Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002792.1 Hibiscus syriacus cultivar Beakdansim tig00005752_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: 82948
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6480 original size:20 final size:20
Alignment explanation
Indices: 6452--6521 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
6442 GGCTTGATTT
*
6452 TACTATAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
6472 TACTGTAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
6492 TACTGTAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
6512 TACTGTAGCA
1 TACTGTAGCA
6522 TATGATTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (20 bp):
TACTGTAGCAGTATCGATAC
Found at i:11202 original size:23 final size:20
Alignment explanation
Indices: 11151--11207 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
11141 GGACTTGATT
*
11151 TTACTGTAGCAGTATCGATA
1 TTACTGTAGTAGTATCGATA
11171 TTACTGTAGTAGTATCGATA
1 TTACTGTAGTAGTATCGATA
11191 TTACTGTAGTAGTATCG
1 TTACTGTAGTAGTATCG
11208 GTACCATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (20 bp):
TTACTGTAGTAGTATCGATA
Found at i:11919 original size:21 final size:22
Alignment explanation
Indices: 11893--11944 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
11883 TGTTCTCAAT
11893 GTATCGATACCCTCCA-CATA-G
1 GTATCGATA-CCTCCACCATAGG
*
11914 GTATCGATACCTCTACCATAGG
1 GTATCGATACCTCCACCATAGG
11936 GTATCGATA
1 GTATCGATA
11945 TTGTTCATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 10 0.36
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (22 bp):
GTATCGATACCTCCACCATAGG
Found at i:15026 original size:18 final size:18
Alignment explanation
Indices: 14995--15029 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14985 ACTATAAATT
*
14995 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
15013 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
15030 CATTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:17457 original size:14 final size:14
Alignment explanation
Indices: 17385--17472 Score: 56
Period size: 14 Copynumber: 6.3 Consensus size: 14
17375 ACCCTACATC
* *
17385 CTAATTCTTACACT
1 CTAAATCTTAAACT
* *
17399 TTAAACCTTAAACAT
1 CTAAATCTTAAAC-T
*
17414 -TAAA-CTTTAAACC
1 CTAAATC-TTAAACT
*
17427 CTAAATCCTT-AATT
1 CTAAAT-CTTAAACT
17441 CTAAATCTTAAACT
1 CTAAATCTTAAACT
* *
17455 CTAATTCCTAAACT
1 CTAAATCTTAAACT
17469 CTAA
1 CTAA
17473 TTCTAATAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
13 4 0.07
14 50 0.86
15 3 0.05
16 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (14 bp):
CTAAATCTTAAACT
Found at i:17475 original size:14 final size:14
Alignment explanation
Indices: 17421--17472 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
17411 CATTAAACTT
*
17421 TAAACCCTAAATCC
1 TAAACTCTAAATCC
* * *
17435 TTAATTCTAAATCT
1 TAAACTCTAAATCC
*
17449 TAAACTCTAATTCC
1 TAAACTCTAAATCC
17463 TAAACTCTAA
1 TAAACTCTAA
17473 TTCTAATAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAACTCTAAATCC
Found at i:17640 original size:2 final size:2
Alignment explanation
Indices: 17633--17674 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17623 ATCTTAACCC
17633 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17675 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17679 original size:2 final size:2
Alignment explanation
Indices: 17674--17704 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17664 TCTCTCTCTC
*
17674 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17705 CTTTACTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20367 original size:3 final size:3
Alignment explanation
Indices: 20347--20416 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
20337 AGATAAGAAA
* * * *
20347 AAT AAT AA- AGT AAA AAT AAT AAA AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20394 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
20417 GGGTAAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 1 0.02
3 57 0.98
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:21819 original size:25 final size:26
