Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009291.1 Hibiscus syriacus cultivar Beakdansim tig00112993_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: 337070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:195 original size:15 final size:15
Alignment explanation
Indices: 171--201 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
161 GCCCGTAAAC
*
171 TAAAGTAAACCAACT
1 TAAAGAAAACCAACT
186 TAAAGAAAACCAACT
1 TAAAGAAAACCAACT
201 T
1 T
202 TGGCTAGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
TAAAGAAAACCAACT
Found at i:6805 original size:21 final size:20
Alignment explanation
Indices: 6781--6819 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
6771 CATCAAGGCC
6781 TTTGTTGAAGCCATGAAATAT
1 TTTGTTGAAGCCAT-AAATAT
6802 TTTGTTGAAGCCATAAAT
1 TTTGTTGAAGCCATAAAT
6820 TCTTACAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTTGAAGCCATAAATAT
Found at i:7619 original size:42 final size:43
Alignment explanation
Indices: 7557--7637 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 43
7547 AAGAAAAATA
*
7557 TGCAAGAGTAAACAAATAAAAATTGCTAAAGC-AAAAATTAAT
1 TGCAAGAGTAAACAAATAAAAATTGATAAAGCTAAAAATTAAT
** * * *
7599 TGCAAGAGTAAGTAATTAAAAGTTGATAAGGCTAAAAAT
1 TGCAAGAGTAAACAAATAAAAATTGATAAAGCTAAAAAT
7638 GTTCGAGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 26 0.81
43 6 0.19
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (43 bp):
TGCAAGAGTAAACAAATAAAAATTGATAAAGCTAAAAATTAAT
Found at i:10760 original size:21 final size:21
Alignment explanation
Indices: 10736--10779 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10726 GTTTGATGGA
*
10736 GTGGCACTGTTAT-CACTTCAT
1 GTGGCACTATT-TCCACTTCAT
*
10757 GTGGCATTATTTCCACTTCAT
1 GTGGCACTATTTCCACTTCAT
10778 GT
1 GT
10780 TGACTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (21 bp):
GTGGCACTATTTCCACTTCAT
Found at i:11303 original size:26 final size:25
Alignment explanation
Indices: 11265--11313 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
11255 AAATAAATTA
11265 TAAAAAAAAATT-ATATAATTATAAT
1 TAAAAAAAAATTAAT-TAATTATAAT
*
11290 TAAATAAATAATTAATTAATTATA
1 TAAA-AAAAAATTAATTAATTATA
11314 TACCTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 15 0.71
27 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAAAAAAAATTAATTAATTATAAT
Found at i:11477 original size:20 final size:19
Alignment explanation
Indices: 11445--11491 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
11435 TTGTTTCCAT
11445 ATTCAAGAA-AATAATATTAA
1 ATTCAA-AATAAT-ATATTAA
*
11465 ATTCAAAATAATATTTTAA
1 ATTCAAAATAATATATTAA
11484 A-TCAAAAT
1 ATTCAAAAT
11492 TTTACCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (19 bp):
ATTCAAAATAATATATTAA
Found at i:11485 original size:19 final size:16
Alignment explanation
Indices: 11452--11491 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 16
11442 CATATTCAAG
11452 AAAATAATATTAAATTC
1 AAAATAATATTAAA-TC
11469 AAAATAATATTTTAAATC
1 AAAATAATA--TTAAATC
11487 AAAAT
1 AAAAT
11492 TTTACCCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATATTAAATC
Found at i:18622 original size:21 final size:21
Alignment explanation
Indices: 18570--18631 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
18560 TTGGTGCAGA
*
18570 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCC-TGAAG
* *
18592 GGGAAACCGATTCCCCCTGTAG
1 GGG-AACCGATACCCCCTGAAG
*
18614 GGGAACCGAAACCCCCTG
1 GGGAACCGATACCCCCTG
18632 GGGTTCTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 13 0.38
22 10 0.29
23 11 0.32
ACGTcount: A:0.26, C:0.32, G:0.27, T:0.15
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:20175 original size:18 final size:18
Alignment explanation
Indices: 20141--20177 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20131 AACAAACACA
*
20141 AGGAACAAGCTCCACCAG
1 AGGAACAAGCACCACCAG
*
20159 AGGAACAAGCACGACCAG
1 AGGAACAAGCACCACCAG
20177 A
1 A
20178 AGATCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.30, G:0.24, T:0.03
Consensus pattern (18 bp):
AGGAACAAGCACCACCAG
Found at i:20539 original size:17 final size:17
Alignment explanation
Indices: 20517--20568 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
20507 TTGATTGTTG
20517 GATGTTTGAATTTGGTT
1 GATGTTTGAATTTGGTT
*
20534 GATGTTT---TAT-G--
1 GATGTTTGAATTTGGTT
20545 GATGTTTGAATTTGGTT
1 GATGTTTGAATTTGGTT
20562 GATGTTT
1 GATGTTT
20569 TATGGATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
11 7 0.26
13 1 0.04
14 4 0.15
15 1 0.04
17 14 0.52
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (17 bp):
GATGTTTGAATTTGGTT
Found at i:20547 original size:28 final size:28
Alignment explanation
Indices: 20515--20582 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
20505 TTTTGATTGT
20515 TGGATGTTTGAATTTGGTTGATGTTTTA
1 TGGATGTTTGAATTTGGTTGATGTTTTA
20543 TGGATGTTTGAATTTGGTTGATGTTTTA
1 TGGATGTTTGAATTTGGTTGATGTTTTA
20571 TGGATGTTTGAA
1 TGGATGTTTGAA
20583 CTTATATTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.51
Consensus pattern (28 bp):
TGGATGTTTGAATTTGGTTGATGTTTTA
Found at i:21477 original size:10 final size:10
Alignment explanation
Indices: 21446--21480 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
21436 AGAAGCATTG
21446 ATCAACAACA
1 ATCAACAACA
**
21456 AGAAACAACA
1 ATCAACAACA
21466 ATCAACAACA
1 ATCAACAACA
21476 ATCAA
1 ATCAA
21481 GAGAGAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.63, C:0.26, G:0.03, T:0.09
Consensus pattern (10 bp):
ATCAACAACA
Found at i:21940 original size:29 final size:28
Alignment explanation
Indices: 21907--21978 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
21897 AACTAAATAA
21907 ACACCAACTTTCTTTTTTCTCCTTCAACT
1 ACACCAACTTTCTTTTTT-TCCTTCAACT
*
21936 ACACCAACTTTCTTTCTTTTCCTTGAACT
1 ACACCAACTTTCTTT-TTTTCCTTCAACT
*
21965 AAACCAA-TTT-TTTT
1 ACACCAACTTTCTTTT
21979 AACTTCACCG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.03
27 3 0.08
28 3 0.08
29 30 0.75
30 3 0.08
ACGTcount: A:0.24, C:0.29, G:0.01, T:0.46
Consensus pattern (28 bp):
ACACCAACTTTCTTTTTTTCCTTCAACT
Found at i:22532 original size:19 final size:21
Alignment explanation
Indices: 22508--22553 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
22498 ATTATTAGGG
*
22508 TAAACTAAC-A-TTTAGTACT
1 TAAACTAACAATTTTAGTAAT
*
22527 TAAACTATCAATTTTAGTAAT
1 TAAACTAACAATTTTAGTAAT
22548 TAAACT
1 TAAACT
22554 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 14 0.61
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAACTAACAATTTTAGTAAT
Found at i:29044 original size:19 final size:19
Alignment explanation
Indices: 29020--29067 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
29010 TCATTGATCA
29020 ATGATGTATGTACATGTGT
1 ATGATGTATGTACATGTGT
*
29039 ATGATGAATGTACATGTGT
1 ATGATGTATGTACATGTGT
*
29058 ATGAAGTATG
1 ATGATGTATG
29068 AATACATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (19 bp):
ATGATGTATGTACATGTGT
Found at i:29084 original size:2 final size:2
Alignment explanation
Indices: 29077--29104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29067 GAATACATTC
29077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29105 GTATTAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29612 original size:23 final size:24
Alignment explanation
Indices: 29567--29616 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
29557 ATCTTTTATA
29567 TATAGTTTAAAATTTTAAGTTAAAT
1 TATAGTTTAAAATTTTAAGTT-AAT
29592 TATA-TTT-AAATTATTAA-TTAAT
1 TATAGTTTAAAATT-TTAAGTTAAT
29614 TAT
1 TAT
29617 TACATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 7 0.29
