTATTTTTTAAGGTGTTTATGTTCGTTTA
Found at i:83369 original size:23 final size:23
Alignment explanation
Indices: 83343--83419 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 23
83333 TGTTCGTTTA
83343 TTTAACGTTCACGAACGTGTTCG
1 TTTAACGTTCACGAACGTGTTCG
83366 TTTATTTAACGTTCACGAACGTGTTCG
1 ----TTTAACGTTCACGAACGTGTTCG
**
83393 TTTAATATTCACGAACGTGTTCG
1 TTTAACGTTCACGAACGTGTTCG
83416 TTTA
1 TTTA
83420 GGGATCGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 25 0.52
27 23 0.48
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (23 bp):
TTTAACGTTCACGAACGTGTTCG
Found at i:83370 original size:27 final size:27
Alignment explanation
Indices: 83332--83419 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
83322 TAAGGTGTTT
83332 GTGTTCGTTTATTTAACGTTCACGAAC
1 GTGTTCGTTTATTTAACGTTCACGAAC
83359 GTGTTCGTTTATTTAACGTTCACGAAC
1 GTGTTCGTTTATTTAACGTTCACGAAC
*
83386 GTGTTCGTTTA-AT-A--TTCACGAAC
1 GTGTTCGTTTATTTAACGTTCACGAAC
83409 GTGTTCGTTTA
1 GTGTTCGTTTA
83420 GGGATCGTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 20 0.33
25 1 0.02
26 1 0.02
27 38 0.63
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
GTGTTCGTTTATTTAACGTTCACGAAC
Found at i:83454 original size:34 final size:34
Alignment explanation
Indices: 83390--83454 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
83380 ACGAACGTGT
* *
83390 TCGTTTAATATTCACGAACGTGTTCGTTTAGGGA
1 TCGTTTAATATTCACGAACATATTCGTTTAGGGA
* *
83424 TCGTTT-ATCATTCGCGAACATATTCTTTTAG
1 TCGTTTAAT-ATTCACGAACATATTCGTTTAG
83455 CATTCGTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 2 0.08
34 24 0.92
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (34 bp):
TCGTTTAATATTCACGAACATATTCGTTTAGGGA
Found at i:83476 original size:23 final size:23
Alignment explanation
Indices: 83424--83477 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
83414 CGTTTAGGGA
*
83424 TCGTTTATCATTCGCGAACATAT
1 TCGTTTAGCATTCGCGAACATAT
* * * *
83447 TCTTTTAGCATTCGTGAATATGT
1 TCGTTTAGCATTCGCGAACATAT
83470 TCGTTTAG
1 TCGTTTAG
83478 AATAAAAAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (23 bp):
TCGTTTAGCATTCGCGAACATAT
Found at i:85872 original size:49 final size:48
Alignment explanation
Indices: 85819--85936 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 48
85809 CTAGTGTAAA
*
85819 TATAATCATATAAAATATGTGAAGTTGATCATGTTTACAACAATATGAG
1 TATAATCATATGAAATATGTGAAGTTGATCATGTTTAC-ACAATATGAG
* * * * * * * *
85868 TATAATTATATGATATCTTTCAAGTTGGTTATGTTTACACAATCTGAG
1 TATAATCATATGAAATATGTGAAGTTGATCATGTTTACACAATATGAG
*
85916 TATGATCATATGAAATATGTG
1 TATAATCATATGAAATATGTG
85937 GAGATATTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
48 24 0.44
49 30 0.56
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (48 bp):
TATAATCATATGAAATATGTGAAGTTGATCATGTTTACACAATATGAG
Found at i:86146 original size:21 final size:21
Alignment explanation
Indices: 86120--86162 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
86110 TCAAAGTTTA
*
86120 ATATTTCATGTGCATCGTGTG
1 ATATTTCATGTACATCGTGTG
* *
86141 ATATTTCGTGTACATTGTGTG
1 ATATTTCATGTACATCGTGTG
86162 A
1 A
86163 ATCGTGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (21 bp):
ATATTTCATGTACATCGTGTG
Found at i:100221 original size:21 final size:21
Alignment explanation
Indices: 100196--100235 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
100186 AAGACTCTAT
100196 TTTCAAAATACAAAAATGACA
1 TTTCAAAATACAAAAATGACA
**
100217 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
100236 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGACA
Found at i:110951 original size:24 final size:24
Alignment explanation
