Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008751.1 Hibiscus syriacus cultivar Beakdansim tig00111842_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: 806611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:3992 original size:18 final size:18
Alignment explanation
Indices: 3959--3993 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3949 GCCTTTATTC
**
3959 ATTTAATCTCTTTTTACT
1 ATTTAATCTCAATTTACT
3977 ATTTAATCTCAATTTAC
1 ATTTAATCTCAATTTAC
3994 CAAAACCCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATCTCAATTTACT
Found at i:7766 original size:13 final size:13
Alignment explanation
Indices: 7748--7781 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
7738 TAGGATTTTC
*
7748 TTTGAAAATAGAT
1 TTTGAAAATAAAT
7761 TTTG-AAATAAAT
1 TTTGAAAATAAAT
7773 TTTGAAAAT
1 TTTGAAAAT
7782 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAAAT
Found at i:10099 original size:21 final size:22
Alignment explanation
Indices: 10044--10119 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
10034 TACAGCAGTG
10044 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* * *
10067 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
10088 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
10111 TGCATCGAT
1 TGCATCGAT
10120 ACACTGTCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.35
22 2 0.05
23 26 0.60
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:13835 original size:20 final size:21
Alignment explanation
Indices: 13796--13835 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13786 AGAAGTTTAA
* *
13796 GATCATCTATTTTCTTTTGAT
1 GATCATCTATTTACTCTTGAT
13817 GATCATC-ATTTACTCTTGA
1 GATCATCTATTTACTCTTGA
13836 AAGTAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (21 bp):
GATCATCTATTTACTCTTGAT
Found at i:13987 original size:22 final size:21
Alignment explanation
Indices: 13945--13984 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13935 AAGACTATTT
13945 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
13966 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
13985 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:26856 original size:20 final size:21
Alignment explanation
Indices: 26831--26882 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
26821 TTTTCCCAAT
*
26831 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
26851 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
26872 TCGCAATGCGA
1 TCGCAATGCGA
26883 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:26895 original size:41 final size:41
Alignment explanation
Indices: 26850--26945 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
26840 GAATAAGTAA
* * *
26850 ATCGCAACGCGA-ATTGGAAAA-ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT--AAAATATCGCAACGAGATACTGACT
* *
26891 ATCGCAATGCGATAATAAAATATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAATAAAATATCGCAACGAGATACTGACT
*
26932 TTCGCAACGCGATA
1 ATCGCAACGCGATA
26946 CTGACTTTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.09
41 40 0.87
42 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATAATAAAATATCGCAACGAGATACTGACT
Found at i:26896 original size:20 final size:20
Alignment explanation
Indices: 26871--26965 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
26861 AATTGGAAAA
*
26871 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
26891 ATCGCAATGCGATAATAAAAT
1 ATCGCAACGCGATACT-GACT
* *
26912 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
26932 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
26952 TTCGCAACGCGATA
1 ATCGCAACGCGATA
26966 ATACATAATC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 48 0.76
21 15 0.24
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:27183 original size:22 final size:22
Alignment explanation
Indices: 27155--27198 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27145 CACTCTCTCA
27155 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
27177 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
27199 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:27489 original size:20 final size:20
Alignment explanation
Indices: 27464--27501 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27454 CGATTCTCTC
27464 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
27484 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
27502 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:28840 original size:18 final size:18
Alignment explanation
Indices: 28819--28863 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28809 TCCACTTCGG
*
28819 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
28837 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
28855 GAGCCATCA
1 GAGCCATCA
28864 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:29390 original size:19 final size:20
Alignment explanation
Indices: 29336--29402 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
29326 TAGTTTACTT
* *
29336 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
29356 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
29376 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
29395 TCGCAACG
1 TCGCAACG
29403 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:29398 original size:39 final size:34
Alignment explanation
Indices: 29355--29442 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 34
29345 GAAAATGACT
29355 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAATG-AA
29394 ATCGCAACGAC-AAA--ATCGCAATGCGAAATGAA
1 ATCGCAACG-CGAAATGATCGCAATGCGAAATGAA
29426 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
29443 AAATCGCAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
31 1 0.02
32 14 0.31
33 16 0.36
34 1 0.02
38 3 0.07
39 9 0.20
40 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAATGAA
Found at i:29448 original size:19 final size:19
Alignment explanation
Indices: 29336--29455 Score: 99
Period size: 19 Copynumber: 6.5 Consensus size: 19
29326 TAGTTTACTT
* **
29336 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
29356 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
29376 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29395 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
29409 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
29427 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
29446 TCGCAACGCG
1 TCGCAACGCG
29456 GAAACAGTGA
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 26 0.31
20 24 0.29
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:31042 original size:33 final size:33
Alignment explanation
Indices: 31000--31126 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
30990 GGAAATTACT
*
31000 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
31033 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
31065 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
31099 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
31127 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:31083 original size:66 final size:66
Alignment explanation
Indices: 31001--31133 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
30991 GAAATTACTA
*
31001 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
31066 T
66 T
* *
31067 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
31132 T
66 T
31133 T
1 T
31134 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:31148 original size:19 final size:20
Alignment explanation
Indices: 31126--31168 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31116 AAATCGCAAC
31126 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
31145 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
31165 GCGA
1 GCGA
31169 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:31327 original size:14 final size:14
Alignment explanation
Indices: 31308--31344 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31298 CATCAATTAA
31308 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31322 ACAAATCACCTTTT
1 ACAAATCAACTTTT
31336 ACAAATCAA
1 ACAAATCAA
31345 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:32765 original size:21 final size:21
Alignment explanation
Indices: 32699--32765 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32689 GTGAATCGGG
*
32699 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
32719 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
32741 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
32762 CTCT
1 CTCT
32766 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:32784 original size:42 final size:41
Alignment explanation
Indices: 32699--32821 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
32689 GTGAATCGGG
* * * * *
32699 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
32741 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
32783 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
32822 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:34889 original size:33 final size:33
Alignment explanation
Indices: 34836--34930 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
34826 GATAATGAGG
* *
34836 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGC-GAAATGACTATCGCAACCAGACA
*
34870 ATCGCAACGCGAAATGACTATCGCGACCAGACA
1 ATCGCAACGCGAAATGACTATCGCAACCAGACA
**
34903 ATCGCAACGCGAAATGAAAATCGCAACC
1 ATCGCAACGCGAAATGACTATCGCAACC
