Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008039.1 Hibiscus syriacus cultivar Beakdansim tig00110526_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: 71202
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:5879 original size:21 final size:22
Alignment explanation
Indices: 5829--5880 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
5819 TGCTGCCATG
5829 ATATGTAAATGATATGCAAAAC
1 ATATGTAAATGATATGCAAAAC
*
5851 ATA-ATAAATGA-AT-CTAAAAC
1 ATATGTAAATGATATGC-AAAAC
5871 ATATGTAAAT
1 ATATGTAAAT
5881 ATAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 10 0.38
21 12 0.46
22 3 0.12
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.29
Consensus pattern (22 bp):
ATATGTAAATGATATGCAAAAC
Found at i:9135 original size:19 final size:20
Alignment explanation
Indices: 9095--9147 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
9085 GAAACCCCTT
9095 TGAAAATACATGATTTTTTTAA
1 TGAAAATACATGA--TTTTTAA
9117 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
9136 TGAAGATACATG
1 TGAAAATACATG
9148 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
22 13 0.43
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:10048 original size:21 final size:22
Alignment explanation
Indices: 9998--10048 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
9988 TACTGCCATG
9998 ATATGTAAATGATATACAAAAC
1 ATATGTAAATGATATACAAAAC
*
10020 ATA-ATAAATGA-AT-CTAAAAC
1 ATATGTAAATGATATAC-AAAAC
10040 ATATGTAAA
1 ATATGTAAA
10049 CATAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 11 0.44
22 3 0.12
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (22 bp):
ATATGTAAATGATATACAAAAC
Found at i:14893 original size:36 final size:36
Alignment explanation
Indices: 14841--14953 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
14831 GATACTATTT
*
14841 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
14877 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
14913 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
14948 ACATCA
1 TCATCA
14954 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:14896 original size:13 final size:11
Alignment explanation
Indices: 14841--14940 Score: 69
Period size: 13 Copynumber: 8.4 Consensus size: 11
14831 GATACTATTT
14841 TCATCACCATAA
1 TCATCACCAT-A
*
14853 TCCATCTCCATTA
1 T-CATCACCA-TA
*
14866 TCA-CGCCTATA
1 TCATCACC-ATA
14877 TCATCACCATA
1 TCATCACCATA
14888 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
14902 TCA-CGCCTATA
1 TCATCACC-ATA
14913 TCATCACCATA
1 TCATCACCATA
14924 TTCCATCACCATA
1 -T-CATCACCATA
14937 TCAT
1 TCAT
14941 GCCAATAACA
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 25 0.35
12 16 0.22
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:14968 original size:33 final size:33
Alignment explanation
Indices: 14924--14992 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
14914 CATCACCATA
*
14924 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
14957 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
14990 TTC
1 TTC
14993 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:19906 original size:11 final size:13
Alignment explanation
Indices: 19874--19903 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19864 TGGTAAAAGA
19874 TGAAAAGGTATGT
1 TGAAAAGGTATGT
19887 TGAAAAGGTATG-
1 TGAAAAGGTATGT
19899 TGAAA
1 TGAAA
19904 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:27795 original size:36 final size:36
Alignment explanation
Indices: 27743--27855 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
27733 GATACTATTT
*
27743 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
27779 TCATCACCATAGTCCATCACCATGATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
27815 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
27850 ACATCA
1 TCATCA
27856 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:27870 original size:33 final size:33
Alignment explanation
Indices: 27755--27894 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
27745 ATCACCATAA
* * *
27755 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
