Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006081.1 Hibiscus syriacus cultivar Beakdansim tig00014407_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: 76907
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:390 original size:12 final size:13
Alignment explanation
Indices: 373--401 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
363 TTATGACATG
373 CATTTAT-ACGCA
1 CATTTATGACGCA
385 CATTTATGACGCA
1 CATTTATGACGCA
398 CATT
1 CATT
402 GCGCGTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (13 bp):
CATTTATGACGCA
Found at i:401 original size:25 final size:25
Alignment explanation
Indices: 352--401 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
342 GTGTCAAAAA
* **
352 TATACGCGCATTTATGACATGCATT
1 TATACGCACATTTATGACACACATT
*
377 TATACGCACATTTATGACGCACATT
1 TATACGCACATTTATGACACACATT
402 GCGCGTCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (25 bp):
TATACGCACATTTATGACACACATT
Found at i:1451 original size:12 final size:12
Alignment explanation
Indices: 1434--1459 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1424 TATGATAATC
1434 AATGAAAAAACA
1 AATGAAAAAACA
1446 AATGAAAAAACA
1 AATGAAAAAACA
1458 AA
1 AA
1460 CCATGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AATGAAAAAACA
Found at i:4096 original size:15 final size:15
Alignment explanation
Indices: 4076--4106 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4066 AAAGGGAAAC
4076 ATGGGTTTAGTGTGA
1 ATGGGTTTAGTGTGA
4091 ATGGGTTTAGTGTGA
1 ATGGGTTTAGTGTGA
4106 A
1 A
4107 CTGATTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (15 bp):
ATGGGTTTAGTGTGA
Found at i:7036 original size:12 final size:12
Alignment explanation
Indices: 7012--7114 Score: 54
Period size: 13 Copynumber: 8.3 Consensus size: 12
7002 AGAAATATAT
7012 ATATATAATAAA
1 ATATATAATAAA
7024 ATATAGTAA-AAA
1 ATATA-TAATAAA
7036 A-ATA-AATGAAA
1 ATATATAAT-AAA
* *
7047 ATAATTTAATATAT
1 AT-ATATAATA-AA
*
7061 ATATATACATATA
1 ATATATA-ATAAA
*
7074 ATA-ATAATAAC
1 ATATATAATAAA
7085 ATGA-ATAATAAAA
1 AT-ATATAAT-AAA
*
7098 ATAAATGAATAAA
1 ATATAT-AATAAA
7111 ATAT
1 ATAT
7115 CCATATAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 23
0.69 0.09 0.23
Matches are distributed among these distances:
9 2 0.03
11 12 0.17
12 19 0.27
13 25 0.36
14 12 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:7094 original size:18 final size:17
Alignment explanation
Indices: 7071--7113 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
7061 ATATATACAT
7071 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
7089 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
7106 ATAA-AATA
1 ATAATAATA
7114 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:7099 original size:51 final size:51
Alignment explanation
Indices: 7005--7125 Score: 119
Period size: 51 Copynumber: 2.5 Consensus size: 51
6995 ATATTAAAGA
* * * * *
7005 AATATATATATATA-ATAAAAT-ATAGTAAAAAAATAAATGAAAATAATTT
1 AATATATATATATACATATAATAATAATAAAAAAATAAATAAAAATAAATG
**
7054 AATATATATATATACATATAATAATAATAACATGAAT-AATAAAAATAAATG
1 AATATATATATATACATATAATAATAATAA-AAAAATAAATAAAAATAAATG
*
7105 AATA-A-A-ATATCCATATAATAA
1 AATATATATATATACATATAATAA
7126 ATAAAGGGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
48 14 0.23
49 15 0.25
50 7 0.11
51 21 0.34
52 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (51 bp):
AATATATATATATACATATAATAATAATAAAAAAATAAATAAAAATAAATG
Found at i:8382 original size:105 final size:105
Alignment explanation
Indices: 8080--8710 Score: 914
Period size: 105 Copynumber: 6.0 Consensus size: 105
8070 GCATTGTTCC
* * ** *
8080 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
8144 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
8186 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
8246 AAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
8286 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
8351 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
8391 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
8456 CAGCGGTCCTTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
8496 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
8561 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
8601 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTCACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
8666 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
8707 GAGT
1 GAGT
8711 GTCACGATAT
Statistics
Matches: 481, Mismatches: 37, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
100 82 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 302 0.63
106 84 0.17
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:9106 original size:105 final size:101
