Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold647
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: 155333
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:15137 original size:51 final size:51
Alignment explanation
Indices: 15050--15149 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
15040 AGATATATGG
*
15050 CATCCGAGCTCGTTGAGAGGTCTGAGTTCATAATGGATGTGATT-CATGTAA
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGTG-TTACATGTAA
* * *
15101 CATCTGAGTTCGTTGAGAGGTCCGAGTTCATTATGGATGTGTTACATGT
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGTGTTACATGT
15150 TATGTGGTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (51 bp):
CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGTGTTACATGTAA
Found at i:26483 original size:49 final size:49
Alignment explanation
Indices: 26404--26585 Score: 265
Period size: 49 Copynumber: 3.7 Consensus size: 49
26394 ACTATTGTGA
* *
26404 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
26453 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* *
26504 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
26553 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
26586 TGCGTACTAG
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 74 0.63
50 2 0.02
51 41 0.35
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:26584 original size:100 final size:100
Alignment explanation
Indices: 26406--26592 Score: 338
Period size: 100 Copynumber: 1.9 Consensus size: 100
26396 TATTGTGAGG
* * *
26406 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
26471 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
*
26506 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCACATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
26571 AAGTGCAGGCTACTATGCGTAC
66 AAGTGCAGGCTACTATGCGTAC
26593 TAGATAGCTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
Found at i:29582 original size:15 final size:15
Alignment explanation
Indices: 29562--29626 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
29552 GTATCTTGGG
29562 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
29577 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
29592 TTT-TTCTA-TCTTTGA
1 TTTCTT-TATTC-TGGA
*
29607 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
29621 TTTCTT
1 TTTCTT
29627 GTTATCTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.27
15 26 0.63
16 4 0.10
ACGTcount: A:0.09, C:0.14, G:0.12, T:0.65
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:29593 original size:30 final size:31
Alignment explanation
Indices: 29558--29626 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
29548 TATCGTATCT
29558 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
*
29588 TGGGTTT-TTCTATCTTTGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
29618 -GGTTTTCTT
1 TGGGTTTCTT
29627 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 7 0.21
30 26 0.76
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.16, T:0.62
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:32243 original size:49 final size:49
Alignment explanation
Indices: 32070--32250 Score: 247
Period size: 49 Copynumber: 3.7 Consensus size: 49
32060 ACTATTGTGA
* * *
32070 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAACT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
32119 GGTCGCATGTGTAGTACTAAGTGCA-GCTACTATGTGTACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* * *
32169 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
32218 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
32251 TGCGTACTAG
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
48 18 0.16
49 55 0.48
50 24 0.21
51 17 0.15
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:32243 original size:99 final size:100
Alignment explanation
Indices: 32072--32257 Score: 320
Period size: 99 Copynumber: 1.9 Consensus size: 100
32062 TATTGTGAGG
* *
32072 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAACTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT
*
32137 AAGTGCA-GCTACTATGTGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
* *
32171 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCACATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT
32236 AAGTGCAGGCTACTATGCGTAC
66 AAGTGCAGGCTACTATGCGTAC
32258 TAGATAGCTT
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
99 68 0.84
100 13 0.16
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
Found at i:38877 original size:35 final size:35
Alignment explanation
Indices: 38836--38902 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
38826 GATGTGTTTA
*
38836 TTTGTGGATGAGATGTACGATGAAGGGCACATTTG
