Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001843.1 Hibiscus syriacus cultivar Beakdansim tig00003732_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: 116380
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7086 original size:28 final size:29
Alignment explanation
Indices: 7019--7115 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 29
7009 GGGCCAATTG
*
7019 TTTTTAATACTTATTATTATGGTTTCAATCT
1 TTTTTAATATTTATTATTATGGTTT-AA-CT
7050 TTTCTTAATATTTATTATTATGGTCTT-A-T
1 TTT-TTAATATTTATTATTATGGT-TTAACT
*
7079 TTTTTAATATTTATTATTAAGGGTTT-ACT
1 TTTTTAATATTTATTATT-ATGGTTTAACT
*
7108 TTTATAAT
1 TTTTTAAT
7116 TAATTTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
28 18 0.31
29 16 0.27
31 4 0.07
32 19 0.32
33 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTTAATATTTATTATTATGGTTTAACT
Found at i:7303 original size:90 final size:89
Alignment explanation
Indices: 7202--7383 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 89
7192 TCCATACTTA
7202 TCAGGGGTCCAATTTTTTCAATATTTGTTATTAGGGACATGCTTTTAAATTTCATTATAATATTT
1 TCAGGGGTCCAATTTTTTCAATATTTGTTATTAGGGACATGCTTTTAAATTTCATTATAATATTT
7267 ATTTGTTGTTATGAATCCAATTCTT
66 A-TTGTTGTTATGAATCCAATTCTT
7292 TCAGGGGTCCAATTTTTTCAATATTTGTTATTAGGGACATGCTTTTAAATTTCATTATAATATTT
1 TCAGGGGTCCAATTTTTTCAATATTTGTTATTAGGGACATGCTTTTAAATTTCATTATAATATTT
7357 ATTGTTGTTATGAATCCAATTCTT
66 ATTGTTGTTATGAATCCAATTCTT
7381 TCA
1 TCA
7384 ATACTTTTTA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 26 0.28
90 66 0.72
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (89 bp):
TCAGGGGTCCAATTTTTTCAATATTTGTTATTAGGGACATGCTTTTAAATTTCATTATAATATTT
ATTGTTGTTATGAATCCAATTCTT
Found at i:7988 original size:30 final size:30
Alignment explanation
Indices: 7952--8072 Score: 233
Period size: 30 Copynumber: 4.0 Consensus size: 30
7942 GCTTGAAAGC
7952 AATGACGATGCTACTAAATATCACTAAACT
1 AATGACGATGCTACTAAATATCACTAAACT
*
7982 AATGACGATGCTATTAAATATCACTAAACT
1 AATGACGATGCTACTAAATATCACTAAACT
8012 AATGACGATGCTACTAAATATCACTAAACT
1 AATGACGATGCTACTAAATATCACTAAACT
8042 AATGACGATGCTACTAAATATCACTAAACT
1 AATGACGATGCTACTAAATATCACTAAACT
8072 A
1 A
8073 TGTTTTTATC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (30 bp):
AATGACGATGCTACTAAATATCACTAAACT
Found at i:10588 original size:21 final size:21
Alignment explanation
Indices: 10564--10620 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
10554 TATCTTTTCA
**
10564 AAAGGATCGATCCCTCGGGAG
1 AAAGGATCGATCCCTCGAAAG
* *
10585 AAAGAATCGATCTCTCGAAAG
1 AAAGGATCGATCCCTCGAAAG
10606 AAAGGATCGATCCCT
1 AAAGGATCGATCCCT
10621 TCTTCATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (21 bp):
AAAGGATCGATCCCTCGAAAG
Found at i:15429 original size:14 final size:15
Alignment explanation
Indices: 15394--15432 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
15384 CAATTTGTTT
15394 TATTTTATTAATTAA
1 TATTTTATTAATTAA
15409 TATTTTATTCAA-TAA
1 TATTTTATT-AATTAA
15424 -ATTTTATTA
1 TATTTTATTA
15433 TTTTTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 8 0.35
15 12 0.52
16 2 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTATTAATTAA
Found at i:15765 original size:29 final size:26
Alignment explanation
Indices: 15731--15800 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 26
15721 ATAAATGTAC
15731 AATTAAATAATAAAAAATATTGAATAAAA
1 AATTAAATAA-AAAAAATATT-AA-AAAA
*
15760 AATTAATTAAACAAAAATATTAAAAAA
1 AATTAAATAAA-AAAAATATTAAAAAA
* *
15787 TATTGAATAAAAAA
1 AATTAAATAAAAAA
15801 TTAATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 3 0.08
27 12 0.33
28 3 0.08
29 18 0.50
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (26 bp):
AATTAAATAAAAAAAATATTAAAAAA
Found at i:15810 original size:15 final size:13
Alignment explanation
Indices: 15738--15813 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 13
15728 TACAATTAAA
15738 TAATAAAAAATAT
1 TAATAAAAAATAT
15751 TGAATAAAAAATTAAT
1 T-AATAAAAAA-T-AT
15767 TAA-ACAAAAATA-
1 TAATA-AAAAATAT
15779 T--TAAAAAATAT
1 TAATAAAAAATAT
15790 TGAATAAAAAATTAAT
1 T-AATAAAAAA-T-AT
15806 TAATAAAA
1 TAATAAAA
15814 TAAAAATGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 20
0.72 0.00 0.28
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 1 0.02
13 2 0.04
14 18 0.35
15 16 0.31
16 6 0.12
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (13 bp):
TAATAAAAAATAT
Found at i:15810 original size:22 final size:22
Alignment explanation
Indices: 15746--15810 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
15736 AATAATAAAA
15746 AATATTGAATAAAAAATTAATT
