Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009109.1 Hibiscus syriacus cultivar Beakdansim tig00112579_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: 85113
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2575 original size:31 final size:31
Alignment explanation
Indices: 2528--2588 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2518 TGCCAAAACG
* *
2528 TAAAATGATAATGTAAGTGACAAAAACTTAA
1 TAAAATAATAACGTAAGTGACAAAAACTTAA
*
2559 TAAAATAATAACGTAAGTGACCAAAACTTA
1 TAAAATAATAACGTAAGTGACAAAAACTTA
2589 TACTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (31 bp):
TAAAATAATAACGTAAGTGACAAAAACTTAA
Found at i:2821 original size:31 final size:32
Alignment explanation
Indices: 2744--2821 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
2734 GTTAACCTTC
* * **
2744 AGTG-ACCACATCTTAATTAAAACTAAATGAA
1 AGTGAACCAAATCTTAATTAAAACAAAACAAA
**
2775 AGTGAAAAAAATCTTAATTAAAACAAAACAAA
1 AGTGAACCAAATCTTAATTAAAACAAAACAAA
2807 AGT-AACCAAATCTTA
1 AGTGAACCAAATCTTA
2822 TGTTTTTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.23
Consensus pattern (32 bp):
AGTGAACCAAATCTTAATTAAAACAAAACAAA
Found at i:3256 original size:32 final size:32
Alignment explanation
Indices: 3195--3291 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 32
3185 ATCCGAACCA
* * *
3195 AAAT-TAACCCGAACGAAAACAAACCGAATCG
1 AAATATAACCCGAACCAAAACAATCTGAATCG
**
3226 AAA-ATAACTTGAACCAAAAACAATCTGAATC-
1 AAATATAACCCGAACC-AAAACAATCTGAATCG
* **
3257 AAATTTAACCCGAACCAAATTAATCTGAATCG
1 AAATATAACCCGAACCAAAACAATCTGAATCG
3289 AAA
1 AAA
3292 GCAATATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
31 27 0.52
32 25 0.48
ACGTcount: A:0.52, C:0.22, G:0.09, T:0.18
Consensus pattern (32 bp):
AAATATAACCCGAACCAAAACAATCTGAATCG
Found at i:17969 original size:19 final size:19
Alignment explanation
Indices: 17945--17986 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
17935 CCCCCTTTGA
*
17945 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
*
17964 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATACCCCCT
17983 -GGGG
1 AGGGG
17987 TTCTGGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:20280 original size:30 final size:30
Alignment explanation
Indices: 20244--20305 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
20234 TAAATGAGAG
*
20244 AAGTGTTAAAGT-AAGGGGAAGTAATTTTTC
1 AAGTGTTAAAGTAAAAGGG-AGTAATTTTTC
20274 AAGTGTTAAAGTAAAAGGGAGTAATTTTTC
1 AAGTGTTAAAGTAAAAGGGAGTAATTTTTC
20304 AA
1 AA
20306 AAACGTCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.32
Consensus pattern (30 bp):
AAGTGTTAAAGTAAAAGGGAGTAATTTTTC
Found at i:25150 original size:70 final size:70
Alignment explanation
Indices: 25034--25166 Score: 212
Period size: 70 Copynumber: 1.9 Consensus size: 70
25024 AAGAGCATAT
* *
25034 AAGAGCAAAAATAGGAGAACAAAACAATCACACATGACTAAAAAACATAGAAGAGCATCCCAAAA
1 AAGAGCAAAAATAGGAGAACAAAACAATCACACAAGACTAAAAAACATAGAAGAACATCCCAAAA
25099 GTCTA
66 GTCTA
* * * *
25104 AAGAGTAAAAATAGGAGAACAAAACAATCCCACAAGGCTAAGAAACATAGAAGAACATCCCAA
1 AAGAGCAAAAATAGGAGAACAAAACAATCACACAAGACTAAAAAACATAGAAGAACATCCCAA
25167 CTGATTTCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 57 1.00
ACGTcount: A:0.56, C:0.19, G:0.15, T:0.11
Consensus pattern (70 bp):
AAGAGCAAAAATAGGAGAACAAAACAATCACACAAGACTAAAAAACATAGAAGAACATCCCAAAA
GTCTA
Found at i:25320 original size:16 final size:16
Alignment explanation
Indices: 25296--25327 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25286 TCTGAAATTG
*
25296 TTTTGAGTTCGAGTTT
1 TTTTAAGTTCGAGTTT
25312 TTTTAAGTTCGAGTTT
1 TTTTAAGTTCGAGTTT
25328 CAATATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.56
Consensus pattern (16 bp):
TTTTAAGTTCGAGTTT
Found at i:26592 original size:81 final size:80
Alignment explanation
Indices: 26437--26597 Score: 259
Period size: 81 Copynumber: 2.0 Consensus size: 80
26427 ATATCAAAGG
* *
26437 TATAGTGCTTGAAAAATTTAGATACCAAATCAATTAAAAATATAAATATCACGTTTATAAGAAAA
1 TATAGTGCTTGAAAAATATAGATACCAAATCAATTAAAAATATAAACATCACGTTTATAAGAAAA
26502 ATCAAATACCAAATA
66 ATCAAATACCAAATA
* ** *
26517 TATAGTGTTTGAAAAATATAGATATTAAATCAATTAAAAAATATAAACATGACGTTTATAAGAAA
1 TATAGTGCTTGAAAAATATAGATACCAAATCAATT-AAAAATATAAACATCACGTTTATAAGAAA
26582 AATCAAATACCAAATA
65 AATCAAATACCAAATA
26598 ATAAACTATA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
80 31 0.42
81 43 0.58
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.29
Consensus pattern (80 bp):
TATAGTGCTTGAAAAATATAGATACCAAATCAATTAAAAATATAAACATCACGTTTATAAGAAAA
ATCAAATACCAAATA
Found at i:27367 original size:18 final size:18
Alignment explanation
Indices: 27339--27377 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
27329 GGTTTTTAGA
*
27339 TTTAGGATTTTGAGACTTT
1 TTTAGGATTTT-AGAATTT
27358 TTTA-GATTTTAGAATTT
