Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005541.1 Hibiscus syriacus cultivar Beakdansim tig00012827_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 86570
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2184 original size:19 final size:19
Alignment explanation
Indices: 2155--2203 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2145 TGGCCTGTAA
*
2155 AATACATTAATATCATTAAT
1 AATA-ATTAATATCAATAAT
*
2175 AATAATTAATATCAATGAT
1 AATAATTAATATCAATAAT
2194 AATAA-TAATA
1 AATAATTAATA
2204 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
AATAATTAATATCAATAAT
Found at i:2205 original size:25 final size:22
Alignment explanation
Indices: 2171--2221 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 22
2161 TTAATATCAT
*
2171 TAATAATAATTAATATCAATGATAA
1 TAATAATAA-TAA-ATAAAT-ATAA
2196 TAATAATAATAAATAAATATAA
1 TAATAATAATAAATAAATATAA
2218 TAAT
1 TAAT
2222 TATTACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 5 0.20
24 3 0.12
25 9 0.36
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATAATAATAAATAAATATAA
Found at i:2559 original size:43 final size:43
Alignment explanation
Indices: 2505--2646 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
2495 ATAACACGGT
*
2505 TCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAAC
1 TCCTACATGATGAGGACGGCTGGTTATCAAAGGTTGACACAAC
* * * * ***
2548 TCCTACATGATGAGGA-GTTCAGG---TC--GGGTGATAACACGGT
1 TCCTACATGATGAGGACG-GCTGGTTATCAAAGGT--TGACACAAC
*
2588 TCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAAC
1 TCCTACATGATGAGGACGGCTGGTTATCAAAGGTTGACACAAC
2631 TCCTACATGATGAGGA
1 TCCTACATGATGAGGA
2647 GTTCAGGTCA
Statistics
Matches: 73, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
38 3 0.04
40 25 0.34
41 1 0.01
42 1 0.01
43 40 0.55
45 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (43 bp):
TCCTACATGATGAGGACGGCTGGTTATCAAAGGTTGACACAAC
Found at i:2591 original size:83 final size:83
Alignment explanation
Indices: 2492--2668 Score: 336
Period size: 83 Copynumber: 2.1 Consensus size: 83
2482 CCATCTAAAA
2492 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAACTCCTACATG
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAACTCCTACATG
*
2557 ATGAGGAGTTCAGGTCGG
66 ATGAGGAGTTCAGGTCAG
2575 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAACTCCTACATG
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAACTCCTACATG
2640 ATGAGGAGTTCAGGTCAG
66 ATGAGGAGTTCAGGTCAG
*
2658 GTGATGACACG
1 GTGATAACACG
2669 ACTCATACAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (83 bp):
GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCAAAGGTTGACACAACTCCTACATG
ATGAGGAGTTCAGGTCAG
Found at i:2678 original size:40 final size:40
Alignment explanation
Indices: 2539--2690 Score: 130
Period size: 40 Copynumber: 3.7 Consensus size: 40
2529 TATCAAAGGT
*
2539 TGACACAACTCCTACATGATGAGGAGTTCAGGTCGGGTGA
1 TGACACAACTCCTACATGATGAGGAGTTCAGGTCAGGTGA
* *** * * *
2579 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCAAAGGT--
1 TGACACAACTCCTACATGATGAGGA-GTTCAGG---TC--AGGTGA
2622 TGACACAACTCCTACATGATGAGGAGTTCAGGTCAGGTGA
1 TGACACAACTCCTACATGATGAGGAGTTCAGGTCAGGTGA
* * *
2662 TGACACGACTCATACATGATGAAGAGTTC
1 TGACACAACTCCTACATGATGAGGAGTTC
2691 TGGCCATCTA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
38 4 0.05
40 51 0.60
41 1 0.01
42 1 0.01
43 25 0.29
45 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (40 bp):
TGACACAACTCCTACATGATGAGGAGTTCAGGTCAGGTGA
Found at i:3837 original size:11 final size:11
Alignment explanation
Indices: 3801--3838 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
3791 CCCTCCTTTA
3801 TTTT-TTTTCT
1 TTTTCTTTTCT
3811 TTTTCTTTT-T
1 TTTTCTTTTCT
3821 TTTTCTTTTCT
1 TTTTCTTTTCT
*
3832 TCTTCTT
1 TTTTCTT
3839 CAAGTGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:10879 original size:30 final size:30
Alignment explanation
Indices: 10845--10917 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
10835 TCTAAATTTG
* *
10845 GATGCATATTATTGGTGATGTGTTATAAAT
1 GATGCATTTTATTGGTAATGTGTTATAAAT
10875 GATGCATTTTATTGGTAATGTGTTATAAAT
1 GATGCATTTTATTGGTAATGTGTTATAAAT
*
10905 AATGCATTTTATT
1 GATGCATTTTATT
10918 ATGCATAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (30 bp):
GATGCATTTTATTGGTAATGTGTTATAAAT
Found at i:16946 original size:28 final size:25
Alignment explanation
Indices: 16915--16968 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 25
16905 ATAATATCAT
*
16915 TAATAATAATTAATACCAATGATAATAA