Indices: 110918--110967 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
110908 AGTCTTCCTG
110918 ATGATATATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
*
110942 ATGATGTATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
110966 AT
1 AT
110968 TGTCATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (24 bp):
ATGATATATAAAACATCTATGTAC
Found at i:114454 original size:17 final size:16
Alignment explanation
Indices: 114433--114472 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
114423 TATCTCTCAT
*
114433 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTCTTTC
114449 TGTTTTTTTCTTCTTTC
1 T-TTTTTTTCTTCTTTC
114466 TTTTTTT
1 TTTTTTT
114473 AGCTCTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTTTTCTTCTTTC
Found at i:117610 original size:24 final size:24
Alignment explanation
Indices: 117578--117651 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
117568 AGTCTTCCTA
*
117578 ATGATGTATAAAATATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
117602 ATGATGTATAAAACATCTATGCAC
1 ATGATGTATAAAACATCTATGTAC
117626 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
117650 AT
1 AT
117652 TTTCATGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:119786 original size:80 final size:80
Alignment explanation
Indices: 119643--119834 Score: 240
Period size: 80 Copynumber: 2.4 Consensus size: 80
119633 CTACTCATAA
* * * ***
119643 ATTTAGGTGTGTATCCCGTACAATACATCACCTTGCTTATAATTGGGTGTATATCATGTACAATA
1 ATTTAGATGTGTATCCCGTACAATACATCATCTTACTTATAATTGGGTGTATATCACACACAATA
* *
119708 TATCACCACTTTTAT
66 TATCACCACCTTCAT
* * * * * * *
119723 ATTTAGATGTGTACCCCTTACGATACATCATCTTACTTGTAGTTGGGTGTGTATCCCACACAATA
1 ATTTAGATGTGTATCCCGTACAATACATCATCTTACTTATAATTGGGTGTATATCACACACAATA
119788 TATCACCACCTTCAT
66 TATCACCACCTTCAT
*
119803 ATTTAGTTGTGTATCCCGTACAATACATCATC
1 ATTTAGATGTGTATCCCGTACAATACATCATC
119835 ACTTTCATAT
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 93 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (80 bp):
ATTTAGATGTGTATCCCGTACAATACATCATCTTACTTATAATTGGGTGTATATCACACACAATA
TATCACCACCTTCAT
Found at i:119814 original size:40 final size:40
Alignment explanation
Indices: 119770--119855 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
119760 TGTAGTTGGG
* *
119770 TGTGTATCCCACACAATATATCACCACCTTCATATTTAGT
1 TGTGTATCCCACACAATACATCACCACCTTCATATTTAGA
** * *
119810 TGTGTATCCCGTACAATACATCATCACTTTCATATTTAGA
1 TGTGTATCCCACACAATACATCACCACCTTCATATTTAGA
119850 TGTGTA
1 TGTGTA
119856 CGCTATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (40 bp):
TGTGTATCCCACACAATACATCACCACCTTCATATTTAGA
Found at i:119907 original size:119 final size:120
Alignment explanation
Indices: 119700--119927 Score: 298
Period size: 119 Copynumber: 1.9 Consensus size: 120
119690 TGTATATCAT
* *
119700 GTACAATATATCACCACTTTTATATTTAGATGTGTACCCCTTACGATACATCATCTTACTTGTAG
1 GTACAATACATCACCACTTTCATATTTAGATGTGTACCCCTTACGATACATCATCTTACTTGTAG
* *
119765 TTGGGTGTGTATCCCACACAATATATCACCACCTTCATATTTAGTTGTGTATCCC
66 TTGGGTGTGTATACCACACAATATATCACCACATTCATATTTAGTTGTGTATCCC
* * * * *
119820 GTACAATACATCATCACTTTCATATTTAGATGTGTA-CGCTATA-TATACATTATCTTGCTTGTA
1 GTACAATACATCACCACTTTCATATTTAGATGTGTACCCCT-TACGATACATCATCTTACTTGTA
* **** *
119883 GTTTGGTGTGTATATGGTACAATATATCACCATATTCATATTTAG
65 GTTGGGTGTGTATACCACACAATATATCACCACATTCATATTTAG
119928 AAATTCTAGA
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
119 57 0.62
120 35 0.38
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (120 bp):
GTACAATACATCACCACTTTCATATTTAGATGTGTACCCCTTACGATACATCATCTTACTTGTAG
TTGGGTGTGTATACCACACAATATATCACCACATTCATATTTAGTTGTGTATCCC
Done.