Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002659.1 Hibiscus syriacus cultivar Beakdansim tig00005440_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: 144091
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2504 original size:18 final size:18
Alignment explanation
Indices: 2481--2523 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2471 TTTTAGATTA
*
2481 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
2499 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
2517 TTTATTT
1 TTTATTT
2524 TAAAAACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:5877 original size:10 final size:11
Alignment explanation
Indices: 5855--5883 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5845 TTTAATGTTT
5855 TGATATATTTA
1 TGATATATTTA
5866 TGATAT-TTTA
1 TGATATATTTA
5876 TGATATAT
1 TGATATAT
5884 CACACCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
TGATATATTTA
Found at i:6176 original size:2 final size:2
Alignment explanation
Indices: 6165--6198 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6155 CTATGAATGA
6165 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6199 TACGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11572 original size:24 final size:24
Alignment explanation
Indices: 11545--11602 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
11535 ATGGGGCCTT
*
11545 AGTATCGATAATGTCACCCTTGGC
1 AGTATCGATAATGCCACCCTTGGC
11569 AGTATCGATAATGCCACCCTTGGC
1 AGTATCGATAATGCCACCCTTGGC
11593 AGTATCGATA
1 AGTATCGATA
11603 CTCCCTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
AGTATCGATAATGCCACCCTTGGC
Found at i:20848 original size:25 final size:25
Alignment explanation
Indices: 20812--20863 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
20802 TCAATCATAT
20812 ACGGGAGAAAGATTGACGTTGGAGA
1 ACGGGAGAAAGATTGACGTTGGAGA
*
20837 ACGGGAGGAAGATTGACGTTGGAGA
1 ACGGGAGAAAGATTGACGTTGGAGA
20862 AC
1 AC
20864 TCATTTTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.40, T:0.15
Consensus pattern (25 bp):
ACGGGAGAAAGATTGACGTTGGAGA
Found at i:27819 original size:159 final size:156
Alignment explanation
Indices: 27588--27917 Score: 439
Period size: 159 Copynumber: 2.1 Consensus size: 156
27578 CATGTGGTTT
* * * *
27588 AAATTTGGTAAAAAAAGTGACTTAAAATAAATCACAAATTTAAGGAATAAGAAGATTATGAAAAA
1 AAATTTGGTAAAAAAAGGGACATAAAATAAATCACAAATTGAAGAAATAAGAAGATTATGAAAAA
27653 TTAAAGGACTAAATTGAGAAAATAAAAAA-AATTATCAAAAAAGAGGAATTGAAAGTACACATGT
66 TTAAAGGACTAAATT--G-AAATAAAAAATAATTATC-AAAAAGAGGAATTGAAAGTACACATGT
*
27717 ATTCTACTATGCTTTAGGAGCATGTAGCTC
127 ATTCTAATATGCTTTAGGAGCATGTAGCTC
* * * * *
27747 AAATTTGGTTAAAAAGGGGACATAAAATAAATGACAAATTGAAGAAATATGGAGATTATGAAAAA
1 AAATTTGGTAAAAAAAGGGACATAAAATAAATCACAAATTGAAGAAATAAGAAGATTATGAAAAA
* ** *
27812 TTGAAGGACTAAATTGAAATAAAAAATTTGTTATCAAAAATAGGAATTGAAAGTACACATGTATT
66 TTAAAGGACTAAATTGAAATAAAAAA-TAATTATCAAAAAGAGGAATTGAAAGTACACATGTATT
* *
27877 CTAATATGGTTTAGGAGCATGT-GACCC
130 CTAATATGCTTTAGGAGCATGTAG-CTC
*
27904 AAATTTTGTAAAAA
1 AAATTTGGTAAAAA
27918 CATAGACTTA
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
156 11 0.07
157 64 0.43
158 5 0.03
159 70 0.47
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (156 bp):
AAATTTGGTAAAAAAAGGGACATAAAATAAATCACAAATTGAAGAAATAAGAAGATTATGAAAAA
TTAAAGGACTAAATTGAAATAAAAAATAATTATCAAAAAGAGGAATTGAAAGTACACATGTATTC
TAATATGCTTTAGGAGCATGTAGCTC
Found at i:28183 original size:19 final size:19
Alignment explanation
Indices: 28149--28185 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28139 ATATCTTATT
28149 TTCATCTTTCACTTTCATA
1 TTCATCTTTCACTTTCATA
28168 TTCAT-TTTCACATTTCAT
1 TTCATCTTTCAC-TTTCAT
28186 TTACATAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (19 bp):
TTCATCTTTCACTTTCATA
Found at i:28311 original size:19 final size:19
Alignment explanation
Indices: 28247--28309 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
28237 TATTTCCATG
*
28247 TTCATAACTTATTTTCAAA
1 TTCATAACTTATTTTTAAA
* * * *
28266 CTCATAACTTAATCTTAGA
1 TTCATAACTTATTTTTAAA
*
28285 TTCATAGCTTATTTTTAAA
1 TTCATAACTTATTTTTAAA
28304 TTCATA
1 TTCATA
28310 GCCCAATGCA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (19 bp):
TTCATAACTTATTTTTAAA
Found at i:36951 original size:312 final size:312
Alignment explanation
Indices: 36372--36994 Score: 1043
Period size: 312 Copynumber: 2.0 Consensus size: 312
36362 CCTCGAATAG
*
36372 TCCAACTTATCTAAGAAAGTTTGAGTATCCACCTACTTTACTAAGAAGGTTTAACAACCTAGTAG
1 TCCAACTTAACTAAGAAAGTTTGAGTATCCACCTACTTTACTAAGAAGGTTTAACAACCTAGTAG
* * *
36437 CAATAACTTTATAGCAGTTAATGCTAGAATCGCATTAGAAAACAAATTTACTCTTTTTCCCTTCC
66 CAATAACTTTATAGCAGCTAATGCTAAAATCGCATTAGAAAACAAATTTACTATTTTTCCCTTCC
* *
36502 ACAAATATCTCGAAACTTTTCGAGTTCTAAAAATTAAATCTCTTTAAGCAGTAATTCAGTGTAAC
131 ACAAATATCTCGAAACTTTTCGAGTTCTAAAAATTAAATCGCTTTAAGCAGTAATTCAGTGCAAC
* *
36567 ATGGTAGGAGGTAATCAATTCATTCCAAATATTACCTACGAAAGGTAATTCTATCAAGTATATTA
196 ATGGTAGGAGGTAATCAATTCATTCCAAAAATTACATACGAAAGGTAATTCTATCAAGTATATTA
*
36632 TAATCAACACGTTGAATTCTTACCAGACAATTACTGTCTACAAATACGACTT
261 TAATCAACACGTTGAATCCTTACCAGACAATTACTGTCTACAAATACGACTT
* *
36684 TCCAACTTAACTAAGAAAGTTTGAGTATCCACCTCCTTTACTAAGAAGGTTTGACAACCTAGTAG
1 TCCAACTTAACTAAGAAAGTTTGAGTATCCACCTACTTTACTAAGAAGGTTTAACAACCTAGTAG
* **
36749 CAATAACTTTATAGCAGCTGATTTTAAAATCGCATTAGAAAACAAATTTACTATTTTTCCCTTCC
66 CAATAACTTTATAGCAGCTAATGCTAAAATCGCATTAGAAAACAAATTTACTATTTTTCCCTTCC
* *
36814 ACAAATATCTCGAAACTTTTTC-AGTTCTAAAAATTCAATCGCTTTAAGCAGTAATTCATTGCAA
131 ACAAATATCTCGAAAC-TTTTCGAGTTCTAAAAATTAAATCGCTTTAAGCAGTAATTCAGTGCAA
* *
36878 CATGGTAGG-GGTAATCAATTCATTCCAAAAATTACATTCGAAAGGTAATTCTATCAAGTCTATT
195 CATGGTAGGAGGTAATCAATTCATTCCAAAAATTACATACGAAAGGTAATTCTATCAAGTATATT
*
36942 ATAAATCAACACGTTGGATCCTTACCAGACAATTACTGTCTACAAATACGACT
260 AT-AATCAACACGTTGAATCCTTACCAGACAATTACTGTCTACAAATACGACT
36995 CACTCTCGTT
Statistics
Matches: 290, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
311 53 0.18
312 232 0.80
313 5 0.02
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (312 bp):
TCCAACTTAACTAAGAAAGTTTGAGTATCCACCTACTTTACTAAGAAGGTTTAACAACCTAGTAG