1 TAATAATAATAAATA--AAT-ATAATAA
16943 TAATAATAATAAATAAATATAATAA
1 TAATAATAATAAATAAATATAATAA
16968 T
1 T
16969 TATTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 3 0.12
28 14 0.56
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
TAATAATAATAAATAAATATAATAA
Found at i:17962 original size:23 final size:23
Alignment explanation
Indices: 17927--17982 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
17917 TTTCTAGAAT
*
17927 GACCATATAGGTTTGTCCCAAAG
1 GACCACATAGGTTTGTCCCAAAG
* *
17950 GACCACATTGGTTTGTCCCGAAG
1 GACCACATAGGTTTGTCCCAAAG
*
17973 GACCATATAG
1 GACCACATAG
17983 AACCCACGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
GACCACATAGGTTTGTCCCAAAG
Found at i:21125 original size:20 final size:19
Alignment explanation
Indices: 21084--21127 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
21074 TTTTTATTTT
21084 AAAAAATTTTAAAATATCA
1 AAAAAATTTTAAAATATCA
*
21103 AAAAGAATTTTGAAAA-ATGA
1 AAAA-AATTTT-AAAATATCA
21123 AAAAA
1 AAAAA
21128 TATTGCCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (19 bp):
AAAAAATTTTAAAATATCA
Found at i:21999 original size:15 final size:15
Alignment explanation
Indices: 21979--22040 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
21969 ACTTGATCCA
*
21979 TTTTCTTTCTTATTT
1 TTTTCTTTCTTGTTT
21994 TTTTC-TTCTTTGTTT
1 TTTTCTTTC-TTGTTT
*
22009 TTTTCTCT-TTGTTT
1 TTTTCTTTCTTGTTT
*
22023 TTTTCTCT-TTGTTT
1 TTTTCTTTCTTGTTT
22037 TTTT
1 TTTT
22041 GTCTTTTTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
14 27 0.63
15 15 0.35
16 1 0.02
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTCTTTCTTGTTT
Found at i:22010 original size:28 final size:28
Alignment explanation
Indices: 21979--22071 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
21969 ACTTGATCCA
*
21979 TTTTCTTTCTTATTTTTTTCTTCTTTGTTT
1 TTTTCTCT-TTATTTTTTTC-TCTTTGTTT
*
22009 TTTTCTCTTTGTTTTTTTCTCTTTGTTT
1 TTTTCTCTTTATTTTTTTCTCTTTGTTT
* *
22037 TTTTGTCTTT-TTGCTCTTTT-TCTTTGATT
1 TTTTCTCTTTATT--T-TTTTCTCTTTGTTT
22066 TTTTCT
1 TTTTCT
22072 TTGCTTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
27 2 0.04
28 18 0.33
29 24 0.44
30 11 0.20
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.77
Consensus pattern (28 bp):
TTTTCTCTTTATTTTTTTCTCTTTGTTT
Found at i:22045 original size:14 final size:14
Alignment explanation
Indices: 21991--22046 Score: 94
Period size: 14 Copynumber: 3.9 Consensus size: 14
21981 TTCTTTCTTA
21991 TTTTTTTCTTCTTTG
1 TTTTTTTC-TCTTTG
22006 TTTTTTTCTCTTTG
1 TTTTTTTCTCTTTG
22020 TTTTTTTCTCTTTG
1 TTTTTTTCTCTTTG
*
22034 TTTTTTTGTCTTT
1 TTTTTTTCTCTTT
22047 TTGCTCTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
14 32 0.80
15 8 0.20
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTCTTTG
Found at i:22054 original size:9 final size:8
Alignment explanation
Indices: 21991--22057 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
21981 TTCTTTCTTA
*
21991 TTTTTTTC
1 TTTTTGTC
21999 TTCTTTGT-
1 TT-TTTGTC
22007 TTTTT-TC
1 TTTTTGTC
*
22014 TCTTTGT-
1 TTTTTGTC
22021 TTTTT-TC
1 TTTTTGTC
* *
22028 TCTTTGTT
1 TTTTTGTC
22036 TTTTTGTC
1 TTTTTGTC
22044 TTTTTGCTC
1 TTTTTG-TC
22053 TTTTT
1 TTTTT
22058 CTTTGATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
6 2 0.04
7 15 0.33
8 18 0.39
9 11 0.24
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.79
Consensus pattern (8 bp):
TTTTTGTC
Found at i:22089 original size:17 final size:17
Alignment explanation
Indices: 22058--22092 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22048 TGCTCTTTTT
**
22058 CTTTGATTTTTTCTTTG
1 CTTTGATTTGATCTTTG
22075 CTTTGATTTGATCTTTG
1 CTTTGATTTGATCTTTG
22092 C
1 C
22093 ACTTTGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (17 bp):
CTTTGATTTGATCTTTG
Found at i:25480 original size:6 final size:6
Alignment explanation
Indices: 25465--25519 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
25455 TACTAACATT
*
25465 AAAT-A AAATAA AAATAA AAAT-G AAATGAA ATATTATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAAT-AA A-A--ATAA AAATAA AAATAA
25515 AAATA
1 AAATA
25520 CCATTATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
5 8 0.19
6 26 0.62
7 1 0.02
8 2 0.05
9 3 0.07
10 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:27370 original size:3 final size:3
Alignment explanation
Indices: 27362--27396 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27352 AAAATATGTA
27362 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27397 GATAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28001 original size:34 final size:34
