Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008609.1 Hibiscus syriacus cultivar Beakdansim tig00111565_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: 282724
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 1 of 2
Found at i:98 original size:22 final size:22
Alignment explanation
Indices: 57--101 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
47 CATTGCATAA
57 AAATTAAACAGTTATAACTCCTG
1 AAATTAAACAG-TATAACTCCTG
80 AAATTAAATCAG-ATAACTCCTG
1 AAATTAAA-CAGTATAACTCCTG
102 TAACTCCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
AAATTAAACAGTATAACTCCTG
Found at i:9262 original size:23 final size:22
Alignment explanation
Indices: 9218--9262 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
9208 TCAGGAGTTA
9218 CAGGAGTTATCTGATTTAATTT
1 CAGGAGTTATCTGATTTAATTT
9240 CAGGAGTTATAACTG-TTTAATTT
1 CAGGAGTTAT--CTGATTTAATTT
9263 TTATGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
CAGGAGTTATCTGATTTAATTT
Found at i:9604 original size:616 final size:615
Alignment explanation
Indices: 7886--9732 Score: 3415
Period size: 615 Copynumber: 3.0 Consensus size: 615
7876 AATTAAATAA
* *
7886 ATTAAATTATTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
1 ATTAAACTGTTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
*
7951 GTTCATGGGAGAGACAAGCTGTTAATATCAGGAGTTACAAGAGTTATCTGATTTAATTTCAGGAG
66 GTTCATGGGAGAGACAAGTTGTTAATATCAGGAGTTACAAGAGTTATCTGATTTAATTTCAGGAG
*
8016 TTATAACTGTTTAATTTTTATGCAATGAACATTGACTCTTTTTTTAGCCAGATTCATCAAGAGGA
131 TTATAACTGTTTAATTTTTATGCAATGAACATGGACTCTTTTTTTAGCCAGATTCATCAAGAGGA
8081 GTTACAAAAAGGGTTTAAATTCAGAATTAAAATCAAATTTAATTTGATTTTCTTGTTGGACGGAT
196 GTTACAAAAAGGGTTTAAATTCAGAATTAAAATCAAATTTAATTTGATTTTCTTGTTGGACGGAT
*
8146 TTACCCTTACTTCTAGCCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACACTCTACAA
261 TTACCCTTACTTCTAGCCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACTCTCTACAA
*
8211 TTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGCTTTCCGATCAGAAGTGCCA
326 TTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGCTTTCCGATCAGAAGTGCAA
* *
8276 TACCACCAGCAGTCCACTCCGGTTTCGAGTGTACGGAATTCGGAGCGACCGTGTTAACCACGGGG
391 TACCACCAGCAGTCCACTCCGGTTTCGGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGG
*
8341 GAAGGTCCGCCTACTGCAACGATTACACACATCGGGGCGAATTCGTTTCTAAGGCAGTGGTTAAT
456 GAAGGTCCGCCTACTGCAGCGATTACACACATCGGGGCGAATTCGTTTCTAAGGCAGTGGTTAAT
8406 ACCACGACACGGTTAATCGGTTCTTTAATTATATATTTCAATATATATTTTTCCAGTCAATGCTA
521 ACCACGACACGGTTAATCGGTTCTTTAATTATATATTTCAATATATATTTTTCCAGTCAATGCTA
*
8471 ATGTCTCGTTTTGCAGCAGTCTATTTTACC
586 ATGCCTCGTTTTGCAGCAGTCTATTTTACC
8501 ATTAAACTGTTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
1 ATTAAACTGTTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
* *
8566 GTTCATGGGAAAGACAAGTTGTTAATATCAGGAGTTACATGAGTTATCTGATTTAATTTCAGGAG
66 GTTCATGGGAGAGACAAGTTGTTAATATCAGGAGTTACAAGAGTTATCTGATTTAATTTCAGGAG
*
8631 TTATAACTGTTTAATTTTTATGCAATGAACATGGACTCTTATTTTAGCCAGATTCATCAAGAGGA
131 TTATAACTGTTTAATTTTTATGCAATGAACATGGACTCTTTTTTTAGCCAGATTCATCAAGAGGA
*
8696 GTTACAAAAAGGGTTTAAATTCATAATTAAAATCAAATTTAATTTGATTTTCTTGTTGGACGGAT
196 GTTACAAAAAGGGTTTAAATTCAGAATTAAAATCAAATTTAATTTGATTTTCTTGTTGGACGGAT
*
8761 TTACCCTTACTTCTAACCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACTCTCTACAA
261 TTACCCTTACTTCTAGCCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACTCTCTACAA
8826 TTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGCTTTCCGATCAGAAGTGCAA
326 TTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGCTTTCCGATCAGAAGTGCAA
*
8891 TACCACCAGCAGTCCACTCCGGTTTTGGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGG
391 TACCACCAGCAGTCCACTCCGGTTTCGGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGG
* * *
8956 GACGGTCCGCCTACTGTAGCGATTACACACATCGGGGCAAATTCGTTTCTAAGGCAGTGGTTAAT
456 GAAGGTCCGCCTACTGCAGCGATTACACACATCGGGGCGAATTCGTTTCTAAGGCAGTGGTTAAT
*
9021 ACCACGACACGGTTAATCGATTCTTTAATTATATATTTCAATATATATTTTTCCAGTCAATGCTA
521 ACCACGACACGGTTAATCGGTTCTTTAATTATATATTTCAATATATATTTTTCCAGTCAATGCTA
* *
9086 ATCCCTCGTTTTGCAACAGTCTATTTTACC
586 ATGCCTCGTTTTGCAGCAGTCTATTTTACC
9116 ATTAAACTGTTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
1 ATTAAACTGTTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
*
9181 GTTCATGGGAGAGACAAGTTGTTAATATCAGGAGTTACAGGAGTTATCTGATTTAATTTCAGGAG
66 GTTCATGGGAGAGACAAGTTGTTAATATCAGGAGTTACAAGAGTTATCTGATTTAATTTCAGGAG
9246 TTATAACTGTTTAATTTTTATGCAATGAACATGGACTCTTTTTTTTAGCCAGATTCATCAAGAGG
131 TTATAACTGTTTAATTTTTATGCAATGAACATGGACTC-TTTTTTTAGCCAGATTCATCAAGAGG
*
9311 AGTTACAAAAAGGGTTTAAATTCAGAATTAAAATCAAATTTAATTTGATTTTCTTATTGGACGGA
195 AGTTACAAAAAGGGTTTAAATTCAGAATTAAAATCAAATTTAATTTGATTTTCTTGTTGGACGGA
9376 TTTACCCTTACTTCTAGCCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACTCTCTACA
260 TTTACCCTTACTTCTAGCCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACTCTCTACA
*
9441 ATTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGTTTTCCGATCAGAAGTGCA
325 ATTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGCTTTCCGATCAGAAGTGCA
* * *
9506 ATACCATCAGCAGTCCACTCCGGTTTCGGGTGTACGGAATTCAGAGCGACCGTGTTAACCTCGGA
390 ATACCACCAGCAGTCCACTCCGGTTTCGGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGG
*
9571 GGAAGGTCCGCCTACTGCAGCGATTACACACATCGGGACGAATTCGTTTCTAAGGCAGTGGTTAA
455 GGAAGGTCCGCCTACTGCAGCGATTACACACATCGGGGCGAATTCGTTTCTAAGGCAGTGGTTAA
*
9636 TACCACGACACGGTTAATCGGTTCTTTAATTATATATTTCAATATATATTTTTCCAATCAATGCT
520 TACCACGACACGGTTAATCGGTTCTTTAATTATATATTTCAATATATATTTTTCCAGTCAATGCT
9701 AATGCCTCGTTTTGCAGCAGTCTATTTTACC
585 AATGCCTCGTTTTGCAGCAGTCTATTTTACC
9732 A
1 A
9733 ACAGAACACC
Statistics
Matches: 1190, Mismatches: 41, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
615 759 0.64
616 431 0.36
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (615 bp):
ATTAAACTGTTATTTTCCTAAATTAAATCAGAATTTAAGATGTATCTGGACTGATTTCAAGCTTT
GTTCATGGGAGAGACAAGTTGTTAATATCAGGAGTTACAAGAGTTATCTGATTTAATTTCAGGAG
TTATAACTGTTTAATTTTTATGCAATGAACATGGACTCTTTTTTTAGCCAGATTCATCAAGAGGA
GTTACAAAAAGGGTTTAAATTCAGAATTAAAATCAAATTTAATTTGATTTTCTTGTTGGACGGAT
TTACCCTTACTTCTAGCCTATAAATAGAGAGCTAAATTCAGCTTCTCAACACACACTCTCTACAA
TTAGAATTCACTCTCCAAGTGTTTTCTAAAGTTGTTCTCTCCGTGCTTTCCGATCAGAAGTGCAA
TACCACCAGCAGTCCACTCCGGTTTCGGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGG
GAAGGTCCGCCTACTGCAGCGATTACACACATCGGGGCGAATTCGTTTCTAAGGCAGTGGTTAAT
ACCACGACACGGTTAATCGGTTCTTTAATTATATATTTCAATATATATTTTTCCAGTCAATGCTA
ATGCCTCGTTTTGCAGCAGTCTATTTTACC
Found at i:16108 original size:48 final size:49
Alignment explanation
Indices: 16032--16139 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 49
16022 AAGTGACGAC
* * *
16032 GAAGATGAACGGCCGGATGGAGTTGTTAACG-ACGACCTCGACGATGAT
1 GAAGATGAACGGCCAGATGCAGTCGTTAACGAACGACCTCGACGATGAT
* * *
16080 GAAGATGAACGGTCAGATGCCGTCGTTAACGACAACGATCTCGACGATGAT
1 GAAGATGAACGGCCAGATGCAGTCGTTAACG--AACGACCTCGACGATGAT
16131 GAAGATGAA
1 GAAGATGAA
16140 TCTTTTGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
48 26 0.51
51 25 0.49
ACGTcount: A:0.32, C:0.19, G:0.31, T:0.19
Consensus pattern (49 bp):
GAAGATGAACGGCCAGATGCAGTCGTTAACGAACGACCTCGACGATGAT
Found at i:18939 original size:24 final size:24
Alignment explanation
Indices: 18895--18964 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 24
18885 ATTTTTAAAT
*
18895 TAAGTTAATAATAAAATATATTTTA
1 TAAGTTAAT-ATAAAATATATTTCA
*
18920 TAAGTTAATATAAAAAATATTTCA
1 TAAGTTAATATAAAATATATTTCA
*
18944 AAAGTTAATATATAAATATAT
1 TAAGTTAATATA-AAATATAT
18965 ATGAATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 24 0.60
25 16 0.40
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAGTTAATATAAAATATATTTCA
Found at i:23347 original size:3 final size:3
Alignment explanation
Indices: 23339--23376 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
23329 TTTAGTACGG
23339 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23377 CGTGTTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36757 original size:2 final size:2
Alignment explanation
Indices: 36750--36799 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
36740 AACTAAAGTA
36750 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
36792 AT AT AT AT
1 AT AT AT AT
36800 TGAAAGGAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37875 original size:20 final size:20
Alignment explanation
Indices: 37852--37896 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
37842 TTAATGGAGC
*
37852 TTGAATTATTTTTGAAAAGT
1 TTGAATTATTTTTGAAAACT
37872 TTGAATTATTTTTGAAAACT
1 TTGAATTATTTTTGAAAACT
37892 TTGAA
1 TTGAA
37897 CAAATTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (20 bp):
TTGAATTATTTTTGAAAACT
Found at i:39148 original size:19 final size:20
Alignment explanation
Indices: 39112--39149 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39102 CTCTAAATCA
