Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2236
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: 102306
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:148 original size:20 final size:20
Alignment explanation
Indices: 119--161 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
109 TTTATCCTAG
119 TTTATTTTTG-TGATTTT-AT
1 TTTATTTTTGAT-ATTTTGAT
138 TTTATTTTTTGATATTTTGAT
1 TTTA-TTTTTGATATTTTGAT
159 TTT
1 TTT
162 GGTTAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (20 bp):
TTTATTTTTGATATTTTGAT
Found at i:1440 original size:20 final size:19
Alignment explanation
Indices: 1395--1440 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1385 ATATTTAATA
*
1395 TTTATTTAAAAATTAAAAT
1 TTTATTTAAAAAATAAAAT
*
1414 TCT-TTTAAAAAATATAAAT
1 TTTATTTAAAAAATA-AAAT
1433 TTTATTTA
1 TTTATTTA
1441 CGTGAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 10 0.45
19 8 0.36
20 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATTTAAAAAATAAAAT
Found at i:1596 original size:2 final size:2
Alignment explanation
Indices: 1589--1646 Score: 107
Period size: 2 Copynumber: 28.5 Consensus size: 2
1579 GTTACCCTTT
1589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1631 TA TA TA TA TA TGA TA T
1 TA TA TA TA TA T-A TA T
1647 TAATCATCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 53 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1785 original size:27 final size:29
Alignment explanation
Indices: 1755--1809 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1745 TATTAACGTA
1755 TTAAA-AT-TTAT-ATAAATATAAAATATT
1 TTAAACATATTATAATAAA-ATAAAATATT
*
1782 TTAAACATATTATAATTAAATAAAATAT
1 TTAAACATATTATAATAAAATAAAATAT
1810 ATAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 13 0.54
30 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAACATATTATAATAAAATAAAATATT
Found at i:1846 original size:19 final size:18
Alignment explanation
Indices: 1768--1872 Score: 83
Period size: 17 Copynumber: 5.9 Consensus size: 18
1758 AAATTTATAT
**
1768 AAATATA-AAATATTTTA
1 AAATATATAAATATAATA
*
1785 AACATATTATAATTA-AATA
1 AA-ATA-TATAAATATAATA
1804 AAATATATAAATATAATA
1 AAATATATAAATATAATA
* *
1822 TGAATATATAAAT-TATTA
1 -AAATATATAAATATAATA
* *
1840 AAAAATATAACT-TAATA
1 AAATATATAAATATAATA
*
1857 AAATATGTAAATATAA
1 AAATATATAAATATAA
1873 AATAAAAAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
17 31 0.45
18 17 0.25
19 17 0.25
20 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATATATAAATATAATA
Found at i:1847 original size:17 final size:17
Alignment explanation
Indices: 1795--1884 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 17
1785 AACATATTAT
*
1795 AATTAAATAAAATATATA
1 AATT-AATAAAAAATATA
* *
1813 AATATAATATGAATATATA
1 AAT-TAATA-AAAAATATA
*
1832 AATTATTAAAAAATATA
1 AATTAATAAAAAATATA
* * *
1849 ACTTAATAAAATATGTA
1 AATTAATAAAAAATATA
1866 AATATAAAATAAAAAATAT
1 AAT-T--AATAAAAAATAT
1885 CCTAATTGTG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
17 22 0.39
18 12 0.21
19 12 0.21
20 10 0.18
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTAATAAAAAATATA
Found at i:2916 original size:24 final size:23
Alignment explanation
Indices: 2880--2928 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
2870 GGCAAGCTCG
2880 AATTATTATTAAAATTATTAT-ATT
1 AATTATTATT-AAATT-TTATAATT
2904 AATTATT-TATAAATTTTATAATT
1 AATTATTAT-TAAATTTTATAATT
2927 AA
1 AA
2929 CTTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 11 0.48
24 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTATTATTAAATTTTATAATT
Found at i:2951 original size:31 final size:31
Alignment explanation
Indices: 2916--2987 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
2906 TTATTTATAA
2916 ATTTTATAATTAACTTTAAATAAAAATTATT
1 ATTTTATAATTAACTTTAAATAAAAATTATT
2947 ATTTTATAATTAACTTTAAATAAAAATTATT
1 ATTTTATAATTAACTTTAAATAAAAATTATT
2978 ATTTTATAAT
1 ATTTTATAAT
2988 AATAATTCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTTTATAATTAACTTTAAATAAAAATTATT
Found at i:3356 original size:27 final size:28
Alignment explanation
Indices: 3293--3375 Score: 132
Period size: 27 Copynumber: 3.0 Consensus size: 28
3283 CTTAATGTCG
* *
3293 GTAGTGGTACCAATGGTAAGTGTTGAAA
1 GTAGTGGAACCAATGGGAAGTGTTGAAA
*
3321 GTAGTGGAACTAATGGGAAGTGTT-AAA
1 GTAGTGGAACCAATGGGAAGTGTTGAAA
3348 GTAGTGGAACCAATGGGAAGTGTTGAAA
1 GTAGTGGAACCAATGGGAAGTGTTGAAA
3376 TATCAATACA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 26 0.52
28 24 0.48
ACGTcount: A:0.35, C:0.06, G:0.34, T:0.25
Consensus pattern (28 bp):
GTAGTGGAACCAATGGGAAGTGTTGAAA
Found at i:3599 original size:16 final size:17
Alignment explanation
Indices: 3580--3612 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3570 TTCAATTTGT
3580 AATGATCT-AAATTTAA
1 AATGATCTGAAATTTAA
*
3596 AATGATTTGAAATTTAA
1 AATGATCTGAAATTTAA
3613 TGACTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (17 bp):
AATGATCTGAAATTTAA
Found at i:4464 original size:15 final size:15
Alignment explanation
Indices: 4444--4474 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4434 AAAGTAATTA
*
4444 TAATTTAATATTATT
1 TAATTTAAAATTATT
4459 TAATTTAAAATTATT
1 TAATTTAAAATTATT
4474 T
1 T
4475 TTCAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTTAAAATTATT
Found at i:4714 original size:24 final size:23