1 AATATTGAATAAAAAATTAATT
* * **
15768 AA-A---CA-AAAATATTAAAA
1 AATATTGAATAAAAAATTAATT
15785 AATATTGAATAAAAAATTAATT
1 AATATTGAATAAAAAATTAATT
15807 AATA
1 AATA
15811 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
21 2 0.07
22 15 0.50
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (22 bp):
AATATTGAATAAAAAATTAATT
Found at i:22635 original size:182 final size:181
Alignment explanation
Indices: 22324--23002 Score: 1060
Period size: 182 Copynumber: 3.7 Consensus size: 181
22314 TGTTTACCTA
* * * *
22324 TTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
*
22389 TTTA-ACGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * * *
22453 CACTTTCAACATATCTGGTATCCTTTTACCGGTATTGTCATTTTGAGATCGG
131 CACTTGCAACAAATCTGGTATCGTTTTACCGGTTTTGTCATTTTGAGA-CGG
*
22505 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-TTAAAAGTATCGACACT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCAT-AAAGTATCGACACT
22569 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* * *
22634 ACACATGCAACAAATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
130 ACACTTGCAACAAATCTGGTATCGTTTTACCGGTTTTGTCATTTTGAGA-CGG
* * *
22687 TTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTTGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
*
22752 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCAA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
22817 CACTTGCAACAAAT-TCGGTATCGTTTTACCGGTTTTGTCATTTTGAGACTGG
131 CACTTGCAACAAATCT-GGTATCGTTTTACCGGTTTTGTCATTTTGAGAC-GG
* * **
22869 TTTTGTCATATTTTTACATGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
* * *
22934 TTTAGGCGCTATAACTTCTTCTCTTTTTATTTCCA-AAAGTGTCGATACTTATATTAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATCG
22998 ACACT
130 ACACT
23003 GTAAATTTAC
Statistics
Matches: 459, Mismatches: 33, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
180 1 0.00
181 63 0.14
182 392 0.85
183 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTGCAACAAATCTGGTATCGTTTTACCGGTTTTGTCATTTTGAGACGG
Found at i:26378 original size:31 final size:31
Alignment explanation
Indices: 26340--26402 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
26330 CCCGAAGGAC
* *
26340 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
26371 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
26402 C
1 C
26403 CTCGACCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:27107 original size:21 final size:21
Alignment explanation
Indices: 27077--27121 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27067 ATTCTGTCGT
*
27077 TTGAAGGGGTA-TCGGTTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
27098 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
27119 TTG
1 TTG
27122 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:29167 original size:199 final size:199
Alignment explanation
Indices: 28903--29630 Score: 1077
Period size: 199 Copynumber: 3.7 Consensus size: 199
28893 AAAAAGTATA
* * * * * * * *
28903 GATACATTATGTAGACCTATTTGCTCATAAAACCGGTATATTTAGACTGGTTGCATTGTTAATTT
1 GATACTTTTTGTACACCTGTTTTCTCA-AAAACCGGTATACTTAGACCGGTTACATTGTTAATTT
* * * *
28968 ACCTATTACATTAT-ATCTATGAATTTCAATATTTTTAGTATCGACACTTATTATAAATGTATCG
65 ACCTAGTACATTATAAT-TATGAGTTTCGATATTTTTAGGATCGACACTTATTATAAATGTATCG
* *
29032 ACACGTTTTAGTGCAATTGGTTTTGAAATACATTCTAGACCAAAAGTATCGGCACTTGTTTTATT
129 ACACGTTTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
*
29097 TGTGTT
194 TGTGTC
* * * *
29103 GATACTTTTTGTACACATGTTTTCTTATAAACCGGTATATTTAGACCGGTTACATTGTTAATTTA
1 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTA
* * * *
29168 CCTATTAC-TCATAATTATGGGTTTCGATATTTTTAGGATCGACATTTATTATAAATGTATCGAC
66 CCTAGTACATTATAATTATGAGTTTCGATATTTTTAGGATCGACACTTATTATAAATGTATCGAC
* * *
29232 GCG-TTTAGTGCATTTGGTTTTGAAATACATTCTGGACCAAAGGTATCGACACTTGTTTTATTTG
131 ACGTTTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTG
29296 TGTC
196 TGTC
* *
29300 GATACTTTTTGTACTCCTGTTTTCTCAAAAATCGGTATACTTAGACCGGTTACATTGTTAATTTA
1 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTA
* *
29365 CCTAGTACATTATAATTATGAGTTTCGATGTTTTTAGGATCAACACTTATTATAAATGTATCGAC
66 CCTAGTACATTATAATTATGAGTTTCGATATTTTTAGGATCGACACTTATTATAAATGTATCGAC
* * *
29430 ACATTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCAACACTTGTTTTATTTG
131 ACGTTTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTG
29495 TGTC
196 TGTC
*
29499 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATACTTAGACCGGTTACATTGTTAATTTA
1 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTA
* *
