Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000416.1 Hibiscus syriacus cultivar Beakdansim tig00000763_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: 93602
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1327 original size:18 final size:17
Alignment explanation
Indices: 1295--1328 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1285 AAAAAAAGAA
*
1295 AACACAAATTTTGAAAT
1 AACACAAACTTTGAAAT
1312 AACACTAAACTTTGAAA
1 AACAC-AAACTTTGAAA
1329 ACCTTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (17 bp):
AACACAAACTTTGAAAT
Found at i:4274 original size:22 final size:22
Alignment explanation
Indices: 4246--4294 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
4236 AATGTCGTTT
4246 AGTAGGTAGGCGGCGACCGGTG
1 AGTAGGTAGGCGGCGACCGGTG
4268 AGTAGGTAGGCGGCGACCGGTG
1 AGTAGGTAGGCGGCGACCGGTG
4290 AGTAG
1 AGTAG
4295 CTATTCGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.49, T:0.14
Consensus pattern (22 bp):
AGTAGGTAGGCGGCGACCGGTG
Found at i:5320 original size:149 final size:148
Alignment explanation
Indices: 5051--5354 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 148
5041 CGAAGTGCCC
* * *
5051 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAGGACCACGTAGAATTCTTTAAGAATC
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAGGACCACATAGAATTCTTTAAGAATC
*
5116 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTTACACATGTTCCAAAGAATATAC
66 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
5181 ATATGTCCCTAAGAACCG
131 ATATGTCCCTAAGAACCG
*
5199 CGTAGACTTGCACCGTAGTGCCATATAATAATGTTCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCAT-AGGACCACATAGAATTCTTTAAGAAT
5264 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
65 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
5329 CATATGTCCCTAAGAACCG
130 CATATGTCCCTAAGAACCG
5348 CGTAGAC
1 CGTAGAC
5355 CCTCGACTCT
Statistics
Matches: 150, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
148 35 0.23
149 115 0.77
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (148 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAGGACCACATAGAATTCTTTAAGAATC
ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
ATATGTCCCTAAGAACCG
Found at i:6580 original size:21 final size:21
Alignment explanation
Indices: 6556--6600 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6546 TCTTGTTCGT
* *
6556 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6577 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6598 TTG
1 TTG
6601 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9195 original size:86 final size:87
Alignment explanation
Indices: 9001--9214 Score: 371
Period size: 86 Copynumber: 2.5 Consensus size: 87
8991 AAAAATTCCG
9001 AGTCGAAT-AA-ATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
1 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
9064 ATAATATTTCACTTCAAATTCA
66 ATAATATTTCACTTCAAATTCA
* * *
9086 AGTTGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCTAGTGAATCCAC-CTAA
1 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
9150 ATAATATTTCACTTCAAATTCA
66 ATAATATTTCACTTCAAATTCA
*
9172 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATCATAAT
1 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAAT
9215 AGTTATTATT
Statistics
Matches: 122, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
85 7 0.06
86 68 0.56
87 47 0.39
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (87 bp):
AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
ATAATATTTCACTTCAAATTCA
Found at i:14495 original size:6 final size:6
Alignment explanation
Indices: 14466--14504 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
14456 CGAGTGTTCG
* * *
14466 ACATAT ACGTAT ACATAT GCATAT ATATAT ACATAT ACA
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACA
14505 GTGGCACTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:34730 original size:23 final size:23
Alignment explanation
Indices: 34700--34747 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
34690 TTTCCGTCTC
34700 TCTCTAACGTTGTATCGTGTTAA
1 TCTCTAACGTTGTATCGTGTTAA
34723 TCTCTAACGTTGTATCGTGTTAA
1 TCTCTAACGTTGTATCGTGTTAA
34746 TC
1 TC
34748 GAAATCGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.44
Consensus pattern (23 bp):
TCTCTAACGTTGTATCGTGTTAA
Found at i:36054 original size:8 final size:8
Alignment explanation
Indices: 36041--36066 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
36031 TGTTATGTAG
36041 ATTTTGAT
1 ATTTTGAT
36049 ATTTTGAT
1 ATTTTGAT
36057 ATTTTGAT
1 ATTTTGAT
36065 AT
1 AT
36067 ATTCATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATTTTGAT
Found at i:36074 original size:16 final size:16
Alignment explanation
Indices: 36041--36074 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36031 TGTTATGTAG
* *
36041 ATTTTGATATTTTGAT
1 ATTTTGATATATTCAT
36057 ATTTTGATATATTCAT
1 ATTTTGATATATTCAT
36073 AT
1 AT
36075 ATATTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTGATATATTCAT
Found at i:37799 original size:21 final size:21
Alignment explanation
Indices: 37765--37805 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37755 TATAGAAAAT
** *
37765 TGTATTTTTTTTTGGATTTTG
1 TGTATTTTAATTTGAATTTTG
37786 TGTATTTTAATTTGAATTTT
1 TGTATTTTAATTTGAATTTT
37806 AATTTGATCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (21 bp):
TGTATTTTAATTTGAATTTTG
Found at i:38898 original size:22 final size:23
Alignment explanation
Indices: 38873--38918 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
38863 CGAAGCCATT
38873 TGGATATACAA-TCCGAATGATA
1 TGGATATACAATTCCGAATGATA
38895 TGGATATACAATTCCGAATGATA
1 TGGATATACAATTCCGAATGATA
38918 T
1 T
38919 CGACTTCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (23 bp):
TGGATATACAATTCCGAATGATA
Found at i:39782 original size:28 final size:28
Alignment explanation
Indices: 39725--39787 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
39715 AATAATATTA
*
39725 ATAAAAAATGAAAAAAAAATATATATAT
1 ATAAAAAATGAAAAAAAAATATATAAAT
*
39753 ATAAAACAATGTAAAAATAAATA-A-AAAT
1 ATAAAA-AATG-AAAAAAAAATATATAAAT
*
39781 ATTAAAA
1 ATAAAAA
39788 TTAGGAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.03
28 14 0.47
29 5 0.17
30 10 0.33
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (28 bp):
ATAAAAAATGAAAAAAAAATATATAAAT
Found at i:40149 original size:34 final size:33
Alignment explanation
Indices: 40111--40197 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
40101 AGTTTTACTT
40111 GGACTCAAA-ATGCTTCGGTTTTAGTGTTTCAATA
1 GGACTCAAATATG-TT-GGTTTTAGTGTTTCAATA
*
40145 GGACTTAAATATGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
* *
40178 GGACTCAATTAAGTTGGTTT
1 GGACTCAAATATGTTGGTTT
40198 ATTTTCTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
33 35 0.73
34 10 0.21
35 3 0.06
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.41
Consensus pattern (33 bp):
GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
Found at i:40258 original size:8 final size:8
Alignment explanation
Indices: 40245--40313 Score: 56
Period size: 8 Copynumber: 8.6 Consensus size: 8
40235 GGGGCCTACA
40245 AAAATAAT
1 AAAATAAT
40253 AAAATAA-
1 AAAATAAT
40260 AAATATAAT
1 AAA-ATAAT
40269 AATAATAAT
1 AA-AATAAT
*
40278 AATA-AAT
1 AAAATAAT
40285 -AAATAA-
1 AAAATAAT
40291 ATAAATATAT
1 A-AAATA-AT
*
40301 AATATAAT
1 AAAATAAT
40309 AAAAT
1 AAAAT
40314 GTTTTTGTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
6 2 0.04
7 8 0.16
8 23 0.47
9 14 0.29
10 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATAAT
Found at i:40270 original size:3 final size:3
Alignment explanation
Indices: 40247--40310 Score: 53
