Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005903.1 Hibiscus syriacus cultivar Beakdansim tig00013868_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: 145609
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:795 original size:20 final size:20
Alignment explanation
Indices: 770--838 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
760 CGTTTCAAAG
770 ATGGTATCGATACCGTCCTT
1 ATGGTATCGATACCGTCCTT
*
790 ATGGTATCGGTACC--CC-T
1 ATGGTATCGATACCGTCCTT
*
807 -TGGTATCGATA-CGTTCTT
1 ATGGTATCGATACCGTCCTT
* *
825 AAGGTATTGATACC
1 ATGGTATCGATACC
839 TCATGAATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
15 1 0.03
16 10 0.26
17 2 0.05
18 3 0.08
19 9 0.23
20 14 0.36
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
ATGGTATCGATACCGTCCTT
Found at i:4932 original size:18 final size:18
Alignment explanation
Indices: 4909--4969 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
4899 AACTAATTTG
4909 ATGATGTTTGACATGGAA
1 ATGATGTTTGACATGGAA
* ****
4927 ATGATGTTT-ACTTCTCG
1 ATGATGTTTGACATGGAA
4944 ATGATGTTTGACATGGAA
1 ATGATGTTTGACATGGAA
4962 ATGATGTT
1 ATGATGTT
4970 ACTTCTCGCT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (18 bp):
ATGATGTTTGACATGGAA
Found at i:4977 original size:34 final size:35
Alignment explanation
Indices: 4908--4977 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4898 CAACTAATTT
4908 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
1 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
4943 GATGATGTTTGACATGGAAATGATG-TTACTTCTC
1 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
4977 G
1 G
4978 CTTGTGATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (35 bp):
GATGATGTTTGACATGGAAATGATGTTTACTTCTC
Found at i:7590 original size:15 final size:16
Alignment explanation
Indices: 7570--7602 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
7560 TCATTCACTG
*
7570 ATTCTACTG-TTCTAT
1 ATTCTAATGCTTCTAT
7585 ATTCTAATGCTTCTAT
1 ATTCTAATGCTTCTAT
7601 AT
1 AT
7603 CTCCTGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTCTAATGCTTCTAT
Found at i:23312 original size:38 final size:35
Alignment explanation
Indices: 23216--23333 Score: 128
Period size: 36 Copynumber: 3.2 Consensus size: 35
23206 TGGAATATTT
* * * *
23216 AGTGCCCTGTGATTGCACCATATGTGCGATACATTT
1 AGTGCCCTATGATTGCACCGTA-GTGCGACACATTC
*
23252 AGTGCCCTATGATTGCATCGTAGATGCGACACATTC
1 AGTGCCCTATGATTGCACCGTAG-TGCGACACATTC
*
23288 AGTGCACCCTATGATTGCACCGTAGGTGCGACATATTC
1 AGTG--CCCTATGATTGCACCGTA-GTGCGACACATTC
*
23326 AATGCCCT
1 AGTGCCCT
23334 GTGAATGTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
35 1 0.01
36 37 0.53
38 31 0.44
39 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (35 bp):
AGTGCCCTATGATTGCACCGTAGTGCGACACATTC
Found at i:27142 original size:43 final size:43
Alignment explanation
Indices: 27089--27216 Score: 220
Period size: 43 Copynumber: 3.0 Consensus size: 43
27079 ATCCCTAATC
*
27089 ATGTTAGTCTACATGTTTATCGACAAATGATACCTTTTATGAT
1 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGAT
* * *
27132 ATGTTCGTCTACATGTTTGTCGAAAAATGATACCTTTTATTAT
1 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGAT
27175 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGA
1 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGA
27217 AGGCATGTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (43 bp):
ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGAT
Found at i:27711 original size:24 final size:23
Alignment explanation
Indices: 27616--27718 Score: 100
Period size: 23 Copynumber: 4.4 Consensus size: 23
27606 GTTCCTTTAC
** *
27616 GTTCG-TTATGTTCATTTATTAT
1 GTTCGTTTATGTTTGTTTATTGT
*
27638 GTTCGTTTACGTTTGTTTATTGT
1 GTTCGTTTATGTTTGTTTATTGT
* * *
27661 GTTCGTTTATGTTAGTTTACATAT
1 GTTCGTTTATGTTTGTTTA-TTGT
* *
27685 GTTCGTTTGTGTTTGTTCATTTGT
1 GTTCGTTTATGTTTGTTTA-TTGT
27709 GTTCGTTTAT
1 GTTCGTTTAT
27719 CATTTAAATG
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
22 5 0.08
23 30 0.47
24 29 0.45
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.59
Consensus pattern (23 bp):
GTTCGTTTATGTTTGTTTATTGT
Found at i:29788 original size:52 final size:52
Alignment explanation
Indices: 29702--29800 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
29692 GTATTTAATT
* * * *
29702 TGAAATTCGAAGTTTTTTTAATTAATTATCTATTTTATTGATGATGTCAACC
1 TGAAATCCAAAGTTTCTTTAATTAATTATCTATTTTATTAATGATGTCAACC
* * *
29754 TGAAATCCAAAGTTTCTTTAGTTAGTTATTTATTTTATTAATGATGT
1 TGAAATCCAAAGTTTCTTTAATTAATTATCTATTTTATTAATGATGT
29801 TTACTCTGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (52 bp):
TGAAATCCAAAGTTTCTTTAATTAATTATCTATTTTATTAATGATGTCAACC
Found at i:31163 original size:18 final size:18