* *
39112 TTTTTCAAAGTTTCATTTTG
1 TTTTTCAAAGATTAATTTTG
39132 TTTTTCAAA-ATTAATTTT
1 TTTTTCAAAGATTAATTTT
39150 TGCTTTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTCAAAGATTAATTTTG
Found at i:46910 original size:21 final size:21
Alignment explanation
Indices: 46877--46942 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
46867 ATCACTCCTT
* *
46877 AAGAATCACATATATATTCCA
1 AAGAACCACATATATGTTCCA
* * * *
46898 AAGAACCAAATATGTGTCCCT
1 AAGAACCACATATATGTTCCA
*
46919 AAGAACCGCATATATGTTCCA
1 AAGAACCACATATATGTTCCA
46940 AAG
1 AAG
46943 GATTACATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGAACCACATATATGTTCCA
Found at i:50788 original size:7 final size:7
Alignment explanation
Indices: 50778--50836 Score: 100
Period size: 7 Copynumber: 8.4 Consensus size: 7
50768 CTCTAAATTA
*
50778 TAAACTC
1 TAAACCC
50785 TAAACCC
1 TAAACCC
50792 TAAACCC
1 TAAACCC
50799 TAAACCC
1 TAAACCC
50806 TAAACCC
1 TAAACCC
50813 TAAACCC
1 TAAACCC
50820 TAAACCC
1 TAAACCC
*
50827 TAAACAC
1 TAAACCC
50834 TAA
1 TAA
50837 CTTACGATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:53159 original size:59 final size:59
Alignment explanation
Indices: 53075--53189 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
53065 TGGTTGAATA
53075 TAAACCGTTAATTAACTAACTGTTAAGGTATATTACTAGCATAATATATATATATAATG
1 TAAACCGTTAATTAACTAACTGTTAAGGTATATTACTAGCATAATATATATATATAATG
*
53134 TAAACCGTTAATTAACTAACTGTTAATGTATATTACTAGCATAATATATATATATA
1 TAAACCGTTAATTAACTAACTGTTAAGGTATATTACTAGCATAATATATATATATA
53190 TATATATATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (59 bp):
TAAACCGTTAATTAACTAACTGTTAAGGTATATTACTAGCATAATATATATATATAATG
Found at i:53184 original size:2 final size:2
Alignment explanation
Indices: 53177--53218 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
53167 TACTAGCATA
53177 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
53219 TTATTTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53274 original size:32 final size:31
Alignment explanation
Indices: 53224--53308 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
53214 TATATTTATT
*
53224 TAATTGATAATATGATATATACCACATCACC
1 TAATTGATGATATGATATATACCACATCACC
* * *
53255 TAATATGATGATATGATATACATCACATCACT
1 TAAT-TGATGATATGATATATACCACATCACC
* * *
53287 TAAGGTAATGACATGATATATA
1 TAA-TTGATGATATGATATATA
53309 TCATATCATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 4 0.09
32 40 0.91
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (31 bp):
TAATTGATGATATGATATATACCACATCACC
Found at i:53635 original size:21 final size:21
Alignment explanation
Indices: 53609--53688 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 21
53599 TTGCATTTCA
53609 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* * ** **
53630 CGTTGCGCT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
53650 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
*
53671 CGTTGCGATAGTTAAAAA
1 CGTTGCGATAGTTGAAAA
53689 AAAGATTTTA
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.31
21 31 0.69
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTTGAAAATCG
Found at i:54277 original size:6 final size:6
Alignment explanation
Indices: 54268--54302 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
54258 CGCCGCCGTC
54268 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
54303 ATAATACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:54500 original size:41 final size:41
Alignment explanation
Indices: 54423--54567 Score: 193
Period size: 41 Copynumber: 3.5 Consensus size: 41
54413 ACAACTGTAG
* *
54423 ACTATCACAACGCGAAATGGAAAATCGCAACGCGATTTTC-
1 ACTATCGCAACGCGAAATGCAAAATCGCAACGCGATTTTCA
** * *
54463 ACTATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCAA-AATCGCAACGCGATTTTCA
* * *
54505 ACTATCGCAATGCGAAATGGAAAATCGCAACGAGATTTTCA
1 ACTATCGCAACGCGAAATGCAAAATCGCAACGCGATTTTCA
54546 ACTATCGCAACGCGAAATGCAA
1 ACTATCGCAACGCGAAATGCAA
54568 CGCGAATTTA
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 17 0.19
41 54 0.61
42 17 0.19
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGCAAAATCGCAACGCGATTTTCA
Found at i:54568 original size:21 final size:21
Alignment explanation
Indices: 54446--54560 Score: 153
Period size: 21 Copynumber: 5.6 Consensus size: 21
54436 GAAATGGAAA
54446 ATCGCAACGCGATTTTC-ACT
1 ATCGCAACGCGATTTTCAACT
54466 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
54487 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
54508 ATCGCAATGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
54528 ATCGCAACGAGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
54549 ATCGCAACGCGA
1 ATCGCAACGCGA
54561 AATGCAACGC
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 30 0.38
21 49 0.62
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:54610 original size:19 final size:19
Alignment explanation
Indices: 54586--54622 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54576 TACGATAGTG
*
54586 GAGATCGCAATGCGAATTA
1 GAGATCGCAATACGAATTA
54605 GAGATCGCAATACGAATT
1 GAGATCGCAATACGAATT
54623 CACGGAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (19 bp):
GAGATCGCAATACGAATTA
Found at i:55053 original size:38 final size:37
Alignment explanation
Indices: 54964--55055 Score: 100
Period size: 38 Copynumber: 2.5 Consensus size: 37
54954 ATATGTATTT
* *
54964 TTATTTTATATTAA-ATTTTTATTTATAATTTTAAAA
1 TTATTTCATATTAACATTTTAATTTATAATTTTAAAA
* *
55000 TTATTTCACT-CTAACATTTTAAATTT-TAATTTCTTAAA
1 TTATTTCA-TATTAACATTTT-AATTTATAATTT-TAAAA
55038 TTATTTCATATTAACATT
1 TTATTTCATATTAACATT
55056 CTATTTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
36 10 0.22
37 13 0.28
38 23 0.50
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.57
Consensus pattern (37 bp):
TTATTTCATATTAACATTTTAATTTATAATTTTAAAA
Found at i:55910 original size:29 final size:29
Alignment explanation
Indices: 55852--55910 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 29
55842 TTATACTACT
* * **
55852 AATTAATTGATTCAACTTTGTCATTTAAA
1 AATTAATTGATTCAAATTTGTAATACAAA
55881 AATTAAATTGATTCAAATTTG-AATACAAA
1 AATT-AATTGATTCAAATTTGTAATACAAA
55910 A
1 A
55911 TCCAATTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (29 bp):
AATTAATTGATTCAAATTTGTAATACAAA
Found at i:60912 original size:41 final size:41
Alignment explanation
Indices: 60866--60947 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
60856 GACTTAGTGA
60866 GGCATTAAACTTATAAAAGAACCTCTAACTATTTAAACATG
1 GGCATTAAACTTATAAAAGAACCTCTAACTATTTAAACATG
60907 GGCATTAAACTTATAAAAGAACCTCTAACTATTTAAACATG
1 GGCATTAAACTTATAAAAGAACCTCTAACTATTTAAACATG
60948 TATGAACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (41 bp):
GGCATTAAACTTATAAAAGAACCTCTAACTATTTAAACATG
Found at i:61067 original size:12 final size:12
Alignment explanation
Indices: 61050--61076 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
61040 CTTATTCCAC
61050 TATCAATATTAT
1 TATCAATATTAT
61062 TATCAATATTAT
1 TATCAATATTAT
61074 TAT
1 TAT
61077 GAAATGACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TATCAATATTAT
Found at i:61552 original size:18 final size:18
Alignment explanation
Indices: 61529--61570 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
61519 TTTGTTTCGT
*
61529 AGGACCACTATGTCCCGA
1 AGGACCACTATATCCCGA
*
61547 AGGACCATTATATCCCGA
1 AGGACCACTATATCCCGA
61565 AGGACC
1 AGGACC
61571 GCGTAGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (18 bp):
AGGACCACTATATCCCGA
Found at i:62436 original size:20 final size:20
Alignment explanation
Indices: 62411--62463 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
62401 GAAATTTCTA
*
62411 TGTATCGATACATGCATGTG
1 TGTATCGATACATGCATATG
62431 TGTATCGATACATGCATATG
1 TGTATCGATACATGCATATG
62451 TGTATCGATACAT
1 TGTATCGATACAT
62464 AGGTATCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCATATG
Found at i:64401 original size:17 final size:17
Alignment explanation
Indices: 64379--64412 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
64369 TATATGTATC
* *
64379 ATTTAATGTTTCTCTTT
1 ATTTAATATTTATCTTT
64396 ATTTAATATTTATCTTT
1 ATTTAATATTTATCTTT
64413 TCATTTTGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTAATATTTATCTTT
Found at i:64798 original size:16 final size:16
Alignment explanation
Indices: 64774--64805 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64764 TTCAGTCAAT
64774 CTTTCCATGACATTTA
1 CTTTCCATGACATTTA
*
64790 CTTTTCATGACATTTA
1 CTTTCCATGACATTTA
64806 GACAGATAAA
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:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (16 bp):
CTTTCCATGACATTTA
Found at i:68762 original size:32 final size:32
Alignment explanation
Indices: 68693--68754 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
68683 GAGTTATTAC
*
68693 CAGATCGGTTAGATTTCGGGTTGGATCAATAT
1 CAGATCGGTTAGATTTCGGGTAGGATCAATAT
