Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001285.1 Hibiscus syriacus cultivar Beakdansim tig00002519_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: 107047
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3559 original size:2 final size:2
Alignment explanation
Indices: 3554--3611 Score: 67
Period size: 2 Copynumber: 32.5 Consensus size: 2
3544 AAAAAAAATA
3554 AT AT AT AT -T AT AT -T AT -T AT A- AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3591 AT AT AT -T AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
3612 ATTCAATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
1 7 0.14
2 42 0.86
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3566 original size:9 final size:9
Alignment explanation
Indices: 3554--3611 Score: 77
Period size: 9 Copynumber: 6.6 Consensus size: 9
3544 AAAAAAAATA
3554 ATATATATT
1 ATATATATT
3563 ATAT-TATT
1 ATATATATT
3571 ATA-ATA-T
1 ATATATATT
3578 ATATATATTAT
1 ATATATA-T-T
3589 ATATATATT
1 ATATATATT
3598 ATATATATT
1 ATATATATT
3607 ATATA
1 ATATA
3612 ATTCAATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.09
8 12 0.27
9 19 0.43
10 1 0.02
11 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATATATT
Found at i:3576 original size:20 final size:19
Alignment explanation
Indices: 3551--3613 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
3541 AAAAAAAAAA
3551 ATAATATATATTATATTATT
1 ATAATATATATTATATTA-T
3571 ATAATATATA-TATATTAT
1 ATAATATATATTATATTAT
3589 AT-ATATATTATATATATTAT
1 ATAATATA-TAT-TATATTAT
3609 ATAAT
1 ATAAT
3614 TCAATTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.13
18 5 0.13
19 7 0.18
20 20 0.51
21 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATATATATTATATTAT
Found at i:3578 original size:13 final size:13
Alignment explanation
Indices: 3557--3613 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
3547 AAAAATAATA
*
3557 TATATTATATTAT
1 TATAATATATTAT
3570 TATAATATA-TAT
1 TATAATATATTAT
*
3582 ATATTATATATATAT
1 -TATAATATAT-TAT
3597 TAT-ATATATTA-
1 TATAATATATTAT
3608 TATAAT
1 TATAAT
3614 TCAATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 3 0.08
12 7 0.18
13 22 0.58
14 3 0.08
15 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATATATTAT
Found at i:3584 original size:11 final size:11
Alignment explanation
Indices: 3551--3611 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
3541 AAAAAAAAAA
3551 ATAATATATAT
1 ATAATATATAT
3562 -T-ATAT-TATT
1 ATAATATATA-T
3571 ATAATATATAT
1 ATAATATATAT
*
3582 ATATTATATAT
1 ATAATATATAT
*
3593 ATATTATATAT
1 ATAATATATAT
*
3604 ATTATATA
1 ATAATATA
3612 ATTCAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 2 0.05
11 32 0.74
12 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATAATATATAT
Found at i:22098 original size:11 final size:11
Alignment explanation
Indices: 22080--22114 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
22070 TGAACAAAGT
22080 AGAATAAAT-A
1 AGAATAAATAA
22090 AGAAATAAATAA
1 AG-AATAAATAA
22102 AGAATAAATAA
1 AGAATAAATAA
22113 AG
1 AG
22115 GCAAGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 18 0.78
12 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (11 bp):
AGAATAAATAA
Found at i:22296 original size:18 final size:19
Alignment explanation
Indices: 22233--22301 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
22223 GGTAAAAACG
*
22233 AAAATAAA-AA-AAACAAT
1 AAAATAAATAATAAAAAAT
22250 AAAATAGAATAATAAAAAAT
1 AAAATA-AATAATAAAAAAT
* *
22270 -AAATCAATAATATAAAAT
1 AAAATAAATAATAAAAAAT
22288 AAAATAATATAATA
1 AAAATAA-ATAATA
22302 TATTATAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.14
18 14 0.33
19 11 0.26
20 12 0.28
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (19 bp):
AAAATAAATAATAAAAAAT
Found at i:22299 original size:28 final size:27
Alignment explanation
Indices: 22233--22299 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
22223 GGTAAAAACG
* *
22233 AAAATAAAAAAAACAATAAAATAGAAT
1 AAAATAAATAAAACAATAAAATAAAAT
* * *
22260 AATAAAAAATAAATCAATAATATAAAAT
1 AA-AATAAATAAAACAATAAAATAAAAT
22288 AAAATAATATAA
1 AAAATAA-ATAA
22300 TATATTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (27 bp):
AAAATAAATAAAACAATAAAATAAAAT
Found at i:22301 original size:23 final size:22
Alignment explanation
Indices: 22235--22301 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
22225 TAAAAACGAA
* *
22235 AATAAAAAAAACAATAAAATAG
1 AATAAAAAAAATAATATAATAG
22257 AATAATAAAAAATAA-ATCAATA-
1 AATAA-AAAAAATAATAT-AATAG
22279 ATATAAAATAAAATAATATAATA
1 A-ATAAAA-AAAATAATATAATA
22302 TATTATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 9 0.24
23 27 0.71
24 2 0.05
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.22
Consensus pattern (22 bp):
AATAAAAAAAATAATATAATAG
Found at i:22311 original size:15 final size:15
Alignment explanation
Indices: 22248--22299 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
22238 AAAAAAAACA
*
22248 ATAAAATAGAATAAT
1 ATAAAATAAAATAAT
*
22263 AAAAAATAAATCAATAAT
1 ATAAAAT-AA--AATAAT
22281 ATAAAATAAAATAAT
1 ATAAAATAAAATAAT
22296 ATAA
1 ATAA
22300 TATATTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 16 0.52
16 1 0.03
17 2 0.06
18 12 0.39
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (15 bp):
ATAAAATAAAATAAT
Found at i:24649 original size:26 final size:26
Alignment explanation
Indices: 24619--24670 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
24609 TTGAGTCCAA
24619 TATCCTTCGTTGTGAAGTTGTAATTG
1 TATCCTTCGTTGTGAAGTTGTAATTG
24645 TATCCTTCGTTGTGAAGTTGTAATTG
1 TATCCTTCGTTGTGAAGTTGTAATTG
