Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 92 of 290
Found at i:30961618 original size:55 final size:53
Alignment explanation
Indices: 30961482--30961690 Score: 199
Period size: 55 Copynumber: 3.9 Consensus size: 53
30961472 ACCCTTTTGA
* * * *
30961482 AACTTACCATTGCCATGTCTCGACATGGTCTTAGATGGTATCCTTACCTTATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTACCTTATG
* * * *
30961535 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTACCTTAT-G
* *** *
30961589 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTACCTTATG
* *
30961642 AAACCTTACCAATTGCCATGCCTT-AGCATGGTCTTACATGGTATCCTTA
1 -AA-CTTACCAA-TGCCATGTCTTGA-CATGGTCTTACATGGGATCCTTA
30961691 AACCCTAATG
Statistics
Matches: 128, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
52 2 0.02
53 44 0.34
54 9 0.07
55 71 0.55
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTACCTTATG
Found at i:30961634 original size:108 final size:110
Alignment explanation
Indices: 30961482--30961682 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
30961472 ACCCTTTTGA
* * *
30961482 AACTTACCATTGCCATGTCTCGACATGGTCTTAGATGGTATCCTTACCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTACCTTA-GAAACCTCACCAA
*
30961545 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * * *
30961590 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTACCTTAGAAACCTCACCAAT
30961655 TGCCATGCCTTAGCATGGTCTTACATGG
66 TGCCATGCCTTAGCATGGTCTTACATGG
30961683 TATCCTTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 1 0.01
108 46 0.57
109 7 0.09
110 27 0.33
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTACCTTAGAAACCTCACCAAT
TGCCATGCCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:30965817 original size:39 final size:40
Alignment explanation
Indices: 30965774--30965941 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
30965764 CTCGTTCAAG
* * * *
30965774 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
30965813 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
30965853 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
30965893 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
30965933 TGCCTTCGG
1 TGCCTTCGG
30965942 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:30965954 original size:40 final size:40
Alignment explanation
Indices: 30965811--30965941 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
30965801 TAACTCATAC
* *
30965811 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
30965851 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
30965891 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
30965931 AATGCCTTCGG
1 AATGCCTTCGG
30965942 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.04
40 79 0.96
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:30965954 original size:80 final size:79
Alignment explanation
Indices: 30965774--30965993 Score: 218
Period size: 80 Copynumber: 2.8 Consensus size: 79
30965764 CTCGTTCAAG
* * * * * * * *
30965774 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-TACAATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACTTAACCCGGATATTGTCACTTAGCACAA-GCCTTCGGGACTTAACCCGGATAT
*
30965838 TAAAACTCGCACGAA
65 TAAAACTCGCACAAA
*
30965853 TGCCTTCGGGACTTAACCCGGA-ATTAGT-A-TCTCGCACAAAGGCCTTCGGGACTTAACCCGGA
1 TGCCTTCGGGACTTAACCCGGATATT-GTCACT-TAGCAC-AA-GCCTTCGGGACTTAACCCGGA
30965915 -ATTAATAACTCGCACAAA
62 TATTAA-AACTCGCACAAA
** *
30965933 TGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCACAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAACCCGGATATTGTCACTTAGCACAAGCCTTCGGGACTTAACCCGGA
30965994 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
77 1 0.01
78 3 0.03
79 50 0.42
80 54 0.46
81 9 0.08
82 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (79 bp):
TGCCTTCGGGACTTAACCCGGATATTGTCACTTAGCACAAGCCTTCGGGACTTAACCCGGATATT
AAAACTCGCACAAA
Found at i:30967125 original size:56 final size:56
Alignment explanation
Indices: 30967054--30967170 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
30967044 TTCTTTATTA
30967054 CCCATACTCCTTATTTTATTCTTCCATTAACAAAACATGTTTCATGACATGTTTTG
1 CCCATACTCCTTATTTTATTCTTCCATTAACAAAACATGTTTCATGACATGTTTTG
* *
30967110 CCCATGCTTCTTATTTTATTCTTCCATTAACAAAACATGTTTCATGACATGTTTTG
1 CCCATACTCCTTATTTTATTCTTCCATTAACAAAACATGTTTCATGACATGTTTTG
30967166 CCCAT
1 CCCAT
30967171 CATTCCTTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.43
Consensus pattern (56 bp):
CCCATACTCCTTATTTTATTCTTCCATTAACAAAACATGTTTCATGACATGTTTTG
Found at i:30973750 original size:40 final size:40
Alignment explanation
Indices: 30973698--30973841 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 40
30973688 TAACTCATAC
* *
30973698 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
30973738 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
30973778 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
30973819 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
30973842 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
39 9 0.10
40 70 0.78
41 11 0.12
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:30978532 original size:3 final size:3
Alignment explanation
Indices: 30978524--30978558 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30978514 GCATTAGTAA
30978524 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30978559 CAGAGACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30979059 original size:15 final size:15
Alignment explanation
Indices: 30979039--30979070 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30979029 AAGAAAATTA
30979039 AAGATCCATGGTTCT
1 AAGATCCATGGTTCT
30979054 AAGATCCATGGTTCT
1 AAGATCCATGGTTCT
30979069 AA
1 AA
30979071 AGCTATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (15 bp):
AAGATCCATGGTTCT
Found at i:30982340 original size:66 final size:66
Alignment explanation
Indices: 30982258--30982428 Score: 225
Period size: 66 Copynumber: 2.6 Consensus size: 66
30982248 GTCAGTAGGC
* * * *
30982258 TCACACGGCCTAGCACACAGGCGTGTGGCTTGGCCGTGTGTCAGAAGCCAGAATACTCACCATTT
1 TCACACGGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAAGCCACAATACTCACCATTT
30982323 T
66 T
* * * * * *
30982324 TCACACGGCCTAGCACACGGGCATGTGGCGTGGCCATGTGTCACAAGTCACTATGCTCATCATTT
1 TCACACGGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAAGCCACAATACTCACCATTT
30982389 T
66 T
* * *
30982390 TCACATGGCCTAGCACATGGGCATGTGGCTTGGCTGTGT
1 TCACACGGCCTAGCACACGGGCATGTGGCTTGGCCGTGT
30982429 AACCCAAGTC
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 90 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (66 bp):
TCACACGGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAAGCCACAATACTCACCATTT
T
Found at i:30985301 original size:16 final size:17
Alignment explanation
Indices: 30985282--30985327 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
30985272 TAAAAAATTA
*
30985282 TAAATATATATAA-CTT
1 TAAATATATAAAATCTT
*
30985298 TAAAAATA-AAAATCTT
1 TAAATATATAAAATCTT
30985314 TAGAATATATAAAA
1 TA-AATATATAAAA
30985328 ACGTTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 5 0.21
18 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAATATATAAAATCTT
Found at i:30986362 original size:3 final size:3
Alignment explanation
Indices: 30986354--30986386 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
30986344 CTATTTAGTT
*
30986354 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30986387 CGCTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:30992627 original size:67 final size:67
Alignment explanation
Indices: 30992528--30992812 Score: 245
Period size: 67 Copynumber: 4.3 Consensus size: 67
30992518 AAGGTATAGG
30992528 GTGTAAGACCATAA-CTCGACTATGGCAGCATAAAGAGTCCACTAGGATAGTAAACATGAGGTAT
1 GTGTAAGACCA-AAGCTCGACTATGGCAGCATAAAGAGTCCACTAGGATAGTAAACATGAGGTAT
30992592 GTT
65 GTT
* * * * * * ** * * *
30992595 GTGTATGATCATAGTTCGACTATGGCAACATAAAGA-TTCTGTCGGGACAGTAAACACGAGGTAT
1 GTGTAAGACCAAAGCTCGACTATGGCAGCATAAAGAGTCCACT-AGGATAGTAAACATGAGGTAT
30992659 GTT
65 GTT
** * ** **
30992662 GTGTAAGACCAAAGCTCGACTATGATAGCATAGAGAGTCTGCTAGGATAGTAAACATGTTGTATG
1 GTGTAAGACCAAAGCTCGACTATGGCAGCATAAAGAGTCCACTAGGATAGTAAACATGAGGTATG
30992727 TT
66 TT
* * * **** * * *
30992729 GTGTAAGACCATAA-CTCGATTATGGCAGTATACAGAGTTTGTTAGCACAGTAAACA-CAGGGTA
1 GTGTAAGACCA-AAGCTCGACTATGGCAGCATAAAGAGTCCACTAGGATAGTAAACATGA-GGTA
30992792 TGTT
64 TGTT
*
30992796 GTGTAAGACCATAGCTC
1 GTGTAAGACCAAAGCTC
30992813 AGCTACGACA
Statistics
Matches: 171, Mismatches: 41, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
66 5 0.03
67 162 0.95
68 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (67 bp):
GTGTAAGACCAAAGCTCGACTATGGCAGCATAAAGAGTCCACTAGGATAGTAAACATGAGGTATG
TT
Found at i:30992828 original size:134 final size:134
Alignment explanation
Indices: 30992528--30992828 Score: 365
Period size: 134 Copynumber: 2.2 Consensus size: 134
30992518 AAGGTATAGG
* * *
30992528 GTGTAAGACCATAACTCGACTATGGCAGCATAAAGAGTCCACTAGGATAGTAAACATGAGGTATG
1 GTGTAAGACCATAGCTCGACTATGACAGCATAGAGAGTCCACTAGGATAGTAAACATGAGGTATG
* * ** * *
30992593 TTGTGTATGATCATAGTTCGACTATGGCAACATAAAGATTCTGTCGGGACAGTAAACACGAGGTA
66 TTGTGTAAGACCATAACTCGACTATGGCAACATAAAGATTCTGTCAGCACAGTAAACACGAGGTA
30992658 TGTT
131 TGTT
* * ** **