68725 CAGATCGGTT-GATTTTCGGTGTAGG-TCAAT
1 CAGATCGGTTAGA-TTTCGG-GTAGGATCAAT
68755 TTTAGATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 21 0.78
33 4 0.15
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (32 bp):
CAGATCGGTTAGATTTCGGGTAGGATCAATAT
Found at i:69439 original size:32 final size:33
Alignment explanation
Indices: 69366--69439 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
69356 GTCCGGTTAA
* *
69366 ATTTT-GTTCGGGTTAAAATTCGATTCGGGTTT
1 ATTTTGGTTTGGGTTAAAATTCGATTCGGGTTG
* * * *
69398 CTTTAGGTTTGGGTT-AATTTCGATTCTGGTTG
1 ATTTTGGTTTGGGTTAAAATTCGATTCGGGTTG
69430 ATTTTGGTTT
1 ATTTTGGTTT
69440 CGTTAAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.15, C:0.08, G:0.26, T:0.51
Consensus pattern (33 bp):
ATTTTGGTTTGGGTTAAAATTCGATTCGGGTTG
Found at i:69449 original size:32 final size:33
Alignment explanation
Indices: 69377--69449 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 33
69367 TTTTGTTCGG
* ** *
69377 GTTAAAATTCGATTCGGGTTTCTTTAGGTTTGG
1 GTTAAATTTCGATTCGGGTTGATTTAGGTTTGC
* *
69410 GTT-AATTTCGATTCTGGTTGATTTTGGTTT-C
1 GTTAAATTTCGATTCGGGTTGATTTAGGTTTGC
69441 GTTAAATTT
1 GTTAAATTT
69450 TGGATCGGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 3 0.09
32 27 0.82
33 3 0.09
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.51
Consensus pattern (33 bp):
GTTAAATTTCGATTCGGGTTGATTTAGGTTTGC
Found at i:71166 original size:322 final size:321
Alignment explanation
Indices: 70581--71222 Score: 1167
Period size: 322 Copynumber: 2.0 Consensus size: 321
70571 TACTACTAAG
* *
70581 ATGAACTAAGTATCATTGTCGAAAATCGCCAGCAAAACTGAAATTGTTTTGTATAAATGACATAT
1 ATGAACTAAGTATCATTGTCGAAAATCACCAGCAAAACTGAAATTATTTTGTATAAATGACATAT
*
70646 AATAATTTCTTCGTTTAATCCTTGTGGTTAAGGATTTTCCAAAAGATGATCAAATATAATGAAAT
66 AATAATATCTTCGTTTAATCCTTGTGGTTAAGGATTTTCCAAAAGATGATCAAATATAATGAAAT
* * *
70711 CTCAAACAACGCCTTCACCTCTTTGTCATTTTTCGCTCACATGCACTCTCGTTTTGTTTTTGTTC
131 CCCAAACAACGCCTTCACCTCTCTGTCATTTTTCGCTCACATGCACTCTCGTTTGGTTTTTGTTC
*
70776 TTTAGTTTTCCGCCATGTAAAAGTGTAAACCCAAGCAGTACTCTGTCTTTCAACTTTTTATTTAC
196 TTTAGTTTTCCGCCATGTAAAAGTGTAAACCCAAGCAGTACCCTGTCTTTCAACTTTTTATTTAC
70841 AAAGAAAAAATGGAGGAAGAATTGCTGAAACGCAACACCGATTGCGTTTATTTCTTAGCCTT
261 AAAGAAAAAATGGAGGAAG-ATTGCTGAAACGCAACACCGATTGCGTTTATTTCTTAGCCTT
*
70903 ATGAACTAAGTATCATTGTCGAAAGTCACCAGCAAAACTGAAATTATTTTGTATAAATGACATAT
1 ATGAACTAAGTATCATTGTCGAAAATCACCAGCAAAACTGAAATTATTTTGTATAAATGACATAT
70968 AATAATATCTTCGTTTAATCCTTGTGGTTAAGGATTTTCCAAAAGATGATCAAATATAATGAAAT
66 AATAATATCTTCGTTTAATCCTTGTGGTTAAGGATTTTCCAAAAGATGATCAAATATAATGAAAT
* *
71033 CCCAAACAACGCCTTCACCTCTCTGTCTTTTTTTGCTCACATGCACTCTCGTTTGGTTTTTGTTC
131 CCCAAACAACGCCTTCACCTCTCTGTCATTTTTCGCTCACATGCACTCTCGTTTGGTTTTTGTTC
*
71098 TTTAGTTTTTCGCCATGTAAAAGTGTAAACCCAAGCAGTACCCTGTCTTTCAACTTTTTATTTAC
196 TTTAGTTTTCCGCCATGTAAAAGTGTAAACCCAAGCAGTACCCTGTCTTTCAACTTTTTATTTAC
*
71163 AAAGAAAAAATGGAGGAAGATTGTTGAAACGCAACACCGATTGCGTTTATTTCTTAGCCT
261 AAAGAAAAAATGGAGGAAGATTGCTGAAACGCAACACCGATTGCGTTTATTTCTTAGCCT
71223 CTCCCCTCAC
Statistics
Matches: 308, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
321 40 0.13
322 268 0.87
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (321 bp):
ATGAACTAAGTATCATTGTCGAAAATCACCAGCAAAACTGAAATTATTTTGTATAAATGACATAT
AATAATATCTTCGTTTAATCCTTGTGGTTAAGGATTTTCCAAAAGATGATCAAATATAATGAAAT
CCCAAACAACGCCTTCACCTCTCTGTCATTTTTCGCTCACATGCACTCTCGTTTGGTTTTTGTTC
TTTAGTTTTCCGCCATGTAAAAGTGTAAACCCAAGCAGTACCCTGTCTTTCAACTTTTTATTTAC
AAAGAAAAAATGGAGGAAGATTGCTGAAACGCAACACCGATTGCGTTTATTTCTTAGCCTT
Found at i:74456 original size:16 final size:17
Alignment explanation
Indices: 74435--74469 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
74425 TACTATTCAC
74435 GTGAATAGTG-AATTTT
1 GTGAATAGTGAAATTTT
74451 GTGAATAGTGAAATTTT
1 GTGAATAGTGAAATTTT
74468 GT
1 GT
74470 CGACGATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (17 bp):
GTGAATAGTGAAATTTT
Found at i:92771 original size:27 final size:27
Alignment explanation
Indices: 92733--92789 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
92723 AACTGGAATT
92733 AATGAGGTTGACAACAGTTCGGTACGA
1 AATGAGGTTGACAACAGTTCGGTACGA
92760 AATGAGGTTGACAACAGTTCGGTACGA
1 AATGAGGTTGACAACAGTTCGGTACGA
92787 AAT
1 AAT
92790 ACCTCAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (27 bp):
AATGAGGTTGACAACAGTTCGGTACGA
Found at i:95189 original size:18 final size:17
Alignment explanation
Indices: 95157--95190 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
95147 TCAGCCGGTC
95157 CGGTTTGAACGGTTCAA
1 CGGTTTGAACGGTTCAA
*
95174 CGGTTCTGATCGGTTCA
1 CGGTT-TGAACGGTTCA
95191 CTAGTAGCGG
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:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAA
Found at i:95737 original size:21 final size:21
Alignment explanation
Indices: 95713--95759 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
95703 ATCCAGGTGA
*
95713 CATACGGGGTGGCATACGAGC
1 CATACGGGGTGACATACGAGC
95734 CATAC-GGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
95754 CATACG
1 CATACG
95760 AGCCAATGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.15
Consensus pattern (21 bp):
CATACGGGGTGACATACGAGC
Found at i:95817 original size:28 final size:27
Alignment explanation
Indices: 95768--95823 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
95758 CGAGCCAATG
* * *
95768 GAGAGGTCGTCATACAGTCTTATACGA
1 GAGAGGTCGCCATACAGGCTTAGACGA
*
95795 GAGAGGGTCGCCATGCAGGCTTAGACGA
1 GAGA-GGTCGCCATACAGGCTTAGACGA
95823 G
1 G
95824 TCATACGAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.27, C:0.20, G:0.34, T:0.20
Consensus pattern (27 bp):
GAGAGGTCGCCATACAGGCTTAGACGA
Found at i:95890 original size:29 final size:29
Alignment explanation
Indices: 95840--96001 Score: 283
Period size: 29 Copynumber: 5.6 Consensus size: 29
95830 GAGCCAAGAG
* *
95840 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
95869 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
95898 A-GTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
95926 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
95955 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
95984 AGGTCGCCATGTAGTCCC
1 AGGTCGCCATGTAGTCCC
96002 ATGTAGTCCT
Statistics
Matches: 129, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
28 28 0.22
29 99 0.77
30 2 0.02
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:95985 original size:86 final size:87
Alignment explanation
Indices: 95840--96001 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 87
95830 GAGCCAAGAG
95840 AGGTCGCCATGCAGCCTAGGCGACCTTGTAGGTCGCCATGTAGTCCCGGCGACCTTGTA-GTCGC
1 AGGTCGCCATGCAGCCTAGGCGACCTTGTAGGTCGCCATGTAGTCCCGGCGACCTTGTAGGTCGC
95904 CATGTAGTCCCGGCGACCTTGT
66 CATGTAGTCCCGGCGACCTTGT
* *
95926 AGGTCGCCATGTAGTCC-CGGCGACCTTGTAGGTCGCCATGTAGTCCCGGCGACCTTGTAGGTCG
1 AGGTCGCCATGCAG-CCTAGGCGACCTTGTAGGTCGCCATGTAGTCCCGGCGACCTTGTAGGTCG
95990 CCATGTAGTCCC
65 CCATGTAGTCCC
96002 ATGTAGTCCT
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
86 54 0.75
87 18 0.25
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.23
Consensus pattern (87 bp):
AGGTCGCCATGCAGCCTAGGCGACCTTGTAGGTCGCCATGTAGTCCCGGCGACCTTGTAGGTCGC
CATGTAGTCCCGGCGACCTTGT
Found at i:96363 original size:26 final size:26
Alignment explanation
Indices: 96308--96358 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
96298 CTTGGTCTCC
**
96308 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
96334 GAGATTGCAGCCGAAAGAAAGAAAG
1 GAGATTGCAGCCG-AAGAAAGAAAG
96359 GGAGAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.08
Consensus pattern (26 bp):
GAGATTGCAGCCGAAGAAAGAAAGAA
Found at i:96634 original size:44 final size:46
Alignment explanation
Indices: 96575--96663 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
96565 GTTTATAGTT
*
96575 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAA
*
96618 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 AAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
96664 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 6 0.15
44 15 0.38
45 5 0.12
46 7 0.17
47 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (46 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAA
Found at i:96738 original size:38 final size:34
Alignment explanation
Indices: 96696--96772 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 34
96686 ATAAAATTAG
96696 TTAGTAAGTTTATAGTATATTATAATGAA-AATAGTTTA
1 TTAGTAAGTTT-TAGT-TA-TATAA--AAGAATAGTTTA
* *
96734 TTAGTTAGTTTTAGTTATATAAAAGAATATTTTA
1 TTAGTAAGTTTTAGTTATATAAAAGAATAGTTTA
96768 TTAGT
1 TTAGT
96773 TGTTTAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 2 0.06
34 13 0.36
35 5 0.14
36 2 0.06
37 4 0.11
38 10 0.28
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (34 bp):
TTAGTAAGTTTTAGTTATATAAAAGAATAGTTTA
