Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005886.1 Hibiscus syriacus cultivar Beakdansim tig00013823_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: 58834
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:989 original size:63 final size:64
Alignment explanation
Indices: 898--1019 Score: 162
Period size: 63 Copynumber: 1.9 Consensus size: 64
888 ATTTATTATT
*
898 TTTAACTTTGAATATTAAAGATAATTATA-CTACTTTGAATATTTTAAA-TT-AAAATAATATCT
1 TTTAACTTTGAATAGTAAAGATAATTATATCT--TTTGAATATTTTAAATTTAAAAATAATATCT
960 A
64 A
* *
961 TTTAATTTTGAATAGTAAA-ATTATTTATATCTTTTGAATATTTTAAATTTAAAAATAAT
1 TTTAACTTTGAATAGTAAAGA-TAATTATATCTTTTGAATATTTTAAATTTAAAAATAAT
1020 TTTATATGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
62 16 0.31
63 26 0.50
64 10 0.19
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (64 bp):
TTTAACTTTGAATAGTAAAGATAATTATATCTTTTGAATATTTTAAATTTAAAAATAATATCTA
Found at i:10433 original size:22 final size:23
Alignment explanation
Indices: 10408--10451 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
10398 AAAATTTTTG
10408 TATA-AACTTTAAAAAATAAAAT
1 TATATAACTTTAAAAAATAAAAT
**
10430 TATATATTTTTAAAAAATAAAA
1 TATATAACTTTAAAAAATAAAA
10452 CGAAGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TATATAACTTTAAAAAATAAAAT
Found at i:10481 original size:19 final size:19
Alignment explanation
Indices: 10457--10505 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
10447 TAAAACGAAG
10457 AAATTTTGAAATAAACTCA
1 AAATTTTGAAATAAACTCA
10476 AAATTTTGAAATAAACTCA
1 AAATTTTGAAATAAACTCA
*
10495 AAACTTTGAAA
1 AAATTTTGAAA
10506 ATCTTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
AAATTTTGAAATAAACTCA
Found at i:16214 original size:22 final size:21
Alignment explanation
Indices: 16164--16222 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
16154 ATATGGAAAA
16164 GAAAAGT-AATT-AAAAATAT
1 GAAAAGTAAATTCAAAAATAT
*
16183 -AAATAATAAATTCAAAAGATAT
1 GAAA-AGTAAATTCAAAA-ATAT
*
16205 GAAAAGTAAATCCAAAAA
1 GAAAAGTAAATTCAAAAA
16223 ACAATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 4 0.12
21 5 0.16
22 15 0.47
23 3 0.09
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.22
Consensus pattern (21 bp):
GAAAAGTAAATTCAAAAATAT
Found at i:17573 original size:31 final size:30
Alignment explanation
Indices: 17514--17597 Score: 141
Period size: 31 Copynumber: 2.7 Consensus size: 30
17504 TGGTGAGCAC
*
17514 ATCTTAATTAAATAAAATAAGAGTGATCAT
1 ATCTTAATTAAATAAAATAAAAGTGATCAT
17544 ATCTTAATTAAATAAAATTAAAAGTGATCAT
1 ATCTTAATTAAATAAAA-TAAAAGTGATCAT
17575 ATCTTAATTAAATAAAAGTAAAA
1 ATCTTAATTAAATAAAA-TAAAA
17598 ATAATCGTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 17 0.33
31 34 0.67
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (30 bp):
ATCTTAATTAAATAAAATAAAAGTGATCAT
Found at i:19207 original size:182 final size:182
Alignment explanation
Indices: 18672--19529 Score: 1148
Period size: 182 Copynumber: 4.7 Consensus size: 182
18662 TGTCGGTTTA
* * * * * **
18672 TGTCGATACTTTATAAAAATATATCGATCCACATCAATATACCAAGAAAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAAC-AGGTAAAAATATGACAAAACC
* * *
18737 GGT-TACGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
65 GGTAT-CGAAAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATA
* * * * *
18801 TAAATATCTACACATTGTGAATTTAAAGGAGAAACAATTTTAGCGCCTATAAAG
129 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * * * *
18855 TATCGATTCTTTATAA-ATATGTATCGATCCACAAAGATATAACAGGTAAATCA-ATGATAAAAC
1 TGTCGATACTTTATAACA-ATGTATCGATCCACAACGATATAACAGGTAAA-AATATGACAAAAC
* * * * * * *
18918 CGGTCTCGAGAA-GACAAAACCGGGTAAGGCGCTATCGGATATATTGAAAGTGTCAATACTGTAA
64 CGGTATCGA-AAGGACAAAACC-GGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAA
*
18982 TATAAGTATCGACACTTTGTGAATTTAAAAGAGAAATAGTTTTAGCGCCTATAAAG