30992662 GTGTAAGACCAAAGCTCGACTATGATAGCATAGAGAGTCTGCTAGGATAGTAAACATGTTGTATG
1 GTGTAAGACCATAGCTCGACTATGACAGCATAGAGAGTCCACTAGGATAGTAAACATGAGGTATG
* ** * *
30992727 TTGTGTAAGACCATAACTCGATTATGGCAGTATACAGAGTT-TGTTAGCACAGTAAACAC-AGGG
66 TTGTGTAAGACCATAACTCGACTATGGCAACATAAAGA-TTCTGTCAGCACAGTAAACACGA-GG
30992790 TATGTT
129 TATGTT
*
30992796 GTGTAAGACCATAGCTC-AGCTACGACAGCATAG
1 GTGTAAGACCATAGCTCGA-CTATGACAGCATAG
30992829 TGTAACACCC
Statistics
Matches: 141, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
133 2 0.01
134 137 0.97
135 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (134 bp):
GTGTAAGACCATAGCTCGACTATGACAGCATAGAGAGTCCACTAGGATAGTAAACATGAGGTATG
TTGTGTAAGACCATAACTCGACTATGGCAACATAAAGATTCTGTCAGCACAGTAAACACGAGGTA
TGTT
Found at i:30994184 original size:13 final size:13
Alignment explanation
Indices: 30994153--30994225 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
30994143 TCCTACAAAT
* *
30994153 ATTTCGTATAAAC
1 ATTTCATATAACC
*
30994166 ACTTCATATAACC
1 ATTTCATATAACC
* * *
30994179 GTTTCATATATCT
1 ATTTCATATAACC
*
30994192 ATTTCTATATAAAC
1 ATTTC-ATATAACC
*
30994206 ATTTCGTATAACC
1 ATTTCATATAACC
30994219 ATTTCAT
1 ATTTCAT
30994226 TTACACATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
13 35 0.78
14 10 0.22
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:30994222 original size:27 final size:26
Alignment explanation
Indices: 30994153--30994225 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 26
30994143 TCCTACAAAT
* * *
30994153 ATTTCGTATAAACACTTCATATAACC
1 ATTTCGTATAACCATTTCATATAAAC
* * * *
30994179 GTTTCATATATCTATTTCTATATAAAC
1 ATTTCGTATAACCATTTC-ATATAAAC
30994206 ATTTCGTATAACCATTTCAT
1 ATTTCGTATAACCATTTCAT
30994226 TTACACATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
26 14 0.40
27 21 0.60
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTTCGTATAACCATTTCATATAAAC
Found at i:30999200 original size:21 final size:21
Alignment explanation
Indices: 30999161--30999200 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30999151 AAAGGTCATG
*
30999161 GATGATTTAAGAGTGACTTAA
1 GATGATTTAAGAGTCACTTAA
30999182 GATGATTTGAA-AGTCACTT
1 GATGATTT-AAGAGTCACTT
30999201 GTTCTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (21 bp):
GATGATTTAAGAGTCACTTAA
Found at i:30999761 original size:27 final size:28
Alignment explanation
Indices: 30999705--30999767 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 28
30999695 GATTGCATGA
30999705 ATATGAATGTGATTGGACCTGATGGGCC
1 ATATGAATGTGATTGGACCTGATGGGCC
* *
30999733 ATATGGATGTGATTGG-GCTGATGGGCC
1 ATATGAATGTGATTGGACCTGATGGGCC
30999760 ATATGAAT
1 ATATGAAT
30999768 TAGATTAGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.30
Consensus pattern (28 bp):
ATATGAATGTGATTGGACCTGATGGGCC
Found at i:30999778 original size:27 final size:27
Alignment explanation
Indices: 30999705--30999778 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
30999695 GATTGCATGA
30999705 ATATGAATGTGATT-GGACCTGATGGGCC
1 ATATGAATGTGATTAGG--CTGATGGGCC
* *
30999733 ATATGGATGTGATTGGGCTGATGGGCC
1 ATATGAATGTGATTAGGCTGATGGGCC
30999760 ATATGAAT-TAGATTAGGCT
1 ATATGAATGT-GATTAGGCT
30999779 TAAAAGGGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.02
27 25 0.61
28 13 0.32
29 2 0.05
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.31
Consensus pattern (27 bp):
ATATGAATGTGATTAGGCTGATGGGCC
Found at i:31007305 original size:17 final size:18
Alignment explanation
Indices: 31007272--31007305 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31007262 TTCAAAGAAG
31007272 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
31007290 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
31007306 CTTCAATCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:31007856 original size:49 final size:49
Alignment explanation
Indices: 31007801--31008022 Score: 210
Period size: 49 Copynumber: 4.7 Consensus size: 49
31007791 GCACATCACA
*
31007801 GTCGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATCGAG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG
* * * * *
31007850 GTCGATGCCATGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCGAT
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG
* * * * *
31007899 GTTGATGCCATGTCCCAGACAGGTCTTAAACTAAC--ACACA-A-C-AG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG
* * *
31007943 G-CTGACGCCATGTACCAGACAGGTCTTACACT-AGCTTGT-ATATCTCGAG
1 GTC-GATGCCATGTCCCAGACAGGTCTTACACTGA-CTT-TCATATATCGAG
* *
31007992 GTAGATG-CATGTCCCAGACATGTCTTACACT
1 GTCGATGCCATGTCCCAGACAGGTCTTACACT
31008023 AGCTCTTGTC
Statistics
Matches: 138, Mismatches: 26, Indels: 19
0.75 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 29 0.21
45 1 0.01
46 3 0.02
47 2 0.01
48 23 0.17
49 79 0.57
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG
Found at i:31007974 original size:93 final size:92
Alignment explanation
Indices: 31007856--31008023 Score: 221
Period size: 93 Copynumber: 1.8 Consensus size: 92
31007846 CGAGGTCGAT
* * * * * *
31007856 GCCATGTCCCAGATAGGTCTTACACTGGCTCT-CATCTATCGATGTTGATGCCATGTCCCAGACA
1 GCCATGTACCAGACAGGTCTTACACTAGCT-TGCATATATCGAGGTAGATG-CATGTCCCAGACA
31007920 GGTCTTAAACTAACACACAACAGGCTGAC
64 GGTCTTAAACTAACACACAACAGGCTGAC
* * *
31007949 GCCATGTACCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGTAGATGCATGTCCCAGACATG
1 GCCATGTACCAGACAGGTCTTACACTAGCTTGCATATATCGAGGTAGATGCATGTCCCAGACAGG
*
31008014 TCTTACACTA
66 TCTTAAACTA
31008024 GCTCTTGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
92 24 0.38
93 40 0.62
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (92 bp):
GCCATGTACCAGACAGGTCTTACACTAGCTTGCATATATCGAGGTAGATGCATGTCCCAGACAGG
TCTTAAACTAACACACAACAGGCTGAC
Found at i:31008022 original size:48 final size:46
Alignment explanation
Indices: 31007951--31008117 Score: 144
Period size: 46 Copynumber: 3.6 Consensus size: 46
31007941 AGGCTGACGC
* * * * **
31007951 CATGTACCAGACAGGTCTTACACTAGCTTGTATATCTCGA-GGTAGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-TATCTCAATGCCA-ATG
*
31007999 CATGTCCCAGACATGTCTTACACTAGCTCTTGTCTCAATGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTTATCTCAATGCCAATG
* * * * *
31008045 CATGTCCCAGACATGTCTTACAATGACACTCATAATGT--A-GCCGATG
1 CATGTCCCAGACATGTCTTACACT-A-GCTC-TTATCTCAATGCCAATG
31008091 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
31008118 ACACATATCA
Statistics
Matches: 100, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 61 0.61
47 6 0.06
48 28 0.28
49 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTTATCTCAATGCCAATG
Found at i:31010988 original size:51 final size:51
Alignment explanation
Indices: 31010912--31011109 Score: 272
Period size: 51 Copynumber: 3.9 Consensus size: 51
31010902 AGATACATGG
* *
31010912 TGGCCTTCACATAGTACCACCCTTGTAG-CCAAAACTATTTTATTCACAAAT
1 TGGCCTTCACATAGTACCACACTTGT-GTCCAAAACTATTTTATTCACAAAC
* *
31010963 TGGCCTTCACATAGTACCACACTTGTGTCCAAAAATATTTTATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAACTATTTTATTCACAAAC
* * * * *
31011014 TGACCTTCACATAGTATCACACTTGTGTCTAAAGCTATTATATTCACAAAC
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAACTATTTTATTCACAAAC
* * *
31011065 TGGCCTTCACATGGTACCACACTTATGTCCAAAGCTATTTTATTC
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAACTATTTTATTC
31011110 CTAAGGTTCA
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 1 0.01
51 129 0.99
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAACTATTTTATTCACAAAC
Found at i:31011195 original size:52 final size:54
Alignment explanation
Indices: 31011133--31011248 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 54
31011123 GGAAAGTTTC
* *
31011133 TCACTGAGCACAATGCCATAGACCTATTTCACTTAG-A-TGCCATGGACTTATT
1 TCACTTAGCACAATGCCATAGACCTATTTCACTTAGAATTACCATGGACTTATT
* * *
31011185 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGTACATTACCATGGACTTATT
1 TCACTTAGCACAATGCCATAGACCTATTTCACTTAG-A-ATTACCATGGACTTATT
31011241 TCACTTAG
1 TCACTTAG
31011249 ATGCCATGGC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
52 32 0.58
55 1 0.02
56 22 0.40
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (54 bp):
TCACTTAGCACAATGCCATAGACCTATTTCACTTAGAATTACCATGGACTTATT
Found at i:31011210 original size:28 final size:27
Alignment explanation
Indices: 31011133--31011276 Score: 165
Period size: 28 Copynumber: 5.4 Consensus size: 27
31011123 GGAAAGTTTC
* * *
31011133 TCACTGAGCACAATGCCATAGACCTATT
1 TCACTTAGCAC-ATGCCATGGACTTATT
31011161 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
31011185 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
* *
31011213 TCACTTAGTACATTACCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
31011241 TCACTTAG---ATGCCATGGCCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
31011265 TCACTTAGCACA
1 TCACTTAGCACA
31011277 ATGTCATATC
Statistics
Matches: 102, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
24 43 0.42
25 1 0.01
27 2 0.02
28 56 0.55
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:31017398 original size:51 final size:51
Alignment explanation
Indices: 31017329--31017526 Score: 342
Period size: 51 Copynumber: 3.9 Consensus size: 51
31017319 GGATACACAA
* *
31017329 TGGCCTTCACATAGTACCACACTTATGTCCAAAGCTATTTTATTCACAAAC