1 TTTAGGATTTTAGAATTT
27375 TTT
1 TTT
27378 TAGACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (18 bp):
TTTAGGATTTTAGAATTT
Found at i:38044 original size:22 final size:24
Alignment explanation
Indices: 38019--38068 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
38009 ACGTCATAAT
38019 TATTTAAAAA-ATTAAAT-AAAAA
1 TATTTAAAAATATTAAATAAAAAA
*
38041 TA-TTAAAAATATTTAATAAAAAA
1 TATTTAAAAATATTAAATAAAAAA
38064 TATTT
1 TATTT
38069 TTTATATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 8 0.33
23 7 0.29
24 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TATTTAAAAATATTAAATAAAAAA
Found at i:38062 original size:23 final size:21
Alignment explanation
Indices: 38022--38067 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
38012 TCATAATTAT
38022 TTAAAAAATTAAATAAAAATA
1 TTAAAAAATTAAATAAAAATA
*
38043 TTAAAAATATTTAATAAAAAATA
1 TTAAAAA-ATTAAAT-AAAAATA
38066 TT
1 TT
38068 TTTTATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 6 0.27
23 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAAAAATTAAATAAAAATA
Found at i:38506 original size:13 final size:13
Alignment explanation
Indices: 38488--38514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38478 TTCACTTCAA
38488 TCAAGCTCGAATT
1 TCAAGCTCGAATT
38501 TCAAGCTCGAATT
1 TCAAGCTCGAATT
38514 T
1 T
38515 TAGGCTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (13 bp):
TCAAGCTCGAATT
Found at i:38567 original size:16 final size:16
Alignment explanation
Indices: 38548--38584 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
38538 TTTTTTTGAG
38548 TTCAACCCTTTTCGAA
1 TTCAACCCTTTTCGAA
*
38564 TTCAACCCTTTTCGAG
1 TTCAACCCTTTTCGAA
38580 TTCAA
1 TTCAA
38585 GTTTCAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.30, G:0.08, T:0.38
Consensus pattern (16 bp):
TTCAACCCTTTTCGAA
Found at i:46884 original size:71 final size:71
Alignment explanation
Indices: 46768--46902 Score: 270
Period size: 71 Copynumber: 1.9 Consensus size: 71
46758 CTTATCCTAA
46768 ATTTAATTATAAACATTTATAATATATAGAGTAAAGTATATAAATAGTATATGAACTTTTAGTAA
1 ATTTAATTATAAACATTTATAATATATAGAGTAAAGTATATAAATAGTATATGAACTTTTAGTAA
46833 GCTTGC
66 GCTTGC
46839 ATTTAATTATAAACATTTATAATATATAGAGTAAAGTATATAAATAGTATATGAACTTTTAGTA
1 ATTTAATTATAAACATTTATAATATATAGAGTAAAGTATATAAATAGTATATGAACTTTTAGTA
46903 CATTTACATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.40
Consensus pattern (71 bp):
ATTTAATTATAAACATTTATAATATATAGAGTAAAGTATATAAATAGTATATGAACTTTTAGTAA
GCTTGC
Found at i:47025 original size:3 final size:3
Alignment explanation
Indices: 47017--47153 Score: 274
Period size: 3 Copynumber: 45.7 Consensus size: 3
47007 TGACGTGACA
47017 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
47065 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
47113 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
47154 AACTCAAACC
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 134 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:61990 original size:2 final size:2
Alignment explanation
Indices: 61985--62040 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
61975 AAAAAATACA
61985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62027 -T AT AT -T AT AT -T AT A
1 AT AT AT AT AT AT AT AT A
62041 AACGTAAGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:64148 original size:17 final size:18
Alignment explanation
Indices: 64116--64149 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
64106 TTTATATTTT
64116 AATATCTTTAAAAATTAC
1 AATATCTTTAAAAATTAC
*
64134 AATAT-TTTGAAAATTA
1 AATATCTTTAAAAATTA
64150 ATATAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (18 bp):
AATATCTTTAAAAATTAC
Found at i:64805 original size:14 final size:15
Alignment explanation
Indices: 64775--64807 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
64765 CGATGTGTAG
64775 TTAAAATATGATTAAA
1 TTAAAATAT-ATTAAA
64791 TTAAAATAT-TTAAA
1 TTAAAATATATTAAA
64805 TTA
1 TTA
64808 TTAATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTAAAATATATTAAA
Found at i:65253 original size:41 final size:41
Alignment explanation
Indices: 65202--65288 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
65192 CGCAAATTCA
*
65202 CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
*
65243 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
*
65284 TGTTG
1 CGTTG
65289 AAAAAAAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
Found at i:65268 original size:22 final size:22
Alignment explanation
Indices: 65202--65273 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
65192 CGCAAATTCA
65202 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
65224 CGTTGC-A-ATTTTTCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
65243 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
65265 CGTTGCGAT