Alignment explanation
Indices: 21765--21821 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
21755 AAAATAGTAA
* **
21765 ATAAATATACATTTATATATATACGT
1 ATAAATAAACATAAATATATATACGT
*
21791 -TAAATAAACATAAATATATATA-TT
1 ATAAATAAACATAAATATATATACGT
21815 ATAAATA
1 ATAAATA
21822 TGTGCTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (26 bp):
ATAAATAAACATAAATATATATACGT
Found at i:25882 original size:4 final size:4
Alignment explanation
Indices: 25873--25897 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25863 ACTTTAACCA
25873 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
25898 GTTTCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:26068 original size:126 final size:116
Alignment explanation
Indices: 25915--26200 Score: 365
Period size: 118 Copynumber: 2.3 Consensus size: 116
25905 TTATTACTCA
* *
25915 ATCTTGTGGTGACTAGATATGGGGTATGATCCACATTATTATGGTTTGGATTATGCTAACCACTA
1 ATCTTGTGGTGACCAGAT-T-GGGTATGATCCACATTATTATGGTTTGGACTATGCTAACCACTA
25980 ACCTTTTTTATTTGATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
64 A-C-----T-TTT-ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
* * *
26041 ATCTTGCGGTGACCAGATCTGAGGTATGATTCACATTATTATGGTTTGGACTCTGCTAACCACTA
1 ATCTTGTGGTGACCAGAT-TG-GGTATGATCCACATTATTATGGTTTGGACTATGCTAACCACTA
* *
26106 ACTTTTATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCGATTTG
64 ACTTTTATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
* *
26159 ACCTTGTGGTGACCCGATTCGGGATATGATCCACATTATTAT
1 ATCTTGTGGTGACCAGATT-GGG-TATGATCCACATTATTAT
26201 TGTTCGAACC
Statistics
Matches: 145, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
117 3 0.02
118 78 0.54
119 3 0.02
120 1 0.01
125 2 0.01
126 58 0.40
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (116 bp):
ATCTTGTGGTGACCAGATTGGGTATGATCCACATTATTATGGTTTGGACTATGCTAACCACTAAC
TTTTATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
Found at i:26218 original size:118 final size:118
Alignment explanation
Indices: 25994--26229 Score: 325
Period size: 118 Copynumber: 2.0 Consensus size: 118
25984 TTTTTATTTG
*
25994 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGATCTTGCGGTGACCAGAT
1 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGACCTTGCGGTGACCAGAT
* * * *
26059 CTGAGGTATGATTCACATTATTATGGTTTGGACTCTGCTAACCACTAACTTTT
66 CTGAGGTATGATCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTT
* * * *
26112 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCGATTTGACCTTGTGGTGACCCGAT
1 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGACCTTGCGGTGACCAGAT
* *
26177 -TCG-GGATATGATCCACATTATTATTGTTCGAAC-CTTACTAACCGCTAACTTTT
66 CT-GAGG-TATGATCCACATTATTATGGTTCGAACTC-TACTAACCACTAACTTTT
26230 CTAACTTAAC
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
117 4 0.04
118 100 0.96
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (118 bp):
ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGACCTTGCGGTGACCAGAT
CTGAGGTATGATCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTT
Found at i:26276 original size:32 final size:33
Alignment explanation
Indices: 26240--26433 Score: 173
Period size: 32 Copynumber: 5.8 Consensus size: 33
26230 CTAACTTAAC
26240 AACATTCTAAC-TTTTATTTTATTGTTCATACT
1 AACATTCTAACTTTTTATTTTATTGTTCATACT
26272 AACATTCTAAC-TTTTATTTTATTGTTCATACT
1 AACATTCTAACTTTTTATTTTATTGTTCATACT
* * * *
26304 AACATTCTAGCTTTTTTTATTGTTCTTATTAACTTACT
1 AACATTCTAAC--TTTTTATT-TTATTGTT--CATACT
* * *
26342 AACATTCTAA-TTTATATTTTATTGCTCATATT
1 AACATTCTAACTTTTTATTTTATTGTTCATACT
* *
26374 AACATACTTACCTTTTTATTTCTATTGTT-ATTACT
1 AACATTC-TAACTTTTTATTT-TATTGTTCA-TACT
**
26409 AAC-TTACTAACACTTTATTTTATTG
1 AACATT-CTAACTTTTTATTTTATTG
26434 CACAAACTAA
Statistics
Matches: 131, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
32 52 0.40
33 7 0.05
34 25 0.19
35 27 0.21
36 6 0.05
38 14 0.11
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (33 bp):
AACATTCTAACTTTTTATTTTATTGTTCATACT
Found at i:26351 original size:70 final size:74