127 TATAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * * *
19038 TGTCGATATTTTATAACAATGTATCGATCTACAATGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * *
19103 GTATCTAAAGGACAAAACCGTTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTATCGAAAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
19168 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * * *
19220 TGTCGATACTTTATAAAAATGTATCGATCAATAACGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * *
19285 GTATCTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTTAAAGTGTCGATACTTTAATATA
66 GTATCGAAAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
19350 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* *
19402 TGTCGATACTTTATAACAATGTATCGGTCCACAACGATATAACATGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * * * *
19467 GTCTCGAAATGACAAAATCGGTAAAGCGCTACAGGATATAATGAAAGTGTCGATACTTTAATA
66 GTATCGAAAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATA
19530 AGTACGCGTA
Statistics
Matches: 601, Mismatches: 66, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
182 407 0.68
183 193 0.32
184 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
GTATCGAAAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:21923 original size:21 final size:21
Alignment explanation
Indices: 21893--21936 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
21883 AAGACAATCA
*
21893 AGAGTGGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
21914 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
21935 AG
1 AG
21937 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGACACTTGAG
Found at i:22007 original size:33 final size:33
Alignment explanation
Indices: 21970--22069 Score: 182
Period size: 33 Copynumber: 3.0 Consensus size: 33
21960 AAATAGATGT
*
21970 AGTGGTGAAAGAAGTTGAGGTGTTGAAGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
22003 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
*
22036 AGTGGTGAAAGAAGTTGATGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
22069 A
1 A
22070 CTTAAGATGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.29, C:0.00, G:0.46, T:0.25
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:22261 original size:2 final size:2
Alignment explanation
Indices: 22254--22287 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
22244 TATATGTTAC
*
22254 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22288 ATAAACACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28481 original size:15 final size:15
Alignment explanation
Indices: 28461--28490 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28451 AGGGGAAGCC
*
28461 AAATTTTTGGGGCAA
1 AAATTTTTGGAGCAA
28476 AAATTTTTGGAGCAA
1 AAATTTTTGGAGCAA
28491 GGAAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (15 bp):
AAATTTTTGGAGCAA
Found at i:29095 original size:36 final size:36
Alignment explanation
Indices: 29037--29146 Score: 98
Period size: 36 Copynumber: 3.1 Consensus size: 36
29027 ATGATTTGTC
* * *
29037 TCACTTGAGACTATTTTACTTAAAAGAAGATTTATT
1 TCACTTGAGATTGTATTACTTAAAAGAAGATTTATT
* * * *
29073 TCCCTTGAGATTGTCATT-CTTAAAA-CAGATCTTGTC
1 TCACTTGAGATTGT-ATTACTTAAAAGAAGAT-TTATT
* * *
29109 TCACTTGAGATTGTTTTACTTGAAAGAATATTTATT
1 TCACTTGAGATTGTATTACTTAAAAGAAGATTTATT
29145 TC
1 TC
29147 TCTCAAGATT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
35 6 0.11
36 45 0.80
37 5 0.09
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (36 bp):
TCACTTGAGATTGTATTACTTAAAAGAAGATTTATT
Found at i:29126 original size:72 final size:73
Alignment explanation
Indices: 29032--29197 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 73
29022 TGCAGATGAT
* * ** *