1 CGTTGCGAT
65274 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 7 0.19
22 16 0.43
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:65388 original size:5 final size:5
Alignment explanation
Indices: 65366--65472 Score: 161
Period size: 5 Copynumber: 22.0 Consensus size: 5
65356 CACGTATTAC
65366 CACGA CCACGA CCACGA CACGA CAC-A CACGA CACGA CAC-A CACGA CACGA
1 CACGA -CACGA -CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
65416 CAC-A CACGA CACGA CACGA CAC-A CACGA CACGA CACGA CAC-A CACGA
1 CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
65463 CACGA CACGA
1 CACGA CACGA
65473 GACGGACGAC
Statistics
Matches: 96, Mismatches: 0, Indels: 11
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.21
5 65 0.68
6 11 0.11
ACGTcount: A:0.41, C:0.43, G:0.16, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:65397 original size:14 final size:15
Alignment explanation
Indices: 65366--65472 Score: 161
Period size: 14 Copynumber: 7.3 Consensus size: 15
65356 CACGTATTAC
65366 CACGACCACGACCACGA
1 CACGA-CACGA-CACGA
65383 CACGACAC-ACACGA
1 CACGACACGACACGA
65397 CACGACAC-ACACGA
1 CACGACACGACACGA
65411 CACGACAC-ACACGA
1 CACGACACGACACGA
65425 CACGACACGACAC-A
1 CACGACACGACACGA
65439 CACGACACGACACGA
1 CACGACACGACACGA
65454 CAC-ACACGACACGA
1 CACGACACGACACGA
65468 CACGA
1 CACGA
65473 GACGGACGAC
Statistics
Matches: 87, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
14 69 0.79
15 10 0.11
16 3 0.03
17 5 0.06
ACGTcount: A:0.41, C:0.43, G:0.16, T:0.00
Consensus pattern (15 bp):
CACGACACGACACGA
Found at i:65482 original size:19 final size:19
Alignment explanation
Indices: 65366--65472 Score: 164
Period size: 19 Copynumber: 5.5 Consensus size: 19
65356 CACGTATTAC
65366 CACGACCACGACCACGACACGA
1 CACGA-CACGA-CAC-ACACGA
65388 CAC-ACACGACACGACAC-A
1 CACGACACGACAC-ACACGA
65406 CACGACACGACACACACGA
1 CACGACACGACACACACGA
65425 CACGACACGACACACACGA
1 CACGACACGACACACACGA
65444 CACGACACGACACACACGA
1 CACGACACGACACACACGA
65463 CACGACACGA
1 CACGACACGA
65473 GACGGACGAC
Statistics
Matches: 83, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.10
19 66 0.80
20 5 0.06
21 1 0.01
22 3 0.04
ACGTcount: A:0.41, C:0.43, G:0.16, T:0.00
Consensus pattern (19 bp):
CACGACACGACACACACGA
Found at i:65975 original size:5 final size:5
Alignment explanation
Indices: 65953--66071 Score: 130
Period size: 5 Copynumber: 22.0 Consensus size: 5
65943 CGCCGCCGTC
* * *
65953 TCGTG TCGTC TCGGG TCGTG TCGTG TCGGG TCGTGG TCGTG TCGTGG TCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGT-G TCGTG TCGT-G TCGTG
66005 TCGTG TCGTGG TCGTG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG TCGTG
1 TCGTG TCGT-G TCGTG TCGT-G TCGT-G TCGT-G TCGT-G TCGTG TCGTG
66055 TCGTGG TCGTGG TCGTG
1 TCGT-G TCGT-G TCGTG
66072 GTAATACGTG
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
5 54 0.52
6 49 0.48
ACGTcount: A:0.00, C:0.19, G:0.45, T:0.35
Consensus pattern (5 bp):
TCGTG
Found at i:65992 original size:6 final size:6
Alignment explanation
Indices: 65966--66073 Score: 153
Period size: 6 Copynumber: 19.5 Consensus size: 6
65956 TGTCGTCTCG
65966 GGTCGT -GTCGT -GTCG- GGTCGT GGTCGT -GTCGT GGTCGT -GTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
66009 -GTCGT GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCGT -GTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
66054 -GTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
66074 AATACGTGTC
Statistics
Matches: 96, Mismatches: 0, Indels: 12
0.89 0.00 0.11
Matches are distributed among these distances:
5 43 0.45
6 53 0.55
ACGTcount: A:0.00, C:0.18, G:0.47, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:65996 original size:11 final size:11
Alignment explanation
Indices: 65953--66071 Score: 142
Period size: 11 Copynumber: 11.0 Consensus size: 11
65943 CGCCGCCGTC
*
65953 TCGT-GTCGTC
1 TCGTGGTCGTG
65963 TCG-GGTCGTG
1 TCGTGGTCGTG
*
65973 TCGT-GTCGGG
1 TCGTGGTCGTG
65983 TCGTGGTCGTG
1 TCGTGGTCGTG
65994 TCGTGGTCGTG
1 TCGTGGTCGTG
66005 TCGT-GTCGTGG
1 TCGTGGTCGT-G
66016 TCGT-GTCGTGG
1 TCGTGGTCGT-G
66027 TCGTGGTCGTGG
1 TCGTGGTCGT-G
66039 TCGTGGTCGTG
1 TCGTGGTCGTG
66050 TCGT-GTCGTGG
1 TCGTGGTCGT-G
66061 TCGTGGTCGTG
1 TCGTGGTCGTG
66072 GTAATACGTG
Statistics
Matches: 99, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
10 30 0.30
11 47 0.47
12 22 0.22
ACGTcount: A:0.00, C:0.19, G:0.45, T:0.35
Consensus pattern (11 bp):
TCGTGGTCGTG
Found at i:66176 original size:22 final size:22
Alignment explanation
Indices: 66151--66217 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
66141 TTTTTTTTCA
66151 ACAAATTTGGAAAATCGCAACG
1 ACAAATTTGGAAAATCGCAACG
* * * **
66173 ACAACTGTAGACTATCGCAACG
1 ACAAATTTGGAAAATCGCAACG
*
66195 ---AATTTGAAAAATCGCAACG
1 ACAAATTTGGAAAATCGCAACG