CAATAACTTTATAGCAGCTAATGCTAAAATCGCATTAGAAAACAAATTTACTATTTTTCCCTTCC
ACAAATATCTCGAAACTTTTCGAGTTCTAAAAATTAAATCGCTTTAAGCAGTAATTCAGTGCAAC
ATGGTAGGAGGTAATCAATTCATTCCAAAAATTACATACGAAAGGTAATTCTATCAAGTATATTA
TAATCAACACGTTGAATCCTTACCAGACAATTACTGTCTACAAATACGACTT
Found at i:38237 original size:21 final size:22
Alignment explanation
Indices: 38211--38252 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
38201 TTCGAGTCAA
*
38211 ATATGCACTGAA-GTGCTTACC
1 ATATGCACTGAATGTCCTTACC
38232 ATATGCACTGAATGTCCTTAC
1 ATATGCACTGAATGTCCTTAC
38253 ACACCACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (22 bp):
ATATGCACTGAATGTCCTTACC
Found at i:38374 original size:30 final size:30
Alignment explanation
Indices: 38331--38387 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
38321 ATACCATATT
*
38331 CACTAAATGTCCTTACACACCATAGTGATG
1 CACTAAATATCCTTACACACCATAGTGATG
* * *
38361 CACTAAGTATCCTTGCACACTATAGTG
1 CACTAAATATCCTTACACACCATAGTG
38388 CTAATCCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (30 bp):
CACTAAATATCCTTACACACCATAGTGATG
Found at i:44417 original size:12 final size:12
Alignment explanation
Indices: 44402--44466 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
44392 CAAAACATAA
44402 ATCAGGTCAAGT
1 ATCAGGTCAAGT
** *
44414 ATCATATCAA-A
1 ATCAGGTCAAGT
44425 ATCCAGGTCAAGT
1 AT-CAGGTCAAGT
* *
44438 ATCAGATC-AGA
1 ATCAGGTCAAGT
44449 ATCCAGGTCAAGT
1 AT-CAGGTCAAGT
44462 ATCAG
1 ATCAG
44467 ATCAGAATTC
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
11 6 0.15
12 27 0.69
13 6 0.15
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (12 bp):
ATCAGGTCAAGT
Found at i:44417 original size:24 final size:24
Alignment explanation
Indices: 44390--44518 Score: 118
Period size: 24 Copynumber: 5.4 Consensus size: 24
44380 TATATCAAAA
*
44390 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAATCA-AAATCCAGGTCAAGT
*
44414 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* *
44438 ATCAGATCAGAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* * * *
44462 ATCAGATCAGAATTCATGTC-AGAT
1 ATCAAATCAAAATCCAGGTCAAG-T
* * *
44486 ATCATATCAGAATCCATGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
*
44510 ATCAGATCA
1 ATCAAATCA
44519 GAATTCAAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 6 0.06
24 85 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAATCAAAATCCAGGTCAAGT
Found at i:44531 original size:24 final size:24
Alignment explanation
Indices: 44404--44522 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
44394 AAACATAAAT
* *
44404 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCAGATCAGAATC
44428 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
44452 CAGGTCAAGTATCAGATCAGAATT
1 CAGGTCAAGTATCAGATCAGAATC
* *
44476 CATGTC-AGATATCATATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
44500 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
44523 TCAAATCAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.02
24 82 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:44537 original size:24 final size:24
Alignment explanation
Indices: 44407--44540 Score: 133
Period size: 24 Copynumber: 5.6 Consensus size: 24
44397 CATAAATCAG
* * * *
44407 GTCAAGTATCATATCAAAATCCAG
1 GTCAAATATCAGATCAGAATCCAT
* *
44431 GTCAAGTATCAGATCAGAATCCAG
1 GTCAAATATCAGATCAGAATCCAT
* *
44455 GTCAAGTATCAGATCAGAATTCAT
1 GTCAAATATCAGATCAGAATCCAT
* *
44479 GTCAGATATCATATCAGAATCCAT
1 GTCAAATATCAGATCAGAATCCAT
* * *
44503 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAATATCAGATCAGAATCCAT
* *
44527 ATCAAAAATCAGAT
1 GTCAAATATCAGAT
44541 AAAATATTCA
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 94 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAATATCAGATCAGAATCCAT
Found at i:46350 original size:36 final size:36
Alignment explanation
Indices: 46303--46375 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
46293 GATAAATTAT
46303 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
46339 AATCTATATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
46375 A
1 A
46376 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:50015 original size:73 final size:72
Alignment explanation
Indices: 49893--50038 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 72
49883 ATTACATTAG
* * *
49893 ATTAAAAATATAACATTTAAATTATATTTAATACTATAATATTTGAAATATATACACTTAAACTA
1 ATTAAAAATATAACATTTAAACTATATTTAATACTATAATATTTAAAATATATAAACTTAAACTA
49958 TAATAAA
66 TAATAAA
* *
49965 ATTAAAAATATTTA-ATTTAATACTATATTTAATACTATGATATTTAAAATATATAAACTTAAAC
1 ATTAAAAATA-TAACATTTAA-ACTATATTTAATACTATAATATTTAAAATATATAAACTTAAAC
50029 TATAATAAA
64 TATAATAAA
50038 A
1 A
50039 GTAAGCTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 16 0.24
73 51 0.76
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (72 bp):
ATTAAAAATATAACATTTAAACTATATTTAATACTATAATATTTAAAATATATAAACTTAAACTA
TAATAAA
Found at i:51873 original size:30 final size:29
Alignment explanation
Indices: 51791--51881 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
51781 AATGTCTATC
* *
51791 TTAGCTCTTTAAGTTTCTGTTTTTGCTAT
1 TTAGCCCTTTAAGTTTCTGTTTTTGTTAT
* *
51820 TTAGACCC-TTAAGTTTCTATTTTTGTTGTT
1 TTAG-CCCTTTAAGTTTCTGTTTTTGTT-AT
* *
51850 TTAGCCCTTTACGTTTATGTTTTTGTTAT
1 TTAGCCCTTTAAGTTTCTGTTTTTGTTAT
51879 TTA
1 TTA
51882 AGTCTTTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (29 bp):
TTAGCCCTTTAAGTTTCTGTTTTTGTTAT
Found at i:57843 original size:66 final size:66
Alignment explanation
Indices: 57745--57906 Score: 197
Period size: 67 Copynumber: 2.4 Consensus size: 66
57735 CAAAATTTAC
* * *
57745 CATCTTTGAGTCGTTTCCCTTGAAACGAATTTTGTCT-CTTGAGACATTTTCTCTT-AAAACA-A
1 CATCTTTGAGTCGTTTCTCTTGAAACAAATTTTGTCTCCTTGAGACAGTTTCT-TTGAAAACACA
57807 AA
65 AA
* * *
57809 TCATCTTTGAGATCGTTTCTATTGAAACAAATTTTGTCTCCCTTGAGGCAGTTTCTTTGGAAACA
1 -CATCTTTGAG-TCGTTTCTCTTGAAACAAATTTTGTCT-CCTTGAGACAGTTTCTTTGAAAACA
57874 CAAA
63 CAAA
57878 -ATCTTTGAGTCTGTTTCTCTTGAAACAAA
1 CATCTTTGAGTC-GTTTCTCTTGAAACAAA
57907 ACCATCTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
65 10 0.12
66 26 0.31
67 27 0.32
68 18 0.21
69 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (66 bp):