Alignment explanation
Indices: 26268--26420 Score: 199
Period size: 70 Copynumber: 2.1 Consensus size: 74
26258 TTATTGTTCA
* * *
26268 TACTAACATTCTAACTTT-TATTTTATTGTTCATACTAACATTC-TAGC-TTT-TTT-TATTGTT
1 TACTAACATTCTAA-TTTATATTTTATTGCTCATACTAACATACTTACCTTTTATTTCTATTGTT
* *
26328 CTTATTAACT
65 ATTACTAACT
*
26338 TACTAACATTCTAATTTATATTTTATTGCTCATATTAACATACTTACCTTTTTATTTCTATTGTT
1 TACTAACATTCTAATTTATATTTTATTGCTCATACTAACATACTTACC-TTTTATTTCTATTGTT
26403 ATTACTAACT
65 ATTACTAACT
26413 TACTAACA
1 TACTAACA
26421 CTTTATTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
69 3 0.04
70 36 0.51
71 3 0.04
73 3 0.04
74 3 0.04
75 23 0.32
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.52
Consensus pattern (74 bp):
TACTAACATTCTAATTTATATTTTATTGCTCATACTAACATACTTACCTTTTATTTCTATTGTTA
TTACTAACT
Found at i:26374 original size:40 final size:38
Alignment explanation
Indices: 26298--26381 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 38
26288 TTTTATTGTT
* * *
26298 CATACTAACATTCTAGCTTTTTTTATTGTTCTTATTAA
1 CATACTAACATTCTAACTTTTTTTATTGCTCATATTAA
* *
26336 CTTACTAACATTCTAATTTATATTTTATTGCTCATATTAA
1 CATACTAACATTCTAACTT-T-TTTTATTGCTCATATTAA
26376 CATACT
1 CATACT
26382 TACCTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 16 0.42
39 1 0.03
40 21 0.55
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.50
Consensus pattern (38 bp):
CATACTAACATTCTAACTTTTTTTATTGCTCATATTAA
Found at i:27088 original size:5 final size:5
Alignment explanation
Indices: 27074--27108 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
27064 TTTCCCCTCG
27074 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
27109 TATCTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:33122 original size:64 final size:63
Alignment explanation
Indices: 33011--33131 Score: 145
Period size: 64 Copynumber: 1.9 Consensus size: 63
33001 CATCGAAGCT
* * * *
33011 ATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTATTTTATTGAAACATCAAATGC
1 ATTTTATGGACCGATACACAACCATGCATCGATACACTCCTACTTTATTAAAACATCAAATGC
* * * *
33074 ATTTTGTGGACCGATACACATCCTATGCATCGATGCACT-CTGCCTTTATTAAAACATC
1 ATTTTATGGACCGATACACAACC-ATGCATCGATACACTCCT-ACTTTATTAAAACATC
33132 GAAGGTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 21 0.44
64 27 0.56
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (63 bp):
ATTTTATGGACCGATACACAACCATGCATCGATACACTCCTACTTTATTAAAACATCAAATGC
Found at i:36063 original size:23 final size:23
Alignment explanation
Indices: 36037--36083 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
36027 AAGAAACAAA
*
36037 AAAAT-TTATATATATTTATAAAT
1 AAAATATT-TATATATTTAGAAAT
*
36060 AAAATATTTATTTATTTAGAAAT
1 AAAATATTTATATATTTAGAAAT
36083 A
1 A
36084 TCAGAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATATTTATATATTTAGAAAT
Found at i:37733 original size:3 final size:3
Alignment explanation
Indices: 37727--37795 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
37717 ATTATTTTTT
* * * *
37727 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
37772 TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
37796 AATGGGTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:38086 original size:122 final size:119
Alignment explanation
Indices: 37937--38221 Score: 346
Period size: 124 Copynumber: 2.3 Consensus size: 119
37927 GAATAAATTC
* *
37937 TTTTCTTTCTTCAGATGAGTTCCTCTCATTATGAACTTTTCGT-TGG-GGATGATGT-TGACCTA
1 TTTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTC-TCTGGAGGATGAT-TCTAACCTA
* *
37999 T-TTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACT
63 TCTT-CTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACT
* * *
38056 TCTTCTTTCTCTTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTGGAAAGGTTGATTCTAAT
1 T-TT-TCT-TC-TTCAGATGAGTTCTTCTCATTATGAACTTTTCTCTGG--AGGATGATTCTAAC
* *
38120 CTATCTTCTTCTGTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACT
60 CTATCTTCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACT
*
38180 TTTTCTTCTTCAGATGAGTTCTTCTCATTACGAACTTCTTCT