Alignment explanation
Indices: 8885--9138 Score: 375
Period size: 105 Copynumber: 2.5 Consensus size: 101
8875 TTCGTTAAAT
* **
8885 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAA
* * *
8950 TTATCTCAAGCAAGATAAAATTCATTTCAAGGGAAA
66 CTATCTCAAGCAAGAAAAAAATCATTTCAAGGGAAA
*
8986 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
9051 AAACTATCTCAAG-AGAGAAAAAAAATCATTTCAAGGGAAA
63 AAACTATCTCAAGCA-AG-AAAAAAATCATTTCAAGGGAAA
* *
9091 TGTTTTCAATGTTTATGTTTCAAGAGAAACGGTCTCAAGCGAGACAAA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
9139 TCTTGTTTTA
Statistics
Matches: 139, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
101 46 0.33
103 4 0.03
104 23 0.17
105 66 0.47
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (101 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAA
CTATCTCAAGCAAGAAAAAAATCATTTCAAGGGAAA
Found at i:9204 original size:36 final size:36
Alignment explanation
Indices: 9108--9210 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 36
9098 AATGTTTATG
* * * * *
9108 TTTCAAGAGAAACGGTCTCAAGCGAGACAAATCTTG
1 TTTCAAGAAAAACAGTCTCAAGTGAAACAAATCTTC
* * ** *
9144 TTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTC
1 TTTCAAGAAAAACAGTCTCAAGTGAAACAAATCTTC
* *
9180 TTTCGAGAAAAACAGTCTCAAGTGAGACAAA
1 TTTCAAGAAAAACAGTCTCAAGTGAAACAAA
9211 GTATGTTTTA
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (36 bp):
TTTCAAGAAAAACAGTCTCAAGTGAAACAAATCTTC
Found at i:9225 original size:36 final size:35
Alignment explanation
Indices: 9104--9227 Score: 97
Period size: 36 Copynumber: 3.5 Consensus size: 35
9094 TTTCAATGTT
* * * *
9104 TATGTTTCAAGAGAAACGGTCTCAAGCGAGACAAA
1 TATGTTTTAAGAAAAACAGTCTCAAGTGAGACAAA
* * ** * *
9139 TCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAA
1 T-ATGTTTTAAGAAAAACAGTCTCAAGTGAGACAAA
* *
9175 TCT-TCTTTCGAGAAAAACAGTCTCAAGTGAGACAAA
1 TATGT-TTT-AAGAAAAACAGTCTCAAGTGAGACAAA
9211 GTATGTTTTAAGAAAAA
1 -TATGTTTTAAGAAAAA
9228 AAAAATTGAG
Statistics
Matches: 65, Mismatches: 19, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
34 1 0.02
35 5 0.08
36 53 0.82
37 5 0.08
38 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (35 bp):
TATGTTTTAAGAAAAACAGTCTCAAGTGAGACAAA
Found at i:9239 original size:72 final size:72
Alignment explanation
Indices: 9108--9245 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
9098 AATGTTTATG
* * * * **
9108 TTTCAAGAGAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATA
1 TTTCAAGAAAAACAGTCTCAAGCGAGACAAATCATGTTTTAAGAAAAAAAAAATTGAGTGAAATA
9173 AATCTTC
66 AATCTTC
* * *
9180 TTTCGAGAAAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGAAAAAAAAAATTGAGTGAGAT
1 TTTCAAGAAAAACAGTCTCAAGCGAGACAAA-TCATGTTTTAAGAAAAAAAAAATTGAGTGAAAT
9244 AA
65 AA
9246 TCATCTGCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 55 0.98
73 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (72 bp):
TTTCAAGAAAAACAGTCTCAAGCGAGACAAATCATGTTTTAAGAAAAAAAAAATTGAGTGAAATA
AATCTTC
Found at i:10693 original size:183 final size:182
Alignment explanation
Indices: 10386--10921 Score: 939
Period size: 183 Copynumber: 2.9 Consensus size: 182
10376 ATCAGGTTTA
* *
10386 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGAAAAAGCAGTGGAGCAAACACCGAATTA
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAAAAAGCAGTGGAGCAAACACCGAATTG
* * ** *
10451 CCAATTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGACAGGGCTTTCGAGTT
66 CCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
10515 TCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTAGAGGGACAAATC
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
10568 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGA-AAAAGCAGTGGAGCAAACACCGAATT
10633 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
65 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
10698 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
10751 ACTGAAGGGTTCATATCATCACAAAGTCTTTGGCCTGATAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGA-AAAAGCAGTGGAGCAAACACCGAATT
*
10816 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTT
65 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
10881 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
10922 CAGATTTAAT
Statistics
Matches: 339, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
182 36 0.11
183 302 0.89
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (182 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAAAAAGCAGTGGAGCAAACACCGAATTG
CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:14456 original size:19 final size:19
Alignment explanation