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
31017380 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
* *
31017431 TGGCCTTCACATAGTACCAAACTTGTGTCCAAAGCTATTATATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
* *
31017482 TGGTCTTCACATAGTACCACACTTGTGTCTAAAGCTATTTTATTC
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
31017527 CTAAGGTTCA
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 139 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
Found at i:31023738 original size:47 final size:47
Alignment explanation
Indices: 31023679--31023800 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
31023669 GCATTGGCAC
31023679 TAAGACAAGGATACCATGTAAGACCATGTTTGGAAAATGACATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAAAATGACATTTGG
* * *
31023726 TAAGACAAGGATACCATGTAAGACCTTGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAAAATGACATTTGG
* * *
31023773 TACGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
31023801 GCAAGGCATG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAAAATGACATTTGG
Found at i:31023907 original size:55 final size:54
Alignment explanation
Indices: 31023779--31023973 Score: 232
Period size: 55 Copynumber: 3.6 Consensus size: 54
31023769 TTGGTACGAT
* * * *
31023779 AAGGATATCATGTAAGACCATGGCAAGGCATGGCATTGATAAGTTCTATAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGA
* * *
31023833 AAGGAAATCATGTAAGACCATATCAAGACATGGCATTGATGAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATAAGG-A
* * * * *
31023889 AAGG-TCCCATGTAAGACCATTTCAAGTCATGGCATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGA
**
31023941 AAGGATACCACATAAGACCATGTCAAGACATGG
1 AAGGATACCATGTAAGACCATGTCAAGACATGG
31023974 AAATGGTAAG
Statistics
Matches: 121, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 4 0.03
53 29 0.24
54 41 0.34
55 42 0.35
56 5 0.04
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGA
Found at i:31023967 original size:53 final size:54
Alignment explanation
Indices: 31023779--31023996 Score: 224
Period size: 54 Copynumber: 4.0 Consensus size: 54
31023769 TTGGTACGAT
* * *
31023779 AAGGATATCATGTAAGACCATGGCAAGGCATGGCATTGATAAGTTCTATAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
* * * *
31023833 AAGGAAATCATGTAAGACCATATCAAGACATGGCATTGATGAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGG-A
* * * * * *
31023889 AAGG-TCCCATGTAAGACCATTTCAAGTCATGGCATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
** * * * * *
31023941 AAGGATACCACATAAGACCATGTCAAGACATGGAAATGGTAAGTTCAAAAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
31023995 AA
1 AA
31023997 AGGTTCCCGA
Statistics
Matches: 138, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.03
53 39 0.28
54 48 0.35
55 42 0.30
56 5 0.04
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
Found at i:31025597 original size:219 final size:219
Alignment explanation
Indices: 31025333--31025780 Score: 860
Period size: 219 Copynumber: 2.0 Consensus size: 219
31025323 TTTTTAATGC
31025333 TTCCAGTTTGGTCCCGAACCATTTCAATTGCATGTTTTAGGGTTTCGAGGGCCCTTTTTAGGGAC
1 TTCCAGTTTGGTCCCGAACCATTTCAATTGCATGTTTTAGGGTTTCGAGGGCCCTTTTTAGGGAC
*
31025398 ATATTGAATGAATGTAAATAAATTAATTTTAAAAGCAAATTTTATGCCCCGAATTAGCAAGTTAA
66 ATATTGAATGAATGTAAATAAATTAATTTTAAAAGCAAATTTTAGGCCCCGAATTAGCAAGTTAA
31025463 GTCAGGTAACGTCTCGTGCTCGACTCCAACGACGGTAATATTCATTTAATACATAAATTACCTAA
131 GTCAGGTAACGTCTCGTGCTCGACTCCAACGACGGTAATATTCATTTAATACATAAATTACCTAA
31025528 CCATCCATTAAAATTATTTCTAAT
196 CCATCCATTAAAATTATTTCTAAT
31025552 TTCCAGTTTGGTCCCGAACCATTTCAATTGCATGTTTTAGGGTTTCGAGGGCCCTTTTTAGGGAC
1 TTCCAGTTTGGTCCCGAACCATTTCAATTGCATGTTTTAGGGTTTCGAGGGCCCTTTTTAGGGAC
*
31025617 ATATTGAATGAATGTAAATAAATTAATTTTAAAAGCAAATTTTAGGCCCCGGATTAGCAAGTTAA
66 ATATTGAATGAATGTAAATAAATTAATTTTAAAAGCAAATTTTAGGCCCCGAATTAGCAAGTTAA
31025682 GTCAGGTAACGTCTCGTGCTCGACTCCAACGACGGTAATATTCATTTAATACATAAATTACCTAA
131 GTCAGGTAACGTCTCGTGCTCGACTCCAACGACGGTAATATTCATTTAATACATAAATTACCTAA
31025747 CCATCCATTAAAATTATTTCTAAT
196 CCATCCATTAAAATTATTTCTAAT
*
31025771 TACCAAGTTT
1 TTCC-AGTTT
31025781 TCAAACCATG
Statistics
Matches: 225, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
219 220 0.98
220 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (219 bp):
TTCCAGTTTGGTCCCGAACCATTTCAATTGCATGTTTTAGGGTTTCGAGGGCCCTTTTTAGGGAC
ATATTGAATGAATGTAAATAAATTAATTTTAAAAGCAAATTTTAGGCCCCGAATTAGCAAGTTAA
GTCAGGTAACGTCTCGTGCTCGACTCCAACGACGGTAATATTCATTTAATACATAAATTACCTAA
CCATCCATTAAAATTATTTCTAAT
Found at i:31030649 original size:25 final size:25
Alignment explanation
Indices: 31030614--31030666 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
31030604 CTCAGTACAG
*
31030614 TTTTAGGAAGTACTAACTACAGTGT
1 TTTTAGAAAGTACTAACTACAGTGT
*
31030639 TTTTAGAAAGTTCTAACTACAGTGT
1 TTTTAGAAAGTACTAACTACAGTGT
31030664 TTT
1 TTT
31030667 CTAAATTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (25 bp):
TTTTAGAAAGTACTAACTACAGTGT
Found at i:31035553 original size:16 final size:16
Alignment explanation
Indices: 31035532--31035562 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31035522 AAATTCAAGG
31035532 TTTCGAGATTTTTGGA
1 TTTCGAGATTTTTGGA
31035548 TTTCGAGATTTTTGG
1 TTTCGAGATTTTTGG
31035563 GACGTTGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.26, T:0.52
Consensus pattern (16 bp):
TTTCGAGATTTTTGGA
Found at i:31047256 original size:39 final size:39
Alignment explanation
Indices: 31047202--31047279 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
31047192 AGGTGCCCCC
*
31047202 GTACTATTCGTGAAAAAGAAATATAGTTTGATGAGATTA
1 GTACTATTCGTGAAAAAGAAATATAGTTCGATGAGATTA
31047241 GTACTATTCGTGAAAAAGAAATATAGTTCGATGAGATTA
1 GTACTATTCGTGAAAAAGAAATATAGTTCGATGAGATTA
31047280 TGTATAGACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (39 bp):
GTACTATTCGTGAAAAAGAAATATAGTTCGATGAGATTA
Found at i:31049821 original size:19 final size:21
Alignment explanation
Indices: 31049797--31049837 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31049787 TATGGCATAG
31049797 ACAT-GGAAT-GGAAAAAGCC
1 ACATGGGAATCGGAAAAAGCC
*
31049816 ACATGGGAATCTGAAAAAGCC
1 ACATGGGAATCGGAAAAAGCC
31049837 A
1 A
31049838 TGAGAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.12
Consensus pattern (21 bp):
ACATGGGAATCGGAAAAAGCC
Found at i:31053350 original size:17 final size:18
Alignment explanation
Indices: 31053308--31053350 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31053298 CGCTGATTCG
31053308 ATTATTCACTTTCTAAAC
1 ATTATTCACTTTCTAAAC
*
31053326 ATTATTCACTTTTTAAAC
1 ATTATTCACTTTCTAAAC
31053344 A-TATTCA
1 ATTATTCA
31053351 AAACCCCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTCACTTTCTAAAC
Found at i:31055099 original size:27 final size:26
Alignment explanation
Indices: 31055057--31055169 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 26
31055047 GTGGATATAG
* *
31055057 GGTAGAATTACAGAAATACCCTTGTA
1 GGTAGAAATACCGAAATACCCTTGTA
*
31055083 GAGTAGAAATACCGAAATACCCCTGTA
1 G-GTAGAAATACCGAAATACCCTTGTA
* *
31055110 GGATAGAATTATCGAAATACCCTTGTA
1 GG-TAGAAATACCGAAATACCCTTGTA
*
31055137 GGGTAGAAATATCGAAATACTCC-TGTA
1 -GGTAGAAATACCGAAATAC-CCTTGTA
31055164 TGGTAG
1 -GGTAG
31055170 GACTACCAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 2 0.03
27 69 0.92
28 4 0.05
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (26 bp):
GGTAGAAATACCGAAATACCCTTGTA
Found at i:31055143 original size:54 final size:54
Alignment explanation
Indices: 31055054--31055163 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
31055044 CAAGTGGATA
*
31055054 TAGGGTAGAATTACAGAAATACCCTTGTAGAGTAGAAATACCGAAATACCCCTG
1 TAGGATAGAATTACAGAAATACCCTTGTAGAGTAGAAATACCGAAATACCCCTG
* * *
31055108 TAGGATAGAATTATC-GAAATACCCTTGTAGGGTAGAAATATCGAAATACTCCTG
1 TAGGATAGAATTA-CAGAAATACCCTTGTAGAGTAGAAATACCGAAATACCCCTG
31055162 TA
1 TA
31055164 TGGTAGGACT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (54 bp):
TAGGATAGAATTACAGAAATACCCTTGTAGAGTAGAAATACCGAAATACCCCTG
Found at i:31063268 original size:79 final size:81
Alignment explanation
Indices: 31063132--31063316 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
31063122 TTGAATGATG
* *
31063132 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
31063196 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
31063211 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
31063273 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
31063291 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31063317 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:31063330 original size:40 final size:40
Alignment explanation
Indices: 31063133--31063316 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
31063123 TGAATGATGT
* * * *
31063133 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
31063173 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
31063213 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
31063251 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
31063292 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31063317 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:31063338 original size:79 final size:79
Alignment explanation