Alignment explanation
Indices: 27932--28005 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
27922 AATCCGTTCA
* * *
27932 TTTATGTTCATTCATTTATGTCTGTGTATATTTG
1 TTTATGTTCATTAATTTATGTCTGTGAATACTTG
* *
27966 TTTATGTTCGTTAATTTATGTCCT-TGAATGCTTG
1 TTTATGTTCATTAATTTATGT-CTGTGAATACTTG
28000 TTTATG
1 TTTATG
28006 CCCGTTCGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (34 bp):
TTTATGTTCATTAATTTATGTCTGTGAATACTTG
Found at i:28606 original size:13 final size:13
Alignment explanation
Indices: 28584--28620 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28574 GGTTCGTTTA
*
28584 TGTTCATTTATTG
1 TGTTCGTTTATTG
*
28597 TGTTTGTTTATTG
1 TGTTCGTTTATTG
28610 TGTTCGTTTAT
1 TGTTCGTTTAT
28621 GTTCGTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.65
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:28655 original size:14 final size:14
Alignment explanation
Indices: 28636--28665 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28626 TTTGCATCCA
28636 TTCATTTATGTTCG
1 TTCATTTATGTTCG
*
28650 TTCATTTGTGTTCG
1 TTCATTTATGTTCG
28664 TT
1 TT
28666 TTTCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.17, T:0.60
Consensus pattern (14 bp):
TTCATTTATGTTCG
Found at i:37740 original size:31 final size:31
Alignment explanation
Indices: 37680--37740 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
37670 ATTTAAAATC
* *
37680 TAATAAATTGATTAATAATATTATCGATTTG
1 TAATAAATTAATTAATAACATTATCGATTTG
* * *
37711 TAATAAATTAATTATTAACGTTATTGATTT
1 TAATAAATTAATTAATAACATTATCGATTT
37741 ATAACCAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
TAATAAATTAATTAATAACATTATCGATTTG
Found at i:38167 original size:41 final size:42
Alignment explanation
Indices: 38044--38613 Score: 433
Period size: 41 Copynumber: 13.9 Consensus size: 42
38034 AAAATCGTAT
* * *
38044 TTTAGTGTCGTTTTTA-TATAAACGCTGCTAAATACT-ATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * * * * * * *
38084 TTTAGTGGCATTTT-TGTACAAATGACACTAAA-ATGTCTTAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATA-CTCATAC
* * *
38125 TTTAGTGGTGTTTTAAGCATAAACGCCTCTAAATACT-ATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * *
38166 TTTAGTGGCATTTTAAGCATAAACACCGCTAAATACTCATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * * *
38208 TTTAGTGGCGTTTTTA-TATAAACGCTGATAAATACTCATAA
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * *
38249 TTTAGTGGAGTTTTAAGTATAAACACCACTAAATACTCATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* *
38291 TTTAGTGGTGTTTTTA-TATAAACGCCGCTAAATACTCATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * * **
38332 TTTAATGGCATTTTTA-TATAAATACCGCTAAATACT-ATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
** * * * * * *
38372 TTTAGTGGTATTTT-TGTACAAATGCCGCTAAAGAGTCTTAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * *
38413 TTTAGTTGCGTTTTAAGCATAAACGCTGCTAAATACTCATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * **
38455 TTTAGTGGCATTTTTA-TATAAACGTTGCTAAATACT-ATAC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
* * * ** *
38495 TTTAGTGGCGTTTGTACA--A-AAACACCAC-AAATGGCTTGTAA
1 TTTAGTGGCGTTT-TA-AGTATAAACGCCGCTAAAT-ACTCATAC
* * *
38536 TTTAGTGGCGTCTTT-A-TACAAACGCTGCTAAAGACTCATAC
1 TTTAGTGGCGT-TTTAAGTATAAACGCCGCTAAATACTCATAC
* *
38577 TTTAGTGGCGTTTTTA-TACAAACGCCG-TAAAATACTC
1 TTTAGTGGCGTTTTAAGTATAAACGCCGCT-AAATACTC
38614 GTAATGACCT
Statistics
Matches: 420, Mismatches: 90, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
39 6 0.01
40 84 0.20
41 226 0.54
42 103 0.25
43 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (42 bp):
TTTAGTGGCGTTTTAAGTATAAACGCCGCTAAATACTCATAC
Found at i:38229 original size:82 final size:82
Alignment explanation
Indices: 38044--38590 Score: 504
Period size: 83 Copynumber: 6.7 Consensus size: 82
38034 AAAATCGTAT
* * * * *
38044 TTTAGTGTCGTTTTTATATAAACGCTGCTAAATACTATACTTTAGTGGCATTTT-TGTACAAATG
1 TTTAGTGGCGTTTTTATATAAACGCTGCTAAATACTATACTTTAGTGGCATTTTAAGCATAAA-C
* *
38108 A-CACTAAA-ATGTCTTAC
65 ACCACTAAATA-CTCATAC
* * *
38125 TTTAGTGGTGTTTTAAGCATAAACGCCT-CTAAATACTATACTTTAGTGGCATTTTAAGCATAAA
1 TTTAGTGGCGTTTTTA-TATAAACG-CTGCTAAATACTATACTTTAGTGGCATTTTAAGCATAAA
*
38189 CACCGCTAAATACTCATAC
64 CACCACTAAATACTCATAC
* * *
38208 TTTAGTGGCGTTTTTATATAAACGCTGATAAATACTCATAATTTAGTGG-AGTTTTAAGTATAAA
1 TTTAGTGGCGTTTTTATATAAACGCTGCTAAATACT-ATACTTTAGTGGCA-TTTTAAGCATAAA
38272 CACCACTAAATACTCATAC
64 CACCACTAAATACTCATAC
* * * * * *