1 TTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TTCT
38222 TCTCCAGATG
Statistics
Matches: 143, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
119 1 0.01
120 30 0.21
121 13 0.09
122 32 0.22
123 3 0.02
124 62 0.43
125 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (119 bp):
TTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTCTGGAGGATGATTCTAACCTATCT
TCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACT
Found at i:38204 original size:36 final size:36
Alignment explanation
Indices: 38163--38254 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
38153 TTGAATAAGC
* *
38163 TCTTCTCATTGTGAACTTTTTCTTCTTCAGATGAGT
1 TCTTCTCATTGTGAACTTCTTCTTCTCCAGATGAGT
**
38199 TCTTCTCATTACGAACTTCTTCTTCTCCAGATGAGT
1 TCTTCTCATTGTGAACTTCTTCTTCTCCAGATGAGT
38235 TCTTCTCATTGTGAACTTCT
1 TCTTCTCATTGTGAACTTCT
38255 CTGGAAAAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.12, T:0.47
Consensus pattern (36 bp):
TCTTCTCATTGTGAACTTCTTCTTCTCCAGATGAGT
Found at i:38423 original size:112 final size:108
Alignment explanation
Indices: 38198--38474 Score: 369
Period size: 112 Copynumber: 2.5 Consensus size: 108
38188 TTCAGATGAG
* * *
38198 TTCTTCTCATTACGAACTTCTTCTTCTCCAGATGAGTTCTTCTCATTGTGAACTTCTCTGGAAAA
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA
* * * * *
38263 GCTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAA
66 GCTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
*
38306 TTCTTCTC-TTCATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-TCTACCT
1 TTCTTCTCATT-ATGAACTTCTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTCT--CT
* * * *
38369 GGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
60 GGAAAAGCTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
38418 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCT
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCT
38475 TCTTCTTCAT
Statistics
Matches: 147, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
107 2 0.01
108 27 0.18
109 20 0.14
110 6 0.04
111 19 0.13
112 71 0.48
113 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (108 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA
GCTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
Found at i:38458 original size:36 final size:36
Alignment explanation
Indices: 38418--38510 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
38408 GTTGAACAAA
38418 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
*
38454 TTCTTCTCATTATGAACTTCTTCTTCTTCATATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
38490 TTCTTCTCATTATGAACTTCT
1 TTCTTCTCATTATGAACTTCT
38511 CTGGAAAAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.49
Consensus pattern (36 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
Found at i:38570 original size:144 final size:147
Alignment explanation
Indices: 38306--38618 Score: 420
Period size: 144 Copynumber: 2.1 Consensus size: 147
38296 GTTGAACAAA
*
38306 TTCTTCTC-TTCATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATT-ATGAACTTCTTCTTCTTCA-ATGACGAGTTCTTCTCATTATGAACTCTA-CTG
* * *
38370 GCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
63 GAAAAGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC
*
38435 TTCTTCTTCTTCAGAT-GAG
128 TTCTTATTCTTCAGATAGAG
*
38454 TTCTTCTCATTATGAACTTCTTCTTCTTC-AT-ATGAGTTCTTCTCATTATGAACTTCT-CTGGA
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAATGACGAGTTCTTCTCATTATGAAC-TCTACTGGA
* * * * * *
38516 AAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTT
65 AAAGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTT
*
38581 CTTATTCTTTAGATGACGAG
130 CTTATTCTTCAGAT-A-GAG
38601 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
38619 CTACCTGGCA
Statistics
Matches: 147, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
144 73 0.50
145 21 0.14
146 5 0.03
147 21 0.14
148 25 0.17
149 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (147 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCAATGACGAGTTCTTCTCATTATGAACTCTACTGGAA
AAGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