24671 GCTCTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (26 bp):
TATCCTTCGTTGTGAAGTTGTAATTG
Found at i:25188 original size:378 final size:378
Alignment explanation
Indices: 24675--25415 Score: 1392
Period size: 378 Copynumber: 2.0 Consensus size: 378
24665 TAATTGGCTC
*
24675 TGAAATTGGAAAGTTGGCAGTTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGTGT
1 TGAAATTGGAAAGTTGACAGTTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGTGT
*
24740 GCACGATTCCCTTTGTCGTGAAGTTGAAACCACGGGTTGTGTGGGTACGATATCCTCCGTCGTGG
66 GCACGATTCCCTTTGTCATGAAGTTGAAACCACGGGTTGTGTGGGTACGATATCCTCCGTCGTGG
24805 AGTTGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTTGTG
131 AGTTGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTTGTG
*
24870 AAGTTGAAATCCAAGTATTGTATGTTACGGGTGGACACGATTCCCTTCGTCGTGAAGTTAAAACC
196 AAGTTGAAATCCAAGTATTGTATGTTACGGGTGGACACGATTCCCTTCGCCGTGAAGTTAAAACC
24935 GTGGATGACCCCTTTATTTTGAAGTTTGGCTTCGAGCTAGATATCCTTCGTTGTGAAGTTAAAAT
261 GTGGATGACCCCTTTATTTTGAAGTTTGGCTTCGAGCTAGATATCCTTCGTTGTGAAGTTAAAAT
25000 CTACTCTCGAGCAAACTATGTCACTTTGAGTTCAAAATCCTCCACTGTGAAGT
326 CTACTCTCGAGCAAACTATGTCACTTTGAGTTCAAAATCCTCCACTGTGAAGT
25053 TGAAATTGGAAAGTTGACAGTTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGTGT
1 TGAAATTGGAAAGTTGACAGTTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGTGT
*
25118 GCACGATTCCCTTTGTCATGAAGTTGAAACCACGGGTTGTGTGGGTACGATATCCTCCGTTGTGG
66 GCACGATTCCCTTTGTCATGAAGTTGAAACCACGGGTTGTGTGGGTACGATATCCTCCGTCGTGG
*
25183 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTTGTG
131 AGTTGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTTGTG
* *
25248 AAGTTGAAATCCAAGTATTGTATGTTACGGGTGGACACGATTCCTTTCGCCGTGAAGTTGAAACC
196 AAGTTGAAATCCAAGTATTGTATGTTACGGGTGGACACGATTCCCTTCGCCGTGAAGTTAAAACC
* *
25313 GTGGATGACCCCTTTATTTTGAAGTTTGGCTTTGAGCTAGATATCCTTCGTTTTGAAGTTAAAAT
261 GTGGATGACCCCTTTATTTTGAAGTTTGGCTTCGAGCTAGATATCCTTCGTTGTGAAGTTAAAAT
*
25378 CTACTCTCGAGCAAACTGTGTCACTTTGAGTTCAAAAT
326 CTACTCTCGAGCAAACTATGTCACTTTGAGTTCAAAAT
25416 ACATATGCAA
Statistics
Matches: 353, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
378 353 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (378 bp):
TGAAATTGGAAAGTTGACAGTTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGTGT
GCACGATTCCCTTTGTCATGAAGTTGAAACCACGGGTTGTGTGGGTACGATATCCTCCGTCGTGG
AGTTGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTTGTG
AAGTTGAAATCCAAGTATTGTATGTTACGGGTGGACACGATTCCCTTCGCCGTGAAGTTAAAACC
GTGGATGACCCCTTTATTTTGAAGTTTGGCTTCGAGCTAGATATCCTTCGTTGTGAAGTTAAAAT
CTACTCTCGAGCAAACTATGTCACTTTGAGTTCAAAATCCTCCACTGTGAAGT
Found at i:26131 original size:21 final size:20
Alignment explanation
Indices: 26106--26159 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
26096 TGAACCCACC
*
26106 TTATTTTCTTTTCTTTTTCTT
1 TTATTTT-TTTTCTTTTCCTT
26127 TTATTTTTTTCTCTTTTCCTT
1 TTATTTTTTT-TCTTTTCCTT
26148 TTATTTTTTTTC
1 TTATTTTTTTTC
26160 AATTTAGGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.80
Consensus pattern (20 bp):
TTATTTTTTTTCTTTTCCTT
Found at i:36503 original size:5 final size:5
Alignment explanation
Indices: 36495--36557 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
36485 AAAAAAACAC
* * *
36495 AATAA AATAG AATAA TAA-AA AAT-A AA-AC AATAA TATAA AATAA AATAA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
36543 AATAA TATAA TATAA
1 AATAA AATAA AATAA
36558 TAGTAAAGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
4 7 0.15
5 38 0.81
6 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:36525 original size:28 final size:27
Alignment explanation
Indices: 36480--36547 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
36470 GGTAAAAACG
*
36480 AAAATAAAA-AAACACAATAAAATAGAAT
1 AAAA-AAAATAAA-ACAATAAAATAAAAT
*
36508 AATAAAAAATAAAACAATAATATAAAAT
1 AA-AAAAAATAAAACAATAAAATAAAAT
36536 AAAATAAAATAA
1 AAAA-AAAATAA
36548 TATAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 28 0.80
29 5 0.14
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.18
Consensus pattern (27 bp):
AAAAAAAATAAAACAATAAAATAAAAT
Found at i:36526 original size:23 final size:22
Alignment explanation
Indices: 36500--36559 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
36490 AACACAATAA
36500 AATAGAATAATAA-AAAATAAAAC
1 AATA-AATAA-AATAAAATAAAAC
*
36523 AATAATATAAAATAAAATAAAAT
1 AATAA-ATAAAATAAAATAAAAC
*
36546 AATATAATATAATA
1 AATA-AATAAAATA
36560 GTAAAGAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 3 0.09
23 28 0.88
24 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAAATAAAATAAAATAAAAC
Found at i:36528 original size:18 final size:18
Alignment explanation
Indices: 36505--36539 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36495 AATAAAATAG
36505 AATAATAAAAAATAAAAC
1 AATAATAAAAAATAAAAC
*
36523 AATAATATAAAATAAAA
1 AATAATAAAAAATAAAA
36540 TAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AATAATAAAAAATAAAAC
Found at i:36550 original size:20 final size:20
Alignment explanation
Indices: 36495--36557 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
36485 AAAAAAACAC
* *
36495 AATAAAATAGAATAATAAAA
1 AATAAAATAAAATAATATAA
*
36515 AAT-AAA-ACAATAATATAA
1 AATAAAATAAAATAATATAA
36533 AATAAAATAAAATAATATAA
1 AATAAAATAAAATAATATAA
*
36553 TATAA
1 AATAA
36558 TAGTAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.35
19 6 0.16
20 18 0.49
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AATAAAATAAAATAATATAA
Found at i:36554 original size:18 final size:18
Alignment explanation
Indices: 36480--36559 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
36470 GGTAAAAACG