29564 CCTAGTACATTATAATTATGGGTTTCGATGTTTTT-GAGATCGACACTTATTATAAATGTATCGA
66 CCTAGTACATTATAATTATGAGTTTCGATATTTTTAG-GATCGACACTTATTATAAATGTATCGA
29628 CAC
130 CAC
29631 TTATTATAAA
Statistics
Matches: 480, Mismatches: 44, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
197 126 0.26
198 102 0.21
199 232 0.48
200 20 0.04
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (199 bp):
GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTA
CCTAGTACATTATAATTATGAGTTTCGATATTTTTAGGATCGACACTTATTATAAATGTATCGAC
ACGTTTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTG
TGTC
Found at i:29628 original size:21 final size:21
Alignment explanation
Indices: 29602--29653 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
29592 TGTTTTTGAG
29602 ATCGACACTTATTATAAATGT
1 ATCGACACTTATTATAAATGT
29623 ATCGACACTTATTATAAATGT
1 ATCGACACTTATTATAAATGT
29644 ATCGACACTT
1 ATCGACACTT
29654 TTTAGTGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
ATCGACACTTATTATAAATGT
Found at i:29801 original size:220 final size:220
Alignment explanation
Indices: 29407--29852 Score: 786
Period size: 220 Copynumber: 2.0 Consensus size: 220
29397 TTTAGGATCA
29407 ACACTTATTATAAATGTATCGACACATTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAA
1 ACACTTATTATAAATGTATCGACACATTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAA
*
29472 AGTATCAACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGATAT
66 AGTATCAACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGATAT
* *
29537 ACTTAGACCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGAG
131 ACTTAGACCGGTTAAATTGTTAATTTACCTAGTACATCATAATTATGGGTTTCGATGTTTTTGAG
29602 ATCGACACTTATTATAAATGTATCG
196 ATCGACACTTATTATAAATGTATCG
*
29627 ACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAA
1 ACACTTATTATAAATGTATCGACACATTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAA
* * *
29692 AGTATTGAA-ACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACTGGTA
66 AGTA-TCAACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGATA
* *
29756 TACTTAGACCGGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGG
130 TACTTAGACCGGTTAAATTGTTAATTTACCTAGTACATCATAATTATGGGTTTCGATGTTTTTGA
*
29821 GATCGACATTTATTATAAATGTATCG
195 GATCGACACTTATTATAAATGTATCG
29847 ACACTT
1 ACACTT
29853 TTTAGTGCAC
Statistics
Matches: 215, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
220 212 0.99
221 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (220 bp):
ACACTTATTATAAATGTATCGACACATTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAA
AGTATCAACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGATAT
ACTTAGACCGGTTAAATTGTTAATTTACCTAGTACATCATAATTATGGGTTTCGATGTTTTTGAG
ATCGACACTTATTATAAATGTATCG
Found at i:30123 original size:24 final size:24
Alignment explanation
Indices: 30086--30132 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
30076 ATTTACATTT
30086 AAATTCAAACTCAAACTCAAATTG
1 AAATTCAAACTCAAACTCAAATTG
* * *
30110 AAATTTAAATTCAAACTCTAATT
1 AAATTCAAACTCAAACTCAAATT
30133 ATAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAACTCAAATTG
Found at i:31357 original size:6 final size:6
Alignment explanation
Indices: 31342--31375 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31332 GTTTGGATCA
* *
31342 TCATCG TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
31376 TGACCACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.32, G:0.06, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:32562 original size:15 final size:15
Alignment explanation
Indices: 32544--32587 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
32534 AGAAGGTTAT
32544 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAGCTG
*
32559 GGTTGAGAAGAGGTG
1 GGTTGAGAAGAGCTG
*
32574 GGTTAAGAAGAGCT
1 GGTTGAGAAGAGCT
32588 TTGAGAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.30, C:0.05, G:0.45, T:0.20
Consensus pattern (15 bp):
GGTTGAGAAGAGCTG
Found at i:33296 original size:199 final size:198
Alignment explanation
Indices: 32954--34229 Score: 2090
Period size: 199 Copynumber: 6.4 Consensus size: 198
32944 TTTTATATCT
* * *
32954 GTTACATTATTAATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTAGGATCGACACTT
1 GTTACATTGTTAATTTACCTAGTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGACACTT
* *
33019 ATTATAAATGTATCGACAC-GTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGAATC
65 ATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
*
33083 GACACTTGTTTTATTTGTGTCGATACTTTTTGTATACATGTTTTCTCAAAAACCGGTATACTTAG
130 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAG
*
33148 ACTG
195 ACCG
*
33152 GTTACATTGTTAATTTACCTAGTACATTATAATTATAGGTTACGATGTTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTAGTACATTATAATTAT-GGTTTCGATGTTTTTGGGATCGACACTT
* * *
33217 GTTATAAATGTATCGACACTTTTTAATGAACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
65 ATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
* *
33282 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAACATCGGTATACTTAG
130 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAG
33347 ACCG
195 ACCG
* * * *
33351 GTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATATTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTAGTACATTATAATTAT-GGTTTCGATGTTTTTGGGATCGACACTT
33416 ATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
65 ATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
* * *
33481 GACACTTGTTTTATTTGTGTCGATACTTTATGTGCACATGTTTTCTCAAAAACCGATATACTTAG
130 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAG
**
33546 ACAT
195 ACCG
33550 GTTACATTGTTAATTTACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTAGTACATTATAATTAT-GGTTTCGATGTTTTTGGGATCGACACTT
* *
33615 CTTATAAATGTATCGACACGTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
65 ATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
* *
33680 GACTCTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAG
130 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAG
*
33745 ACCA
195 ACCG
* * *
33749 GTTAAATTGTTAATTTACCTA-TTCTATCATAATTATGAGTTTCGATGTTTTTGGGATCGACACT
1 GTTACATTGTTAATTTACCTAGTAC-ATTATAATTATG-GTTTCGATGTTTTTGGGATCGACACT
33813 TATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTAT
64 TATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTAT
* *
33878 CGACACTTGTTTTATTTGTGTCGATACTTTTTGTACATATGTTTTCTCAAAAACTGGTATACTTA
129 CGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTA
*
33943 GACCA
194 GACCG
*
33948 GTTACATTGTTAATTTACCTAGTACATTATAATTATGATTTTCGATGTTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTAGTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGACACTT
*
34013 ATTATAAATGTATCGACAC-GTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
65 ATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATC
* *
34077 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTTG
130 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAG
34142 ACCG
195 ACCG
* * * *
34146 GTTAAATTGTTAATTTACCTATTACATCATAATTATTGGTTTCGATATTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTAGTACATTATAATTA-TGGTTTCGATGTTTTTGGGATCGACACTT
34211 ATTATAAATGTATCGACAC
65 ATTATAAATGTATCGACAC
34230 ATAAGTTTAC
Statistics
Matches: 1006, Mismatches: 66, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
198 264 0.26
199 740 0.74
200 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (198 bp):
GTTACATTGTTAATTTACCTAGTACATTATAATTATGGTTTCGATGTTTTTGGGATCGACACTTA
TTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCG
ACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAGA
CCG
Found at i:34624 original size:19 final size:19
Alignment explanation
Indices: 34600--34650 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
34590 ATTACATTCA
*
34600 TATACAAAATTATAAATCG
1 TATACAAAATTAAAAATCG
*
34619 TATACAAAATTAAAAATCT
1 TATACAAAATTAAAAATCG
34638 TATACAAAATTAA
1 TATACAAAATTAA
34651 CCCTACATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
TATACAAAATTAAAAATCG
Found at i:38222 original size:261 final size:261
Alignment explanation
Indices: 37756--38274 Score: 984
Period size: 261 Copynumber: 2.0 Consensus size: 261
37746 GTGTGCCATC
*
37756 TTCCTTCATCCTTTTGTATTCAGCCATACTGTCAACATTTAAAATTTGTAATCAATTTAAAGTTC
1 TTCCTTCATCCTTTTGCATTCAGCCATACTGTCAACATTTAAAATTTGTAATCAATTTAAAGTTC
37821 TTAAATACTTTAATCCAATTACCATTTCAACAATAATAACAAAAATACATTGATACTTACTAGAA
66 TTAAATACTTTAATCCAATTACCATTTCAACAATAATAACAAAAATACATTGATACTTACTAGAA
* *
37886 GTACATATATCTACCCTTTGGTTGCTTTCCACCCATTGACTTCATTTTTCCTTCATATATCAGTT
131 ATACATATATCCACCCTTTGGTTGCTTTCCACCCATTGACTTCATTTTTCCTTCATATATCAGTT
*
37951 TGCGCAAATCAAATCAAATACTGCTTACATACACTTTATTCAATATACAAAAATCAATAACCATT
196 TGCACAAATCAAATCAAATACTGCTTACATACACTTTATTCAATATACAAAAATCAATAACCATT
38016 A
261 A
* *
38017 TTCCTTCATCCTTTTGCATTCGGCCATACTGTCAACATTTAAAATTTGTAATCAATTTAAAGTTT
1 TTCCTTCATCCTTTTGCATTCAGCCATACTGTCAACATTTAAAATTTGTAATCAATTTAAAGTTC
38082 TTAAATACTTTAATCCAATTACCATTTCAACAATAATAACAAAAATACATTGATACTTACTAGAA
66 TTAAATACTTTAATCCAATTACCATTTCAACAATAATAACAAAAATACATTGATACTTACTAGAA
38147 ATACATATATCCACCCTTTGGTTGCTTTCCACCCATTGACTTCATTTTTCCTTCATATATCAGTT