Indices: 31063185--31063349 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
31063175 GGACTAAGAT
* * **
31063185 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
31063250 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
31063264 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
31063327 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
31063343 CCGAAGG
1 CCGAAGG
31063350 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:31069770 original size:25 final size:25
Alignment explanation
Indices: 31069718--31069811 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
31069708 GAGGAAGTGC
*
31069718 AAAAGGGCTATGCCCCAG-TTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
31069742 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
31069767 AAAAGGGCTTTGCCTCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
31069792 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
31069812 ATTTAAAGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
24 17 0.26
25 48 0.74
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:31069824 original size:24 final size:24
Alignment explanation
Indices: 31069793--31069838 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
31069783 AGTTTATCGA
**
31069793 AAAGGGCTTTGCC-CCAGTTATTT
1 AAAGGGCTAGGCCTCCAGTTATTT
31069816 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
31069839 ATGATAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTT
Found at i:31069836 original size:50 final size:51
Alignment explanation
Indices: 31069719--31069836 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 51
31069709 AGGAAGTGCA
31069719 AAAG-GGCTATGCC-CCAG-TTACCGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAGAGGCTATGCCTCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
* * ***
31069767 AAA-AGGGCTTTGCCT-CAGTTTATCGAAAAGGGCTTTGCCCCAG-TTATTT
1 AAAGA-GGCTATGCCTCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
*
31069816 AAAGAGGCTAGGCCTCCAGTT
1 AAAGAGGCTATGCCTCCAGTT
31069837 ATATGATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
48 3 0.05
49 25 0.44
50 29 0.51
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (51 bp):
AAAGAGGCTATGCCTCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:31070049 original size:31 final size:31
Alignment explanation
Indices: 31070014--31070150 Score: 184
Period size: 31 Copynumber: 4.4 Consensus size: 31
31070004 CGTTTACAGT
*
31070014 AAAGGCTTCGGCCTAGTGATATGAATAATGA
1 AAAGGCTTCGGCCTAGTGATATGATTAATGA
* * *
31070045 AAAGGCTTCGACCGAGTGATATGATTTATGA
1 AAAGGCTTCGGCCTAGTGATATGATTAATGA
* **
31070076 AAAGGCTTCAGCCTAGTGATATGATTTTTGA
1 AAAGGCTTCGGCCTAGTGATATGATTAATGA
* * *
31070107 AAAGGCTTCGGCCCAGTGGTTTGATTAATGA
1 AAAGGCTTCGGCCTAGTGATATGATTAATGA
31070138 AAAGGCTTCGGCC
1 AAAGGCTTCGGCC
31070151 CAGTAACCGT
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCTAGTGATATGATTAATGA
Found at i:31070190 original size:28 final size:28
Alignment explanation
Indices: 31070014--31070193 Score: 112
Period size: 31 Copynumber: 6.0 Consensus size: 28
31070004 CGTTTACAGT
* *
31070014 AAAGGCTTCGGCCTAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGT-ATATG-TTAA-GA
* * *
31070045 AAAGGCTTCGACCGAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATG--TTAAGA
* * **
31070076 AAAGGCTTCAGCCTAGTGATATGATTTTTGA
1 AAAGGCTTCGGCCCAGT-ATATG--TTAAGA
* *
31070107 AAAGGCTTCGGCCCAGTGGTTTGATTAATGA
1 AAAGGCTTCGGCCCAGT-ATATG-TTAA-GA
*
31070138 AAAGGCTTCGGCCCAGTA-ACCGTTAA-A
1 AAAGGCTTCGGCCCAGTATA-TGTTAAGA
31070165 CAAAGGCTTCGGCCCAGTATATGTTAAGA
1 -AAAGGCTTCGGCCCAGTATATGTTAAGA
31070194 CTGAATGTGG
Statistics
Matches: 123, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 23 0.19
29 6 0.05
30 3 0.02
31 88 0.72
32 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (28 bp):
AAAGGCTTCGGCCCAGTATATGTTAAGA
Found at i:31073719 original size:250 final size:250
Alignment explanation
Indices: 31073273--31073741 Score: 604
Period size: 250 Copynumber: 1.9 Consensus size: 250
31073263 GAAGAACTCC
* * * * * *
31073273 AGAGTTTGAACTAGAAATTGAGAAATTGGCCTAAAAACTGCGGAAAGAATCCATTTGACGCGGTA
1 AGAGTTTGAACCAGAAATTGAGAAATTGGCCCAAAAACTACGAAAAGAAGCCATTTGACGCCGTA
** * * * *
31073338 AACGACCAAATCTAGGATTTGAAACCATATCTTACACCGAGGAAATTTTCTAGTTTGACAAACCG
66 AACGACCAAATCTAGGATTCAAAACCATATCTTACACCAAAGAAATTTTCTAGTTCGACAAACCA
* *
31073403 ACAGAGATGGTTGAACAAACTATATGCCAACTCGCAGCGGCACTAGATGAACAAAAACCCTTATG
131 ACAGAGATGGTCGAACAAACAATATGCCAACTCGCAGCGGCACTAGATGAACAAAAACCCTTATG
* *
31073468 TATAACCTATTTAGTGGGAGGAACGTTGTTTGAGTTAAAATCGGGTTTGAACTTT
196 TATAACCTATCTAGTAGGAGGAACGTTGTTTGAGTTAAAATCGGGTTTGAACTTT
* * *
31073523 AGAGTTTGAACCAGAAATTGAGAAATTGGCCCAAAAACTATGAAAAGCAGCCATTTGATGCCGTA
1 AGAGTTTGAACCAGAAATTGAGAAATTGGCCCAAAAACTACGAAAAGAAGCCATTTGACGCCGTA
* * **
31073588 AATGACCAAATCCTA-GATTCAAAACCATATCTTACACCAAATAAATTTTCTCA-TTCGATGAAC
66 AACGACCAAAT-CTAGGATTCAAAACCATATCTTACACCAAAGAAATTTTCT-AGTTCGACAAAC
* * * * *
31073651 CAA-ACGAGATGGTCGAAGAGAA-AATATGTCAACTCGCAGCGGCACTAGATGAACAACAGCCTT
129 CAACA-GAGATGGTCGAACA-AACAATATGCCAACTCGCAGCGGCACTAGATGAACAAAAACCCT
* *
31073714 TATGTATAATCTATCTGGTAGGAGGAAC
192 TATGTATAACCTATCTAGTAGGAGGAAC
31073742 ACCGTTCAAG
Statistics
Matches: 185, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
249 1 0.01
250 178 0.96
251 6 0.03
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (250 bp):
AGAGTTTGAACCAGAAATTGAGAAATTGGCCCAAAAACTACGAAAAGAAGCCATTTGACGCCGTA
AACGACCAAATCTAGGATTCAAAACCATATCTTACACCAAAGAAATTTTCTAGTTCGACAAACCA
ACAGAGATGGTCGAACAAACAATATGCCAACTCGCAGCGGCACTAGATGAACAAAAACCCTTATG
TATAACCTATCTAGTAGGAGGAACGTTGTTTGAGTTAAAATCGGGTTTGAACTTT
Found at i:31079332 original size:17 final size:17
Alignment explanation
Indices: 31079295--31079330 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31079285 CAAAAATCTG
*
31079295 AATTTATTTCCGATTTA
1 AATTTATTTCCAATTTA
31079312 AATTTATTTCCAATATTA
1 AATTTATTTCCAAT-TTA
31079330 A
1 A
31079331 TTAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTTATTTCCAATTTA
Found at i:31079377 original size:18 final size:18
Alignment explanation
Indices: 31079356--31079398 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31079346 CACTGATTTG
*
31079356 ATTATTCACTTTCTAAAC
1 ATTATTCACTTTCAAAAC
31079374 ATTATTCACTTTCAAAAC
1 ATTATTCACTTTCAAAAC
31079392 ATT-TTCA
1 ATTATTCA
31079399 AAACCCCCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATTCACTTTCAAAAC
Found at i:31082659 original size:19 final size:20
Alignment explanation
Indices: 31082615--31082660 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
31082605 AAGATGACAC
*
31082615 CAAATTAACTTGTTGTTTTA
1 CAAATTAACTTGTTATTTTA
**
31082635 TTAATTAACTT-TTATTTTA
1 CAAATTAACTTGTTATTTTA
31082654 CAAATTA
1 CAAATTA
31082661 CCTTAATAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (20 bp):
CAAATTAACTTGTTATTTTA
Found at i:31085268 original size:19 final size:20
Alignment explanation
Indices: 31085224--31085269 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
31085214 AAGATGACAC
*
31085224 CAAATTAACTTGTTGTTTTA
1 CAAATTAACTTGTTATTTTA
**
31085244 TTAATTAACTT-TTATTTTA
1 CAAATTAACTTGTTATTTTA
31085263 CAAATTA
1 CAAATTA
31085270 CCTTAATAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (20 bp):
CAAATTAACTTGTTATTTTA
Found at i:31087481 original size:30 final size:30
Alignment explanation
Indices: 31087423--31087481 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
31087413 TTTACGAGCC
* * *
31087423 TAGGGGCCAAAGTGCAAATATGTGAAAGTT
1 TAGGGGCCAAAATGAAAATATGTAAAAGTT
* *
31087453 TAGGGGTCAAAATGAAAATTTGTAAAAGT
1 TAGGGGCCAAAATGAAAATATGTAAAAGT
31087482 ATGATTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (30 bp):
TAGGGGCCAAAATGAAAATATGTAAAAGTT
Found at i:31087738 original size:18 final size:20
Alignment explanation
Indices: 31087702--31087747 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
31087692 AGTTGTAAGT
31087702 ATATATATGTGAATAATTTG
1 ATATATATGTGAATAATTTG
*
31087722 ATAT-TATGTG-ATTATTTG
1 ATATATATGTGAATAATTTG
31087740 ATGATATA
1 AT-ATATA
31087748 ACATGTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (20 bp):
ATATATATGTGAATAATTTG
Found at i:31088177 original size:50 final size:50
Alignment explanation
Indices: 31088101--31088330 Score: 184
Period size: 50 Copynumber: 4.6 Consensus size: 50
31088091 TGTAAGTCAC
* * *
31088101 GTGTGTAGTACTAATTGCGGGTTACTATGTGTACCAGATTGATAGGTCGCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAG-TTGATAGGTCGCA
* * * **
31088152 -TGTGTAGTACTAAGTGCAAGCTACTATGCGTACCCGTT-A-ACTTCGATCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGTTGATAGGTCG--CA
* * * * ** *
31088201 TGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGTTGGTTAACTC-AA
1 -GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGTT-GATAGGTCGCA
* * *
31088252 GTGTGTAGTACTAAGTGCAGGCTAATACGTGTACTAGATTGATAGG-CTGCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAG-TTGATAGGTC-GCA
*
31088303 -TGTGTAATACTAAGTGCAGGCTACTATG
1 GTGTGTAGTACTAAGTGCAGGCTACTATG
31088331 CATACCAAGG
Statistics
Matches: 142, Mismatches: 27, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
47 4 0.03
48 1 0.01
49 5 0.04
50 91 0.64
51 38 0.27
54 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (50 bp):
GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGTTGATAGGTCGCA
Found at i:31088560 original size:16 final size:16
Alignment explanation
Indices: 31088539--31088570 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31088529 AGAATGGAGT
31088539 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
31088555 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
31088571 TAAAACAATT
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:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:31090310 original size:251 final size:250
Alignment explanation
Indices: 31089827--31090323 Score: 922
Period size: 251 Copynumber: 2.0 Consensus size: 250
31089817 TACAACACGG
* * * ** *
31089827 GCAGAGACACGGCCATGTGTCTTAGTCTTGTGGAGGACACGCCTAGCACTCGGGCGTGTGGCTTG
1 GCAGAAACACGACCATGTGTCTCAACCTTGTGGAGGACACGCCTAGCACACGGGCGTGTGGCTTG
31089892 GCCGTGTGGATCAATTTGTTTTGCTGACGTCATAAACAGAGAGTTACACGGCCTGAGGATACAGG
66 GCCGTGTGGATCAATTTGTTTTGCTGACGTCATAAACAGAGAGTTACACGGCCTGAGGATACAGG
31089957 CATGTTGAATACAGACGAGCGCGTCCCTGTGTCCACACGGGCGTGTGACCCTATTTCATGAAAAT
131 CATGTTGAATACAGACGAGCGCGTCCCTGTGTCCACACGGGCGTGTGACCCTATTTCATGAAAAT
31090022 TTCTCTAAGTTTTCCCAGAGCTTTCTAAAGTCCTCGATTTAGTCCCGAACCTCCC
196 TTCTCTAAGTTTTCCCAGAGCTTTCTAAAGTCCTCGATTTAGTCCCGAACCTCCC
*
31090077 GCAGAAACACGACCATGTGTCTCAACCTTGTGGAGGATACGGCCTAGCACACGGGCGTGTGGCTT
1 GCAGAAACACGACCATGTGTCTCAACCTTGTGGAGGACAC-GCCTAGCACACGGGCGTGTGGCTT
31090142 GGCCGTGTGGATCAATTTGTTTTGCTGACGTCATAAACAGAGAGTTACACGGCCTGAGGATACAG
65 GGCCGTGTGGATCAATTTGTTTTGCTGACGTCATAAACAGAGAGTTACACGGCCTGAGGATACAG
31090207 GCATGTTGAATACAGACGAGCGCGTCCCTGTGTCCACACGGGCGTGTGACCCTATTTCATGAAAA
130 GCATGTTGAATACAGACGAGCGCGTCCCTGTGTCCACACGGGCGTGTGACCCTATTTCATGAAAA
31090272 TTTCTCTAAGTTTTCCCAGAGCTTTCTAAAGTCCTCGATTTAGTCCCGAACC
195 TTTCTCTAAGTTTTCCCAGAGCTTTCTAAAGTCCTCGATTTAGTCCCGAACC
31090324 ACCCCGATGT
Statistics
Matches: 239, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
250 34 0.14
251 205 0.86
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (250 bp):
GCAGAAACACGACCATGTGTCTCAACCTTGTGGAGGACACGCCTAGCACACGGGCGTGTGGCTTG
GCCGTGTGGATCAATTTGTTTTGCTGACGTCATAAACAGAGAGTTACACGGCCTGAGGATACAGG
CATGTTGAATACAGACGAGCGCGTCCCTGTGTCCACACGGGCGTGTGACCCTATTTCATGAAAAT
TTCTCTAAGTTTTCCCAGAGCTTTCTAAAGTCCTCGATTTAGTCCCGAACCTCCC
Found at i:31098235 original size:21 final size:21
Alignment explanation
Indices: 31098201--31098240 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31098191 AATAGTCATG
*
31098201 GATGATTTAAGAGTGACTTAA
1 GATGATTTAAGAGTCACTTAA
**
31098222 GATGATTTGCGAGTCACTT
1 GATGATTTAAGAGTCACTT
31098241 TTTGTTTAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (21 bp):
GATGATTTAAGAGTCACTTAA
Found at i:31098784 original size:27 final size:28
Alignment explanation
Indices: 31098726--31098801 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 28
31098716 ATTGCATGAC
*
31098726 TATGAATGTGAGTGGGCCTAATGGGCCA
1 TATGAATGTGATTGGGCCTAATGGGCCA
*
31098754 TATGAATGTGATTGGGCC-GATGGGCCA
1 TATGAATGTGATTGGGCCTAATGGGCCA
*
31098781 TATGAATGAGATTGGGCCTAA
1 TATGAATGTGATTGGGCCTAA
31098802 AGGGGCTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.26
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTAATGGGCCA
Found at i:31107312 original size:17 final size:18
Alignment explanation
Indices: 31107279--31107312 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31107269 TTCAAAGAAG
31107279 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
31107297 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
31107313 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:31113538 original size:3 final size:3
Alignment explanation
Indices: 31113530--31113555 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31113520 AGTTCGTGTG
31113530 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
31113556 GTAAGGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:31129001 original size:28 final size:26
Alignment explanation
Indices: 31128969--31129046 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 26
31128959 TCTTGTGCAA
31128969 ATTTTAAATTAAAAAATTTTAATCTTTT
1 ATTTTAAATTAAAAAA--TTAATCTTTT
***
31128997 ATTTTTTTTTAAAAAATTAATCTTTTT
1 ATTTTAAATTAAAAAATTAATC-TTTT
* *
31129024 ACTTATTTAATTTAAAAATTAAT
1 A-TT-TTAAATTAAAAAATTAAT
31129047 AATATTTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
26 6 0.15
27 5 0.12
28 15 0.37
29 15 0.37
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTAAATTAAAAAATTAATCTTTT
Found at i:31129195 original size:58 final size:58
Alignment explanation
Indices: 31129132--31129248 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
31129122 ATATGGGGCG
*
31129132 TTATACTTTTTCACTTAAATATTTTATTTTTAATTCTAGTAATTAATGTAAAATAATA
1 TTATACTTTTTCACTTAAATATTTTATTTTTAATTCTAGTAATTAATGCAAAATAATA
31129190 TTATACTTTTTCACTTAAATATTTTATTTTTAATTCTAGTAATTAATGCAAAATAATA
1 TTATACTTTTTCACTTAAATATTTTATTTTTAATTCTAGTAATTAATGCAAAATAATA
31129248 T
1 T
31129249 GTGTTTGTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (58 bp):
TTATACTTTTTCACTTAAATATTTTATTTTTAATTCTAGTAATTAATGCAAAATAATA
Found at i:31133167 original size:23 final size:21
Alignment explanation
Indices: 31133141--31133184 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31133131 AAGTTTGGAA
31133141 GATCATGCATATACTAGTGGATG
1 GATC-TGCAT-TACTAGTGGATG
* *
31133164 GATCTTCATTATTAGTGGATG
1 GATCTGCATTACTAGTGGATG
31133185 AGCCATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 4 0.21
23 4 0.21
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (21 bp):
GATCTGCATTACTAGTGGATG
Found at i:31134305 original size:3 final size:3
Alignment explanation
Indices: 31134297--31134326 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
31134287 AATTAAATGA
*
31134297 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31134327 TATTTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:31141640 original size:16 final size:16
Alignment explanation
Indices: 31141619--31141686 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
31141609 TTTGGTTCGC
31141619 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
31141635 TGTATTGGATTAGGGG
1 TGTATTGGATTAGAGG
*
31141651 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
31141667 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
31141683 TGTA
1 TGTA
31141687 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:31141726 original size:45 final size:41
Alignment explanation
Indices: 31141667--31141776 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
31141657 GGATTAGAGG
*
31141667 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
31141709 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
31141752 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
31141777 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:31141939 original size:16 final size:16
Alignment explanation
Indices: 31141902--31141943 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31141892 TTAATCATAT
*
31141902 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
31141918 TT-AAATATATTATAA
1 TTAAAATATATTATAA
31141933 TTAAAATATAT
1 TTAAAATATAT
31141944 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:31141950 original size:14 final size:15
Alignment explanation
Indices: 31141911--31141952 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31141901 TTTAAACATA
*
31141911 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31141926 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31141940 A-TATAATTTAATA
1 ATTATAATTAAATA
31141953 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31142050 original size:120 final size:121
Alignment explanation
Indices: 31141905--31142168 Score: 446
Period size: 120 Copynumber: 2.2 Consensus size: 121
31141895 ATCATATTTA
31141905 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
31141970 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-GATAAATT-
66 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATG-TAAATTG
*
31142025 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
31142090 TATTCTTATATGAATTTATTAAAATCATAATATATGATACTATAAAATGTAATTTG
66 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTAAATTG
*
31142146 AA-ATAATTAATATTAAATA-ATTA
1 AACATAATTATTATTAAATATATTA
31142169 ATGTTGACAA
Statistics
Matches: 137, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
119 4 0.03
120 130 0.95
121 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTAAATTG
Found at i:31142070 original size:14 final size:15
Alignment explanation
Indices: 31142021--31142072 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31142011 ATAAAAGATA
31142021 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
31142036 TATTAAATATATTAT
1 AATTAAATATATTAT
31142051 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
31142064 AATTTAATA
1 AATTAAATA
31142073 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:31142135 original size:61 final size:61
Alignment explanation
Indices: 31141950--31142137 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
31141940 ATATAATTTA
* * *
31141950 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
** * * * * * * * *
31142011 ATAAAA--GAT-A-AATTAACATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT
31142069 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
31142131 ATAAAAT
1 ATAAAAT
31142138 GTAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
57 3 0.03
58 3 0.03
59 29 0.31
60 14 0.15
61 38 0.40
62 3 0.03
63 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
Found at i:31149831 original size:42 final size:42
Alignment explanation
Indices: 31149751--31149831 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
31149741 CGTGTCCCTG
** * **
31149751 CCCGTGTGACTCACATGGCCTAGACACACGCCTGTGTCCTTA
1 CCCGTGTGACTCACACAGCCTAGACACACACCCATGTCCTTA
* *
31149793 CCCGTGTGACTCACACAGCCTGGATACACACCCATGTCC
1 CCCGTGTGACTCACACAGCCTAGACACACACCCATGTCC
31149832 CTAGTCTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.38, G:0.20, T:0.21
Consensus pattern (42 bp):
CCCGTGTGACTCACACAGCCTAGACACACACCCATGTCCTTA
Found at i:31153367 original size:51 final size:51
Alignment explanation
Indices: 31153312--31153411 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
31153302 CTACCACATA
*
31153312 ACATGTAA-CACATCCATAATGAACTTGAACCTATCAACGAGCTCAGATGTT
1 ACATG-AATCACATCCATAATGAACTTGAACCTATCAACAAGCTCAGATGTT
* * * * *
31153363 ACATGAATCGCATCCATTATGAACTTGGACCTCTCAACAAGCTCGGATG
1 ACATGAATCACATCCATAATGAACTTGAACCTATCAACAAGCTCAGATG
31153412 CTCGTATCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (51 bp):
ACATGAATCACATCCATAATGAACTTGAACCTATCAACAAGCTCAGATGTT
Found at i:31157373 original size:18 final size:17
Alignment explanation
Indices: 31157350--31157391 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
31157340 TTATATTTTA
31157350 AAAAATATTAATTACT-AT
1 AAAAATATTAA-TA-TGAT
*
31157368 AAAAATGTTAATATGAT
1 AAAAATATTAATATGAT
31157385 AAAAATA
1 AAAAATA
31157392 ATTTCTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAAATATTAATATGAT
Found at i:31158903 original size:21 final size:21
Alignment explanation
Indices: 31158853--31158903 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
31158843 GATAAAAAAT
31158853 TATA-ACATT-TTTTTATGAA
1 TATATACATTATTTTTATGAA
* *
31158872 TAAATATATTATTTTTAT-AA
1 TATATACATTATTTTTATGAA
31158892 TATATAGCATTA
1 TATATA-CATTA
31158904 AGCATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 11 0.44
21 11 0.44
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (21 bp):
TATATACATTATTTTTATGAA
Found at i:31159991 original size:32 final size:32
Alignment explanation
Indices: 31159923--31159984 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
31159913 CATCAATCAT
*
31159923 TTCAATATGTAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
*
31159955 TTCAATATCTAACAAGTTTAAAACATAATA
1 TTCAATATCTAACAAGCTTAAAACATAATA
31159985 TGTTCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.31
Consensus pattern (32 bp):
TTCAATATCTAACAAGCTTAAAACATAATAAA
Found at i:31160001 original size:32 final size:32
Alignment explanation
Indices: 31159933--31160001 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
31159923 TTCAATATGT
* *
31159933 AACAAGCTTAAAACATAATAAATTCAATATCT
1 AACAAGCTTAAAACATAATAAATTCAAAATCC
* **
31159965 AACAAGTTTAAAACATAATATGTTCAAAATCC
1 AACAAGCTTAAAACATAATAAATTCAAAATCC
31159997 AACAA
1 AACAA
31160002 ACTAATTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (32 bp):
AACAAGCTTAAAACATAATAAATTCAAAATCC
Found at i:31165035 original size:14 final size:15
Alignment explanation
Indices: 31165016--31165045 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31165006 TAACGCCTTC
31165016 TTTTTTCTATATAATT
1 TTTTTTCTATATAA-T
31165032 TTTTTTCTATATAA
1 TTTTTTCTATATAA
31165046 CCCTAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTCTATATAAT
Found at i:31170080 original size:42 final size:42
Alignment explanation
Indices: 31170002--31170111 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
31169992 TCGATGCCGA
**
31170002 TGCCATGTCCCAGACATGGTCTTACAGGGGACCTCATATTGG
1 TGCCATGTCCCAGACATGGTCTTACAGGAAACCTCATATTGG
* * * ***
31170044 TGCCATGTCGCAGACATGGTCTTACATGAAATCTCATATCAA
1 TGCCATGTCCCAGACATGGTCTTACAGGAAACCTCATATTGG
* * *
31170086 CGCCATATCCCAGATATGGTCTTACA
1 TGCCATGTCCCAGACATGGTCTTACA
31170112 CTGGCACATA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (42 bp):
TGCCATGTCCCAGACATGGTCTTACAGGAAACCTCATATTGG
Found at i:31170163 original size:48 final size:48
Alignment explanation
Indices: 31170044--31170256 Score: 215
Period size: 48 Copynumber: 4.6 Consensus size: 48
31170034 CTCATATTGG
* ** *
31170044 TGCCATGTCGCAGACATGGTCTTACA-TGAAATCTCATATCAACGCC-A
1 TGCCATGTCCCAGACATGGTCTTACACTG-GCTCACATATCAACGCCGA
* * * *
31170091 T---A--TCCCAGATATGGTCTTACACTGGCACATATATCAACGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGCCGA
* * * * *
31170134 TGCCATGTCCTAGATATGGTCTTATACTGGCTCACATATTAATGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGCCGA
* * * *
31170182 TGTCATGTCCCAGACATGGTCTTACACTAGTTCACATATCAACACCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGCCGA
31170230 TGCCATGTCCCAGACATGGTCTTACAC
1 TGCCATGTCCCAGACATGGTCTTACAC
31170257 GAGATTTCGT
Statistics
Matches: 134, Mismatches: 25, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
42 28 0.21
43 4 0.03
44 1 0.01
46 1 0.01
47 1 0.01
48 99 0.74
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (48 bp):
TGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGCCGA
Found at i:31177710 original size:24 final size:24
Alignment explanation
Indices: 31177679--31177724 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
31177669 AATTATTTTC
31177679 AAAAATT-AAAAAATTAAATATTCT
1 AAAAATTAAAAAAATT-AATATTCT
31177703 AAAAATTAAAAAAATTAATATT
1 AAAAATTAAAAAAATTAATATT
31177725 AAATGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAATTAAAAAAATTAATATTCT
Found at i:31178449 original size:4 final size:4
Alignment explanation
Indices: 31178440--31178510 Score: 54
Period size: 4 Copynumber: 16.5 Consensus size: 4
31178430 TTTTTTCTTC
* *
31178440 TTTA TTTA TTTA TTTA TTTA CTTTC TTTAA GTTT- TTTA TTTG TCCTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTT-A -TTTA TTTA TTTA T--TTA
*
31178488 TTTA TTTTA TTTA TTTG TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TT
31178511 ATTGATTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 3 0.06
4 38 0.70
5 7 0.13
6 6 0.11
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:31178500 original size:23 final size:22
Alignment explanation
Indices: 31178441--31178505 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
31178431 TTTTTCTTCT
* *
31178441 TTATTTATTTATTTATTT-ACT
1 TTATTTATTTATTTATTTGTCC
*
31178462 TTCTTTAAGTTT-TTTATTTGTCC
1 TTATTT-A-TTTATTTATTTGTCC
31178485 TTATTTATTTTATTTATTTGT
1 TTATTTA-TTTATTTATTTGT
31178506 TTATTATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.14
22 12 0.34
23 18 0.51
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (22 bp):
TTATTTATTTATTTATTTGTCC
Found at i:31178600 original size:57 final size:55
Alignment explanation
Indices: 31178526--31178640 Score: 144
Period size: 57 Copynumber: 2.1 Consensus size: 55
31178516 TTTTAAAAAA
**
31178526 TTTGAAATGTATATTTAAAATGT-TTTATAATATTTTTTTAAATTTTAAATATATATT
1 TTTGAAATGTATATTTAAAAT-TCTAAATAATATTTTTTT-AATTTTAAATATAT-TT
* *
31178583 TTTGAAAT-TATTTTTTAAAATTCTAAATATTATTTTTTTAATTTTAAATATATTT
1 TTTGAAATGTA-TATTTAAAATTCTAAATAATATTTTTTTAATTTTAAATATATTT
31178638 TTT
1 TTT
31178641 AATAATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
55 5 0.10
56 17 0.33
57 30 0.58
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (55 bp):
TTTGAAATGTATATTTAAAATTCTAAATAATATTTTTTTAATTTTAAATATATTT
Found at i:31178625 original size:21 final size:22
Alignment explanation
Indices: 31178589--31178642 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
31178579 TATTTTTGAA
31178589 ATTATTTTTTAAAATTCTAAAT
1 ATTATTTTTTAAAATTCTAAAT
* *
31178611 ATTATTTTTT-TAATTTTAAAT
1 ATTATTTTTTAAAATTCTAAAT
31178632 A-TATTTTTTAA
1 ATTATTTTTTAA
31178643 TAATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.29
21 10 0.36
22 10 0.36
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTATTTTTTAAAATTCTAAAT
Found at i:31178646 original size:22 final size:22
Alignment explanation
Indices: 31178582--31178646 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
31178572 AAATATATAT
31178582 TTTTGAAAT-TATTTTTTAA-AA
1 TTTT-AAATATATTTTTTAATAA
*
31178603 TTCTAAATATTATTTTTT--TAA
1 TTTTAAATA-TATTTTTTAATAA
31178624 TTTTAAATATATTTTTTAATAA
1 TTTTAAATATATTTTTTAATAA
31178646 T
1 T
31178647 ATAAAACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 12 0.32
21 13 0.35
22 12 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAAATATATTTTTTAATAA
Found at i:31178922 original size:20 final size:19
Alignment explanation
Indices: 31178882--31178925 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
31178872 AATAGAAAAA
*
31178882 TATTTGTTAAAAAAGGATT
1 TATTTGTTAAAAAAGAATT
*
31178901 TATTTGTTAAAAAATAACTT
1 TATTTGTTAAAAAAGAA-TT
31178921 TATTT
1 TATTT
31178926 AATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (19 bp):
TATTTGTTAAAAAAGAATT
Found at i:31183645 original size:40 final size:40
Alignment explanation
Indices: 31183596--31183859 Score: 353
Period size: 40 Copynumber: 6.7 Consensus size: 40
31183586 GCTCCTCGTT
*