* * *
36480 AAAATAAAAAAACACAAT
1 AAAATAAAATAATATAAT
*
36498 AAAATAGAATAATA-AA-
1 AAAATAAAATAATATAAT
*
36514 AAATAAAACAATAATATAAAAT
1 AAA-ATAA-AATAATAT--AAT
36536 AAAATAAAATAATATAAT
1 AAAATAAAATAATATAAT
*
36554 ATAATA
1 AAAATA
36560 GTAAAGAACC
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
16 3 0.06
17 4 0.08
18 26 0.53
20 8 0.16
21 5 0.10
22 3 0.06
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (18 bp):
AAAATAAAATAATATAAT
Found at i:36558 original size:10 final size:10
Alignment explanation
Indices: 36495--36564 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
36485 AAAAAAACAC
* *
36495 AATAAAATAG
1 AATAATATAA
*
36505 AATAATAAAA
1 AATAATATAA
*
36515 AATAA-A-AC
1 AATAATATAA
36523 AATAATATAA
1 AATAATATAA
*
36533 AATAAAATAA
1 AATAATATAA
36543 AATAATATAA
1 AATAATATAA
*
36553 TATAATAGTAA
1 AATAATA-TAA
36564 A
1 A
36565 GAACCAAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
8 6 0.12
9 2 0.04
10 37 0.77
11 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.24
Consensus pattern (10 bp):
AATAATATAA
Found at i:36708 original size:2 final size:2
Alignment explanation
Indices: 36701--36733 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36691 ATATTCGTAC
36701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36734 AAATGGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42099 original size:32 final size:34
Alignment explanation
Indices: 42036--42099 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
42026 TTTAAAAATG
42036 GTTTTTGAAAATATATAGTATGGTTTTGAAAATAC
1 GTTTTTGAAAATATATAGTA-GGTTTTGAAAATAC
42071 GTTTTT-AAAATCATATA-TA-GTTTTGAAAA
1 GTTTTTGAAAAT-ATATAGTAGGTTTTGAAAA
42100 CATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 10 0.36
34 7 0.25
35 11 0.39
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44
Consensus pattern (34 bp):
GTTTTTGAAAATATATAGTAGGTTTTGAAAATAC
Found at i:42111 original size:15 final size:15
Alignment explanation
Indices: 42091--42122 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42081 TCATATATAG
42091 TTTTGAAAACATATT
1 TTTTGAAAACATATT
42106 TTTTGAAAACATATT
1 TTTTGAAAACATATT
42121 TT
1 TT
42123 AAAAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTGAAAACATATT
Found at i:42119 original size:33 final size:34
Alignment explanation
Indices: 42036--42119 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 34
42026 TTTAAAAATG
*
42036 GTTTTTGAAAATATATAGTATGGTTTTGAAAATAC
1 GTTTTTGAAAACATATAGTA-GGTTTTGAAAATAC
42071 GTTTTT-AAAATCATATA-TA-GTTTTGAAAACATA-
1 GTTTTTGAAAA-CATATAGTAGGTTTTG-AAA-ATAC
*
42104 TTTTTTGAAAACATAT
1 GTTTTTGAAAACATAT
42120 TTTAAAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
32 6 0.14
33 13 0.30
34 13 0.30
35 11 0.26
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (34 bp):
GTTTTTGAAAACATATAGTAGGTTTTGAAAATAC
Found at i:42122 original size:14 final size:14
Alignment explanation
Indices: 42091--42133 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
42081 TCATATATAG
42091 TTTTGAAAACATATT
1 TTTTGAAAACATA-T
42106 TTTTGAAAACATAT
1 TTTTGAAAACATAT
**
42120 TTTAAAAAACATAT
1 TTTTGAAAACATAT
42134 ATATAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (14 bp):
TTTTGAAAACATAT
Found at i:42311 original size:21 final size:20
Alignment explanation
Indices: 42225--42382 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
42215 AAATGACCAA
**
42225 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
42244 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
42264 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
42284 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
42305 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
42326 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
42346 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
42367 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
42383 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:42411 original size:20 final size:20
Alignment explanation
Indices: 42349--42542 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
42339 CGATTTTCCA
* ** *
42349 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
42369 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
42389 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42409 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
42429 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
42449 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42469 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
42489 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
42509 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
42530 AAATCGCAACGCG
1 AAATCGCAACGCG
42543 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:42433 original size:60 final size:60
Alignment explanation
Indices: 42349--42542 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
42339 CGATTTTCCA
* ** * *
42349 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
42409 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
42469 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
42530 AAATCGCAACGCG
1 AAATCGCAACGCG
42543 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:42964 original size:33 final size:33
Alignment explanation
Indices: 42925--42995 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
42915 TTCACTTAGA
*
42925 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
42958 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
42991 TTTCA
1 TTTCA