Alignment explanation
Indices: 31142--31179 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31132 TTACCATGTA
31142 AAGAAAATTACTTTTTAT
1 AAGAAAATTACTTTTTAT
31160 AAGAAAATTACTTTTTAT
1 AAGAAAATTACTTTTTAT
31178 AA
1 AA
31180 CCCTAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
AAGAAAATTACTTTTTAT
Found at i:36380 original size:6 final size:6
Alignment explanation
Indices: 36369--36398 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
36359 TCTCGTCTCG
36369 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
36399 ACGTTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:36703 original size:21 final size:20
Alignment explanation
Indices: 36485--36733 Score: 175
Period size: 21 Copynumber: 11.9 Consensus size: 20
36475 CGTTGCGATT
*
36485 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
36504 TTAGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
36527 TTCGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
36546 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
36569 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
36588 TTGGAATAAATCGCAAGGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
36611 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
36630 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * *
36653 TTCGACTATAGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
**
36672 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
* *
36693 TTCGACTATCGCAACGTGAAC
1 TTGGACTATCGCAA-GCGAAC
36714 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
36734 TATGTAAATC
Statistics
Matches: 179, Mismatches: 33, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
19 48 0.27
21 93 0.52
23 38 0.21
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:36718 original size:42 final size:42
Alignment explanation
Indices: 36488--36708 Score: 374
Period size: 42 Copynumber: 5.3 Consensus size: 42
36478 TGCGATTTTG
*
36488 GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
36530 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
36572 GACTATCGCAACGAACTTGGAATAAATCGCAAGGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
36614 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
36656 GACTATAGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
36696 GACTATCGCAACG
1 GACTATCGCAACG
36709 TGAACTTGGA
Statistics
Matches: 169, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 30 0.18
41 1 0.01
42 138 0.82
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:36718 original size:84 final size:83
Alignment explanation
Indices: 36488--36733 Score: 363
Period size: 84 Copynumber: 3.0 Consensus size: 83
36478 TGCGATTTTG
*
36488 GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTT-GGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
*
36553 AAATCGCAACGCGAACTTC
65 AAATCGCAATGCGAACTTC
* * *
36572 GACTATCGCAACGAACTTGGAATAAATCGCAAGGCGAACTTGGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGG-ATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
36637 AAATCGCAATGCGAACTTC
65 AAATCGCAATGCGAACTTC
* * *
36656 GACTATAGCAACGAATTTGGA-AAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGAC
1 GACTATCGCAACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGCAAC--GAATTTGGAA
36720 T--ATCGCAATGCGAA
64 TAAATCGCAATGCGAA
36734 TATGTAAATC
Statistics
Matches: 148, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
82 42 0.28
83 2 0.01
84 104 0.70
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (83 bp):
GACTATCGCAACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATA
AATCGCAATGCGAACTTC
Found at i:44297 original size:21 final size:19
Alignment explanation
Indices: 44261--44304 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
44251 CAAAAACCCT
44261 AAAAGATATATTTAAAATTA
1 AAAAGATATATTTAAAA-TA
44281 AAAAGATA-ATTCCTAAAATA
1 AAAAGATATATT--TAAAATA
44301 AAAA
1 AAAA
44305 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAGATATATTTAAAATA
Found at i:47246 original size:14 final size:15
Alignment explanation
Indices: 47217--47248 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
47207 AAATAATTAA
47217 AATAATATATTTTAT
1 AATAATATATTTTAT
47232 AATAATATA-TTTAT
1 AATAATATATTTTAT
47246 AAT
1 AAT
47249 TATTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:51201 original size:21 final size:21
Alignment explanation
Indices: 51177--51216 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
51167 TTTATTTTAT
51177 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
51198 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
51217 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:51252 original size:32 final size:33