34931 GCGAAATAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 45 0.82
34 10 0.18
ACGTcount: A:0.39, C:0.27, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGACTATCGCAACCAGACA
Found at i:34935 original size:20 final size:19
Alignment explanation
Indices: 34807--34972 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
34797 TCTTTTGGTT
*
34807 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
34826 GATAATGAGGATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
34846 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
34864 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
34880 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
34898 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
34913 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
34933 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
34952 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
34971 GA
1 GA
34973 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 44 0.37
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:34990 original size:19 final size:19
Alignment explanation
Indices: 34968--35015 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
34958 AAAATCGCAA
*
34968 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
34987 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
35007 TGCGATTTT
1 TGCGATTTT
35016 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:35616 original size:20 final size:20
Alignment explanation
Indices: 35531--35624 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
35521 CGCTATGTAA
* *
35531 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
* *
35551 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
35571 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
35592 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
35612 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
35625 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:35642 original size:21 final size:21
Alignment explanation
Indices: 35613--35705 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
35603 ATAGTAAGTA
35613 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
35634 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
35654 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
35675 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
35695 TCGCATTGCGA
1 TCGCATTGCGA
35706 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:35643 original size:41 final size:41
Alignment explanation
Indices: 35556--35686 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
35546 TCAGTATCGT
* * * ** *
35556 GTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATTATCGC
1 GTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT-TCGC
*
35597 ATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTCGC
1 GTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTCGC
* **
35638 GTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAATTCGC
1 GTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAATTCGC
35679 GTTGCGAT
1 GTTGCGAT
35687 TTACTTATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 71 0.92
42 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
GTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTCGC
Found at i:35687 original size:41 final size:41
Alignment explanation
Indices: 35613--35705 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
35603 ATAGTAAGTA
35613 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
35654 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
35695 TCGCATTGCGA
1 TCGCATTGCGA
35706 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:35848 original size:19 final size:19
Alignment explanation
Indices: 35804--35850 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
35794 GGAGATCGTG
*
35804 TTGCGAATTAGCGATCGCA
1 TTGCGATTTAGCGATCGCA
35823 TTGCGATTTAGCGATCGCA
1 TTGCGATTTAGCGATCGCA
35842 TTGCGATTT
1 TTGCGATTT
35851 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (19 bp):
TTGCGATTTAGCGATCGCA
Found at i:37358 original size:33 final size:33
Alignment explanation
Indices: 37314--37421 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 33
37304 TCATCACCAC
* *
37314 CATCATCATGACCATGACCATGAGGAAGATCAT
1 CATCACCATGACCATGACCAAGAGGAAGATCAT
* * ** *
37347 CATGACCATGACAATGAGGAAGAGGACGATCAT
1 CATCACCATGACCATGACCAAGAGGAAGATCAT
** * *
37380 CATCACCATGACCATGAGGAACAGGACGATCAT
1 CATCACCATGACCATGACCAAGAGGAAGATCAT
*
37413 CTTCACCAT
1 CATCACCAT
37422 AAGGAGGGAG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (33 bp):
CATCACCATGACCATGACCAAGAGGAAGATCAT
Found at i:37399 original size:27 final size:27
Alignment explanation
Indices: 37315--37369 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
37305 CATCACCACC
37315 ATCATCATGACCATGACCATGAGGAAG
1 ATCATCATGACCATGACCATGAGGAAG
*
37342 ATCATCATGACCATGACAATGAGGAAG
1 ATCATCATGACCATGACCATGAGGAAG
37369 A
1 A
37370 GGACGATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (27 bp):
ATCATCATGACCATGACCATGAGGAAG
Found at i:39609 original size:50 final size:51
Alignment explanation
Indices: 39508--39610 Score: 181
Period size: 50 Copynumber: 2.0 Consensus size: 51
39498 TTAATCAACA
*
39508 AACGATTAACATTCCAAATAGAAGATTTTTTTTCTTTAAAATAAAATGTTG
1 AACGATTAACATTCCAAATAGAAGATTTTTTTTCTTTAAAATAAAAAGTTG
*
39559 AACGATTAACATTTCAAATAGAAGA-TTTTTTTCTTTAAAATAAAAAGTTG
1 AACGATTAACATTCCAAATAGAAGATTTTTTTTCTTTAAAATAAAAAGTTG
39609 AA
1 AA
39611 AGTCAAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 26 0.52
51 24 0.48
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (51 bp):
AACGATTAACATTCCAAATAGAAGATTTTTTTTCTTTAAAATAAAAAGTTG
Found at i:45841 original size:6 final size:6
Alignment explanation
Indices: 45830--45889 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
45820 CACTTTTAAT
45830 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC
45878 TTCATC TTCATC
1 TTCATC TTCATC
45890 CCCTACTCTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCATC
Found at i:46887 original size:226 final size:226
Alignment explanation
Indices: 46489--46948 Score: 634
Period size: 226 Copynumber: 2.0 Consensus size: 226
46479 AACATAACTA
* * * *
46489 GTTAATTACTGAAAATATTATCAATCATAATAACATAACATGTAGCGCTTATGTAACGTAATATG
1 GTTAATTACTGAAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATGTAACGTAATAGG
* * * *
46554 TAGCACATTTTTAAAGATGATGGGGCCTTAGAAATCCGACGATAACAAAATATGTTAATTACTTC
66 TAGCACATTTTTAAAGATGATGGAGCCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTTA
* * * * *
46619 ATTTTTTATCAATATTATCAACAAATTATGTAGCGTCTAAAATATTACCAAAGTTTAAGCTGATT
131 AATTGTTATCAATATTATCAACAAATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGATG
*
46684 GAGCCTTAGAAATCTGACGATAACAAAATAG
196 GAGCCTTAGAAATCCGACGATAACAAAATAG
* * * * *
46715 GTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGTGTTTATTTAATGTAATAGG
1 GTTAATTACTGAAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATGTAACGTAATAGG
* * *
46780 TAGCGCCTTTTTAAAGCA-GATGGAGCTTTAAAAATCCGACGATAACAAAATAGGTTAATTACTT
66 TAGCACATTTTTAAAG-ATGATGGAGCCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTT
* * * * *
46844 AAATTGTTATTAATATTATCAACATATTAGGTAGCGCCTAAAATATTATCAAATTTTAAGTTGAT
130 AAATTGTTATCAATATTATCAACAAATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGAT
* * *
46909 GGGGCCTTAGAAGTCCGACGATAACAAAATAT
195 GGAGCCTTAGAAATCCGACGATAACAAAATAG
46941 GTTAATTA
1 GTTAATTA
46949 TTTATTTTGT
Statistics
Matches: 203, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
226 202 1.00
227 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (226 bp):
GTTAATTACTGAAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATGTAACGTAATAGG
TAGCACATTTTTAAAGATGATGGAGCCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTTA
AATTGTTATCAATATTATCAACAAATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGATG
GAGCCTTAGAAATCCGACGATAACAAAATAG
Found at i:46989 original size:108 final size:108
Alignment explanation
Indices: 46811--47095 Score: 374
Period size: 108 Copynumber: 2.6 Consensus size: 108
46801 GGAGCTTTAA
* * **
46811 AAATCCGACGATAACAAAATAGGTTAATTACTTAAATTGTTATTAATATTATCAACATATTAGGT
1 AAATCCGACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATTATCAACATATTAGGT
* * * * *
46876 AGCGCCTAAAATATTATCAAATTTTAAGTTGATGGGGCCTTAG
66 TGCGCCTAAAATATTAACAAAGTTTAAGTTAATAGGGCCTTAG
*
46919 AAGTCCGACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATTATCAACATATTAGGT
1 AAATCCGACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATTATCAACATATTAGGT
* *
46984 TGCGCCTAAAATGTTAACAAAGTTTAAGTTAATAGGGCCTTCG
66 TGCGCCTAAAATATTAACAAAGTTTAAGTTAATAGGGCCTTAG
* * * * * * *
47027 AAAACCCACGACAACAAAATATGTTAATT-TATTATTTTGTTATAAATAAATATTAACATACTAG
1 AAATCCGACGATAACAAAATATGTTAATTAT-TTATTTTGTTATTAAT-ATTATCAACATATTAG
47091 GTTGC
64 GTTGC
47096 ACCCAATAAT
Statistics
Matches: 155, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 1 0.01
108 136 0.88
109 18 0.12
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (108 bp):
AAATCCGACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATTATCAACATATTAGGT
TGCGCCTAAAATATTAACAAAGTTTAAGTTAATAGGGCCTTAG
Found at i:47354 original size:38 final size:38
Alignment explanation
Indices: 47293--47366 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
47283 TACATTATCA
* *