42996 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:43119 original size:20 final size:20
Alignment explanation
Indices: 43075--43184 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
43065 TGCAGAAGAG
*
43075 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
43096 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
43116 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
43137 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
43151 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
43170 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
43185 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:43132 original size:41 final size:38
Alignment explanation
Indices: 43068--43184 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
43058 TTCAATTTGC
* *
43068 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
43106 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
43147 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
43180 AGAAT
1 AGAAT
43185 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:43154 original size:14 final size:14
Alignment explanation
Indices: 43135--43191 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
43125 GAGAAATGAA
43135 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
43149 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
43168 AATCGCAACGAGAG
1 AATCGCAACGAGAG
43182 AATCGCAACG
1 AATCGCAACG
43192 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:43167 original size:33 final size:33
Alignment explanation
Indices: 43127--43207 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
43117 CGCAACGAGA
43127 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
43160 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
43193 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
43208 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:43225 original size:19 final size:19
Alignment explanation
Indices: 43203--43330 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
43193 GAAACCAAAA
*
43203 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43222 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
43236 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43255 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
43269 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
43289 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
43309 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
43329 TC
1 TC
43331 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:43244 original size:14 final size:14
Alignment explanation
Indices: 43225--43281 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
43215 TTTCATTTCG
43225 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
43239 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
43258 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
43272 CGTTGCGATT
1 CGTTGCGATT
43282 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:43250 original size:33 final size:33
Alignment explanation
Indices: 43208--43330 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
43198 CAAAATCGCA
43208 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
43241 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
43274 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
43315 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
43331 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:43292 original size:21 final size:21
Alignment explanation
Indices: 43266--43330 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
43256 CGCGTTGCGA
43266 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
43287 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
43307 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
43328 TTC
1 TTC
43331 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:45182 original size:93 final size:93
Alignment explanation
Indices: 45023--45490 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
45013 TAGATTGCTT
* *
45023 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45088 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45116 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45181 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45209 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45274 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45302 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45366 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45394 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45459 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45486 AGTAA
1 AGTAA
45491 TGCAATCCAT
Statistics
Matches: 372, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
92 98 0.26
93 274 0.74
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:45473 original size:185 final size:186
Alignment explanation
Indices: 45023--45490 Score: 904
Period size: 185 Copynumber: 2.5 Consensus size: 186
45013 TAGATTGCTT
* *
45023 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45088 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
45153 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
45209 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45274 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
45339 GTGTATTC-TTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
45394 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45459 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
45491 TGCAATCCAT
Statistics
Matches: 280, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