27789 AGTCCATCACCATGATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCAT-ATCACGCCAATAACATCATCC---T
27827 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
27860 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
27893 TC
1 TC
27895 ATTCATCAAC
Statistics
Matches: 92, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 42 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:32214 original size:24 final size:26
Alignment explanation
Indices: 32171--32219 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
32161 CATTTGTTAA
32171 GGCATCAGAAGAGCCTTACATCAAGT
1 GGCATCAGAAGAGCCTTACATCAAGT
32197 GGCATCAG-A-AGCCTTACATCAAG
1 GGCATCAGAAGAGCCTTACATCAAG
32220 CGATAATCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 14 0.61
25 1 0.04
26 8 0.35
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (26 bp):
GGCATCAGAAGAGCCTTACATCAAGT
Found at i:32352 original size:15 final size:15
Alignment explanation
Indices: 32341--32369 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32331 ACTCAAAAAG
32341 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
32356 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
32370 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:36253 original size:24 final size:26
Alignment explanation
Indices: 36210--36257 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
36200 CATTTGTTAA
36210 GGCATCAGAAGAGCCTTACATCAAGT
1 GGCATCAGAAGAGCCTTACATCAAGT
36236 GGCATCAG-A-AGCCTTACATCAA
1 GGCATCAGAAGAGCCTTACATCAA
36258 AGACTCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.59
25 1 0.05
26 8 0.36
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (26 bp):
GGCATCAGAAGAGCCTTACATCAAGT
Found at i:46257 original size:13 final size:14
Alignment explanation
Indices: 46229--46264 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
46219 ATACTATTTT
*
46229 CATCACCATCTTTC
1 CATCACCATCTCTC
46243 CATCACCATC-CTC
1 CATCACCATCTCTC
46256 CATCACCAT
1 CATCACCAT
46265 TCACGCCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.25, C:0.47, G:0.00, T:0.28
Consensus pattern (14 bp):
CATCACCATCTCTC
Found at i:47825 original size:22 final size:22
Alignment explanation
Indices: 47765--47827 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
47755 ATTGAGTACA
* *
47765 AAAAGAAAAGAAAAGACAAAAAG
1 AAAAGAAAA-ATAAGAAAAAAAG
*
47788 AAAA-AAAAATTCAGAAAAAAAG
1 AAAAGAAAAA-TAAGAAAAAAAG
47810 AAAAGAAAAATAAGAAAA
1 AAAAGAAAAATAAGAAAA
47828 GTAAAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.03
22 24 0.71
23 9 0.26
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (22 bp):
AAAAGAAAAATAAGAAAAAAAG
Found at i:49037 original size:13 final size:12
Alignment explanation
Indices: 49015--49091 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 12
49005 AATTGAGCAC
49015 AAAAAGAAAAGA
1 AAAAAGAAAAGA
49027 AAAGACA-AAAAGA
1 AAA-A-AGAAAAGA
*
49040 AAAAAAAAATTCAGAA
1 AAAAAGAAA---AG-A
49056 AAAAAGAAAAGAA
1 AAAAAGAAAAG-A
49069 AAATAAGAAAAGTA
1 AAA-AAGAAAAG-A
49083 AAAAAGAAA
1 AAAAAGAAA
49092 GCAAGCCAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
11 1 0.02
12 7 0.13
13 23 0.42
14 13 0.24
15 2 0.04
16 9 0.16
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:49042 original size:23 final size:23
Alignment explanation
Indices: 49016--49079 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
49006 ATTGAGCACA
*
49016 AAAAGAAAAGAA-AAGACAAAAAG
1 AAAAGAAAA-AATAAGAAAAAAAG
*
49039 AAAA-AAAAAATTCAGAAAAAAAG
1 AAAAGAAAAAA-TAAGAAAAAAAG
49062 AAAAG-AAAAATAAGAAAA
1 AAAAGAAAAAATAAGAAAA
49080 GTAAAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 11 0.31
23 22 0.63
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (23 bp):
AAAAGAAAAAATAAGAAAAAAAG
Found at i:50304 original size:14 final size:13
Alignment explanation
Indices: 50286--50324 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
50276 AAAAAATTCT
50286 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
50299 GAAAAATAAGAAAA
1 GAAAAA-AAGAAAA
*
50313 GTAAAAAAGAAA
1 GAAAAAAAGAAA
50325 GCAAGCCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:50311 original size:22 final size:22
Alignment explanation