47293 TTAACCTTTAGAGTATCCGTACTTTTAGAGTAAATAAC
1 TTAACCTTTAGAATATCCATACTTTTAGAGTAAATAAC
*
47331 TTAACCTTTAGAATATTCATACTTTTAGAGTAAATA
1 TTAACCTTTAGAATATCCATACTTTTAGAGTAAATA
47367 TCCATATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (38 bp):
TTAACCTTTAGAATATCCATACTTTTAGAGTAAATAAC
Found at i:47698 original size:75 final size:75
Alignment explanation
Indices: 47567--47709 Score: 173
Period size: 75 Copynumber: 1.9 Consensus size: 75
47557 ATTGTATATA
* * *
47567 TTTACCGTTTACATTATTAGTAAACTTTAAACAAACAGTTAGGCATTTTGACGTAATAGATAGCG
1 TTTACCGTTTACATTATTAGTAAACTTTAAACAAACAGTTAGACAATTTAACGTAATAGATAGCG
47632 CCTATTTTAT
66 CCTATTTTAT
* * * * *
47642 TTTACTGTTTACATTATTATTAACAC-TTAAACAAACCAG-TAGATAATTTAATGTAATAGGTAG
1 TTTACCGTTTACATTATTAGTAA-ACTTTAAACAAA-CAGTTAGACAATTTAACGTAATAGATAG
*
47705 TGCCT
64 CGCCT
47710 GTTTAACATA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 52 0.91
76 5 0.09
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (75 bp):
TTTACCGTTTACATTATTAGTAAACTTTAAACAAACAGTTAGACAATTTAACGTAATAGATAGCG
CCTATTTTAT
Found at i:47810 original size:75 final size:75
Alignment explanation
Indices: 47710--47893 Score: 271
Period size: 75 Copynumber: 2.5 Consensus size: 75
47700 GGTAGTGCCT
*
47710 GTTTAACATAATAGGTAGTGTCTATTTTATTTTACCGTTTACATTATTAGTAACCTTT-AAACAA
1 GTTTAACATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAA-CTTTCAAACAA
47774 ACCGATAGGTA
65 ACCGATAGGTA
* * * *
47785 TTTTAACGTAACAGGTAATGCCTATTTTATTTTACCGTTTACATTATTAGTAACTTTCAAACAAA
1 GTTTAACATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAACTTTCAAACAAA
*
47850 CCGGTAGGTA
66 CCGATAGGTA
* **
47860 GTTTAATATAATAGGTAGCACCTATTTTATTTTA
1 GTTTAACATAATAGGTAGTGCCTATTTTATTTTA
47894 ACAGGATAAG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 4 0.04
75 91 0.96
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (75 bp):
GTTTAACATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAACTTTCAAACAAA
CCGATAGGTA
Found at i:54187 original size:30 final size:30
Alignment explanation
Indices: 54145--54203 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
54135 TAAACCCATT
*
54145 AAAATTTTGCTCGATTCA-TGCTAGTTAAA
1 AAAATTTTGCTCGACTCATTGCTAGTTAAA
*
54174 AAAATTGTTGCTCGACTCATTGCTCGTTAA
1 AAAATT-TTGCTCGACTCATTGCTAGTTAA
54204 GCTTGTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 11 0.42
31 9 0.35
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (30 bp):
AAAATTTTGCTCGACTCATTGCTAGTTAAA
Found at i:55255 original size:20 final size:20
Alignment explanation
Indices: 55208--55437 Score: 193
Period size: 20 Copynumber: 11.2 Consensus size: 20
55198 AATGACCAAT
55208 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
55227 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
55247 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
55267 AAGATCGCAACGTGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
55289 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
*
55309 AAAATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
55331 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
55351 AAAATCGCAACGCGATTCAT
1 AAAATCGCAACGCGATTCAG
55371 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
55393 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
55413 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
55433 AAAAT
1 AAAAT
55438 GAGTAAATTC
Statistics
Matches: 173, Mismatches: 22, Indels: 31
0.77 0.10 0.14
Matches are distributed among these distances:
18 1 0.01
19 24 0.14
20 99 0.57
21 2 0.01
22 42 0.24
23 5 0.03
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:55357 original size:62 final size:62
Alignment explanation
Indices: 55291--55437 Score: 267
Period size: 62 Copynumber: 2.4 Consensus size: 62
55281 ATCTTCCAAG
*
55291 AATCGCAATGCGATTCATAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCATAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATTCAGAA
*
55353 AATCGCAACGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCATAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATTCAGAA
*
55415 AATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTCATAAAAT
55438 GAGTAAATTC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (62 bp):
AATCGCAACGCGATTCATAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATTCAGAA
Found at i:55399 original size:42 final size:41
Alignment explanation
Indices: 55208--55437 Score: 174
Period size: 42 Copynumber: 5.6 Consensus size: 41
55198 AATGACCAAT
* * *
55208 AAAATCGCAACGCGATATC--AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTCAGAAAATCGCAACGCGATTCAG
* ** * *
55247 AAAATCGCAACGTTGA--AAAGAAGATCGCAACGTGATCTTCCA-
1 AAAATCGCAACG-CGATTTCAGAAAATCGCAACGCGA--TT-CAG
* * * *
55289 AGAATCGCAATGCGA-TTCATAAAATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGATTTCAGAAAATCGCAACGCGA--TT-CAG
* *
55331 AGAATCGCAACGCGA-TTCAGAAAATCGCAACGCGATTCAT
1 AAAATCGCAACGCGATTTCAGAAAATCGCAACGCGATTCAG
*
55371 AAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGAT-TT-CAGAAAATCGCAACGCGATTCAG
55413 AAAATCGCAACGCGA-TTCAGAAAAT
1 AAAATCGCAACGCGATTTCAGAAAAT
55438 GAGTAAATTC
Statistics
Matches: 156, Mismatches: 23, Indels: 23
0.77 0.11 0.11
Matches are distributed among these distances:
39 16 0.10
40 36 0.23
41 2 0.01
42 99 0.63
43 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTCAGAAAATCGCAACGCGATTCAG
Found at i:55595 original size:6 final size:6
Alignment explanation
Indices: 55533--55592 Score: 102
Period size: 6 Copynumber: 10.0 Consensus size: 6
55523 GACACGTATT
55533 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
55581 GCCACG GCCACG
1 ACCACG ACCACG
55593 GCCCGAGACG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.50, G:0.20, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:56147 original size:21 final size:21
Alignment explanation
Indices: 56121--56165 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
56111 CGTGGTCGTG
56121 GTCGTGGTCGTGGTAATACGT
1 GTCGTGGTCGTGGTAATACGT
56142 GTCGTGGTCGTGGTAATACGT
1 GTCGTGGTCGTGGTAATACGT
56163 GTC
1 GTC
56166 TTCGACACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.38, T:0.33
Consensus pattern (21 bp):
GTCGTGGTCGTGGTAATACGT
Found at i:56155 original size:6 final size:6
Alignment explanation
Indices: 56092--56134 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
56082 TCTCGTCTCG
56092 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
56135 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:56310 original size:40 final size:41
Alignment explanation
Indices: 56251--56376 Score: 159
Period size: 42 Copynumber: 3.1 Consensus size: 41
56241 GAATTTACTC
* *
56251 ATTTTCTGAATCGCATTGCGATTCTTGGA-ATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGGAGATCGCGTTGCG
*
56291 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGG-AGATCGCGTTGCG
* * * *
56333 CTTTTCTAAATCGCGTTGCGGTT-TT-CATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGGAGATCGCGTTGCG
56372 ATTTT
1 ATTTT
56377 GTTGGTCATT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 16 0.21
40 26 0.34
41 3 0.04
42 31 0.41
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (41 bp):
ATTTTCTAAATCGCGTTGCGATTCTTGGAGATCGCGTTGCG
Found at i:56347 original size:20 final size:20
Alignment explanation
Indices: 56251--56376 Score: 121
Period size: 20 Copynumber: 6.2 Consensus size: 20
56241 GAATTTACTC
* *
56251 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
56271 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
56291 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
56311 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
56333 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* *
56353 GTTTTC-ATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
56372 ATTTT
1 ATTTT
56377 GTTGGTCATT
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.20
20 49 0.55
21 9 0.10
22 13 0.15
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:57931 original size:18 final size:16
Alignment explanation
Indices: 57910--57940 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57900 CTTCTAATTT
57910 TTTTTTGAGTTCAAGC
1 TTTTTTGAGTTCAAGC
57926 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
57941 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:64438 original size:14 final size:14
Alignment explanation
Indices: 64421--64448 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64411 ATCATAACAA
64421 AATTATATAACTAT
1 AATTATATAACTAT
64435 AATTATATAACTAT
1 AATTATATAACTAT
64449 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:66324 original size:21 final size:21
Alignment explanation
Indices: 66298--66463 Score: 95
Period size: 21 Copynumber: 7.6 Consensus size: 21
66288 GATTTACATA
66298 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
66319 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* **
66340 TTCGCGTTGCGATTTTCCAAATTCG
1 TTCGCATTGCGATAGTCC-AA---G
* * * * *
66365 ACTATCGCAATGCGA-ACTTCGAC
1 --T-TCGCATTGCGATAGTCCAAG
* *
66388 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
66409 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* *
66430 TTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
66451 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
66464 TTTCCAAATT
Statistics
Matches: 114, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