TTATTCTTCAGATAGAG
Found at i:38601 original size:256 final size:256
Alignment explanation
Indices: 38146--38719 Score: 997
Period size: 256 Copynumber: 2.2 Consensus size: 256
38136 TAGAATTATG
* ** * *
38146 CAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTTTCTTCTTCAGATGAGTTCTTCTCATTAC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAC
*
38211 GAACTTCTTCTTCTCCAGATGAGTTCTTCTCATTGTGAACTTCTCTGGAAAAGCTGATCCATCAA
66 GAACTTCTTCTTCTCCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGCTGATCCATCAA
*
38276 GTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCTTCATGAATTTCTTCTTCTTCAGATGA
131 GTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCTTCATGAATTTCTTATTCTTCAGATGA
38341 CGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
196 CGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
*
38402 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAC
* * *
38467 GAACTTCTTCTTCTTCATATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCAA
66 GAACTTCTTCTTCTCCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGCTGATCCATCAA
*
38532 GTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATT-ATGAATTTCTTATTCTTTAGATG
131 GTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTC-TTCATGAATTTCTTATTCTTCAGATG
38596 ACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
195 ACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
38658 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA---CTTCTTCTTCTTCAGATGAGTTCTTCT
38720 TACTCGAACT
Statistics
Matches: 302, Mismatches: 12, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
256 273 0.90
257 2 0.01
259 27 0.09
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (256 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAC
GAACTTCTTCTTCTCCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGCTGATCCATCAA
GTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCTTCATGAATTTCTTATTCTTCAGATGA
CGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
Found at i:38675 original size:112 final size:112
Alignment explanation
Indices: 38454--38985 Score: 581
Period size: 112 Copynumber: 4.8 Consensus size: 112
38444 TTCAGATGAG
38454 TTCTTCTCATTATGAACTTCTTCTTC-TT-CAT-ATGAGTTCTTCTCATTATGAACT-T-CTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCTTTACATGATGAGTTCTTCTCATTATGAACTCTAC-CTG
* * * *
38514 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAA
65 GAAAAGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
* * * *
38562 TTCTTCTCATTATGAATTTCTTATTCTTTAGATGACGAGTTCTTCTCATTATGAACTCTACCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCTTTACATGATGAGTTCTTCTCATTATGAACTCTACCTGG
* * * *
38627 CAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
66 AAAAGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
* * *
38674 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCA-GATGAGTTC-T-TC--T-T--ACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCTT-TACATGATGAGTTCTTCTCATTATGAACTCTACCTG
** * ** * *
38731 GTCATGTTGATCCATTGAATGATGAATTTAAGCAAAAAGTTGAACAAG
65 GAAAAGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
* * * * * *
38779 TTCTTCTCATTATGAACTTTTTCTGCCTTCTTCA-GATGAGTTTTTCTCATTATGAACTTTTCGC
1 TTCTTCTCATTATGAACTTCTTCT-TCTT-TACATGATGAGTTCTTCTCATTATGAACTCTAC-C
* *
38843 TGGAAAAGCTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
63 TGGAAAAGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
* * **
38893 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCA-GATGAGTTCTTCTTATTATGAACTCTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCTT-TACATGATGAGTTCTTCTCATTATGAACTCTACCTG
* *
38957 GAAAAGCTGATCCATCAAATGATGGATTT
65 GAAAAGTTGATCCATCAAATGATGAATTT
38986 GAATCTTTGC
Statistics
Matches: 359, Mismatches: 50, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
105 71 0.20
106 16 0.04
107 2 0.01
108 27 0.08
109 2 0.01
110 5 0.01
111 24 0.07
112 109 0.30
113 38 0.11
114 65 0.18
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTTACATGATGAGTTCTTCTCATTATGAACTCTACCTGG
AAAAGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
Found at i:38906 original size:219 final size:215
Alignment explanation
Indices: 38519--38940 Score: 632
Period size: 219 Copynumber: 1.9 Consensus size: 215
38509 CTCTGGAAAA
* * *
38519 GTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTT
1 GTTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTC
* * * *
38584 ATTCTTTAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGAT
66 ATTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCATCAAATGAT
38649 GAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGT
129 GAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGT
38714 TCTTCTTACTCGAACTGGTCAT
194 TCTTCTTACTCGAACTGGTCAT
* *
38736 GTTGATCCATTGAA-TGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTT
1 GTTGATCCA-TCAAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA---TT
* * * * *
38800 TCTGCCTTCTTCAGAT-GAGTTTTTCTCATTATGAACTTTTCGCTGGAAAAGCTGATCCATCAAA
62 TCT-CATTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAGCTAATCCATCAAA
38864 TGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT
125 TGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT
38929 GAGTTCTTCTTA
190 GAGTTCTTCTTA
38941 TTATGAACTC
Statistics
Matches: 185, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
217 51 0.28
218 25 0.14
219 95 0.51
220 5 0.03
221 9 0.05
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (215 bp):
GTTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTC
ATTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCATCAAATGATGA
ATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTC
TTCTTACTCGAACTGGTCAT
Found at i:39851 original size:115 final size:115
Alignment explanation
Indices: 39690--40167 Score: 832
Period size: 115 Copynumber: 4.2 Consensus size: 115
39680 GATCATGCAG
* * * * * * *
39690 TTCATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCTTACCGAACCAAATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
39754 AACACTTCCAGAAGATGATATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
* *
39804 TTCATTTTTCAAATCCAATGATTGGTTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
39869 AACACTTCCAGAAGATGCTATTGGTTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
*
39919 TTCATCTTTCAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
39984 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
40034 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
40099 AATACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
40149 TTCATCTTTCAAATCCAAT
1 TTCATCTTTCAAATCCAAT
40168 TAATGTTTGG
Statistics
Matches: 346, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 22 0.06
115 324 0.94
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
Found at i:41059 original size:19 final size:17
Alignment explanation
Indices: 41035--41083 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
41025 TCCATAAAAG
41035 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
41054 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
41070 AATAAATTGAATTT
1 AATAAATTGAATTT
41084 GGAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:52125 original size:18 final size:17
Alignment explanation
Indices: 52104--52137 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52094 AAATATTAAT
52104 ATAAATATTATAAAAATA
1 ATAAATA-TATAAAAATA
*
52122 ATAAGTATATAAAAAT
1 ATAAATATATAAAAAT
52138 TTTGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAAATATATAAAAATA
Found at i:52664 original size:23 final size:23
Alignment explanation
Indices: 52638--52684 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
52628 AAGAAACAAA
*
52638 AAAAT-TTATATATATTTATAAAT
1 AAAATATT-TATATATTTAGAAAT
*
52661 AAAATATTTATTTATTTAGAAAT
1 AAAATATTTATATATTTAGAAAT
52684 A
1 A
52685 TCAGAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATATTTATATATTTAGAAAT
Found at i:54289 original size:3 final size:3
Alignment explanation
Indices: 54281--54355 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
54271 AATTATTTTT
* *