31183596 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
31183636 C-AATCGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAAT-GCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
31183676 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
31183716 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
31183756 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
31183795 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
31183836 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31183860 CATCATTCAA
Statistics
Matches: 205, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 52 0.25
40 139 0.68
41 12 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:31193848 original size:15 final size:15
Alignment explanation
Indices: 31193828--31193857 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31193818 AATACAAAAA
31193828 ATATGTTTTGGATTG
1 ATATGTTTTGGATTG
*
31193843 ATATGTTTTGTATTG
1 ATATGTTTTGGATTG
31193858 GAATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTG
Found at i:31194555 original size:41 final size:42
Alignment explanation
Indices: 31194436--31194562 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 42
31194426 ACATAGGATC
* * * *
31194436 CGATATGTGTTTTCGTGTAAAACCACGTCTGGGACGTTGGCAT
1 CGATATGTG-ATTCGTGTAAGACCATGTCTGGGACATTGGCAT
* * *
31194479 CGATATGTGGTTACGTATAAGACCATGTATGGGACATTGGCAT
1 CGATATGTGATT-CGTGTAAGACCATGTCTGGGACATTGGCAT
* * * *
31194522 CG-TATTTGATTCGTGTAAGACCTTGTCTAGGACAGTGGCAT
1 CGATATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCAT
31194563 TAATATGAGA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 25 0.36
42 9 0.13
43 36 0.51
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (42 bp):
CGATATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCAT
Found at i:31197551 original size:19 final size:21
Alignment explanation
Indices: 31197508--31197556 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 21
31197498 AATTTTAAAA
31197508 TTAATAATTTTAAAAAATTATAT
1 TTAA-AATTTTAAAAAA-TATAT
31197531 TTAAAATTTT-AAAAA-ATAT
1 TTAAAATTTTAAAAAATATAT
31197550 TTAAAAT
1 TTAAAAT
31197557 ATACATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.42
21 5 0.19
22 6 0.23
23 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAATTTTAAAAAATATAT
Found at i:31197639 original size:9 final size:9
Alignment explanation
Indices: 31197625--31197694 Score: 59
Period size: 10 Copynumber: 7.2 Consensus size: 9
31197615 AATATATTTT
31197625 AAAAAATTAA
1 AAAAAATT-A
31197635 AAAAAATTA
1 AAAAAATTA
*
31197644 AAAATATTA
1 AAAAAATTA
*
31197653 TAAAAACACTA
1 -AAAAA-ATTA
*
31197664 AAAATATTA
1 AAAAAATTA
*
31197673 AAAATATTTA
1 AAAA-AATTA
31197683 AAACAAATTA
1 AAA-AAATTA
31197693 AA
1 AA
31197695 CATATTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 16 0.33
10 28 0.58
11 4 0.08
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAAATTA
Found at i:31197699 original size:29 final size:28
Alignment explanation
Indices: 31197618--31197706 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 28
31197608 TAAAAATAAT
* *
31197618 ATATTTTAAAAAATTAAAAAAAATTAAAA
1 ATATTTAAAAAAATT-AAAAATATTAAAA
* *
31197647 ATATTATAAAAACACTAAAAATATTAAAA
1 ATATT-TAAAAAAATTAAAAATATTAAAA
* *
31197676 ATATTTAAAACAAATTAAACATATTTAAA
1 ATATTTAAAA-AAATTAAAAATATTAAAA
31197705 AT
1 AT
31197707 TTAAAATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.10
29 38 0.76
30 7 0.14
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATTTAAAAAAATTAAAAATATTAAAA
Found at i:31197815 original size:20 final size:21
Alignment explanation
Indices: 31197792--31197830 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31197782 TTATATTATT
31197792 AAAAAAT-ATATTTAAAATAA
1 AAAAAATAATATTTAAAATAA
31197812 AAAAAATAATATTTAAAAT
1 AAAAAATAATATTTAAAAT
31197831 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATAATATTTAAAATAA
Found at i:31197943 original size:9 final size:9
Alignment explanation
Indices: 31197929--31197984 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
31197919 AATAATAAAC
31197929 AAATAAATA
1 AAATAAATA
31197938 AAATAAATA
1 AAATAAATA
* *
31197947 AGGACAAATA
1 A-AATAAATA
**
31197957 AAATACTTA
1 AAATAAATA
*
31197966 AAA-AAATT
1 AAATAAATA
31197974 AAATAAATA
1 AAATAAATA
31197983 AA
1 AA
31197985 TAAGAAAGAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
8 5 0.14
9 23 0.66
10 7 0.20
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:31198500 original size:15 final size:17
Alignment explanation
Indices: 31198475--31198513 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
31198465 GATTTTTTAT
*
31198475 TAAATTTTTTTATTTT-
1 TAAATATTTTTATTTTC
*
31198491 TCAATATTTTTATTTTC
1 TAAATATTTTTATTTTC
31198508 TAAATA
1 TAAATA
31198514 ATTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TAAATATTTTTATTTTC
Found at i:31206409 original size:9 final size:9
Alignment explanation
Indices: 31206395--31206424 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
31206385 CAATTGTGAA
31206395 AAACATGTT
1 AAACATGTT
31206404 AAACATGTT
1 AAACATGTT
31206413 AAACATGTT
1 AAACATGTT
31206422 AAA
1 AAA
31206425 AGTGATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (9 bp):
AAACATGTT
Found at i:31206438 original size:18 final size:18
Alignment explanation
Indices: 31206417--31206451 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31206407 CATGTTAAAC
*
31206417 ATGTTAAAAGTGATTATT
1 ATGTGAAAAGTGATTATT
*
31206435 ATGTGATAAGTGATTAT
1 ATGTGAAAAGTGATTAT
31206452 GAGGGCATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (18 bp):
ATGTGAAAAGTGATTATT
Found at i:31206738 original size:16 final size:16
Alignment explanation
Indices: 31206717--31206748 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31206707 AGGAACTTTA
31206717 TAAAATATGCATCGAT
1 TAAAATATGCATCGAT
31206733 TAAAATATGCATCGAT
1 TAAAATATGCATCGAT
31206749 ATGTCCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
TAAAATATGCATCGAT
Found at i:31208658 original size:46 final size:46
Alignment explanation
Indices: 31208555--31208768 Score: 188
Period size: 46 Copynumber: 4.6 Consensus size: 46
31208545 ACATTATGGG
* ** * * * * *
31208555 AGCCAGTGTAAGATCATGTCTAAGACATAGCAACGACATTGAGAGGAG
1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTTGAGATG-T
*
31208603 AGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTTGAGATGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTTGAGATGT
* *
31208648 CAGCCAGTGTAAGA-CATGTCTGGGACATGCATCAG-TTATGAGATGT
1 -AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCT-TGAGATGT
* * *
31208694 -GTCAGTGTAAGACCATGTCTGGGACATAGCAT-TGACTTGATGGATG-
1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTTGA--GATGT
*
31208740 AGCCAGTGTAAGACCATGTTTGGGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATG
31208769 GTATCGGCAT
Statistics
Matches: 142, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
44 11 0.08
45 19 0.13
46 59 0.42
47 41 0.29
48 12 0.08
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (46 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTTGAGATGT
Found at i:31208756 original size:47 final size:45
Alignment explanation
Indices: 31208513--31208768 Score: 186
Period size: 47 Copynumber: 5.5 Consensus size: 45
31208503 TTTGTGCGCT
* *
31208513 AGTGTAAGACATGTCTGAGACATGCATAGGCCACATT-ATGG--GAGCC
1 AGTGTAAGACATGTCTGGGACATGCAT-TG--AC-TTGATGGATGAGCC
** ** * *
31208559 AGTGTAAGATCATGTCTAAGACATAGCAACGACATTGAGAGGA-GAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATTGAC-TTGA-TGGATGAGCC
* *
31208607 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGA--GATGTCAGCC
1 AGTGTAAGACATGTCTGGGACATGCAT-TGACTTGATGGATG--AGCC
* * * *
31208653 AGTGTAAGACATGTCTGGGACATGCA-TCAGTT-ATGAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATTGACTTGATG-GATGAGCC
31208697 AGTGTAAGACCATGTCTGGGACATAGCATTGACTTGATGGATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATTGACTTGATGGATGAGCC
*
31208744 AGTGTAAGACCATGTTTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
31208769 GTATCGGCAT
Statistics
Matches: 172, Mismatches: 22, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
43 3 0.02
44 14 0.08
45 19 0.11
46 54 0.31
47 63 0.37
48 19 0.11
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATTGACTTGATGGATGAGCC
Found at i:31222955 original size:114 final size:114
Alignment explanation
Indices: 31222755--31223073 Score: 520
Period size: 114 Copynumber: 2.8 Consensus size: 114
31222745 TTAATAATGG
* *
31222755 AATTGCAATATTTTCTATAATGGATGGATGTCAAATAATATGTACTTTATCAAATCAAAGATGTA
1 AATTGCAATATTTTCTGTAATGGATGGATGTCAAATAATATCTACTTTATCAAATCAAAGATGTA
*
31222820 CACATTGTTTGAGACTGAAATATCGAATAATGGAATTGCAATATTTAGA
66 CACATTGTTTGAGACTGAAATATAGAATAATGGAATTGCAATATTTAGA
*
31222869 AATTGTAATATTTTCTGTAATGGATGGATGTCAAATAATATCTACTTTATCAAATCAAAGATGTA
1 AATTGCAATATTTTCTGTAATGGATGGATGTCAAATAATATCTACTTTATCAAATCAAAGATGTA
* *
31222934 CACATTGTTTGAGAGTGAAATATTGAATAATGGAATTGCAATATTTAGA
66 CACATTGTTTGAGACTGAAATATAGAATAATGGAATTGCAATATTTAGA
* *
31222983 AATTGCAATTTTTTCTGTAAT--A--GATGTCAAATAATATCTACTTTATCAAATAAAAGATGTA
1 AATTGCAATATTTTCTGTAATGGATGGATGTCAAATAATATCTACTTTATCAAATCAAAGATGTA
* *
31223044 CACATTATTTGATACTGAAATATAGAATAA