20 13 0.11
21 84 0.74
22 3 0.03
25 1 0.01
26 1 0.01
27 3 0.03
28 9 0.08
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:66452 original size:111 final size:111
Alignment explanation
Indices: 66258--66663 Score: 706
Period size: 111 Copynumber: 3.7 Consensus size: 111
66248 GTTTCCAGAT
66258 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
66323 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
*
66369 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCG
1 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
66434 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
* *
66480 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCAATA-TCCAAGTTCG
1 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
* *
66544 CATTGCGATAGTTGAAGTTCGCTTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
* * * *
66590 TCGCAATACGAACTTCGACTATCGCAATGCGATTTACATATTTGCATTACGATAGTCCAAGTTCG
1 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
66655 CGTTGCGAT
66 CATTGCGAT
66664 TTTCCAAATT
Statistics
Matches: 279, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
110 100 0.36
111 179 0.64
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (111 bp):
TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
Found at i:66475 original size:21 final size:21
Alignment explanation
Indices: 66390--66475 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 21
66380 ACTTCGACTA
* * *
66390 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
* *
66410 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAT
* * *
66431 TCGCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAT
* **
66452 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATAGTCCAAAT
66473 TCG
1 TCG
66476 ACTATCGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 12 0.22
21 43 0.78
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:66563 original size:21 final size:20
Alignment explanation
Indices: 66501--66573 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
66491 ACTTCGACTA
* *
66501 TCGCATTGCGATTTACATA-T
1 TCGCATTGCGATATCCA-AGT
*
66521 TCGCATTGCAATATCCAAGT
1 TCGCATTGCGATATCCAAGT
**
66541 TCGCATTGCGATAGTTGAAGT
1 TCGCATTGCGATA-TCCAAGT
*
66562 TCGCTTTGCGAT
1 TCGCATTGCGAT
66574 TTTCCAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 16 0.36
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATATCCAAGT
Found at i:66654 original size:221 final size:222
Alignment explanation
Indices: 66258--66663 Score: 724
Period size: 221 Copynumber: 1.8 Consensus size: 222
66248 GTTTCCAGAT
* *
66258 TCGCAATGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCCAAGTTCG
*
66323 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTATCGCAATGCGAACTTCGAC
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTATCGCAATACGAACTTCGAC
* * *
66388 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTT
131 TATCGCAATGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTT
66453 CGCGTTGCGATTTTCCAAATTCGACTA
196 CGCGTTGCGATTTTCCAAATTCGACTA
66480 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCAATA-TCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCCAAGTTCG
* *
66544 CATTGCGATAGTTGAAGTTCGCTTTGCGATTTTCCAAATTCGACTATCGCAATACGAACTTCGAC
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTATCGCAATACGAACTTCGAC
*
66609 TATCGCAATGCGATTTACATATTTGCATTACGATAGTCCAAGTTCGCGTTGCGAT
131 TATCGCAATGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCGTTGCGAT
66664 TTTCCAAATT
Statistics
Matches: 175, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
221 123 0.70
222 52 0.30
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (222 bp):
TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCCAAGTTCG
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTATCGCAATACGAACTTCGAC
TATCGCAATGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTT
CGCGTTGCGATTTTCCAAATTCGACTA
Found at i:66669 original size:21 final size:21
Alignment explanation
Indices: 66645--66747 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
66635 ATTACGATAG
66645 TCCAAGTTCGCGTTGCGATTT
1 TCCAAGTTCGCGTTGCGATTT
* **
66666 TCCAAATT--CGTTGCGATAG
1 TCCAAGTTCGCGTTGCGATTT
* *
66685 TCGAAGTCCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGA-TT-T
* **
66708 TCCAAATT--CGTTGCGATAG
1 TCCAAGTTCGCGTTGCGATTT
*
66727 TCGAAGTTCGCGTTGCGATTT
1 TCCAAGTTCGCGTTGCGATTT
66748 ATTCCAAATT
Statistics
Matches: 59, Mismatches: 17, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
19 20 0.34
20 1 0.02
21 32 0.54
22 1 0.02
23 5 0.08
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (21 bp):
TCCAAGTTCGCGTTGCGATTT
Found at i:66724 original size:42 final size:42
Alignment explanation
Indices: 66639--66770 Score: 232
Period size: 42 Copynumber: 3.2 Consensus size: 42
66629 ATTTGCATTA
*
66639 CGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
*
66679 CGATAGTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
66721 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
66763 CGATAGTC
1 CGATAGTC
66771 CAAAATCGCA
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 22 0.25
41 2 0.02
42 63 0.72
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
Found at i:66761 original size:21 final size:21
Alignment explanation
Indices: 66695--66766 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
66685 TCGAAGTCCG
66695 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
66716 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
66735 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
66758 CGTTGCGAT
1 CGTTGCGAT
66767 AGTCCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 8 0.20
21 25 0.61
23 8 0.20
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:67511 original size:21 final size:21
Alignment explanation
Indices: 67485--67726 Score: 253
Period size: 21 Copynumber: 11.4 Consensus size: 21
67475 ATTTTGGACT
67485 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
67506 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
* *
67527 ATCGCAATGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
67548 ATCGCAACACGAATTTGGAATAA
1 ATCGC-A-ACGAATTTGGAATAA
67571 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
67592 ATTGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
67613 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
67634 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
67655 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
67676 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
67697 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTGGAATAA
67718 ATCGCAACG
1 ATCGCAACG
67727 CGAACTTCGA
Statistics
Matches: 188, Mismatches: 19, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
19 29 0.15
21 110 0.59
22 2 0.01
23 47 0.25
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:67651 original size:63 final size:63
Alignment explanation
Indices: 67527--67766 Score: 231
Period size: 63 Copynumber: 3.8 Consensus size: 63
67517 AACTTCGACT
* * * *
67527 ATCGCAA-TGAACTTGGAATAAATCGCAACACGAATTTGGAATAAATCGCAACGAATTTGGAATA
1 ATCGCAACCGAACTTGGAAT--ATCGCAACGCGAACTTCGAAT-AATCGCAACGAATTTGGAATA
67591 A
63 A
* * * *
67592 ATTGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAACGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAAT--ATCGCAACGCGAACTTCGAATAATCGCAACGAATTTGGAATAA
* * * *
67655 ATCGCAACGCGAACTTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGAATTTAGAATAA
1 ATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTCGAAT-AATCGCAACGAATTTGGAATAA
* * *
67718 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACT-ATCGCAA
1 ATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTCGAATAATCGCAA
67767 TGCGAATATG
Statistics
Matches: 149, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
61 9 0.06
63 86 0.58
65 54 0.36
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (63 bp):
ATCGCAACCGAACTTGGAATATCGCAACGCGAACTTCGAATAATCGCAACGAATTTGGAATAA
Found at i:67742 original size:21 final size:21
Alignment explanation
Indices: 67613--67772 Score: 134
Period size: 21 Copynumber: 7.6 Consensus size: 21
67603 TTTGGAATAA
67613 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
67634 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
67653 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
67676 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* * *
67695 AAATCGCAA--CGAATTTAGAAT
1 --ATCGCAACGCGAACTTCGACT
67716 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
67739 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
67760 ATCGCAATGCGAA
1 ATCGCAACGCGAA
67773 TATGTAAATC
Statistics
Matches: 121, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
19 20 0.17
21 81 0.67
23 20 0.17
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:67772 original size:42 final size:41
Alignment explanation
Indices: 67595--67766 Score: 188
Period size: 42 Copynumber: 4.1 Consensus size: 41
67585 GGAATAAATT
*
67595 GCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
1 GCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATC
*
67637 GCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATC
1 GCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATC
* * * *
67679 GCAACGAATTTGGAATAAATCGCAA--CGAATTTAGAATAAATC
1 GCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACT--ATC