Found at i:99014 original size:17 final size:17
Alignment explanation
Indices: 98992--99025 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
98982 ACAATGATTT
*
98992 TTAGTATCAAATCATTA
1 TTAGTATCAAATAATTA
99009 TTAGTATCAAATAATTA
1 TTAGTATCAAATAATTA
99026 AATATTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAGTATCAAATAATTA
Found at i:99261 original size:11 final size:11
Alignment explanation
Indices: 99231--99512 Score: 94
Period size: 11 Copynumber: 23.9 Consensus size: 11
99221 ATTAGTAATA
99231 ATTATTAAATC
1 ATTATTAAATC
99242 ATTAGTATTAAATC
1 A-T--TATTAAATC
99256 ATTATTATAAT-
1 ATTATTA-AATC
* *
99267 ATTACTAAATA
1 ATTATTAAATC
* * *
99278 ATAAAT-AATT
1 ATTATTAAATC
*
99288 ATTATAAAATC
1 ATTATTAAATC
*
99299 ATTATTATAATG
1 ATTATTA-AATC
99311 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
99325 ATTACTAAATC
1 ATTATTAAATC
99336 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
99351 A-T-TTAAATC
1 ATTATTAAATC
99360 ATTATTAAATC
1 ATTATTAAATC
* *
99371 ATTTTTATAATT
1 ATTATTA-AATC
*
99383 ATTACTAAATC
1 ATTATTAAATC
*
99394 ATTATTATAATG
1 ATTATTA-AATC
99406 ATTATTATCAAATC
1 ATTA-T-T-AAATC
* *
99420 ATTACTATATGATT
1 ATTA-T-TA-AATC
*
99434 ATTATCAAATC
1 ATTATTAAATC
*
99445 ATTACTAAATC
1 ATTATTAAATC
99456 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
99471 A-T-TTAAATC
1 ATTATTAAATC
99480 ATTATTAAATC
1 ATTATTAAATC
* *
99491 ATTTTTATAATG
1 ATTATTA-AATC
*
99503 ATTAATAAAT
1 ATTATTAAAT
99513 ACATAGAAAT
Statistics
Matches: 204, Mismatches: 34, Indels: 66
0.67 0.11 0.22
Matches are distributed among these distances:
8 12 0.06
9 2 0.01
10 13 0.06
11 83 0.41
12 36 0.18
13 5 0.02
14 35 0.17
15 6 0.03
16 12 0.06
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:99302 original size:14 final size:14
Alignment explanation
Indices: 99231--99328 Score: 67
Period size: 14 Copynumber: 7.1 Consensus size: 14
99221 ATTAGTAATA
*
99231 ATTATTAAATCATT
1 ATTATAAAATCATT
* *
99245 AGTATTAAATCATT
1 ATTATAAAATCATT
* * *
99259 ATTATAATATTACT
1 ATTATAAAATCATT
* *
99273 A-AATAATAAATAATT
1 ATTAT-A-AAATCATT
99288 ATTATAAAATCATT
1 ATTATAAAATCATT
*
99302 ATTAT--AATGATT
1 ATTATAAAATCATT
*
99314 ATTATCAAATCATT
1 ATTATAAAATCATT
99328 A
1 A
99329 CTAAATCATC
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
12 11 0.17
13 2 0.03
14 43 0.66
15 7 0.11
16 2 0.03
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (14 bp):
ATTATAAAATCATT
Found at i:99397 original size:14 final size:13
Alignment explanation
Indices: 99350--99448 Score: 65
Period size: 14 Copynumber: 8.2 Consensus size: 13
99340 AATCATTAAA
99350 TATT-TAAATCAT
1 TATTATAAATCAT
99362 TA-T-TAAATCAT
1 TATTATAAATCAT
*
99373 T-TT-T--ATAAT
1 TATTATAAATCAT
99382 TATTACTAAATCAT
1 TATTA-TAAATCAT
*
99396 TATTAT-AATGAT
1 TATTATAAATCAT
99408 TATTATCAAATCAT
1 TATTAT-AAATCAT
* *
99422 TACTAT--ATGAT
1 TATTATAAATCAT
99433 TATTATCAAATCAT
1 TATTAT-AAATCAT
99447 TA
1 TA
99449 CTAAATCATC
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 21 0.31
12 14 0.21
13 1 0.01
14 25 0.37
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.47
Consensus pattern (13 bp):
TATTATAAATCAT
Found at i:99511 original size:23 final size:23
Alignment explanation
Indices: 99352--99512 Score: 69
Period size: 23 Copynumber: 6.8 Consensus size: 23
99342 TCATTAAATA
*
99352 TTTA-AATCATTATTAAATCATT
1 TTTATAATCATTAATAAATCATT
* *
99374 TTTATAATTATTACTAAATCATT
1 TTTATAATCATTAATAAATCATT
* *
99397 ATTATAATGATTATTATCAAATCATT
1 TTTATAATCATTA--AT-AAATCATT
** *
99423 ACTAT-ATGATTATTATCAAATCATT
1 TTTATAATCATTA--AT-AAATCATT
** * * * * *
99448 ACTA-AATCATCAAATCATTAAATA
1 TTTATAATCAT-TAATAAAT-CATT
*
99472 TTTA-AATCATTATTAAATCATT
1 TTTATAATCATTAATAAATCATT
*
99494 TTTATAATGATTAATAAAT
1 TTTATAATCATTAATAAAT
99513 ACATAGAAAT
Statistics
Matches: 109, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
22 10 0.09
23 45 0.41
24 12 0.11
25 29 0.27
26 13 0.12
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTATAATCATTAATAAATCATT
Found at i:99532 original size:120 final size:118
Alignment explanation
Indices: 99247--99533 Score: 422
Period size: 120 Copynumber: 2.4 Consensus size: 118
99237 AAATCATTAG
* *
99247 TATTAAATCATTATTATAATATTACTAAATA-AT-AAATAAT-TATTATAAAATCATTATTATAA
1 TATTAAATCATTTTTATAATATTACTAAATACATAAAATAATATATTATAAAATCATTACTATAA
99309 TGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
** *
99362 TATTAAATCATTTTTATAATTATTACTAAAT-CATTATTATAATGATTATTATCAAATCATTACT
1 TATTAAATCATTTTTATAA-TATTACTAAATACA-TAAAATAAT-A-TATTATAAAATCATTACT
99426 AT-ATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
62 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
99482 TATTAAATCATTTTTATAATGATTAATAAATACATAGAAATACATATATTAT
1 TATTAAATCATTTTTATAAT-ATTACTAAATACATA-AAATA-ATATATTAT
99534 TACTAATGAG
Statistics
Matches: 153, Mismatches: 8, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
115 18 0.12
116 12 0.08
117 1 0.01
118 5 0.03
119 1 0.01
120 90 0.59
121 24 0.16
122 2 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (118 bp):
TATTAAATCATTTTTATAATATTACTAAATACATAAAATAATATATTATAAAATCATTACTATAA
TGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:102362 original size:26 final size:24
Alignment explanation
Indices: 102304--102362 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
102294 CTAATAAACC
*
102304 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
102328 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
102356 TAATAAT
1 TAATAAT
102363 AATGATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:102370 original size:55 final size:57
Alignment explanation
Indices: 102304--102415 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 57
102294 CTAATAAACC
* * *
102304 TAATAATGATTT-G-ATAATTACTATTAATCTAATGATT-TGATATTTAATGATTTAA
1 TAATAATGATTTAGCATAATCACTAATAAT-TAATGATTATAATATTTAATGATTTAA
* *
102359 TAATAATGATTTAGTCATAATCACTAATAATTATTTATTATAATATTTAATGATTTA
1 TAATAATGATTTAG-CATAATCACTAATAATTAATGATTATAATATTTAATGATTTA
102416 GATTTGATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
55 12 0.25
56 1 0.02
57 6 0.12
58 29 0.60
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (57 bp):
TAATAATGATTTAGCATAATCACTAATAATTAATGATTATAATATTTAATGATTTAA
Found at i:102379 original size:14 final size:14
Alignment explanation
Indices: 102304--102371 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
102294 CTAATAAACC
*
102304 TAATAATGATTTGA
1 TAATAATGATTTAA
*
102318 TAATTACT-A-TTAA
1 TAA-TAATGATTTAA
* *
102331 T-CTAATGATTTGA
1 TAATAATGATTTAA
*
102344 TATTTAATGATTTAA
1 TA-ATAATGATTTAA
102359 TAATAATGATTTA
1 TAATAATGATTTA
102372 GTCATAATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
11 3 0.07
12 1 0.02
13 8 0.20
14 14 0.34
15 15 0.37
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (14 bp):
TAATAATGATTTAA
Found at i:103203 original size:28 final size:28
Alignment explanation
Indices: 103166--103219 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
103156 TATATATAAT
*
103166 ATATAACTTAAACTAATAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
103194 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
103220 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:103226 original size:28 final size:28
Alignment explanation
Indices: 103161--103226 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
103151 TTTTATATAT
*
103161 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
103189 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
103217 ATAATTTATA
1 ATAATATATA
103227 CTAACAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:103229 original size:21 final size:21
Alignment explanation
Indices: 103196--103243 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
103186 CTAATATAAT
103196 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
103217 ATAATTTATACTAACAAAC-A
1 ATAACTTAAACTAACAAACTA
103237 ATTAACT
1 A-TAACT
103244 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:103793 original size:45 final size:46
Alignment explanation
Indices: 103737--103828 Score: 177
Period size: 45 Copynumber: 2.0 Consensus size: 46
103727 CCATGCACAG
103737 TTCCCACGTCCCATGCACAGCATGCATCCC-CAACTCCCCCATGCA
1 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
103782 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
103828 T
1 T
103829 GCTCCAATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 30 0.65
46 16 0.35
ACGTcount: A:0.23, C:0.48, G:0.11, T:0.18
Consensus pattern (46 bp):
TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
Found at i:103918 original size:29 final size:29
Alignment explanation
Indices: 103876--103966 Score: 164
Period size: 29 Copynumber: 3.1 Consensus size: 29
103866 AATACCACAC
* *
103876 AGGTCGCTCGGATGCCATGGCAACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