Indices: 50267--50312 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
50257 AATTGAGTAC
**
50267 AAAAAGAAAAAAAAATTCTGAA
1 AAAAAGAAAAAAAAATTAAGAA
50289 AAAAAGAAAAGAAAAA-TAAGAA
1 AAAAAGAAAA-AAAAATTAAGAA
50311 AA
1 AA
50313 GTAAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (22 bp):
AAAAAGAAAAAAAAATTAAGAA
Found at i:51519 original size:18 final size:18
Alignment explanation
Indices: 51498--51553 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
51488 AAAATTGAGT
51498 ACAAAAAGAAAAAAAAAG
1 ACAAAAAGAAAAAAAAAG
51516 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAA--AG
*
51536 AAAAAAAGAAAAGAAAAA
1 ACAAAAAGAAAA-AAAAA
51554 TAAGAAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 16 0.47
19 1 0.03
20 13 0.38
21 4 0.12
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (18 bp):
ACAAAAAGAAAAAAAAAG
Found at i:51529 original size:20 final size:20
Alignment explanation
Indices: 51498--51558 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
51488 AAAATTGAGT
51498 ACAAAAAG--AAAAAAAAAG
1 ACAAAAAGAAAAAAAAAAAG
**
51516 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAAAAAG
*
51536 AAAAAAAGAAAAGAAAAATAAG
1 ACAAAAAGAAAA-AAAAA-AAG
51558 A
1 A
51559 AAAGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.24
20 19 0.56
21 4 0.12
22 3 0.09
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.03
Consensus pattern (20 bp):
ACAAAAAGAAAAAAAAAAAG
Found at i:51552 original size:22 final size:20
Alignment explanation
Indices: 51500--51561 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 20
51490 AATTGAGTAC
*
51500 AAAAAG-AAAAAAA-AAGAC
1 AAAAAGAAAAAAAATAAGAA
*
51518 AAAAAGAAAAAAAATCAGAA
1 AAAAAGAAAAAAAATAAGAA
51538 AAAAAGAAAAGAAAAATAAGAA
1 AAAAAG-AAA-AAAAATAAGAA
51560 AA
1 AA
51562 GTAAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 6 0.16
19 7 0.19
20 9 0.24
21 3 0.08
22 12 0.32
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAAAATAAGAA
Found at i:51561 original size:20 final size:19
Alignment explanation
Indices: 51500--51561 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 19
51490 AATTGAGTAC
* *
51500 AAAAAGAAAAAAAAA-GAC
1 AAAAAGAAAAAAAAATAAA
51518 AAAAAG-AAAAAAAATCAGAA
1 AAAAAGAAAAAAAAAT-A-AA
51538 AAAAAGAAAAGAAAAATAAGA
1 AAAAAGAAAA-AAAAATAA-A
51559 AAA
1 AAA
51562 GTAAAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 8 0.22
18 6 0.17
20 8 0.22
21 8 0.22
22 6 0.17
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATAAA
Found at i:52783 original size:22 final size:21
Alignment explanation
Indices: 52748--52792 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
52738 AATTGAGTAC
* * *
52748 AAAAAGGAAAAAAATTCAGAA
1 AAAAAGAAAAAAAAATAAGAA
52769 AAAAAGAAAAGAAAAATAAGAA
1 AAAAAGAAAA-AAAAATAAGAA
52791 AA
1 AA
52793 GTAAAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (21 bp):
AAAAAGAAAAAAAAATAAGAA
Found at i:52784 original size:14 final size:13
Alignment explanation
Indices: 52765--52804 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
52755 AAAAAAATTC
52765 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
52778 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
52792 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
52805 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:54164 original size:75 final size:73
Alignment explanation
Indices: 54075--54228 Score: 247
Period size: 75 Copynumber: 2.0 Consensus size: 73
54065 GACATACCAA
54075 TTCATTCTTCCGCAGCCATCTCTTTCTATC-TTTATTTCGTTTCTTTCTATTTCCAATATTTTTA
1 TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTTATTTCGTTTCTTTCTATTTCC-ATA-TTTTA
54139 TTATTATCCAT
64 TTA-TATCCAT
54150 TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTATTTCGTTTCTTTCTATTTCCATATTTT
1 TTCATTCTTCCGCAGCCATCTCTTTCTATC--T-TTTATTTCGTTTCTTTCTATTTCCATATTTT
54215 ATTATATCCAT
63 ATTATATCCAT
54226 TTC
1 TTC
54229 TTAATTACAC
Statistics
Matches: 75, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
75 30 0.40
76 10 0.13
77 8 0.11
78 3 0.04
79 24 0.32
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.55
Consensus pattern (73 bp):
TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTTATTTCGTTTCTTTCTATTTCCATATTTTATT
ATATCCAT
Found at i:54191 original size:39 final size:39
Alignment explanation
Indices: 54075--54191 Score: 95
Period size: 39 Copynumber: 3.1 Consensus size: 39
54065 GACATACCAA
*
54075 TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTCGT
1 TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTT-AT
* * * **
54115 TTCTTTCTATTTC-CA---ATAT-TTT-TAT-TATTATCCAT
1 TTCATTC--TTCCGCAGCCATCTCTTTCTATCT-TTATTTAT
54150 TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTAT
1 TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTAT
54189 TTC
1 TTC
54192 GTTTCTTTCT
Statistics
Matches: 56, Mismatches: 11, Indels: 21
0.64 0.12 0.24
Matches are distributed among these distances:
33 3 0.05
34 2 0.04
35 8 0.14
36 7 0.12
37 6 0.11
38 6 0.11
39 12 0.21
40 7 0.12
41 2 0.04
42 3 0.05
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (39 bp):
TTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTAT
Found at i:54487 original size:20 final size:20
Alignment explanation
Indices: 54462--54503 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54452 AATTGAGTAC
*
54462 AAAAGAAAAAAAAATCAGAA
1 AAAAGAAAAAAAAATAAGAA
*
54482 AAAAGAAAGAAAAATAAGAA
1 AAAAGAAAAAAAAATAAGAA
54502 AA
1 AA
54504 GTAAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAAAAATAAGAA
Found at i:55700 original size:18 final size:18
Alignment explanation
Indices: 55679--55784 Score: 108
Period size: 18 Copynumber: 5.7 Consensus size: 18
55669 AAAATTGAGT
55679 ACAAAAAGAAAAAAAAAG
1 ACAAAAAGAAAAAAAAAG
55697 ACAAAAAGAAAAAAAAAATCAG
1 ACAAAAAG--AAAAAAAA--AG
* *
55719 AAAAAAAGACAAAAAAAG
1 ACAAAAAGAAAAAAAAAG
55737 ACAAAAAGAAAAAAAAA-
1 ACAAAAAGAAAAAAAAAG
*
55754 ATCAAAAA-AAAAGAAAAG
1 A-CAAAAAGAAAAAAAAAG
*
55772 AAAAATAAGAAAA
1 ACAAA-AAGAAAA
55785 GTAAAAAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.16
18 34 0.46
19 4 0.05
20 15 0.20
22 9 0.12
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (18 bp):
ACAAAAAGAAAAAAAAAG
Found at i:55702 original size:8 final size:7
Alignment explanation
Indices: 55690--55796 Score: 53
Period size: 8 Copynumber: 14.4 Consensus size: 7
55680 CAAAAAGAAA
55690 AAAAAAG
1 AAAAAAG
55697 ACAAAAAG
1 A-AAAAAG
55705 AAAAAA-
1 AAAAAAG
*
55711 AAAATCAG
1 AAAA-AAG
55719 AAAAAAAG
1 -AAAAAAG
55727 ACAAAAAAAG
1 ---AAAAAAG
55737 ACAAAAAG
1 A-AAAAAG
55745 AAAAAA-
1 AAAAAAG
55751 AAAATCAA-
1 AAAA--AAG
55759 AAAAAA-
1 AAAAAAG
*
55765 AGAAAAG
1 AAAAAAG
55772 AAAAATA-
1 AAAAA-AG
*
55779 AGAAAAG
1 AAAAAAG
55786 TAAAAAAG
1 -AAAAAAG
55794 AAA
1 AAA
55797 GCAAGCCAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
6 16 0.20
7 24 0.30
8 29 0.36
9 4 0.05
10 8 0.10
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:55792 original size:40 final size:40
Alignment explanation
Indices: 55681--55776 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
55671 AATTGAGTAC
*
55681 AAAAAGAAAAAAAAAGACAAAAAGAAAAAAAAAATCAGAA
1 AAAAAGAAAAAAAAAGACAAAAAGAAAAAAAAAATCAAAA
*
55721 AAAAAGACAAAAAAAGACAAAAAGAAAAAAAAAATCAAAA
1 AAAAAGAAAAAAAAAGACAAAAAGAAAAAAAAAATCAAAA
55761 AAAAAGAAAAGAAAAA
1 AAAAAGAAAA-AAAAA
55777 TAAGAAAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 47 0.90
41 5 0.10
ACGTcount: A:0.83, C:0.05, G:0.09, T:0.02
Consensus pattern (40 bp):
AAAAAGAAAAAAAAAGACAAAAAGAAAAAAAAAATCAAAA
Found at i:57314 original size:573 final size:573
Alignment explanation
Indices: 56220--57369 Score: 2255
Period size: 573 Copynumber: 2.0 Consensus size: 573
56210 CCTCAATCAT
*
56220 TCATTTTAAGCATTATGTACTTTCATTAAAAGTCTTGTATCAACCGAATAGCTATGTAACCATTC
1 TCATTATAAGCATTATGTACTTTCATTAAAAGTCTTGTATCAACCGAATAGCTATGTAACCATTC
56285 GGCCAAGCCCTCTCATTTCCTATAAATAGAGTGGCTTGCCATCATCTGTAGTCATCTCATCTCAT
66 GGCCAAGCCCTCTCATTTCCTATAAATAGAGTGGCTTGCCATCATCTGTAGTCATCTCATCTCAT
56350 ATATAAAAATTACTCTTGTGAGTTAATTTCTCTTCATGTTCTTTGTGAACTTTATCGATTAAGCA
131 ATATAAAAATTACTCTTGTGAGTTAATTTCTCTTCATGTTCTTTGTGAACTTTATCGATTAAGCA
*
56415 AGTATAATTCCTATACTTGTGGCGTCATTCCTTCCATCCTGATTCCGAAATTCCTAGATTAATAT
196 AGTATAATTCCTATACTTGTGGCGTCATTCCTTCCATCCTGATTCCAAAATTCCTAGATTAATAT