25 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TATAGTTTAAAATTTTAAGTTAAT
Found at i:35252 original size:13 final size:14
Alignment explanation
Indices: 35236--35290 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 14
35226 AAAGTAAACT
35236 GTCAA-AGGTCAAA
1 GTCAACAGGTCAAA
35249 GTCAA-AGGTCAACA
1 GTCAACAGGTCAA-A
*
35263 GGCAAGTCAGGTCAAA
1 GTCAA--CAGGTCAAA
35279 GTCAACAGGTCA
1 GTCAACAGGTCA
35291 TACCAGTTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 12 0.33
14 12 0.33
16 5 0.14
17 7 0.19
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (14 bp):
GTCAACAGGTCAAA
Found at i:35259 original size:20 final size:20
Alignment explanation
Indices: 35222--35283 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
35212 TTTGACTTTT
*
35222 GGTCAAAGT-AAACTGTCAAA
1 GGTCAAAGTCAAA-GGTCAAA
35242 GGTCAAAGTCAAAGGTCAACA
1 GGTCAAAGTCAAAGGTCAA-A
35263 GG-C-AAGTC--AGGTCAAA
1 GGTCAAAGTCAAAGGTCAAA
35279 -GTCAA
1 GGTCAA
35284 CAGGTCATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.03
16 2 0.05
17 8 0.22
19 5 0.14
20 15 0.41
21 6 0.16
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
GGTCAAAGTCAAAGGTCAAA
Found at i:35871 original size:25 final size:25
Alignment explanation
Indices: 35843--35908 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
35833 GGGGTGACTA
35843 GGGATTTTGGGATTTTGGAAAATTG
1 GGGATTTTGGGATTTTGGAAAATTG
*
35868 GGGATTTTAGGATTTTGGAAAATTG
1 GGGATTTTGGGATTTTGGAAAATTG
*
35893 GGGATTTTGGTATTTT
1 GGGATTTTGGGATTTT
35909 ATATCTTGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (25 bp):
GGGATTTTGGGATTTTGGAAAATTG
Found at i:38506 original size:20 final size:19
Alignment explanation
Indices: 38459--38512 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
38449 ACTTAGGCTG
**
38459 GTTCAAGTTGACTCAGTTT
1 GTTCAAGTTGACTCAGTCA
*
38478 GGTCTAAGTTGACTCAGATCA
1 GTTC-AAGTTGACTCAG-TCA
38499 GTTCAAGTTGACTC
1 GTTCAAGTTGACTC
38513 GAATTGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (19 bp):
GTTCAAGTTGACTCAGTCA
Found at i:41533 original size:26 final size:26
Alignment explanation
Indices: 41501--41563 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
41491 ATTTAGAGAG
41501 TTATTAATTTATCGATAAATTAATAA
1 TTATTAATTTATCGATAAATTAATAA
41527 TTATTAATTTATCGATAAATTAATAA
1 TTATTAATTTATCGATAAATTAATAA
41553 TTATTAATTTA
1 TTATTAATTTA
41564 AAGAGTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATTAATAA
Found at i:43156 original size:19 final size:20
Alignment explanation
Indices: 43118--43158 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
43108 TTAACTTTTT
43118 GGTCAAAGTCAAAGATCAAC
1 GGTCAAAGTCAAAGATCAAC
*
43138 GGTCAAAGTC-AATATCAAC
1 GGTCAAAGTCAAAGATCAAC
43157 GG
1 GG
43159 GCATGTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (20 bp):
GGTCAAAGTCAAAGATCAAC
Found at i:43187 original size:18 final size:18
Alignment explanation
Indices: 43145--43187 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
43135 AACGGTCAAA
* * *
43145 GTCAATATCAACGGGCAT
1 GTCAATGTCAACAGGCAG
43163 GTCAATGTCAACAGGCAG
1 GTCAATGTCAACAGGCAG
43181 GTCAATG
1 GTCAATG
43188 CCTAGGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (18 bp):
GTCAATGTCAACAGGCAG
Found at i:43265 original size:20 final size:20
Alignment explanation
Indices: 43242--43288 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
43232 TTGGTTTGAT
* *
43242 TTGACTCATATTGAATCAAG
1 TTGACTCAAATCGAATCAAG
* *
43262 TTGACTCAAATCGATTCGAG
1 TTGACTCAAATCGAATCAAG
43282 TTGACTC
1 TTGACTC
43289 GAACCAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (20 bp):
TTGACTCAAATCGAATCAAG
Found at i:43298 original size:20 final size:20
Alignment explanation
Indices: 43260--43298 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43250 TATTGAATCA
* *
43260 AGTTGACTCAAATCGATTCG
1 AGTTGACTCAAACCAATTCG
*
43280 AGTTGACTCGAACCAATTC
1 AGTTGACTCAAACCAATTC
43299 TAAAGTCGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTTGACTCAAACCAATTCG
Found at i:58069 original size:20 final size:20
Alignment explanation
Indices: 58044--58090 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
58034 AATTTAATCA
58044 TTCATTTTTTTACATTTACT
1 TTCATTTTTTTACATTTACT
58064 TTCATTTTTTTACATTTACT
1 TTCATTTTTTTACATTTACT
58084 TTC-TTTT
1 TTCATTTT
58091 ACTCTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCATTTTTTTACATTTACT
Found at i:75773 original size:15 final size:15
Alignment explanation
Indices: 75749--75784 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
75739 CACGAAAATG
75749 AAAA-AAGAAAAACA
1 AAAAGAAGAAAAACA
*
75763 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAACA
75778 AAAAGAA
1 AAAAGAA
75785 AACGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAACA
Found at i:83033 original size:49 final size:49
Alignment explanation
Indices: 82956--83367 Score: 558
Period size: 49 Copynumber: 8.4 Consensus size: 49
82946 TTATACTGAA
* * * ** *
82956 ATGCATTAAATTTTCATTAGTGGTACCTTTCTGCCAAAAATACACCATT
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
*
83005 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAAAGCACCA-T
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
* * * *
83053 ATGCATTTAACTTGCATTAGTGGCACATTTCTGCAAAAAAAATGCACCGTT
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGC--CAAAAATGCACCATT
* * *
83104 ATGCATTTAACTTGCATTAGTGACACCTTTCTACC-AAAAGGCACCATC
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
** * *
83152 ATGCAGCTAACTTGCATTAGTGACACGTTTTTGCCAAAAATGCACCATT
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
* * *
83201 ATACATTTAACTTGCATTAGTGACATCTTTATGCCAAAAATGCACCATT
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
*
83250 ATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATT
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
* * *
83299 ATGCATTTAACTTGCATTAGTGGCACCTGTATGCCCAAAAATGCACCATT
1 ATGCATTTAACTTGCATTAGTGACACCTTTCTG-CCAAAAATGCACCATT
83349 ATGCATTTAACTTGCATTA
1 ATGCATTTAACTTGCATTA
83368 TAGCAGTTCA
Statistics
Matches: 320, Mismatches: 38, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
48 73 0.23
49 170 0.53
50 45 0.14
51 32 0.10
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (49 bp):
ATGCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATT
Found at i:83117 original size:99 final size:98
Alignment explanation
Indices: 82956--83367 Score: 576
Period size: 99 Copynumber: 4.2 Consensus size: 98
82946 TTATACTGAA
* * * * *
82956 ATGCATTAAATTTTCATTAGTGGTACCTTTCTGCCAAAAATACACCATTATGCATTTAACTTGCA
1 ATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCA
* *
83021 TTAGTGACACCTTTCTGCCAAAAAAGCACCA-T
66 TTAGTGACACCTTTATGCCAAAAATGCACCATT
* * *
83053 ATGCATTTAACTTGCATTAGTGGCACATTTCTGCAAAAAAAATGCACCGTTATGCATTTAACTTG
1 ATGCATTTAACTTGCATTAGTGGCACCTTTCTGC--CAAAAATGCACCATTATGCATTTAACTTG
* * * *
83118 CATTAGTGACACCTTTCTACC-AAAAGGCACCATC
64 CATTAGTGACACCTTTATGCCAAAAATGCACCATT
** * * * *
83152 ATGCAGCTAACTTGCATTAGTGACACGTTTTTGCCAAAAATGCACCATTATACATTTAACTTGCA
1 ATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCA
*
83217 TTAGTGACATCTTTATGCCAAAAATGCACCATT
66 TTAGTGACACCTTTATGCCAAAAATGCACCATT
83250 ATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCA
1 ATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCA
* *
83315 TTAGTGGCACCTGTATGCCCAAAAATGCACCATT
66 TTAGTGACACCTTTATG-CCAAAAATGCACCATT
83349 ATGCATTTAACTTGCATTA
1 ATGCATTTAACTTGCATTA
83368 TAGCAGTTCA
Statistics
Matches: 277, Mismatches: 33, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