Indices: 14423--14459 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
14413 TGCAGATGAT
14423 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
14442 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
14460 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:16204 original size:18 final size:17
Alignment explanation
Indices: 16183--16225 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
16173 ATATATACAT
16183 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
16201 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
16218 ATAA-AATA
1 ATAATAATA
16226 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:16204 original size:56 final size:55
Alignment explanation
Indices: 16106--16213 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 55
16096 ATATTAAAGA
16106 AATATATATATATAATAACAATAAAATATAGTAAAAAAAATAAATAAAAATAATTT
1 AATATATATATATAATAACAATAAAATATAGTAAAAAAAAT-AATAAAAATAATTT
* **
16162 AATATATATATAT-ATATACATATAATAATA-A-TAACATGAATAATAAAAATAA
1 AATATATATATATAATA-ACA-ATAA-AATATAGTAAAAAAAATAATAAAAATAA
16214 ATGAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
55 14 0.30
56 23 0.50
57 5 0.11
58 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (55 bp):
AATATATATATATAATAACAATAAAATATAGTAAAAAAAATAATAAAAATAATTT
Found at i:16633 original size:37 final size:37
Alignment explanation
Indices: 16583--16687 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
16573 GTGCTTGTGG
* * * *
16583 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAAATCT
* * * *
16620 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAATTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAAATCT
* *
16657 ATCCTATTTTTAAGAGTTTAAATCGTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
16688 GACGAAAATG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAAATCT
Found at i:17183 original size:31 final size:32
Alignment explanation
Indices: 17148--17216 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
17138 GTTAATTTTT
*
17148 AATTTAAATC-CTAAACTTTAAATAAAATATC
1 AATTTAAACCTCTAAACTTTAAATAAAATATC
* *
17179 AATTT-AACCTCTAAACTTTATATGAAATATC
1 AATTTAAACCTCTAAACTTTAAATAAAATATC
*
17210 ATTTTAA
1 AATTTAA
17217 CCCTTGAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 3 0.09
31 28 0.88
32 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39
Consensus pattern (32 bp):
AATTTAAACCTCTAAACTTTAAATAAAATATC
Found at i:17217 original size:31 final size:31
Alignment explanation
Indices: 17158--17218 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
17148 AATTTAAATC
17158 CTAAACTTTAAATAAAATATCAATTTAACCT
1 CTAAACTTTAAATAAAATATCAATTTAACCT
* * *
17189 CTAAACTTTATATGAAATATCATTTTAACC
1 CTAAACTTTAAATAAAATATCAATTTAACC
17219 CTTGAACCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (31 bp):
CTAAACTTTAAATAAAATATCAATTTAACCT
Found at i:22641 original size:29 final size:29
Alignment explanation
Indices: 22598--22657 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
22588 ATAAGTGTCA
*
22598 AATAAAACTTGGGGTAAGGAAAAAGAAGC
1 AATAAAACTTAGGGTAAGGAAAAAGAAGC
22627 AATAAAACTTAGGGTAAGGAAAAAGAAGC
1 AATAAAACTTAGGGTAAGGAAAAAGAAGC
22656 AA
1 AA
22658 CCAAGATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.25, T:0.13
Consensus pattern (29 bp):
AATAAAACTTAGGGTAAGGAAAAAGAAGC
Found at i:25399 original size:27 final size:28
Alignment explanation
Indices: 25361--25422 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
25351 AGGACTTCCT
25361 TTCTTGGTTTGGGAA-GGGGATGGTATG
1 TTCTTGGTTTGGGAAGGGGGATGGTATG
*
25388 TTCTTGGTTTGGGAAGGGGGATGGTCTG
1 TTCTTGGTTTGGGAAGGGGGATGGTATG
25416 TTCTTGG
1 TTCTTGG
25423 AGAAATCCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 15 0.45
28 18 0.55
ACGTcount: A:0.11, C:0.06, G:0.44, T:0.39
Consensus pattern (28 bp):
TTCTTGGTTTGGGAAGGGGGATGGTATG
Found at i:32859 original size:16 final size:16
Alignment explanation
Indices: 32838--32871 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
32828 GCCCTCTACT
*
32838 CCGTCTTCATCTTATA
1 CCGTCTTCACCTTATA
32854 CCGTCTTCACCTTATA
1 CCGTCTTCACCTTATA
32870 CC
1 CC
32872 TTAACCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.38, G:0.06, T:0.38
Consensus pattern (16 bp):
CCGTCTTCACCTTATA
Found at i:34631 original size:20 final size:20
Alignment explanation
Indices: 34606--34658 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
34596 TCTTACCTTT
34606 GGTATCGGTACTACATGAAC
1 GGTATCGGTACTACATGAAC
34626 GGTATCGGTACTACATGAAC
1 GGTATCGGTACTACATGAAC
34646 GGTATCGGTACTA
1 GGTATCGGTACTA
34659 TTCATGCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
GGTATCGGTACTACATGAAC
Found at i:37665 original size:13 final size:13
Alignment explanation