131 ATACATATATCCACCCTTTGGTTGCTTTCCACCCATTGACTTCATTTTTCCTTCATATATCAGTT
38212 TGCACAAATCAAATCAAATACTGCTTACATACACTTTATTCAATATACAAAAATCAATAACCA
196 TGCACAAATCAAATCAAATACTGCTTACATACACTTTATTCAATATACAAAAATCAATAACCA
38275 CTCTTTGTGG
Statistics
Matches: 252, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
261 252 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (261 bp):
TTCCTTCATCCTTTTGCATTCAGCCATACTGTCAACATTTAAAATTTGTAATCAATTTAAAGTTC
TTAAATACTTTAATCCAATTACCATTTCAACAATAATAACAAAAATACATTGATACTTACTAGAA
ATACATATATCCACCCTTTGGTTGCTTTCCACCCATTGACTTCATTTTTCCTTCATATATCAGTT
TGCACAAATCAAATCAAATACTGCTTACATACACTTTATTCAATATACAAAAATCAATAACCATT
A
Found at i:38405 original size:21 final size:19
Alignment explanation
Indices: 38349--38416 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
38339 CATTTATACA
*
38349 ACCTAAAATATCATTTTCT
1 ACCTATAATATCATTTTCT
*
38368 ACCTATAATATCATTTTTT
1 ACCTATAATATCATTTTCT
38387 ACCTATAATATCATCTTT-T
1 ACCTATAATATCAT-TTTCT
*
38406 ACATATAATAT
1 ACCTATAATAT
38417 TAAATAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 42 0.93
20 3 0.07
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.46
Consensus pattern (19 bp):
ACCTATAATATCATTTTCT
Found at i:39172 original size:182 final size:181
Alignment explanation
Indices: 38804--40004 Score: 1574
Period size: 182 Copynumber: 6.6 Consensus size: 181
38794 TACGCGTACT
* * * *
38804 TATTAAATTATCGATACTTTCAATATATCCGGTA-TCGT-TTTACCGGTTTTGTCATTTTTAGAC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGT--TATTTACCTGTTTTGTCATTTTGAGAC
* *
38867 ATGG-TTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACA
64 -CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACA
*
38931 CTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
128 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
38985 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACTG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
* * * * *
39050 GTTTTGTCATA-TTTTAGGCTGTTGTATTGTTATGGATCAATACATTTTCATAAAGTGTCGACAC
66 GTTTTGTCATATTTTTA-CCTGTTATATTGTTATGGATCGATACATTTT-TTAAAGTATCGACAC
39114 GTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTA
129 -TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* * **** *
39167 TATTAAATTATTGACACTTTCAAAATATCCGGTAACGCTTTACCGGTTTTGTCATTTCT-AGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTT-TGAGACC
* *
39231 GATTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTTTAAAGTATCGACAC
*
39296 TTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
129 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
39349 TATTAAAGTATCAACACTTTCAACATATCCGGTAGTTATTTACCTCTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
* ** * *
39414 GTTTTATCATA-TTTTAGGTTGTTATATTGTTATGGATAGATACATTTTTTAAAGTGTCGACACG
66 GTTTTGTCATATTTTTA-CCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACAC-
39478 TTT-TAGGCGCTATAACTTCTTCTC---TAAATT-CAGAAAGTGTCGATACTTA
129 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* *
39527 TATTAAATTATCGACACTTTCAATATATCCGGTA-TCGT-TTTA-CTGGTTTTGTCATTTTTAGA
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGT--TATTTACCT-GTTTTGTCATTTTGAGA
* * * *
39589 CCTGTTTTATCCTATTTTTACCTGTTATATTGTTATGGATTGATACATTTTTTAAAGTATCGACA
63 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACA
39654 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
128 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
*
39708 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
* * * ** *
39773 GTTTTGTCATA-TTTTAGGCTGTTATATTATTATGGATCGATATATTTGCATAAAGTGTCGACA-
66 GTTTTGTCATATTTTTA-CCTGTTATATTGTTATGGATCGATACATTT-TTTAAAGTATCGACAC
* * * *
39836 TGTTTTAGGCGTTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTTGATACTTA
129 T-TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *** *
39890 TATTAAATTATCGACACTTTCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTTTTAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCA-TTTTGAGACC
* * * * *
39955 TGTTTTGTCCTGTTTTTACCTGTTATATTATTATGGATCGATATATTTTT
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
40005 CATTTGTATC
Statistics
Matches: 902, Mismatches: 85, Indels: 65
0.86 0.08 0.06
Matches are distributed among these distances:
177 8 0.01
178 147 0.16
179 6 0.01
180 15 0.02
181 252 0.28
182 407 0.45
183 62 0.07
184 5 0.01
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (181 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTT
TATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:39854 original size:541 final size:543
Alignment explanation