Alignment explanation
Indices: 51211--51308 Score: 155
Period size: 32 Copynumber: 3.0 Consensus size: 33
51201 TTTGTTTCAA
51211 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
51243 TTATCGAACTTGGAAG-TTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
51275 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
51308 T
1 T
51309 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 42 0.69
33 19 0.31
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:51337 original size:13 final size:13
Alignment explanation
Indices: 51294--51348 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
51284 TTGGAAGTAT
51294 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
51307 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
51321 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
51334 TTAAGTATTTGAA
1 TTAAGTATTTCAA
51347 TT
1 TT
51349 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:51570 original size:21 final size:21
Alignment explanation
Indices: 51544--51600 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
51534 TGGAGCGTGG
*
51544 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
51565 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
51586 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
51601 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:51791 original size:15 final size:15
Alignment explanation
Indices: 51766--51820 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
51756 ATCTGGAATA
*
51766 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
51781 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
51796 TAAAAAACCGGTTTTT
1 T-TAAAACCGGTTTTT
51812 TTAAAACCG
1 TTAAAACCG
51821 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:51804 original size:16 final size:17
Alignment explanation
Indices: 51768--51817 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
51758 CTGGAATATT
*
51768 AAAATCGGTTTTTTT--
1 AAAACCGGTTTTTTTAA
*
51783 ATAACCGG-TTTTTTAA
1 AAAACCGGTTTTTTTAA
51799 AAAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
51816 AA
1 AA
51818 CCGAAACCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 7 0.24
17 10 0.34
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAACCGGTTTTTTTAA
Found at i:51936 original size:15 final size:17
Alignment explanation
Indices: 51910--51941 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
51900 TTCTATGAGA
51910 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
51926 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
51942 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:55128 original size:2 final size:2
Alignment explanation
Indices: 55123--55154 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55113 TATATTTGTG
55123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55155 CAAGGCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57179 original size:545 final size:545
Alignment explanation
Indices: 56143--57223 Score: 2135
Period size: 545 Copynumber: 2.0 Consensus size: 545
56133 AAGGTTTTGC
*
56143 AACAGTTAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
1 AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
56208 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
66 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
56273 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
131 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
56338 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
196 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
56403 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
261 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
56468 TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
326 TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
56533 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
391 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
56598 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
456 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
56663 TGTTTAATTAGCTTATTTATTATTA
521 TGTTTAATTAGCTTATTTATTATTA
56688 AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
1 AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
*
56753 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATGGTTTTGTGTCACC
66 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
56818 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
131 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
56883 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
196 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
56948 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