97 73 0.26
98 94 0.34
99 110 0.40
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (98 bp):
ATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCA
TTAGTGACACCTTTATGCCAAAAATGCACCATT
Found at i:87301 original size:20 final size:20
Alignment explanation
Indices: 87276--87332 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 20
87266 CGATGTTGCC
*
87276 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCCTACCA
* *
87296 TGGTATCAATACTACCCTACTA
1 TGGTATCGATAC--CCCTACCA
*
87318 TGGTACCGATACCCC
1 TGGTATCGATACCCC
87333 CTTATGGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 14 0.47
22 16 0.53
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (20 bp):
TGGTATCGATACCCCTACCA
Found at i:93682 original size:78 final size:79
Alignment explanation
Indices: 93561--93859 Score: 474
Period size: 79 Copynumber: 3.8 Consensus size: 79
93551 TTGTTATTGC
* **
93561 ACCCATATGCATTTCAGAGATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTT
1 ACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTT
*
93626 TATGCTAACAATGT
66 TATGCTGACAATGT
* * *
93640 ACCCATATACATTT-AGCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATTTTTATTT
1 ACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTT
93704 TATGCTGACAATGT
66 TATGCTGACAATGT
* *
93718 ACCCATATACATTTCAGCTATGGCATCCTTTAATGCCAATAATGCACCCATATGCATTTTTCTTT
1 ACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTT
93783 TATGCTGACAATGT
66 TATGCTGACAATGT
* * * *
93797 ACCCATATACATTTTAGCTATGGCATCATTTCATGACAATAATACACCCATATGCATTATTCT
1 ACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCT
93860 ATTTTCATTC
Statistics
Matches: 203, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
78 72 0.35
79 131 0.65
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.36
Consensus pattern (79 bp):
ACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTT
TATGCTGACAATGT
Found at i:93731 original size:34 final size:34
Alignment explanation
Indices: 93679--93811 Score: 95
Period size: 34 Copynumber: 3.6 Consensus size: 34
93669 TCATGCCAAT
*
93679 AATGCACCCATATGCATTTTTATTTTATGCTGAC
1 AATGCACCCATATACATTTTTATTTTATGCTGAC
* ** *
93713 AATGTACCCATATACATTTCAGCTATGGCATCCTTTAATGCCAAT
1 AATGCACCCATATACATTT----T-T---AT--TTT-ATGCTGAC
* *
93758 AATGCACCCATATGCATTTTTCTTTTATGCTGAC
1 AATGCACCCATATACATTTTTATTTTATGCTGAC
*
93792 AATGTACCCATATACATTTT
1 AATGCACCCATATACATTTT
93812 AGCTATGGCA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
34 40 0.53
35 3 0.04
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 2 0.03
44 3 0.04
45 22 0.29
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (34 bp):
AATGCACCCATATACATTTTTATTTTATGCTGAC
Found at i:94402 original size:19 final size:21
Alignment explanation
Indices: 94358--94409 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
94348 CGATGTTGTC
94358 TGGTATCGATACTACCCTACTA
1 TGGTATCGATACTACCCTA-TA
*
94380 TGGTACCGATACT-CCCT-TA
1 TGGTATCGATACTACCCTATA
94399 TGGTATCGATA
1 TGGTATCGATA
94410 TCAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (21 bp):
TGGTATCGATACTACCCTATA
Found at i:94477 original size:75 final size:75
Alignment explanation
Indices: 94324--94485 Score: 197
Period size: 75 Copynumber: 2.2 Consensus size: 75
94314 TACTTCCTCT
* *
94324 TGGTATCGATACCAAAATTAGGTTCGATGTTGTCTGGTATCGATACTACCCTACTATGGTACCGA
1 TGGTATCGATACCAAAATTAGATTCGATGTTGTCTGGTATCGATACTACCCTACAATGGTACCGA
*
94389 TACTCCCTTA
66 TACTCCCTAA
* *
94399 TGGTATCGATATCAAAATTAGATTCGATGTT-TACTTGGTATC-A-A-TACCCTTACAATGGTAT
1 TGGTATCGATACCAAAATTAGATTCGATGTTGT-C-TGGTATCGATACTACCC-TACAATGGTAC
* *
94460 CGATATTGCCTCAA
63 CGATACTCCCT-AA
94474 TGGTATCGATAC
1 TGGTATCGATAC
94486 TGATTGAATC
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
73 5 0.07
74 20 0.27
75 43 0.57
76 7 0.09
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (75 bp):
TGGTATCGATACCAAAATTAGATTCGATGTTGTCTGGTATCGATACTACCCTACAATGGTACCGA
TACTCCCTAA
Found at i:97878 original size:14 final size:14
Alignment explanation
Indices: 97839--97883 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
97829 AGGATTGAGG
97839 ATTTTAGAATTTAAA
1 ATTTTAGAATTT-AA
* *
97854 ATTTAAAAATTTAA
1 ATTTTAGAATTTAA
*
97868 ATTTTAGAATTAAA
1 ATTTTAGAATTTAA
97882 AT
1 AT
97884 ATACACAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTTTAGAATTTAA
Found at i:98159 original size:19 final size:19
Alignment explanation
Indices: 98132--98191 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
98122 ACTATGTTTA
*
98132 TATACACAAAGCAATACAC
1 TATAAACAAAGCAATACAC
98151 TATAAACAAAGCAATACAC
1 TATAAACAAAGCAATACAC
98170 TATAAACAAAGCAATACAC
1 TATAAACAAAGCAATACAC
98189 TAT
1 TAT
98192 GTTTATTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.55, C:0.22, G:0.05, T:0.18
Consensus pattern (19 bp):
TATAAACAAAGCAATACAC
Found at i:98229 original size:37 final size:37
Alignment explanation
Indices: 98175--98254 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
98165 TACACTATAA
* ** *
98175 ACAAAGCAATACACTATGTTTATTTACACAAACCAAC
1 ACAAACCAATACACTATGTACATATACACAAACCAAC
* *
98212 CCAAACCAATACACTATGTACATATGCACAAACCAAC
1 ACAAACCAATACACTATGTACATATACACAAACCAAC
98249 ACAAAC
1 ACAAAC
98255 ATCAATATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.19
Consensus pattern (37 bp):
ACAAACCAATACACTATGTACATATACACAAACCAAC
Found at i:100058 original size:35 final size:36
Alignment explanation
Indices: 99990--100063 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 36
99980 CCTTAGGTTC
** * *
99990 ATAAGGAATTACCAGCTTGATCGGTGCTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCGAAGATAAACCTAT
* *
100026 ATAAGG-ATTACCAGTTTGATCGAAGATAAACCTCT
1 ATAAGGAATTACCAGCTTGATCGAAGATAAACCTAT
100061 ATA
1 ATA
100064 TACTTCATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 26 0.81
36 6 0.19
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCGAAGATAAACCTAT
Found at i:101872 original size:17 final size:17
Alignment explanation
Indices: 101852--101957 Score: 92
Period size: 17 Copynumber: 6.1 Consensus size: 17
101842 TTTAACTAAG
101852 TAGTTCATTGATTAAAC
1 TAGTTCATTGATTAAAC
101869 TAGTTCATTCAAGATT--AC
1 TAGTTCATT---GATTAAAC
* * *
101887 AAGTTCAATGAATAAAGC
1 TAGTTCATTGATTAAA-C
101905 TAGTTCATT-ATTTAAAC
1 TAGTTCATTGA-TTAAAC
* *
101922 TAGTTCATTCATCAAAC
1 TAGTTCATTGATTAAAC
*
101939 TAGTTCATTTATTAAAC
1 TAGTTCATTGATTAAAC
101956 TA
1 TA
101958 ACTCTTAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
15 3 0.04
17 43 0.60
18 22 0.31
20 4 0.06
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (17 bp):
TAGTTCATTGATTAAAC
Found at i:102505 original size:21 final size:22
Alignment explanation
Indices: 102480--102523 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
102470 TTAAGGCCAA
*
102480 ATTCA-CCTTCAAATTG-TCTAG
1 ATTCATCC-TCAAAATGATCTAG
102501 ATTCATCCTCAAAATGATCTAG
1 ATTCATCCTCAAAATGATCTAG
102523 A
1 A
102524 ATATTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTCATCCTCAAAATGATCTAG
Found at i:105777 original size:11 final size:11
Alignment explanation
Indices: 105761--105786 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
105751 ACCACAATCT
105761 AATGCAACTAA
1 AATGCAACTAA
105772 AATGCAACTAA
1 AATGCAACTAA
105783 AATG
1 AATG
105787 ATGTGCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (11 bp):
AATGCAACTAA
Found at i:114303 original size:12 final size:12
Alignment explanation
Indices: 114259--114309 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
114249 CAAAGCATTT