Indices: 38804--39947 Score: 1519
Period size: 541 Copynumber: 2.1 Consensus size: 543
38794 TACGCGTACT
* * * * * * * ** * *
38804 TATTAAATTATCGATACTTTCAATATATCCGGTATCGTTTTACCGGTTTTGTCATTTTTAGACAT
1 TATTAAAGTATCAACACTTTCAACATATCCGATAGCGATTTACCTCTTTTGTCATTTTGAGAC-C
* * ** *
38869 GG-TTTGTCCTATTTTTA-CCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACAC
65 GGTTTTATCATA-TTTTAGGTTGTTATATTGTTATGGATAGATACATTTTTTAAAGTATCGACAC
38932 TTTATAGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATC
129 TTTATAGGCGCTATAACTTATTCTC--TTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATC
*
38997 GACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACTGGTTTTGTCATAT
192 GACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACTGGTTTTATCATAT
* * *
39062 TTTAGGCTGTTGTATTGTTATGGATCAATACATTTTCATAAAGTGTCGACACGTTTTAGGCGCTA
257 TTTAGCCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTATCGACACGTTTTAGGCGCTA
* *
39127 TAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATTGACACTTTCAAAA
322 TAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAAAA
* *
39192 TATCCGGTAACGCTTTACCGGTTTTGTCATTTCTAGACCGATTTTGTCCTATTTTTACCTGTTAT
387 TATCCGGTAACGATTTACCGGTTTTGTCATTTCTAGACCGATTTTGTCATATTTTTACCTGTTAT
* ***
39257 ATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTGTAGGCGCTATAACTTCTTCTCT
452 ATTATTATGGATCGATACATTTGCATAAAGTATCGACACTTTGTAGGCGCTATAACTTCTTCTCT
*
39322 TTTAAATTCCAAAAGTGTCGATACTTA
517 TTTAAATTCAAAAAGTGTCGATACTTA
* **
39349 TATTAAAGTATCAACACTTTCAACATATCCGGTAGTTATTTACCTCTTTTGTCATTTTGAGACCG
1 TATTAAAGTATCAACACTTTCAACATATCCGATAGCGATTTACCTCTTTTGTCATTTTGAGACCG
*
39414 GTTTTATCATATTTTAGGTTGTTATATTGTTATGGATAGATACATTTTTTAAAGTGTCGACACGT
66 GTTTTATCATATTTTAGGTTGTTATATTGTTATGGATAGATACATTTTTTAAAGTATCGACAC-T
* *
39479 TT-TAGGCGCTATAACTTCTTCTC-TAAATT-CAGAAAGTGTCGATACTTATATTAAATTATCGA
130 TTATAGGCGCTATAACTTATTCTCTTAAATTCCA-AAAGTGTCGATACTTATATTAAAGTATCGA
* * *
39541 CACTTTCAATATATCCGGTA-TCGT-TTTA-CTGGTTTTGTCATTTTTAGACCT-GTTTTATCCT
194 CACTTTCAACATATCCGGTAGT--TATTTACCT-GTTTTGTCATTTTGAGA-CTGGTTTTATCAT
** *
39602 ATTTTTA-CCTGTTATATTGTTATGGATTGATACATTTT-TTAAAGTATCGACAC-TTTATAGGC
255 A-TTTTAGCCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTATCGACACGTTT-TAGGC
39664 GCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAAGTATCGACACTTT
318 GCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAAGTATCGACACTTT
* *** * * *
39728 CAACATATCCGGTAGTTATTTACCTGTTTTGTCATTT-TGAGACCGGTTTTGTCATA-TTTTAGG
382 CAAAATATCCGGTAACGATTTACCGGTTTTGTCATTTCT-AGACCGATTTTGTCATATTTTTA-C
* * * *
39791 CTGTTATATTATTATGGATCGATATATTTGCATAAAGTGTCGACA-TGTTTTAGGCGTTATAACT
445 CTGTTATATTATTATGGATCGATACATTTGCATAAAGTATCGACACT-TTGTAGGCGCTATAACT
*
39855 TCTTCTCTTTTAAATTCAAAAAGTGTTGATACTTA
509 TCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
* * * *
39890 TATTAAATTATCGACACTTTCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTT
1 TATTAAAGTATCAACACTTTCAACATATCCGATAGCGATTTACCTCTTTTGTCATTTT
39948 TTAGACCTGT
Statistics
Matches: 527, Mismatches: 58, Indels: 32
0.85 0.09 0.05
Matches are distributed among these distances:
540 10 0.02
541 266 0.50
542 112 0.21
543 8 0.02
544 7 0.01
545 121 0.23
546 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (543 bp):
TATTAAAGTATCAACACTTTCAACATATCCGATAGCGATTTACCTCTTTTGTCATTTTGAGACCG
GTTTTATCATATTTTAGGTTGTTATATTGTTATGGATAGATACATTTTTTAAAGTATCGACACTT
TATAGGCGCTATAACTTATTCTCTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACA
CTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACTGGTTTTATCATATTTTA
GCCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTATCGACACGTTTTAGGCGCTATAAC
TTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAAAATATC
CGGTAACGATTTACCGGTTTTGTCATTTCTAGACCGATTTTGTCATATTTTTACCTGTTATATTA
TTATGGATCGATACATTTGCATAAAGTATCGACACTTTGTAGGCGCTATAACTTCTTCTCTTTTA
AATTCAAAAAGTGTCGATACTTA
Found at i:39955 original size:21 final size:22
Alignment explanation
Indices: 39931--39972 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
39921 ATAGCGCTTT
39931 ACCTGTTTTGTCAT-TTTTTAG
1 ACCTGTTTTGTCATGTTTTTAG
*
39952 ACCTGTTTTGTCCTGTTTTTA
1 ACCTGTTTTGTCATGTTTTTA
39973 CCTGTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.57
Consensus pattern (22 bp):
ACCTGTTTTGTCATGTTTTTAG
Found at i:46567 original size:35 final size:35
Alignment explanation
Indices: 46492--46569 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
46482 TCTAAACCCT
*
46492 AAATTGAAGTATTTTAGAATTTCAGGTTTAATATG
1 AAATTGAAGTATTTTAGAATTTCAGGTTTAATATA
* * * **