103905 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
103934 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
103963 AGGT
1 AGGT
103967 TACTGTAGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:107292 original size:167 final size:168
Alignment explanation
Indices: 107016--107351 Score: 665
Period size: 167 Copynumber: 2.0 Consensus size: 168
107006 ATGATAAGAG
107016 AACAAGTCATTTGATTGACACAAATTTAGTTAGAACACATAATTTACCAGATTGTAAATATACAA
1 AACAAGTCATTTGATTGACACAAATTTAGTTAGAACACATAATTTACCAGATTGTAAATATACAA
107081 CTGATGTCAACTGCTCATCAAGTAACTGAGAAGCAAATGCTGAGCACCTATTGGCCTCAATAGCA
66 CTGATGTCAACTGCTCATCAAGTAACTGAGAAGCAAATGCTGAGCACCTATTGGCCTCAATAGCA
107146 TAC-TTCTTATGATACTTTCACCACAAACAACTGCATC
131 TACTTTCTTATGATACTTTCACCACAAACAACTGCATC
107183 AACAAGTCATTTGATTGACACAAATTTAGTTAGAACACATAATTTACCAGATTGTAAATATACAA
1 AACAAGTCATTTGATTGACACAAATTTAGTTAGAACACATAATTTACCAGATTGTAAATATACAA
107248 CTGATGTCAACTGCTCATCAAGTAACTGAGAAGCAAATGCTGAGCACCTATTGGCCTCAATAGCA
66 CTGATGTCAACTGCTCATCAAGTAACTGAGAAGCAAATGCTGAGCACCTATTGGCCTCAATAGCA
107313 TACTTTCTTATGATACTTTCACCACAAACAACTGCATC
131 TACTTTCTTATGATACTTTCACCACAAACAACTGCATC
107351 A
1 A
107352 CAAAAGAAAT
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
167 133 0.79
168 35 0.21
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (168 bp):
AACAAGTCATTTGATTGACACAAATTTAGTTAGAACACATAATTTACCAGATTGTAAATATACAA
CTGATGTCAACTGCTCATCAAGTAACTGAGAAGCAAATGCTGAGCACCTATTGGCCTCAATAGCA
TACTTTCTTATGATACTTTCACCACAAACAACTGCATC
Found at i:114263 original size:6 final size:6
Alignment explanation
Indices: 114252--114293 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
114242 GGAAATAGGG
*
114252 ATGGGT ATGGGT ATGGGT ATGTGT ATGGGT ATGGGT ATGGGT
1 ATGGGT ATGGGT ATGGGT ATGGGT ATGGGT ATGGGT ATGGGT
114294 CGGGTTTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
ATGGGT
Found at i:116721 original size:20 final size:21
Alignment explanation
Indices: 116696--116747 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
116686 TTTTCCCAAT
116696 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
116716 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
116737 TCGCAATGCGA
1 TCGCAATGCGA
116748 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:116760 original size:41 final size:42
Alignment explanation
Indices: 116715--116870 Score: 160
Period size: 41 Copynumber: 3.8 Consensus size: 42
116705 GAATAAGTAA
** *
116715 ATCGCAACGCGA-ATTGGTAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
*
116756 ATCGCAACGCGATAAT-ACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
* ** *
116797 TTCGCAACGCGATATTGAC--TTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
* * * * *
116837 TTCGCAACGAGATAAT-ACATAATCGCAATGCGAT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGAT
116871 TTTCAAAGTT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
39 2 0.02
40 32 0.33
41 59 0.61
42 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (42 bp):
ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
Found at i:116761 original size:20 final size:20
Alignment explanation
Indices: 116736--116850 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
116726 AATTGGTAAA
*
116736 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
116756 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
116777 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
116797 TTCGCAACGCGATATTGACT
1 ATCGCAACGCGATACTGACT
* *
116817 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
116837 TTCGCAACGAGATA
1 ATCGCAACGCGATA
116851 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 62 0.77
21 15 0.19
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:116835 original size:40 final size:40
Alignment explanation
Indices: 116734--116870 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 40
116724 CGAATTGGTA
* *
116734 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
116774 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATATTGAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
116816 -TTTCGCAACGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
116855 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
116871 TTTCAAAGTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.39
41 46 0.56
42 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:117607 original size:24 final size:24
Alignment explanation
Indices: 117580--117633 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
117570 GTATTCGAAA
*
117580 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
117604 TTTGAAATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
117628 TTTGAT
1 TTTGAT
117634 GATGTTTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:117825 original size:12 final size:12
Alignment explanation
Indices: 117808--117832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117798 ATATAATCCT
117808 GAAGAAGAAAAA
1 GAAGAAGAAAAA
117820 GAAGAAGAAAAA
1 GAAGAAGAAAAA
117832 G
1 G
117833 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:120118 original size:19 final size:19
Alignment explanation
Indices: 120096--120160 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
120086 GGAAATTACT
120096 ATCGCAATGCGAAATGAGA
1 ATCGCAATGCGAAATGAGA
120115 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAGA
*
120129 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAGA
*
120148 ATCGCAACGCGAA
1 ATCGCAATGCGAA
120161 TTTCGGAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 11 0.28
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.56
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAGA
Found at i:120138 original size:33 final size:33
Alignment explanation
Indices: 120096--120222 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
120086 GGAAATTACT
*
120096 ATCGCAATGCGAAATGAGAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
120129 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
120161 TTTCGGAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
120195 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
120223 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:120207 original size:66 final size:66
Alignment explanation
Indices: 120101--120229 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
120091 TTACTATCGC
* *
120101 AATGCGAAATGAGAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTTCG
120166 G
66 G
*
120167 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTT
120230 AATTTCGCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.15
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTTCG
G
Found at i:120218 original size:19 final size:19
Alignment explanation
Indices: 120096--120226 Score: 58
Period size: 19 Copynumber: 7.7 Consensus size: 19
120086 GGAAATTACT
* *
120096 ATCGCAATGCGAAATGAGA
1 ATCGCAAAGCGAAATGAAA
*
120115 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
*
120129 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
120148 ATCGCAACGCG-AAT----
1 ATCGCAAAGCGAAATGAAA
* * *
120162 TTCGGAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
120181 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
120195 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
120214 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
120227 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 24 0.29
15 8 0.10
16 4 0.05
17 4 0.05
18 7 0.09
19 35 0.43
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:120244 original size:19 final size:19
Alignment explanation
Indices: 120222--120263 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
120212 AAATCGCAAC
120222 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
120241 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
120260 GCGA
1 GCGA
120264 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:120264 original size:19 final size:19
Alignment explanation
Indices: 120231--120297 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
120221 CGCGAATTTA
120231 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
120250 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
120267 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
120283 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
120298 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:120423 original size:14 final size:14
Alignment explanation
Indices: 120404--120440 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
120394 CATCAATTAA
120404 ACAAATCAACTTTT
1 ACAAATCAACTTTT
120418 ACAAATCAACTTTT
1 ACAAATCAACTTTT
120432 ACAAATCAA
1 ACAAATCAA
120441 TTAAACAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:121856 original size:21 final size:21
Alignment explanation
Indices: 121790--121856 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