CATCTTTGAGTCGTTTCTCTTGAAACAAATTTTGTCTCCTTGAGACAGTTTCTTTGAAAACACAA
A
Found at i:57894 original size:31 final size:31
Alignment explanation
Indices: 57859--57933 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
57849 CCTTGAGGCA
57859 GTTTCT-TTGGAAACACAAA-ATCTTTGAGTCT
1 GTTTCTCTT-GAAACA-AAACATCTTTGAGTCT
57890 GTTTCTCTTGAAACAAAACCATCTTTGAGTC-
1 GTTTCTCTTGAAACAAAA-CATCTTTGAGTCT
*
57921 ATTTC-CTTGAAAC
1 GTTTCTCTTGAAAC
57934 GAATTTTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 11 0.28
31 16 0.40
32 13 0.32
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (31 bp):
GTTTCTCTTGAAACAAAACATCTTTGAGTCT
Found at i:57913 original size:99 final size:95
Alignment explanation
Indices: 57792--57998 Score: 247
Period size: 97 Copynumber: 2.1 Consensus size: 95
57782 CTTGAGACAT
* * * *
57792 TTTCTCTTAAAACAAAATCATCTTTGAGATCGTTTCTATTGAAACAAATTTTGTCTCCCTTGAGG
1 TTTCTCTTGAAACAAAACCATCTTTGAG-TCATTTC-ATTGAAACAAATTTTGTCTCCCTTGAGA
* * *
57857 CAGTTTCT-TTGGAAACA-CAAAATCTTTGAGTCTG
64 AAGCTTCTCTT-GAAACATC---ATCTTTGAGTCGG
* * *
57891 TTTCTCTTGAAACAAAACCATCTTTGAGTCATTTCCTTGAAACGAATTTTGTCTCTCTTGAGAAA
1 TTTCTCTTGAAACAAAACCATCTTTGAGTCATTTCATTGAAACAAATTTTGTCTCCCTTGAGAAA
*
57956 GCTTCTCTTGAAGCATCATCTTTGAGTCGG
66 GCTTCTCTTGAAACATCATCTTTGAGTCGG
57986 TTTCTCTTGAAAC
1 TTTCTCTTGAAAC
57999 TATCATCCCT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
95 25 0.26
97 35 0.37
98 9 0.09
99 26 0.27
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (95 bp):
TTTCTCTTGAAACAAAACCATCTTTGAGTCATTTCATTGAAACAAATTTTGTCTCCCTTGAGAAA
GCTTCTCTTGAAACATCATCTTTGAGTCGG
Found at i:57919 original size:32 final size:31
Alignment explanation
Indices: 57745--57933 Score: 107
Period size: 32 Copynumber: 5.8 Consensus size: 31
57735 CAAAATTTAC
* **
57745 CATCTTTGAGTCGTTTCCCTTGAAACGAATTT
1 CATCTTTGAGTCGTTTCTCTTGAAAC-AAAAT
** * * *
57777 TGTCTCTTGAGACATTTTCTCTTAAAACAAAAT
1 CATCT-TTGAGTC-GTTTCTCTTGAAACAAAAT
* *
57810 CATCTTTGAGATCGTTTCTATTGAAACAAATTT
1 CATCTTTGAG-TCGTTTCTCTTGAAACAAA-AT
** *
57843 TGTCTCCCTTGAGGCAGTTTCT-TTGGAAACACAAA-
1 CATCT---TTGAGTC-GTTTCTCTT-GAAACA-AAAT
*
57878 -ATCTTTGAGTCTGTTTCTCTTGAAACAAAAC
1 CATCTTTGAGTC-GTTTCTCTTGAAACAAAAT
*
57909 CATCTTTGAGTCATTTC-CTTGAAAC
1 CATCTTTGAGTCGTTTCTCTTGAAAC
57934 GAATTTTGTC
Statistics
Matches: 121, Mismatches: 23, Indels: 28
0.70 0.13 0.16
Matches are distributed among these distances:
30 11 0.09
31 22 0.18
32 35 0.29
33 17 0.14
34 14 0.12
35 3 0.02
36 17 0.14
37 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (31 bp):
CATCTTTGAGTCGTTTCTCTTGAAACAAAAT
Found at i:58566 original size:3 final size:3
Alignment explanation
Indices: 58551--58622 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
58541 TCTACAAAAC
*
58551 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58597 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
58623 CATATTACAA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 3 0.05
3 62 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:60082 original size:2 final size:2
Alignment explanation
Indices: 60075--60101 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60065 CCTTATCTTG
60075 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60102 TTCGTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60696 original size:17 final size:17
Alignment explanation
Indices: 60650--60696 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
60640 GTGGCGACTC
*
60650 CAAAATCAAATTGTTTT
1 CAAAATCAAATTTTTTT
60667 CAAAATCAAATTTTTTT
1 CAAAATCAAATTTTTTT
60684 CAAAATCAAATTT
1 CAAAATCAAATTT
60697 CATCGCCTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (17 bp):
CAAAATCAAATTTTTTT
Found at i:63301 original size:50 final size:49
Alignment explanation
Indices: 63237--63332 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 49
63227 AACTTGACTC
* * *
63237 ATCATATCATCTATGATTCTAATGAATTAGATCCATTAATTTTAAAAATG
1 ATCACATCATCTATGATTCTAATGAATTAAATCAATTAA-TTTAAAAATG
* *
63287 ATCACATCATCTATGATTTTAATGAATTAAATTAATTAATTTAAAA
1 ATCACATCATCTATGATTCTAATGAATTAAATCAATTAATTTAAAA
63333 TATTTTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 7 0.17
50 34 0.83
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (49 bp):
ATCACATCATCTATGATTCTAATGAATTAAATCAATTAATTTAAAAATG
Found at i:71393 original size:37 final size:37
Alignment explanation
Indices: 71308--71393 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 37
71298 ATTAAACATT
71308 TTTTATAATTTTAATTTTGTAAAAAAATTTATATAAATA
1 TTTTATAA-TTTAATTTTGTAAAAAAA-TTATATAAATA
*
71347 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAA-AAAATTATATAAATA
71383 TTTTATAATTT
1 TTTTATAATTT
71394 GTAATATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
36 10 0.24
37 22 0.52
38 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (37 bp):
TTTTATAATTTAATTTTGTAAAAAAATTATATAAATA
Found at i:72769 original size:16 final size:16
Alignment explanation
Indices: 72748--72786 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
72738 AACATAAAAA
*
72748 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
72764 AAACATATCCATTAAG
1 AAACATATCCATTAAG
72780 AAACATA
1 AAACATA
72787 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:84567 original size:21 final size:21
Alignment explanation
Indices: 84542--84610 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
84532 CACTTGATGT
84542 ATCGATGCACCTTGACTATGC
1 ATCGATGCACCTTGACTATGC
* *
84563 ATCGATGTACCTTGAATATGC
1 ATCGATGCACCTTGACTATGC
84584 ATCGATGCACCTTGACTATGC
1 ATCGATGCACCTTGACTATGC
84605 ATCGAT
1 ATCGAT
84611 TCACACACAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (21 bp):
ATCGATGCACCTTGACTATGC
Found at i:85716 original size:28 final size:28
Alignment explanation
Indices: 85644--85716 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
85634 CGATTTCATA
*
85644 AATATAATCATTTA-AAAAATATAAAAAT
1 AATA-AATCAGTTATAAAAATATAAAAAT
* *
85672 AATAAATTTAGTT-TAAAAATATTAAAAT
1 AATAAA-TCAGTTATAAAAATATAAAAAT
*
85700 ATTAAATCAGTTATAAA
1 AATAAATCAGTTATAAA
85717 TAAACTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 7 0.19
28 30 0.81