46527 TAATTGAATTATTTTGGAATTTGGGGTTTAGA-ATA
1 AAATTGAAGTATTTTAGAATTTCAGGTTTA-ATATA
46562 AAATTGAA
1 AAATTGAA
46570 AACTGTGTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTCAGGTTTAATATA
Found at i:49565 original size:112 final size:112
Alignment explanation
Indices: 49109--49571 Score: 732
Period size: 112 Copynumber: 4.1 Consensus size: 112
49099 TTGTCGGTTT
**
49109 GTGTCGATATTTTATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATATTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
49174 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
49221 GTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGT--AAAAATGACAAAATC
1 GTGTCGATATTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
49284 AGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
49331 GTGTCAATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAAAAAATATGACAAAA
1 GTGTCGATATTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAA-ATGACAAAA
49396 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
49445 GTGCCGATATTTTATAAAAATGTATCGATCCATAACAGTATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATATTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
49510 GGTCTATAAATGACAAAATAAGTAAAGCGCTACCAGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
49557 GTGTCGATACTTTAT
1 GTGTCGATATTTTAT
49572 TATAAGTATC
Statistics
Matches: 322, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
110 104 0.32
112 110 0.34
113 10 0.03
114 98 0.30
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATATTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:50184 original size:23 final size:23
Alignment explanation
Indices: 50149--50196 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
50139 AAATATATCA
*
50149 ATATAAACACTACCTATTACATT
1 ATATAAACACTACCTAATACATT
* * *
50172 ATATAAGCGCTACCTAATATATT
1 ATATAAACACTACCTAATACATT
50195 AT
1 AT
50197 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACACTACCTAATACATT
Found at i:52496 original size:18 final size:18
Alignment explanation
Indices: 52469--52504 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52459 AAGATTATAT
* *
52469 TAATTTTATATAGTTTTA
1 TAATTCTATATAGGTTTA
52487 TAATTCTATATAGGTTTA
1 TAATTCTATATAGGTTTA
52505 AAGGTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (18 bp):
TAATTCTATATAGGTTTA
Found at i:53962 original size:2 final size:2
Alignment explanation
Indices: 53955--53983 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53945 AATTTAGTAA
53955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53984 AAACAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56026 original size:84 final size:84
Alignment explanation
Indices: 55853--56231 Score: 365
Period size: 84 Copynumber: 4.6 Consensus size: 84
55843 GCTATGTTGT
** * * ** * *
55853 AAATGATGTGCCTAAGAGATGAGCGTAGTCGAACTTGAATATC-TTTGTTGGCAGATAACCCTCC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTC
* *** *
55917 TAGCCTGGCGTTATGCCGC
66 TAGACTTAAGTTATGCTGC
* *
55936 AAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTC
* * *
56001 TAGCCTTAAGTTATACTGT
66 TAGACTTAAGTTATGCTGC
* * *
56020 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTC
*
56085 TCGACTTAAGTTATGCTGC
66 TAGACTTAAGTTATGCTGC
* * * * * ** * *
56104 AAATGACGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--TT--TGGCAGACAATCCTT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTT
* * *
56165 CTCGATTTAAGCTATGCTGC
65 CTAGACTTAAGTTATGCTGC
* * *
56185 AAATGATGTACCGTT-GAGCTGAGCGTAGTCGAACTCAAATGTCTTTT
1 AAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
56232 TTTTTGGCAA
Statistics
Matches: 243, Mismatches: 48, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
80 23 0.09
81 40 0.16
82 2 0.01
83 37 0.15
84 115 0.47
85 26 0.11
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (84 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTC
TAGACTTAAGTTATGCTGC
Found at i:56636 original size:106 final size:106
Alignment explanation
Indices: 56445--57709 Score: 2073
Period size: 106 Copynumber: 11.9 Consensus size: 106
56435 GTGAAGTTTA
* * *
56445 AAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCG
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
56510 ATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
56551 AAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
56616 ATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
56657 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
56722 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