56480 CAAGTGGGTTGAAGACACTATCACCACCCTCAAGCAAGTTTGTGAAGATTGGGATTGTGCTCCTT
261 CAAGTGGGTTGAAGACACTATCACCACCCTCAAGCAAGTTTGTGAAGATTGGGATTGTGCTCCTT
56545 AACATTATTTCATCTTTGGCGTGTTTGAGATACAACATCACCATCATCTTTATTTCATCATCAAC
326 AACATTATTTCATCTTTGGCGTGTTTGAGATACAACATCACCATCATCTTTATTTCATCATCAAC
56610 ATCCTTCATCAAGACCATACCAACTTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTCATT
391 ATCCTTCATCAAGACCATACCAACTTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTCATT
56675 TCTTTCTATTTCCATTATTTTTATTATTATCCATTTCTTAATTTCACCATTAATATTATTTTCTT
456 TCTTTCTATTTCCATTATTTTTATTATTATCCATTTCTTAATTTCACCATTAATATTATTTTCTT
56740 TCTTATTTTCATTGCAGCCAATCTTATAATTCAAGGACATCAGTACTTGTCAA
521 TCTTATTTTCATTGCAGCCAATCTTATAATTCAAGGACATCAGTACTTGTCAA
56793 TCATTATAAGCATTATGTACTTTCATTAAAAGTCTTGTATCAACCGAATAGCTATGTAACCATTC
1 TCATTATAAGCATTATGTACTTTCATTAAAAGTCTTGTATCAACCGAATAGCTATGTAACCATTC
56858 GGCCAAGCCCTCTCATTTCCTATAAATAGAGTGGCTTGCCATCATCTGTAGTCATCTCATCTCAT
66 GGCCAAGCCCTCTCATTTCCTATAAATAGAGTGGCTTGCCATCATCTGTAGTCATCTCATCTCAT
56923 ATATAAAAATTACTCTTGTGAGTTAATTTCTCTTCATGTTCTTTGTGAACTTTATCGATTAAGCA
131 ATATAAAAATTACTCTTGTGAGTTAATTTCTCTTCATGTTCTTTGTGAACTTTATCGATTAAGCA
56988 AGTATAATTCCTATACTTGTGGCGTCATTCCTTCCATCCTGATTCCAAAATTCCTAGATTAATAT
196 AGTATAATTCCTATACTTGTGGCGTCATTCCTTCCATCCTGATTCCAAAATTCCTAGATTAATAT
57053 CAAGTGGGTTGAAGACACTATCACCACCCTCAAGCAAGTTTGTGAAGATTGGGATTGTGCTCCTT
261 CAAGTGGGTTGAAGACACTATCACCACCCTCAAGCAAGTTTGTGAAGATTGGGATTGTGCTCCTT
*
57118 AACATTGTTTCATCTTTGGCGTGTTTGAGATACAACATCACCATCATCTTTATTTCATCATCAAC
326 AACATTATTTCATCTTTGGCGTGTTTGAGATACAACATCACCATCATCTTTATTTCATCATCAAC
*
57183 ATCCTTCATCAAGTCCATACCAACTTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTCATT
391 ATCCTTCATCAAGACCATACCAACTTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTCATT
57248 TCTTTCTATTTCCATTATTTTTATTATTATCCATTTCTTAATTTCACCATTAATATTATTTTCTT
456 TCTTTCTATTTCCATTATTTTTATTATTATCCATTTCTTAATTTCACCATTAATATTATTTTCTT
*
57313 TCTTATTTTCATTGCATCCAATCTTATAATTCAAGGACATCAGTACTTGTCAA
521 TCTTATTTTCATTGCAGCCAATCTTATAATTCAAGGACATCAGTACTTGTCAA
57366 TCAT
1 TCAT
57370 AGATCAGGGC
Statistics
Matches: 572, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
573 572 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (573 bp):
TCATTATAAGCATTATGTACTTTCATTAAAAGTCTTGTATCAACCGAATAGCTATGTAACCATTC
GGCCAAGCCCTCTCATTTCCTATAAATAGAGTGGCTTGCCATCATCTGTAGTCATCTCATCTCAT
ATATAAAAATTACTCTTGTGAGTTAATTTCTCTTCATGTTCTTTGTGAACTTTATCGATTAAGCA
AGTATAATTCCTATACTTGTGGCGTCATTCCTTCCATCCTGATTCCAAAATTCCTAGATTAATAT
CAAGTGGGTTGAAGACACTATCACCACCCTCAAGCAAGTTTGTGAAGATTGGGATTGTGCTCCTT
AACATTATTTCATCTTTGGCGTGTTTGAGATACAACATCACCATCATCTTTATTTCATCATCAAC
ATCCTTCATCAAGACCATACCAACTTCATTCTTCCGCAGCCATCTCTTTCTATCTTTATTTCATT
TCTTTCTATTTCCATTATTTTTATTATTATCCATTTCTTAATTTCACCATTAATATTATTTTCTT
TCTTATTTTCATTGCAGCCAATCTTATAATTCAAGGACATCAGTACTTGTCAA
Found at i:57535 original size:23 final size:21
Alignment explanation
Indices: 57509--57576 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
57499 CTCCTTCAAC
57509 AAAATTGAGTACAAAAAGAAAAG
1 AAAATT-AG-ACAAAAAGAAAAG
*
57532 -AAA--AGACAAAAAGAAAAAA
1 AAAATTAGACAAAAAG-AAAAG
*
57551 AAAATTCAGAAAAAAAGAAAAG
1 AAAATT-AGACAAAAAGAAAAG
57573 AAAA
1 AAAA
57577 ATAAGAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
18 8 0.22
19 6 0.16
20 3 0.08
22 11 0.30
23 9 0.24
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.07
Consensus pattern (21 bp):
AAAATTAGACAAAAAGAAAAG
Found at i:57543 original size:13 final size:12
Alignment explanation
Indices: 57521--57597 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 12
57511 AATTGAGTAC
57521 AAAAAGAAAAGA
1 AAAAAGAAAAGA
57533 AAAGACA-AAAAGA
1 AAA-A-AGAAAAGA
*
57546 AAAAAAAAATTCAGAA
1 AAAAAGAAA---AG-A
57562 AAAAAGAAAAGAA
1 AAAAAGAAAAG-A
57575 AAATAAGAAAAGTA
1 AAA-AAGAAAAG-A
57589 AAAAAGAAA
1 AAAAAGAAA
57598 GCAAGCCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
11 1 0.02
12 7 0.13
13 23 0.42
14 13 0.24
15 2 0.04
16 9 0.16
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:58790 original size:18 final size:18
Alignment explanation