Alignment explanation
Indices: 4677--4729 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
4667 AAGCAAGAAG
* *
4677 AAAAAAAAGGAAAGGAAATGAGA
1 AAAAAAAAGAAAAGGAAATAAGA
**
4700 AAAAAAAAGAAAAAGTTAATAAGA
1 AAAAAAAAG-AAAAGGAAATAAGA
4724 AAAAAA
1 AAAAAA
4730 GAAAGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (23 bp):
AAAAAAAAGAAAAGGAAATAAGA
Found at i:4915 original size:21 final size:18
Alignment explanation
Indices: 4871--4906 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4861 TTAAAAAATT
4871 ATTTATAATTATATATTA
1 ATTTATAATTATATATTA
4889 ATTTATAA-TATAT-TTA
1 ATTTATAATTATATATTA
4905 AT
1 AT
4907 ATAATTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATAATTATATATTA
Found at i:5783 original size:16 final size:16
Alignment explanation
Indices: 5762--5828 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
5752 AATATATATA
5762 ATAAATATTTTAAAAT
1 ATAAATATTTTAAAAT
* *
5778 ATAAATAATTTATATTATT
1 ATAAAT-ATTT-TA-AAAT
* *
5797 ATTAATATATTAAAAT
1 ATAAATATTTTAAAAT
*
5813 TTAATATATTTTAAAA
1 ATAA-ATATTTTAAAA
5829 CATGATTATA
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
16 10 0.26
17 16 0.42
18 5 0.13
19 7 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATATTTTAAAAT
Found at i:5826 original size:25 final size:25
Alignment explanation
Indices: 5766--5828 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
5756 TATATAATAA
5766 ATATTTTAAAATATAAATAATTTAT
1 ATATTTTAAAATATAAATAATTTAT
* *
5791 ATTATTATTAATATATTAA-AATTTAAT
1 A-TATT-TTAAAATATAAATAATTT-AT
5818 ATATTTTAAAA
1 ATATTTTAAAA
5829 CATGATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 6 0.19
26 13 0.41
27 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTTTAAAATATAAATAATTTAT
Found at i:6011 original size:5 final size:5
Alignment explanation
Indices: 5979--6025 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
5969 TATTTCAAAA
* * * *
5979 ATTTT ATCTT ATTTT GTTTT -TGTG ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
6026 AATTTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
4 2 0.06
5 32 0.94
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:6030 original size:24 final size:24
Alignment explanation
Indices: 5978--6037 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
5968 GTATTTCAAA
* *
5978 AATTTTATCTTATTTTGTTTTTGT
1 AATTTTATTTTATTTTATTTTTGT
*
6002 GATTTTATTTTATTTTATTTTAT-T
1 AATTTTATTTTATTTTATTTT-TGT
6026 AATTTTAATTTT
1 AATTTT-ATTTT
6038 GATTAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (24 bp):
AATTTTATTTTATTTTATTTTTGT
Found at i:6844 original size:26 final size:27
Alignment explanation
Indices: 6794--6869 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
6784 ATATCGCGCG
*
6794 ATAAAAAATATATATTAT-TATAAAA-AA
1 ATAAAAAATA-ATAATATATA-AAAATAA
*
6821 ATAAAAAATAATAATATATAAAAATAT
1 ATAAAAAATAATAATATATAAAAATAA
*
6848 ATTAAAAAT-ATAATATAATAAA
1 ATAAAAAATAATAATAT-ATAAA
6870 TATTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 17 0.40
27 26 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAAAATAATAATATATAAAAATAA
Found at i:6880 original size:24 final size:25
Alignment explanation
Indices: 6797--6879 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 25
6787 TCGCGCGATA
* * * *
6797 AAAAATATATATTATTATAAAAAAATA
1 AAAAATATA-A-TATAATAAATATATT
*
6824 AAAAATAATAATATATAAAAATATATT
1 AAAAAT-ATAATATA-ATAAATATATT
*
6851 AAAAATATAATATAATAAATATTTT
1 AAAAATATAATATAATAAATATATT
6876 AAAA
1 AAAA
6880 TTTAAATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 13 0.28
26 11 0.23
27 20 0.43
28 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAAATATAATATAATAAATATATT
Found at i:7215 original size:13 final size:13
Alignment explanation
Indices: 7197--7222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7187 ATTATATTAA
7197 AATTTTAAAAAAT
1 AATTTTAAAAAAT
7210 AATTTTAAAAAAT
1 AATTTTAAAAAAT
7223 TTTAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTTTAAAAAAT
Found at i:7800 original size:30 final size:30
Alignment explanation
Indices: 7764--7898 Score: 243
Period size: 30 Copynumber: 4.5 Consensus size: 30
7754 TATAAAATCA
* *
7764 TAAGATAAAAGGCTCTCTTTCATACTGAGT
1 TAAGATAAAAGGCTCTATTTCATACCGAGT
7794 TAAGATAAAAGGCTCTATTTCATACCGAGT
1 TAAGATAAAAGGCTCTATTTCATACCGAGT
7824 TAAGATAAAAGGCTCTATTTCATACCGAGT
1 TAAGATAAAAGGCTCTATTTCATACCGAGT
*
7854 TAAGATAAAAGGCTCAATTTCATACCGAGT
1 TAAGATAAAAGGCTCTATTTCATACCGAGT
7884 TAAGATAAAAGGCTC
1 TAAGATAAAAGGCTC
7899 GTGGCTCTGC
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (30 bp):
TAAGATAAAAGGCTCTATTTCATACCGAGT
Found at i:9866 original size:32 final size:32
Alignment explanation
Indices: 9830--9893 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
9820 AGCTAACGAA
9830 TAAATTAAATT-T-AAATATTTTAATATTTAATT
1 TAAA-TAAATTATCAAATATTTT-ATATTTAATT
* *
9862 TAAATAATTTATCAAATATTTTATTTTTAATT
1 TAAATAAATTATCAAATATTTTATATTTAATT
9894 AATATGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 5 0.18
32 14 0.50
33 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
TAAATAAATTATCAAATATTTTATATTTAATT
Found at i:10169 original size:11 final size:11
Alignment explanation
Indices: 10153--10177 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10143 GATATGATAA
10153 AAAAATAATAT