261 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
*
57013 TGAAAATATGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
326 TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
57078 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
391 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
57143 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
456 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
57208 TGTTTAATTAGCTTAT
521 TGTTTAATTAGCTTAT
57224 AAATGTATGA
Statistics
Matches: 533, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
545 533 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (545 bp):
AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
TGTTTAATTAGCTTATTTATTATTA
Found at i:63929 original size:2 final size:2
Alignment explanation
Indices: 63922--63957 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
63912 GAGTTGTTAC
63922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63958 AACCTGACGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68559 original size:11 final size:11
Alignment explanation
Indices: 68541--68617 Score: 82
Period size: 11 Copynumber: 7.0 Consensus size: 11
68531 GTTCATGAAT
68541 ATGTTTGTTTA
1 ATGTTTGTTTA
*
68552 ACGTTTGTTTA
1 ATGTTTGTTTA
**
68563 ATGTTCATTTA
1 ATGTTTGTTTA
*
68574 ACGTTTGTTTA
1 ATGTTTGTTTA
**
68585 ATGTTCATTTA
1 ATGTTTGTTTA
*
68596 ATGTTCGTTTA
1 ATGTTTGTTTA
*
68607 GTGTTTGTTTA
1 ATGTTTGTTTA
68618 TCATTTGTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 53 1.00
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.57
Consensus pattern (11 bp):
ATGTTTGTTTA
Found at i:68583 original size:33 final size:33
Alignment explanation
Indices: 68543--68628 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
68533 TCATGAATAT
68543 GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
1 GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
* ** * **
68576 GTTTGTTTAATGTTCATTTAATGTTCGTTTAGT
1 GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
* *
68609 GTTTGTTTATCATTTGTTTA
1 GTTTGTTTAACGTTTGTTTA
68629 TATAATCAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.19, C:0.07, G:0.16, T:0.58
Consensus pattern (33 bp):
GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
Found at i:68617 original size:22 final size:22
Alignment explanation
Indices: 68548--68611 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
68538 AATATGTTTG
68548 TTTAACGTTTGTTTAATGTTCA
1 TTTAACGTTTGTTTAATGTTCA
68570 TTTAACGTTTGTTTAATGTTCA
1 TTTAACGTTTGTTTAATGTTCA
* * *
68592 TTTAATGTTCGTTTAGTGTT
1 TTTAACGTTTGTTTAATGTT
68612 TGTTTATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (22 bp):
TTTAACGTTTGTTTAATGTTCA
Found at i:70612 original size:24 final size:25
Alignment explanation
Indices: 70574--70624 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
70564 TGTTCTTATG
*
70574 ACACATTTTTCTCTGCTCTTGTGGC
1 ACACATTTTTCTCTGCTCTTGGGGC
*
70599 ACACA-TTTTCTCTGTTCTTGGGGC
1 ACACATTTTTCTCTGCTCTTGGGGC
70623 AC
1 AC
70625 GATCTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (25 bp):
ACACATTTTTCTCTGCTCTTGGGGC
Found at i:74340 original size:21 final size:21
Alignment explanation
Indices: 74316--74363 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
74306 TTGACATACA
74316 AAATGTTCTCTAAAAGCAACC
1 AAATGTTCTCTAAAAGCAACC
74337 AAATGTTCTCTAAAAGCAACC
1 AAATGTTCTCTAAAAGCAACC
74358 AAATGT
1 AAATGT
74364 CCACAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (21 bp):
AAATGTTCTCTAAAAGCAACC
Found at i:74372 original size:21 final size:21
Alignment explanation
Indices: 74327--74374 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
74317 AATGTTCTCT
* * *
74327 AAAAGCAACCAAATGTTCTCT
1 AAAAGCAACCAAATGTCCACA
74348 AAAAGCAACCAAATGTCCACA
1 AAAAGCAACCAAATGTCCACA
74369 AAAAGC
1 AAAAGC
74375 CTCAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAAGCAACCAAATGTCCACA
Found at i:75886 original size:24 final size:24
Alignment explanation
Indices: 75858--75940 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
75848 TCAGAAATGA
75858 AACAGAATTCAGATAAGATATCAG
1 AACAGAATTCAGATAAGATATCAG
* * * *
75882 AACAGAATCCAGATCAGAAATCAT
1 AACAGAATTCAGATAAGATATCAG
*
75906 AACAGAATTCAGGTAATG-TATCAG
1 AACAGAATTCAGATAA-GATATCAG
*
75930 AACAAAATTCA
1 AACAGAATTCA
75941 AGTCGGAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 47 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
AACAGAATTCAGATAAGATATCAG
Found at i:75950 original size:48 final size:48
Alignment explanation
Indices: 75847--75952 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
75837 AAACGGAGAT
* * *