66214 ACAA
1 ACAA
66218 CTGCAGACTA
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
19 13 0.42
22 18 0.58
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (22 bp):
ACAAATTTGGAAAATCGCAACG
Found at i:66200 original size:41 final size:41
Alignment explanation
Indices: 66149--66235 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
66139 TCTTTTTTTT
* * *
66149 CAACAAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGAAAAATCGCAACGACAACTGCAGACTATCG
66190 CAACGAATTTGAAAAATCGCAACGACAACTGCAGACTATCG
1 CAACGAATTTGAAAAATCGCAACGACAACTGCAGACTATCG
66231 CAACG
1 CAACG
66236 CGACGCGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (41 bp):
CAACGAATTTGAAAAATCGCAACGACAACTGCAGACTATCG
Found at i:66233 original size:22 final size:21
Alignment explanation
Indices: 66164--66235 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
66154 AATTTGGAAA
66164 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTG-AGACT
** **
66186 ATCGCAACGA-ATTTGA-AAA
1 ATCGCAACGACAACTGAGACT
66205 ATCGCAACGACAACTGCAGACT
1 ATCGCAACGACAACTG-AGACT
66227 ATCGCAACG
1 ATCGCAACG
66236 CGACGCGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (21 bp):
ATCGCAACGACAACTGAGACT
Found at i:66263 original size:20 final size:20
Alignment explanation
Indices: 66238--66345 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
66228 TCGCAACGCG
*
66238 ACGCGAAATGGAAAATCGCA
1 ACGCGAAATGCAAAATCGCA
* * *
66258 ACGCGAATTTCAACTATCGCA
1 ACGCGAAATGCAA-AATCGCA
*
66279 ACGCGAAATGAAAAATCGCA
1 ACGCGAAATGCAAAATCGCA
** * *
66299 ACGCGATTTTCAACTATCGCA
1 ACGCGAAATGCAA-AATCGCA
*
66320 ACGCGAAATGGAAAATCGCA
1 ACGCGAAATGCAAAATCGCA
66340 ACGCGA
1 ACGCGA
66346 TTTTCAACTA
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 37 0.54
21 31 0.46
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
ACGCGAAATGCAAAATCGCA
Found at i:66295 original size:41 final size:41
Alignment explanation
Indices: 66238--66366 Score: 240
Period size: 41 Copynumber: 3.1 Consensus size: 41
66228 TCGCAACGCG
*
66238 ACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
*
66279 ACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
66320 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
66361 ACGCGA
1 ACGCGA
66367 TTTTCAACTA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
Found at i:66395 original size:21 final size:21
Alignment explanation
Indices: 66252--66384 Score: 153
Period size: 21 Copynumber: 6.4 Consensus size: 21
66242 GAAATGGAAA
66252 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAATTTCAACT
* * **
66273 ATCGCAACGCGAA-ATGAAAA
1 ATCGCAACGCGAATTTCAACT
*
66293 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
* ** *
66314 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTCAACT
*
66334 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
*
66355 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
66376 ATCGCAACG
1 ATCGCAACG
66385 TGAAATGCAA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
20 30 0.33
21 61 0.67
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAATTTCAACT
Found at i:67077 original size:26 final size:27
Alignment explanation
Indices: 67026--67077 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
67016 CTAACTGCTT
* *
67026 AATACATGTGCATATTTCTTTAACAGC
1 AATACACGTGCATAGTTCTTTAACAGC
67053 AATACACGTGCAT-GTTCTTTAACAG
1 AATACACGTGCATAGTTCTTTAACAG
67078 TCTAACATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (27 bp):
AATACACGTGCATAGTTCTTTAACAGC
Found at i:67174 original size:36 final size:36
Alignment explanation
Indices: 67127--67339 Score: 322
Period size: 36 Copynumber: 5.9 Consensus size: 36
67117 AGATGAACAA
* * *
67127 TTGAATCGAAAGTGCGGGTGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
*
67163 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-TT
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
* *
67198 CTTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
67235 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCA-T
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
*
67270 CTTGAATCGAAAGCGCCGATGCTTCCTTTCGTTCACT
1 -TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
*
67307 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
67340 TTCTTATTCA
Statistics
Matches: 161, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
35 2 0.01
36 157 0.98
37 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
Found at i:67244 original size:72 final size:72
Alignment explanation
Indices: 67127--67344 Score: 382
Period size: 72 Copynumber: 3.0 Consensus size: 72
67117 AGATGAACAA
*
67127 TTGAATCGAAAGTGCGGGTGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
67192 GTTCTTC
66 GTTCTTC
67199 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
*
67264 GTTCATC
66 GTTCTTC
* * * *