1 TTTGTGGATGAGATGTACGATAAAGGGCACATTTG
38871 TTTGTGGATGAGATGTACGATAAAGGGCACAT
1 TTTGTGGATGAGATGTACGATAAAGGGCACAT
38903 GTGCTAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (35 bp):
TTTGTGGATGAGATGTACGATAAAGGGCACATTTG
Found at i:42762 original size:42 final size:43
Alignment explanation
Indices: 42708--42810 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 43
42698 GATTTATGTA
** *
42708 TAAGACCATGTCTGGGACATCGGCATCG-TATCTG-ATTTCATG
1 TAAGACCATGTCTGGGACAGAGGCATCGATAT-TGAATTACATG
* *
42750 TAAGACCCTGTCTGGGATAGAGGCATCGATATTGAATTACATG
1 TAAGACCATGTCTGGGACAGAGGCATCGATATTGAATTACATG
* *
42793 TAAGACCACGTTTGGGAC
1 TAAGACCATGTCTGGGAC
42811 GTCAGCATTG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
42 26 0.52
43 24 0.48
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACAGAGGCATCGATATTGAATTACATG
Found at i:49447 original size:40 final size:40
Alignment explanation
Indices: 49392--49573 Score: 251
Period size: 40 Copynumber: 4.6 Consensus size: 40
49382 TATTCGAATG
*
49392 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
49432 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
49472 ATATCCGGGCCAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * *
49512 ATATCCGGGCTAAGACCCAAAGGCATTTCTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
49552 ATATCC-GGCTAAATCTCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
49574 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 12 0.09
40 114 0.89
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:57104 original size:24 final size:24
Alignment explanation
Indices: 57072--57148 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
57062 AAGTCTGTCA
* *
57072 GGAGAGGATTTAGGTGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
57096 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
57120 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
57144 GGAGA
1 GGAGA
57149 ACAGTGTTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.31, C:0.03, G:0.43, T:0.23
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:58596 original size:27 final size:26
Alignment explanation
Indices: 58556--58662 Score: 160
Period size: 27 Copynumber: 4.0 Consensus size: 26
58546 AGGAAGCGTC
* *
58556 CTGGTGGCTATGCCACTATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
58583 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
58610 CTGGTGGCTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
58637 CTGGTGGCTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
58663 TTGGCAGCCA
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
26 12 0.16
27 61 0.81
28 2 0.03
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:61110 original size:21 final size:21
Alignment explanation
Indices: 61061--61110 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
61051 TTTCGTGTTA
* * **
61061 TTCATTTTAACCTTTTTTTAT
1 TTCATTTTAAACTTGTTGCAT
61082 TATCATTTTAAACTTGTTGCAT
1 T-TCATTTTAAACTTGTTGCAT
61104 TTCATTT
1 TTCATTT
61111 GTGTTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.60
Consensus pattern (21 bp):
TTCATTTTAAACTTGTTGCAT
Found at i:73603 original size:44 final size:45
Alignment explanation
Indices: 73407--73611 Score: 159
Period size: 44 Copynumber: 4.6 Consensus size: 45
73397 AGCGGCGAAT
* *
73407 CTTATC-CTCCTGAGGTAGCAGGGGAGCAGATTTTAG-CCACTAGC
1 CTTATCTC-CCTGAGGTAGCAAGGGAGCAGATTTAAGACCACTAGC
* * * * ** *
73451 CTTATATCCCTAAGGTAGCAAGGAAGCAG-GTTAATGATTA-TAGT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAA-GACCACTAGC
* * * * *** * **
73495 TTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATGGCAAAT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGACCACTAGC
* *
73540 CTTATCTTCCTGAGGTAGCAAGGGAGCAGATTTTAG-CCACTAGC
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGACCACTAGC
*
73584 CTTATCTCCCTGAGGTAGCAAAGGAGCA
1 CTTATCTCCCTGAGGTAGCAAGGGAGCA
73612 AGCTAATGAT
Statistics
Matches: 124, Mismatches: 32, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
43 3 0.02
44 82 0.66
45 39 0.31
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (45 bp):
CTTATCTCCCTGAGGTAGCAAGGGAGCAGATTTAAGACCACTAGC
Found at i:73622 original size:133 final size:133
Alignment explanation
Indices: 73404--73655 Score: 380
Period size: 133 Copynumber: 1.9 Consensus size: 133
73394 CAAAGCGGCG
*
73404 AATCTTATCCTCCTGAGGTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATATCCCTAAGGTAG
1 AATCTTATCCTCCTGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATATCCCTAAGGTAG
* * * *
73469 CAAGGAAGCAGGTTAATGATTATAGTTTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATG
66 CAAGGAAGCAAGCTAATGATTACAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATG
73534 GCA
131 GCA
* * *
73537 AATCTTATCTTCCTGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAG
1 AATCTTATCCTCCTGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATATCCCTAAGGTAG
* * * *
73602 CAAAGG-AGCAAGCTAATGATTGCAGTCTTCTCTTCTTGAGGTAGTAAGGGAGCA
66 C-AAGGAAGCAAGCTAATGATTACAGTCTTATCTTCCTGAGGTAGCAAGGGAGCA
73656 AACTAATGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
133 102 0.96
134 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (133 bp):
AATCTTATCCTCCTGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATATCCCTAAGGTAG
CAAGGAAGCAAGCTAATGATTACAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATG
GCA
Found at i:75592 original size:16 final size:16
Alignment explanation
Indices: 75571--75612 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
75561 TCAATTGTTA
*
75571 TTTTTATATATTCTTT
1 TTTTTATATATTCTTG
*
75587 TTTTTATATATTGTTG
1 TTTTTATATATTCTTG
*
75603 TATTTATATA
1 TTTTTATATA
75613 ATTTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTATATATTCTTG
Found at i:75892 original size:23 final size:23
Alignment explanation
Indices: 75864--75909 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
75854 CAAATTTCTT
75864 CTTTTTCGTATTATTCATTTTAAC
1 CTTTTTCGTATTA-TCATTTTAAC
**
75888 CTTTTTTTTATTATCATTTTAA
1 CTTTTTCGTATTATCATTTTAA
75910 ACTTGTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.63
Consensus pattern (23 bp):
CTTTTTCGTATTATCATTTTAAC
Found at i:76706 original size:16 final size:15
Alignment explanation
Indices: 76681--76715 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
76671 TTTGTTAAAA
76681 TGATTAATCTCAAGG
1 TGATTAATCTCAAGG
76696 TGATCTAATCTCAAGG
1 TGAT-TAATCTCAAGG
76712 TGAT
1 TGAT
76716 ATGATCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (15 bp):
TGATTAATCTCAAGG
Found at i:93965 original size:42 final size:42
Alignment explanation
Indices: 93893--93982 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
93883 TACGTGTAAA
*
93893 ACCATATCTGGGATATGGCATCTGTATGAGACTTCGTATAAG
1 ACCATATCTGGGATATGACATCTGTATGAGACTTCGTATAAG
* * * * *
93935 ACCATATTTGGGATATGATATC-GATGTGAGATTTCGTGTAAG
1 ACCATATCTGGGATATGACATCTG-TATGAGACTTCGTATAAG
93977 ACCATA
1 ACCATA
93983 GCTAGACTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (42 bp):
ACCATATCTGGGATATGACATCTGTATGAGACTTCGTATAAG
Found at i:99937 original size:6 final size:6
Alignment explanation
Indices: 99907--100086 Score: 104
Period size: 6 Copynumber: 29.3 Consensus size: 6
99897 AAGAAACATT
* * * *
99907 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAG- GTGACAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
99956 ATCAGA ATCAGA ATCAAA ATTAG- GTGACAGA ATCAGA ATCAGT A-CAGGTA
1 ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCA-G-A
* * *
100006 A-CAAA ATCAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
*
100054 ATCAGT ATCAGGTA A-CAGA ATCAGA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
100087 GTGAATGCAA
Statistics
Matches: 133, Mismatches: 24, Indels: 34
0.70 0.13 0.18
Matches are distributed among these distances:
5 10 0.08
6 105 0.79
7 14 0.11
8 4 0.03
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:99997 original size:37 final size:37
Alignment explanation
Indices: 99916--100036 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 37
99906 TATCAGAACT
* * *
99916 AGAATCAAAATGAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAAAATCAGGTGACAGAATC
* *
99953 AAAATCAGAATCAGAATCAAAATTAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAAAATCAGGTGACAGAATC
* *
99990 AGAATCAGTA-CAGGTAA-CAAAATCA-G-AATCAGAATC
1 AGAATCAGAATCA-G-AATCAAAATCAGGTGA-CAGAATC
100026 AGAATCAGAAT
1 AGAATCAGAAT
100037 TAGGTGACAG
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.01
36 19 0.27
37 48 0.69
38 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.17
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAAAATCAGGTGACAGAATC
Found at i:100053 original size:25 final size:25
Alignment explanation
Indices: 100019--100086 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
100009 AAATCAGAAT
* *
100019 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
*
100044 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
100069 CAGAATCAGAATCAGAAT
1 CAGAATCAGAATCAGAAT
100087 GTGAATGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:100064 original size:37 final size:36
Alignment explanation
Indices: 99983--100064 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 36
99973 AATTAGGTGA
*
99983 CAGAATCAGAATCAGTACAGGTAACAAAATCAGAAT
1 CAGAATCAGAATCAGAACAGGTAACAAAATCAGAAT
* * *
100019 CAGAATCAGAATCAGAATTAGGTGACAGAATCAGAAT
1 CAGAATCAGAATCAGAA-CAGGTAACAAAATCAGAAT
*