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAAATCAGTTATAAAAATATAAAAAT
Found at i:94544 original size:46 final size:46
Alignment explanation
Indices: 94494--94805 Score: 178
Period size: 46 Copynumber: 6.8 Consensus size: 46
94484 TTAGTAATTT
* *
94494 TTCATTAATTTTAGTTATGGTC-TCTTTTCATGCATTAATACATCCA
1 TTCATCAATTTTAGTTATGG-CATCCTTTCATGCATTAATACATCCA
* * ** * *
94540 TTCATGC-ATTTTAATCATGGCATCCTTTCATGCCCTAATGCATCCT
1 TTCAT-CAATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCA
* *
94586 TTCATGCAA-TTTAGTTATGGCATCCTTTCATGCATT-TTA-AT-TA
1 TTCAT-CAATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCA
* * * * * * *
94629 TGGCATC-CTTTCATGCCTTAAT-GCATCCGTTCATGCCTTAATGCATCCG
1 T-TCATCAATTTTA-G--TT-ATGGCATCCTTTCATGCATTAATACATCCA
* * * * *
94678 TTCATGC-ATTTTACTTATGACATCCTTTCATGCCTTAATGCATCCG
1 TTCAT-CAATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCA
* * * * * *
94724 TTTATGC-ATTTTAATTATGGCATCCTTTCATGCCTTAATGCACCCT
1 TTCAT-CAATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCA
* *
94770 TTCATGC-ATTTTAATTATGGCATCCCTTCATGCATT
1 TTCAT-CAATTTTAGTTATGGCATCCTTTCATGCATT
94806 TTAGTTATGG
Statistics
Matches: 213, Mismatches: 39, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
43 5 0.02
44 6 0.03
45 4 0.02
46 183 0.86
47 4 0.02
48 5 0.02
49 6 0.03
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (46 bp):
TTCATCAATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCA
Found at i:94584 original size:20 final size:20
Alignment explanation
Indices: 94559--95129 Score: 174
Period size: 26 Copynumber: 24.6 Consensus size: 20
94549 TTTAATCATG
*
94559 GCATCCTTTCATGCCCTAAT
1 GCATCCTTTCATGCCTTAAT
*
94579 GCATCCTTTCATGCAATTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
94604 GGCATCCTTTCATGCATTTTAATTAT
1 -GCATCCTTTCATGC--CTT-A--AT
94630 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
94651 GCATCCGTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
94671 GCATCCGTTCATGCATTTTACTTAT
1 GCATCCTTTCATGC--CTTA---AT
94696 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
94717 GCATCCGTTT-ATGCATTTTAATTAT
1 GCATCC-TTTCATGC--CTT-A--AT
94742 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
94763 GCACCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
* *
94788 GGCATCCCTTCATGCATTTTAGTTAT
1 -GCATCCTTTCATGC--CTTA---AT
**
94814 GGCATCCTTTCATAACTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
94835 GCATCCATTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
94860 GGCATCCATTCATGCCATTTAATTAT
1 -GCATCCTTTCATGCC--TT-A--AT
*
94886 GGCATCATTTCATGCCTTTTAATTAT
1 -GCATCCTTTCATGCC--TT-A--AT
*
94912 GGCATCCTTTCATGCCTTTAT
1 -GCATCCTTTCATGCCTTAAT
*
94933 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
94958 GGCATCCTTTAATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
94979 GCAT-TTGTTCATGCATTTTAATTAT
1 GCATCCT-TTCATGC--CTT-A--AT
*
95004 GGCATCATTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
95025 GCATCCTTTCATGCATTTTAATTTT
1 GCATCCTTTCATGC--CTTAA---T
95050 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
**
95071 GCATCCTTTCATGTATTTTAATTAT
1 GCATCCTTTCATG--CCTT-A--AT
95096 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
95117 GCATCCTTTCATG
1 GCATCCTTTCATG
95130 TATTTTAGTT
Statistics
Matches: 445, Mismatches: 44, Indels: 124
0.73 0.07 0.20
Matches are distributed among these distances:
19 1 0.00
20 141 0.32
21 23 0.05
22 21 0.05
23 9 0.02
24 23 0.05
25 24 0.05
26 201 0.45
27 2 0.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:94603 original size:92 final size:91
Alignment explanation
Indices: 94501--94805 Score: 343
Period size: 92 Copynumber: 3.3 Consensus size: 91
94491 TTTTTCATTA
*
94501 ATTTTAGTTATGGTC-TCTTTTCATGCATTAATACATCCATTCATGCATTTTAATCATGGCATCC
1 ATTTTAGTTATGG-CATCCTTTCATGCATTAATACATCCATTCATGCATTTTAAT-ATGGCATCC
*
94565 TTTCATGCCCTAATGCATCCTTTCATGC
64 TTTCATGCCTTAATGCATCCTTTCATGC
* * *
94593 AATTTAGTTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC--CTT-A-AT-GC
1 ATTTTAGTTATGGCATCCTTTCATGCA--TTAA-TA---CATCCATTCATGCATTTTAATATGGC
* *
94653 ATCCGTTCATGCCTTAATGCATCCGTTCATGC
60 ATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * * *
94685 ATTTTACTTATGACATCCTTTCATGCCTTAATGCATCCGTTTATGCATTTTAATTATGGCATCCT
1 ATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCATTCATGCATTTTAA-TATGGCATCCT
*
94750 TTCATGCCTTAATGCACCCTTTCATGC
65 TTCATGCCTTAATGCATCCTTTCATGC
* *
94777 ATTTTAATTATGGCATCCCTTCATGCATT
1 ATTTTAGTTATGGCATCCTTTCATGCATT
94806 TTAGTTATGG
Statistics
Matches: 178, Mismatches: 22, Indels: 26
0.79 0.10 0.12
Matches are distributed among these distances:
86 11 0.06
88 2 0.01
89 2 0.01
90 4 0.02
91 3 0.02
92 133 0.75
93 2 0.01
94 4 0.02
95 3 0.02
96 2 0.01
98 12 0.07
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (91 bp):
ATTTTAGTTATGGCATCCTTTCATGCATTAATACATCCATTCATGCATTTTAATATGGCATCCTT
TCATGCCTTAATGCATCCTTTCATGC
Found at i:94610 original size:72 final size:72
Alignment explanation
Indices: 94534--95305 Score: 536
Period size: 72 Copynumber: 11.0 Consensus size: 72
94524 TGCATTAATA
* * * *
94534 CATCCATTCATGCATTTTAATCATGGCATCCTTTCATGCCCTAATGCATCCTTTCATGCAATTTA
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
94599 GTTATGG
66 GTTATGG
* *
94606 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC--CTTA
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
94669 ---AT-G
66 GTTATGG
* * *
94672 CATCCGTTCATGCATTTTACTTATGACATCCTTTCATGCCTTAATGCATCCGTTT-ATGCATTTT
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC-TTTCATGCATTTT
*
94736 AATTATGG
65 AGTTATGG
* * * *
94744 CATCCTTTCATGC--CTT-A--AT-GCACCCTTTCATGCATTTTAATTATGGCATCCCTTCATGC
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATGC
94803 ATTTTAGTTATGG
60 ATTTTAGTTATGG
** * * *
94816 CATCCTTTCAT--AACTT-A--AT-GCATCCATTCATGCATTTTAATTATGGCATCCATTCATGC
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATG-
*
94875 CA-TTTAATTATGG
59 CATTTTAGTTATGG
* * *
94888 CATCATTTCATGCCTTTTAATTATGGCATCCTTTCATGCCTTTATGCATCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
94953 GTTATGG
66 GTTATGG
* * * * *