Indices: 37647--37673 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37637 GCATATGGGT
37647 TCATTTGATAAGC
1 TCATTTGATAAGC
37660 TCATTTGATAAGC
1 TCATTTGATAAGC
37673 T
1 T
37674 AATAGAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TCATTTGATAAGC
Found at i:39479 original size:36 final size:36
Alignment explanation
Indices: 39381--39501 Score: 104
Period size: 36 Copynumber: 3.4 Consensus size: 36
39371 CATTCACATA
* *
39381 ACATTGAATGTGTTGCATCTACA-GTGCAATCATA-G
1 ACATTAAATGTGTTGCATCTA-AGGTGCAATCAAATG
* ***
39416 AGCACTAAATGTGCAACATCTAAGGTGCAATCAAATG
1 A-CATTAAATGTGTTGCATCTAAGGTGCAATCAAATG
* * * *
39453 ACATTGAATGTGTTGCACCTATGGTGCAATCACATTG
1 ACATTAAATGTGTTGCATCTAAGGTGCAATCA-AATG
39490 -CATTAAATGTGT
1 ACATTAAATGTGT
39502 CATACAATTA
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
35 2 0.03
36 60 0.90
37 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (36 bp):
ACATTAAATGTGTTGCATCTAAGGTGCAATCAAATG
Found at i:39797 original size:17 final size:17
Alignment explanation
Indices: 39754--39801 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
39744 AAAGAATCAG
* *
39754 TAAAAGAAACAATACAA
1 TAAAAGAAATAGTACAA
*
39771 TAAGAA-AAATAGTATAA
1 TAA-AAGAAATAGTACAA
39788 TAAAAGAAATAGTA
1 TAAAAGAAATAGTA
39802 AGGTGAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.19
Consensus pattern (17 bp):
TAAAAGAAATAGTACAA
Found at i:43569 original size:21 final size:21
Alignment explanation
Indices: 43545--43599 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
43535 TCCAAATGAG
* *
43545 ATATGTCTCGAATGACCGCAT
1 ATATGTCTCGAAGGACCACAT
*
43566 ATATGT-TCCAAAGGACCACAT
1 ATATGTCT-CGAAGGACCACAT
*
43587 ATATGTCCCGAAG
1 ATATGTCTCGAAG
43600 AACCGTGTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (21 bp):
ATATGTCTCGAAGGACCACAT
Found at i:47473 original size:21 final size:20
Alignment explanation
Indices: 47463--47516 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
47453 CTTATTGAGA
47463 GTATCGATACTCTTACCCTGG
1 GTATCGATACTCTTA-CCTGG
47484 GTATCGATACTCTTACCCTGG
1 GTATCGATACTCTTA-CCTGG
*
47505 GTATCAATACTC
1 GTATCGATACTC
47517 CCTTGAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (20 bp):
GTATCGATACTCTTACCTGG
Found at i:48668 original size:24 final size:25
Alignment explanation
Indices: 48639--48685 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
48629 AATCTGTTTG
48639 TTTATGTTTG-TTCATTTATGTCCC
1 TTTATGTTTGTTTCATTTATGTCCC
48663 TTTATGTTTGTTTCATTTATGTC
1 TTTATGTTTGTTTCATTTATGTC
48686 TGTGTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (25 bp):
TTTATGTTTGTTTCATTTATGTCCC
Found at i:48693 original size:25 final size:25
Alignment explanation
Indices: 48641--48704 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
48631 TCTGTTTGTT
*
48641 TATGTTTG-TTCATTTATGTCCCTT
1 TATGTTTGTTTCATTTATGTCCCTG
**
48665 TATGTTTGTTTCATTTATGTCTGTG
1 TATGTTTGTTTCATTTATGTCCCTG
*
48690 TATGTTCGTTT-ATTT
1 TATGTTTGTTTCATTT
48705 CCGTTCGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 12 0.34
25 23 0.66
ACGTcount: A:0.12, C:0.11, G:0.16, T:0.61
Consensus pattern (25 bp):
TATGTTTGTTTCATTTATGTCCCTG
Found at i:48793 original size:16 final size:18
Alignment explanation
Indices: 48768--48804 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
48758 AATCATTAAT
48768 ATTTTAAAACACAAAT-A
1 ATTTTAAAACACAAATCA
*
48785 ATTTT-AAACTCAAATCA
1 ATTTTAAAACACAAATCA
48802 ATT
1 ATT
48805 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTTTAAAACACAAATCA
Found at i:52739 original size:35 final size:35
Alignment explanation
Indices: 52658--52773 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
52648 TAAAATCATC
*
52658 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTCCAATACTAGTGGGAAAACCTAATTT-AGCAT
** *
52694 ATTTGTAATACTAGTGGGAAAACTTAATTTAGCAT
1 ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
52729 ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
1 ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
*
52764 GTTTCCAATA
1 ATTTCCAATA
52774 TTGAGCATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 46 0.64
36 26 0.36
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (35 bp):
ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
Found at i:55286 original size:12 final size:12
Alignment explanation
Indices: 55241--55286 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
55231 AAAATACGGT
*
55241 ATGAACAGTACT
1 ATGAACAGTACC
* *
55253 GTGAACATTA--
1 ATGAACAGTACC
55263 ATGAACAGTACC
1 ATGAACAGTACC
55275 ATGAACAGTACC
1 ATGAACAGTACC
55287 TGCTACAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 8 0.29
12 20 0.71