100056 CAGTATCAG
1 CAGAATCAG
100065 GTAACAGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 16 0.40
37 24 0.60
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (36 bp):
CAGAATCAGAATCAGAACAGGTAACAAAATCAGAAT
Found at i:100079 original size:31 final size:31
Alignment explanation
Indices: 99916--100086 Score: 131
Period size: 31 Copynumber: 5.5 Consensus size: 31
99906 TATCAGAACT
* * *
99916 AGAATCAAAATGAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* * *
99947 AGAATCAAAATCAGAATCAGAATCA--AAATT
1 AGAATCAGAATCAGAATCAGAATCAGGTAA-C
* *
99977 AG-GTGACAGAATCAGAATCAGTA-CAGGTAAC
1 AGAAT--CAGAATCAGAATCAGAATCAGGTAAC
* *
100008 AAAATCAGAATCAGAATCAGAATCA-G-AATT
1 AGAATCAGAATCAGAATCAGAATCAGGTAA-C
* *
100038 AG-GTGACAGAATCAGAATCAGTATCAGGTAAC
1 AGAAT--CAGAATCAGAATCAGAATCAGGTAAC
100070 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
100087 GTGAATGCAA
Statistics
Matches: 109, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
29 5 0.05
30 22 0.20
31 73 0.67
32 6 0.06
33 3 0.03
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.18
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:100311 original size:27 final size:26
Alignment explanation
Indices: 100205--100311 Score: 90
Period size: 27 Copynumber: 4.0 Consensus size: 26
100195 CATGGCTGCC
* * *
100205 AGAACAGATATTGTGACAGAGTCAGC-
1 AGAACAGATATTGTGGCAAAGCCA-CT
* *
100231 AGATACAGATATTGTGGCAGAGCCACC
1 AGA-ACAGATATTGTGGCAAAGCCACT
* * *
100258 AGAATAGATATTTTTGGCATAGCCACT
1 AGAACAGATA-TTGTGGCAAAGCCACT
*
100285 AGAAACAGATAATGTGGCAAAGCCACT
1 AG-AACAGATATTGTGGCAAAGCCACT
100312 TAACAAAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 10 0.15
27 50 0.75
28 7 0.10
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (26 bp):
AGAACAGATATTGTGGCAAAGCCACT
Found at i:100939 original size:27 final size:27
Alignment explanation
Indices: 100909--101322 Score: 390
Period size: 27 Copynumber: 15.3 Consensus size: 27
100899 GGGGCAAAAT
* *
100909 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
100936 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
100963 AGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* * *
100990 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
101017 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
101044 GGT-ATTTCTACTCTACAAGGGTATTTT
1 GGTAATTT-TACCCTACAAGGGTATTTC
101071 GGT-ATTTATACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* * *
101098 GGTAATTTTACCCTATAGGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
101125 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
101152 GAT-ATTTCTACCCTATAAGTGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* *
101179 AGT-ATTTCTACCCTACAAGGGTATTTT
1 GGTAATTT-TACCCTACAAGGGTATTTC
* * * * *
101206 AGTAATTCTACCTTACAGGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
* * * *
101233 AGTAATTCTACCCTACAGGGGTCTTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
101260 GAT-ATTTTAACCCTACAAGGGTATATC
1 GGTAATTTT-ACCCTACAAGGGTATTTC
* * *
101287 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
**
101314 AATAATTTT
1 GGTAATTTT
101323 GTAAATCAAG
Statistics
Matches: 325, Mismatches: 54, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
26 13 0.04
27 298 0.92
28 14 0.04
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:101049 original size:81 final size:81
Alignment explanation
Indices: 100911--101320 Score: 475
Period size: 81 Copynumber: 5.1 Consensus size: 81
100901 GGCAAAATGG
* * * * *
100911 TAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCC
1 TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
*
100976 TACAAGGGTATTTCGA
66 TACAGGGGTATTTCGA
* * * *
100992 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTATTTCTACTC
1 TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
* * *
101057 TACAAGGGTATTTTGG
66 TACAGGGGTATTTCGA
* * * * * *
101073 TATTTATACCCTACAAGGGTATTTCGGTAATTTTACCCTATAGGGGTATTTTAGTAATTCTACCC
1 TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
101138 TACAGGGGTATTTCGA
66 TACAGGGGTATTTCGA
* * * * * * *
101154 TATTTCTACCCTATAAGTGTATTTCAGTATTTCTACCCTACAAGGGTATTTTAGTAATTCTACCT
1 TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
*
101219 TACAGGGGTATTT-TA
66 TACAGGGGTATTTCGA
* * * * *
101234 GTAATTCTACCCTACAGGGGTCTTTCGAT-ATTTTAACCCTACAAGGGTATATC-GATAATTCTA
1 -TAATTCTACCCTACAAGGGTATTTCGGTAATTCT-ACCCTACAAGGGTATTTCAG-TAATTCTA
*
101297 CCCTACAGGGGTATTTCAA
63 CCCTACAGGGGTATTTCGA
101316 TAATT
1 TAATT
101321 TTGTAAATCA
Statistics
Matches: 280, Mismatches: 45, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
80 5 0.02
81 274 0.98
82 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (81 bp):
TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
TACAGGGGTATTTCGA
Found at i:101335 original size:27 final size:27
Alignment explanation
Indices: 101305--101473 Score: 144
Period size: 27 Copynumber: 6.3 Consensus size: 27
101295 TACCCTACAG
* * *
101305 GGGTATTTCAATAATTTTGTAAATCAA
1 GGGTATTTCAGTAATTTTATAAATCGA
*** * * * *
101332 GGGTAAAACGGTAATTCTGTAAATCGG
1 GGGTATTTCAGTAATTTTATAAATCGA
* * *
101359 GGGTAGTTT-GGTAATTTTATAAGTTGA
1 GGGTA-TTTCAGTAATTTTATAAATCGA
*
101386 GGGTATTTCAGTAATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTATAAATCGA
*
101413 GGGTATTTCAGTAATTTTA-CAATCGA
1 GGGTATTTCAGTAATTTTATAAATCGA
* * * *
101439 CGATATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTATAAATCGA
101466 GGGTATTT
1 GGGTATTT
101474 GGGTAATTCG
Statistics
Matches: 112, Mismatches: 27, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
26 25 0.22
27 87 0.78
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTATAAATCGA
Found at i:101347 original size:54 final size:53
Alignment explanation
Indices: 101126--101349 Score: 128
Period size: 54 Copynumber: 4.2 Consensus size: 53
101116 GGGTATTTTA
* * * * * *** *
101126 GTAATTCTACCCTACAGGGGTATTTCGATATTTCTACCCTATAAGTGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCAATATTT-TAACATACAAGGGTAAAACG
* * * * * * * * *****
101180 GTATTTCTACCCTACAAGGGTATTTTAGTAATTCTACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCAAT-ATTTTAACATACAAGGGTAAAACG
* * * * *
101234 GTAATTCTACCCTACAGGGGTCTTTCGATATTTTAACCCTACAAGGGTATATCG
1 GTAATTCTACCCTACAGGGGTATTTCAATATTTTAA-CATACAAGGGTAAAACG
*
101288 ATAATTCTACCCTACAGGGGTATTTCAATAATTTTGTAA-AT-CAAGGGTAAAACG
1 GTAATTCTACCCTACAGGGGTATTTCAAT-A-TTT-TAACATACAAGGGTAAAACG
101342 GTAATTCT
1 GTAATTCT
101350 GTAAATCGGG
Statistics
Matches: 134, Mismatches: 31, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
53 5 0.04
54 118 0.88
55 5 0.04
56 3 0.02
57 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (53 bp):
GTAATTCTACCCTACAGGGGTATTTCAATATTTTAACATACAAGGGTAAAACG
Found at i:101445 original size:26 final size:27
Alignment explanation
Indices: 101389--101465 Score: 120
Period size: 26 Copynumber: 2.9 Consensus size: 27
101379 AAGTTGAGGG
* *
101389 TATTTCAGTAATTTTACAAATCGAGGG
1 TATTTCAGTAATTTTACAAATCGACGA
101416 TATTTCAGTAATTTTAC-AATCGACGA
1 TATTTCAGTAATTTTACAAATCGACGA
*
101442 TATTTCGGTAATTTTACAAATCGA
1 TATTTCAGTAATTTTACAAATCGA
101466 GGGTATTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 23 0.50
27 23 0.50
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (27 bp):
TATTTCAGTAATTTTACAAATCGACGA
Found at i:101478 original size:27 final size:27
Alignment explanation
Indices: 101352--101481 Score: 156
Period size: 27 Copynumber: 4.9 Consensus size: 27
101342 GTAATTCTGT
* *
101352 AAATCGGGGGTAGTTT-GGTAATTTTAT
1 AAATCGAGGGTA-TTTCGGTAATTTTAC
* * *
101379 AAGTTGAGGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTCGGTAATTTTAC
*
101406 AAATCGAGGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTCGGTAATTTTAC
* *
101433 -AATCGACGATATTTCGGTAATTTTAC
1 AAATCGAGGGTATTTCGGTAATTTTAC
*
101459 AAATCGAGGGTATTTGGGTAATT
1 AAATCGAGGGTATTTCGGTAATT
101482 CGGTAAACTA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 26 0.30
27 62 0.70
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (27 bp):
AAATCGAGGGTATTTCGGTAATTTTAC
Found at i:101480 original size:53 final size:53
Alignment explanation
Indices: 101352--101481 Score: 163
Period size: 53 Copynumber: 2.4 Consensus size: 53
101342 GTAATTCTGT
* * * * *
101352 AAATCGGGGGTAGTTTGGTAATTTTATAAGTTGAGGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTGGTAATTTTACAAGTCGACGATATTTCAGTAATTTTAC
* *
101406 AAATCGAGGGTATTTCAGTAATTTTACAA-TCGACGATATTTCGGTAATTTTAC
1 AAATCGAGGGTATTT-GGTAATTTTACAAGTCGACGATATTTCAGTAATTTTAC
101459 AAATCGAGGGTATTTGGGTAATT
1 AAATCGAGGGTATTT-GGTAATT
101482 CGGTAAACTA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
53 44 0.67
54 22 0.33
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (53 bp):
AAATCGAGGGTATTTGGTAATTTTACAAGTCGACGATATTTCAGTAATTTTAC
Found at i:107202 original size:40 final size:41
Alignment explanation
Indices: 107128--107221 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 41
107118 TATCTCAATA
*
107128 TCGCACACTTAGTGCCTCTTCTAGCCGAAGCTATTCC-AAC
1 TCGCACACTTAGTGCCTCTTCTAGACGAAGCTATTCCGAAC
* *
107168 TCGCACACTTAGTGCCAT-TTGTAGTAGGAA-CTATTCCGAAC
1 TCGCACACTTAGTGCC-TCTTCTAG-ACGAAGCTATTCCGAAC
* *
107209 -CGTAGACTTAGTG
1 TCGCACACTTAGTG
107222 TGGAACATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
40 39 0.85
41 7 0.15
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
TCGCACACTTAGTGCCTCTTCTAGACGAAGCTATTCCGAAC