94960 CATCCTTTAATGC--CTT-A--AT-GCAT-TTGTTCATGCATTTTAATTATGGCATCATTTCATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCT-TTCATGC--CTT-A--AT-GCATCCTTTCATG
*
95018 C--CTTA---AT-G
59 CATTTTAGTTATGG
* * *
95026 CATCCTTTCATGCATTTTAATTTTGACATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTTA
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* *
95091 ATTATGA
66 GTTATGG
* ** * *
95098 CATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATGTATTTTAGTTATGACATCTTTTCTTGC
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATG--CCTTA---ATG-CATCCTTTCATGC
*
95157 --CTT-G--AT-G
60 ATTTTAGTTATGG
* * * *
95164 CATCCGTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGTATCATTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* * *
95229 ATCATGT
66 GTTATGG
* * *
95236 CATCCTTTCATGCATTTTAATTATGGCATACTTTCATGTCTTAATGCATCCGTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
95301 GTTAT
66 GTTAT
95306 TAACTCGGTT
Statistics
Matches: 558, Mismatches: 80, Indels: 124
0.73 0.10 0.16
Matches are distributed among these distances:
65 1 0.00
66 135 0.24
67 18 0.03
68 19 0.03
69 6 0.01
70 19 0.03
71 20 0.04
72 315 0.56
73 5 0.01
74 2 0.00
75 1 0.00
76 2 0.00
77 2 0.00
78 13 0.02
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (72 bp):
CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
GTTATGG
Found at i:94711 original size:66 final size:66
Alignment explanation
Indices: 94520--94733 Score: 284
Period size: 66 Copynumber: 3.2 Consensus size: 66
94510 ATGGTCTCTT
* * *
94520 TTCATGCATTAATACATCCATTCATGCATTTTAATCATGGCATCCTTTCATGCCCTAATGCATCC
1 TTCATGCATTAATGCATCCATTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
*
94585 T
66 G
*
94586 TTCATGCAATTTAGTTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
1 TTCATGC-A-TTA---AT-GCATCCATTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
94651 GCATCCG
60 GCATCCG
* * * *
94658 TTCATGCCTTAATGCATCCGTTCATGCATTTTACTTATGACATCCTTTCATGCCTTAATGCATCC
1 TTCATGCATTAATGCATCCATTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
94723 G
66 G
*
94724 TTTATGCATT
1 TTCATGCATT
94734 TTAATTATGG
Statistics
Matches: 131, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
66 65 0.50
67 3 0.02
68 3 0.02
70 3 0.02
71 2 0.02
72 55 0.42
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.41
Consensus pattern (66 bp):
TTCATGCATTAATGCATCCATTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
G
Found at i:94802 original size:138 final size:136
Alignment explanation
Indices: 94520--94776 Score: 344
Period size: 138 Copynumber: 1.9 Consensus size: 136
94510 ATGGTCTCTT
*
94520 TTCATGCATTAATACATCCATTCATGCATTTTAATCATGGCATCCTTTCATGCCCTAATGCATCC
1 TTCATGCATTAATACATCCATTCATGCATTTTAATCATGACATCCTTTCATGCCCTAATGCATCC
* * *
94585 TTTCATGCAATTTAGTTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAA
66 TTTCATGCAATTTAATTATGGCATCCTTTCATGCA-CTTAA-TATGGCACCCTTTCATGCCTTAA
*
94650 TGCATCCG
129 TGCATCCC
* * * * * *
94658 TTCATGCCTTAATGCATCCGTTCATGCATTTTACTTATGACATCCTTTCATGCCTTAATGCATCC
1 TTCATGCATTAATACATCCATTCATGCATTTTAATCATGACATCCTTTCATGCCCTAATGCATCC
*
94723 GTTT-ATGCATTTTAATTATGGCATCCTTTCATGC-CTT-A-AT-GCACCCTTTCATGC
66 -TTTCATGCAATTTAATTATGGCATCCTTTCATGCACTTAATATGGCACCCTTTCATGC
94777 ATTTTAATTA
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
132 13 0.12
133 2 0.02
135 1 0.01
136 2 0.02
138 86 0.80
139 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (136 bp):
TTCATGCATTAATACATCCATTCATGCATTTTAATCATGACATCCTTTCATGCCCTAATGCATCC
TTTCATGCAATTTAATTATGGCATCCTTTCATGCACTTAATATGGCACCCTTTCATGCCTTAATG
CATCCC
Found at i:94839 original size:46 final size:46
Alignment explanation
Indices: 94789--95248 Score: 589
Period size: 46 Copynumber: 9.9 Consensus size: 46
94779 TTTAATTATG
* * **
94789 GCATCCCTTCATGCATTTTAGTTATGGCATCCTTTCATAACTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* *
94835 GCATCCATTCATGCATTTTAATTATGGCATCCATTCATGCCATTTAATTAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC--TT-A--AT
* * *
94886 GGCATCATTTCATGCCTTTTAATTATGGCATCCTTTCATGCCTTTAT
1 -GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* *
94933 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTAATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* *
94979 GCAT-TTGTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAAT
1 GCATCCT-TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* *
95025 GCATCCTTTCATGCATTTTAATTTTGACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* *
95071 GCATCCTTTCATGTATTTTAATTATGACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* * * * * *
95117 GCATCCTTTCATGTATTTTAGTTATGACATCTTTTCTTGCCTTGAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* *
95163 GCATCCGTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
* * * *
95209 GTATCATTTCATGCATTTTAATCATGTCATCCTTTCATGC
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC
95249 ATTTTAATTA
Statistics
Matches: 366, Mismatches: 40, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.00
46 318 0.87
47 3 0.01
48 2 0.01
49 1 0.00
50 2 0.01
51 2 0.01
52 37 0.10
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
Found at i:100791 original size:2 final size:2
Alignment explanation
Indices: 100779--100822 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
100769 TACATATGTT
*
100779 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100821 TA
1 TA
100823 ATAGTTACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:100794 original size:12 final size:12
Alignment explanation
Indices: 100769--100818 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
100759 AATTACTTAT
* *
100769 TACATATGTTTA
1 TACATATATATA
100781 TACATATATATA
1 TACATATATATA
*
100793 TATATATATATA
1 TACATATATATA
*
100805 TATATATATATA
1 TACATATATATA
100817 TA
1 TA
100819 TATAATAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (12 bp):
TACATATATATA
Found at i:101270 original size:135 final size:135
Alignment explanation
Indices: 101090--101850 Score: 868
Period size: 135 Copynumber: 5.6 Consensus size: 135
101080 TCTTTTTTCT
* * * *
101090 GGAAGAAT-AAATCTGAAAGAAGAAGAATCTGCTCCACTGCTCTTTAGGGGAGGTTAGACTCGAG