Period size: 3 Copynumber: 20.7 Consensus size: 3
40237 GGCCTACAAA
*
40247 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT
40293 AAAT ATAT AAT -AT AAT AA
1 -AAT A-AT AAT AAT AAT AA
40311 AATGTTTTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 6 0.11
3 30 0.56
4 18 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40796 original size:84 final size:84
Alignment explanation
Indices: 40656--41637 Score: 940
Period size: 84 Copynumber: 11.8 Consensus size: 84
40646 CTGAATGAAA
* * * * * * * *
40656 TCGAACTCGAAGGTC-TT-TAG-CAGATATCTCTTCTTGCCTTGAGCTATGCTGCAAATGATGGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGAT-GT
* * * *
40718 TCCTTTG-AGCTGAGTGGAG
65 GCCTTCGAAGCTGAGCGTAG
* * * *
40737 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCCGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* * * *
40802 CCCTCGAAGTTGAGTGTAA
66 CCTTCGAAGCTGAGCGTAG
* * * * *
40821 TCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* *
40883 CCTT-GGAGTTGAGCGTAG
66 CCTTCGAAGCTGAGCGTAG
* * * * *
40901 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTATGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
*
40966 GCCTT-GGAGCTGAGCGTAG
65 GCCTTCGAAGCTGAGCGTAG
* * * * * * *
40985 TCGAAATCGAAGGTCTTTAGGTCACAGATAACCCTTCTAGTCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
41050 GCCCTCGAAGCTGAGTGTAA
65 GCCTTCGAAGCTGAGCGTAG
* * * * *
41070 TCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
*
41132 CCTT-GGAGCTGAGCGTAG
66 CCTTCGAAGCTGAGCGTAG
* * *
41150 TCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
41215 GCCTT-GAAGCTGAGCGTAG
65 GCCTTCGAAGCTGAGCGTAG
* * * * * * *
41234 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGCTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
41299 GCCCTCGAAGCTGAGTGTAA
65 GCCTTCGAAGCTGAGCGTAG
* * * * *
41319 TCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
*
41381 CCTTAG-AGCTGAGCGTAG
66 CCTTCGAAGCTGAGCGTAG
* * *
41399 TCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
41464 GCCTT-GAAGCTGAGCGTAG
65 GCCTTCGAAGCTGAGCGTAG
* * * * * ** *
41483 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATAATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
41548 GCCCTCGAAGCTGAGTGTAA
65 GCCTTCGAAGCTGAGCGTAG
* * * ** ** * *
41568 TCGAACTCGAGGGTCTTCGGTTGGCAGATAACCCTTCTTAACTTAAGTTATATTGCAAATGATAT
1 TCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
41633 GCCTT
65 GCCTT
41638 GGAGTTGTGT
Statistics
Matches: 744, Mismatches: 134, Indels: 42
0.81 0.15 0.05
Matches are distributed among these distances:
80 81 0.11
81 131 0.18
82 3 0.00
83 12 0.02
84 392 0.53
85 125 0.17
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
CCTTCGAAGCTGAGCGTAG
Found at i:41114 original size:249 final size:249
Alignment explanation
Indices: 40700--41641 Score: 1519
Period size: 249 Copynumber: 3.8 Consensus size: 249
40690 TGCCTTGAGC
* * * * * *
40700 TATGCTGCAAATGATGGTTCCTTTG-AGCTGAGTGGAGTCGAACTCGAAGGTC-TTTGTTGACAG
1 TATGCTGCAAATGAT-ATGCC-TTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
* *
40763 ATAACCCTTCTAGCCTTGAGTTATGCCGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACT
64 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * *
40828 CGAGGGTCTTTGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTT
129 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCT
* * *
40893 GAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTATGT
194 GAGCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGT
* * *
40949 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGGTCACAGAT
1 TATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
* *
41014 AACCCTTCTAGTCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
41079 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGA
131 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGA
41144 GCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGT
196 GCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGT
*
41198 TATGCTGTAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
1 TATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
* *
41263 AACCCTTCTAGCCTTGAGCTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
*
41328 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGA
131 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGA
41393 GCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGT
196 GCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGT
*
41447 TATGCTGTAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
1 TATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
** *
41512 AACCCTTCTAGCCTTGAGTTATATTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* ** * * *
41577 AGGGTCTTCGGTTGGCAGATAACCCTTCTTAACTTAAGTTATATTGCAAATGATATGCCTTGGAG
131 AGGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAG
41642 TTGTGTTGAA
Statistics
Matches: 650, Mismatches: 37, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
247 3 0.00
248 27 0.04
249 572 0.88
250 1 0.00
253 47 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (249 bp):
TATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGA
GCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGT
Found at i:41993 original size:110 final size:110
Alignment explanation
Indices: 41784--42429 Score: 967
Period size: 110 Copynumber: 5.9 Consensus size: 110
41774 TTGTGCAGTT
* * *
41784 TCGAGGCCAATATCATTCGCCGTGAAGTTGAAATTGACTC----TGAAACTGGAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
** * * *
41845 TGACAACCAGTCGCCCCTCCGCTGTGAAGTTGAACTTGTGTTATC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
41890 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTTTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
41955 TGACAGTCAATCACCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
42000 TCGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * *
42065 TGACACTCAGACGCCCATTCGCTATGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
42110 TCGAGTCCAATATCATTCGCTGTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
42175 TGACAGTCAGCCTCCCATTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
42220 TCAAGTCCAATATCATTCGCTGTAAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
42285 TGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGTTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
42330 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATCGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
42395 TGACCGTCAGTCGTCCCTTCGCTGTGAAGTTGAGC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
42430 AACCACCATC
Statistics
Matches: 487, Mismatches: 49, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
106 37 0.08
110 450 0.92
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (110 bp):
TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:46421 original size:33 final size:33
Alignment explanation
Indices: 46384--46454 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
46374 AAAATGCTTC
* *
46384 AGTTTTAGTGTTTCAATAGGACCCAAATATGTT
1 AGTTTTAATGTTTCAATAGGACCCAAATACGTT
*
46417 AGTTTTAATGTTTCAATAGGACTCAAATACGTT
1 AGTTTTAATGTTTCAATAGGACCCAAATACGTT
*
46450 GGTTT
1 AGTTT
46455 ATTTTCTAAA
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:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (33 bp):
AGTTTTAATGTTTCAATAGGACCCAAATACGTT
Found at i:46515 original size:8 final size:8
Alignment explanation
Indices: 46502--46575 Score: 71
Period size: 9 Copynumber: 8.8 Consensus size: 8
46492 GGGGCCTGCA
46502 AAAATAAT
1 AAAATAAT
46510 AAAATAA-
1 AAAATAAT
46517 AAATATAAT
1 AAA-ATAAT
46526 AATAATAAT