38291 TTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTCATACTTTAATGGCATTTTTA-TATAAAT
1 TTTAGTGGCGTTTTTATATAAACGCTGCTAAATACT-ATACTTTAGTGGCATTTTAAGCATAAAC
*
38355 ACCGCTAAATACT-ATAC
65 ACCACTAAATACTCATAC
** * * * * * * *
38372 TTTAGTGGTATTTTTGTACAAATGCCGCTAAAGAGTCT-TACTTTAGTTGCGTTTTAAGCATAAA
1 TTTAGTGGCGTTTTTATATAAACGCTGCTAAATA--CTATACTTTAGTGGCATTTTAAGCATAAA
* **
38436 CGCTGCTAAATACTCATAC
64 CACCACTAAATACTCATAC
* * * *
38455 TTTAGTGGCATTTTTATATAAACGTTGCTAAATACTATACTTTAGTGGCGTTTGT-A-CAAAAAC
1 TTTAGTGGCGTTTTTATATAAACGCTGCTAAATACTATACTTTAGTGGCATTT-TAAGCATAAAC
* ** *
38518 ACCAC-AAATGGCTTGTAA
65 ACCACTAAAT-ACTCATAC
* * * *
38536 TTTAGTGGCGTCTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGGCGTTTT
1 TTTAGTGGCGTTTTTATATAAACGCTGCTAAATACT-ATACTTTAGTGGCATTTT
38591 TATACAAACG
Statistics
Matches: 389, Mismatches: 60, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
80 4 0.01
81 109 0.28
82 118 0.30
83 156 0.40
84 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (82 bp):
TTTAGTGGCGTTTTTATATAAACGCTGCTAAATACTATACTTTAGTGGCATTTTAAGCATAAACA
CCACTAAATACTCATAC
Found at i:38374 original size:164 final size:163
Alignment explanation
Indices: 38044--38590 Score: 566
Period size: 164 Copynumber: 3.3 Consensus size: 163
38034 AAAATCGTAT
* * * * *
38044 TTTAGTGTCGTTTTTATATAAACGCTGCTAAATACT-ATACTTTAGTGGCA-TTTT-TGTACAAA
1 TTTAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGG-AGTTTTAAGTATAAA
* * * * * *
38106 TGA-CACTAAA-ATGTCTTACTTTAGTGGTGTTTTAAGCATAAACGCCTCTAAATACTATACTTT
65 -CACCACTAAATA-CTCATACTTTAGTGGTGTTTTTA-TATAAACGCCGCTAAATACTATACTTT
*
38169 AGTGGCATTTTAAGCATAAACACCGCTAAATACTCATAC
127 AGTGGCATTTTTA-CATAAACACCGCTAAATACT-ATAC
* * * *
38208 TTTAGTGGCGTTTTTATATAAACGCTGATAAATACTCATAATTTAGTGGAGTTTTAAGTATAAAC
1 TTTAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGGAGTTTTAAGTATAAAC
*
38273 ACCACTAAATACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTCATACTTTAAT
66 ACCACTAAATACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACT-ATACTTTAGT
* *
38338 GGCATTTTTATATAAATACCGCTAAATACTATAC
130 GGCATTTTTACATAAACACCGCTAAATACTATAC
** * * * * * * * *
38372 TTTAGTGGTATTTTTGTACAAATGCCGCTAAAGAGTCTTACTTTAGTTGCGTTTTAAGCATAAAC
1 TTTAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGGAGTTTTAAGTATAAAC
* ** ** **
38437 GCTGCTAAATACTCATACTTTAGTGGCATTTTTATATAAACGTTGCTAAATACTATACTTTAGTG
66 ACCACTAAATACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTG
* * * * * * *
38502 GCGTTTGTACAAAAACACCAC-AAATGGCTTGTAA
131 GCATTTTTACATAAACACCGCTAAAT-AC-TATAC
* *
38536 TTTAGTGGCGTCTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGGCGTTTT
1 TTTAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGGAGTTTT
38591 TATACAAACG
Statistics
Matches: 320, Mismatches: 55, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
162 4 0.01
163 26 0.08
164 186 0.58
165 52 0.16
166 51 0.16
167 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (163 bp):
TTTAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCATACTTTAGTGGAGTTTTAAGTATAAAC
ACCACTAAATACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTG
GCATTTTTACATAAACACCGCTAAATACTATAC
Found at i:43614 original size:23 final size:23
Alignment explanation
Indices: 43583--43655 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
43573 ATAGGTAAAA
*
43583 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
43606 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
43629 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
43652 ATAT
1 ATAT
43656 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:44104 original size:23 final size:23
Alignment explanation
Indices: 44078--44145 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
44068 TAAAACTATG
44078 ATGTAATAAGTAGCGCTTATATA
1 ATGTAATAAGTAGCGCTTATATA
* *
44101 ATGTAATATGTAGCGTTTATATA
1 ATGTAATAAGTAGCGCTTATATA
* *
44124 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAAGTAGCGCTTATAT
44146 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATGTAATAAGTAGCGCTTATATA
Found at i:44159 original size:490 final size:489
Alignment explanation
Indices: 43161--45485 Score: 3748
Period size: 490 Copynumber: 4.8 Consensus size: 489
43151 TTTTTACCTG
* *
43161 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATT
*
43226 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGACGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
43291 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