75847 ATCAGAAATGA-AACAGAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCATAACAGAATTCAGATAAGATATCAGAACAAAATCAAG
*
75894 ATCAGAAATCATAACAGAATTCAGGTAATG-TATCAGAACAAAATTCAAG
1 ATCAGAAATCATAACAGAATTCAGATAA-GATATCAGAACAAAA-TCAAG
*
75943 -TCGGAAATCA
1 ATCAGAAATCA
75953 AATAAAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
47 10 0.20
48 36 0.71
49 5 0.10
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCATAACAGAATTCAGATAAGATATCAGAACAAAATCAAG
Found at i:78863 original size:23 final size:23
Alignment explanation
Indices: 78815--78872 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
78805 TATTATATGA
* **
78815 CACTACGGTGCAATTCTACGTGG
1 CACTATGGTGCAATTCTACGCAG
78838 CACTATGGTGCAATTCTACGCAG
1 CACTATGGTGCAATTCTACGCAG
78861 CACT-TCGGTGCA
1 CACTAT-GGTGCA
78873 TTTATACGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
CACTATGGTGCAATTCTACGCAG
Found at i:83829 original size:25 final size:26
Alignment explanation
Indices: 83801--83856 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
83791 TACAACTCTT
* * *
83801 TTAATGAATATTTAATTT-GGAATAG
1 TTAAAGAAGATTTAATTTCGGAATAA
*
83826 TTAAAGAAGATTTTATTTCGGAATAA
1 TTAAAGAAGATTTAATTTCGGAATAA
83852 TTAAA
1 TTAAA
83857 ATAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (26 bp):
TTAAAGAAGATTTAATTTCGGAATAA
Found at i:90433 original size:16 final size:17
Alignment explanation
Indices: 90394--90438 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
90384 GTTTATGAGG
*
90394 GAATTGAAATCTGTGAAG
1 GAATTGAAATCTGT-AAC
90412 GAATTGAAATCTGT-AC
1 GAATTGAAATCTGTAAC
*
90428 GAATTGGAATC
1 GAATTGAAATC
90439 CAATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (17 bp):
GAATTGAAATCTGTAAC
Found at i:91061 original size:37 final size:37
Alignment explanation
Indices: 91020--91096 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
91010 AACCTGAACC
91020 CGACCCGAATATCACACTTAAAAAACCCGACCCGACT
1 CGACCCGAATATCACACTTAAAAAACCCGACCCGACT
*
91057 CGACCCGAATATCACACTTAAAAAACCCGACCCTACT
1 CGACCCGAATATCACACTTAAAAAACCCGACCCGACT
91094 CGA
1 CGA
91097 ACAAAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.14
Consensus pattern (37 bp):
CGACCCGAATATCACACTTAAAAAACCCGACCCGACT
Found at i:91316 original size:38 final size:37
Alignment explanation
Indices: 91273--91349 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
91263 TTAAACCCAA
91273 ACTCGA-CCTGAATATCACACTTAAAAAAACCCGACCCG
1 ACTCGATCC-GAATATCACACTT-AAAAAACCCGACCCG
*
91311 ACTCGATCCGAATATCACACTTAAAAAACCCGACTCG
1 ACTCGATCCGAATATCACACTTAAAAAACCCGACCCG
91348 AC
1 AC
91350 CCGAACAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 16 0.43
38 19 0.51
39 2 0.05
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.17
Consensus pattern (37 bp):
ACTCGATCCGAATATCACACTTAAAAAACCCGACCCG
Found at i:91371 original size:257 final size:246
Alignment explanation
Indices: 90967--91562 Score: 813
Period size: 257 Copynumber: 2.4 Consensus size: 246
90957 TATAATGTAA
*
90967 AATTATATATATTTTTCGGGTCGGTCCCGTTTTTTTCACCCTAAACCTGAACCCGACCCGAATAT
1 AATTATATATATTTTT-GGGTCGGT-CCGTTTTTTTCACCATAAACCTGAACCCGACCCGAATAT
* *
91032 CACACTT-AAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCTACTCG
64 CACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCG
*
91096 AACAAAATAAAATTTCAT-CCGACCCTAATATATGAATTAGAAATCCGACCCGACCCGACCCGAC
129 AACAAAATAAAATTTCATCCCGACCCGAATATATGAATTAGAAAT---A--CGACCCGACCCGA-
* **
91160 CCGA-AATAATAAAAATTTAATTTTATTTAATAAAAACAGTGACTTAATCCGACTCGACCGACCC
188 --AATAATAA-AAAAAAATAATTTTATTTAATAAAAACAGTGACTTAATCCGA--C--CCGACCC
91224 G
246 G
* ** * *
91225 AATTATATATATTTTTGGGTCGGTCCGATTTTTTT-ACCTTAAACCCAAACTCGACCTGAATATC
1 AATTATATATATTTTTGGGTCGGTCCG-TTTTTTTCACCATAAACCTGAACCCGACCCGAATATC
* *
91289 ACACTTAAAAAAACCCGACCCGACTCGATCCGAATATCACACTTAAAAAACCCGACTCGACCCGA
65 ACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGA
* *
91354 ACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATACGACCCGACCCTAAAT
130 ACAAAATAAAATTTCAT----CCCGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAAT
*
91419 AATAAAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
191 AATAAAAAAAAATAATTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
*
91475 AATTATATATATTTTCGGGTCGGTCCTGTTTTTTTCACCATAAACCTGAACCCGACCCGAATATC
1 AATTATATATATTTTTGGGTCGGTCC-GTTTTTTTCACCATAAACCTGAACCCGACCCGAATATC
91540 ACACTTAAAAAAACCCGACCCGA
65 ACACTTAAAAAAACCCGACCCGA
91563 ATAAAATAAA
Statistics
Matches: 306, Mismatches: 22, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
250 40 0.13
251 48 0.16
252 1 0.00
254 40 0.13
255 5 0.02
256 33 0.11
257 97 0.32
258 16 0.05
259 1 0.00
262 25 0.08
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (246 bp):