1 GGAAG-ATCAAATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCAAG
* * * * *
101154 AAAATTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAGACTGTGATTTACTTCACTAC
65 AAAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAATCAGAATGTGATTTACTTCGCTAC
101219 TCTTCA
130 TCTTCA
* * * * ** *
101225 GGAATACCAAATCTGAAAGAAGTACAATCTATTCCGCTACTCTTTAGGGGAGGTCAGACTCAAGG
1 GGAAGATCAAATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCAAGA
* * * *
101290 AAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAATCATAATGTGATTTGCTTCGTTTCT
66 AAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAATCAGAATGTGATTTACTTCGCTACT
101355 CTTCA
131 CTTCA
* * * * *
101360 GGAAGACCAAATCCGAAAGAAGAAGAATATGCTCTGCTACTCTTTAGGGGAGGTCAGACTCAAGG
1 GGAAGATCAAATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCAAGA
* * * *
101425 AATCTTTGATCCACTTCTCTTCTTTTCAGGGAAGATTGAATCA-AATGTGATTTACTTCGCTTCT
66 AAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAATCAGAATGTGATTTACTTCGCTACT
101489 CTTCA
131 CTTCA
* * * * * *
101494 AGAAGATCATATATGAAGGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTTAGACTCAAGG
1 GGAAGATCAAATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCAAGA
* * *
101559 AAA-TCTTGATCCACTTTCTCTGCTCTTCAGGGAAGAATT-AAT-AGATTGTGATTTGCTTTGCT
66 AAACT-TTGATCCAC-TTCTCTGCTCTTCAGGGAAG-ATTGAATCAGAATGTGATTTACTTCGCT
* * *
101621 GCTATTAA
128 ACTCTTCA
** *
101629 ATAAGATCAAATATGAAAGAAGAAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCTAA
1 GGAAGATCAAATCTGAAAGAAG-AAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTC-AA
* * * * * * * * *
101694 AAAAACTTTGATCCACTTTTTTGTTCTTCAAGGAAGATTAAATC-GGATTTGATTTACTTCACTA
64 GAAAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAATCAGAATGTGATTTACTTCGCTA
* * *
101758 ATTTTTA
129 CTCTTCA
* * * *
101765 GGAAGATCAAATCTGAAAGAAGAAAGAATCTCCTCCACTACTCTTTAGGGGAGGTTAGACTCGAG
1 GGAAGATCAAATCTGAAAGAAG-AAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCAAG
101830 AAAAACTTTGATCCACTTCTC
65 -AAAACTTTGATCCACTTCTC
101851 CGTACCCGAG
Statistics
Matches: 534, Mismatches: 81, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
133 1 0.00
134 93 0.17
135 274 0.51
136 151 0.28
137 14 0.03
138 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (135 bp):
GGAAGATCAAATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCAAGA
AAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAATCAGAATGTGATTTACTTCGCTACT
CTTCA
Found at i:104350 original size:13 final size:13
Alignment explanation
Indices: 104286--104342 Score: 96
Period size: 13 Copynumber: 4.4 Consensus size: 13
104276 GTCATAAATC
104286 TATGACGCGCATT
1 TATGACGCGCATT
*
104299 TATGACACGCATT
1 TATGACGCGCATT
*
104312 TATGACACGCATT
1 TATGACGCGCATT
104325 TATGACGCGCATT
1 TATGACGCGCATT
104338 TATGA
1 TATGA
104343 TGTGCATTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:104422 original size:85 final size:84
Alignment explanation
Indices: 104322--104483 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 84
104312 TATGACACGC
* * * *
104322 ATTTATGACGCGCATTTATGA-TGTGCATTGCGAGTCATTGAAGCCCCCATCA-TAAATGAAGAT
1 ATTTATGACACGCATTTATGACT-TACATTGCGAGTCATTGAAGCACACATCATTAAA--AAGAT
*
104385 GACACACATTTGTGTTTCATAA
63 GACACACATTCGTGTTTCATAA
* * *
104407 ATTTATGACATGCATTTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAAAAGATGAC
1 ATTTATGACACGCATTTATGACTTACATTGCGAGTCATTGAAGCACACATCATTAAAAAGATGAC
104472 ACACATTCGTGT
66 ACACATTCGTGT
104484 GTCGTGATTG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 19 0.28
85 43 0.64
86 5 0.07
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGACTTACATTGCGAGTCATTGAAGCACACATCATTAAAAAGATGAC
ACACATTCGTGTTTCATAA
Found at i:104941 original size:36 final size:36
Alignment explanation
Indices: 104891--104963 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
104881 AAATTTAAGT
*
104891 ATGAAAAACTCTTTTTACTCACATTTGTCAATTCAA
1 ATGAAAAACACTTTTTACTCACATTTGTCAATTCAA
104927 ATGAAAAACACTTTTTACTCACATTTGTCAATTCAA
1 ATGAAAAACACTTTTTACTCACATTTGTCAATTCAA
104963 A
1 A
104964 GTAGGGCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (36 bp):
ATGAAAAACACTTTTTACTCACATTTGTCAATTCAA
Found at i:106966 original size:2 final size:2
Alignment explanation
Indices: 106959--107030 Score: 55
Period size: 2 Copynumber: 38.5 Consensus size: 2
106949 AACTAAAATA
* *
106959 AT AT AT AT AT AT AT AT A- AT AT A- AT AT TT AT AT A- AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
106997 AA AT AT TT AT AT AA AA AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
107031 ACTTATAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
1 5 0.09
2 51 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:108816 original size:3 final size:3
Alignment explanation
Indices: 108808--108864 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
108798 ATTTTTATTA
** **
108808 AAT AAT AAT AAT AAT AAT ATAT AAT AAT TTT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
108854 AAT AAT AAT AA
1 AAT AAT AAT AA
108865 AACGAAATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:109682 original size:76 final size:76
Alignment explanation
Indices: 109019--109655 Score: 1148
Period size: 76 Copynumber: 8.4 Consensus size: 76
109009 AGGTCCTAAG
*
109019 AACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109084 GGCTTTTTGGA
66 GGCTTTTTGGA
* *
109095 AACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
*
109160 GGCTTTTTGAA
66 GGCTTTTTGGA
* *
109171 AACATCATGCACTGCAGAACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109236 GGCTTTTTGGA
66 GGCTTTTTGGA
* *
109247 AACATCATGCACTGCAGGACTTACAGATGACTCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109312 GGCTTTTTGGA
66 GGCTTTTTGGA
109323 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109388 GGCTTTTTGGA
66 GGCTTTTTGGA
*
109399 AACATCATGCACTGTAGGACTTACAGATTACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109464 GGCTTTTTGGA
66 GGCTTTTTGGA
*
109475 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGGA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109540 GGCTTTTTGGA
66 GGCTTTTTGGA
* * *