121780 GTGAATCGGG
*
121790 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
121810 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
121832 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
121853 CTCT
1 CTCT
121857 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:121875 original size:42 final size:41
Alignment explanation
Indices: 121790--121912 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
121780 GTGAATCGGG
* * * *
121790 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
121832 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
121874 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
121913 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:122303 original size:91 final size:90
Alignment explanation
Indices: 122128--122312 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
122118 ATTTCAAACT
* *
122128 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
122193 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
122221 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
122285 GTATTGGCATCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
122312 T
1 T
122313 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:124043 original size:40 final size:38
Alignment explanation
Indices: 123999--124118 Score: 134
Period size: 40 Copynumber: 3.1 Consensus size: 38
123989 TCTTTTGGTT
*
123999 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAGAATCGCAACGC
** *
124038 GGAAATGACTATCGCAACGCGCGACGA-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAA--CGCGA-AATGAGAATCGCAACGC
* *
124079 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAGAATCGCAACGC
124117 GA
1 GA
124119 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
37 1 0.01
38 19 0.28
40 28 0.42
41 14 0.21
42 5 0.07
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAGAATCGCAACGC
Found at i:124090 original size:19 final size:19
Alignment explanation
Indices: 123999--124118 Score: 132
Period size: 19 Copynumber: 6.1 Consensus size: 19
123989 TCTTTTGGTT
*
123999 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
124018 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
124038 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
124058 GCGACGAGAGAATCGCAACGC
1 GAAATGA-A-AATCGCAACGC
124079 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
124098 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
124117 GA
1 GA
124119 TTTTGGTTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
19 37 0.44
20 31 0.37
21 16 0.19
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:124148 original size:20 final size:19
Alignment explanation
Indices: 124114--124198 Score: 98
Period size: 20 Copynumber: 4.4 Consensus size: 19
124104 AAAATCGCAA
**
124114 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
124133 TGCGATTTTTTATTTCTCGT
1 TGCGA-TTTTTATTTCGCGT
**
124153 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
*
124173 TGCGATTTTCATTTCGCGT
1 TGCGATTTTTATTTCGCGT
124192 TGCGATT
1 TGCGATT
124199 CTCTCGTCGC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 24 0.44
20 31 0.56
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:124233 original size:20 final size:20
Alignment explanation
Indices: 124150--124238 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
124140 TTTTATTTCT
*
124150 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
**
124170 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
** *
124189 CGTTGCGATTCTC-TCGTCGCG
1 CGTTGCGATAGTCAT-TTC-CG
124210 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
124230 CGTTGCGAT
1 CGTTGCGAT
124239 TCTCATTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 15 0.26
20 25 0.44
21 15 0.26
22 1 0.02
ACGTcount: A:0.11, C:0.25, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:124244 original size:20 final size:20
Alignment explanation
Indices: 124163--124267 Score: 99
Period size: 20 Copynumber: 5.2 Consensus size: 20
124153 TGCGATAGTT
*
124163 ATTTCCGCGTTGCGATTTTC
1 ATTTCCGCGTTGCGATTCTC
124183 ATTT-CGCGTTGCGATTCTC
1 ATTTCCGCGTTGCGATTCTC
* **
124202 -TCGTCGCGCGTTGCGATAGTC
1 AT-TTC-CGCGTTGCGATTCTC
124223 ATTTCCGCGTTGCGATTCTC
1 ATTTCCGCGTTGCGATTCTC
* * *
124243 ATTAT-CTCGTTACGATTTTC
1 ATT-TCCGCGTTGCGATTCTC
124263 ATTTC
1 ATTTC
124268 AACCAAAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.01
19 16 0.23
20 35 0.51
21 16 0.23
22 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTTCCGCGTTGCGATTCTC
Found at i:124265 original size:40 final size:40
Alignment explanation
Indices: 124168--124267 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
124158 TAGTTATTTC
*
124168 CGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCTCGTCG
1 CGCGTTGCGATTTTCATTTCCGCGTTGCGATTCTCTC-TAG
** *
124208 CGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCAT-TAT
1 CGCGTTGCGATTTTCATTTCCGCGTTGCGATTCTC-TCTAG
* *
124248 CTCGTTACGATTTTCATTTC
1 CGCGTTGCGATTTTCATTTC
124268 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
40 34 0.68
41 15 0.30
42 1 0.02
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (40 bp):
CGCGTTGCGATTTTCATTTCCGCGTTGCGATTCTCTCTAG
Found at i:124938 original size:20 final size:20
Alignment explanation
Indices: 124765--124937 Score: 186
Period size: 20 Copynumber: 8.6 Consensus size: 20
124755 CGCTATGTAA
*
124765 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGT
* *
124785 ATCACGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGT
*
124805 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGT
124825 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
124845 ATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
* ** *
124865 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--AAGTCAGT
* * *
124886 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGAAAGTCAGT
* *
124906 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
124926 ATCGCATTGCGA
1 ATCGCGTTGCGA
124938 TTTTCCCAAT
Statistics
Matches: 138, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
19 3 0.02
20 121 0.88
21 12 0.09
22 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:124957 original size:61 final size:61
Alignment explanation
Indices: 124765--124959 Score: 162
Period size: 61 Copynumber: 3.2 Consensus size: 61
124755 CGCTATGTAA
* * * * * * * ***
124765 ATCGCGTTGCGAAAGTCAGAATCACGTTGCGAAAGTCAGAATCGCGTTGCGAAAGT-CAGA-
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCA-AT
* * * * * * ** *
124825 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* *
124886 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
124948 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
124960 TTACTTATTC
Statistics
Matches: 111, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
60 49 0.44
61 60 0.54
62 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:125049 original size:21 final size:21
Alignment explanation
Indices: 125009--125049 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
124999 ACTGTAGACC
** *
125009 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
125030 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
125050 GCGAATTTGC
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:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:133159 original size:83 final size:81
Alignment explanation
Indices: 133031--133181 Score: 205
Period size: 83 Copynumber: 1.8 Consensus size: 81
133021 AGATCTCTTA
* * *
133031 ATTTTTATGCTAATTATAATGACGTATTTTCCAACAATAATTTACAAACCAAATTAGCACATATT
1 ATTTTTATGCTAATTATAATGACATATTTTCCAAAAATAAATTACAAACCAAATTAGCACATATT
133096 TTTAAGGATTATATTT
66 TTTAAGGATTATATTT
* * * *
133112 ATTTTCTATGCTAATTATAAATGATATATTTT-TAAAAATTAAATTACATACCAAATTAGCACTT
1 ATTTT-TATGCTAATTAT-AATGACATATTTTCCAAAAA-TAAATTACAAACCAAATTAGCACAT
133176 ATTTTT
63 ATTTTT
133182 TAATTTCCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
81 5 0.08
82 16 0.27
83 39 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (81 bp):
ATTTTTATGCTAATTATAATGACATATTTTCCAAAAATAAATTACAAACCAAATTAGCACATATT
TTTAAGGATTATATTT
Found at i:134613 original size:31 final size:30
Alignment explanation
Indices: 134567--134644 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
134557 TTCGATAATA
*
134567 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
134598 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
134629 TAATAAGTATTTTATA
1 TAATAA-TATTTTATA
134645 TTTTTTAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 34 0.85
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:135404 original size:31 final size:31
Alignment explanation
Indices: 135346--135413 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
135336 TCAGTAAAGT
*
135346 TTAAAAAATTATAAAATACTGATTAAATTTA
1 TTAAAAAATTATAAAATACTGAATAAATTTA