114259 TTATTTTACTTG
1 TTATTTTACTTG
*
114271 TTCATTTT-TTTG
1 TT-ATTTTACTTG
114283 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
114297 TTATTTTCCTTG
1 TTATTTTACTTG
114309 T
1 T
114310 CTTTTAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.67
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:126370 original size:17 final size:17
Alignment explanation
Indices: 126335--126470 Score: 134
Period size: 17 Copynumber: 7.9 Consensus size: 17
126325 AGCTATGCAC
* *
126335 TTCATTTATT-AAGTAG
1 TTCATTGATTAAACTAG
126351 TTCATTGATTAAACTAG
1 TTCATTGATTAAACTAG
*
126368 TTCATTCATTAAACTAG
1 TTCATTGATTAAACTAG
*
126385 TTCATTCATTAAACTAG
1 TTCATTGATTAAACTAG
*
126402 TTCATTCAAGATT--ACAAG
1 TTCATT---GATTAAACTAG
* *
126420 TTCATTGAATAAAGTTAG
1 TTCATTGATTAAA-CTAG
*
126438 TTCATTAATTAAACTAG
1 TTCATTGATTAAACTAG
*
126455 TTCATTTATTAAACTA
1 TTCATTGATTAAACTA
126471 AATCTTAATT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.03
16 9 0.09
17 63 0.62
18 23 0.23
20 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (17 bp):
TTCATTGATTAAACTAG
Found at i:136828 original size:12 final size:13
Alignment explanation
Indices: 136797--136830 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
136787 AAATTAGATG
*
136797 CACTTAATTAAAT
1 CACTTAAATAAAT
136810 CACTTAAATAAAT
1 CACTTAAATAAAT
136823 -ACTTAAAT
1 CACTTAAAT
136831 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTAAATAAAT
Found at i:140078 original size:19 final size:20
Alignment explanation
Indices: 140054--140094 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
140044 ACTTAGGGTC
140054 CGTTTG-TTTTCATGGAAAA
1 CGTTTGATTTTCATGGAAAA
140073 CGTTTGATTTTCATGGAAAA
1 CGTTTGATTTTCATGGAAAA
140093 CG
1 CG
140095 GATTCCGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTTGATTTTCATGGAAAA
Found at i:140132 original size:14 final size:14
Alignment explanation
Indices: 140113--140147 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
140103 AAAATGAATT
140113 ACATTTTCTAGAAA
1 ACATTTTCTAGAAA
*
140127 ACATTTTCTGGAAA
1 ACATTTTCTAGAAA
*
140141 TCATTTT
1 ACATTTT
140148 ACAGTTTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (14 bp):
ACATTTTCTAGAAA
Found at i:140964 original size:21 final size:21
Alignment explanation
Indices: 140938--140991 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
140928 TAAAGGTAAT
*
140938 TCTTTTTTATTTTATCTTTTA
1 TCTTTTTTATTTTATATTTTA
*
140959 TCTTTTATT-TCTTATATTTTA
1 TCTTTT-TTATTTTATATTTTA
*
140980 TTTTGTTTTATT
1 TCTT-TTTTATT
140992 ATGATCGCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (21 bp):
TCTTTTTTATTTTATATTTTA
Found at i:140981 original size:14 final size:13
Alignment explanation
Indices: 140940--140983 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
140930 AAGGTAATTC
140940 TTTTT-TATTTTA
1 TTTTTATATTTTA
*
140952 TCTTTTATCTTTTA
1 T-TTTTATATTTTA
140966 TTTCTTATATTTTA
1 TTT-TTATATTTTA
140980 TTTT
1 TTTT
140984 GTTTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.04
13 7 0.26
14 19 0.70
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTATATTTTA
Found at i:141416 original size:20 final size:20
Alignment explanation
Indices: 141310--141418 Score: 60
Period size: 20 Copynumber: 5.2 Consensus size: 20
141300 TTTTTTTATC
*
141310 TTTTTATATTATATATTTTTA
1 TTTTTATATTATATA-TATTA
*
141331 TATTGTTAATATTATCTATATTA
1 T-TT-TT-ATATTATATATATTA
* * * *
141354 TGTTTATATAATGCATGTACT-
1 TTTTTATATTAT--ATATATTA
** *
141375 TTTTTATACCAT-TATAAATA
1 TTTTTATATTATATAT-ATTA
141395 TTTTTATATTATATATATTA
1 TTTTTATATTATATATATTA
141415 TTTT
1 TTTT
141419 CAAATCAATT
Statistics
Matches: 65, Mismatches: 15, Indels: 17
0.67 0.15 0.18
Matches are distributed among these distances:
18 2 0.03
19 2 0.03
20 23 0.35
21 15 0.23
22 7 0.11
23 7 0.11
24 9 0.14
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTTATATTATATATATTA
Found at i:147970 original size:15 final size:15
Alignment explanation
Indices: 147946--147979 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
147936 ATTATATTAG
147946 TTTTTTTA-TTTTTA
1 TTTTTTTATTTTTTA
147960 TTTTCTTTATTTTTTA
1 TTTT-TTTATTTTTTA
147976 TTTT
1 TTTT
147980 AATTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 4 0.22
16 10 0.56
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:147991 original size:21 final size:22
Alignment explanation
Indices: 147947--147991 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
147937 TTATATTAGT
* **
147947 TTTTTTATTTTTATTTTCTTTA
1 TTTTTTATTTTAATTTTCAATA
147969 TTTTTTATTTTAATTTT-AATA
1 TTTTTTATTTTAATTTTCAATA
147990 TT
1 TT
147992 AGTTCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTATTTTAATTTTCAATA
Found at i:152142 original size:53 final size:54
Alignment explanation
Indices: 152055--152160 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 54
152045 GCTCATAAGC
152055 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTA
1 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTA
* * *
152109 TTATTTTT-TCAATATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATT
152161 TTACCCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 41 0.84
54 8 0.16
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (54 bp):
TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTA
Found at i:152354 original size:40 final size:40
Alignment explanation
Indices: 152310--152431 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
152300 ACCGTAGTGC
152310 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
152350 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
152390 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
152430 TA
1 TA
152432 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:155038 original size:19 final size:19
Alignment explanation
Indices: 155014--155058 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
155004 CTTTAATTTG
155014 TTTATTTAATTATTTTT-CT
1 TTTATTTAATT-TTTTTACT
*
155033 TTTATTTAATTTTTTTATT
1 TTTATTTAATTTTTTTACT
155052 TTTATTT
1 TTTATTT
155059 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTAATTTTTTTACT
Found at i:155136 original size:23 final size:24
Alignment explanation
Indices: 155104--155148 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
155094 TTATTAATAA
155104 TATTTATTA-TTATATTATTTTTC
1 TATTTATTATTTATATTATTTTTC
* *
155127 TATTTTTTATTTATTTTATTTT
1 TATTTATTATTTATATTATTTT
155149 AATATATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (24 bp):
TATTTATTATTTATATTATTTTTC
Found at i:157957 original size:5 final size:5
Alignment explanation
Indices: 157943--158008 Score: 55
Period size: 5 Copynumber: 13.0 Consensus size: 5
157933 GAGGTAACCC
* * **
157943 ATTTT GTTTT ATTTT CATTTT A-TTT ATTTC ATTCC A-TTT ATTTT ATTTTTT
1 ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A--TTTT
157994 ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT
158009 TTTCTTTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 6 0.12
5 34 0.68
6 5 0.10
7 5 0.10
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:157974 original size:14 final size:14
Alignment explanation
Indices: 157950--158012 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
157940 CCCATTTTGT
157950 TTTATTTTCATTTTA
1 TTTA-TTTCATTTTA
**
157965 TTTATTTCATTCCA
1 TTTATTTCATTTTA
*
157979 TTTATTTTA-TTT-
1 TTTATTTCATTTTA
*
157991 TTTATTTTATTTTA
1 TTTATTTCATTTTA
*
158005 TTTTTTTC
1 TTTATTTC
158013 TTTGAACAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 9 0.23
13 4 0.10
14 22 0.56
15 4 0.10