AATTATATATATTTTTGGGTCGGTCCGTTTTTTTCACCATAAACCTGAACCCGACCCGAATATCA
CACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAA
CAAAATAAAATTTCATCCCGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAATAA
AAAAAAATAATTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
Found at i:91715 original size:207 final size:206
Alignment explanation
Indices: 91318--91774 Score: 584
Period size: 207 Copynumber: 2.2 Consensus size: 206
91308 CCGACTCGAT
*
91318 CCGAATATCACACTTAAAAAACCCGACTCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCC
1 CCGAATATCACACTTAAAAAA----ACTCGACCCGAACAAAATAAAATTTCAT----CCCGACCC
*
91383 GAATATATGAATTAGAAATACGACCCGACCCTAAATAATAAAAAAAAATATTTTTATTTAATAAA
58 GAATATATGAATTAGAAATACGACCCGACCCTAAATAAT-AAAAAAAATATTTTTATTTAAAAAA
91448 AACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCTGTTTTTTTCAC
122 AACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCTGTTTTTTTCAC
91513 CAT-AAACCTG-A-ACCCGAC
187 CATAAAACC-GAACACCCGAC
* *
91531 CCGAATATCACACTTAAAAAAACCCGACCCGAATAAAATAAAATTTCAT-CCGACCCGAATATAT
1 CCGAATATCACACTTAAAAAAACTCGACCCGAACAAAATAAAATTTCATCCCGACCCGAATATAT
* * *
91595 GAATTAGAAATCCGACCCGACCCGACTCGAAATAAT-AAAGAATTATTTTTATTTAAAAAAAACA
66 GAATTAGAAATACGACCCGA-CC--CT--AAATAATAAAAAAAATATTTTTATTTAAAAAAAACA
* * * * *
91659 GTGACTTAATCCGACTCGACCTGAATTATATATATTTTTGGGTTGGT-CTGGTTTTTTTCACCCT
126 GTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCT-GTTTTTTTCACCAT
91723 AAAACCGAACCCGACCCGAC
190 AAAACCGAA--C-ACCCGAC
*
91743 CCGAATATCACACTTAAAAAAACTCGATCCGA
1 CCGAATATCACACTTAAAAAAACTCGACCCGA
91775 CCCAACCAAA
Statistics
Matches: 218, Mismatches: 14, Indels: 25
0.85 0.05 0.10
Matches are distributed among these distances:
204 34 0.16
205 2 0.01
206 2 0.01
207 84 0.39
208 6 0.03
209 32 0.15
212 37 0.17
213 21 0.10
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (206 bp):
CCGAATATCACACTTAAAAAAACTCGACCCGAACAAAATAAAATTTCATCCCGACCCGAATATAT
GAATTAGAAATACGACCCGACCCTAAATAATAAAAAAAATATTTTTATTTAAAAAAAACAGTGAC
TTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCTGTTTTTTTCACCATAAAACC
GAACACCCGAC
Found at i:96193 original size:23 final size:23
Alignment explanation
Indices: 96167--96211 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
96157 CACCACAGCT
*
96167 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
96190 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
96212 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:96460 original size:149 final size:149
Alignment explanation
Indices: 96190--96494 Score: 601
Period size: 149 Copynumber: 2.0 Consensus size: 149
96180 CGAAGTGCCC
*
96190 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
96255 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
96320 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
96339 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
96404 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
96469 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
96488 CGTAGAC
1 CGTAGAC
96495 CCTCGACTCT
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:96854 original size:18 final size:19
Alignment explanation
Indices: 96816--96854 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
96806 ATTTCCTATC
*
96816 AATTCTTATACCATCACAT
1 AATTCTTATAACATCACAT
*
96835 AATTCTTTTAACAT-ACAT
1 AATTCTTATAACATCACAT
96853 AA
1 AA
96855 CATATCATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCTTATAACATCACAT
Found at i:96925 original size:16 final size:16
Alignment explanation
Indices: 96880--96926 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
96870 TATAATAGAA
*
96880 ATACTTATAAGTCATAT
1 ATACTTAT-AGTCACAT
*
96897 A-ACTTAAAG-CACAT
1 ATACTTATAGTCACAT
96911 ATACTTATAGTCACAT
1 ATACTTATAGTCACAT
96927 TGCTTATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.20
15 9 0.36
16 10 0.40
17 1 0.04
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (16 bp):
ATACTTATAGTCACAT
Found at i:96968 original size:2 final size:2
Alignment explanation
Indices: 96961--96998 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
96951 TCTCTTAGAC
96961 AT AT AT AT AT 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 AT AT AT AT AT
96999 TCACATGTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98043 original size:21 final size:21
Alignment explanation
Indices: 98019--98063 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
98009 TCTTGTTCGT
* *
98019 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
98040 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
98061 TTG
1 TTG
98064 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:100350 original size:6 final size:6
Alignment explanation