* *
135377 TTAAAAGATTATAAAATTA-TTAATAAATTTA
1 TTAAAAAATTATAAAA-TACTGAATAAATTTA
135408 TCTAAA
1 T-TAAA
135414 TACTATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
TTAAAAAATTATAAAATACTGAATAAATTTA
Found at i:135421 original size:31 final size:31
Alignment explanation
Indices: 135346--135429 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
135336 TCAGTAAAGT
* * * * *
135346 TTAAAAAATTATAAAATACTGATTAAATTTA
1 TTAAAAGACTATAAAATAATTAATAAATTTA
* *
135377 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAGACTATAAAATAATTAATAAATTTA
*
135408 TCT-AAATACTATAAAATAATTA
1 T-TAAAAGACTATAAAATAATTA
135430 TTATATTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (31 bp):
TTAAAAGACTATAAAATAATTAATAAATTTA
Found at i:136017 original size:32 final size:32
Alignment explanation
Indices: 135981--136045 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
135971 TATCAGCATT
* * * *
135981 TGATTTCCCTCATTCTAATGATCCTAAAAAGG
1 TGATTTCACTCAATCCAACGATCCTAAAAAGG
*
136013 TGATTTCACTCAATCCAACGATCTTAAAAAGG
1 TGATTTCACTCAATCCAACGATCCTAAAAAGG
136045 T
1 T
136046 ATAAAGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (32 bp):
TGATTTCACTCAATCCAACGATCCTAAAAAGG
Found at i:142326 original size:21 final size:21
Alignment explanation
Indices: 142300--142373 Score: 148
Period size: 21 Copynumber: 3.5 Consensus size: 21
142290 CTCTACTTGT
142300 AGTATCGATACCTGAGGGTCA
1 AGTATCGATACCTGAGGGTCA
142321 AGTATCGATACCTGAGGGTCA
1 AGTATCGATACCTGAGGGTCA
142342 AGTATCGATACCTGAGGGTCA
1 AGTATCGATACCTGAGGGTCA
142363 AGTATCGATAC
1 AGTATCGATAC
142374 TAAAAATGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (21 bp):
AGTATCGATACCTGAGGGTCA
Found at i:142767 original size:32 final size:32
Alignment explanation
Indices: 142731--142794 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
142721 AAATCTTAAC
142731 ACTTCAAAGGATTATAAATACACTATCTTAGT
1 ACTTCAAAGGATTATAAATACACTATCTTAGT
142763 ACTTCAAAGGATTATAAATACACTATCTTAGT
1 ACTTCAAAGGATTATAAATACACTATCTTAGT
142795 TTTAAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (32 bp):
ACTTCAAAGGATTATAAATACACTATCTTAGT
Found at i:150342 original size:51 final size:51
Alignment explanation
Indices: 150261--150363 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
150251 CATTTTGATA
* * *
150261 ACCTACAAAATGTGTCCCTTTCAAGTAGCTAAACTTGTGTA-GACAATATTG
1 ACCTACAAAATGCGCCCCTTTCAAGCAGCTAAACTTGTG-AGGACAATATTG
*
150312 ACCTACAAAATGCGCCCCTTTCAAGCAGCTAAATTTGTGAGGACAATATTG
1 ACCTACAAAATGCGCCCCTTTCAAGCAGCTAAACTTGTGAGGACAATATTG
150363 A
1 A
150364 AAAGACAGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (51 bp):
ACCTACAAAATGCGCCCCTTTCAAGCAGCTAAACTTGTGAGGACAATATTG
Found at i:165590 original size:12 final size:12
Alignment explanation
Indices: 165573--165612 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
165563 ACAGCAGCCC
165573 CCCCCTTAGCAG
1 CCCCCTTAGCAG
165585 CCCCCTTAGCAG
1 CCCCCTTAGCAG
165597 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
165610 CCC
1 CCC
165613 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:165601 original size:13 final size:13
Alignment explanation
Indices: 165572--165612 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
165562 TACAGCAGCC
165572 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
165585 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
165597 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
165610 CCC
1 CCC
165613 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:168901 original size:15 final size:16
Alignment explanation
Indices: 168873--168904 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
168863 AAAATCTTTC
168873 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
168889 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
168904 T
1 T
168905 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:169679 original size:16 final size:16
Alignment explanation
Indices: 169655--169688 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
169645 TATCGCCGAC
*
169655 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
169671 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
169687 CG
1 CG
169689 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:170118 original size:11 final size:12
Alignment explanation
Indices: 170091--170129 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
170081 TACAGCAGCC
*
170091 CCCCCTTAACAG
1 CCCCCTTAGCAG
170103 CCCCCTTAGCAG
1 CCCCCTTAGCAG
170115 CCCCCTTAGCAG
1 CCCCCTTAGCAG
170127 CCC
1 CCC
170130 ATGTGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.18, C:0.54, G:0.13, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:172830 original size:14 final size:13
Alignment explanation
Indices: 172808--172841 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
172798 ATTTTCTATA
*
172808 TTAATTATAATTC
1 TTAATTATAAATC
172821 TTATATTATAAATC
1 TTA-ATTATAAATC
172835 TTAATTA
1 TTAATTA
172842 ATTTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATTATAAATC
Found at i:172851 original size:13 final size:13
Alignment explanation
Indices: 172835--172871 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
172825 ATTATAAATC
172835 TTAATTAATTTCA
1 TTAATTAATTTCA
172848 TTAATTAATTTCA
1 TTAATTAATTTCA
*
172861 TTAAATAATTT
1 TTAATTAATTT
172872 ATTTATTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATTAATTTCA
Found at i:173500 original size:12 final size:12
Alignment explanation
Indices: 173475--173590 Score: 105
Period size: 12 Copynumber: 9.9 Consensus size: 12
173465 TATATAGTTA
* *
173475 ATACTTATACAT
1 ATACATATATAT
*
173487 ATACATACATAT
1 ATACATATATAT
* *
173499 ATACATACATAC
1 ATACATATATAT
*
173511 ATACACTTTATAT
1 ATACA-TATATAT
*
173524 TTA-ATATATAT
1 ATACATATATAT
173535 AT--ATATATAT
1 ATACATATATAT
*
173545 ATATATATATAT
1 ATACATATATAT
*
173557 ATATATATATAT
1 ATACATATATAT
*
173569 ATATATATATAT
1 ATACATATATAT
173581 ATACAT-TATA
1 ATACATATATA
173591 CATATGTTAT
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
10 10 0.11
11 11 0.12
12 63 0.70
13 6 0.07
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (12 bp):
ATACATATATAT
Found at i:173534 original size:2 final size:2
Alignment explanation
Indices: 173527--173583 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
173517 TTTATATTTA
173527 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
173569 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
173584 CATTATACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:173745 original size:18 final size:17
Alignment explanation
Indices: 173722--173760 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
173712 TATTCAGTCT
* *
173722 ATTTTACAATTTTTTCA
1 ATTTTAAAATTATTTCA
173739 CATTTTAAAATTATTTCA
1 -ATTTTAAAATTATTTCA
173757 ATTT
1 ATTT
173761 AATCCCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAAAATTATTTCA
Found at i:175450 original size:13 final size:13
Alignment explanation
Indices: 175406--175450 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
175396 TATTTTCTAT
175406 ATTAATTATAATC
1 ATTAATTATAATC
*
175419 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
175434 -TTAATTATAATC
1 ATTAATTATAATC
175446 ATTAA
1 ATTAA
175451 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:175760 original size:17 final size:18
Alignment explanation
Indices: 175738--175776 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
175728 TTTGAAAATT
175738 TTGGGAA-GAGAGAGAAA
1 TTGGGAATGAGAGAGAAA
*
175755 TTGGGAATTTAGAGAGAAA
1 TTGGGAA-TGAGAGAGAAA
175774 TTG
1 TTG
175777 AGCAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.23
Consensus pattern (18 bp):
TTGGGAATGAGAGAGAAA
Found at i:176084 original size:15 final size:14
Alignment explanation
Indices: 176060--176100 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
176050 GTCACTCATG
176060 TTTA-ATTATATAC
1 TTTATATTATATAC
176073 TTATATATTATATAC
1 TT-TATATTATATAC
176088 TTTATA-TATATAC
1 TTTATATTATATAC
176101 ACACACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.35
14 6 0.23
15 11 0.42
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATATTATATAC
Found at i:176231 original size:8 final size:8
Alignment explanation
Indices: 176215--176260 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
176205 ATAGCATGAG
*
176215 TATACAAA
1 TATATAAA
176223 TATATAAA
1 TATATAAA
176231 TATAT-AA
1 TATATAAA
*
176238 TATATAAG
1 TATATAAA
176246 TATATAAA
1 TATATAAA
176254 CTATATA
1 -TATATA
176261 GTATATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.21
8 20 0.61
9 6 0.18
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (8 bp):
TATATAAA
Found at i:176239 original size:15 final size:15
Alignment explanation
Indices: 176221--176252 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
176211 TGAGTATACA