109551 AACATCATGCACTTTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAATCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
109616 GGCTTTTTGGA
66 GGCTTTTTGGA
*
109627 AACATCATGCACTTTAGGACTTACAGATG
1 AACATCATGCACTGTAGGACTTACAGATG
109656 TGGGAAATAG
Statistics
Matches: 545, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 545 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (76 bp):
AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
GGCTTTTTGGA
Found at i:110360 original size:22 final size:22
Alignment explanation
Indices: 110335--110413 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
110325 CATAAAGCTT
110335 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
110357 TCATCTTTAAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
110379 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
110401 TCATCTTTGAAAA
1 TCATCTTTGAAAA
110414 ATGTAGATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:114511 original size:72 final size:72
Alignment explanation
Indices: 114421--114555 Score: 207
Period size: 72 Copynumber: 1.9 Consensus size: 72
114411 TATAATGGGT
** *
114421 TAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAAGCAT
1 TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAAGCAT
114486 AACAGAC
66 AACAGAC
* * * *
114493 TAGCTGAATATTATCCATAAAACCAGGGCTATTAACCAATTGTTTTAGGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAAGC
114556 TTTATTGTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAAGCAT
AACAGAC
Found at i:118596 original size:11 final size:10
Alignment explanation
Indices: 118570--118595 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
118560 CAGAAAAAAT
118570 AAAAAATTAA
1 AAAAAATTAA
118580 AAAAAATTAA
1 AAAAAATTAA
118590 AAAAAA
1 AAAAAA
118596 AAACAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:118603 original size:18 final size:18
Alignment explanation
Indices: 118563--118604 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
118553 ATTTATTCAG
*
118563 AAAAAATAAAAAATTAAA
1 AAAAAATAAAAAATAAAA
*
118581 AAAAATTAAAAAA-AAAA
1 AAAAAATAAAAAATAAAA
118598 ACAAAAA
1 A-AAAAA
118605 GTTAGAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAAAATAAAA
Found at i:120492 original size:2 final size:2
Alignment explanation
Indices: 120485--120521 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
120475 TTTATCATAA
120485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
120522 CATAGGTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:121729 original size:3 final size:3
Alignment explanation
Indices: 121721--121782 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
121711 ATTTTTATTA
** ** **
121721 AAT AAT AAT AAT AAT AAT -AT ATAT AAT AAT TTT AAT TTT AAT TTT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
121766 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
121783 AACGAAATGA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:121970 original size:2 final size:2
Alignment explanation
Indices: 121963--121987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
121953 TGTGTTGCAA
121963 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
121988 CTTCTTACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123865 original size:57 final size:56
Alignment explanation
Indices: 123798--123938 Score: 178
Period size: 57 Copynumber: 2.5 Consensus size: 56
123788 TCGATACTTC
**
123798 CAAGAAATAAATTCAACAATTTATTTCTTTGTACAAAATAGA-ATCATACTTGATTCT
1 CAAGAAATAAATTCAACAATTTATTTCTTT-TACAAAATA-ACATCATACAAGATTCT
*
123855 CAAGAAATAAATTCAACAATTTTAATTCTTTTACAAAATAACATCATACAAGATTCT
1 CAAGAAATAAATTCAACAA-TTTATTTCTTTTACAAAATAACATCATACAAGATTCT
* * *
123912 -ATGAAAATAAATTTAATAATTTATTTC
1 CAAG-AAATAAATTCAACAATTTATTTC
123939 CACCTATGAA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
56 10 0.14
57 54 0.73
58 10 0.14
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (56 bp):
CAAGAAATAAATTCAACAATTTATTTCTTTTACAAAATAACATCATACAAGATTCT
Found at i:126986 original size:453 final size:454
Alignment explanation
Indices: 126139--127043 Score: 1641
Period size: 453 Copynumber: 2.0 Consensus size: 454
126129 TGGGCAATTC
126139 ATAATTCTGATTGCCGGAGGTCTTCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGGCAGCCTAC
1 ATAATTCTGATTGCCGGAGGTCTTCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGGCAGCCTAC
126204 TACCTTACCTCCCCCTCACCCCATTACATATATGGGAATAGGGTCAACTAATTTTTTTTCTTATA
66 TACCTTACCTCCCCCTCACCCCATTACATATATGGGAATAGGGTCAACTAATTTTTTTTCTTATA
*
126269 ATCATTAATACAAAAAATTAGCCACTTAAAATAAACTTAAAGGTAGATACAAACAGATATGACCG
131 ATCATTAATACAAAAAACTAGCCACTTAAAATAAACTTAAAGGTAGATACAAACAGATATGACCG
* *
126334 CATCGACAAATAAACCACAAAGGAGATCAAGCTACCATTGAAAATCGTAAATCAAAATCAAACGA
196 CATCGAAAAATAAACCACAAAAGAGATCAAGCTACCATTGAAAATCGTAAATCAAAATCAAACGA
*
126399 CATGATAAAAATATCCACGAACGCAAATTGTGTATCCAAATTTAATTTGAAGGTCCAAAGCAAGA
261 CATGATAAAAATATCCACGAACGCAAATTGCGTATCCAAATTTAATTTGAAGGTCCAAAGCAAGA
* *
126464 GAAATAAGCTTGATAACAAATCAGAGCTATCTCGATCATTAGTAGTAATGTCAAATCCAATCCTG
326 GAAATAAGCATGATAACAAATCAGAGCTATCTCGATCATTAGTAGTAATATCAAATCCAATCCTG
*
126529 ATAAAAAAACAAAAATAACGACCAAACGACAAAAAATGTGCCAAAACATAGAAAGAAATGTGTA
391 ATAAAAAAACAAAAATAACGACCAAACGACAAAAAATATGCCAAAACATAGAAAGAAATGTGTA
* *
126593 ATAATTCTGATTGCCGGAGGTCTTCGACGGAAGCTGCTCTCAACCTGGCGTT-GGGTCAGCCTAC
1 ATAATTCTGATTGCCGGAGGTCTTCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGGCAGCCTAC
126657 TACCTTACCTCCCCCTCACCCCATTACATATATGGGAATAGGGTCAACTAATTTTTTTTCTTATA
66 TACCTTACCTCCCCCTCACCCCATTACATATATGGGAATAGGGTCAACTAATTTTTTTTCTTATA
* *
126722 ATCATTAATACAAAAAACTAGTCACTTAAAATAAACTTAAAGGTATATACAAACAGATATGACCG
131 ATCATTAATACAAAAAACTAGCCACTTAAAATAAACTTAAAGGTAGATACAAACAGATATGACCG
* **
126787 CATCGAAAAATAAACCACAAAAGAGATCAAGCTACCATTGAAAATCGTAAATCAGAATCAAGTGA
196 CATCGAAAAATAAACCACAAAAGAGATCAAGCTACCATTGAAAATCGTAAATCAAAATCAAACGA
*
126852 CATGATAAAAATATTCACGAACGCAAATTGCGTATCCAAATTTAATTTGAAGGTCCAAAGCAAGA
261 CATGATAAAAATATCCACGAACGCAAATTGCGTATCCAAATTTAATTTGAAGGTCCAAAGCAAGA
*
126917 GAAATAAGCATGATAACAAATCAGAGCTATCTCGATCATTAGTAGTAATATCAAATCCAATCTTG
326 GAAATAAGCATGATAACAAATCAGAGCTATCTCGATCATTAGTAGTAATATCAAATCCAATCCTG
* *