* *
67721 GCAACGCGAACTTCGACT-ATCGCAACGCGAACTTCGACTATC
1 GCAA--CGAACTTGGAATAATCGCAACGCGAACTTCGACTATC
67763 GCAA
1 GCAA
67767 TGCGAATATG
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
40 9 0.08
42 85 0.76
44 18 0.16
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
GCAACGAACTTGGAATAATCGCAACGCGAACTTCGACTATC
Found at i:73718 original size:23 final size:23
Alignment explanation
Indices: 73692--73735 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
73682 AAGGAACGCG
73692 TAGAATTTGTC-CGAAGGACCATA
1 TAGAA-TTGTCTCGAAGGACCATA
73715 TAGAATTGTCTCGAAGGACCA
1 TAGAATTGTCTCGAAGGACCA
73736 AATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (23 bp):
TAGAATTGTCTCGAAGGACCATA
Found at i:74158 original size:15 final size:15
Alignment explanation
Indices: 74138--74182 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
74128 ATATAAAGCC
74138 CTCATATAAAATATA
1 CTCATATAAAATATA
*
74153 CTCATATAAAACACT-
1 CTCATATAAAATA-TA
*
74168 TTCATATAAAATATA
1 CTCATATAAAATATA
74183 ATAACATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCATATAAAATATA
Found at i:74160 original size:28 final size:30
Alignment explanation
Indices: 74108--74182 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
74098 TATCAATTTA
* *
74108 CTCATATAAAACATATTCGCATATAAAGC-C-
1 CTCATAT-AAA-ATATACGCATATAAAACACT
*
74138 CTCATATAAAATATACTCATATAAAACACT
1 CTCATATAAAATATACGCATATAAAACACT
*
74168 TTCATATAAAATATA
1 CTCATATAAAATATA
74183 ATAACATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 14 0.36
29 4 0.10
30 21 0.54
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.31
Consensus pattern (30 bp):
CTCATATAAAATATACGCATATAAAACACT
Found at i:79475 original size:24 final size:24
Alignment explanation
Indices: 79435--79489 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
79425 GAAGTGCCAA
* *
79435 GTAG-ATTTGTCCGAAAGAACCAT
1 GTAGAATTCGTCCGAAAGAACCAC
* *
79458 GTAGAATTCGTCCTAAAGGACCAC
1 GTAGAATTCGTCCGAAAGAACCAC
*
79482 ATAGAATT
1 GTAGAATT
79490 ATCCCGAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (24 bp):
GTAGAATTCGTCCGAAAGAACCAC
Found at i:79503 original size:23 final size:23
Alignment explanation
Indices: 79473--79579 Score: 160
Period size: 23 Copynumber: 4.7 Consensus size: 23
79463 ATTCGTCCTA
79473 AAGGACCACATAGAATTATCCCG
1 AAGGACCACATAGAATTATCCCG
*
79496 AAGGACCACATAGAATTGTCCCG
1 AAGGACCACATAGAATTATCCCG
* *
79519 AAGGACTACATAGAATTGTCCCG
1 AAGGACCACATAGAATTATCCCG
* *
79542 AAGGACCACTTAGATTTATCCCG
1 AAGGACCACATAGAATTATCCCG
*
79565 AATGACCACATAGAA
1 AAGGACCACATAGAA
79580 CCCACAACTC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (23 bp):
AAGGACCACATAGAATTATCCCG
Found at i:79530 original size:46 final size:46
Alignment explanation
Indices: 79459--79579 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 46
79449 AAGAACCATG
**
79459 TAGAATTCGTCCTAAAGGACCACATAGAATTATCCCGAAGGACCACA
1 TAGAATT-GTCCCGAAGGACCACATAGAATTATCCCGAAGGACCACA
* * *
79506 TAGAATTGTCCCGAAGGACTACATAGAATTGTCCCGAAGGACCACT
1 TAGAATTGTCCCGAAGGACCACATAGAATTATCCCGAAGGACCACA
* * *
79552 TAGATTTATCCCGAATGACCACATAGAA
1 TAGAATTGTCCCGAAGGACCACATAGAA
79580 CCCACAACTC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 58 0.89
47 7 0.11
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (46 bp):
TAGAATTGTCCCGAAGGACCACATAGAATTATCCCGAAGGACCACA
Found at i:79793 original size:15 final size:15
Alignment explanation
Indices: 79712--79793 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
79702 ATAATGTATC
79712 TTCACGTAGAATC-TT
1 TTCACGTAGAA-CATT
* *
79727 TTCACTTAGCACATT
1 TTCACGTAGAACATT
** *
79742 TTCATATACAACATT
1 TTCACGTAGAACATT
*
79757 TTCATGTAGAACATTT
1 TTCACGTAGAACA-TT
*
79773 TTCACGTAGAACAGT
1 TTCACGTAGAACATT
79788 TTCACG
1 TTCACG
79794 AAACATTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
14 1 0.02
15 40 0.73
16 14 0.25
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (15 bp):
TTCACGTAGAACATT
Found at i:82041 original size:21 final size:20
Alignment explanation
Indices: 82015--82067 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
82005 ATTGGGGCAT
* *
82015 GGGTATCGATACTGGTTTAAA
1 GGGTATCGATACT-GCTGAAA
**
82036 GGGTATAAATACTGCTGAAA
1 GGGTATCGATACTGCTGAAA
*
82056 GAGTATCGATAC
1 GGGTATCGATAC
82068 CATAAGGCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (20 bp):
GGGTATCGATACTGCTGAAA
Found at i:82970 original size:22 final size:22
Alignment explanation
Indices: 82942--83003 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
82932 AGTCGAGGGT
*
82942 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCATTCGGGACATA
82964 TACATAGGTCATTCGGGACATA
1 TACATAGGTCATTCGGGACATA
82986 TACATAGGTCATTCGGGA
1 TACATAGGTCATTCGGGA
83004 TAAATTTCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (22 bp):
TACATAGGTCATTCGGGACATA
Found at i:83690 original size:16 final size:17
Alignment explanation
Indices: 83663--83696 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
83653 TTCTTCATTC
83663 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
83680 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
83696 T
1 T
83697 GACACATCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:84842 original size:38 final size:38
Alignment explanation
Indices: 84800--84881 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
84790 AAAATTTACT
*
84800 AAATAATAAAACCATTCGCTTGAATTAAGTAATAAACA
1 AAATAATAAAACAATTCGCTTGAATTAAGTAATAAACA
* *
84838 AAATAATAAAATAATTTGCTTGAATTAAGTAATAAACA
1 AAATAATAAAACAATTCGCTTGAATTAAGTAATAAACA
84876 AAATAA
1 AAATAA
84882 ATCAAGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (38 bp):
AAATAATAAAACAATTCGCTTGAATTAAGTAATAAACA
Found at i:87913 original size:14 final size:15
Alignment explanation
Indices: 87882--87918 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
87872 ATAAATTAGT
87882 TAAAA-ATTTAAAAG
1 TAAAATATTTAAAAG
*
87896 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
87910 TAAAATATT
1 TAAAATATT
87919 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:91280 original size:50 final size:52
Alignment explanation
Indices: 91211--91348 Score: 154
Period size: 59 Copynumber: 2.6 Consensus size: 52
91201 CACACTCTAA
**
91211 TTTGCCTTTTCATCACGACTAGGAGGGTTA-G-TTAGAGCCATATTATCAAG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCAAG
* **
91261 TTTGTCTTTTCATTGCGACTAGGAGGGTTCTATAGGACACTTAGAGCCATATTATTGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGG---T-TAGG--A-TTAGAGCCATATTATCAAG
91320 TTTGCCTTTTCATTGCGACTAGGAGGGTT
1 TTTGCCTTTTCATTGCGACTAGGAGGGTT
91349 CAATATAACA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
50 24 0.33
53 1 0.01
54 2 0.03
55 2 0.03
56 1 0.01
59 43 0.59
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (52 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCAAG
Found at i:91360 original size:59 final size:59
Alignment explanation
Indices: 91242--91362 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
91232 GGAGGGTTAG
* * *
91242 TTAGAGCCATATTATCAAGTTTGTCTTTTCATTGCGACTAGGAGGGTTCTATAGGACAC
1 TTAGAGCCATATTATCAAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGAACAC
** *
91301 TTAGAGCCATATTATTGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATATAACAC
1 TTAGAGCCATATTATCAAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGAACAC
91360 TTA
1 TTA
91363 TCCATCTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCAAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGAACAC
Found at i:99934 original size:34 final size:35
Alignment explanation
Indices: 99891--99960 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
99881 CATAAAAAAC
* *
99891 CCCATAAAACTGAAATT-ATATTCTCTTAATCTAA
1 CCCAGAAAACTGAAATTAACATTCTCTTAATCTAA
*
99925 CCCAGAAAACTGAAATTAACATTCTTTTAATCTAA
1 CCCAGAAAACTGAAATTAACATTCTCTTAATCTAA
99960 C
1 C
99961 ACTCTTCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.33
Consensus pattern (35 bp):
CCCAGAAAACTGAAATTAACATTCTCTTAATCTAA
Found at i:109735 original size:37 final size:37
Alignment explanation
Indices: 109668--109740 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
109658 AGGAGAAATG
*
109668 GAAAATGTTGCAGCATTCTCAATAACATTCCTGGGCA
1 GAAAATGTTGCAGCATTCTCAACAACATTCCTGGGCA
* * *
109705 GAAAATGTTGCAGTATTCT-AGACGATATTCCTGGGC
1 GAAAATGTTGCAGCATTCTCA-ACAACATTCCTGGGC
109741 GCAAAAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (37 bp):
GAAAATGTTGCAGCATTCTCAACAACATTCCTGGGCA
Found at i:113136 original size:21 final size:21
Alignment explanation
Indices: 113103--113165 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
113093 CTACCCCTAA
*
113103 CTTAAACACTAAATTATAAAT
1 CTTAAACACTAAATCATAAAT
*
113124 CTTAAAC-CTTAAATCATAACTT
1 CTTAAACAC-TAAATCATAA-AT
* * *
113146 CATAACCTCTAAATCATAAA
1 CTTAAACACTAAATCATAAA
113166 CTCTAACCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 16 0.47
22 16 0.47
23 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.32
Consensus pattern (21 bp):
CTTAAACACTAAATCATAAAT
Found at i:113161 original size:22 final size:21
Alignment explanation
Indices: 113111--113180 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
113101 AACTTAAACA
*
113111 CTAAATTATAAA-TCTTAAACCT
1 CTAAATCATAAACTC-T-AACCT
113133 -TAAATCAT-AACTTCATAACCT
1 CTAAATCATAAAC-TC-TAACCT
113154 CTAAATCATAAACTCTAACC-
1 CTAAATCATAAACTCTAACCT
113174 CTAAATC
1 CTAAATC