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTCATTTTA
Found at i:158010 original size:12 final size:12
Alignment explanation
Indices: 157979--158003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
157969 TTTCATTCCA
157979 TTTATTTTATTT
1 TTTATTTTATTT
157991 TTTATTTTATTT
1 TTTATTTTATTT
158003 T
1 T
158004 ATTTTTTTCT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:160466 original size:19 final size:19
Alignment explanation
Indices: 160442--160486 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
160432 ATTTAATTTG
160442 TTTATTTAATTATTTT-TCT
1 TTTATTTAATT-TTTTATCT
*
160461 TTTATTTAATTTTTTATTT
1 TTTATTTAATTTTTTATCT
160480 TTTATTT
1 TTTATTT
160487 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTAATTTTTTATCT
Found at i:160559 original size:23 final size:24
Alignment explanation
Indices: 160533--160577 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
160523 TTATTATTAA
160533 TATTTATTA-TTATATTATTTTTC
1 TATTTATTATTTATATTATTTTTC
* *
160556 TATTTTTTATTTATTTTATTTT
1 TATTTATTATTTATATTATTTT
160578 AATATATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (24 bp):
TATTTATTATTTATATTATTTTTC
Found at i:161675 original size:10 final size:11
Alignment explanation
Indices: 161650--161675 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
161640 ACTGACTTAT
161650 TTTTTTCTTTC
1 TTTTTTCTTTC
161661 TTTTTTCTTTC
1 TTTTTTCTTTC
161672 TTTT
1 TTTT
161676 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:170748 original size:16 final size:16
Alignment explanation
Indices: 170710--170761 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 16
170700 CGATTAAATT
**
170710 TATATAATATTGTTATT
1 TATATAATATT-TTAAA
170727 TATATAATATTTTAAA
1 TATATAATATTTTAAA
*
170743 TATATAA-A-ATTAAA
1 TATATAATATTTTAAA
170757 TATAT
1 TATAT
170762 TTAAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 10 0.31
17 11 0.34
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TATATAATATTTTAAA
Found at i:174391 original size:15 final size:15
Alignment explanation
Indices: 174371--174401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
174361 CTTTAGAGGA
*
174371 TCTAAATTAGGAAAC
1 TCTAAACTAGGAAAC
174386 TCTAAACTAGGAAAC
1 TCTAAACTAGGAAAC
174401 T
1 T
174402 GACTAATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (15 bp):
TCTAAACTAGGAAAC
Found at i:179862 original size:34 final size:34
Alignment explanation
Indices: 179818--179885 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
179808 TAGACATAAC
*
179818 AAAAAGCTTAATCAGAGGTTGTGATACGAAATAG
1 AAAAAACTTAATCAGAGGTTGTGATACGAAATAG
179852 AAAAAACTTAATCAGAGGTTGTGATACGAAATAG
1 AAAAAACTTAATCAGAGGTTGTGATACGAAATAG
179886 TGATAGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.24
Consensus pattern (34 bp):
AAAAAACTTAATCAGAGGTTGTGATACGAAATAG
Found at i:182530 original size:11 final size:11
Alignment explanation
Indices: 182492--182572 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
182482 AAAAAAAATA
*
182492 TCAAGCTCAAT
1 TCAAGCTCGAT
* *
182503 TGAAGCTCAAGAC
1 TCAAGCTC--GAT
182516 TCAAGCTCGAT
1 TCAAGCTCGAT
*
182527 TCAAGCTCAAT
1 TCAAGCTCGAT
*
182538 TCAAGAAGCTCAAT
1 TC---AAGCTCGAT
*
182552 TCAAACTCGAT
1 TCAAGCTCGAT
182563 TCAAGCTCGA
1 TCAAGCTCGA
182573 CATATTAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
11 37 0.66
13 8 0.14
14 11 0.20
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:182548 original size:14 final size:14
Alignment explanation
Indices: 182529--182555 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
182519 AGCTCGATTC
182529 AAGCTCAATTCAAG
1 AAGCTCAATTCAAG
182543 AAGCTCAATTCAA
1 AAGCTCAATTCAA
182556 ACTCGATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (14 bp):
AAGCTCAATTCAAG
Found at i:182553 original size:25 final size:25
Alignment explanation
Indices: 182518--182567 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
182508 CTCAAGACTC
* *
182518 AAGCTCGATTCAAGCTCAATTCAAG
1 AAGCTCAATTCAAACTCAATTCAAG
*
182543 AAGCTCAATTCAAACTCGATTCAAG
1 AAGCTCAATTCAAACTCAATTCAAG
182568 CTCGACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (25 bp):
AAGCTCAATTCAAACTCAATTCAAG
Found at i:182568 original size:36 final size:35
Alignment explanation
Indices: 182492--182570 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 35
182482 AAAAAAAATA
*
182492 TCAAGCTCAATTGAAGCTCAAGACTCAAGCTCGAT
1 TCAAGCTCAATTGAAGCTCAAGACTCAAACTCGAT
*
182527 TCAAGCTCAATTCAAGAAGCTC-A-ATTCAAACTCGAT
1 TCAAGCTCAATT---GAAGCTCAAGACTCAAACTCGAT
182563 TCAAGCTC
1 TCAAGCTC
182571 GACATATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 12 0.31
36 19 0.49
37 1 0.03
38 7 0.18
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (35 bp):
TCAAGCTCAATTGAAGCTCAAGACTCAAACTCGAT
Found at i:183991 original size:28 final size:28
Alignment explanation
Indices: 183960--184026 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
183950 TTAAAACTTA
* * *
183960 AAACCTAAACCCTTAACCCCTGAACTAT
1 AAACCTAAACCCTTAAACCCTAAACCAT
*
183988 AAACCCTAAA-CTTTAAACCCTAAACCAT
1 AAA-CCTAAACCCTTAAACCCTAAACCAT
184016 AAACTCTAAAC
1 AAAC-CTAAAC
184027 ACTAAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 25 0.78
29 6 0.19
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (28 bp):
AAACCTAAACCCTTAAACCCTAAACCAT
Found at i:183997 original size:7 final size:7
Alignment explanation
Indices: 183958--184032 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
183948 ACTTAAAACT
*
183958 TAAAACC
1 TAAACCC
183965 TAAACCC
1 TAAACCC
*
183972 TTAACCCC
1 -TAAACCC
* **
183980 TGAACTA
1 TAAACCC
183987 TAAACCC
1 TAAACCC
**
183994 TAAACTT
1 TAAACCC
184001 TAAACCC
1 TAAACCC
*
184008 TAAACCA
1 TAAACCC
*
184015 TAAACTC
1 TAAACCC
*
184022 TAAACAC
1 TAAACCC
184029 TAAA
1 TAAA
184033 TTATAAAACC
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
7 44 0.88
8 6 0.12
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:183999 original size:14 final size:14
Alignment explanation
Indices: 183977--184026 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
183967 AACCCTTAAC
*
183977 CCCTGAACTATAAA
1 CCCTAAACTATAAA
*
183991 CCCTAAACTTTAAA
1 CCCTAAACTATAAA
*
184005 CCCTAAACCATAAA
1 CCCTAAACTATAAA
*
184019 CTCTAAAC
1 CCCTAAAC
184027 ACTAAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (14 bp):
CCCTAAACTATAAA
Found at i:184039 original size:21 final size:21
Alignment explanation
Indices: 183987--184032 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
183977 CCCTGAACTA
* * *
183987 TAAACCCTAAACTTTAAACCC
1 TAAACCATAAACTCTAAACAC
184008 TAAACCATAAACTCTAAACAC
1 TAAACCATAAACTCTAAACAC
184029 TAAA
1 TAAA
184033 TTATAAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCATAAACTCTAAACAC
Found at i:184184 original size:14 final size:14
Alignment explanation
Indices: 184165--184194 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
184155 TATAATTATC
*
184165 AATAATGTATTTTT
1 AATAATGTAATTTT
184179 AATAATGTAATTTT
1 AATAATGTAATTTT
184193 AA
1 AA
184195 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:186025 original size:42 final size:42
Alignment explanation
Indices: 185978--186062 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
185968 TCAAGATCTA
185978 GGCTTCCAAAATTTGTAGGATACAAATCCAATTATAAAGTAG
1 GGCTTCCAAAATTTGTAGGATACAAATCCAATTATAAAGTAG
186020 GGCTTCCAAAATTTGTAGGATACAAATCCAATTATAAAGTAG
1 GGCTTCCAAAATTTGTAGGATACAAATCCAATTATAAAGTAG
186062 G
1 G
186063 CCTTGATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (42 bp):
GGCTTCCAAAATTTGTAGGATACAAATCCAATTATAAAGTAG