1 AAAAATAATAT
10164 AAAAATAATAT
1 AAAAATAATAT
10175 AAA
1 AAA
10178 TACATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:10291 original size:23 final size:23
Alignment explanation
Indices: 10261--10307 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
10251 GTTTAAGCCA
*
10261 ATAACTTCATGCAATTATGGTGG
1 ATAACTTCATGCAATAATGGTGG
10284 ATAACTTCATGCAATAATGGTGG
1 ATAACTTCATGCAATAATGGTGG
10307 A
1 A
10308 AAAAGCTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (23 bp):
ATAACTTCATGCAATAATGGTGG
Found at i:11481 original size:16 final size:16
Alignment explanation
Indices: 11451--11505 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
11441 AAATTTAACA
11451 ACCTGAAACTC-AAATG
1 ACCT-AAACTCAAAATG
**
11467 ACCTAAACTTGAAATG
1 ACCTAAACTCAAAATG
*
11483 ATCC-GAACTCAAAATG
1 A-CCTAAACTCAAAATG
11499 ACCTAAA
1 ACCTAAA
11506 AATTTAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 7 0.23
16 22 0.71
17 2 0.06
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (16 bp):
ACCTAAACTCAAAATG
Found at i:13976 original size:26 final size:28
Alignment explanation
Indices: 13933--13985 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
13923 TTGGGAGATG
*
13933 GGGGAGAAAGAAAGAAAGGAAGGAAAAA
1 GGGGAGAAAGAAAGAAAGAAAGGAAAAA
*
13961 GGGGA-AAAGAGA-AAAGAAAGGAAAA
1 GGGGAGAAAGAAAGAAAGAAAGGAAAA
13986 GTATAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 6 0.26
28 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (28 bp):
GGGGAGAAAGAAAGAAAGAAAGGAAAAA
Found at i:15991 original size:3 final size:3
Alignment explanation
Indices: 15985--16075 Score: 71
Period size: 3 Copynumber: 29.7 Consensus size: 3
15975 TATCCAAAAA
* * *
15985 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT TAT TAT AAT ACT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
16030 AAA AAT AAAT AA- AAT AAT ATAT AA- ATAT AAT ATT AAT ATAT AAT AA
1 AAT AAT -AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT A-AT AAT AA
16076 ATATTTTAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
2 5 0.07
3 55 0.75
4 13 0.18
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:16055 original size:16 final size:18
Alignment explanation
Indices: 16034--16080 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
16024 TACTAAAAAA
16034 ATAAATAAA-A-TAATAT
1 ATAAATAAATATTAATAT
16050 ATAAATATAATATTAATAT
1 ATAAATA-AATATTAATAT
16069 AT-AATAAATATT
1 ATAAATAAATATT
16081 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 5 0.18
19 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAAATATTAATAT
Found at i:16061 original size:13 final size:13
Alignment explanation
Indices: 16033--16074 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
16023 ATACTAAAAA
*
16033 AATAAATAAA-AT
1 AATATATAAATAT
16045 AATATATAAATAT
1 AATATATAAATAT
16058 AATAT-TAATATAT
1 AATATATAA-ATAT
16071 AATA
1 AATA
16075 AATATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATATAAATAT
Found at i:16067 original size:22 final size:21
Alignment explanation
Indices: 15995--16079 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 21
15985 AATAATAATA
15995 ATAATAATAATAATA-ATAAAT
1 ATAAT-ATAATAATATATAAAT
* * * *
16016 -TATTATAATACTAAAAAAAT
1 ATAATATAATAATATATAAAT
*
16036 A-AATAAAATAATATATAAAT
1 ATAATATAATAATATATAAAT
16056 ATAATATTAAT-ATATAATAAAT
1 ATAATA-TAATAATAT-ATAAAT
16078 AT
1 AT
16080 TTTAAAATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
19 8 0.16
20 23 0.46
21 8 0.16
22 11 0.22
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATATAATAATATATAAAT
Found at i:16084 original size:19 final size:19
Alignment explanation
Indices: 16044--16080 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16034 ATAAATAAAA
16044 TAATATATAAATATAATAT
1 TAATATATAAATATAATAT
16063 TAATATAT-AATA-AATAT
1 TAATATATAAATATAATAT
16080 T
1 T
16081 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATATATAAATATAATAT
Found at i:17397 original size:184 final size:183
Alignment explanation
Indices: 16870--17412 Score: 676
Period size: 184 Copynumber: 2.9 Consensus size: 183
16860 TTCATGCATG
* * ** * * *
16870 TAGAAGCAAATTATGGTACGGTAAGCATGCTTC-GGCCAACGCAAAATCCTAAGAGAAAGGTAGG
1 TAGAAGCAAATTATGATACAGTAAGCATGCTTCAATCCGACGCAAAATACGAAGAGAAAGGTAGG
* * *** * *
16934 AATGCTGATCAAGAACATGCATCCAAACAATTTCGTTTGAAAGTTTGAAAGCCTATTATTAA-GA
66 AATGCTAATCAAGCACATGCATTTGAACAATTTCGTTTGAAAGTTTG-AAGCATTTTATTAAGGA
* *
16998 ATGCGTCGATTTCCACAATGATAAGAATTCTGTTACTTTCACAGTTCGTGCACA
130 ATGTGTCGATTTCCACAATGATAAGAATTCGGTTACTTTCACAGTTCGTGCACA
* *
17052 TGGAAGCAAATTATGATACAGTAAGCATGCTTCGAAGAAATCCCGACGCAAAACACGAAGAGAAA
1 TAGAAGCAAATTATGATACAGTAAGCATGCTTC-----AAT-CCGACGCAAAATACGAAGAGAAA
* *
17117 GGTAGGAATGCTAATCAAGCACATGCATTTGAACAATTTCGTTTAAAAGTTTGAACCATTATTAT
60 GGTAGGAATGCTAATCAAGCACATGCATTTGAACAATTTCGTTTGAAAGTTTGAAGCATT-TTAT
* *
17182 CAAGGAATGTCTCGATTTCCACAATGATAAGAATTCGGTTACTTTCACAGTTCGTGCACA
124 TAAGGAATGTGTCGATTTCCACAATGATAAGAATTCGGTTACTTTCACAGTTCGTGCACA
* ** *
17242 TAGAAGCAAATTATGATACAGTAAGCATGCTTCAATCCGATGCATTATACGAAAAGAAAGGTAGG
1 TAGAAGCAAATTATGATACAGTAAGCATGCTTCAATCCGACGCAAAATACGAAGAGAAAGGTAGG
* * * *
17307 AATACAAATCAAGCACAAGCATTTGAACAATTTCGTTTGAAAGTTTGAATGAATTTTATTAAGGA
66 AATGCTAATCAAGCACATGCATTTGAACAATTTCGTTTGAAAGTTTGAA-GCATTTTATTAAGGA
* ***