176221 AATATATAAATATAT
1 AATATATAAATATAT
*
176236 AATATATAAGTATAT
1 AATATATAAATATAT
176251 AA
1 AA
176253 ACTATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATATATAAATATAT
Found at i:176495 original size:15 final size:14
Alignment explanation
Indices: 176472--176567 Score: 77
Period size: 15 Copynumber: 6.4 Consensus size: 14
176462 TGGCATGTTA
176472 TATAGTTTATATACT
1 TATA-TTTATATACT
*
176487 TATACTTTATATATTT
1 TATA-TTTATATA-CT
176503 TATACTTTATATA-T
1 TATA-TTTATATACT
* *
176517 ATATATATATTATTCT
1 -TATATTTA-TATACT
*
176533 TATATATATATACT
1 TATATTTATATACT
*
176547 TATATATTATATACA
1 TATAT-TTATATACT
176562 TATATT
1 TATATT
176568 ATAAGTATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 15 0.22
15 39 0.57
16 15 0.22
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (14 bp):
TATATTTATATACT
Found at i:176499 original size:9 final size:9
Alignment explanation
Indices: 176469--176515 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
176459 CATTGGCATG
*
176469 TTATATAGT
1 TTATATACT
176478 TTATATAC-
1 TTATATACT
176486 -T-TATACT
1 TTATATACT
176493 TTATATA-T
1 TTATATACT
176501 TT-TATACT
1 TTATATACT
176509 TTATATA
1 TTATATA
176516 TATATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
6 5 0.16
7 5 0.16
8 7 0.22
9 15 0.47
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.57
Consensus pattern (9 bp):
TTATATACT
Found at i:176499 original size:17 final size:16
Alignment explanation
Indices: 176479--176559 Score: 66
Period size: 16 Copynumber: 5.2 Consensus size: 16
176469 TTATATAGTT
176479 TATATACTTATACTTTA
1 TATATACTTATA-TTTA
*
176496 TATAT-TTTATACTTTA
1 TATATACTTATA-TTTA
*
176512 TATATA--TATATATA
1 TATATACTTATATTTA
*
176526 T-TATTCTTATA--TA
1 TATATACTTATATTTA
176539 TATATACTTATATATTA
1 TATATACTTATAT-TTA
176556 TATA
1 TATA
176560 CATATATTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
13 6 0.11
14 13 0.25
15 8 0.15
16 15 0.28
17 11 0.21
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATACTTATATTTA
Found at i:176507 original size:16 final size:16
Alignment explanation
Indices: 176472--176516 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
176462 TGGCATGTTA
*
176472 TATAGTTTATATA-CT
1 TATACTTTATATATCT
*
176487 TATACTTTATATATTT
1 TATACTTTATATATCT
176503 TATACTTTATATAT
1 TATACTTTATATAT
176517 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (16 bp):
TATACTTTATATATCT
Found at i:176512 original size:31 final size:30
Alignment explanation
Indices: 176472--176559 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
176462 TGGCATGTTA
176472 TATAGTTTATATACTTATACTTTATATATT-T
1 TATA-TTTATATACTTATA-TTTATATATTCT
*
176503 TATACTTTATATA--TATATATATATTATTCT
1 TATA-TTTATATACTTATATTTATA-TATTCT
*
176533 TATATATATATACTTATATATTATATA
1 TATATTTATATACTTATAT-TTATATA
176560 CATATATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
28 5 0.10
29 15 0.31
30 5 0.10
31 19 0.40
32 4 0.08
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.56
Consensus pattern (30 bp):
TATATTTATATACTTATATTTATATATTCT
Found at i:176515 original size:2 final size:2
Alignment explanation
Indices: 176510--176570 Score: 53
Period size: 2 Copynumber: 33.0 Consensus size: 2
176500 TTTTATACTT
*
176510 TA TA TA TA TA TA TA TA T- TA T- TC T- TA TA TA TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
176549 TA TA T- TA TA TA CA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
176571 AGTATAATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
1 6 0.12
2 43 0.86
3 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:176538 original size:21 final size:22
Alignment explanation
Indices: 176470--176724 Score: 83
Period size: 21 Copynumber: 11.5 Consensus size: 22
176460 ATTGGCATGT
*
176470 TATATAGT-TTATATACTTATACTT
1 TATATA-TATTATATA-TTATA-TA
*
176494 TATATATTTTATACT-TTATATA
1 TATATATATTATA-TATTATATA
*
176516 TATATATA-TAT-TATTCTTATA
1 TATATATATTATATATT-ATATA
176537 TATATATACTTATATA-T-TATA
1 TATATATA-TTATATATTATATA
* * *
176558 TACATATATTATA-AGTATAATG
1 TATATATATTATATATTAT-ATA
* * *
176580 TATACTTATATTGTATGCATAAGTACA
1 TATA--TATATTATAT--ATTA-TATA
* *
176607 -ATGTACATTATA-A-TATATA
1 TATATATATTATATATTATATA
* * *
176626 TACATGTATTATATTATCATA-A
1 TATATATATTATA-TATTATATA
* *
176648 CAT-TCATCA-TACATATTATATA
1 TATAT-AT-ATTATATATTATATA
* *
176670 CATATTATATTAT-TATGTATGTA
1 TATA-TATATTATATAT-TATATA
176693 TATATATA-TATATA-TATATA
1 TATATATATTATATATTATATA
176713 TATATATATTAT
1 TATATATATTAT
176725 TTAGTCTATT
Statistics
Matches: 172, Mismatches: 30, Indels: 61
0.65 0.11 0.23
Matches are distributed among these distances:
19 5 0.03
20 30 0.17
21 41 0.24
22 34 0.20
23 26 0.15
24 29 0.17
25 1 0.01
26 2 0.01
27 3 0.02
28 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (22 bp):
TATATATATTATATATTATATA
Found at i:176565 original size:29 final size:28
Alignment explanation
Indices: 176469--176570 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 28
176459 CATTGGCATG
* *
176469 TTATATAGTTTATATACTTATACTTTATATA
1 TTATATACTATATATA--TATAC-TTATATA
* *
176500 TTTTATACTTTATATATATA--TATATA
1 TTATATACTATATATATATACTTATATA
176526 TTAT-T-CTTATATATATATACTTATATA
1 TTATATAC-TATATATATATACTTATATA
176553 TTATATAC-ATATAT-TATA
1 TTATATACTATATATATATA
176571 AGTATAATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
24 1 0.02
25 12 0.19
26 13 0.21
27 16 0.26
28 1 0.02
29 5 0.08
31 14 0.23
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (28 bp):
TTATATACTATATATATATACTTATATA
Found at i:176576 original size:19 final size:19
Alignment explanation
Indices: 176514--176589 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
176504 ATACTTTATA
**
176514 TATATATATATATTATTCT
1 TATATATATATATTATAAT
176533 TATATATATATACTTATATAT
1 TATATATATATA-TTATA-AT
* *
176554 TATATACATATATTATAAG
1 TATATATATATATTATAAT
*
176573 TATA-ATGTATACTTATA
1 TATATATATATA-TTATA
176590 TTGTATGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.10
19 22 0.46
20 9 0.19
21 12 0.25
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (19 bp):
TATATATATATATTATAAT
Found at i:176588 original size:53 final size:54
Alignment explanation
Indices: 176478--176590 Score: 128
Period size: 53 Copynumber: 2.1 Consensus size: 54
176468 GTTATATAGT
* * *
176478 TTATATACTTATACTTTATATATTTTATACTTTATATATATATATATATTATTC
1 TTATATACTTATACTTTATATATTATATACTATATATATATATATATATTATAC
176532 TTATATA-TATATAC-TTATATATTATATAC-ATATAT-TATA-AGTATAATGTATAC
1 TTATATACT-TATACTTTATATATTATATACTATATATATATATA-TAT-AT-TATAC
176585 TTATAT
1 TTATAT
176591 TGTATGCATA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
50 1 0.02
51 7 0.13
52 7 0.13
53 25 0.48
54 12 0.23
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (54 bp):
TTATATACTTATACTTTATATATTATATACTATATATATATATATATATTATAC
Found at i:176601 original size:24 final size:24
Alignment explanation
Indices: 176556--176601 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
176546 TTATATATTA
*
176556 TATACATATATTATAAGTATAATG
1 TATACATATATTATAAGCATAATG
* * *
176580 TATACTTATATTGTATGCATAA
1 TATACATATATTATAAGCATAA
176602 GTACAATGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (24 bp):
TATACATATATTATAAGCATAATG
Found at i:176698 original size:2 final size:2
Alignment explanation
Indices: 176660--176721 Score: 69
Period size: 2 Copynumber: 33.0 Consensus size: 2
176650 TTCATCATAC
* * *
176660 AT AT -T AT AT AC AT AT -T AT AT -T AT -T AT GT AT GT 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
176698 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
176722 TATTTAGTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:176755 original size:19 final size:18
Alignment explanation
Indices: 176731--176771 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
176721 TTATTTAGTC
*
176731 TATTTTACAACTTTTTTCA
1 TATTTTACAA-TTATTTCA
176750 TATTTTACAATTATTTCA
1 TATTTTACAATTATTTCA
176768 -ATTT
1 TATTT
176772 GATATCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTACAATTATTTCA
Found at i:182616 original size:14 final size:13
Alignment explanation
Indices: 182594--182631 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
182584 ATTTTCTATA
182594 TTAATTATAATTC
1 TTAATTATAATTC
*
182607 TTATATTATAAATC
1 TTA-ATTATAATTC
182621 TTAATTATAAT
1 TTAATTATAAT
182632 CATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATTATAATTC
Found at i:182637 original size:13 final size:12
Alignment explanation
Indices: 182594--182637 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 12
182584 ATTTTCTATA
182594 TTAATTATAATTC
1 TTAATTATAA-TC
182607 TTATATTATAAATC
1 TTA-ATTAT-AATC
182621 TTAATTATAATC
1 TTAATTATAATC
182633 ATTAA
1 -TTAA
182638 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 10 0.36
15 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAATTATAATC
Done.