Found at i:111549 original size:43 final size:43
Alignment explanation
Indices: 111501--111656 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 43
111491 GTTATCGAGA
111501 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
** * * *
111544 TGTGATTATGTGTAACACCATGTCTGGGACATTAGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* * * * * * *
111587 TATGATTTCATGTAAGACCCTGGCTGGGACA-AGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
** *
111628 ATGTGA-TAGTTGTAAGACCATATCTAGGA
1 -TGTGATTACATGTAAGACCATGTCTAGGA
111657 TATGGAATTG
Statistics
Matches: 89, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
41 18 0.20
42 9 0.10
43 62 0.70
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
Found at i:112485 original size:13 final size:13
Alignment explanation
Indices: 112469--112496 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
112459 AATGTGGAAT
112469 TGAGTAGTAGAAA
1 TGAGTAGTAGAAA
112482 TGAGTAGTAGAAA
1 TGAGTAGTAGAAA
112495 TG
1 TG
112497 GTGCAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (13 bp):
TGAGTAGTAGAAA
Found at i:118390 original size:43 final size:42
Alignment explanation
Indices: 118342--118494 Score: 177
Period size: 43 Copynumber: 3.6 Consensus size: 42
118332 TATCAAGATG
118342 TGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTATTA
1 TGATTACATGTAAGACCATGTCT-GGACATTGGCATTGTATTA
** *
118385 TGATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTATTT
1 TGATTACATGTAAGACCATGTCT-GGACATTGGCATTGTATTA
* * *
118428 TGATTTCATGTAAGACCCTGTCTGCGACA-TGGCATTGGT-TTG
1 TGATTACATGTAAGACCATGTCTG-GACATTGGCATT-GTATTA
*
118470 TGA-TAGCATGTAAGACCATATCTGG
1 TGATTA-CATGTAAGACCATGTCTGG
118495 GATATGGTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 64 0.67
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (42 bp):
TGATTACATGTAAGACCATGTCTGGACATTGGCATTGTATTA
Found at i:123206 original size:27 final size:26
Alignment explanation
Indices: 123172--123265 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 26
123162 GCATGGCTGT
* *
123172 CAGAACAGATAATGTGACAGAGTCAC
1 CAGAACAGATAATGTGGCAGAGCCAC
123198 CAGATACAGATAATCGTGGCAGAGCCAC
1 CAGA-ACAGATAAT-GTGGCAGAGCCAC
123226 CAGAACAGATATATGTGGCAGAGCCAC
1 CAGAACAGATA-ATGTGGCAGAGCCAC
*
123253 CAGATCAGATAAT
1 CAGAACAGATAAT
123266 TATGGTATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
26 6 0.10
27 39 0.63
28 17 0.27
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (26 bp):
CAGAACAGATAATGTGGCAGAGCCAC
Found at i:123277 original size:27 final size:27
Alignment explanation
Indices: 123172--123282 Score: 118
Period size: 27 Copynumber: 4.1 Consensus size: 27
123162 GCATGGCTGT
* * *
123172 CAGAACAGATAA-TGTGACAGAGTCAC
1 CAGATCAGATAATTGTGGCAGAGCCAC
*
123198 CAGATACAGATAATCGTGGCAGAGCCAC
1 CAGAT-CAGATAATTGTGGCAGAGCCAC
*
123226 CAGAACAGAT-ATATGTGGCAGAGCCAC
1 CAGATCAGATAAT-TGTGGCAGAGCCAC
* * *
123253 CAGATCAGATAATTATGGTATAGCCAC
1 CAGATCAGATAATTGTGGCAGAGCCAC
123280 CAG
1 CAG
123283 GATGCTTCCT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.08
27 48 0.68
28 17 0.24
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
CAGATCAGATAATTGTGGCAGAGCCAC
Found at i:123278 original size:54 final size:54
Alignment explanation
Indices: 123172--123282 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
123162 GCATGGCTGT
* *
123172 CAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCAC
1 CAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCAC
* * * *
123226 CAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTATGGTATAGCCAC
1 CAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCAC
123280 CAG
1 CAG
123283 GATGCTTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 32 0.64
55 18 0.36
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (54 bp):
CAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCAC
Found at i:123412 original size:26 final size:28
Alignment explanation
Indices: 123370--123442 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 28
123360 AAAGTAACCG
* *
123370 TAGGGGTATAAT-GGTAATTTTGCAC-C-
1 TAGGGGTAT-ATCAGTAATTTTCCACACA
*
123396 TAGGGGTATATCAGTAA-CTTCCACACA
1 TAGGGGTATATCAGTAATTTTCCACACA
123423 TAGGGGTAT-TCAAGTAATTT
1 TAGGGGTATATC-AGTAATTT
123443 CACTATTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 7 0.18
26 16 0.42
27 14 0.37
28 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (28 bp):
TAGGGGTATATCAGTAATTTTCCACACA
Found at i:129123 original size:27 final size:27
Alignment explanation
Indices: 129093--129178 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
129083 GTGACTAAGT
129093 CACCAGATCAGATAATTGTGGCATAGC
1 CACCAGATCAGATAATTGTGGCATAGC
* * **