1 AA-AATAAT
46535 AATAATAA-
1 AA-AATAAT
46543 ATAAATAAAT
1 A-AAAT-AAT
46553 AAAATATAT
1 AAAATA-AT
*
46562 AATATAAT
1 AAAATAAT
46570 AAAATA
1 AAAATA
46576 GTTTTATAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
7 3 0.05
8 23 0.40
9 29 0.51
10 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:46527 original size:3 final size:3
Alignment explanation
Indices: 46504--46575 Score: 64
Period size: 3 Copynumber: 24.3 Consensus size: 3
46494 GGCCTGCAAA
*
46504 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT
46549 AAAT AA- AAT ATAT AAT -AT AAT AA- AAT A
1 -AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
46576 GTTTTATAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 10 0.17
3 36 0.60
4 14 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:46538 original size:17 final size:16
Alignment explanation
Indices: 46505--46575 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
46495 GCCTGCAAAA
*
46505 ATAATAAAATAAAAAT
1 ATAATAAAATAATAAT
46521 ATAAT--AATAATAAT
1 ATAATAAAATAATAAT
46535 AATAAT-AAAT-A-AAT
1 -ATAATAAAATAATAAT
46549 A-AATAAAATATATAAT
1 ATAATAAAATA-ATAAT
46565 ATAATAAAATA
1 ATAATAAAATA
46576 GTTTTATAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
12 3 0.06
13 5 0.11
14 11 0.23
15 7 0.15
16 12 0.26
17 9 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATAAAATAATAAT
Found at i:46554 original size:38 final size:37
Alignment explanation
Indices: 46503--46575 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 37
46493 GGGCCTGCAA
46503 AAATAATAAAATAAAA-ATATAATAATAATAATAATAAT
1 AAATAATAAAATAAAATATATAAT-ATAATAA-AATAAT
46541 AAATAA-ATAAATAAAATATATAATATAATAAAATA
1 AAATAATA-AAATAAAATATATAATATAATAAAATA
46576 GTTTTATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
37 5 0.15
38 21 0.64
39 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (37 bp):
AAATAATAAAATAAAATATATAATATAATAAAATAAT
Found at i:46761 original size:42 final size:41
Alignment explanation
Indices: 46690--46774 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 41
46680 AGATTGGGGT
* *
46690 AATGCTTGGGGTTTTCTTTAGGTGAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
46731 AATGCTTAGGGTTTTGCTTTAGGTAAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTT-CTTTAGGTAAAGGCAACTTCCATACG
46773 AA
1 AA
46775 GCGATGGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 14 0.34
42 27 0.66
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (41 bp):
AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
Found at i:49178 original size:2 final size:2
Alignment explanation
Indices: 49173--49221 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
49163 AAAAGAGAAT
49173 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
49215 TA TA TA T
1 TA TA TA T
49222 TAGGTCAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58715 original size:21 final size:21
Alignment explanation
Indices: 58686--58855 Score: 132
Period size: 21 Copynumber: 8.3 Consensus size: 21
58676 CAACTCAGTT
*
58686 TCCAAATTCACGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
**
58707 TCGGAATTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* * **
58728 TCCAAAAT--CATTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
*
58747 TCTAAATTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* **
58768 TCCGAATTCGCGTTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
** * *
58789 TCTGAATTCGTGTTACGATAG
1 TCCAAATTCGCGTTGCGATAG
* * **
58810 TCCAAAAT--CATTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
*
58829 TCTAAATTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
58850 TCCAAA
1 TCCAAA
58856 ATCATTGCGA
Statistics
Matches: 108, Mismatches: 37, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
19 26 0.24
21 82 0.76
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (21 bp):