Indices: 58769--58824 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
58759 AAAATTGAGT
58769 ACAAAAAGAAAAAAAAAG
1 ACAAAAAGAAAAAAAAAG
58787 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAA--AG
*
58807 AAAAAAAGAAAAGAAAAA
1 ACAAAAAGAAAA-AAAAA
58825 TAAGAAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 16 0.47
19 1 0.03
20 13 0.38
21 4 0.12
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (18 bp):
ACAAAAAGAAAAAAAAAG
Found at i:58800 original size:20 final size:20
Alignment explanation
Indices: 58769--58829 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
58759 AAAATTGAGT
58769 ACAAAAAG--AAAAAAAAAG
1 ACAAAAAGAAAAAAAAAAAG
**
58787 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAAAAAG
*
58807 AAAAAAAGAAAAGAAAAATAAG
1 ACAAAAAGAAAA-AAAAA-AAG
58829 A
1 A
58830 AAAGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.24
20 19 0.56
21 4 0.12
22 3 0.09
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.03
Consensus pattern (20 bp):
ACAAAAAGAAAAAAAAAAAG
Found at i:58823 original size:22 final size:20
Alignment explanation
Indices: 58771--58832 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 20
58761 AATTGAGTAC
*
58771 AAAAAG-AAAAAAA-AAGAC
1 AAAAAGAAAAAAAATAAGAA
*
58789 AAAAAGAAAAAAAATCAGAA
1 AAAAAGAAAAAAAATAAGAA
58809 AAAAAGAAAAGAAAAATAAGAA
1 AAAAAG-AAA-AAAAATAAGAA
58831 AA
1 AA
58833 GTAAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 6 0.16
19 7 0.19
20 9 0.24
21 3 0.08
22 12 0.32
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAAAATAAGAA
Found at i:58832 original size:20 final size:19
Alignment explanation
Indices: 58771--58832 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 19
58761 AATTGAGTAC
* *
58771 AAAAAGAAAAAAAAA-GAC
1 AAAAAGAAAAAAAAATAAA
58789 AAAAAG-AAAAAAAATCAGAA
1 AAAAAGAAAAAAAAAT-A-AA
58809 AAAAAGAAAAGAAAAATAAGA
1 AAAAAGAAAA-AAAAATAA-A
58830 AAA
1 AAA
58833 GTAAAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 8 0.22
18 6 0.17
20 8 0.22
21 8 0.22
22 6 0.17
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATAAA
Found at i:60053 original size:14 final size:13
Alignment explanation
Indices: 60034--60073 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
60024 AAAAAAATTC
60034 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
60047 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
60061 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
60074 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:61284 original size:14 final size:13
Alignment explanation
Indices: 61265--61304 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
61255 AAAAAAATTC
61265 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
61278 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
61292 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
61305 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:62493 original size:22 final size:22
Alignment explanation
Indices: 62480--62524 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
62470 AATTGAGTAC
62480 AAAAAGAAAA-AAAATTCAGAA
1 AAAAAGAAAAGAAAATTCAGAA
* *
62501 AAAAAGAAAAGAAAAATAAGAA
1 AAAAAGAAAAGAAAATTCAGAA
62523 AA
1 AA
62525 GTAAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (22 bp):
AAAAAGAAAAGAAAATTCAGAA
Found at i:62516 original size:14 final size:13
Alignment explanation
Indices: 62497--62536 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
62487 AAAAAAATTC
62497 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
62510 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
62524 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
62537 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:63728 original size:9 final size:9
Alignment explanation
Indices: 63714--63785 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
63704 AATTGAGTAC
63714 AAAAAGAAA
1 AAAAAGAAA
*
63723 AAAAAG-AC
1 AAAAAGAAA
63731 AAAAAGAAA
1 AAAAAGAAA
* *
63740 AAAAATCAGA
1 AAAAA-GAAA
63750 AAAAAGAAA
1 AAAAAGAAA
63759 AGAAAA-ATAA
1 A-AAAAGA-AA
* *
63769 GAAAAG-TA
1 AAAAAGAAA
63777 AAAAAGAAA
1 AAAAAGAAA