129120 CACCAAAACAGAT-ATGTGTGGCGGAGC
1 CACCAGATCAGATAAT-TGTGGCATAGC
129147 CACCAGATCAGATAATTGTGGCATAGC
1 CACCAGATCAGATAATTGTGGCATAGC
129174 CACCA
1 CACCA
129179 AGACGCTTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.04
27 45 0.92
28 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (27 bp):
CACCAGATCAGATAATTGTGGCATAGC
Found at i:130432 original size:16 final size:17
Alignment explanation
Indices: 130411--130442 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
130401 TGATGAAAAG
130411 AAATAAAAA-GAAGAAA
1 AAATAAAAAGGAAGAAA
130427 AAATAAAAAGGAAGAA
1 AAATAAAAAGGAAGAA
130443 TGGTCAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (17 bp):
AAATAAAAAGGAAGAAA
Found at i:133685 original size:48 final size:48
Alignment explanation
Indices: 133582--134322 Score: 734
Period size: 48 Copynumber: 15.0 Consensus size: 48
133572 CAAGATAAAT
* * *
133582 ATATATATGTGTGGTAAACCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
133630 ATA--TATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
133676 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
133724 ACATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
133772 ATATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 --ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *** * *
133822 ACATGTATATGTGGTAAAGCCGAATATATATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTA-ATGT-G-AAA----TAT-G-T-A--TGAG
* ** * * * ** *
133882 ATATGTATGA-GAT-ATATATATGTGGTAAAGCCGAATG-GCTA-ATG--TGAA
1 ATATGTAT-ATG-TGGTA-A-A-GCCG-AATGGCTAATGTGAAATATGTATGAG
* * ** * * *
133930 ATATGTATGA-GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTAT-ATG-T-GGTA-AAGCCG-AATGGCTAA-------TGTGAAATATGTATGAG
*
133989 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
134037 ATA--TATATGTGGTAAAGACGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
134083 ATA--TATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGCATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
134129 ATATGTATATGTGGTAAAGCCGAATGGCTAATATAAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
134177 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
134225 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * *
134273 AGATGTATATTTGGTAAAGCCGAATGGCTAATGAGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
134321 AT
1 AT
134323 GTGTGTATAT
Statistics
Matches: 600, Mismatches: 55, Indels: 76
0.82 0.08 0.10
Matches are distributed among these distances:
46 131 0.22
48 342 0.57
49 4 0.01
50 52 0.09
51 3 0.00
54 1 0.00
55 12 0.02
56 6 0.01
57 7 0.01
58 3 0.00
59 12 0.02
60 14 0.02
61 4 0.01
62 1 0.00
63 5 0.01
64 3 0.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:133860 original size:71 final size:71
Alignment explanation
Indices: 133774--133917 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 71
133764 TGTATGAGAT
* *
133774 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGACATGTATATGTGGTAA
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGACATATATATGTGGTAA
133839 AGCCGA
66 AGCCGA
*
133845 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAA
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGACATATATATGTGGTAA
133910 AGCCGA
66 AGCCGA
133916 AT
1 AT
133918 GGCTAATGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (71 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGACATATATATGTGGTAA
AGCCGA
Found at i:133940 original size:119 final size:120
Alignment explanation
Indices: 133729--133965 Score: 449
Period size: 119 Copynumber: 2.0 Consensus size: 120
133719 ATGAGACATG
133729 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATGTATATGTGGTAAAGC
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATA-GTATATGTGGTAAAGC
133794 CGAATGGCTAATGTGAAATATGTATGAGACATGTATATGTGGTAAAGCCGAATATA
65 CGAATGGCTAATGTGAAATATGTATGAGACATGTATATGTGGTAAAGCCGAATATA
133850 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATA-TATATGTGGTAAAGCC
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATAGTATATGTGGTAAAGCC
*
133914 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAAT
66 GAATGGCTAATGTGAAATATGTATGAGACATGTATATGTGGTAAAGCCGAAT
133966 GGCTAATGTG
Statistics
Matches: 115, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
119 67 0.58
121 48 0.42
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (120 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATAGTATATGTGGTAAAGCC
GAATGGCTAATGTGAAATATGTATGAGACATGTATATGTGGTAAAGCCGAATATA
Found at i:134131 original size:236 final size:237
Alignment explanation
Indices: 133847--134322 Score: 803
Period size: 236 Copynumber: 2.0 Consensus size: 237
133837 AAAGCCGAAT
*
133847 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATATATATGTGGTAAAG
1 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATATATATGTGGTAAAG
* * *
133912 CCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGA
66 CCGAATGGCTAATATAAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGA
*
133977 AATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTAT-GAGATAT
131 AATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATAGAGATAT
*
134041 ATATGTGGTAAAGACGAATGGCTAAT-ATGAAATATGTATGAG
196 ATATGTGGTAAAGACGAATGGCTAATGA-GAAATATGTAGGAG
* *
134083 ATATATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGGTAAAG
1 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATATATATGTGGTAAAG
134148 CCGAATGGCTAATATAAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGA
66 CCGAATGGCTAATATAAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGA
* * *
134213 AATATGTATGAGATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAGAGATG
131 AATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTAT-AGAGATA
* *
134278 TATATTTGGTAAAGCCGAATGGCTAATGAGAAATATGTAGGAG
195 TATATGTGGTAAAGACGAATGGCTAATGAGAAATATGTAGGAG
134321 AT
1 AT
134323 GTGTGTATAT
Statistics
Matches: 224, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
236 178 0.79
238 45 0.20
239 1 0.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (237 bp):
ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATATATATGTGGTAAAG
CCGAATGGCTAATATAAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGA
AATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATAGAGATAT
ATATGTGGTAAAGACGAATGGCTAATGAGAAATATGTAGGAG
Found at i:134791 original size:20 final size:20
Alignment explanation
Indices: 134763--134800 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
134753 TGAGGGTAAC
*
134763 TATAGATATGAATGAAATGA
1 TATAGATATGAATCAAATGA
*
134783 TATATATATGAATCAAAT
1 TATAGATATGAATCAAAT
134801 AAACAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (20 bp):
TATAGATATGAATCAAATGA
Found at i:137831 original size:28 final size:29
Alignment explanation
Indices: 137787--137900 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
137777 TACCTCTATC
* *
137787 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
137815 TGGTCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
137844 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
137873 TGGCCCGTTAGGCCC-AATCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
137901 ATCATCCTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 26 0.35
29 48 0.64
30 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:137859 original size:57 final size:57
Alignment explanation
Indices: 137778--137893 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 57
137768 AATTTCACAT
* * *
137778 ACCTCTATCTGGCCCATTAAGCCC-AATCATATTCATATGGTCCATTAGGCCCAAATC
1 ACCTCTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCC-AATC
* * * *
137835 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCAATC
1 ACCTCTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAATC
137892 AC
1 AC
137894 ATTCATAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 27 0.53
58 24 0.47
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (57 bp):
ACCTCTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAATC
Found at i:139244 original size:16 final size:16
Alignment explanation
Indices: 139223--139254 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
139213 AAGTTTAGGA
139223 TTTCGGGATTTTTGGG
1 TTTCGGGATTTTTGGG
139239 TTTCGGGATTTTTGGG
1 TTTCGGGATTTTTGGG
139255 GGGTTACAGC
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:0.06, C:0.06, G:0.38, T:0.50
Consensus pattern (16 bp):
TTTCGGGATTTTTGGG
Found at i:145254 original size:28 final size:28
Alignment explanation
Indices: 145191--145313 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
145181 ATATTAAGTC
*
145191 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
145218 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
145246 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
145274 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
145303 CGCACACTTAG
1 CGCACACTTAG
145314 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:151446 original size:40 final size:40
Alignment explanation
Indices: 151402--151492 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
151392 GGACTAAGAT
* * *
151402 CCGAAGGTATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
*
151442 CCGAAGGCCTTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
*
151482 CCTAAGGCATT
1 CCGAAGGCATT
151493 GAATGAGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
39 2 0.05
40 42 0.95
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
Done.