TCCAAATTCGCGTTGCGATAG
Found at i:58743 original size:40 final size:40
Alignment explanation
Indices: 58711--58877 Score: 262
Period size: 40 Copynumber: 4.1 Consensus size: 40
58701 CGATAGTCGG
58711 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
* * * *
58751 AATTCGCGTTGCGATAGTCCGAATTCGCGTTGCGATTTTCTG
1 AATTCGCGTTGCGATAGTCCAAAAT--CATTGCGATTTTCTA
* *
58793 AATTCGTGTTACGATAGTCCAAAATCATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
58833 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
58873 AATTC
1 AATTC
58878 ACGACCACGA
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 79 0.70
42 34 0.30
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (40 bp):
AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
Found at i:58761 original size:61 final size:60
Alignment explanation
Indices: 58684--58877 Score: 183
Period size: 61 Copynumber: 3.2 Consensus size: 60
58674 CACAACTCAG
*
58684 TTTCCAAATTCACGTTGCGATAGTCGGAATTCGCGTTGCGATAGTCCAAAATCATTGCGAT
1 TTTCCAAATTC-CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGAT
* ** ** * * *
58745 TTTCTAAATTCGCGTTGCGATAGTCCGAATTCGCGTTGCGATTTTCTGAATTCGTGTTACGAT
1 TTTCCAAATTC-CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATC--ATTGCGAT
** * * ** **
58808 AGTCCAAAAT-CATTGCGATTTTCTAAATTCGCGTTGCGATAGTCCAAAATCATTGCGAT
1 TTTCCAAATTCCGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGAT
*
58867 TTTCTAAATTC
1 TTTCCAAATTC
58878 ACGACCACGA
Statistics
Matches: 100, Mismatches: 30, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
59 12 0.12
61 76 0.76
63 12 0.12
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (60 bp):
TTTCCAAATTCCGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGAT
Found at i:58784 original size:82 final size:82
Alignment explanation
Indices: 58690--58852 Score: 272
Period size: 82 Copynumber: 2.0 Consensus size: 82
58680 TCAGTTTCCA
*
58690 AATTCACGTTGCGATAGTCGGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTAAATT
1 AATTCACGTTGCGATAGTCGGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
58755 CGCGTTGCGATAGTCCG
66 CGCGTTGCGATAGTCCG
* ** * *
58772 AATTCGCGTTGCGATTTTCTGAATTCGTGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
1 AATTCACGTTGCGATAGTCGGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
58837 CGCGTTGCGATAGTCC
66 CGCGTTGCGATAGTCC
58853 AAAATCATTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (82 bp):
AATTCACGTTGCGATAGTCGGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
CGCGTTGCGATAGTCCG
Found at i:58865 original size:19 final size:19
Alignment explanation
Indices: 58804--58866 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
58794 ATTCGTGTTA
58804 CGATAGTCCAAAATCATTG
1 CGATAGTCCAAAATCATTG
** * * *
58823 CGATTTTCTAAATTCGCGTTG
1 CGATAGTCCAAAAT--CATTG
58844 CGATAGTCCAAAATCATTG
1 CGATAGTCCAAAATCATTG
58863 CGAT
1 CGAT
58867 TTTCTAAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (19 bp):
CGATAGTCCAAAATCATTG
Found at i:59717 original size:21 final size:21
Alignment explanation
Indices: 59691--59823 Score: 142
Period size: 21 Copynumber: 6.3 Consensus size: 21
59681 ATTTTGGACT
*
59691 ATCGCAACGCGAATTCGGAAA
1 ATCGCAACGCGAATTCAGAAA
* ** **
59712 ATCGCAACGTGAATTTGGACT
1 ATCGCAACGCGAATTCAGAAA
* * *
59733 ATCGCAATGCAAATTTAGAAA
1 ATCGCAACGCGAATTCAGAAA
59754 ATCG-AAGCGCGAATTCAGAAA
1 ATCGCAA-CGCGAATTCAGAAA
* **
59775 ATCGCAGCGCGAATTCAGACT
1 ATCGCAACGCGAATTCAGAAA
59796 ATCGCAACGCGAATTCAGAAA
1 ATCGCAACGCGAATTCAGAAA
59817 ATCGCAA
1 ATCGCAA
59824 TGATTTTGGA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
20 2 0.02
21 88 0.97
22 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAATTCAGAAA
Found at i:59775 original size:63 final size:63
Alignment explanation
Indices: 59698--59820 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 63