29032 TTGTCTCACTTGAGACTATTTTACTTAAAAGAAGATTTATTTCCCTTGAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGATTGTTTTACTTAAAAGAAGATTTATTTCCCTCAAGATTATCATTCTTAAA
29097 AC-AGATC
66 ACGAGATC
* * * **
29104 TTGTCTCACTTGAGATTGTTTTACTTGAAAGAATATTTATTTCTCTCAAGATTATTTTTCTTAAA
1 TTGTCTCACTTGAGATTGTTTTACTTAAAAGAAGATTTATTTCCCTCAAGATTATCATTCTTAAA
*
29169 ACGAGATT
66 ACGAGATC
* * *
29177 TTATCTCGCTTGAGATAGTTT
1 TTGTCTCACTTGAGATTGTTT
29198 CTCTCGAAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 57 0.72
73 22 0.28
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44
Consensus pattern (73 bp):
TTGTCTCACTTGAGATTGTTTTACTTAAAAGAAGATTTATTTCCCTCAAGATTATCATTCTTAAA
ACGAGATC
Found at i:29348 original size:36 final size:35
Alignment explanation
Indices: 29267--29348 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
29257 AAAACATTTC
** * *
29267 CCTTGAAATGAATTATGTCTCTCTTGAGATAGTTT
1 CCTTGAAACAAATTATGTCTCCCTTGAGACAGTTT
* *
29302 CCTTTAAAACAAATTTTGTCTCCCTTGAGACAGTTT
1 CC-TTGAAACAAATTATGTCTCCCTTGAGACAGTTT
29338 CTCTTGAAACA
1 C-CTTGAAACA
29349 TAAACATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 2 0.05
36 35 0.92
37 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (35 bp):
CCTTGAAACAAATTATGTCTCCCTTGAGACAGTTT
Found at i:29363 original size:101 final size:101
Alignment explanation
Indices: 29211--29618 Score: 667
Period size: 101 Copynumber: 4.0 Consensus size: 101
29201 TCGAAACAGA
29211 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * *
29276 GAATTATGTCTCTCTTGAGATAGTTTCCTTTAAAAC
66 GAATTTTGTCTCTCTTGAGATAATTTCCCTTAAAAC
29312 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * * * *
29377 GATTTTTGTCTCTCTTGAGATAGTTTCTCTCGAAACAGA
66 GAATTTTGTCTCTCTTGAGATAATTTCCCT-TAAA-A-C
29416 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
29481 GAA--TTGTCTCTCTTGAGATAATTTCCCTTAAAAC
66 GAATTTTGTCTCTCTTGAGATAATTTCCCTTAAAAC
* *
29515 AAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
29580 GTATTTTGTCTCTCTTGAGATAATTTCCCTTGAAAC
66 GAATTTTGTCTCTCTTGAGATAATTTCCCTTAAAAC
29616 AAA
1 AAA
29619 ACTTTTGAAA
Statistics
Matches: 287, Mismatches: 15, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
99 65 0.23
100 1 0.00
101 127 0.44
102 26 0.09
103 1 0.00
104 67 0.23
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (101 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTGTCTCTCTTGAGATAATTTCCCTTAAAAC
Found at i:29591 original size:203 final size:204
Alignment explanation
Indices: 29173--29625 Score: 777
Period size: 203 Copynumber: 2.2 Consensus size: 204
29163 CTTAAAACGA
* *
29173 GATTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
1 GATTTTGTCTCTCTTGAGATAGTTTCTCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
*
29238 TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTATGTCTCTCTTGAGATAGTTTC
66 TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTATGTCTCTCTTGAGATAATTTC
* *
29303 CTTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
131 CCTTAAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
29368 CCTTGAAAT
196 CCTTGAAAT
29377 GATTTTTGTCTCTCTTGAGATAGTTTCTCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTT
1 GA-TTTTGTCTCTCTTGAGATAGTTTCTCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTT
29442 CTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA-T-TGTCTCTCTTGAGATAATTT
65 CTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTATGTCTCTCTTGAGATAATTT
*
29505 CCCTTAAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACATTT
130 CCCTTAAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTT
29570 CCCTTGAAAT
195 CCCTTGAAAT
* * * *
29580 GTATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACA-AAACTTTTG
1 G-ATTTTGTCTCTCTTGAGATAGTTTCTCTCGAAACAGAAAATTTTG
29626 AAATTGTTTC
Statistics
Matches: 237, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
202 8 0.03