Found at i:186821 original size:22 final size:23
Alignment explanation
Indices: 186787--186830 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
186777 ATACATATAT
186787 ATAAGTAAGATAATAAT-GAAAAA
1 ATAAGTAAGATAA-AATAGAAAAA
*
186810 ATAA-TAATATAAAATAGAAAA
1 ATAAGTAAGATAAAATAGAAAA
186831 CCGAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (23 bp):
ATAAGTAAGATAAAATAGAAAAA
Found at i:186848 original size:2 final size:2
Alignment explanation
Indices: 186841--186944 Score: 78
Period size: 2 Copynumber: 53.5 Consensus size: 2
186831 CCGAATGTAA
*
186841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** *
186882 A- AT GGG AA AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT A- AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
186920 A- AT ACT GAT GAT AT AA AT AT AT AT A
1 AT AT A-T -AT -AT AT AT AT AT AT AT A
186945 ATAAAGTTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
1 7 0.08
2 71 0.85
3 5 0.06
4 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (2 bp):
AT
Found at i:200688 original size:9 final size:9
Alignment explanation
Indices: 200638--200692 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
200628 AATAAAGAGG
200638 ATAAAA-AA
1 ATAAAATAA
200646 ATAAAATAA
1 ATAAAATAA
*
200655 AGT-AAATAC
1 A-TAAAATAA
*
200664 A-AAAATGA
1 ATAAAATAA
*
200672 ATAGAATAA
1 ATAAAATAA
200681 ATAAAATAA
1 ATAAAATAA
200690 ATA
1 ATA
200693 GAATGAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
8 11 0.30
9 25 0.68
10 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (9 bp):
ATAAAATAA
Found at i:200710 original size:18 final size:17
Alignment explanation
Indices: 200624--200708 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 17
200614 GTAACGTAAT
* *
200624 AAAAAATAAAGAGGATA
1 AAAAAATAAATAGAATA
200641 AAAAAATAAAATAAAGTAAATA
1 AAAAAAT-AAAT--AG--AATA
* *
200663 CAAAAATGAATAGAATA
1 AAAAAATAAATAGAATA
200680 AATAAAATAAATAGAATGA
1 AA-AAAATAAATAGAAT-A
200699 AGAAAAATAA
1 A-AAAAATAA
200709 TAACACTAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
17 12 0.22
18 16 0.30
19 11 0.20
20 3 0.06
21 3 0.06
22 9 0.17
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAAAATAAATAGAATA
Found at i:200800 original size:18 final size:19
Alignment explanation
Indices: 200777--200821 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
200767 TAAAAGGAAG
200777 AAAGAAAGAATA-A-AAATA
1 AAAGAAA-AATAGATAAATA
200795 AAAG-AAAATAGATAAATA
1 AAAGAAAAATAGATAAATA
200813 AAAGAAAAA
1 AAAGAAAAA
200822 ACGTATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 3 0.12
18 13 0.54
19 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAGAAAAATAGATAAATA
Found at i:200872 original size:22 final size:23
Alignment explanation
Indices: 200838--200881 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
200828 ATACATATAT
200838 ATAAGTAAGATAATAAT-GAAAAA
1 ATAAGTAAGATAA-AATAGAAAAA
*
200861 ATAA-TAATATAAAATAGAAAA
1 ATAAGTAAGATAAAATAGAAAA
200882 CCGAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (23 bp):
ATAAGTAAGATAAAATAGAAAAA
Found at i:200973 original size:39 final size:39
Alignment explanation
Indices: 200890--200975 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
200880 AACCGAATGT
200890 AATATATATATATACATATAAAATAATGGGAAATATAAA
1 AATATATATATATACATATAAAATAATGGGAAATATAAA
* * * *
200929 TATATATATATATATATATAATAAT-AT-TGATGATATAAA
1 AATATATATATATACATATAA-AATAATGGGA-AATATAAA
200968 AATATATA
1 AATATATA
200976 ATAAAGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.05
39 35 0.88
40 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (39 bp):
AATATATATATATACATATAAAATAATGGGAAATATAAA
Found at i:204441 original size:20 final size:20
Alignment explanation
Indices: 204416--204453 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
204406 CCTCTTATTT
*
204416 TGCGTTTGATTCGTTTCCCC
1 TGCGTTAGATTCGTTTCCCC
204436 TGCGTTAGATTCGTTTCC
1 TGCGTTAGATTCGTTTCC
204454 TGGTAGTCTA
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:0.08, C:0.26, G:0.21, T:0.45
Consensus pattern (20 bp):
TGCGTTAGATTCGTTTCCCC
Found at i:208322 original size:17 final size:17
Alignment explanation
Indices: 208293--208325 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
208283 ATCGAATTGA
208293 CTCGACTCGGACTCGAG
1 CTCGACTCGGACTCGAG
208310 CTCGAGCTC-GACTCGA
1 CTCGA-CTCGGACTCGA
208326 ATTCTTAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.18
Consensus pattern (17 bp):
CTCGACTCGGACTCGAG
Found at i:218242 original size:21 final size:21
Alignment explanation
Indices: 218217--218272 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
218207 TAGTGGCAGA
*
218217 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGAG
218238 TGCATGGATGCACTGCAGGAG
1 TGCATGGATGCACTGCAGGAG
*
218259 TGCATGTATGCACT
1 TGCATGGATGCACT
218273 TTGACACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGAG
Found at i:218519 original size:21 final size:21
Alignment explanation
Indices: 218495--218534 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
218485 ATATTTAATG
218495 AAAAAGATAACAATTGTTAAC
1 AAAAAGATAACAATTGTTAAC
* *
218516 AAAATGATATCAATTGTTA
1 AAAAAGATAACAATTGTTA
218535 CCATTTGTTT
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:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATAACAATTGTTAAC
Found at i:221767 original size:21 final size:21
Alignment explanation
Indices: 221737--221815 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
221727 ACTAGTGGCA
221737 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
221758 GGTGCCTGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
221779 GTTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
**
221800 ACTGCATGGATGCACT
1 GGTGCATGGATGCACT
221816 TTGACACCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:222711 original size:15 final size:15
Alignment explanation
Indices: 222691--222775 Score: 98
Period size: 15 Copynumber: 5.7 Consensus size: 15
222681 ATTTTATTAT
222691 TATGTGAATATGTTA
1 TATGTGAATATGTTA
* *
222706 TATGTGAAAATGTTT
1 TATGTGAATATGTTA
* *
222721 TACGTGAAAATGTTA
1 TATGTGAATATGTTA
*
222736 TATGTGAATATGTTC
1 TATGTGAATATGTTA
* * *
222751 TATGTGAATGTGATC
1 TATGTGAATATGTTA
222766 TATGTGAATA
1 TATGTGAATA
222776 AATGTCTGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (15 bp):
TATGTGAATATGTTA
Found at i:224700 original size:24 final size:24
Alignment explanation
Indices: 224663--224720 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
224653 GTCCTTCGGG
*
224663 ACAAA-TCTATGTGGCACTTAGGT
1 ACAAATTCTACGTGGCACTTAGGT
* *
224686 ACATATTCTACGTGGCACTTCGGT
1 ACAAATTCTACGTGGCACTTAGGT
*
224710 GCAAATTCTAC
1 ACAAATTCTAC
224721 ACGGTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (24 bp):
ACAAATTCTACGTGGCACTTAGGT
Found at i:230334 original size:24 final size:24
Alignment explanation
Indices: 230307--230386 Score: 135
Period size: 24 Copynumber: 3.3 Consensus size: 24
230297 AGTGATTTAA
230307 AGTTGGTTGTTCCTTTCATTTTTG
1 AGTTGGTTGTTCCTTTCATTTTTG
*
230331 AGTTGGTTGTTCCCTTCATTTTTG
1 AGTTGGTTGTTCCTTTCATTTTTG
230355 AGTTGGTTGTTCCCTTT-ATTTTTG
1 AGTTGGTTGTT-CCTTTCATTTTTG
230379 AGTTGGTT
1 AGTTGGTT
230387 TTGAATCTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
24 49 0.92
25 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.56
Consensus pattern (24 bp):
AGTTGGTTGTTCCTTTCATTTTTG
Found at i:231362 original size:15 final size:15
Alignment explanation
Indices: 231339--231423 Score: 80
Period size: 15 Copynumber: 5.7 Consensus size: 15