*
43356 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
*
43421 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
* * * *
43486 CACTGTTAAAAAAATTGAAACACAAATTACATAACTTTAAAAAATGTATCGATCCTTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAA
* *
43551 AAGTATGGACACTTTCAACATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
391 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATGTA
*
43616 ATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
456 ATAGGTAGCGCTTATATAATGTAATAGGTAGTGC
*
43650 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTTTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATT
43715 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
43780 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
43845 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTTATAAAATATCAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATA-TTTTATAAAATATCAA
* * * *
43910 AACAATCAATTATTTTTTTGTGTAAATGAAATTATTAAATTAATATTATATGTGGAAAACATGAA
260 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
*
43975 ACACTATTAAAAAAATTGAAGCATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAA
325 ACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAA
*
44040 AAAGTATGGACACTTTCAATATAATAGGTAAAACTATGATGTAATAAGTAGCGCTTATATAATGT
390 AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATGT
* *
44105 AATATGTAGCGTTTATATAATGTAATAGGTAGTGC
455 AATAGGTAGCGCTTATATAATGTAATAGGTAGTGC
*
44140 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATT
*
44205 AATTTAAGGTTATCTTTTGAGTGAGCTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
44270 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
*
44335 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
* * *
44400 ATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
44465 CACTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAA
* *
44529 AAGTATGGACACTTACAATAT-ATCATGT-AAAA-AT-ATG-----A-T---G------TAA--T
391 AAGTATGGACACTTTCAATATAAT-AGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATGT
* *
44573 -AT--GTAGCACTTATATAATGTAATAGGTGGTGC
455 AATAGGTAGCGCTTATATAATGTAATAGGTAGTGC
*
44605 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTTTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATT
* *
44670 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTATTAATTATAGGTGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
*
44735 TTA-TTTTTATGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
44799 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
44864 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
44929 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
326 CACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAA
* * * * * *
44994 AAAGGATCGATACTTTACAATATATTAGGTAAAAATATGATGTAATAGGTATCGCTTATATAATG
390 AAAGTATGGACACTTT-CAATATAATAGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATG
*
45059 TAATAGGTAGCGCTTATATAATGTAATAGGTAGCGC
454 TAATAGGTAGCGCTTATATAATGTAATAGGTAGTGC
* *
45095 TTATATTGTAAAGTATCTATCTTTTTTATAGAAGTGTCCATACTTATTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATT
* * * **
45160 AATTTAAGATTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
* * * * *
45225 TTATTTTTTATGTTACGCTATATATTATCATTAAATTAAAAACAATAAACGTATATATTATATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
* * *
45290 TTATTATTATATTTGGTTAATATTATTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
*
45355 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTA----G-------G---
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
45406 ---TATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATTGATCATTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTAT-AA
*
45467 AAAATATGGACACTTTCAA
390 AAAGTATGGACACTTTCAA
45486 CGTATTATAA
Statistics
Matches: 1726, Mismatches: 79, Indels: 79
0.92 0.04 0.04
Matches are distributed among these distances:
464 193 0.11
465 155 0.09
466 67 0.04
467 11 0.01
468 6 0.00
469 2 0.00
470 6 0.00
472 55 0.03
473 14 0.01
474 4 0.00
476 2 0.00
479 2 0.00
480 2 0.00
485 6 0.00
486 2 0.00
487 7 0.00
488 81 0.05
489 320 0.19
490 624 0.36
491 167 0.10
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (489 bp):
TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATT
AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAA
AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATGTA
ATAGGTAGCGCTTATATAATGTAATAGGTAGTGC
Found at i:44990 original size:22 final size:22
Alignment explanation