67271 TTGAATCGAAAGCGCCGATGCTTCCTTTCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
67336 GTTCTTC
66 GTTCTTC
67343 TT
1 TT
67345 ATTCACCTTC
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 139 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (72 bp):
TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
GTTCTTC
Found at i:76551 original size:20 final size:20
Alignment explanation
Indices: 76457--76825 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
76447 GATTTTCCAT
* ** *
76457 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
76477 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
76497 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
76517 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
76537 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
76557 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
76577 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
76597 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
76617 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
76637 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
76657 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
76677 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
76697 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
76717 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
76737 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
76757 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
76777 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
76797 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
76817 AATCACAAC
1 AATCGCAAC
76826 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:77536 original size:24 final size:24
Alignment explanation
Indices: 77497--77543 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
77487 AAATTTGGTC
77497 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
77521 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
77544 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:77735 original size:12 final size:12
Alignment explanation
Indices: 77718--77742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77708 ATATAATCCT
77718 GAAGAAGAAAAA
1 GAAGAAGAAAAA
77730 GAAGAAGAAAAA
1 GAAGAAGAAAAA
77742 G
1 G
77743 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:80066 original size:19 final size:19
Alignment explanation
Indices: 80044--80369 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
80034 CGGAAAATAC
*
80044 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
80063 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
80077 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
80097 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
80111 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
80130 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
80149 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
80163 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
80182 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
80201 AATCGCAA--CG--AT-AG
1 AATCGCAATGCGAAATGAA
80215 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
80234 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
80253 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
80272 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
80291 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
80310 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
80324 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
80343 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
80362 AATCGCAA
1 AATCGCAA
80370 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 49 0.18
15 4 0.01
16 13 0.05
17 12 0.04
18 5 0.02
19 173 0.64
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:80131 original size:33 final size:34
Alignment explanation
Indices: 80044--80369 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
80034 CGGAAAATAC
* *
80044 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
80077 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
80111 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
80149 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
80182 AATCGCAATGCGAAATGAAAATCGCAACGAT-AG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
80215 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
80253 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
80291 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
80323 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
80362 AATCGCAA
1 AATCGCAA
80370 CGAGATAATC
Statistics
Matches: 258, Mismatches: 11, Indels: 43
0.83 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 110 0.43
34 33 0.13
35 9 0.03
36 6 0.02