231329 ATTTTATTAT
231339 TATGTGAATATGTTA
1 TATGTGAATATGTTA
* *
231354 TATGCGAATATGTTT
1 TATGTGAATATGTTA
* * *
231369 TACGTAAAAATGTTA
1 TATGTGAATATGTTA
*
231384 TATGTGAATATGTTC
1 TATGTGAATATGTTA
* * * *
231399 TACGTGAATGTGATC
1 TATGTGAATATGTTA
231414 TATGTGAATA
1 TATGTGAATA
231424 AATGACACTT
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (15 bp):
TATGTGAATATGTTA
Found at i:231559 original size:23 final size:23
Alignment explanation
Indices: 231533--231576 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
231523 GGGTTCTACA
*
231533 TGGTCTTTTCGGACAATTCTATG
1 TGGTCCTTTCGGACAATTCTATG
*
231556 TGGTCCTTTGGGACAATTCTA
1 TGGTCCTTTCGGACAATTCTA
231577 CACGGTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (23 bp):
TGGTCCTTTCGGACAATTCTATG
Found at i:231587 original size:23 final size:22
Alignment explanation
Indices: 231526--231591 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
231516 GAGTTGAGGG
*
231526 TTCTACATGGTCTTTTCGGACAA
1 TTCTACATGGTC-TTTGGGACAA
**
231549 TTCTATGTGGTCCTTTGGGACAA
1 TTCTACATGGT-CTTTGGGACAA
*
231572 TTCTACACGGTACTTTGGGA
1 TTCTACATGGT-CTTTGGGA
231592 AAAATCTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (22 bp):
TTCTACATGGTCTTTGGGACAA
Found at i:231648 original size:24 final size:23
Alignment explanation
Indices: 231593--231649 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
231583 ACTTTGGGAA
*
231593 AAATCTATGTGGCACTTCGGTGC
1 AAATCTACGTGGCACTTCGGTGC
* *
231616 ATATTCTACGTGGCACTTTGGTGC
1 A-AATCTACGTGGCACTTCGGTGC
231640 AAATCCTACG
1 AAAT-CTACG
231650 CGACAGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (23 bp):
AAATCTACGTGGCACTTCGGTGC
Found at i:234141 original size:36 final size:36
Alignment explanation
Indices: 234095--234226 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
234085 TAAAATCATT
*
234095 TCACTAGAGATT-TTTATTCTTAAAACATATTTTATC
1 TCACTAGAGATTGTTT-TTCTTAAAACAAATTTTATC
* * * *
234131 TCATTCGAGATTGTTTATCTTAAACCAAATTTTATC
1 TCACTAGAGATTGTTTTTCTTAAAACAAATTTTATC
* *
234167 TCACTAGAGATTG-TTTTCTTAAAACACATTTTGTC
1 TCACTAGAGATTGTTTTTCTTAAAACAAATTTTATC
*
234202 TCACTATAGATTGTTTTTCTTAAAA
1 TCACTAGAGATTGTTTTTCTTAAAA
234227 TCTCACTTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 30 0.37
36 49 0.60
37 3 0.04
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.45
Consensus pattern (36 bp):
TCACTAGAGATTGTTTTTCTTAAAACAAATTTTATC
Found at i:235016 original size:75 final size:76
Alignment explanation
Indices: 234893--235040 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 76
234883 GAGAGTTCTC
* * * *
234893 ATCCATTACAAAAGAAGTTGGATAAATATTTCTGATGAAAAAGTTCATATATGAGA-G-CTTGTT
1 ATCCATAACAAAAGAAGATGGATAAACATTTCTGATCAAAAAGTTCATA-ATGAGATGACTTGTT
234956 CAACCTTGACTA
65 CAACCTTGACTA
* ** *
234968 ATCCATAACAGAAGAAGATGGATCCACATTTCTGATCAATAAGTTCATAATGAGATGAACTTGTT
1 ATCCATAACAAAAGAAGATGGATAAACATTTCTGATCAAAAAGTTCATAATGAGATG-ACTTGTT
235033 CAACCTTG
65 CAACCTTG
235041 CTATGTTCAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
74 6 0.10
75 42 0.68
77 14 0.23
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (76 bp):
ATCCATAACAAAAGAAGATGGATAAACATTTCTGATCAAAAAGTTCATAATGAGATGACTTGTTC
AACCTTGACTA
Found at i:238210 original size:25 final size:25
Alignment explanation
Indices: 238176--238227 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
238166 AATATGTAAA
* * *
238176 CTCCTAGTCATCTGAAGATGAGGGT
1 CTCCTAGTCACCCGAAAATGAGGGT
238201 CTCCTAGTCACCCGAAAATGAGGGT
1 CTCCTAGTCACCCGAAAATGAGGGT
238226 CT
1 CT
238228 GCTTGCACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (25 bp):
CTCCTAGTCACCCGAAAATGAGGGT
Found at i:242241 original size:20 final size:20
Alignment explanation
Indices: 242216--242263 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
242206 ATTGAATTTG
242216 TTCAAAGTTTTCAAAAATAA
1 TTCAAAGTTTTCAAAAATAA
242236 TTCAAAGTTTTCAAAAATAA
1 TTCAAAGTTTTCAAAAATAA
242256 TTCAAAGT
1 TTCAAAGT
242264 CTATTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (20 bp):
TTCAAAGTTTTCAAAAATAA
Found at i:244730 original size:20 final size:19
Alignment explanation
Indices: 244705--244761 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
244695 AAAAAAATAC
244705 TTTTAATAATAAATACATAT
1 TTTTAATAATAAATACAT-T
*
244725 TTTTAATCATAGAA-A-ATT
1 TTTTAATAATA-AATACATT
244743 TTTGTACATAATAAATACA
1 TTT-TA-ATAATAAATACA
244762 ATTGGTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 4 0.13
19 6 0.20
20 17 0.57
21 3 0.10
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (19 bp):
TTTTAATAATAAATACATT
Found at i:246476 original size:17 final size:17
Alignment explanation
Indices: 246454--246563 Score: 94
Period size: 17 Copynumber: 6.2 Consensus size: 17
246444 AATTAAGAGT
*
246454 TAGTTTAATAAATGAAC
1 TAGTTTAATCAATGAAC
* *
246471 TAGTTTGATGAATGAAC
1 TAGTTTAATCAATGAAC
*
246488 TAGTTTAATTAATGAAC
1 TAGTTTAATCAATGAAC
* *
246505 TAACTTTATTCAATGAAC
1 T-AGTTTAATCAATGAAC
* *
246523 TAACTTTATTCAATGAAC
1 T-AGTTTAATCAATGAAC
*
246541 TAGAACTTTATTCAATGAAC
1 TAG---TTTAATCAATGAAC
246561 TAG
1 TAG
246564 ATGCATGAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
17 32 0.40
18 32 0.40
20 17 0.21
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (17 bp):
TAGTTTAATCAATGAAC
Found at i:246546 original size:24 final size:21
Alignment explanation
Indices: 246506--246564 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 21
246496 TTAATGAACT
246506 AACTTTATTCAATGAACT---
1 AACTTTATTCAATGAACTAGA
246524 AACTTTATTCAATGAACTAG-
1 AACTTTATTCAATGAACTAGA
246544 AACTTTATTCAATGAACTAGA
1 AACTTTATTCAATGAACTAGA
246565 TGCATGAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.47
20 20 0.53
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
AACTTTATTCAATGAACTAGA
Found at i:246552 original size:38 final size:36
Alignment explanation
Indices: 246481--246562 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 36
246471 TAGTTTGATG
*
246481 AATGAACT-AGTTTAATTAATGAACTAACTTTATTC
1 AATGAACTAACTTTAATTAATGAACTAACTTTATTC
246516 AATGAACTAACTTT-ATTCAATGAACTAGAACTTTATTC
1 AATGAACTAACTTTAATT-AATGAACT--AACTTTATTC
246554 AATGAACTA
1 AATGAACTA
246563 GATGCATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 11 0.26
36 12 0.29
38 19 0.45
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (36 bp):
AATGAACTAACTTTAATTAATGAACTAACTTTATTC
Found at i:246564 original size:20 final size:18
Alignment explanation
Indices: 246481--246562 Score: 114
Period size: 18 Copynumber: 4.5 Consensus size: 18
246471 TAGTTTGATG
*
246481 AATGAACT-AGTTTAATT-
1 AATGAACTAACTTT-ATTC
246498 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
246516 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
246534 AATGAACTAGAACTTTATTC
1 AATGAACT--AACTTTATTC
246554 AATGAACTA
1 AATGAACTA
246563 GATGCATGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
17 11 0.18
18 31 0.52
20 18 0.30
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:248121 original size:30 final size:29
Alignment explanation
Indices: 248073--248143 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
248063 ATCTTTTTAG
*
248073 ATATTAAATTTTCAAAAGTTATATAATAA
1 ATATTAACTTTTCAAAAGTTATATAATAA
*
248102 ATATTACACTTTTTAAAAGTTATATAATAA
1 ATATTA-ACTTTTCAAAAGTTATATAATAA
248132 ATATTAAACTTT
1 ATATT-AACTTT
248144 AATGATCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 6 0.16
30 31 0.82
31 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (29 bp):
ATATTAACTTTTCAAAAGTTATATAATAA
Found at i:248479 original size:12 final size:12