63786 GCAAGCCAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
8 13 0.28
9 21 0.45
10 13 0.28
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:63734 original size:17 final size:17
Alignment explanation
Indices: 63712--63744 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
63702 AAAATTGAGT
63712 ACAAAAAGAAAAAAAAG
1 ACAAAAAGAAAAAAAAG
63729 ACAAAAAGAAAAAAAA
1 ACAAAAAGAAAAAAAA
63745 TCAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAAAAAAG
Found at i:63742 original size:19 final size:19
Alignment explanation
Indices: 63712--63765 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
63702 AAAATTGAGT
63712 ACAAAAAG--AAAAAAAAG
1 ACAAAAAGAAAAAAAAAAG
*
63729 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAA-AAG
63749 A-AAAAAGAAAAGAAAAA
1 ACAAAAAGAAAA-AAAAA
63766 TAAGAAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 8 0.26
19 16 0.52
20 7 0.23
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (19 bp):
ACAAAAAGAAAAAAAAAAG
Found at i:63770 original size:14 final size:13
Alignment explanation
Indices: 63714--63785 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
63704 AATTGAGTAC
63714 AAAAAGAAAA-AA
1 AAAAAGAAAAGAA
*
63726 AAGACA-AAAAGAA
1 AA-AAAGAAAAGAA
**
63739 AAAAA-ATCAG-A
1 AAAAAGAAAAGAA
63750 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
63763 AAATAAGAAAAGTA
1 AAA-AAGAAAAGAA
63777 AAAAAGAAA
1 AAAAAGAAA
63786 GCAAGCCAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
11 6 0.12
12 14 0.29
13 16 0.33
14 12 0.25
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:63773 original size:19 final size:19
Alignment explanation
Indices: 63715--63779 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 19
63705 ATTGAGTACA
*
63715 AAAAGAAAAAAAAGACAAA-
1 AAAAGAAAAATAAGA-AAAG
* *
63734 AAGAAAAAAAATCAGAAAAAAG
1 AA-AAGAAAAAT-A-AGAAAAG
63756 AAAAGAAAAATAAGAAAAG
1 AAAAGAAAAATAAGAAAAG
63775 TAAAA
1 -AAAA
63780 AAGAAAGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 8 0.22
20 12 0.33
21 12 0.33
22 4 0.11
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (19 bp):
AAAAGAAAAATAAGAAAAG
Found at i:64996 original size:14 final size:13
Alignment explanation
Indices: 64977--65016 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
64967 AAAAAAATTC
64977 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
64990 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
65004 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
65017 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:66227 original size:14 final size:13
Alignment explanation
Indices: 66208--66247 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
66198 AAAAAAATTC
66208 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
66221 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
66235 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
66248 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:67441 original size:18 final size:18
Alignment explanation
Indices: 67420--67475 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
67410 AAAATTGAGT
67420 ACAAAAAGAAAAAAAAAG
1 ACAAAAAGAAAAAAAAAG
67438 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAA--AG
*
67458 AAAAAAAGAAAAGAAAAA
1 ACAAAAAGAAAA-AAAAA
67476 TAAGAAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 16 0.47
19 1 0.03
20 13 0.38
21 4 0.12
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (18 bp):
ACAAAAAGAAAAAAAAAG
Found at i:67451 original size:20 final size:20
Alignment explanation
Indices: 67420--67480 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
67410 AAAATTGAGT
67420 ACAAAAAG--AAAAAAAAAG
1 ACAAAAAGAAAAAAAAAAAG
**
67438 ACAAAAAGAAAAAAAATCAG
1 ACAAAAAGAAAAAAAAAAAG
*
67458 AAAAAAAGAAAAGAAAAATAAG
1 ACAAAAAGAAAA-AAAAA-AAG
67480 A
1 A
67481 AAAGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.24
20 19 0.56
21 4 0.12
22 3 0.09
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.03
Consensus pattern (20 bp):
ACAAAAAGAAAAAAAAAAAG
Found at i:67474 original size:22 final size:20
Alignment explanation
Indices: 67422--67483 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 20