Indices: 44965--45009 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44955 ATTACATAAC
* *
44965 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGGATCGATACTT
*
44987 TTTATAAAAAGGATCGATACTT
1 TTTAAAAAAAGGATCGATACTT
45009 T
1 T
45010 ACAATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGGATCGATACTT
Found at i:45059 original size:23 final size:23
Alignment explanation
Indices: 45028--45100 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
45018 TTAGGTAAAA
* *
45028 ATATGATGTAATAGGTATCGCTT
1 ATATAATGTAATAGGTAGCGCTT
45051 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
45074 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
45097 ATAT
1 ATAT
45101 TGTAAAGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:49623 original size:25 final size:25
Alignment explanation
Indices: 49590--49639 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
49580 CACCACTATA
*
49590 GATCCGACCTTTTGCGGCA-TTTTT
1 GATCCGACCTATTGCGGCAGTTTTT
49614 GATCTCGACCTATTGCGGCAGTTTTT
1 GATC-CGACCTATTGCGGCAGTTTTT
49640 TCACAAACGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 14 0.61
26 5 0.22
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.40
Consensus pattern (25 bp):
GATCCGACCTATTGCGGCAGTTTTT
Found at i:52419 original size:10 final size:10
Alignment explanation
Indices: 52404--52443 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
52394 AAATATACAA
52404 ATAAACGAAC
1 ATAAACGAAC
52414 ATAAACGAATC
1 ATAAACGAA-C
52425 -TAAACGAAC
1 ATAAACGAAC
*
52434 ATAAAGGAAC
1 ATAAACGAAC
52444 CAACATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 1 0.04
10 25 0.93
11 1 0.04
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:52626 original size:14 final size:14
Alignment explanation
Indices: 52609--52644 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52599 GATATAAACA
*
52609 AACATAAATGAATG
1 AACATAAATAAATG
52623 AACATAAATAAATG
1 AACATAAATAAATG
*
52637 AATATAAA
1 AACATAAA
52645 CGAACTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (14 bp):
AACATAAATAAATG
Found at i:52992 original size:18 final size:17
Alignment explanation
Indices: 52964--53001 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
52954 AAAGAGATAA
52964 CTTTTACAAATCTCTAT
1 CTTTTACAAATCTCTAT
52981 CTTTTCACAAATCTCTAT
1 CTTTT-ACAAATCTCTAT
52999 CTT
1 CTT
53002 ACAAGGTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (17 bp):
CTTTTACAAATCTCTAT
Found at i:53269 original size:21 final size:22
Alignment explanation
Indices: 53243--53283 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53233 TCAAGACATA
*
53243 GAGTATTGGTAAT-CCTTTAAT
1 GAGTATCGGTAATACCTTTAAT
*
53264 GAGTATCGGTATTACCTTTA
1 GAGTATCGGTAATACCTTTA
53284 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (22 bp):
GAGTATCGGTAATACCTTTAAT
Found at i:53416 original size:20 final size:20
Alignment explanation
Indices: 53391--53442 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
53381 AACATATGGT
53391 AGTATCGATACTGCCTAGAG
1 AGTATCGATACTGCCTAGAG
53411 AGTATCGATACTGCCTAGAG
1 AGTATCGATACTGCCTAGAG
*
53431 AGTATCTATACT
1 AGTATCGATACT
53443 TCTCTTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTGCCTAGAG
Found at i:55969 original size:21 final size:20
Alignment explanation
Indices: 55927--55965 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55917 TGGCCGTTTC
*
55927 TAGCCGTTGGAGATGATTTG
1 TAGCCGTTGGAGATAATTTG
55947 TAGCCGTTAGG-GATAATTT
1 TAGCCGTT-GGAGATAATTT
55966 TGTACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (20 bp):
TAGCCGTTGGAGATAATTTG
Found at i:56846 original size:21 final size:21
Alignment explanation
Indices: 56820--56864 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56810 GATTTCTGGG
* *
56820 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
56841 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
56862 CAA
1 CAA
56865 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:58628 original size:23 final size:22
Alignment explanation
Indices: 58540--58620 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
58530 ATCATTATAT
*
58540 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
*
58562 GGCACTTCGGTGTAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
58584 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
58607 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
58621 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 40 0.73
23 15 0.27