184 6 0.02
185 138 0.49
186 136 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:45578 original size:19 final size:19
Alignment explanation
Indices: 45538--45666 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
45528 TAGTTTACTT
* *
45538 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
45558 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
45577 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
45596 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
45610 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
45629 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
45643 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
45662 TCGCA
1 TCGCA
45667 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:45617 original size:33 final size:32
Alignment explanation
Indices: 45574--45666 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
45564 CGCGAAACCA
**
45574 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
45606 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
45639 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
45667 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:45664 original size:52 final size:52
Alignment explanation
Indices: 45538--45666 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
45528 TAGTTTACTT
**
45538 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
45590 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
45643 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
45667 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:45684 original size:19 final size:19
Alignment explanation
Indices: 45662--45819 Score: 173
Period size: 19 Copynumber: 8.6 Consensus size: 19
45652 GAAACCAAAA
*
45662 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45681 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45700 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
45716 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
45733 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
45752 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
45771 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
* *
45790 TCGCGTTGCGATTTTAAGT
1 TCGCGTTGCGATTTTCATT
*
45809 TCGTGTTGCGA
1 TCGCGTTGCGA
45820 AAGTAAACTA
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
14 7 0.06
16 5 0.04
17 5 0.04
19 101 0.86
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45729 original size:52 final size:54
Alignment explanation
Indices: 45667--45804 Score: 190
Period size: 52 Copynumber: 2.5 Consensus size: 54
45657 CAAAATCGCA
45667 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCG
** * *
45719 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGG--T-TCG
*
45776 TTGCGATTATCATTTCGCGTTGCGATTTT
1 TTGCGATTTTCATTTCGCGTTGCGATTTT
45805 AAGTTCGTGT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
52 44 0.58
53 1 0.01
57 31 0.41
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (54 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCG
Found at i:47755 original size:14 final size:14
Alignment explanation
Indices: 47736--47771 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
47726 ATTGTTTAAT
47736 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
47750 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
47764 TGATTTGT
1 TGATTTGT
47772 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:47894 original size:19 final size:19
Alignment explanation
Indices: 47878--47975 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
47868 AAAAATGACT
47878 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47897 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
47916 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
47930 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47949 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
47969 ATCGCAA
1 ATCGCAA
47976 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48007 original size:53 final size:53
Alignment explanation
Indices: 47878--47994 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
47868 AAAAATGACT
47878 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
47930 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
47983 ATCGCAATGCGA
1 ATCGCAATGCGA
47995 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:48012 original size:19 final size:19
Alignment explanation
Indices: 47984--48185 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
47974 AACGAGAGAA
* *
47984 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
48003 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
48019 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
48036 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
48055 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
48071 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
48088 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
48107 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
48123 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
48140 TCCGCATTGCGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
48157 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
48173 TCGCATTGCGATT
1 TCGCATTGCGATT
48186 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 10, Indels: 44
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.03
14 23 0.15
15 1 0.01
16 22 0.15
17 20 0.13
18 2 0.01
19 72 0.48
20 6 0.04
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:48027 original size:33 final size:33
Alignment explanation