54281 TAA TAA TAA TAA -ATA TAA TAA TTA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
54326 TAA TTA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54356 AATGGGTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.02
3 60 0.97
4 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:54300 original size:12 final size:12
Alignment explanation
Indices: 54283--54353 Score: 115
Period size: 12 Copynumber: 5.9 Consensus size: 12
54273 TTATTTTTTA
*
54283 ATAATAATAAAT
1 ATAATAATAATT
* *
54295 ATAATAATTATA
1 ATAATAATAATT
54307 ATAATAATAATT
1 ATAATAATAATT
54319 ATAATAATAATT
1 ATAATAATAATT
54331 ATAATAATAATT
1 ATAATAATAATT
54343 ATAATAATAAT
1 ATAATAATAAT
54354 AAAATGGGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:74640 original size:14 final size:15
Alignment explanation
Indices: 74621--74651 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
74611 TTATGCGCAG
74621 TGTATCGATAC-CTA
1 TGTATCGATACACTA
74635 TGTATCGATACACTA
1 TGTATCGATACACTA
74650 TG
1 TG
74652 ATAGTGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (15 bp):
TGTATCGATACACTA
Found at i:74659 original size:21 final size:21
Alignment explanation
Indices: 74635--74713 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
74625 TCGATACCTA
74635 TGTATCGATACACTATGATAG
1 TGTATCGATACACTATGATAG
* *
74656 TGTATCAATGCATTCCT-TGA-ATG
1 TGTATCGATACA---CTATGATA-G
*
74679 TGTATCGATACACTATCATAG
1 TGTATCGATACACTATGATAG
74700 TGTATCGATACACT
1 TGTATCGATACACT
74714 TGTCGGGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.04
21 27 0.57
22 2 0.04
23 14 0.30
24 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (21 bp):
TGTATCGATACACTATGATAG
Found at i:75799 original size:15 final size:15
Alignment explanation
Indices: 75779--75816 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
75769 TATCTTTGGT
75779 TTAGATAATGATGGC
1 TTAGATAATGATGGC
*
75794 TTAGATAATGATGGT
1 TTAGATAATGATGGC
75809 TTAGATAA
1 TTAGATAA
75817 CGAAAAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (15 bp):
TTAGATAATGATGGC
Found at i:77222 original size:18 final size:19
Alignment explanation
Indices: 77189--77224 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
77179 TACTTAAGTG
*
77189 TAAAATTTTGTTTGAAACT
1 TAAAATATTGTTTGAAACT
77208 TAAAATATT-TTTGAAAC
1 TAAAATATTGTTTGAAAC
77225 AATTTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (19 bp):
TAAAATATTGTTTGAAACT
Found at i:78911 original size:13 final size:13
Alignment explanation
Indices: 78893--78920 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
78883 CAAAGTTAAC
78893 GAGTTGACTTAGT
1 GAGTTGACTTAGT
78906 GAGTTGACTTAGT
1 GAGTTGACTTAGT
78919 GA
1 GA
78921 CTGGACCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (13 bp):
GAGTTGACTTAGT
Found at i:80318 original size:6 final size:6
Alignment explanation
Indices: 80309--80335 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
80299 AACCCGTCTT
80309 CGTCCC CGTCCC CGTCCC CGTCCC CGT
1 CGTCCC CGTCCC CGTCCC CGTCCC CGT
80336 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.63, G:0.19, T:0.19
Consensus pattern (6 bp):
CGTCCC
Found at i:81555 original size:28 final size:27
Alignment explanation
Indices: 81524--81582 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
81514 TTTAACAATA
81524 TTAAAATA-GAATAAAATTTATTTTTAAC
1 TTAAAATAGGAATAAAA--TATTTTTAAC
* *
81552 TT-AAATAGGATTAAAATATTTTTAAG
1 TTAAAATAGGAATAAAATATTTTTAAC
81578 TTAAA
1 TTAAA
81583 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 11 0.41
27 7 0.26
28 9 0.33
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (27 bp):
TTAAAATAGGAATAAAATATTTTTAAC
Found at i:81592 original size:28 final size:28
Alignment explanation
Indices: 81561--81618 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
81551 CTTAAATAGG
* *
81561 ATTAA-AATATTTTTAAGTTAAATTAAAA
1 ATTAATAATATTTATAA-TTAAAGTAAAA
*
81589 ATTAATAATATTTATAATTTAAGTAAAA
1 ATTAATAATATTTATAATTAAAGTAAAA
81617 AT
1 AT
81619 ATAACACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTAATAATATTTATAATTAAAGTAAAA
Done.