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:55933 original size:21 final size:22
Alignment explanation
Indices: 55872--55943 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
55862 CTAAGTGGCA
*
55872 TATGAAATATTTCCCGAAGGACC
1 TATG-AATATGTCCCGAAGGACC
* *
55895 TGTGAATATGTTCCGAAGGACC
1 TATGAATATGTCCCGAAGGACC
*
55917 TATGAGT-TGTCCCGAAGGACC
1 TATGAATATGTCCCGAAGGACC
55938 TATGAA
1 TATGAA
55944 ACCCTCGACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 18 0.43
22 21 0.50
23 3 0.07
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (22 bp):
TATGAATATGTCCCGAAGGACC
Found at i:59582 original size:35 final size:35
Alignment explanation
Indices: 59513--59620 Score: 180
Period size: 35 Copynumber: 3.1 Consensus size: 35
59503 TCATTTCCAC
*
59513 TACTAGTGGGATAACCTAATTTGAGCATATTTGCAA
1 TACTAGTGGGAAAACCTAATTT-AGCATATTTGCAA
59549 TACTAGTGGGAAAACCTAATTTAGCATATTTGCAA
1 TACTAGTGGGAAAACCTAATTTAGCATATTTGCAA
* *
59584 TACTAATGGGAAAACCTAATTTAGCATATTTCCAA
1 TACTAGTGGGAAAACCTAATTTAGCATATTTGCAA
59619 TA
1 TA
59621 TTGAGCATTA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 48 0.70
36 21 0.30
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (35 bp):
TACTAGTGGGAAAACCTAATTTAGCATATTTGCAA
Found at i:63646 original size:37 final size:37
Alignment explanation
Indices: 63571--63652 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
63561 TTTAAATGAT
* * *
63571 AACGAACACAATAAAAGAACATAAACAAACGGATGTA
1 AACGAACACAATAAAAGAACAGAAACAAACAGACGTA
* *
63608 AACGAACACAATAAATGAACAGAAACGAACTAG-CGTA
1 AACGAACACAATAAAAGAACAGAAACAAAC-AGACGTA
63645 AACGAACA
1 AACGAACA
63653 TAAACAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 38 0.97
38 1 0.03
ACGTcount: A:0.57, C:0.18, G:0.15, T:0.10
Consensus pattern (37 bp):
AACGAACACAATAAAAGAACAGAAACAAACAGACGTA
Found at i:63695 original size:23 final size:23
Alignment explanation
Indices: 63669--63717 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
63659 AACCTGTACA
* *
63669 AACATAACAAATGAACATAATCG
1 AACACAACAAATGAACATAAACG
* *
63692 AACACAATAAATGAACGTAAACG
1 AACACAACAAATGAACATAAACG
63715 AAC
1 AAC
63718 GTAAACAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (23 bp):
AACACAACAAATGAACATAAACG
Found at i:63954 original size:34 final size:34
Alignment explanation
Indices: 63911--63993 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
63901 AAATGAAAGG
*
63911 ACATTAACGAACATACACAGACATAAATAAACGA
1 ACATAAACGAACATACACAGACATAAATAAACGA
* * *
63945 ACATAAACGATCACACACCGACATAAATAAACGA
1 ACATAAACGAACATACACAGACATAAATAAACGA
* *
63979 ATATAAATGAACATA
1 ACATAAACGAACATA
63994 AATGAACGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.55, C:0.20, G:0.08, T:0.16
Consensus pattern (34 bp):
ACATAAACGAACATACACAGACATAAATAAACGA
Found at i:65506 original size:20 final size:20
Alignment explanation
Indices: 65481--65522 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
65471 TAAATTAACA
65481 AATAGACATAGATAAGATTT
1 AATAGACATAGATAAGATTT
65501 AATAGACATAGATAAGATTT
1 AATAGACATAGATAAGATTT
65521 AA
1 AA
65523 AAGAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (20 bp):
AATAGACATAGATAAGATTT
Found at i:66282 original size:28 final size:27
Alignment explanation
Indices: 66241--66318 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
66231 ATAAATAATT
*
66241 AAAAAT-TAAAAATAAAGAAAAAGAAGA
1 AAAAATATATAAATAAAGAAAAA-AAGA
*
66268 AAAAATATATAAATAAA-ACAAATAAATA
1 AAAAATATATAAATAAAGA-AAA-AAAGA
66296 AAATAATA-ATAAA-AAAGAAAAAA
1 AAA-AATATATAAATAAAGAAAAAA
66319 TAATATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
26 2 0.05
27 13 0.30
28 24 0.55
29 5 0.11
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (27 bp):
AAAAATATATAAATAAAGAAAAAAAGA
Found at i:66285 original size:24 final size:23
Alignment explanation
Indices: 66252--66327 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 23
66242 AAAATTAAAA
*
66252 ATAAAGAAAAAGAAGAAAAAATAT
1 ATAAATAAAAAGAA-AAAAAATAT
*
66276 ATAAATAAAACAAATAAATAAAATA-
1 ATAAATAAAA-AGA-AAA-AAAATAT
66301 AT-AATAAAAAAGAAAAAATAATAT
1 ATAAAT-AAAAAGAAAAAA-AATAT
66325 ATA
1 ATA
66328 TATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
22 2 0.05
23 7 0.17
24 16 0.38
25 10 0.24
26 7 0.17
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (23 bp):
ATAAATAAAAAGAAAAAAAATAT
Found at i:66316 original size:46 final size:46
Alignment explanation
Indices: 66259--66403 Score: 145
Period size: 46 Copynumber: 3.1 Consensus size: 46
66249 AAAATAAAGA
* * *
66259 AAAAGAAGAAAAAATATATAAATAAAACAAATAAATAAAATAATAAT
1 AAAA-AAGAAAAAATATATATATAATATAAATAAATAAAATAATAAT
66306 AAAAAAGAAAAAATAATATATATATATATATAATAAATAAAA-ACATAA-