203 123 0.52
204 4 0.02
205 102 0.43
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (204 bp):
GATTTTGTCTCTCTTGAGATAGTTTCTCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTATGTCTCTCTTGAGATAATTTC
CCTTAAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
CCTTGAAAT
Found at i:29913 original size:2 final size:2
Alignment explanation
Indices: 29906--29947 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
29896 TTTATGTTAC
29906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29947 A
1 A
29948 ATAACACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31720 original size:18 final size:18
Alignment explanation
Indices: 31697--31735 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31687 GAAAAAATAT
*
31697 GAAGAAGGAAAGAGGGAG
1 GAAGAAGAAAAGAGGGAG
*
31715 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGAGGGAG
31733 GAA
1 GAA
31736 ATGAGGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.03
Consensus pattern (18 bp):
GAAGAAGAAAAGAGGGAG
Found at i:33053 original size:199 final size:199
Alignment explanation
Indices: 32621--33304 Score: 832
Period size: 199 Copynumber: 3.4 Consensus size: 199
32611 ATATTTTTTC
* * * *
32621 TAAAAGTATC-AACAAAAAAACATTGAAACCAATAATTATAATGTAATAGGTAAATTAACAATGT
1 TAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * **
32685 AACCGGTATAAATATACCGG--TTAATTAGAAAACATGTCAACATAATGTATCGACACTTGTGT-
66 AACCGGTATAAATATACCGGTTTTAA-GAGAAAATAGGTCATCATAATGTATCGACACTAAT-TA
*
32747 AATTTGTGTCGATACTTATTTTCCGTAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGAT
129 AATTTGTGTCGATACTTA-TTTCCATAATGAAT-CCCAAACGAGGTGCACGCATAAAGTGTCGAT
*
32812 ACAATTAT
192 ACATTTAT
* * * *
32820 TAATAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAATATGTAAATTTACAATG
1 TAAAAGTATCGAT-CCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATG
* * *
32884 TAACCGGTATAAATATACTGGTTTTAAGAGAAAATAGGTCATCATAAAGTATCAACACTAATTAA
65 TAACCGGTATAAATATACCGGTTTTAAGAGAAAATAGGTCATCATAATGTATCGACACTAATTAA
* *
32949 ATTTGTGTCGATACATT-TTATCCATAATGAATTCCAAACG-GGTGCACACATAAAGTGTCGATA
130 ATTTGTGTCGATAC-TTATT-TCCATAATGAATCCCAAACGAGGTGCACGCATAAAGTGTCGATA
33012 CATTTAT
193 CATTTAT
* * * *
33019 TAAAAGTATCGATCCTAAAAACATCGAAACCGATAATTACAATGTGATAGGTAAATTTACAATGT
1 TAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * * * * **
33084 ACCCGATAGAAATATACCGGTTTTATGAAAAAATAGGTC-TAAATAATGTATCGATACTCTTTAA
66 AACCGGTATAAATATACCGGTTTTAAGAGAAAATAGGTCAT-CATAATGTATCGACACTAATTAA
* * *
33148 GTTTGTGTCGATACTTGTTTCCAGAATGAATGCCC-AACGAGGTGCACGCATAAAGTGTCGATAC
130 ATTTGTGTCGATACTTATTTCCATAATGAAT-CCCAAACGAGGTGCACGCATAAAGTGTCGATAC
33212 ATTTA-
194 ATTTAT
* * *
33217 -AAATGTTATCGATCCAAAAAACATGGAAACCAATAATTATAATGTAATAGGTAAACTTACAATG
1 TAAAAG-TATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATG
*
33281 TTACCGGTATAAATATACCGGTTT
65 TAACCGGTATAAATATACCGGTTT
33305 ACTTATAAAA
Statistics
Matches: 418, Mismatches: 54, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
197 4 0.01
198 96 0.23
199 184 0.44
200 69 0.17
201 59 0.14
202 6 0.01
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (199 bp):
TAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT
AACCGGTATAAATATACCGGTTTTAAGAGAAAATAGGTCATCATAATGTATCGACACTAATTAAA
TTTGTGTCGATACTTATTTCCATAATGAATCCCAAACGAGGTGCACGCATAAAGTGTCGATACAT
TTAT
Found at i:33456 original size:23 final size:23
Alignment explanation
Indices: 33406--33450 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33396 TGCTTATTTT
* *
33406 ATTATATAATCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
33429 ATTATATAAGCGCTACTTAATA
1 ATTATATAAGCGCTACCTAATA
33451 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:33758 original size:22 final size:22
Alignment explanation