17372 ATGTGTCGATTTTCGTGATGATAAGAATTCGGGTTACTTTC
130 ATGTGTCGATTTCCACAATGATAAGAATTC-GGTTACTTTC
17413 TAGAAATTAC
Statistics
Matches: 310, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
182 30 0.10
184 103 0.33
185 16 0.05
188 4 0.01
189 72 0.23
190 85 0.27
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (183 bp):
TAGAAGCAAATTATGATACAGTAAGCATGCTTCAATCCGACGCAAAATACGAAGAGAAAGGTAGG
AATGCTAATCAAGCACATGCATTTGAACAATTTCGTTTGAAAGTTTGAAGCATTTTATTAAGGAA
TGTGTCGATTTCCACAATGATAAGAATTCGGTTACTTTCACAGTTCGTGCACA
Found at i:27876 original size:5 final size:5
Alignment explanation
Indices: 27868--27921 Score: 76
Period size: 5 Copynumber: 11.0 Consensus size: 5
27858 TAATTTTTTT
*
27868 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAAA ATTAA A-TAA AATAA ATT-A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATT-AA ATTAA ATTAA ATTAA ATTAA
27917 ATTAA
1 ATTAA
27922 TTTTTTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
4 8 0.18
5 32 0.71
6 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATTAA
Found at i:28214 original size:22 final size:23
Alignment explanation
Indices: 28189--28239 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
28179 TTATTAATTA
*
28189 TAAATAATAAATAT-AAATATTT
1 TAAATAAAAAATATAAAATATTT
*
28211 TAAATAAAAAATTTAAAATATTT
1 TAAATAAAAAATATAAAATATTT
28234 TCAAAT
1 T-AAAT
28240 GACGATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 9 0.36
24 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATAAAAAATATAAAATATTT
Found at i:33422 original size:27 final size:31
Alignment explanation
Indices: 33381--33456 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 31
33371 TTTAGTCAAA
* * *
33381 TTTTTAAATTCAATTAATTGATTTATTTAATC
1 TTTTAAAATTAAATT-ATCGATTTATTTAATC
33413 TTTTAAAATTTAAAATTGATCGATTTATTTAATC
1 TTTTAAAA-TT-AAATT-ATCGATTTATTTAATC
33447 TTTTAAAATT
1 TTTTAAAATT
33457 TATAACTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.18
33 4 0.11
34 27 0.71
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (31 bp):
TTTTAAAATTAAATTATCGATTTATTTAATC
Found at i:46339 original size:67 final size:67
Alignment explanation
Indices: 46231--46363 Score: 266
Period size: 67 Copynumber: 2.0 Consensus size: 67
46221 GTAACAAAAG
46231 TAACAAAGATGAAGAGAGTATAACCTGTGGCTTAGAAAGGAGAAGGACATCACGGTGAATACCGG
1 TAACAAAGATGAAGAGAGTATAACCTGTGGCTTAGAAAGGAGAAGGACATCACGGTGAATACCGG
46296 AA
66 AA
46298 TAACAAAGATGAAGAGAGTATAACCTGTGGCTTAGAAAGGAGAAGGACATCACGGTGAATACCGG
1 TAACAAAGATGAAGAGAGTATAACCTGTGGCTTAGAAAGGAGAAGGACATCACGGTGAATACCGG
46363 A
66 A
46364 CAACCACCAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.17
Consensus pattern (67 bp):
TAACAAAGATGAAGAGAGTATAACCTGTGGCTTAGAAAGGAGAAGGACATCACGGTGAATACCGG
AA
Found at i:50741 original size:14 final size:13
Alignment explanation
Indices: 50715--50748 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
50705 TAAATTTTAA
50715 TTTATTAATAATT
1 TTTATTAATAATT
50728 TTTATTATATAATT
1 TTTATTA-ATAATT
50742 TTT-TTAA
1 TTTATTAA
50749 ATATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 10 0.50
14 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATTAATAATT
Found at i:50752 original size:15 final size:14
Alignment explanation
Indices: 50715--50744 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
50705 TAAATTTTAA
50715 TTTATTA-ATAATT
1 TTTATTATATAATT
50728 TTTATTATATAATT
1 TTTATTATATAATT
50742 TTT
1 TTT
50745 TTAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTATATAATT
Found at i:55911 original size:36 final size:36
Alignment explanation
Indices: 55761--55898 Score: 213
Period size: 36 Copynumber: 3.8 Consensus size: 36
55751 CGAACCTTCT
55761 GGTGACTTTTGTTGGTCCCAAGAACTATTCGTTGTA
1 GGTGACTTTTGTTGGTCCCAAGAACTATTCGTTGTA
* * * *
55797 GGTGACTTTTGTGGGTTCCAGGAAGTATTCGTTGTA
1 GGTGACTTTTGTTGGTCCCAAGAACTATTCGTTGTA
* * *
55833 GGTGACTTCTGTTGGTCCCAAGGACTATTCATTGTA
1 GGTGACTTTTGTTGGTCCCAAGAACTATTCGTTGTA
55869 GGTGACTTTTGTTGGTCCCAAGAACTATTC
1 GGTGACTTTTGTTGGTCCCAAGAACTATTC
55899 TTTACAGGTG
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.38
Consensus pattern (36 bp):
GGTGACTTTTGTTGGTCCCAAGAACTATTCGTTGTA
Found at i:56398 original size:210 final size:210
Alignment explanation
Indices: 56036--56884 Score: 1369
Period size: 210 Copynumber: 4.0 Consensus size: 210
56026 CTTGGTTTTT
** *
56036 CCAACCAGATGTCGGTTGCACTGGCTTTACTTGACCTGCTTTATTATCCCATGCACTTTCCTCTC
1 CCAACCAGATGTCAATTGCACTGGCTTTACTTGACTTGCTTTATTATCCCATGCACTTTCCTCTC
* ** * *
56101 TCCCTTGGTCCAGCTGGGTATTGTTTCCAACGAAGCTAGATTCATTAACTGTTGCAATCTTCTTC
66 TCCCTTGGTCCGGCTGGGTATCATTTCCAATGAAGCTAGATTCATTAACTGCTGCAATCTTCTTC
* *
56166 CCCCAAGAACAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGGT
131 CCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGAT
56231 GGAATCTTTTGTCCC
196 GGAATCTTTTGTCCC
**
56246 CCAACCAGATGTTGATTGCACTGGCTTTACTTGACTTGCTTTATTATCCCATGCACTTTCCTCTC
1 CCAACCAGATGTCAATTGCACTGGCTTTACTTGACTTGCTTTATTATCCCATGCACTTTCCTCTC
* *
56311 TCCCTTGATCCGGCTGGGTATTATTTCCAATGAAGCTAGATTCATTAACTGCTGCAATCTTCTTC
66 TCCCTTGGTCCGGCTGGGTATCATTTCCAATGAAGCTAGATTCATTAACTGCTGCAATCTTCTTC
* *
56376 CCCCAAGAAGAAACATTATCCCAGCCACTAAATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGGT
131 CCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGAT
56441 GGAATCTTTTGTCCC
196 GGAATCTTTTGTCCC
* * *
56456 CCAACCAGATGTCAATTGCACTGGCTTTCCTTGAATTGCTTCATTATCCCATGCACTTTCCTCTC
1 CCAACCAGATGTCAATTGCACTGGCTTTACTTGACTTGCTTTATTATCCCATGCACTTTCCTCTC
56521 TCCCTTGGTCCGGCTGGGTATCATTTCCAATGAAGCTAGATTCATTAACTGCTGCAATCTTCTTC
66 TCCCTTGGTCCGGCTGGGTATCATTTCCAATGAAGCTAGATTCATTAACTGCTGCAATCTTCTTC
*
56586 CCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCATCCAAGGTTTTTGTAGGGAT
131 CCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGAT
56651 GGAATCTTTTGTCCC
196 GGAATCTTTTGTCCC
* *
56666 CCAACCAGATGTCAATTGCACAGGCTTTACTTGACTTGCTTTATTACCCCATGCACTTTCCTCTC
1 CCAACCAGATGTCAATTGCACTGGCTTTACTTGACTTGCTTTATTATCCCATGCACTTTCCTCTC
* *** * * **
56731 TCCCTTGGTCCCGCCATGTATCATTTTCAATGAAGCCAGATTCACGAACTG-TGGCAATCTTCTT
66 TCCCTTGGTCCGGCTGGGTATCATTTCCAATGAAGCTAGATTCATTAACTGCT-GCAATCTTCTT
56795 CCCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGA
130 CCCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGA
**
56860 CAGAATCTCTTT-TCCC
195 TGGAATCT-TTTGTCCC
*
56876 CCGACCAGA
1 CCAACCAGA
56885 CCATGGCTGT
Statistics
Matches: 600, Mismatches: 37, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
209 1 0.00
210 596 0.99
211 3 0.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (210 bp):
CCAACCAGATGTCAATTGCACTGGCTTTACTTGACTTGCTTTATTATCCCATGCACTTTCCTCTC
TCCCTTGGTCCGGCTGGGTATCATTTCCAATGAAGCTAGATTCATTAACTGCTGCAATCTTCTTC
CCCCAAGAAGAAACATTATCCCAGCCACTAGATTTGGAAGATTCGTCCAAGGTTTTTGTAGGGAT
GGAATCTTTTGTCCC
Found at i:61582 original size:145 final size:145
Alignment explanation
Indices: 61319--61608 Score: 544
Period size: 145 Copynumber: 2.0 Consensus size: 145
61309 AATATTTTTT
61319 CAGGACACTTAACTAATAGCAGATTGTTGATAGTTGGCACTTAGTCCTATTTTGCCACGAGATCC
1 CAGGACACTTAACTAATAGCAGATTGTTGATAGTTGGCACTTAGTCCTATTTTGCCACGAGATCC
*
61384 AGTACCCCAGAAGAATTTGCATCTATTTCACATACCACTGTGATTACTGATAAGTCATATAATGC
66 AGTACCCCAGAAGAATTTGCATCTATTTCACATACCACTGTGATTACTAATAAGTCATATAATGC
61449 CATGCCATCAGTTAA
131 CATGCCATCAGTTAA
*
61464 CAGGACACTTAACTAATAGCAGATTGTTGATAGTTGGCACTTAGTCCTATTTTGCCATGAGATCC
1 CAGGACACTTAACTAATAGCAGATTGTTGATAGTTGGCACTTAGTCCTATTTTGCCACGAGATCC
* *
61529 AGTACCTCAGAAGAATTTGCATCTATTTCACATACCCCTGTGATTACTAATAAGTCATATAATGC
66 AGTACCCCAGAAGAATTTGCATCTATTTCACATACCACTGTGATTACTAATAAGTCATATAATGC
61594 CATGCCATCAGTTAA
131 CATGCCATCAGTTAA
61609 AAGAGCAAAA
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 141 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (145 bp):
CAGGACACTTAACTAATAGCAGATTGTTGATAGTTGGCACTTAGTCCTATTTTGCCACGAGATCC
AGTACCCCAGAAGAATTTGCATCTATTTCACATACCACTGTGATTACTAATAAGTCATATAATGC
CATGCCATCAGTTAA
Found at i:62130 original size:2 final size:2
Alignment explanation
Indices: 62123--62166 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
62113 CGTAAGCCCA
62123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62165 AT
1 AT
62167 CCCTTTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65886 original size:2 final size:2
Alignment explanation
Indices: 65881--65910 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
65871 CACACACACA
65881 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
65911 CACTTGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:70230 original size:25 final size:25
Alignment explanation
Indices: 70183--70230 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
70173 AATATTTAAG
** * *
70183 TAATATTTAATTTAATTATAATATA
1 TAATATTTAAAATAATAAAAATATA
70208 TAATATTTAAAATAATAAAAATA
1 TAATATTTAAAATAATAAAAATA
70231 CTTTTATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATATTTAAAATAATAAAAATATA
Found at i:70392 original size:11 final size:12
Alignment explanation
Indices: 70363--70416 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
70353 ATTTTATTAA
70363 ATATT-ATATATT
1 ATATTAATAT-TT
70375 ATATTAATATTT
1 ATATTAATATTT
70387 AT-TTAATA-TT
1 ATATTAATATTT
*
70397 ATATCAATATTT
1 ATATTAATATTT
70409 AT-TTAATA
1 ATATTAATA
70417 ATATTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 4 0.11
11 16 0.43
12 13 0.35
13 4 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTAATATTT
Found at i:70395 original size:22 final size:22
Alignment explanation
Indices: 70370--70426 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
70360 TAAATATTAT
70370 ATATTATATTAATATTTATTTA
1 ATATTATATTAATATTTATTTA
*
70392 ATATTATATCAATATTTATTTA
1 ATATTATATTAATATTTATTTA
70414 ATA--ATATTAATAT
1 ATATTATATTAATAT
70427 AAAAATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.27
22 24 0.73
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTATATTAATATTTATTTA
Found at i:70428 original size:11 final size:11
Alignment explanation
Indices: 70362--70454 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
70352 AATTTTATTA
70362 AATATTATATAT
1 AATATTA-ATAT
*
70374 TATATTAATAT
1 AATATTAATAT
*
70385 -TTATTTAATAT
1 AATA-TTAATAT
* *
70396 TATATCAATAT
1 AATATTAATAT
* *
70407 -TTATTTA-AT
1 AATATTAATAT
70416 AATATTAATAT
1 AATATTAATAT
* *
70427 AAAAATATATAT
1 AATATTA-ATAT
70439 AATA-TAATTAT
1 AATATTAA-TAT
70450 AATAT
1 AATAT
70455 ATTTATTTGA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
9 2 0.03
10 12 0.19
11 33 0.53
12 15 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (11 bp):
AATATTAATAT