Indices: 100339--100375 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
100329 CTCTCGTCAC
100339 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
100376 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:101354 original size:46 final size:46
Alignment explanation
Indices: 101287--101379 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
101277 ATCTTTCCAA
*
101287 TTCAATTTATTTCATTCACAAACGTCAAGATTCAAATTTTTAACCT
1 TTCAATTTATTTCATTCACAAACGTCAAGATTCAAATTTCTAACCT
101333 TTCAATTTATTTCATTCACAAACGTCAAGATTCAAATTTCTAACCT
1 TTCAATTTATTTCATTCACAAACGTCAAGATTCAAATTTCTAACCT
101379 T
1 T
101380 ACTTAAATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.41
Consensus pattern (46 bp):
TTCAATTTATTTCATTCACAAACGTCAAGATTCAAATTTCTAACCT
Found at i:101555 original size:19 final size:19
Alignment explanation
Indices: 101531--101567 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
101521 TATTATGTTA
101531 ATTAAA-TTAATAAAATAAT
1 ATTAAATTTAA-AAAATAAT
101550 ATTAAATTTAAAAAATAA
1 ATTAAATTTAAAAAATAA
101568 ATAAAGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAATTTAAAAAATAAT
Found at i:101942 original size:16 final size:16
Alignment explanation
Indices: 101921--101951 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
101911 AATAAATAAA
101921 GAACATAAACGAACAC
1 GAACATAAACGAACAC
101937 GAACATAAACGAACA
1 GAACATAAACGAACA
101952 ATTTTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:101998 original size:10 final size:10
Alignment explanation
Indices: 101983--102083 Score: 58
Period size: 10 Copynumber: 9.1 Consensus size: 10
101973 CATTTAAATG
101983 ATAAACGAAC
1 ATAAACGAAC
101993 ATAAACGAAC
1 ATAAACGAAC
*
102003 GTAAACGAAGAC
1 ATAAACG-A-AC
*
102015 AAACGAACGAAC
1 ATA--AACGAAC
*
102027 ATAAACGGACATA
1 ATAAAC-GA-A-C
*
102040 ATAAATGAAC
1 ATAAACGAAC
*
102050 ATAAATGAACAC
1 ATAAACG-A-AC
102062 AATAAACGAAC
1 -ATAAACGAAC
*
102073 ATAAACAAAC
1 ATAAACGAAC
102083 A
1 A
102084 ACACAAACAC
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
10 36 0.50
11 7 0.10
12 13 0.18
13 12 0.17
14 4 0.06
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:102051 original size:23 final size:23
Alignment explanation
Indices: 101993--102083 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
101983 ATAAACGAAC
* *
101993 ATAAACGAACGTAAACGAAGACA
1 ATAAACGAACATAAACGAACACA
* *
102016 A-ACGAACGAACATAAACGGACATA
1 ATA--AACGAACATAAACGAACACA
* *
102040 ATAAATGAACATAAATGAACACA
1 ATAAACGAACATAAACGAACACA
*
102063 ATAAACGAACATAAACAAACA
1 ATAAACGAACATAAACGAACA
102084 ACACAAACAC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
22 1 0.02
23 35 0.65
24 17 0.31
25 1 0.02
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.11
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:102091 original size:23 final size:23
Alignment explanation
Indices: 101985--102091 Score: 67
Period size: 23 Copynumber: 4.6 Consensus size: 23
101975 TTTAAATGAT
*
101985 AAACGAACATAAACGAACGTAAAC
1 AAAC-AACATAAACGAACATAAAC
**
102009 GAAGACAA-ACGAACGAACATAAAC
1 -AA-ACAACATAAACGAACATAAAC
** * *
102033 GGACATA-ATAAATGAACATAAAT
1 AAACA-ACATAAACGAACATAAAC
*
102056 GAAC-ACAATAAACGAACATAAAC
1 AAACAAC-ATAAACGAACATAAAC
*
102079 AAACAACACAAAC
1 AAACAACATAAAC
102092 ACAAAAAAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
21 1 0.02
22 3 0.05
23 38 0.60
24 15 0.24
25 4 0.06
26 2 0.03
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.09
Consensus pattern (23 bp):
AAACAACATAAACGAACATAAAC
Found at i:102384 original size:14 final size:14
Alignment explanation
Indices: 102357--102398 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
102347 GAACATAAAT
*
102357 GAACATAAATGAAC
1 GAACATAAACGAAC
*
102371 GAATATAAACGAAC
1 GAACATAAACGAAC
*
102385 GAACCTAAACGAAC
1 GAACATAAACGAAC
102399 ATATAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:104623 original size:2 final size:2
Alignment explanation
Indices: 104612--104657 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
104602 TTGTTTCTTT
* *
104612 TC TC -C TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
104653 TC TC T
1 TC TC T
104658 TTTTAATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:108008 original size:20 final size:20
Alignment explanation
Indices: 107983--108023 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
107973 GTCTGATAAA
*
107983 TATTATCCACAATCATAGGT
1 TATTATCCACAATCAAAGGT
*
108003 TATTATCCATAATCAAAGGT
1 TATTATCCACAATCAAAGGT
108023 T
1 T
108024 GCCGTAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (20 bp):
TATTATCCACAATCAAAGGT
Found at i:116488 original size:23 final size:23
Alignment explanation