37 5 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:80305 original size:161 final size:157
Alignment explanation
Indices: 80072--80391 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
80062 AAATCCCAAC
*
80072 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
80137 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
*
80202 ATCGCAACGATAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
80229 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
80293 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
80358 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
80390 AT
1 AT
80392 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 119 0.78
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:80407 original size:52 final size:52
Alignment explanation
Indices: 80072--80391 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
80062 AAATCCCAAC
80072 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
80125 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
80177 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
80229 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
80286 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
80338 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
80390 AT
1 AT
80392 TATAAACGCA
Statistics
Matches: 253, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 183 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 44 0.17
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:80478 original size:18 final size:18
Alignment explanation
Indices: 80398--80497 Score: 136
Period size: 18 Copynumber: 5.6 Consensus size: 18
80388 AAATTATAAA
80398 CGCATTGCGATTTTCATTT
1 CGCATTGCGA-TTTCATTT
80417 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGA-TTTCATTT
*
80437 CGCATTGCGA-TTC-TCT
1 CGCATTGCGATTTCATTT
80453 CG--TTGCGATTTCATTT
1 CGCATTGCGATTTCATTT
80469 CGCATTGCGATTTCATTT
1 CGCATTGCGATTTCATTT
80487 CGCATTGCGAT
1 CGCATTGCGAT
80498 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 8 0.11
17 3 0.04
18 25 0.34
19 10 0.14
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (18 bp):
CGCATTGCGATTTCATTT
Found at i:80623 original size:14 final size:14
Alignment explanation
Indices: 80604--80640 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
80594 CATCAATTAC
80604 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
80618 ACAAATCATCTTTT
1 ACAAATCAACTTTT
80632 ACAAATCAA
1 ACAAATCAA
80641 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:80652 original size:12 final size:12
Alignment explanation
Indices: 80635--80707 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
80625 ATCTTTTACA
80635 AATCAATTAAAC
1 AATCAATTAAAC
*
80647 AATCAA--AAATTG
1 AATCAATTAAA--C
**
80659 AATCAACTTTTAC
1 AATCAA-TTAAAC
80672 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
80685 AATCAA-AAAAC
1 AATCAATTAAAC
80696 AATCAATTAAAC
1 AATCAATTAAAC
80708 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:80669 original size:38 final size:38
Alignment explanation
Indices: 80621--80693 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
80611 AACTTTTACA
*
80621 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
80659 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
80694 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:82545 original size:19 final size:19
Alignment explanation
Indices: 82505--82639 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
82495 TAGTTTACTT
* *
82505 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
82525 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
82544 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
82563 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
82577 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
82596 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
82610 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
82629 TCGCAATGCGA
1 TCGCAACGCGA
82640 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:82580 original size:14 final size:14
Alignment explanation
Indices: 82561--82617 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
82551 GCGAAATGAA
*
82561 AATCGCAACGACAG
1 AATCGCAACGAAAG
82575 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
82592 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
82608 AATCGCAACG
1 AATCGCAACG
82618 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:82584 original size:33 final size:33
Alignment explanation
Indices: 82542--82634 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
82532 GCGAAACCAA
*
82542 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
82575 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
82608 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