113181 TTATCTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 9 0.21
21 17 0.40
22 13 0.31
23 3 0.07
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (21 bp):
CTAAATCATAAACTCTAACCT
Found at i:122792 original size:16 final size:16
Alignment explanation
Indices: 122768--122801 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
122758 TATCGCCGAC
*
122768 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
122784 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
122800 CG
1 CG
122802 TGATTAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:124234 original size:29 final size:30
Alignment explanation
Indices: 124202--124260 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
124192 TATTTCATCG
* * *
124202 CTAAAT-ATTTTTATAATTTTTTAATGTGA
1 CTAAATAATTGTTACAATTTATTAATGTGA
*
124231 CTAAATAATTGTTACAATTTATTATTGTGA
1 CTAAATAATTGTTACAATTTATTAATGTGA
124261 AAGAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (30 bp):
CTAAATAATTGTTACAATTTATTAATGTGA
Found at i:124366 original size:98 final size:97
Alignment explanation
Indices: 124246--124565 Score: 222
Period size: 98 Copynumber: 3.2 Consensus size: 97
124236 TAATTGTTAC
*
124246 AATTTATTATTGTGAAAGAATATTATTTGTCACAAATTTTTATAATGAGAAATTAATATTTGTTA
1 AATTTTTTATTGTGAAAGAATATTA-TTGTCACAAATTTTTATAATGAGAAATTAATATTTGTTA
* **
124311 TAAATTGCTATTTTGATTAAATAAATTTGTCGT
65 TAAATTGATATTTTGATTAAATAAATTTGTCAA
* ** * * * **
124344 AATTTTTTATTTTGACAA-AATATTA-TG--ACTAAATAAATT-TGAT-ATAACTTTTTACTTTG
1 AATTTTTTATTGTGA-AAGAATATTATTGTCAC-AAAT-TTTTATAATGAGAAATTAATA-TTTG
* * * * * * * *
124403 ATTAAATTTAATGTGTTATTGTGACTAAATCATTTTGTTAC
62 -TT--A-TAAAT-TGATATTTTGATTAAATAAATTTGTCAA
* * * *
124444 AATTTGTTATTGTGAAATAATATTACTTGTCATAAATTTTTATATTGAGAAATTAATATTTGTTA
1 AATTTTTTATTGTGAAAGAATATTA-TTGTCACAAATTTTTATAATGAGAAATTAATATTTGTTA
* * *
124509 GAAATTAATATTTTGATTAAATAAATTTATCAA
65 TAAATTGATATTTTGATTAAATAAATTTGTCAA
* *
124542 AACTTTTTATTTTGACAA-AATATT
1 AATTTTTTATTGTGA-AAGAATATT
124566 TTGACTAAAT
Statistics
Matches: 162, Mismatches: 43, Indels: 34
0.68 0.18 0.14
Matches are distributed among these distances:
94 9 0.06
95 11 0.07
96 6 0.04
98 58 0.36
99 13 0.08
100 41 0.25
102 6 0.04
103 10 0.06
104 8 0.05
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (97 bp):
AATTTTTTATTGTGAAAGAATATTATTGTCACAAATTTTTATAATGAGAAATTAATATTTGTTAT
AAATTGATATTTTGATTAAATAAATTTGTCAA
Found at i:124577 original size:198 final size:196
Alignment explanation
Indices: 124226--124632 Score: 589
Period size: 198 Copynumber: 2.1 Consensus size: 196
124216 AATTTTTTAA
*
124226 TGTGACTAAATAATTGTTACAATTTATTATTGTGAAAGAATATTATTTGTCACAAATTTTTATAA
1 TGTGACTAAATAATTGTTACAATTTATTATTGTGAAAGAATATTACTTGTCACAAATTTTTATAA
* ** * ** *
124291 TGAGAAATTAATATTTGTTATAAATTGCTATTTTGATTAAATAAATTTGTCGTAATTTTTTATTT
66 TGAGAAATTAATATTTGTTAGAAATTAATATTTTGATTAAATAAATTTATCAAAACTTTTTATTT
* * * *
124356 TGACAAAATATTATGACTAAATAAATTTGATATAACTTTTTACTTTGATTAAATTTAATGTGTTA
131 TGACAAAATATTATGACTAAATAAATTTAACATAACTTTTTACTTTAAATAAATTTAATGTGTTA
124421 T
196 T
* * * *
124422 TGTGACTAAATCATTTTGTTACAATTTGTTATTGTGAAATAATATTACTTGTCATAAATTTTTAT
1 TGTGACTAAAT-A-ATTGTTACAATTTATTATTGTGAAAGAATATTACTTGTCACAAATTTTTAT
*
124487 ATTGAGAAATTAATATTTGTTAGAAATTAATATTTTGATTAAATAAATTTATCAAAACTTTTTAT
64 AATGAGAAATTAATATTTGTTAGAAATTAATATTTTGATTAAATAAATTTATCAAAACTTTTTAT
* * * *
124552 TTTGACAAAATATTTTGACTAAATAAATTTAACATAATTTTTTATTTTAAATAAATTTAATTTGT
129 TTTGACAAAATATTATGACTAAATAAATTTAACATAACTTTTTACTTTAAATAAATTTAATGTGT
124617 TAT
194 TAT
* *
124620 TTTGTCTAAATAA
1 TGTGACTAAATAA
124633 ATTATCATAA
Statistics
Matches: 185, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
196 11 0.06
197 2 0.01
198 172 0.93
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (196 bp):
TGTGACTAAATAATTGTTACAATTTATTATTGTGAAAGAATATTACTTGTCACAAATTTTTATAA
TGAGAAATTAATATTTGTTAGAAATTAATATTTTGATTAAATAAATTTATCAAAACTTTTTATTT
TGACAAAATATTATGACTAAATAAATTTAACATAACTTTTTACTTTAAATAAATTTAATGTGTTA
T
Found at i:124700 original size:21 final size:21
Alignment explanation
Indices: 124676--124716 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
124666 TTTTATTTAA
*
124676 ATTTGTTATTATAAATAAAAT
1 ATTTGTTATGATAAATAAAAT
* *
124697 ATTTTTTATGATAACTAAAA
1 ATTTGTTATGATAAATAAAA
124717 ATATATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTGTTATGATAAATAAAAT
Found at i:124769 original size:27 final size:29
Alignment explanation
Indices: 124712--124770 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
124702 TTATGATAAC
* *
124712 TAAAAATATATTTTAAAATCTTATAACAA
1 TAAAAATATATATTAAAATCATATAACAA
124741 TAAAAATA-ATATTAAATATCAT-TAA-AA
1 TAAAAATATATATTAAA-ATCATATAACAA
124768 TAA
1 TAA
124771 CATAAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 10 0.37
29 12 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAAAATATATATTAAAATCATATAACAA
Found at i:128281 original size:20 final size:20
Alignment explanation
Indices: 128244--128286 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
128234 ATTCCACCAC
*
128244 ATGCAACTATATACTCCTAA
1 ATGCAACTACATACTCCTAA
* *
128264 ATGCATCTACATAGTCCTAA
1 ATGCAACTACATACTCCTAA
128284 ATG
1 ATG
128287 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATACTCCTAA
Found at i:136269 original size:18 final size:18
Alignment explanation
Indices: 136235--136280 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
136225 ATGATATGTA
136235 CAAATGAGAATGCTGTGG
1 CAAATGAGAATGCTGTGG
*
136253 CAAACTGAG-ATGTTGTGG
1 CAAA-TGAGAATGCTGTGG
136271 -AAATG-GAATG
1 CAAATGAGAATG
136281 GTGGTAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 5 0.20
17 3 0.12
18 12 0.48
19 4 0.16
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.24
Consensus pattern (18 bp):
CAAATGAGAATGCTGTGG
Found at i:137812 original size:20 final size:20
Alignment explanation
Indices: 137775--137817 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
137765 ATTCCACCAC
*
137775 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
137795 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
137815 ATG
1 ATG
137818 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:138338 original size:11 final size:11
Alignment explanation
Indices: 138322--138346 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
138312 AAATCTATTG
138322 TTTTATTTTAT
1 TTTTATTTTAT
138333 TTTTATTTTAT
1 TTTTATTTTAT
138344 TTT
1 TTT
138347 AACTAATGTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:139470 original size:418 final size:414
Alignment explanation
Indices: 138688--139531 Score: 1124
Period size: 418 Copynumber: 2.0 Consensus size: 414
138678 TATAAAACTT
* * * *
138688 TTACTATATAACATTTTATGCACCAAAAAATAGGGAAAATGTTTCTGATAGTATAATTTTTCATA
1 TTACTATATAACATTTTATACACCAAAAAATAGGGAAAATGGTTCTGATAATATAATGTTTCATA
*
138753 ATGATTAAAATATATAACTATAAAAATAATTAATTACAAAAAACTTGAATTTTATTATCTAATGT
66 ATGATTAAAATATATAACTAAAAAAATAATTAATTACAAAAAACTTGAATTTTATTATCTAATGT
* * *
138818 GATAATTTTTCTATAACAATAACTATAAATTATAATTACAAACTTATCAATATAACTTTTGAAAC
131 GATAATTTTTCTATAACAATAAATATAAATTATAATTAAAAAATTATCAATATAACTTTTGAAAC
*
138883 AAAAAAAAAAAAGTGGAGAAAAATATTTATCACAATATATGTTATCAATATAATTAAAATTTATA
196 ----AAAAAAAAGTGGAGAAAAATAGTTATCACAATATATGTTATCAATATAATTAAAATTTATA
* * * * * *
138948 ACTACAAGTATAATCTGTCATAAAAATGTGAATACCATTATTTTTTGTGACATTGTTTTTTTGTA
257 ACTACAAATATAATCTGTCACAAAAACGTGAATAACATTATTTTTTGTGACACTGATTTTTTGTA
* *
139013 ATAATTATAAACACTATAGTTACAAAAATTATTACTATATAATTTTTTTGGG-ACAAA-AATATG
322 ATAATTATAAACACTATAGTTACAAAAATTATCACTATATAACTTTTTTGGGCA-AAACAATATG
* *
139076 GAGGAAAATCATTATGATAATATATTTTG
386 GAGGAAAATCATTATGACAATATATTTTA
* *
139105 TTACTATATAACATTTTTTACACTAAAAAATAGGGAGAAATGGTTCTGATAATATAATGTTTCAT
1 TTACTATATAACATTTTATACACCAAAAAATAGGGA-AAATGGTTCTGATAATATAATGTTTCAT
* * *
139170 AATGATTAAAATATATATATGTACAAAAATATAATTTATTA-AAAAAACTTGAATTTTATTATTT
65 AATGATTAAAATATATA-A-CTA-AAAAA-ATAATTAATTACAAAAAACTTGAATTTTATTATCT
* * *
139234 GATGTGATAATTTTTTCTATAACAATAAATATAAATTATAATTATAAAAATTGTTAATATAACTT
126 AATGTGATAA-TTTTTCTATAACAATAAATATAAATTATAATTA-AAAAATTATCAATATAACTT
* * * *
139299 TTGAAAC-AAAAAAA-TTGAGAAAAAATAGTTATGACAATATATGTTATCACTATAGTTAAAATT
189 TTGAAACAAAAAAAAGTGGAG-AAAAATAGTTATCACAATATATGTTATCAATATAATTAAAATT
* * * *
139362 TATAACTACAAATATAATTTGTCACAAAAGCGTGAATAACGTTATTTTTTGTGATACT-ATTTTT
253 TATAACTACAAATATAATCTGTCACAAAAACGTGAATAACATTATTTTTTGTGACACTGATTTTT
* * * * *
139426 TGTAATAATTATTAACACTTATAGTTACAAAATTTGTCACTATATGACTTTTTTGTGCAAAACAA
318 TGTAATAATTATAAACAC-TATAGTTACAAAAATTATCACTATATAACTTTTTTGGGCAAAACAA
* * *
139491 TATGGAGGGAAATCTTTGTGACAATATATTTTA
382 TATGGAGGAAAATCATTATGACAATATATTTTA
*
139524 TCACTATA
1 TTACTATA
139532 ATTAAACATA
Statistics
Matches: 372, Mismatches: 44, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
417 59 0.16
418 172 0.46
419 39 0.10
420 2 0.01
421 35 0.09
422 42 0.11
423 23 0.06
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (414 bp):
TTACTATATAACATTTTATACACCAAAAAATAGGGAAAATGGTTCTGATAATATAATGTTTCATA
ATGATTAAAATATATAACTAAAAAAATAATTAATTACAAAAAACTTGAATTTTATTATCTAATGT
GATAATTTTTCTATAACAATAAATATAAATTATAATTAAAAAATTATCAATATAACTTTTGAAAC
AAAAAAAAGTGGAGAAAAATAGTTATCACAATATATGTTATCAATATAATTAAAATTTATAACTA
CAAATATAATCTGTCACAAAAACGTGAATAACATTATTTTTTGTGACACTGATTTTTTGTAATAA
TTATAAACACTATAGTTACAAAAATTATCACTATATAACTTTTTTGGGCAAAACAATATGGAGGA