Indices: 116458--116501 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
116448 TGTACTTCTG
*
116458 TGCTGAATCATTCAGCACTGATT
1 TGCTGAATCAGTCAGCACTGATT
116481 TGCTGAATCAGTCAGCACTGA
1 TGCTGAATCAGTCAGCACTGA
116502 ATCATTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (23 bp):
TGCTGAATCAGTCAGCACTGATT
Found at i:121599 original size:14 final size:14
Alignment explanation
Indices: 121577--121618 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
121567 ATTAGTTATA
121577 TTTTAATTAAAATG
1 TTTTAATTAAAATG
*
121591 TTTTTATT-AAA--
1 TTTTAATTAAAATG
121602 TTTTAATTAAAATG
1 TTTTAATTAAAATG
121616 TTT
1 TTT
121619 AAACATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 7 0.30
12 3 0.13
13 3 0.13
14 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TTTTAATTAAAATG
Found at i:121619 original size:13 final size:13
Alignment explanation
Indices: 121578--121620 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
121568 TTAGTTATAT
121578 TTTAATTAAAATG
1 TTTAATTAAAATG
*
121591 TTTTTATT-AAAT-
1 -TTTAATTAAAATG
121603 TTTAATTAAAATG
1 TTTAATTAAAATG
121616 TTTAA
1 TTTAA
121621 ACATTCTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 9 0.36
14 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
TTTAATTAAAATG
Found at i:124250 original size:20 final size:20
Alignment explanation
Indices: 124206--124251 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
124196 GTATTAAGGA
124206 ACATTTAGGATCATATAGAT
1 ACATTTAGGATCATATAGAT
* * *
124226 GCATTTAGGATCATGTAGTT
1 ACATTTAGGATCATATAGAT
124246 ACATTT
1 ACATTT
124252 GGTGGGATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (20 bp):
ACATTTAGGATCATATAGAT
Found at i:126546 original size:103 final size:103
Alignment explanation
Indices: 126424--126636 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
126414 GGGTCTACGC
* * *
126424 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAATTCTGGTGAGACATATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
126489 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
126527 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
126592 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
126630 GGTCCTT
1 GGTCCTT
126637 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:131754 original size:187 final size:185
Alignment explanation
Indices: 131441--131813 Score: 656
Period size: 187 Copynumber: 2.0 Consensus size: 185
131431 CAAAGAAGAA
131441 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAACCATGAAGGGACTCA
1 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAACCATGAAGGGACTCA
*
131506 CCAATCAGTTGAAGATGTAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGCTTCTGGTA
66 CCAATCAGTTGAAGATATAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGCTTCTGGTA
131571 TCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
131 TCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
131626 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAAATCCATGAAGGGACT
1 TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAAT-AAAAAAAAA-CCATGAAGGGACT
* * * *
131691 CACCAATCAGTTGAAGATATAGCTAGAGTTGTTTCCATGTTCCTGAAAGAATTAGAAGCTTCTGG
64 CACCAATCAGTTGAAGATATAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGCTTCTGG
* * *
131756 TATTTGTAAGCCATCATCCATCGCTATCACTTCATATGCATGGTAGCCCTTATCCCC
129 TATCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
131813 T
1 T
131814 GATTTGATCA
Statistics
Matches: 178, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
185 41 0.23
186 9 0.05
187 128 0.72
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (185 bp):
TCTTGGTCACCATTTTCTGGACTATTTGGTCAGCTCGAAATAAAAAAAAACCATGAAGGGACTCA
CCAATCAGTTGAAGATATAGCGAGAGTTATTTCCATATTCCTGAAAGAATGAGAAGCTTCTGGTA
TCTGTAAGCCATCATCCACCGCTATCACTTCATATGCATGGTAGCCCTCATCCCC
Found at i:132813 original size:14 final size:14
Alignment explanation
Indices: 132794--132859 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
132784 ACCTAACTTA
132794 AAACCCTAAATCAT
1 AAACCCTAAATCAT
*
132808 AAACCCTAAATCTT
1 AAACCCTAAATCAT
* * *
132822 AAACCATAACT-TT
1 AAACCCTAAATCAT
132835 ACAACCTCTAAATCAT
1 A-AACC-CTAAATCAT
*
132851 AAACTCTAA
1 AAACCCTAA
132860 TTTAGGGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 3 0.07
14 30 0.71
15 7 0.17
16 2 0.05
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:132874 original size:14 final size:14
Alignment explanation
Indices: 132857--132894 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
132847 TCATAAACTC
*
132857 TAATTTAGGGTTTA
1 TAATTAAGGGTTTA
132871 TAATTAAGGGTTT-
1 TAATTAAGGGTTTA
132884 TAAATTAAGGG
1 T-AATTAAGGG
132895 CAGAGTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (14 bp):
TAATTAAGGGTTTA
Done.