Found at i:70546 original size:63 final size:65
Alignment explanation
Indices: 70405--70546 Score: 147
Period size: 63 Copynumber: 2.2 Consensus size: 65
70395 TTATATCAAT
* *
70405 ATTTATTTAATAATA-TTAATATAAAAATATATATAATATAATTATAATATATTTATTTGAACTA
1 ATTTATTTAATAATATTTAATATAAAAAAATATATAATATAA-TATAATATATTTATATGAACTA
70469 A
65 A
* *
70470 ATTT-TTTAA-AATATTTGAT-TAAAAAAATATATAATATAA-A-AAT-TATTTTATAT-AATTA
1 ATTTATTTAATAATATTTAATATAAAAAAATATATAATATAATATAATATA-TTTATATGAACTA
70528 A
65 A
*
70529 TTTTTTATTTAATAATAT
1 --ATTTATTTAATAATAT
70547 AATTATTTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
59 7 0.11
60 9 0.14
61 4 0.06
62 5 0.08
63 28 0.42
64 9 0.14
65 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (65 bp):
ATTTATTTAATAATATTTAATATAAAAAAATATATAATATAATATAATATATTTATATGAACTAA
Found at i:70549 original size:20 final size:19
Alignment explanation
Indices: 70516--70563 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
70506 TAAAAATTAT
*
70516 TTTATATAATTAATTTTTTA
1 TTTA-ATAATTAATTATTTA
70536 TTTAATAATATAATTATTTA
1 TTTAATAAT-TAATTATTTA
70556 TTTAATAA
1 TTTAATAA
70564 AATTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATAATTAATTATTTA
Found at i:70571 original size:16 final size:16
Alignment explanation
Indices: 70515--70571 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
70505 ATAAAAATTA
* * *
70515 TTTTATATAATTAATT
1 TTTTATTTAATAAAAT
70531 TTTTATTTAATAATATAAT
1 TTTTATTTAAT-A-A-AAT
70550 TATTTATTTAATAAAAT
1 T-TTTATTTAATAAAAT
70567 TTTTA
1 TTTTA
70572 AAGGGATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 14 0.41
17 4 0.12
18 2 0.06
19 4 0.12
20 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTTAATAAAAT
Found at i:70753 original size:25 final size:23
Alignment explanation
Indices: 70724--70799 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 23
70714 CACATTTTTA
70724 AAATTTAAAATTTTAAAAATTAAAT
1 AAATTTAAAATTTTAAAAA--AAAT
*
70749 AAATTAATTAAATTTTAAAAAAAAT
1 AAATT--TAAAATTTTAAAAAAAAT
*
70774 AAATTATTAAAATTTTATATAAAAAT
1 AAA-T-TTAAAATTTTA-AAAAAAAT
70800 TAAAATAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
25 21 0.49
26 8 0.19
27 14 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTTAAAATTTTAAAAAAAAT
Found at i:70797 original size:28 final size:28
Alignment explanation
Indices: 70728--70808 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
70718 TTTTTAAAAT
*
70728 TTAAAATTTTA-AAAATTAAATAAATTAA
1 TTAAAATTTTATAAAA-AAAATAAATTAA
70756 TT-AAA-TTT-TAAAAAAAATAAATT-A
1 TTAAAATTTTATAAAAAAAATAAATTAA
* * *
70780 TTAAAATTTTATATAAAAATTAAAATAA
1 TTAAAATTTTATAAAAAAAATAAATTAA
70808 T
1 T
70809 CGAATCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
24 3 0.07
25 12 0.27
26 10 0.23
27 15 0.34
28 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAAAATTTTATAAAAAAAATAAATTAA
Found at i:70941 original size:21 final size:22
Alignment explanation
Indices: 70917--70957 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
70907 AGTTATATAA
70917 AATTAA-TATCAATTTATTTTT
1 AATTAAGTATCAATTTATTTTT
*
70938 AATTAAGTATCGATTTATTT
1 AATTAAGTATCAATTTATTT
70958 GATCAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (22 bp):
AATTAAGTATCAATTTATTTTT
Found at i:77820 original size:17 final size:17
Alignment explanation
Indices: 77798--77866 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 17
77788 ACATTCATAT
77798 AATCAAACCAAAAGTTA
1 AATCAAACCAAAAGTTA
* *
77815 AATC-AATC-ATA--T-
1 AATCAAACCAAAAGTTA
*
77827 AATCAAATCAAAAGTTA
1 AATCAAACCAAAAGTTA
* *
77844 AATCAATCGAAAAGTTA
1 AATCAAACCAAAAGTTA
77861 AATCAA
1 AATCAA
77867 TAAAACTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
12 4 0.10
13 5 0.12
14 2 0.05
15 2 0.05
16 4 0.10
17 24 0.59
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.23
Consensus pattern (17 bp):
AATCAAACCAAAAGTTA
Found at i:77863 original size:29 final size:29
Alignment explanation
Indices: 77792--77851 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
77782 AAACCTACAT
*
77792 TCATATAATCAAACCAAAAGTTAAATCAA
1 TCATATAATCAAATCAAAAGTTAAATCAA
77821 TCATATAATCAAATCAAAAGTTAAATCAA
1 TCATATAATCAAATCAAAAGTTAAATCAA
77850 TC
1 TC
77852 GAAAAGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (29 bp):
TCATATAATCAAATCAAAAGTTAAATCAA
Found at i:77867 original size:17 final size:16
Alignment explanation
Indices: 77806--77871 Score: 70
Period size: 17 Copynumber: 4.3 Consensus size: 16
77796 ATAATCAAAC
77806 CAAAAGTTAAATCAAT
1 CAAAAGTTAAATCAAT
*
77822 C-ATA--T-AATCAAAT
1 CAAAAGTTAAATC-AAT
77835 CAAAAGTTAAATCAAT
1 CAAAAGTTAAATCAAT
77851 CGAAAAGTTAAATCAAT
1 C-AAAAGTTAAATCAAT
77868 -AAAA
1 CAAAA
77872 CTTTCAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
12 4 0.10
13 5 0.12
14 2 0.05
15 6 0.14
16 6 0.14
17 19 0.45
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
CAAAAGTTAAATCAAT
Found at i:77948 original size:17 final size:17
Alignment explanation
Indices: 77928--77964 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
77918 AATACAGTAA
*
77928 ATATTTAATAAAATTAT
1 ATATTTAATAAAATAAT
*
77945 ATATTTAATTAAATAAT
1 ATATTTAATAAAATAAT
77962 ATA
1 ATA
77965 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTAATAAAATAAT
Found at i:85317 original size:2 final size:2
Alignment explanation