AAATCATTATGACAATATATTTTA
Found at i:139527 original size:179 final size:178
Alignment explanation
Indices: 139330--139786 Score: 426
Period size: 178 Copynumber: 2.5 Consensus size: 178
139320 AAAATAGTTA
* * * *
139330 TGACAATATATGTTATCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAGCGT
1 TGACAATATATTTTATCACTATAATTAAAA-TTATAACTACAAA-A-AATTTTTCACAAAAACGT
* * * * *
139395 GAATAACGTTATTTTTTGTGA-TACTATTTTTTGTAATAATTATTA-ACACTTATAGTTACAAAA
63 GAATAACATTATTTGTTGTGACAAC--TTTTTTGTAACAATAATTATA-ACTTATAGTTACAAAA
** * * *
139458 TTTGTCACTATATGA-CT-TTTTTGTGCAAAACAATA-TGGAGGGA-AATC-TTTG
125 CATATCACTATATGATCTGTTTTTGTACAAAACAAAATTGGA--GATAATCATTTG
* * *
139509 TGACAATATATTTTATCACTATAATTAAACA-TATAACGACAAAAAATTTTTTTTACTAAAAACT
1 TGACAATATATTTTATCACTATAATTAAA-ATTATAACTACAAAAAA--TTTTTCAC-AAAAACG
** * *
139573 TGAATCTCATTATTTGTTGTGACAACTTTTTTGTAACAATAATTATATCTTATAGTTTCAAAACA
62 TGAATAACATTATTTGTTGTGACAACTTTTTTGTAACAATAATTATAACTTATAGTTACAAAACA
*
139638 TATCACTATATGATTTTGTTTTTGTACAAAACAAAATTGGAGATAATCATTTG
127 TATCACTATATGA-TCTGTTTTTGTACAAAACAAAATTGGAGATAATCATTTG
* * * **
139691 TGACTATATATTTTGTCACTATAATTAAAATATATAATTACAAACAAAATTTTTCACAACAAATT
1 TGACAATATATTTTATCACTATAATTAAAAT-TATAACTAC-AA-AAAATTTTTCACAA-AAACG
* ** *
139756 TAAATCTCATTATTTGTTGTGATAACTTTTT
62 TGAATAACATTATTTGTTGTGACAACTTTTT
139787 CTGTCATAGT
Statistics
Matches: 231, Mismatches: 30, Indels: 30
0.79 0.10 0.10
Matches are distributed among these distances:
176 2 0.01
177 1 0.00
178 60 0.26
179 51 0.22
180 6 0.03
181 21 0.09
182 37 0.16
183 47 0.20
184 2 0.01
185 4 0.02
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.41
Consensus pattern (178 bp):
TGACAATATATTTTATCACTATAATTAAAATTATAACTACAAAAAATTTTTCACAAAAACGTGAA
TAACATTATTTGTTGTGACAACTTTTTTGTAACAATAATTATAACTTATAGTTACAAAACATATC
ACTATATGATCTGTTTTTGTACAAAACAAAATTGGAGATAATCATTTG
Found at i:139821 original size:15 final size:16
Alignment explanation
Indices: 139793--139822 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
139783 TTTTCTGTCA
139793 TAGTTACTAAAATTTT
1 TAGTTACTAAAATTTT
139809 TAGTTAC-AAAATTT
1 TAGTTACTAAAATTT
139823 ATCATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TAGTTACTAAAATTTT
Found at i:141780 original size:29 final size:30
Alignment explanation
Indices: 141723--141781 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
141713 CTGGGATGTG
141723 CATTATCTCGTGAATAAAAAAGTTCGAGAA
1 CATTATCTCGTGAATAAAAAAGTTCGAGAA
* *
141753 CATTATCTCGTGGAT-TAAAAGTTCGAGAA
1 CATTATCTCGTGAATAAAAAAGTTCGAGAA
141782 TTCACCCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (30 bp):
CATTATCTCGTGAATAAAAAAGTTCGAGAA
Found at i:141984 original size:20 final size:20
Alignment explanation
Indices: 141959--141997 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
141949 TGACATACGA
141959 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
141979 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
141998 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:141991 original size:9 final size:9
Alignment explanation
Indices: 141959--141997 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
141949 TGACATACGA
141959 ATACGAGCC
1 ATACGAGCC
*
141968 ATACAAGCC
1 ATACGAGCC
141977 ATATACGAGCC
1 --ATACGAGCC
141988 ATACGAGCC
1 ATACGAGCC
141997 A
1 A
141998 ATGGAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (9 bp):
ATACGAGCC
Found at i:142107 original size:29 final size:29
Alignment explanation
Indices: 142004--142107 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
141994 GCCAATGGAG
* **
142004 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
142033 AGGTCGCCATGTAGTCCTGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
**
142062 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
142091 AGGTCGCCATGTAGTCC
1 AGGTCGCCATGTAGTCC
142108 TAGCTCACGA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:142587 original size:41 final size:41
Alignment explanation
Indices: 142542--142630 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
142532 TATATGATTG
* *
142542 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
142583 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
142624 TTAGTTT
1 TTAGTTT
142631 GTTTGTTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:142888 original size:16 final size:16
Alignment explanation
Indices: 142856--142902 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
142846 TTTAAAAAGT
*
142856 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
142872 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
142888 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
142903 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:142897 original size:15 final size:14
Alignment explanation
Indices: 142877--142907 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
142867 GTTTATTAGT
142877 TTATTATATTATAAG
1 TTATTATATTA-AAG
142892 TTATTATATTAAAG
1 TTATTATATTAAAG
142906 TT
1 TT
142908 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:145080 original size:17 final size:17
Alignment explanation
Indices: 145058--145090 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
145048 CAATGATTTT
*
145058 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
145075 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
145091 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:145107 original size:24 final size:22
Alignment explanation
Indices: 145075--145143 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
145065 AAATCATTAC
145075 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
145097 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
145122 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
145144 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:145363 original size:35 final size:37
Alignment explanation
Indices: 145282--145368 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
145272 TTAGTATTCT
* * *
145282 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
145320 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
145355 ATAATTATTATAAA
1 ATAATTATTATAAA
145369 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:145389 original size:12 final size:13
Alignment explanation
Indices: 145298--145642 Score: 151
Period size: 14 Copynumber: 25.1 Consensus size: 13
145288 ATTAGTAATA
145298 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
145312 AGTATTAAATCATT
1 ATTA-TAAATCATT
145326 ATTATAAAT-A--
1 ATTATAAATCATT
145336 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
145347 ATAACTAAATAATT
1 ATTA-TAAATCATT
145361 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
145375 ATTAT-AATGATT
1 ATTATAAATCATT
145387 ATTATCAAATCATT
1 ATTAT-AAATCATT
145401 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
145420 AAATATTTAAATCATT
1 --AT-TATAAATCATT
* *
145436 ATTTTTTATAATGATT
1 A--TTATA-AATCATT
145452 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
145466 ATTAT-AATGATT
1 ATTATAAATCATT
145478 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
145492 ACTAT-AATGATT
1 ATTATAAATCATT
145504 ATTATCAAATCATT
1 ATTAT-AAATCATT
145518 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
145537 AAATATTTAAATCATT
1 --AT-TATAAATCATT
145553 A-T-TAAATCATT
1 ATTATAAATCATT
* *
145564 TTTAT-AATGATT
1 ATTATAAATCATT
145576 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
145590 ATTAT-AATGATT
1 ATTATAAATCATT
145602 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
145616 ACTAT-AATGATT
1 ATTATAAATCATT
145628 ATTATCAAATCATT
1 ATTAT-AAATCATT
145642 A
1 A
145643 CTAAATCATC
Statistics
Matches: 266, Mismatches: 28, Indels: 74
0.72 0.08 0.20
Matches are distributed among these distances:
10 4 0.02
11 24 0.09
12 66 0.25
13 10 0.04
14 96 0.36
15 8 0.03
16 24 0.09
17 2 0.01
18 6 0.02
19 22 0.08
20 2 0.01
21 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:145470 original size:26 final size:26
Alignment explanation
Indices: 145441--145642 Score: 222
Period size: 26 Copynumber: 8.0 Consensus size: 26
145431 TCATTATTTT
145441 TTATAATGATTATTA-CTAAATCATTA
1 TTATAATGATTATTATC-AAATCATTA
145467 TTATAATGATTATTATCAAATCATTA
1 TTATAATGATTATTATCAAATCATTA
*
145493 CTATAATGATTATTATCAAATCATTA
1 TTATAATGATTATTATCAAATCATTA
* * * * * * *
145519 CTA-AATCATCA-AATC-ATTAAATA
1 TTATAATGATTATTATCAAATCATTA
* * *
145542 TT-TAA--ATCATTATTAAATCATTT
1 TTATAATGATTATTATCAAATCATTA
145565 TTATAATGATTATTA-CTAAATCATTA
1 TTATAATGATTATTATC-AAATCATTA
145591 TTATAATGATTATTATCAAATCATTA
1 TTATAATGATTATTATCAAATCATTA
*
145617 CTATAATGATTATTATCAAATCATTA
1 TTATAATGATTATTATCAAATCATTA
145643 CTAAATCATC
Statistics
Matches: 149, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.03
22 2 0.01
23 14 0.09
24 6 0.04
25 6 0.04
26 115 0.77
27 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
TTATAATGATTATTATCAAATCATTA
Found at i:145623 original size:124 final size:124
Alignment explanation
Indices: 145438--145700 Score: 517
Period size: 124 Copynumber: 2.1 Consensus size: 124
145428 AAATCATTAT
145438 TTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT
1 TTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT
*
145503 TATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCA
66 TATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATAA
145562 TTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT
1 TTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT
145627 TATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATAA
66 TATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATAA
145686 TTTTTATAATGATTA
1 TTTTTATAATGATTA
145701 ATAAATACAT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 138 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (124 bp):
TTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT
TATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATAA
Found at i:148588 original size:26 final size:24
Alignment explanation
Indices: 148530--148588 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
148520 CTAATAAACC
*
148530 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
148554 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
148582 TAATAAT
1 TAATAAT
148589 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:149466 original size:28 final size:28
Alignment explanation
Indices: 149399--149459 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
149389 ATTTTTTATA
*
149399 TAATATAATATAACTTAAACTAATAAAC
1 TAATATAATATAACTTAAACTAACAAAC
149427 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
149455 TAATA
1 TAATA
149460 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:149469 original size:21 final size:21
Alignment explanation
Indices: 149436--149484 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
149426 CTAATATAAT
149436 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
149457 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
149478 ATTAACT
1 A-TAACT
149485 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:149878 original size:21 final size:21
Alignment explanation
Indices: 149853--149924 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
149843 ACGCAACTAT
149853 GGATGCAACACATGCAGCTAC
1 GGATGCAACACATGCAGCTAC
* *
149874 GGATGCAGGA-ATC-TCCCAGCTAT
1 GGATGCA--ACA-CAT-GCAGCTAC
*
149897 GGATGCAACGCATGCAGCTAC
1 GGATGCAACACATGCAGCTAC
149918 GGATGCA
1 GGATGCA
149925 GGAATCTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 22 0.55
22 3 0.08
23 15 0.38
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (21 bp):
GGATGCAACACATGCAGCTAC
Found at i:149900 original size:23 final size:23
Alignment explanation
Indices: 149867--149937 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
149857 GCAACACATG
149867 CAGCTACGGATGCAGGAATCTCC
1 CAGCTACGGATGCAGGAATCTCC
* ** *
149890 CAGCTATGGATGCA--ACGCAT-G
1 CAGCTACGGATGCAGGAATC-TCC
149911 CAGCTACGGATGCAGGAATCTCC
1 CAGCTACGGATGCAGGAATCTCC
149934 CAGC
1 CAGC
149938 CCCAGCTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
21 15 0.42
22 2 0.06
23 19 0.53
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (23 bp):
CAGCTACGGATGCAGGAATCTCC
Found at i:149956 original size:50 final size:44
Alignment explanation
Indices: 149849--149937 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
149839 AATAACGCAA
*
149849 CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
1 CTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCCCAG
149893 CTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCCCAG
1 CTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCCCAG
149937 C
1 C
149938 CCCAGCTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (44 bp):
CTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCCCAG
Found at i:150063 original size:20 final size:20
Alignment explanation
Indices: 150038--150075 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
150028 ACGTGCATGG
*
150038 CCCATGCACAGTTCCCACGT
1 CCCATGCACAGCTCCCACGT
150058 CCCATGCACAGCTCCCAC
1 CCCATGCACAGCTCCCAC
150076 ATGCATCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.50, G:0.13, T:0.16
Consensus pattern (20 bp):
CCCATGCACAGCTCCCACGT
Found at i:150087 original size:20 final size:20
Alignment explanation
Indices: 150064--150101 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
150054 ACGTCCCATG
*
150064 CACAGCTCCCACATGCATCC
1 CACAACTCCCACATGCATCC
*
150084 CACAACTCCCCCATGCAT
1 CACAACTCCCACATGCAT
150102 GCTCCAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.50, G:0.08, T:0.16
Consensus pattern (20 bp):
CACAACTCCCACATGCATCC
Found at i:150194 original size:29 final size:29
Alignment explanation
Indices: 150161--150264 Score: 181
Period size: 29 Copynumber: 3.6 Consensus size: 29
150151 AACACCACAC
*
150161 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
150190 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
150219 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
150248 AGCTCGCCCGGATGCCA
1 AGGTCGCCCGGATGCCA
150265 CTGTAGACTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.17, C:0.37, G:0.31, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:152330 original size:21 final size:21
Alignment explanation
Indices: 152306--152353 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
152296 CCTAATATTG
152306 CAATGTCAAAATTAGGCGCAA
1 CAATGTCAAAATTAGGCGCAA
*
152327 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGCGCAA
*
152348 TAATGT
1 CAATGT
152354 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (21 bp):
CAATGTCAAAATTAGGCGCAA
Found at i:154406 original size:183 final size:177
Alignment explanation
Indices: 153961--154413 Score: 459
Period size: 178 Copynumber: 2.5 Consensus size: 177
153951 AGATTCTGCA
* * * *
153961 AATATATGTTATCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAACGTGAAT
1 AATATATTTTATCACTATAATTAAAATATATAACTACAAA-AAAATTTGTCACAAAAACGTGAAT
** * * * * * ** *
154026 AACGTTATTTTTTGTGA-TACTATTTTTTGTAATAATTATTAACACTTATAGTTACAAAATTTGT
65 CTCATTATTTGTTGTGACAAC--TTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATAT
* * *
154090 CACTATATGACTTTTTTGTGCAAAAAAATATGGAGGGAAATCTTTGTGAC
128 CACTATATGACTTTTTTGTACAAAAAAAAATGGAGAGAAATCTTTGTGAC
* * * *
154140 AATATATTTTATCACTATAATT-AAACATATAACGACAAAAAATATATT-TTACTAAAAACTTGA
1 AATATATTTTATCACTATAATTAAAATATATAACTACAAAAAA-AT-TTGTCAC-AAAAACGTGA
* *
154203 ATCTCATTATTTGTTGTGACAACTTTTTTGTAACAATAATTATA-TCTTATAGTTTCAAAACATA
63 ATCTCATTATTTGTTGTGACAACTTTTTTGTAACAATAATTA-ACACTTATAGTTACAAAACATA
* * *
154267 TCACTATATGATTTTCTTTTTGTACAAAAAAAAATTGA-AGATAATCATTTTTGAC
127 TCACTATATGA--CT-TTTTTGTACAAAAAAAAATGGAGAGA-AATC-TTTGTGAC
* * * *
154322 TATATATTTTGTCACTATAATTAAAATATATAATTACAAACAAAATTTGTCACAACAAATC-TAA
1 AATATATTTTATCACTATAATTAAAATATATAACTACAAA-AAAATTTGTCACAA-AAA-CGTGA
154386 ATCTCATTATTTGTTGTGACAACTTTTT
63 ATCTCATTATTTGTTGTGACAACTTTTT
154414 CTGTCATAGT
Statistics
Matches: 226, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
177 2 0.01
178 62 0.27
179 47 0.21
180 5 0.02
181 23 0.10
182 31 0.14
183 52 0.23
184 4 0.02
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (177 bp):
AATATATTTTATCACTATAATTAAAATATATAACTACAAAAAAATTTGTCACAAAAACGTGAATC
TCATTATTTGTTGTGACAACTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATATCAC
TATATGACTTTTTTGTACAAAAAAAAATGGAGAGAAATCTTTGTGAC
Found at i:154448 original size:15 final size:16
Alignment explanation
Indices: 154420--154449 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
154410 TTTTCTGTCA
154420 TAGTTACTAAAATTTT
1 TAGTTACTAAAATTTT
154436 TAGTTAC-AAAATTT
1 TAGTTACTAAAATTT
154450 GTCATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TAGTTACTAAAATTTT
Found at i:156091 original size:21 final size:21
Alignment explanation
Indices: 156066--156113 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
156056 CCTAATATTG
156066 CAATGTCAAAATTAAGTGCAA
1 CAATGTCAAAATTAAGTGCAA
*
156087 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAAGTGCAA
*
156108 TAATGT
1 CAATGT
156114 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAAGTGCAA
Found at i:158200 original size:41 final size:41
Alignment explanation
Indices: 158094--158188 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
158084 ATATTTGTAT
* * *
158094 TTTAGTGGCATTTGTATGAAAATGCCGCTATAGACTTCTAC
1 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTTATAC
* *
158135 TTTAGTGGCGTTCGTATGAGAACGCCGCTATAGACTTATAC
1 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTTATAC
158176 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
158189 TTGTTAAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTTATAC
Found at i:162458 original size:21 final size:21
Alignment explanation
Indices: 162420--162489 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
162410 ATGAAGCAAG
* *
162420 GGAAGCAGAGAGAGCAGCAGT
1 GGAAGCAGACAGAGCAGCAGC
* *
162441 GGAAGCAGCCAGATCAGCAGC
1 GGAAGCAGACAGAGCAGCAGC
* * * *
162462 GAAAGCAGAGAAAGAAGCAGC
1 GGAAGCAGACAGAGCAGCAGC
*
162483 GGCAGCA
1 GGAAGCA
162490 CAGAGAGAAG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.37, T:0.03
Consensus pattern (21 bp):
GGAAGCAGACAGAGCAGCAGC
Found at i:162498 original size:21 final size:21
Alignment explanation
Indices: 162456--162522 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
162446 CAGCCAGATC
** * *
162456 AGCAGCGAAAGCAGAGAAAGA
1 AGCAGCGGCAGCACAGAGAGA
162477 AGCAGCGGCAGCACAGAGAGA
1 AGCAGCGGCAGCACAGAGAGA
* * *
162498 AGCAACGGCAGCATAGAGGGA
1 AGCAGCGGCAGCACAGAGAGA
162519 AGCA
1 AGCA
162523 ACATATCAGC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.19, G:0.36, T:0.01
Consensus pattern (21 bp):
AGCAGCGGCAGCACAGAGAGA
Done.