66 CACATTGTTTGAGACTGAAATATAGAATAA
31223074 AAGACTTAAA
Statistics
Matches: 193, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
110 64 0.33
112 1 0.01
114 128 0.66
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (114 bp):
AATTGCAATATTTTCTGTAATGGATGGATGTCAAATAATATCTACTTTATCAAATCAAAGATGTA
CACATTGTTTGAGACTGAAATATAGAATAATGGAATTGCAATATTTAGA
Found at i:31235534 original size:93 final size:93
Alignment explanation
Indices: 31235422--31235593 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31235412 GCCCATAAGT
* *
31235422 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31235487 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
31235515 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
31235580 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
31235594 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:31235589 original size:46 final size:46
Alignment explanation
Indices: 31235414--31235589 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
31235404 TGTAACCCGC
* *
31235414 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
31235460 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
31235506 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
31235553 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
31235590 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:31238019 original size:30 final size:30
Alignment explanation
Indices: 31237975--31238063 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
31237965 CAAAGATAAC
31237975 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
31238004 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
31238034 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
31238064 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:31238023 original size:15 final size:15
Alignment explanation
Indices: 31237975--31238054 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
31237965 CAAAGATAAC
*
31237975 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
31237989 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
31238004 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
31238019 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
31238034 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
31238049 AAGAAA
1 AAGAAA
31238055 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:31238063 original size:15 final size:15
Alignment explanation
Indices: 31237986--31238063 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
31237976 AGAAAACCGA
31237986 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
31238001 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
31238015 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
31238030 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
31238046 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
31238061 ATA
1 ATA
31238064 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31241129 original size:93 final size:93
Alignment explanation
Indices: 31241017--31241187 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
31241007 GCCCATAAGT
* *
31241017 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31241082 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
31241110 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
31241175 CGAGTTCGGATGC
66 CGAGCTCGGATGC
31241188 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:31241184 original size:46 final size:46
Alignment explanation
Indices: 31241009--31241184 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
31240999 TGTAACCCGC
* *
31241009 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
31241055 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
31241105 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
31241148 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
31241185 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 65 0.58
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:31244456 original size:18 final size:20
Alignment explanation
Indices: 31244415--31244459 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
31244405 TAATCCAAGC
* *
31244415 TCAATATCAGTCAATATTTT
1 TCAATATCAATCAATATTTG
31244435 TCAATATCAATC-A-ATTTG
1 TCAATATCAATCAATATTTG
31244453 TCAATAT
1 TCAATAT
31244460 TATGCAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (20 bp):
TCAATATCAATCAATATTTG
Found at i:31244456 original size:28 final size:28
Alignment explanation
Indices: 31244424--31244478 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
31244414 CTCAATATCA
* * *
31244424 GTCAATATTTTTCAATATCAATCAATTT
1 GTCAATATTATGCAATAACAATCAATTT
*
31244452 GTCAATATTATGCAGTAACAATCAATT
1 GTCAATATTATGCAATAACAATCAATT
31244479 ATTCAGTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (28 bp):
GTCAATATTATGCAATAACAATCAATTT
Found at i:31244485 original size:18 final size:18
Alignment explanation
Indices: 31244458--31244524 Score: 116
Period size: 18 Copynumber: 3.7 Consensus size: 18
31244448 ATTTGTCAAT
*
31244458 ATTATGCAGTAACAATCA
1 ATTATTCAGTAACAATCA
*
31244476 ATTATTCAGTAGCAATCA
1 ATTATTCAGTAACAATCA
31244494 ATTATTCAGTAACAATCA
1 ATTATTCAGTAACAATCA
31244512 ATTATTCAGTAAC
1 ATTATTCAGTAAC
31244525 GGTCAGTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (18 bp):
ATTATTCAGTAACAATCA
Found at i:31244537 original size:36 final size:36
Alignment explanation
Indices: 31244464--31244540 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
31244454 CAATATTATG
* *
31244464 CAGTAACAATCAATTATTCAGTAGCAATCAATTATT
1 CAGTAACAATCAATTATTCAGTAACAATCAATCATT
** *
31244500 CAGTAACAATCAATTATTCAGTAACGGTCAGTCATT
1 CAGTAACAATCAATTATTCAGTAACAATCAATCATT
31244536 CAGTA
1 CAGTA
31244541 CTTTTATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (36 bp):
CAGTAACAATCAATTATTCAGTAACAATCAATCATT
Found at i:31244659 original size:47 final size:43
Alignment explanation
Indices: 31244604--31244773 Score: 116
Period size: 47 Copynumber: 3.7 Consensus size: 43
31244594 ACCATCACAC
31244604 CAGT-ACAGTACGACACATAGTGCCTCATCGGCCAAGCCGAAGTAAA
1 CAGTAACAGTACGACACATAGTGCCTCATCGG--AA-CCGAAGT-AA
* * *
31244650 CAGTAACAGTACGATAC-TCAGTACCTCATCGGATTAAACCGAACTAA
1 CAGTAACAGTACGACACAT-AGTGCCTCATCGG----AACCGAAGTAA
* *
31244697 CAGTAGCAGTACGACACACATGGTGCCTCATC-G-ACTCGAAGTCAA
1 CAGTAACAGTACG--ACACATAGTGCCTCATCGGAAC-CGAAGT-AA
*
31244742 -AGTAATAGTACGACACTTATAGTGCCTCATCG
1 CAGTAACAGTACGACAC--ATAGTGCCTCATCG
31244774 AATCAAGGTC
Statistics
Matches: 99, Mismatches: 13, Indels: 25
0.72 0.09 0.18
Matches are distributed among these distances:
42 4 0.04
43 2 0.02
44 27 0.27
45 2 0.02
46 5 0.05
47 37 0.37
48 7 0.07
49 14 0.14
50 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (43 bp):
CAGTAACAGTACGACACATAGTGCCTCATCGGAACCGAAGTAA
Found at i:31245771 original size:17 final size:17
Alignment explanation
Indices: 31245749--31245785 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
31245739 AATCCCTAAT
*
31245749 TTTCCTTTCTTTCTTTC
1 TTTCCTTTCTTTCCTTC
31245766 TTTCCTTTCTTTCCTTC
1 TTTCCTTTCTTTCCTTC
31245783 TTT
1 TTT
31245786 TCTTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCCTTTCTTTCCTTC
Found at i:31245773 original size:9 final size:9
Alignment explanation
Indices: 31245749--31245785 Score: 60
Period size: 8 Copynumber: 4.3 Consensus size: 9
31245739 AATCCCTAAT
31245749 TTTCCTTTC
1 TTTCCTTTC
31245758 TTT-CTTTC
1 TTTCCTTTC
31245766 TTTCCTTTC
1 TTTCCTTTC
31245775 TTTCC-TTC
1 TTTCCTTTC
31245783 TTT
1 TTT
31245786 TCTTCTCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTCCTTTC
Found at i:31245969 original size:24 final size:25
Alignment explanation
Indices: 31245919--31245969 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
31245909 AGTAATTATA
* *
31245919 TAATTGTATTACAAATGTATGTATT
1 TAATTGTATTACAAATATATATATT
* *
31245944 TAATT-TATTACACATATATATTTT
1 TAATTGTATTACAAATATATATATT
31245968 TA
1 TA
31245970 TTACCATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
TAATTGTATTACAAATATATATATT
Found at i:31247416 original size:16 final size:15
Alignment explanation
Indices: 31247389--31247433 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
31247379 AAAGCCCATA
31247389 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
31247404 ATAAAGAAAATCCATG
1 ATAAAG-AAATCCAAG
*
31247420 ATAAGGAAATCCAA
1 ATAAAGAAATCCAA
31247434 TTTACATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31249501 original size:16 final size:15
Alignment explanation
Indices: 31249474--31249518 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 15
31249464 AAAGCCCAGA
31249474 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
31249489 ATAAAGAAAATCCATG
1 ATAAAG-AAATCCAAG
31249505 ATAAAGAAATCCAA
1 ATAAAGAAATCCAA
31249519 TTTACAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31250791 original size:13 final size:13
Alignment explanation
Indices: 31250773--31250805 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
31250763 CAGTTTCGAC
31250773 CACGGGCTAGACA
1 CACGGGCTAGACA
31250786 CACGGGCTAGACA
1 CACGGGCTAGACA
31250799 CACGGGC
1 CACGGGC
31250806 GTGTGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.33, T:0.06
Consensus pattern (13 bp):
CACGGGCTAGACA
Done.