Indices: 85310--85337 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
85300 CATGAAAGAA
85310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85338 GCATGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90250 original size:17 final size:18
Alignment explanation
Indices: 90191--90251 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 18
90181 TATTCATATG
90191 ATAT-AATTATATTATTT
1 ATATAAATTATATTATTT
* * *
90208 TTATATCATAATATTATTT
1 ATATA-AATTATATTATTT
*
90227 A-AAAAATTATA-TATTT
1 ATATAAATTATATTATTT
90243 ATATAAATT
1 ATATAAATT
90252 TTAATGTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
16 6 0.18
17 14 0.42
18 2 0.06
19 11 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATAAATTATATTATTT
Found at i:90288 original size:14 final size:14
Alignment explanation
Indices: 90242--90289 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
90232 ATTATATATT
90242 TATATAAATTTTAA
1 TATATAAATTTTAA
* * *
90256 TGTATTAAAATTTAT
1 TATA-TAAATTTTAA
*
90271 TATATAATTTTTAA
1 TATATAAATTTTAA
90285 TATAT
1 TATAT
90290 TTATATTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:90297 original size:29 final size:28
Alignment explanation
Indices: 90233--90300 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
90223 ATTTAAAAAA
* *
90233 TTATATATTTATATAAATTTTAATGTAT
1 TTATATTTTTATATAAATTTTAATATAT
* * *
90261 TAAAATTTATTATATAATTTTTAATATAT
1 TTATATTT-TTATATAAATTTTAATATAT
90290 TTATATTTTTA
1 TTATATTTTTA
90301 CATTATAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
TTATATTTTTATATAAATTTTAATATAT
Found at i:90625 original size:28 final size:29
Alignment explanation
Indices: 90594--90654 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
90584 AATTATATTT
90594 ATATAATAATTT-TAAAATATATAATATA
1 ATATAATAATTTATAAAATATATAATATA
* ** *
90622 ATAT-ATCATTTATATTATATATTATATA
1 ATATAATAATTTATAAAATATATAATATA
90650 ATATA
1 ATATA
90655 TTATGTGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATAATAATTTATAAAATATATAATATA
Found at i:90635 original size:14 final size:14
Alignment explanation
Indices: 90587--90655 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
90577 TAAATAAAAT
90587 TATAT-TTATATAA
1 TATATATTATATAA
90600 TA-AT-TT-TA-AA
1 TATATATTATATAA
*
90610 -ATATATAATATAA
1 TATATATTATATAA
*
90623 TATATCATT-TATAT
1 TATAT-ATTATATAA
90637 TATATATTATATAA
1 TATATATTATATAA
90651 TATAT
1 TATAT
90656 TATGTGCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
9 1 0.02
10 4 0.09
11 3 0.07
12 6 0.13
13 7 0.16
14 22 0.49
15 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATATTATATAA
Found at i:90655 original size:12 final size:12
Alignment explanation
Indices: 90568--90658 Score: 60
Period size: 12 Copynumber: 7.2 Consensus size: 12
90558 TTATATTTTA
90568 TATATAATATA-
1 TATATAATATAT
* *
90579 AATAAAATTATATT
1 TATATAA-TATA-T
90593 TATATAATA-AT
1 TATATAATATAT
* *
90604 TTTAAAATATAT
1 TATATAATATAT
*
90616 AATATAATATATCATT
1 TATAT-A-ATAT-A-T
*
90632 TATATTATATAT
1 TATATAATATAT
90644 TATATAATATAT
1 TATATAATATAT
90656 TAT
1 TAT
90659 GTGCAATTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
11 13 0.22
12 24 0.40
13 4 0.07
14 13 0.22
15 1 0.02
16 5 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (12 bp):
TATATAATATAT
Found at i:91592 original size:16 final size:16
Alignment explanation
Indices: 91563--91618 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
91553 AAATAAATAA
* *
91563 TAATTAAAAATTAAAT
1 TAATTTAAATTTAAAT
91579 TAATTTAAATTTAAA-
1 TAATTTAAATTTAAAT
* * *
91594 AAAATTATATTTAAAT
1 TAATTTAAATTTAAAT
91610 TCAATTTAA
1 T-AATTTAA
91619 TTTCAACTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
15 12 0.40
16 13 0.43
17 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAAATTTAAAT
Found at i:91607 original size:26 final size:25
Alignment explanation
Indices: 91568--91618 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
91558 AATAATAATT
*
91568 AAAAATTAAATTAATTTAAATTTAA
1 AAAAATTAAATTAAATTAAATTTAA
* *
91593 AAAAATTATATTTAAATTCAATTTAA
1 AAAAATTA-AATTAAATTAAATTTAA
91619 TTTCAACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAAATTAAATTAAATTAAATTTAA
Found at i:93520 original size:20 final size:19
Alignment explanation
Indices: 93460--93529 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 19
93450 ATATATACTT
93460 TTTAAATATTTA-TT-ATA
1 TTTAAATATTTATTTAATA
*
93477 TTT-AATACTTATTTAATA
1 TTTAAATATTTATTTAATA
93495 -TTAAATAATTTATTTAATA
1 TTTAAAT-ATTTATTTAATA
93514 TTTAAAT-TTT-TTTAAT
1 TTTAAATATTTATTTAAT
93530 TAAACAATCT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.15
17 13 0.28
18 9 0.20
19 11 0.24
20 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAATATTTATTTAATA
Found at i:96671 original size:115 final size:115
Alignment explanation
Indices: 96540--96779 Score: 324
Period size: 115 Copynumber: 2.1 Consensus size: 115
96530 TTTCAAAAAC
* **
96540 ATCTTATAAAAATTTTTTGAGTTGAATCTAGATAAATTTCTTTAAATTTAG-ATTAGTTTAA-AT
1 ATCTTATAAAAATTTTTCGAGTTGAATCTAGATAAATTTCTACAAA-TTAGTATTAGTTTAATAT
* * *
96603 TCATATTACTATTTGATAAATAAAATAAATTTAAATTTAATTATAAAAATAT
65 TCAGATTACTATTTAATAAATAAAATAAATTTAAATTTAACTAT-AAAATAT
* * * * *
96655 ATCTTATAAAATTTTTTCGAGTTGAATTTGGATAAATTTCTACAAATTCGTATTAGTTTAATTTT