82635 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:82631 original size:52 final size:54
Alignment explanation
Indices: 82505--82639 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
82495 TAGTTTACTT
*
82505 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
82563 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
82610 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
82640 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:82657 original size:19 final size:19
Alignment explanation
Indices: 82635--82763 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
82625 AAAATCGCAA
82635 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
82654 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
82668 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
82687 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
82701 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
82720 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
82739 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
82759 TGCGA
1 TGCGA
82764 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:82677 original size:33 final size:33
Alignment explanation
Indices: 82635--82726 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
82625 AAAATCGCAA
82635 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
82668 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
82701 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
82727 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:82966 original size:93 final size:93
Alignment explanation
Indices: 82807--83186 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
82797 TTGAATGGAT
82807 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
82872 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
82900 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
82965 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
82993 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
83057 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
83085 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
83150 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
83178 AAATTTACT
1 AAATTTACT
83187 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:83120 original size:185 final size:186
Alignment explanation
Indices: 82807--83186 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
82797 TTGAATGGAT
82807 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
82872 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
82937 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
82993 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
83057 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
83122 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
83178 AAATTTACT
1 AAATTTACT
83187 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:84908 original size:14 final size:14
Alignment explanation
Indices: 84889--84943 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
84879 TTGAAATGAA
84889 AATCGCAACGAGAG
1 AATCGCAACGAGAG
84903 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
84920 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
84936 AATCGCAA
1 AATCGCAA
84944 GGTTGAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:84926 original size:33 final size:33
Alignment explanation
Indices: 84881--84996 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
84871 TCTTTTGGTT
84881 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * * *
84914 GAGATGACAATCGCAACGAGAGAATCGCAAGGTT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACG-C
84948 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
84981 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
84997 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
33 45 0.61
34 29 0.39
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:84994 original size:19 final size:17
Alignment explanation
Indices: 84883--85001 Score: 58
Period size: 14 Copynumber: 7.1 Consensus size: 17
84873 TTTTGGTTGA
84883 AATGAAAATCGCAA-CG
1 AATGAAAATCGCAAGCG
*
84899 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAA-GCG
*
84915 AGATGACAATCGCAA-CG
1 A-ATGAAAATCGCAAGCG
* *
84932 -A-GAGAATCGCAAGGTTG
1 AATGAAAATCGCAA-G-CG
84949 AAATGAAAATCGCAA-CG
1 -AATGAAAATCGCAAGCG
*
84966 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAA-GCG
84982 AAATGAAAATCGCAATGCG
1 -AATGAAAATCGCAA-GCG
85001 A
1 A
85002 TTTTGGTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 30
0.67 0.08 0.26
Matches are distributed among these distances:
14 30 0.38
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 24 0.31
20 10 0.13
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (17 bp):
AATGAAAATCGCAAGCG
Done.