59688 ACTATCGCAA
* * ** * *
59698 CGCGAATTCGGAAAATCGCAACGTGAATTTGGACTATCGCAATGCAAATTTAGAAAATCGAAG
1 CGCGAATTCAGAAAATCGCAACGCGAATTCAGACTATCGCAACGCAAATTCAGAAAATCGAAG
* *
59761 CGCGAATTCAGAAAATCGCAGCGCGAATTCAGACTATCGCAACGCGAATTCAGAAAATCG
1 CGCGAATTCAGAAAATCGCAACGCGAATTCAGACTATCGCAACGCAAATTCAGAAAATCG
59821 CAATGATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (63 bp):
CGCGAATTCAGAAAATCGCAACGCGAATTCAGACTATCGCAACGCAAATTCAGAAAATCGAAG
Found at i:65307 original size:44 final size:42
Alignment explanation
Indices: 65220--65370 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 42
65210 TGAGAAATTT
*
65220 ATCGA-ATTGAAAAAAATTAGGGGCATTAATCGTAAAGGTAAAA
1 ATCGATATTG-AAAAAATTAGGGGC-TTAATTGTAAAGGTAAAA
*
65263 ATCGATATTGAAAAAATTAGGGGTCTCAATTGTAAAGGTAAAAA
1 ATCGATATTGAAAAAATTAGGGG-CTTAATTGTAAAGGT-AAAA
* * * * *
65307 AT-AAGATTGAAAAAATTTTGGGGCCTTAATTATAAAAGTAAAA
1 ATCGATATTGAAAAAA-TTAGGGG-CTTAATTGTAAAGGTAAAA
*
65350 ATTG-TGATTGAAAAAATTAGG
1 ATCGAT-ATTGAAAAAATTAGG
65371 AGCGTTATAA
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
43 51 0.57
44 39 0.43
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (42 bp):
ATCGATATTGAAAAAATTAGGGGCTTAATTGTAAAGGTAAAA
Found at i:65531 original size:13 final size:14
Alignment explanation
Indices: 65511--65538 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
65501 ATTATAAAGG
65511 TAAAAAAATAAGAT
1 TAAAAAAATAAGAT
65525 TAAAAAAATAAGAT
1 TAAAAAAATAAGAT
65539 CCAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (14 bp):
TAAAAAAATAAGAT
Found at i:65641 original size:44 final size:45
Alignment explanation
Indices: 65541--65643 Score: 106
Period size: 44 Copynumber: 2.3 Consensus size: 45
65531 AATAAGATCC
*
65541 AATTAAAAAAATAAATTAAAGGTATCAATTATAAAAATAAAAAACTA
1 AATTAAAAAAAT-AATTAAAGGCATCAATTATAAAAATAAAAAAC-A
* * * *
65588 GATT--TAAAATAGTTAGAA-GCATCAATTATAAAGATAAAAAA-A
1 AATTAAAAAAATAATTA-AAGGCATCAATTATAAAAATAAAAAACA
65630 AATTAAAAAAATAA
1 AATTAAAAAAATAA
65644 GACCTATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
42 4 0.09
44 31 0.69
45 7 0.16
47 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (45 bp):
AATTAAAAAAATAATTAAAGGCATCAATTATAAAAATAAAAAACA
Found at i:77470 original size:23 final size:23
Alignment explanation
Indices: 77444--77493 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
77434 GTTTGTATTT
77444 GTTCCTGCATTAAGTTAGCTTTG
1 GTTCCTGCATTAAGTTAGCTTTG
77467 GTTCCTGCATTAAGTTAGCTTTG
1 GTTCCTGCATTAAGTTAGCTTTG
77490 GTTC
1 GTTC
77494 TTTAAGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (23 bp):
GTTCCTGCATTAAGTTAGCTTTG
Found at i:77500 original size:19 final size:21
Alignment explanation
Indices: 77452--77501 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
77442 TTGTTCCTGC
77452 ATTAAGTTAGCTTTGGTTCCT
1 ATTAAGTTAGCTTTGGTTCCT
77473 GCATTAAGTTAGCTTTGGTT-CT
1 --ATTAAGTTAGCTTTGGTTCCT
77495 -TTAAGTT
1 ATTAAGTT
77502 GCTGATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.26
22 2 0.07
23 18 0.67
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (21 bp):
ATTAAGTTAGCTTTGGTTCCT
Found at i:86686 original size:15 final size:15
Alignment explanation
Indices: 86666--86694 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
86656 CATATAAAGT
86666 TAATGTTAATGTCAC
1 TAATGTTAATGTCAC
86681 TAATGTTAATGTCA
1 TAATGTTAATGTCA
86695 AATAATTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (15 bp):
TAATGTTAATGTCAC
Found at i:93136 original size:16 final size:16
Alignment explanation
Indices: 93103--93132 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
93093 CATTTAGTAC
93103 TTCAATTTACATTTTA
1 TTCAATTTACATTTTA
93119 TTCAATTTA-ATTTT
1 TTCAATTTACATTTT
93133 TATTGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (16 bp):
TTCAATTTACATTTTA
Done.