Indices: 47990--48199 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
47980 AGAATCGCAA
*
47990 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
48023 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
48061 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
48094 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
48127 TGCGATTTTCATTTCCGCATTGCGATT-TCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
48160 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
48193 TGCGATT
1 TGCGATT
48200 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 15, Indels: 30
0.77 0.08 0.16
Matches are distributed among these distances:
31 9 0.06
32 18 0.12
33 76 0.52
34 13 0.09
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:48185 original size:52 final size:52
Alignment explanation
Indices: 47984--48154 Score: 315
Period size: 52 Copynumber: 3.3 Consensus size: 52
47974 AACGAGAGAA
* *
47984 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
48036 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
48088 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
48140 TCCGCATTGCGATTT
1 T-CGCATTGCGATTT
48155 CATGTTGGGA
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.89
53 13 0.11
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:50495 original size:12 final size:12
Alignment explanation
Indices: 50478--50502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50468 TCTTCGGGGA
50478 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50490 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50502 C
1 C
50503 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:50710 original size:24 final size:24
Alignment explanation
Indices: 50676--50722 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
50666 CTGAAACATC
50676 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
50700 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
50723 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:51429 original size:20 final size:20
Alignment explanation
Indices: 51401--51630 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
51391 AAATTTCAGT
* * *
51401 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51421 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
51441 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51461 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
51481 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
51501 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
51521 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
51541 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
51561 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
51581 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
51601 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
51621 GTTGCGATTT
1 GTTGCGATTT
51631 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:51647 original size:21 final size:21
Alignment explanation
Indices: 51617--51699 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
51607 ATTTTCATAT
*
51617 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
51638 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
51659 TCGCATTGTGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
51680 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
51700 TTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:51903 original size:17 final size:17
Alignment explanation
Indices: 51883--51917 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
51873 AATATATAAA
*
51883 TTTTGAAAACATATTAT
1 TTTTGAAAACATAATAT
51900 TTTTGAAAACATAATAT
1 TTTTGAAAACATAATAT
51917 T
1 T
51918 ATAAAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (17 bp):
TTTTGAAAACATAATAT
Found at i:53171 original size:4 final size:4
Alignment explanation
Indices: 53164--53223 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
53154 ATTAATTTAA
* *
53164 ATTT ATTTT ATTT ATTT A-AT ATTT ATTTT ATTTT ATTTT AATT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT A-TTT A-TTT A-TTT ATTT ATTT
53211 ATTT ACTTT ATTT
1 ATTT A-TTT ATTT
53224 TAACCCTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 2 0.04
4 24 0.50
5 22 0.46
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:53176 original size:9 final size:9
Alignment explanation
Indices: 53164--53223 Score: 68
Period size: 9 Copynumber: 6.4 Consensus size: 9
53154 ATTAATTTAA
53164 ATTTATTTT
1 ATTTATTTT
53173 ATTTATTTAAT
1 ATTTATTT--T
53184 ATTTATTTT
1 ATTTATTTT
53193 ATTTTATTTT
1 A-TTTATTTT
*
53203 AATTA-TTT
1 ATTTATTTT
*
53211 ATTTACTTT
1 ATTTATTTT
53220 ATTT
1 ATTT
53224 TAACCCTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
8 7 0.16
9 20 0.44
10 9 0.20
11 9 0.20
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTATTTT
Found at i:54304 original size:15 final size:16
Alignment explanation
Indices: 54284--54323 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
54274 TATTTTAAAC
54284 ATTTTAAAAAAT-TAA
1 ATTTTAAAAAATATAA
* *
54299 ATTTTATAAAATATAT
1 ATTTTAAAAAATATAA
54315 ATTTTAAAA
1 ATTTTAAAA
54324 CTACTTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAAAAAATATAA
Found at i:55600 original size:20 final size:20
Alignment explanation
Indices: 55553--55605 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
55543 GTCATTTGTA
*
55553 AAATT-ATATTTTAGGTATG
1 AAATTCATATTTTAGGTATC
* *
55572 ATTATTCATATTTTAGGTGTC
1 A-AATTCATATTTTAGGTATC
55593 AAATTCATATTTT
1 AAATTCATATTTT
55606 CATTTGGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (20 bp):