1 AAAAAAGAAAAAAT-ATATATATA-ATATA-AATAAATAAAATA-ATAAT
* * * *
66354 AAAATAG-TAATATATATATAT-ATATAAATTAATAAAATAAATAAT
1 AAAAAAGAAAAAATATATATATAATATAAATAAATAAAAT-AATAAT
66399 AAAAA
1 AAAAA
66404 CATATATATA
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
43 10 0.12
44 9 0.11
45 5 0.06
46 18 0.22
47 16 0.19
48 10 0.12
49 15 0.18
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (46 bp):
AAAAAAGAAAAAATATATATATAATATAAATAAATAAAATAATAAT
Found at i:66341 original size:40 final size:40
Alignment explanation
Indices: 66297--66420 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 40
66287 AAATAAATAA
66297 AATAATAATAAAA-AAGAAAAAATAATATATATATATATAT
1 AATAATAATAAAATAA-AAAAAATAATATATATATATATAT
*
66337 AATAAATAA-AAACATAAAAAATAGTAATATATATATATATAT
1 AAT-AATAATAAA-ATAAAAAA-AATAATATATATATATATAT
* *
66379 AA-ATTAATAAAATAAATAATAAAAACATATATATATATATAT
1 AATAATAATAAAATAAA-AA-AAATA-ATATATATATATATAT
66421 GTAATCTAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
40 15 0.21
41 17 0.24
42 40 0.56
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (40 bp):
AATAATAATAAAATAAAAAAAATAATATATATATATATAT
Found at i:66370 original size:44 final size:43
Alignment explanation
Indices: 66296--66425 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 43
66286 CAAATAAATA
66296 AAATAATAATAAA-AA-AGAAAAAATAATATATATATATATATAAT
1 AAATAA-AATAAATAATA-AAAAAAT-ATATATATATATATATAAT
*
66340 AAATAAAA-ACATAA-AAAATAGTAATATATATATATATATA-AAT
1 AAATAAAATAAATAATAAAA-A--AATATATATATATATATATAAT
* * *
66383 TAATAAAATAAATAATAAAAACATATATATATATATATGTAAT
1 AAATAAAATAAATAATAAAAAAATATATATATATATATATAAT
66426 CTAAAAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
42 21 0.28
43 19 0.26
44 27 0.36
45 7 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (43 bp):
AAATAAAATAAATAATAAAAAAATATATATATATATATATAAT
Found at i:66484 original size:31 final size:31
Alignment explanation
Indices: 66432--66490 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
66422 TAATCTAAAA
*
66432 AAAAAATATATTAAAGTAAAAAAGAAAATGT
1 AAAAAATATATTAAAGAAAAAAAGAAAATGT
*
66463 AAAAAA-ATATTACATGAAAAAAAGAAAA
1 AAAAAATATATTA-AAGAAAAAAAGAAAA
66491 GAAAATTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (31 bp):
AAAAAATATATTAAAGAAAAAAAGAAAATGT
Found at i:67073 original size:37 final size:37
Alignment explanation
Indices: 66962--67073 Score: 163
Period size: 37 Copynumber: 3.0 Consensus size: 37
66952 ACGCTTGTGG
*
66962 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAAC-TCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AACTTCT
* *
66999 ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTTCT
* *
67036 ATCCTATTTCTAAGAGTTTGAATCCTAGTAAACTTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTTCT
67073 A
1 A
67074 ACGTTATGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 2 0.03
37 65 0.97
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTTCT
Found at i:67770 original size:33 final size:34
Alignment explanation
Indices: 67668--67779 Score: 199
Period size: 34 Copynumber: 3.3 Consensus size: 34
67658 GGTCTTGGGA
*
67668 TTCAAGAGAAACATTTTCAAAGGTTTTTTTGTGT
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
67702 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
*
67736 TTCAAGAGAAACAATTTCAAAGGATTTTTT-TGT
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
67769 TTCAAGAGAAA
1 TTCAAGAGAAA
67780 TTGTCTCAAG
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
33 14 0.18
34 62 0.82
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (34 bp):
TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
Found at i:67812 original size:37 final size:36
Alignment explanation
Indices: 67764--68132 Score: 319
Period size: 36 Copynumber: 10.4 Consensus size: 36
67754 AAAGGATTTT
* * *
67764 TTTGTTTCAAGAGAAATTGTCTCAAGGGAGGCAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
67800 TTTTGTTTCAAGAGAAACATAT-TC---AGAG-----A
1 -TTTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA
*
67829 TTGGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
1 TT--TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
67867 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
67904 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAG----A--CAAAA
67946 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
67982 CTTAGTTCCAAAAGAAATTGTCTCAATG-GAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAA
* * *
68019 TTTGTTT-AATGTA-AAAATAT-TC-A-A-AG----AT
1 TTTGTTTCAA-G-AGAAACTGTCTCAAGAGAGACAAAA
*
68047 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
68083 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
68119 TTTGTTTCAAGAGA
1 TTTGTTTCAAGAGA