1 ATCTTATAAAAATTTTTCGAGTTGAATCTAGATAAATTTCTACAAATTAGTATTAGTTTAATATT
* *
96720 GAGATTATTATTTAATAAATAAAATAAATTTAAATTTAACTATAAAATAT
66 CAGATTACTATTTAATAAATAAAATAAATTTAAATTTAACTATAAAATAT
96770 AT-TTATAAAA
1 ATCTTATAAAA
96780 GACAATTGAT
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
114 11 0.10
115 59 0.54
116 40 0.36
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (115 bp):
ATCTTATAAAAATTTTTCGAGTTGAATCTAGATAAATTTCTACAAATTAGTATTAGTTTAATATT
CAGATTACTATTTAATAAATAAAATAAATTTAAATTTAACTATAAAATAT
Found at i:97315 original size:24 final size:25
Alignment explanation
Indices: 97288--97346 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
97278 TATATTTATA
97288 TTTTATAT-TATGATCATATT-GTTT
1 TTTTATATATATGAT-ATATTAGTTT
* *
97312 TTTTATATCATATTATATTTTAGTTT
1 TTTTATAT-ATATGATATATTAGTTT
97338 TTTTATATA
1 TTTTATATA
97347 ATTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 8 0.27
25 5 0.17
26 17 0.57
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.64
Consensus pattern (25 bp):
TTTTATATATATGATATATTAGTTT
Found at i:97332 original size:18 final size:19
Alignment explanation
Indices: 97295--97332 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
97285 ATATTTTATA
* *
97295 TTATGATCATATTGTTTTT
1 TTATGATCATATTATATTT
97314 TTAT-ATCATATTATATTT
1 TTATGATCATATTATATTT
97332 T
1 T
97333 AGTTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATGATCATATTATATTT
Found at i:97674 original size:40 final size:40
Alignment explanation
Indices: 97619--97695 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
97609 AGTTATGCGT
* * * *
97619 AAGTCAGCAGAAAAATAGAATAT-AAAGGAAATAGAGAACA
1 AAGTCAACAAAAAAATAAAACATAAAAGG-AATAGAGAACA
97659 AAGTCAACAAAAAAATAAAACATAAAAGGAATAGAGA
1 AAGTCAACAAAAAAATAAAACATAAAAGGAATAGAGA
97696 GGAATAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 27 0.84
41 5 0.16
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.12
Consensus pattern (40 bp):
AAGTCAACAAAAAAATAAAACATAAAAGGAATAGAGAACA
Found at i:98680 original size:10 final size:9
Alignment explanation
Indices: 98645--98677 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
98635 TATAATTTTT
98645 TTAAAAATA
1 TTAAAAATA
*
98654 TTAAATATA
1 TTAAAAATA
98663 -TAAAAATA
1 TTAAAAATA
98671 TTAAAAA
1 TTAAAAA
98678 ATAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAATA
Found at i:99054 original size:21 final size:20
Alignment explanation
Indices: 99025--99063 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
99015 TATTTTTATT
*
99025 TAAATTTAATTATAAATATA
1 TAAATTTAATTAAAAATATA
99045 TAAATATTAATTAAAAATA
1 TAAAT-TTAATTAAAAATA
99064 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATTTAATTAAAAATATA
Found at i:99082 original size:34 final size:34
Alignment explanation
Indices: 99044--99108 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
99034 TTATAAATAT
* *
99044 ATAAATATTAATTAAAAATAATATTTTAATTCAA
1 ATAAATAATAATTAAAAATAATAATTTAATTCAA
* * *
99078 ATAAATAATAATTGAAATTTATAATTTAATT
1 ATAAATAATAATTAAAAATAATAATTTAATT
99109 GTTTTTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (34 bp):
ATAAATAATAATTAAAAATAATAATTTAATTCAA
Found at i:99316 original size:38 final size:37
Alignment explanation
Indices: 99253--99357 Score: 97
Period size: 38 Copynumber: 2.8 Consensus size: 37
99243 TAAGTAAATG
*
99253 TTTTTTATATATAATATAAAAATATTTAATATTTAAA
1 TTTTTTATATATAATAAAAAAATATTTAATATTTAAA
* * *
99290 TTTTTTATATAT-TTAAAAAATTATATTTTATATTTATA
1 TTTTTTATATATAATAAAAAA--ATATTTAATATTTAAA
** *
99328 -TTTAAATATATATTAAATATAAATATTTAA
1 TTTTTTATATATAATAAA-A-AAATATTTAA
99358 ATAAAATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
36 6 0.11
37 21 0.38
38 26 0.46
39 1 0.02
40 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
TTTTTTATATATAATAAAAAAATATTTAATATTTAAA
Found at i:99339 original size:25 final size:26
Alignment explanation
Indices: 99295--99360 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
99285 TTAAATTTTT
* **
99295 TATATATTTAAAAAATTATATTTTATA
1 TATATATTT-AAATATTATATTAAATA
*
99322 TTTATATTTAAATA-TATATTAAATA
1 TATATATTTAAATATTATATTAAATA
*
99347 TAAATATTTAAATA
1 TATATATTTAAATA
99361 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 21 0.64
26 4 0.12
27 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATATTTAAATATTATATTAAATA
Found at i:99751 original size:29 final size:31
Alignment explanation
Indices: 99691--99768 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 31
99681 ATATATTTTA
99691 TAATTAAATTTAAGTAAATTTTATTAATAAA-
1 TAATT-AATTTAAGTAAATTTTATTAATAAAT
*
99722 TAA-TAATTTAAATTAAA-TTTATTTAA-AAAT
1 TAATTAATTT-AAGTAAATTTTA-TTAATAAAT
99752 TAATTAATTATAA-TAAA
1 TAATTAATT-TAAGTAAA
99769 AAAATTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
29 12 0.29
30 18 0.44
31 10 0.24
32 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
TAATTAATTTAAGTAAATTTTATTAATAAAT
Found at i:99927 original size:28 final size:27
Alignment explanation
Indices: 99872--99928 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
99862 TAATATTTAT
* *
99872 ATATTTTTATAATTAAATTTAAATAAA
1 ATATTTTTATAATAAAATATAAATAAA
* *
99899 ATATTTTTATTATAAAATAATAATTAAA
1 ATATTTTTATAATAAAAT-ATAAATAAA
99927 AT
1 AT
99929 TTATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTTTTATAATAAAATATAAATAAA
Done.