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:61869 original size:18 final size:18
Alignment explanation
Indices: 61848--61890 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
61838 AAATACTTGT
61848 TTCAGAACAAATATATGC
1 TTCAGAACAAATATATGC
** *
61866 TTCAGATTAAATATATGT
1 TTCAGAACAAATATATGC
61884 TTCAGAA
1 TTCAGAA
61891 ATATTATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TTCAGAACAAATATATGC
Found at i:65505 original size:192 final size:190
Alignment explanation
Indices: 65188--65570 Score: 716
Period size: 192 Copynumber: 2.0 Consensus size: 190
65178 AACAAAATTA
65188 AAGTTTAATAGAGATTTAGAGATAATGGTTGAAACTTTTTGAATTGAGACAAATGAAATGTTTGA
1 AAGTTTAATAGAGATTTAGAGATAATGGTTGAAACTTTTTGAATTGAGACAAATGAAATGTTTGA
65253 TTTATGGATATTCCTTCAACTCGTTCCACGATACTACGGCTCCAGCAAAGACATCATCGAGGTAA
66 TTTATGGATATTCCTTCAACTCGTTCCACGATACTACGGCTCCAGCAAAGACATCATCGAGGTAA
65318 CAAAGAAAACGCAACTGAATTTCAATTCAAATATATATTGAATGATATCTTAACAACAATATAG
131 CAAAGAAAACGCAACTGAA-TTCAATTC-AA-ATATATTGAATGATATCTTAACAAC-ATATAG
65382 AAGTTTAATAGAGATTTAGAGATAATGGTTGAAAC-TTTTGAATTGAGACAAATG-AATGTTTGA
1 AAGTTTAATAGAGATTTAGAGATAATGGTTGAAACTTTTTGAATTGAGACAAATGAAATGTTTGA
65445 TTTATGGATATTCCTTCAACTCGTTCCACGATACTACGGCTCCAGCAAAGACATCATCGAGGTAA
66 TTTATGGATATTCCTTCAACTCGTTCCACGATACTACGGCTCCAGCAAAGACATCATCGAGGTAA
65510 CAAAGAAAACGCAACTGAATTCAATTCAAATATATTGAATGATATCTTAACAACATATAG
131 CAAAGAAAACGCAACTGAATTCAATTCAAATATATTGAATGATATCTTAACAACATATAG
65570 A
1 A
65571 CACCAAAACA
Statistics
Matches: 189, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
188 7 0.04
189 25 0.13
190 2 0.01
191 8 0.04
192 93 0.49
193 19 0.10
194 35 0.19
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (190 bp):
AAGTTTAATAGAGATTTAGAGATAATGGTTGAAACTTTTTGAATTGAGACAAATGAAATGTTTGA
TTTATGGATATTCCTTCAACTCGTTCCACGATACTACGGCTCCAGCAAAGACATCATCGAGGTAA
CAAAGAAAACGCAACTGAATTCAATTCAAATATATTGAATGATATCTTAACAACATATAG
Found at i:67621 original size:22 final size:23
Alignment explanation
Indices: 67593--67655 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
67583 AATATCGATA
* * *
67593 CCTTTTTTTAGCGTTGGAAATAC
1 CCTTTTTCTAGCGCTAGAAATAC
*
67616 CCTTTTTCTAGCGCTAGTAATAC
1 CCTTTTTCTAGCGCTAGAAATAC
*
67639 CCTTTTTCTAGCACTAG
1 CCTTTTTCTAGCGCTAG
67656 TATCGATACC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (23 bp):
CCTTTTTCTAGCGCTAGAAATAC
Found at i:67656 original size:23 final size:23
Alignment explanation
Indices: 67611--67657 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
67601 TAGCGTTGGA
*
67611 AATACCCTTTTTCTAGCGCTAGT
1 AATACCCTTTTTCTAGCACTAGT
67634 AATACCCTTTTTCTAGCACTAGT
1 AATACCCTTTTTCTAGCACTAGT
67657 A
1 A
67658 TCGATACCAA
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:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (23 bp):
AATACCCTTTTTCTAGCACTAGT
Found at i:73175 original size:45 final size:46
Alignment explanation
Indices: 73118--73225 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 46
73108 TGCACCAATC
*
73118 CATGCATTGATGCACCATGA-ATTAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACCATGAGATTAAA-TGAAACATCGAATGCATTT
**
73163 CATGCATCGATGCA-C-TGAGGATTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACCATGA-GATTAAATG-AAACATCGAATGCATTT
* *
73209 TATGCATCGATACACCA
1 CATGCATCGATGCACCA
73226 GCCATGCATC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 17 0.33
46 28 0.54
47 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (46 bp):
CATGCATCGATGCACCATGAGATTAAATGAAACATCGAATGCATTT
Found at i:73287 original size:17 final size:19
Alignment explanation
Indices: 73259--73307 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
73249 TATTTTGAAA
73259 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
73277 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
73296 CACCGATGCACT
1 CATCGATGCACT
73308 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:74652 original size:19 final size:20
Alignment explanation
Indices: 74628--74675 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
74618 AATGATTTTC
*
74628 TTTTGAAAACAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
* *
74647 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
74667 TTTTGAAAA
1 TTTTGAAAA
74676 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:76072 original size:21 final size:20
Alignment explanation
Indices: 76046--76165 Score: 134
Period size: 21 Copynumber: 5.8 Consensus size: 20
76036 AGGATGTCAA
*
76046 AGTGCATCCATGCACCGTTGC
1 AGTGCATCCATGCACC-CTGC
*