Alignment explanation
Indices: 248459--248493 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
248449 ATTTTGTTTA
*
248459 ATAAATTTAAAT
1 ATAATTTTAAAT
248471 ATAATTTTAAA-
1 ATAATTTTAAAT
248482 ATAATTTTAAAT
1 ATAATTTTAAAT
248494 TTTCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATTTTAAAT
Found at i:248517 original size:21 final size:20
Alignment explanation
Indices: 248479--248516 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
248469 ATATAATTTT
248479 AAAATAATTTTAAATTTTCA
1 AAAATAATTTTAAATTTTCA
248499 AAAATAAATTTT-AATTTT
1 AAAAT-AATTTTAAATTTT
248517 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATAATTTTAAATTTTCA
Found at i:252155 original size:21 final size:21
Alignment explanation
Indices: 252122--252164 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
252112 TCTCGTTTAT
* * *
252122 CGCTTTTGTGGTCATAGCGGG
1 CGCTATTGCGGTCATAGAGGG
252143 CGCTATTGCGGTCATAGAGGG
1 CGCTATTGCGGTCATAGAGGG
252164 C
1 C
252165 ACTTTTGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.21, G:0.37, T:0.28
Consensus pattern (21 bp):
CGCTATTGCGGTCATAGAGGG
Found at i:252641 original size:21 final size:21
Alignment explanation
Indices: 252579--252641 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
252569 TTCTGATATA
*
252579 CCCGCTAT-AGCCACAAAAGTG
1 CCCGCTATGA-CCACAAAAGCG
* * *
252600 CCCTCTATGACCGCAATAGCG
1 CCCGCTATGACCACAAAAGCG
*
252621 CCCGCTATGATCACAAAAGCG
1 CCCGCTATGACCACAAAAGCG
252642 ATAAACGAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (21 bp):
CCCGCTATGACCACAAAAGCG
Found at i:253492 original size:21 final size:21
Alignment explanation
Indices: 253468--253519 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
253458 TCCTAATCTT
253468 TAAATCTTAAACTATAAAT-AC
1 TAAATCTTAAACTAT-AATCAC
* *
253489 TAAACCTTAAACTATAATCCC
1 TAAATCTTAAACTATAATCAC
253510 TAAATCTTAA
1 TAAATCTTAA
253520 GTCATAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATCTTAAACTATAATCAC
Found at i:253514 original size:42 final size:42
Alignment explanation
Indices: 253468--253549 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
253458 TCCTAATCTT
* *
253468 TAAATCTTAAACT-ATAAATACTAAACCTTAAACTATAATCCC
1 TAAATCTT-AACTCATAAACACTAAACCCTAAACTATAATCCC
* *
253510 TAAATCTTAAGTCATAAACACTAAACCCTAAACTTTAATC
1 TAAATCTTAACTCATAAACACTAAACCCTAAACTATAATC
253550 TTTAAACCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.30
Consensus pattern (42 bp):
TAAATCTTAACTCATAAACACTAAACCCTAAACTATAATCCC
Found at i:253555 original size:28 final size:26
Alignment explanation
Indices: 253489--253598 Score: 80
Period size: 28 Copynumber: 4.0 Consensus size: 26
253479 CTATAAATAC
*
253489 TAAACCTTAAA-CTATAATCCCTAAATCT
1 TAAATCTTAAACCTA-AA-CCCTAAA-CT
* *
253517 TAAGTCATAAACACTAAACCCTAAACT
1 TAAATCTTAAAC-CTAAACCCTAAACT
* * *
253544 TTAATCTTTAAACCCTAAGCCGTAAGCAC-
1 TAAATC-TTAAA-CCTAAACCCTAA--ACT
253573 TAAATCTTAAACCTAAACCCTAAACT
1 TAAATCTTAAACCTAAACCCTAAACT
253599 CAGTTATGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
25 2 0.03
27 16 0.25
28 33 0.52
29 8 0.12
30 5 0.08
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.27
Consensus pattern (26 bp):
TAAATCTTAAACCTAAACCCTAAACT
Found at i:253574 original size:42 final size:42
Alignment explanation
Indices: 253481--253597 Score: 103
Period size: 42 Copynumber: 2.8 Consensus size: 42
253471 ATCTTAAACT
* * * * *
253481 ATAAATACTAAACCTTAAACTATAATCCCTAAATCTTAAGTC
1 ATAAACACTAAACCCTAAACTATAATCCCTAAACCCTAAGCC
* **
253523 ATAAACACTAAACCCTAAACTTTAATCTTTAAACCCTAAGCC
1 ATAAACACTAAACCCTAAACTATAATCCCTAAACCCTAAGCC
* * * *
253565 GTAAGCACTAAATCTTAAACCTA-AA-CCCTAAAC
1 ATAAACACTAAACCCTAAA-CTATAATCCCTAAAC
253598 TCAGTTATGT
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
41 6 0.10
42 51 0.86
43 2 0.03
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (42 bp):
ATAAACACTAAACCCTAAACTATAATCCCTAAACCCTAAGCC
Found at i:254859 original size:12 final size:12
Alignment explanation
Indices: 254837--254873 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
254827 TTGAGTTTCG
254837 GGAGAGAAGAAGA
1 GGAG-GAAGAAGA
254850 GGAGGAAGAAGA
1 GGAGGAAGAAGA
*
254862 AGAGGAAGAAGA
1 GGAGGAAGAAGA
254874 AGATGCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (12 bp):
GGAGGAAGAAGA
Found at i:254861 original size:15 final size:15
Alignment explanation
Indices: 254841--254876 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
254831 GTTTCGGGAG
*
254841 AGAAGAAGAGGAGGA
1 AGAAGAAGAGGAAGA
254856 AGAAGAAGAGGAAGA
1 AGAAGAAGAGGAAGA
254871 AGAAGA
1 AGAAGA
254877 TGCATAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAGGAAGA
Found at i:254874 original size:12 final size:12
Alignment explanation
Indices: 254842--254876 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
254832 TTTCGGGAGA
*
254842 GAAGAAGAGGAG
1 GAAGAAGAAGAG
254854 GAAGAAGAAGAG
1 GAAGAAGAAGAG
254866 GAAGAAGAAGA
1 GAAGAAGAAGA
254877 TGCATAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAG
Found at i:255063 original size:11 final size:11
Alignment explanation
Indices: 255001--255068 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
254991 TTCGTTTTCA
*
255001 AGCTTGAATCA
1 AGCTTGAATCG
*
255012 AGTTTGAATCG
1 AGCTTGAATCG
** *
255023 AGCTCAAAATTG
1 AGCT-TGAATCG
*
255035 AGCTTGAACCG
1 AGCTTGAATCG
255046 AGC-TGAATCG
1 AGCTTGAATCG
255056 AGCTTGAATCG
1 AGCTTGAATCG
255067 AG
1 AG
255069 TTTTGAGTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
10 9 0.20
11 27 0.61
12 8 0.18
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (11 bp):
AGCTTGAATCG
Found at i:255787 original size:27 final size:27
Alignment explanation
Indices: 255727--255827 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 27
255717 TAAATTTCAA
* *
255727 AATAA-AAATATATTTTTAAATGACA-AT
1 AATAATAAA-ATATTTTTAAATTA-AGTT
*
255754 AAAAATAAAATATTTTTAAATTAAGTT
1 AATAATAAAATATTTTTAAATTAAGTT
* *
255781 AATAATAAGATATATTT-AA-TAAGTT
1 AATAATAAAATATTTTTAAATTAAGTT
*
255806 AAT-ATAAAAATATTTTTTAATT
1 AATAAT-AAAATATTTTTAAATT
255828 TAATATATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
24 2 0.03
25 18 0.30
26 5 0.08
27 33 0.54
28 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (27 bp):
AATAATAAAATATTTTTAAATTAAGTT
Found at i:255852 original size:25 final size:27
Alignment explanation
Indices: 255807--255864 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
255797 TAATAAGTTA
* *
255807 ATATA-AAAATATTTTTTAATTTAA-T
1 ATATATAAAATATTTATAAATTTAAGT
255832 ATATATAAAATA-TTATAAATTTAAGT
1 ATATATAAAATATTTATAAATTTAAGT
*
255858 ATTTATA
1 ATATATA
255865 CGCTAAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATATAAAATATTTATAAATTTAAGT
Found at i:257265 original size:7 final size:7
Alignment explanation
Indices: 257253--257291 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
257243 TTATATTATC
257253 ATCTGCA
1 ATCTGCA
257260 ATCTGCA
1 ATCTGCA
257267 ATCTGCA
1 ATCTGCA
257274 ATCTGCA
1 ATCTGCA
257281 ATCTGCA
1 ATCTGCA
257288 ATCT
1 ATCT
257292 TTAACTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (7 bp):
ATCTGCA
Found at i:261435 original size:21 final size:21
Alignment explanation
Indices: 261388--261437 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
261378 TCGACTTTGG
* * *
261388 AACTTTTCCTGGGATGCAACT
1 AACTTTTCATGGGACGCAACC
* *
261409 AGCTTTTCATGGGACGTAACC
1 AACTTTTCATGGGACGCAACC
261430 AACTTTTC
1 AACTTTTC
261438 TTGTGAAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (21 bp):
AACTTTTCATGGGACGCAACC
Done.