126982 ATAAAAAAATAAAAATAACGACCAAACGACAAAAAATATGTCAAAACATAGAAAGAAATGTG
391 ATAAAAAAACAAAAATAACGACCAAACGACAAAAAATATGCCAAAACATAGAAAGAAATGTG
127044 ACATAAATGC
Statistics
Matches: 433, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
453 382 0.88
454 51 0.12
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (454 bp):
ATAATTCTGATTGCCGGAGGTCTTCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGGCAGCCTAC
TACCTTACCTCCCCCTCACCCCATTACATATATGGGAATAGGGTCAACTAATTTTTTTTCTTATA
ATCATTAATACAAAAAACTAGCCACTTAAAATAAACTTAAAGGTAGATACAAACAGATATGACCG
CATCGAAAAATAAACCACAAAAGAGATCAAGCTACCATTGAAAATCGTAAATCAAAATCAAACGA
CATGATAAAAATATCCACGAACGCAAATTGCGTATCCAAATTTAATTTGAAGGTCCAAAGCAAGA
GAAATAAGCATGATAACAAATCAGAGCTATCTCGATCATTAGTAGTAATATCAAATCCAATCCTG
ATAAAAAAACAAAAATAACGACCAAACGACAAAAAATATGCCAAAACATAGAAAGAAATGTGTA
Found at i:127131 original size:56 final size:56
Alignment explanation
Indices: 127064--127175 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
127054 AAAATAAAAT
127064 ATGTCATGAAAAGAGAGTTAATAAAAAATATAATATAATAAAATAAAGAAAAATAA
1 ATGTCATGAAAAGAGAGTTAATAAAAAATATAATATAATAAAATAAAGAAAAATAA
127120 ATGTCATGAAAAGAGAGTTAATAAAAAATATAATATAATAAAATAAAGAAAAATAA
1 ATGTCATGAAAAGAGAGTTAATAAAAAATATAATATAATAAAATAAAGAAAAATAA
127176 TGAATACCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (56 bp):
ATGTCATGAAAAGAGAGTTAATAAAAAATATAATATAATAAAATAAAGAAAAATAA
Found at i:128882 original size:12 final size:12
Alignment explanation
Indices: 128865--128903 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
128855 AGTAGTAAGG
128865 GAAATGTTCTCT
1 GAAATGTTCTCT
128877 GAAATGTTCTCT
1 GAAATGTTCTCT
128889 GAAAT-TCTCTCT
1 GAAATGT-TCTCT
128901 GAA
1 GAA
128904 TTTTCCCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (12 bp):
GAAATGTTCTCT
Found at i:131016 original size:22 final size:22
Alignment explanation
Indices: 130969--131016 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
130959 TTTCTTTAAA
* * *
130969 AAAAATAGAATAATTATTTCTT
1 AAAAATAGAATAATTAGTTATC
130991 AAAAA-AGAATAATTAAGTTATC
1 AAAAATAGAATAATT-AGTTATC
131013 AAAA
1 AAAA
131017 TAAAATTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
AAAAATAGAATAATTAGTTATC
Found at i:136648 original size:17 final size:17
Alignment explanation
Indices: 136625--136663 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
136615 TAGCTTATTA
136625 TTTTTTTCTCT-TTCTT
1 TTTTTTTCTCTCTTCTT
136641 TCTTTTTTCTCTCTTCTT
1 T-TTTTTTCTCTCTTCTT
136659 TTTTT
1 TTTTT
136664 ATTTCACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTCTCTCTTCTT
Found at i:136653 original size:19 final size:16
Alignment explanation
Indices: 136625--136668 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
136615 TAGCTTATTA
136625 TTTTTTTCTCTTTCTTT
1 TTTTTTTCTC-TTCTTT
136642 CTTTTTTCTCTCTTCTTT
1 -TTTTTT-TCTCTTCTTT
136660 TTTTATTTC
1 TTTT-TTTC
136669 ACTCTCACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTCTCTTCTTT
Found at i:136673 original size:19 final size:18
Alignment explanation
Indices: 136626--136673 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
136616 AGCTTATTAT
*
136626 TTTTTTCTCT-TTCTTTC
1 TTTTTTCACTCTTCTTTC
* *
136643 TTTTTTCTCTCTTCTTTT
1 TTTTTTCACTCTTCTTTC
136661 TTTATTTCACTCT
1 TTT-TTTCACTCT
136674 CACTGCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 10 0.37
18 9 0.33
19 8 0.30
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCACTCTTCTTTC
Found at i:137028 original size:29 final size:27
Alignment explanation
Indices: 136978--137033 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
136968 AATATAATAA
* * *
136978 TGATAATATTAAAATTATACATGAATT
1 TGATAAAATTAAAATGATACATAAATT
137005 TGATAAAATGTAAACATGATACATAAATT
1 TGATAAAAT-TAAA-ATGATACATAAATT
137034 CTAATATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 12 0.50
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (27 bp):
TGATAAAATTAAAATGATACATAAATT
Found at i:137578 original size:18 final size:19
Alignment explanation
Indices: 137555--137594 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
137545 TCAAAAAATC
* *
137555 ATTTTAAATATTATTA-TA
1 ATTTTAAAAAATATTACTA
137573 ATTTTAAAAAATATTACTA
1 ATTTTAAAAAATATTACTA
137592 ATT
1 ATT
137595 ACATTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTAAAAAATATTACTA
Found at i:142998 original size:20 final size:19
Alignment explanation
Indices: 142953--143010 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
142943 TCCAACATTG
*
142953 GTAACAATTGGTTATCTTTT
1 GTAACAATTAG-TATCTTTT
142973 -TAACAATTAGTATCCTTTT
1 GTAACAATTAGTAT-CTTTT
142992 GTAACAATTAGTATCTTTT
1 GTAACAATTAGTATCTTTT
143011 CATTAAACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 3 0.09
19 19 0.54
20 13 0.37
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (19 bp):
GTAACAATTAGTATCTTTT
Found at i:143186 original size:29 final size:30
Alignment explanation
Indices: 143116--143175 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
143106 CAATTTAAGG
143116 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATG-TTTTTGGACTTGAATTGAATTTA
143147 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
143176 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:143330 original size:17 final size:17
Alignment explanation
Indices: 143308--143372 Score: 91
Period size: 16 Copynumber: 4.0 Consensus size: 17
143298 TATTGCTCGG
143308 AGGGTATCTATACCCCC
1 AGGGTATCTATACCCCC
*
143325 AGGGTATCCATA-CCCC
1 AGGGTATCTATACCCCC
*
143341 -GGGTATCGATACCCCC
1 AGGGTATCTATACCCCC
143357 A-GGTATCTATACCCCC
1 AGGGTATCTATACCCCC
143373 TGGCTGCAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 10 0.23
16 22 0.51
17 11 0.26
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (17 bp):
AGGGTATCTATACCCCC
Found at i:143427 original size:21 final size:21
Alignment explanation
Indices: 143403--143444 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
143393 ATTTGAATTT
143403 TATGAAGTA-GTACCGATACCC
1 TATGAAG-AGGTACCGATACCC
143424 TATGAAGAGGTACCGATACCC
1 TATGAAGAGGTACCGATACCC
143445 CTATCTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (21 bp):
TATGAAGAGGTACCGATACCC
Done.