68133 GACAAAACTT
Statistics
Matches: 275, Mismatches: 23, Indels: 69
0.75 0.06 0.19
Matches are distributed among these distances:
28 16 0.06
29 7 0.03
30 18 0.07
31 1 0.00
32 4 0.01
33 4 0.01
34 4 0.01
35 4 0.01
36 93 0.34
37 81 0.29
38 5 0.02
39 2 0.01
40 1 0.00
42 35 0.13
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:67946 original size:42 final size:40
Alignment explanation
Indices: 67833--67980 Score: 202
Period size: 42 Copynumber: 3.8 Consensus size: 40
67823 CAGAGATTGG
* *
67833 TGTTTCAAGAGAAACTGTCTCAAAAGAGAC--A-AAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACAAAATT
*
67870 TGTTTCAAGGGAAACTGTCTCAAGAGAG----ACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACAAAATT
67906 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA--CAAAATT
67948 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
67981 ACTTAGTTCC
Statistics
Matches: 100, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
35 1 0.01
36 32 0.32
37 26 0.26
40 1 0.01
42 40 0.40
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (40 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACAAAATT
Found at i:67959 original size:115 final size:108
Alignment explanation
Indices: 67833--68132 Score: 339
Period size: 115 Copynumber: 2.8 Consensus size: 108
67823 CAGAGATTGG
*
67833 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
* *
67898 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATT
66 ACAAAATTTGTTTCAAGAGAAA-TG--TAAAAAGAGACAAA-G---AATT
* * ** *
67948 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAATG-GA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAA-GAGA
* ** *
68012 GACAAAATTTGTTT-------AATGTAAAAATATTCAAAGATTT
65 GACAAAATTTGTTTCAAGAGAAATGTAAAAAGAGACAAAGAATT
*
68049 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
*
68113 ATAAAATTTGTTTCAAGAGA
66 ACAAAATTTGTTTCAAGAGA
68133 GACAAAACTT
Statistics
Matches: 157, Mismatches: 19, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
99 1 0.01
100 35 0.22
101 36 0.23
104 1 0.01
105 9 0.06
107 2 0.01
108 2 0.01
115 70 0.45
116 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (108 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAATTTGTTTCAAGAGAAATGTAAAAAGAGACAAAGAATT
Found at i:68147 original size:22 final size:21
Alignment explanation
Indices: 68068--68147 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
68058 GGAAACTGTC
68068 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
68089 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
*
68104 TCAAGAGAGATAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
68125 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAA-TTTGTT
68147 T
1 T
68148 GAGTAAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 1 0.02
19 1 0.02
20 4 0.09
21 22 0.47
22 7 0.15
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:68440 original size:116 final size:116
Alignment explanation
Indices: 68235--68464 Score: 381
Period size: 116 Copynumber: 2.0 Consensus size: 116
68225 CCTGAAGATA
* *
68235 AATGTTGCTAGTGAGTATGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
1 AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
*
68300 GAAGTTAAGCCTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATT
66 GAAGTTAAGCCTTGAATTGAATATCCTTCGCCGTGAAGTTGAAATCCAATT
* *
68351 AATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGT
1 AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
* *
68416 GAAGTTGAGCCTT-AACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
66 GAAGTTAAGCCTTGAA-TTGAATATCCTTCGCCGTGAAGTTGAAATCCAA
68465 GCTTATATTG
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 2 0.02
116 104 0.98
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (116 bp):
AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
GAAGTTAAGCCTTGAATTGAATATCCTTCGCCGTGAAGTTGAAATCCAATT
Found at i:72919 original size:22 final size:21
Alignment explanation
Indices: 72895--72947 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
72885 AAAATAATTA
*
72895 AAAAAATAAAGAAAAAAGAAGA
1 AAAAAATAAAGAAAAAA-AACA
* *
72917 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAAAAAAACA
*
72938 AATAAATAAA
1 AAAAAATAAA
72948 ATAATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (21 bp):
AAAAAATAAAGAAAAAAAACA
Found at i:72955 original size:12 final size:11
Alignment explanation
Indices: 72885--72958 Score: 51
Period size: 12 Copynumber: 6.3 Consensus size: 11
72875 AATAGTGAGT
72885 AAAATAATTAAA
1 AAAATAA-TAAA
72897 AAAATAA-AGAA
1 AAAATAATA-AA
* *
72908 AAAAGAAGAAA
1 AAAATAATAAA
*
72919 AAAATATAGAAA
1 AAAATA-ATAAA
*
72931 TAAAACAAATAAA
1 -AAAA-TAATAAA
72944 TAAAATAATAAA