76067 AGTGCATTCATGCACTCCTGC
1 AGTGCATCCATGCAC-CCTGC
76088 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
76109 AGTGCATCCATTCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
76130 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
76151 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
76166 TCCATTTCGA
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.05
20 14 0.16
21 50 0.59
22 14 0.16
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:76110 original size:42 final size:44
Alignment explanation
Indices: 76046--76168 Score: 148
Period size: 42 Copynumber: 2.9 Consensus size: 44
76036 AGGATGTCAA
** *
76046 AGTGCATCCATGCACCGTTGCAGTGCATTCATGCACTCCTG-C-
1 AGTGCATCCATGCACCCATGCAGTGCATCCATGCACTCCTGACT
* *
76088 AGTGCATCCATGCACCCCTGCAGTGCATCCATTCA--CCTGCACT
1 AGTGCATCCATGCACCCATGCAGTGCATCCATGCACTCCTG-ACT
*
76131 AGTGCATCGATGCA-CCATGCAGTGCATCCATGCACTCC
1 AGTGCATCCATGCACCCATGCAGTGCATCCATGCACTCC
76169 ATTTCGAATG
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.06
42 50 0.72
43 13 0.19
44 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (44 bp):
AGTGCATCCATGCACCCATGCAGTGCATCCATGCACTCCTGACT
Found at i:76146 original size:22 final size:23
Alignment explanation
Indices: 76088--76165 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 23
76078 GCACTCCTGC
*
76088 AGTGCATCCATGCACCCCTG--C-
1 AGTGCATCCATGCA-CCATGCACT
*
76109 AGTGCATCCATTCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
76131 AGTGCATCGATGCACCATG--C-
1 AGTGCATCCATGCACCATGCACT
76151 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
76166 TCCATTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.04
20 16 0.33
21 15 0.31
22 14 0.29
23 2 0.04
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:77613 original size:65 final size:65
Alignment explanation
Indices: 77477--77635 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 65
77467 GCACTAAGAG
* * * *
77477 TGCACCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGA
* *
77541 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-TA
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-
*
77604 TA
64 GA
* * *
77606 TGGATCGATGCATGAAATGCATTCAATGTT
1 TGCATCGATGCATCAAATGCATTCGATGTT
77636 CAATTTAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 27 0.33
65 52 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGA
Found at i:77683 original size:65 final size:64
Alignment explanation
Indices: 77476--77685 Score: 184
Period size: 65 Copynumber: 3.2 Consensus size: 64
77466 TGCACTAAGA
* * * * *
77476 GTGCACCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGAT
77538 TG
63 TG
*
77540 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCAATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGG-AT
77605 AT-
63 -TG
* **
77607 G-G-ATCGATGCATGAAATGCATTCAATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCAATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGAT
77668 TG
63 TG
*
77670 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
77686 CTCTGAAAAT
Statistics
Matches: 123, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
62 4 0.03
63 6 0.05
64 49 0.40
65 56 0.46
66 5 0.04
67 2 0.02
68 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTCATAAAATCTCAGTGCATCGATGCATGGATTG
Found at i:78753 original size:21 final size:21
Alignment explanation
Indices: 78729--78772 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
78719 CCAGAGGAGG
*
78729 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
78750 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
78771 AG
1 AG
78773 CTCCCAGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:85717 original size:19 final size:20
Alignment explanation
Indices: 85675--85719 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
85665 GGTACTACCC
* * *
85675 TTTTGAGTTCTCGATACTAC
1 TTTTGAGTTATCGATACCAA
85695 TTTTGAG-TATCGATACCAA
1 TTTTGAGTTATCGATACCAA
85714 TTTTGA
1 TTTTGA
85720 TTACTGGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (20 bp):
TTTTGAGTTATCGATACCAA
Found at i:86099 original size:28 final size:28
Alignment explanation
Indices: 86067--86130 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
86057 TTATTATAAC
86067 TCAAGGGTATTTTGATTATTTTATCCAT
1 TCAAGGGTATTTTGATTATTTTATCCAT
* *
86095 TCAAGGGAATTTTGGTTATTTTATCCAT
1 TCAAGGGTATTTTGATTATTTTATCCAT
86123 TCAAGGGT
1 TCAAGGGT
86131 GTTTAAGGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (28 bp):
TCAAGGGTATTTTGATTATTTTATCCAT
Done.