AAATTCATATTTTAGGTATC
Found at i:62168 original size:22 final size:22
Alignment explanation
Indices: 62142--62201 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
62132 TTAGTGCAGA
62142 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
62164 GGGAACCGATTCCCCC-TGTAG
1 GGGAATCGATACCCCCTTGAAG
62185 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
62202 GAGGGTTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:66235 original size:16 final size:16
Alignment explanation
Indices: 66206--66245 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
66196 ATTAAATAAG
66206 AAAA-TAAAAATGCAT
1 AAAATTAAAAATGCAT
* *
66221 AAATTTAAAAGTGCAT
1 AAAATTAAAAATGCAT
66237 AAAATTAAA
1 AAAATTAAA
66246 TATCAGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (16 bp):
AAAATTAAAAATGCAT
Found at i:66331 original size:31 final size:30
Alignment explanation
Indices: 66269--66338 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
66259 ATGCAATAAA
* **
66269 AAAATGTTAGTAGTTAGTAATTAGCGGTTAG
1 AAAA-GTTAGTAGTTAGAAATTAGCAATTAG
* *
66300 AAAGGTTAGTTGTTAGAAAATTAGCAATTAG
1 AAAAGTTAGTAGTTAG-AAATTAGCAATTAG
66331 AAAAGTTA
1 AAAAGTTA
66339 ACAGTTAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAAGTTAGTAGTTAGAAATTAGCAATTAG
Found at i:66624 original size:127 final size:129
Alignment explanation
Indices: 66445--66725 Score: 367
Period size: 127 Copynumber: 2.2 Consensus size: 129
66435 AAATAAAATA
* * * *
66445 AATAAAA-AAAAGTTAGTGGGTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCC-GAAT-
1 AATAAAATAAAAGTTAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAG-ATC
* * * * *
66507 CGGATCACCATAAGGTCG-ATTCAAATATTAGAAACAATAAATAAAT-A-AACAATTGTTAGAGT
65 CAG-TCACCACAAGATCGAATT-AAATATTAGAAACAATAAATAAATAATAACAATGGTTAAAGT
*
66569 GC
128 AC
*
66571 AATAAAATAAAAGTCAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAGATCC
1 AATAAAATAAAAGTTAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAGATCC
*
66636 AGTCACCACAAGATCGAATTGAATATTAGAAACAATAAATAAATAAATAACAATGGTTAAAGTAC
66 AGTCACCACAAGATCGAATTAAATATTAGAAACAATAAATAAAT-AATAACAATGGTTAAAGTAC
*
66701 AATAAAATAAAAATTAGTAGTTAGC
1 AATAAAATAAAAGTTAGTAGTTAGC
66726 TTGAAATAAA
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
126 7 0.05
127 83 0.62
128 6 0.04
129 1 0.01
130 37 0.28
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.23
Consensus pattern (129 bp):
AATAAAATAAAAGTTAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAGATCC
AGTCACCACAAGATCGAATTAAATATTAGAAACAATAAATAAATAATAACAATGGTTAAAGTAC
Found at i:68768 original size:58 final size:57
Alignment explanation
Indices: 68637--68768 Score: 135
Period size: 58 Copynumber: 2.3 Consensus size: 57
68627 TAATGAAAAG
* ** * *
68637 TCAAGTGATC-ATTTGTAACTTTTAATAGTTGGAGACTCAACAAAGCAACTCCTATAG
1 TCAAGGGATCAATTTGTAACTTTTAATAGTCAGAGACTCAACAAA-CAAATCCTATAA
* * *
68694 TTAAGGGATCATTTTGTAACTTTTGATAGTCAGAGAACTCAACAAA-AAATACCTTATAA
1 TCAAGGGATCAATTTGTAACTTTTAATAGTCAGAG-ACTCAACAAACAAAT-CC-TATAA
68753 TCAAGGGA-CAATTTGT
1 TCAAGGGATCAATTTGT
68769 GTATCTTACC
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
57 11 0.18
58 29 0.48
59 21 0.34
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (57 bp):
TCAAGGGATCAATTTGTAACTTTTAATAGTCAGAGACTCAACAAACAAATCCTATAA
Found at i:70381 original size:33 final size:33
Alignment explanation
Indices: 70331--70406 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
70321 AGATTGAATT
* *
70331 GTTGTTTCCTATCGACTTAATCGCTAAGTAATC
1 GTTGTTTCTTATAGACTTAATCGCTAAGTAATC
*
70364 TTTGTTTCTTATAGACTTAATCGCTAAGTAATC
1 GTTGTTTCTTATAGACTTAATCGCTAAGTAATC
70397 GTTGTTTCTT
1 GTTGTTTCTT
70407 TTTGTTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.46
Consensus pattern (33 bp):
GTTGTTTCTTATAGACTTAATCGCTAAGTAATC
Found at i:87642 original size:13 final size:13
Alignment explanation
Indices: 87624--87654 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
87614 TTGTTCATAA
87624 CATCATAACTCAC
1 CATCATAACTCAC
*
87637 CATCATAACTTAC
1 CATCATAACTCAC
87650 CATCA
1 CATCA
87655 CATCTCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (13 bp):
CATCATAACTCAC
Found at i:92243 original size:30 final size:30
Alignment explanation
Indices: 92209--92283 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
92199 AAATGGATTT
* * *
92209 AGTTTAGTGATCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAAA
*
92239 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
*
92269 AGTTTAGGGACCAAA
1 AGTTTAGTGACCAAA
92284 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:92678 original size:16 final size:16
Alignment explanation
Indices: 92657--92688 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
92647 CATATGAATC
92657 TCTTCCTATTCTCCAG
1 TCTTCCTATTCTCCAG
92673 TCTTCCTATTCTCCAG
1 TCTTCCTATTCTCCAG
92689 AAAAGACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.06, T:0.44
Consensus pattern (16 bp):
TCTTCCTATTCTCCAG
Found at i:94605 original size:31 final size:31
Alignment explanation
Indices: 94567--94781 Score: 335
Period size: 31 Copynumber: 6.9 Consensus size: 31
94557 GAGTCGAGGG
* *
94567 TTACCTATGTTATTCGGGATATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
94598 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
94629 TTACCTATGTTCTTCGGGACATATGGACA-T
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
94659 GTTACCTATGTTCTTCGGGATATATGGACAGT
1 -TTACCTATGTTCTTCGGGACATATGGACAGT
94691 TTACCTATGTTCTTCGGGACATATGGACA-T
1 TTACCTATGTTCTTCGGGACATATGGACAGT
** *
94721 GTTACCTATGTTCTTCGGGACATATGGGTAGA
1 -TTACCTATGTTCTTCGGGACATATGGACAGT