67412 AATTGAGTAC
*
67422 AAAAAG-AAAAAAA-AAGAC
1 AAAAAGAAAAAAAATAAGAA
*
67440 AAAAAGAAAAAAAATCAGAA
1 AAAAAGAAAAAAAATAAGAA
67460 AAAAAGAAAAGAAAAATAAGAA
1 AAAAAG-AAA-AAAAATAAGAA
67482 AA
1 AA
67484 GTAAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 6 0.16
19 7 0.19
20 9 0.24
21 3 0.08
22 12 0.32
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAAAATAAGAA
Found at i:67483 original size:20 final size:19
Alignment explanation
Indices: 67422--67483 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 19
67412 AATTGAGTAC
* *
67422 AAAAAGAAAAAAAAA-GAC
1 AAAAAGAAAAAAAAATAAA
67440 AAAAAG-AAAAAAAATCAGAA
1 AAAAAGAAAAAAAAAT-A-AA
67460 AAAAAGAAAAGAAAAATAAGA
1 AAAAAGAAAA-AAAAATAA-A
67481 AAA
1 AAA
67484 GTAAAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 8 0.22
18 6 0.17
20 8 0.22
21 8 0.22
22 6 0.17
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATAAA
Found at i:68704 original size:14 final size:13
Alignment explanation
Indices: 68685--68724 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
68675 AAAAAAATTC
68685 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
68698 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
68712 AGTAAAAAAGAAA
1 AGAAAAAAAGAAA
68725 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:69117 original size:19 final size:19
Alignment explanation
Indices: 69095--69173 Score: 88
Period size: 19 Copynumber: 4.0 Consensus size: 19
69085 AAAATTGAGT
69095 ACAAAAAGAAAAAAAAAAG
1 ACAAAAAGAAAAAAAAAAG
69114 ACAAAAAGAAAAAAAAATCAG
1 ACAAAAAGAAAAAAAAA--AG
* * *
69135 AAAAAAAGAAAAGAAAAAT
1 ACAAAAAGAAAAAAAAAAG
69154 A-AGAAAAGAAAAAAAGAAAG
1 ACA-AAAAGAAAAAAA-AAAG
69174 TAATTCAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.02
19 30 0.59
20 3 0.06
21 17 0.33
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.03
Consensus pattern (19 bp):
ACAAAAAGAAAAAAAAAAG
Found at i:69119 original size:13 final size:13
Alignment explanation
Indices: 69097--69172 Score: 84
Period size: 13 Copynumber: 5.7 Consensus size: 13
69087 AATTGAGTAC
69097 AAAAAGAAAA-AA
1 AAAAAGAAAAGAA
*
69109 AAAAGACAAAAAGAA
1 AAAA-A-GAAAAGAA
*
69124 AAAAA-AATCAGAA
1 AAAAAGAA-AAGAA
69137 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
69150 AAATAAGAAAAGAA
1 AAA-AAGAAAAGAA
69164 AAAAAGAAA
1 AAAAAGAAA
69173 GTAATTCAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
12 6 0.11
13 23 0.42
14 20 0.36
15 6 0.11
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:70362 original size:9 final size:9
Alignment explanation
Indices: 70344--70414 Score: 67
Period size: 9 Copynumber: 8.0 Consensus size: 9
70334 AATTGAGTAC
70344 AAAAAGAAA
1 AAAAAGAAA
*
70353 AAAAACAAA
1 AAAAAGAAA
70362 AAGAAA-AAA
1 AA-AAAGAAA
*
70371 AAATTAGAAA
1 AAA-AAGAAA
70381 AAAAAGAAA
1 AAAAAGAAA
70390 AAAAA-AAA
1 AAAAAGAAA
* *
70398 GAAAAG-TA
1 AAAAAGAAA
70406 AAAAAGAAA
1 AAAAAGAAA
70415 GCAAGCCAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
8 14 0.28
9 27 0.54
10 9 0.18
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:70362 original size:15 final size:15
Alignment explanation
Indices: 70342--70397 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 15
70332 AAAATTGAGT
70342 ACAAAAAGAAAAAAA
1 ACAAAAAGAAAAAAA
70357 ACAAAAAG-AAAAAA
1 ACAAAAAGAAAAAAA
**
70371 A-AATTAGAAAAAAA
1 ACAAAAAGAAAAAAA
*
70385 AGAAAAA-AAAAAA
1 ACAAAAAGAAAAAA
70398 GAAAAGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.11
14 20 0.57
15 11 0.31
ACGTcount: A:0.86, C:0.04, G:0.07, T:0.04
Consensus pattern (15 bp):
ACAAAAAGAAAAAAA
Found at i:70411 original size:13 final size:12
Alignment explanation
Indices: 70344--70414 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
70334 AATTGAGTAC
70344 AAAAAGAAAAAA
1 AAAAAGAAAAAA
70356 AACAAA-AAGAAAA
1 AA-AAAGAA-AAAA
** *
70369 AAAAATTAGAAA
1 AAAAAGAAAAAA
70381 AAAAAGAAAAAA
1 AAAAAGAAAAAA
*
70393 AAAAAGAAAAGTA
1 AAAAAGAAAA-AA
70406 AAAAAGAAA
1 AAAAAGAAA
70415 GCAAGCCAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
12 29 0.59
13 20 0.41
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAA
Done.