Indices: 33718--33759 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33708 ATTTTACATA
** *
33718 TTTAGTAATCGTTTTATAATAC
1 TTTAGTAATAATTTAATAATAC
33740 TTTAGTAATAATTTAATAAT
1 TTTAGTAATAATTTAATAAT
33760 TATTAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTAGTAATAATTTAATAATAC
Found at i:38279 original size:32 final size:32
Alignment explanation
Indices: 38238--38300 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
38228 TTTCGATGTA
*
38238 TTGATTGAAATTACATGAAAGAAGTTTCCTCC
1 TTGACTGAAATTACATGAAAGAAGTTTCCTCC
38270 TTGACTGAAATTACATGAAAGAAGTTTCCTC
1 TTGACTGAAATTACATGAAAGAAGTTTCCTC
38301 TTTCTTGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGACTGAAATTACATGAAAGAAGTTTCCTCC
Found at i:39443 original size:13 final size:13
Alignment explanation
Indices: 39425--39449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39415 ACAGACGCGT
39425 ATATGAAGACTGC
1 ATATGAAGACTGC
39438 ATATGAAGACTG
1 ATATGAAGACTG
39450 TTCAACTGTG
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:40013 original size:2 final size:2
Alignment explanation
Indices: 40006--40049 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
39996 GACAGACATG
40006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40048 TA
1 TA
40050 CTCTCTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43318 original size:23 final size:22
Alignment explanation
Indices: 43292--43356 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 22
43282 TTAATTATGT
*
43292 AAATAAATTTTTAAATATTATAA
1 AAAT-AATTATTAAATATTATAA
*
43315 AAAT-A-TATTATA-ATTATAA
1 AAATAATTATTAAATATTATAA
*
43334 AAATAATTCTTAAATAATTATAA
1 AAATAATTATTAAAT-ATTATAA
43357 TTATATTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 11 0.32
20 6 0.18
21 6 0.18
23 11 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATTATTAAATATTATAA
Found at i:44071 original size:16 final size:16
Alignment explanation
Indices: 44050--44081 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
44040 TATGAGTAGG
44050 CACAAGTAAAATTTCA
1 CACAAGTAAAATTTCA
44066 CACAAGTAAAATTTCA
1 CACAAGTAAAATTTCA
44082 GGTGGACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
CACAAGTAAAATTTCA
Found at i:45139 original size:36 final size:37
Alignment explanation
Indices: 45099--45183 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 37
45089 CAATTTCAAA
45099 CATTAGTCAATGATTTATAAAG-TACTTATTATTAGT
1 CATTAGTCAATGATTTATAAAGTTACTTATTATTAGT
* * *
45135 CATTAGCCAATGGTTTATAAAGTTATAGTTATTATTAGT
1 CATTAGTCAATGATTTATAAAG-T-TACTTATTATTAGT
45174 CATTA-TCAAT
1 CATTAGTCAAT
45184 CCCTGATTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 20 0.48
38 4 0.10
39 18 0.43
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (37 bp):
CATTAGTCAATGATTTATAAAGTTACTTATTATTAGT
Found at i:46663 original size:42 final size:42
Alignment explanation
Indices: 46604--46718 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
46594 CATTTCGTAA
* *
46604 TAAAGTTCAATGCACCAACCTTATCCCGTATACTTCTCGGAG
1 TAAAGTTCAACGCACCAACCTTATCCCGTATACTTATCGGAG
* *
46646 TAAAGTTTAACGCACCAACCTTATCTCGTATACTTATCGGAG
1 TAAAGTTCAACGCACCAACCTTATCCCGTATACTTATCGGAG
* ** * *
46688 CAAAACTCAATGTACCAACCTTA-CCTCGTAT
1 TAAAGTTCAACGCACCAACCTTATCC-CGTAT
46719 CTCTTATAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 60 0.98
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (42 bp):
TAAAGTTCAACGCACCAACCTTATCCCGTATACTTATCGGAG
Found at i:57816 original size:19 final size:18
Alignment explanation
Indices: 57792--57831 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
57782 AAATGGGGGA
57792 AATGAGGAACGAATTTGGG
1 AATGAGGAACGAA-TTGGG
57811 AATGAGGAACGAATTGGG
1 AATGAGGAACGAATTGGG
57829 AAT
1 AAT
57832 TTAGAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20
Consensus pattern (18 bp):
AATGAGGAACGAATTGGG
Done.