*
94753 TTACCTATGTTCTTTGGGACATATGGACA
1 TTACCTATGTTCTTCGGGACATATGGACA
94782 TATTATTATA
Statistics
Matches: 170, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
30 2 0.01
31 167 0.98
32 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:94885 original size:30 final size:30
Alignment explanation
Indices: 94851--94911 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
94841 CCTTAAGTTC
* *
94851 TCAGTAATGTACATGGGCTTATAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGATA
* *
94881 TCAGTACTATATATGGGCCTATAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGATA
94911 T
1 T
94912 TAAAAGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (30 bp):
TCAGTAATATACATGGGCCTATAAAAGATA
Found at i:94927 original size:30 final size:30
Alignment explanation
Indices: 94860--94927 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
94850 CTCAGTAATG
* **
94860 TACATGGGCTTATAAAAGATATCAGTACTA
1 TACATGGGCCTATAAAAGATATCAAAACTA
* * *
94890 TATATGGGCCTATAAAAGATATTAAAAGTA
1 TACATGGGCCTATAAAAGATATCAAAACTA
94920 TACATGGG
1 TACATGGG
94928 ATAGTACATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (30 bp):
TACATGGGCCTATAAAAGATATCAAAACTA
Found at i:95065 original size:6 final size:6
Alignment explanation
Indices: 95054--95154 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
95044 AATGTATTAC
* * * *
95054 ATGATA ATGATA TTGATG TTGATA ATGATA GA-GATC ATGATA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA
* * * * * * * *
95102 TTGATG TTGATA ATGATA GA-GATC ATGATA ACGATA TTGATG TTGATA
1 ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA ATGATA ATGATA
95150 ATGAT
1 ATGAT
95155 GCTATTTATG
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
5 2 0.03
6 69 0.95
7 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.37
Consensus pattern (6 bp):
ATGATA
Found at i:95078 original size:18 final size:18
Alignment explanation
Indices: 95055--95154 Score: 119
Period size: 18 Copynumber: 5.6 Consensus size: 18
95045 ATGTATTACA
95055 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** **
95073 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
95091 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** **
95109 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
*
95127 TGATAACGATATTGATGT
1 TGATAATGATATTGATGT
95145 TGATAATGAT
1 TGATAATGAT
95155 GCTATTTATG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:95093 original size:36 final size:36
Alignment explanation
Indices: 95053--95154 Score: 195
Period size: 36 Copynumber: 2.8 Consensus size: 36
95043 AAATGTATTA
95053 CATGATAATGATATTGATGTTGATAATGATAGAGAT
1 CATGATAATGATATTGATGTTGATAATGATAGAGAT
95089 CATGATAATGATATTGATGTTGATAATGATAGAGAT
1 CATGATAATGATATTGATGTTGATAATGATAGAGAT
*
95125 CATGATAACGATATTGATGTTGATAATGAT
1 CATGATAATGATATTGATGTTGATAATGAT
95155 GCTATTTATG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (36 bp):
CATGATAATGATATTGATGTTGATAATGATAGAGAT
Found at i:97609 original size:64 final size:65
Alignment explanation
Indices: 97523--97732 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 65
97513 TGCACTAAGA
* * * * *
97523 GTGCACCGGTGCATCAAGTGCATTTGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGG-TTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGATTG
** * *
97587 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGAA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGAT
97651 T-
64 TG
* ** *
97652 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGGAT
97715 TG
64 TG
*
97717 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
97733 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGATTG
Found at i:97657 original size:19 final size:19
Alignment explanation
Indices: 97633--97671 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
97623 AAAATCCTCA
* *
97633 GTGCATCGGTGCATGGAAT
1 GTGCATCGATGCATGAAAT
97652 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
97671 G
1 G
97672 CATTCGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:104218 original size:22 final size:21
Alignment explanation
Indices: 104176--104215 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
104166 GAGTTTATTT
*
104176 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
104197 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
104216 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:106241 original size:19 final size:19
Alignment explanation
Indices: 106217--106256 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
106207 AAAATCCTCA
* *
106217 GTGCATCGGTGCATGGAAT
1 GTGCATCGATGCATGAAAT
106236 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
106255 GT
1 GT
106257 ATTCGATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:106305 original size:65 final size:64
Alignment explanation
Indices: 106151--106316 Score: 187
Period size: 65 Copynumber: 2.6 Consensus size: 64
106141 GTGCACTAAG
*
106151 AGTGCATCGATGCATGG-CTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 AGTGCATCGATGCATGGAATGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CT
106215 C
64 C
* * * **
106216 AGTGCATCGGTGCATGGAAT-GTGCATCGATGCATGAAATGTATTCGATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGAATGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
* *
106278 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGGAATGGTGCATCGATGCATCA
106317 CTCTGAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 22 0.26
65 57 0.66
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATGGAATGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTC
Done.