1 -AAAATAATAAA
72956 AAA
1 AAA
72959 GTTAAAATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
10 1 0.02
11 18 0.35
12 19 0.37
13 13 0.25
14 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:73033 original size:44 final size:42
Alignment explanation
Indices: 72946--73067 Score: 127
Period size: 46 Copynumber: 2.7 Consensus size: 42
72936 CAAATAAATA
* * *
72946 AAATAATAAAAAAGTTAAAATAATATATATATATATATATATAAAT
1 AAATAATAAAAAAG--AACAT-ATATATATATAAATATATA-AAAC
* * *
72992 AAAAACATAAAAATAGTAATATATATATATATAAATTTATAAAAC
1 AAATA-ATAAAAA-AG-AACATATATATATATAAATATATAAAAC
73037 AAATAATAAAAAAGAACATATATATATATAA
1 AAATAATAAAAAAGAACATATATATATATAA
73068 TCTAAAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
42 16 0.24
43 2 0.03
44 7 0.10
45 7 0.10
46 21 0.31
47 12 0.18
48 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (42 bp):
AAATAATAAAAAAGAACATATATATATATAAATATATAAAAC
Found at i:73720 original size:37 final size:36
Alignment explanation
Indices: 73626--73721 Score: 151
Period size: 35 Copynumber: 2.7 Consensus size: 36
73616 TGGATCTTAT
*
73626 TTTTAGGAGTTTGAATCATAGT-AAACTCTATCCTA
1 TTTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTA
*
73661 TTTTAGGAG-TTGAATTCTAGTAAAACTCTATCCTA
1 TTTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTA
73696 TGTTTAGGAGTTTGAATCCTAGTAAA
1 T-TTTAGGAGTTTGAATCCTAGTAAA
73722 CTTCTAACGT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 10 0.18
35 23 0.42
36 8 0.15
37 14 0.25
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (36 bp):
TTTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTA
Found at i:74380 original size:34 final size:36
Alignment explanation
Indices: 74319--74398 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
74309 GGTCTTGGAA
74319 TTCAAGAGAAACATTTTCAAAGC-TTTTTTTTGTGT
1 TTCAAGAGAAACATTTTCAAAGCTTTTTTTTTGTGT
* *
74354 TTCAAGAGAATA-A-TTTCAAAGGTTTTTTTTTTTGT
1 TTCAAGAGAA-ACATTTTCAAAGCTTTTTTTTTGTGT
74389 TTC-AGAGAAA
1 TTCAAGAGAAA
74399 TTGTCTCATG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 1 0.02
34 14 0.34
35 25 0.61
36 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (36 bp):
TTCAAGAGAAACATTTTCAAAGCTTTTTTTTTGTGT
Found at i:74474 original size:15 final size:15
Alignment explanation
Indices: 74456--74513 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
74446 GATTGGTGTT
74456 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
74471 TCAAGAGACAAAACTTTGTT
1 TCAAGAG---AAAC--TGTC
*
74491 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
74506 TCAAGAGA
1 TCAAGAGA
74514 GACAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 17 0.50
17 4 0.12
18 4 0.12
20 9 0.26
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:74537 original size:36 final size:36
Alignment explanation
Indices: 74452--74639 Score: 213
Period size: 36 Copynumber: 5.1 Consensus size: 36
74442 CAGAGATTGG
74452 TGTTTCAAGAGAAACTGTCTC-A-AGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
74487 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
74523 TGTTTCAAGAGAAACTGTCTCAACAGAGACAAAGGCAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC--A---AAA-TT
*
74565 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
74601 AGTTCCAAAAGAAATTGTCTCAATG-GAGAC-AAATT
1 TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATT
74636 TGTT
1 TGTT
74640 AATGTAAAAA
Statistics
Matches: 133, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
35 27 0.20
36 57 0.43
37 13 0.10
38 1 0.01
40 1 0.01
41 3 0.02
42 31 0.23
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:74579 original size:78 final size:78
Alignment explanation
Indices: 74485--74633 Score: 226
Period size: 78 Copynumber: 1.9 Consensus size: 78
74475 GAGACAAAAC
* * * *
74485 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAACAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAACAGA
74550 GACAAAGGCAAAT
66 GACAAAGGCAAAT
* * **
74563 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACTTAGTTCCAAAAGAAATTGTCTCAATGGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAACAGA
74628 GACAAA
66 GACAAA
74634 TTTGTTAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (78 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAACAGA
GACAAAGGCAAAT
Found at i:74720 original size:22 final size:20
Alignment explanation
Indices: 74681--74723 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
74671 GGAAACTGTC
*
74681 TCAAGAGAGATAAATTTGTT
1 TCAAGAGAGAAAAATTTGTT
74701 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGA-AAAA-TTTGTT
74723 T
1 T
74724 TGAGTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (20 bp):
TCAAGAGAGAAAAATTTGTT
Done.