56763 AAGTTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
56828 TTATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
56869 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
** *
56934 ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * *
56975 AAGTTGTTTGTTAACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
57040 ATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
57081 GAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
57146 ATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
57187 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
57252 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * *
57293 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCATTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
57358 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
57399 AAGTTGTTTATTGACAACCAGCGGTCCCTTCTTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
57464 ATATCCTTCGCT-TGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
57504 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * *
57569 ATATCATTCGCTGTGAAATTGAAATTGGCTCTAAAAGTGGA
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
57610 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * *
57675 ATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAA
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
57710 TGAAATTGGA
Statistics
Matches: 1079, Mismatches: 79, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
105 102 0.09
106 977 0.91
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
Found at i:65588 original size:59 final size:58
Alignment explanation
Indices: 65517--65771 Score: 155
Period size: 59 Copynumber: 4.3 Consensus size: 58
65507 ATATTAACAT
*
65517 TAAAAAATATATTTTA-TTTTTCTTAACTTATTGAGTATATTTTATTCTC-ACTTTAAC
1 TAAAAAATATATTTTAGTTTTTCTTAACTTATT-AGTATATTTTATTCTCTACCTTAAC
* * * * * *
65574 TAAAAAATATATATTTTAGTCCTATCTTAATTTATAAAATATATATTATTC-CTACCTTAAC
1 T-AAAAA-ATATATTTTAGT-TTTTCTTAACTTAT-TAGTATATTTTATTCTCTACCTTAAC
* * * * * *
65635 TTAAAAATATATTTTATTTTTATCTTAACTTGTTACGTATATTATATTCT-TAACTTAAAT
1 TAAAAAATATATTTTAGTTTT-TCTTAACTTATTA-GTATATTTTATTCTCTACCTT-AAC
** * * * * *
65695 TATTAAATATATTATA-TTCTTACATTAAATTATTA-AATATTATTTATTCT-TATCTTAAC
1 TAAAAAATATATTTTAGTT-TTTC-TTAACTTATTAGTATA-T-TTTATTCTCTACCTTAAC
65754 TTAAAAATATATATTTTA
1 -TAAAAA-ATATATTTTA
65772 CTTTAATTTT
Statistics
Matches: 149, Mismatches: 33, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
57 1 0.01
58 10 0.07
59 51 0.34
60 47 0.32
61 40 0.27
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (58 bp):
TAAAAAATATATTTTAGTTTTTCTTAACTTATTAGTATATTTTATTCTCTACCTTAAC
Found at i:65627 original size:30 final size:30
Alignment explanation
Indices: 65510--65768 Score: 160
Period size: 30 Copynumber: 8.7 Consensus size: 30
65500 AAATCACATA
* *
65510 TTAACATTAAAAAATATATTTTATT-TT-TC
1 TTAAC-TTATAAAATATATATTATTCTTATC
** * * *
65539 TTAACTTATTGAGTATATTTTATTCTCA-C
1 TTAACTTATAAAATATATATTATTCTTATC
* * *
65568 TTTAAC-TAAAAAATATATATTTTAGTCCTATC
1 -TTAACTTATAAAATATATA--TTATTCTTATC
* * *
65600 TTAATTTATAAAATATATATTATTCCTACC
1 TTAACTTATAAAATATATATTATTCTTATC
* *
65630 TTAACTTA-AAAATATATTTTATTTTTATC
1 TTAACTTATAAAATATATATTATTCTTATC
* * ** *
65659 TTAACTTGTTACGTATAT-TATATTCTTAAC
1 TTAACTTATAAAATATATAT-TATTCTTATC
* *
65689 TTAAATTATTAAATATAT-TATATTCTTA-C
1 TTAACTTATAAAATATATAT-TATTCTTATC
* *
65718 ATTAAATTATTAAATAT-TATTTATTCTTATC
1 -TTAACTTATAAAATATATA-TTATTCTTATC
65749 TTAACTTA-AAAATATATATT
1 TTAACTTATAAAATATATATT
65769 TTACTTTAAT
Statistics
Matches: 182, Mismatches: 34, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
28 15 0.08
29 50 0.27
30 92 0.51
31 12 0.07
32 13 0.07
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAACTTATAAAATATATATTATTCTTATC
Found at i:65752 original size:119 final size:118
Alignment explanation
Indices: 65510--65765 Score: 279
Period size: 119 Copynumber: 2.1 Consensus size: 118
65500 AAATCACATA
* * *
65510 TTAACATTAAAAAATATATTTTATTTTTCTTAACTTATTGAGTATATTTTATTCTCACTTTAACT
1 TTAAC-TT-AAAAATATATTTTATTTTTCTTAACTTATTGAGTATATTATATTCTAACTTTAAAT
* *
65575 AAAAAATATATATTTTAGTCCTATCTTAATTTATAAAATATATATTATTCCTACC
64 AAAAAATATATATTATAGTCCTATCTTAAATTATAAAATATATATTATTCCTACC
*
65630 TTAACTTAAAAATATATTTTATTTTTATCTTAACTTGTT-ACGTATATTATATTCTTAAC-TTAA
1 TTAACTTAAAAATATATTTTA-TTTT-TCTTAACTTATTGA-GTATATTATATTC-TAACTTTAA
* ** * * * * *
65693 ATTATTAA-ATATATTATATTCTTA-CATTAAATTATTAAATAT-TATTTATTCTTATC
62 ATAAAAAATATATATTATAGTCCTATC-TTAAATTATAAAATATATA-TTATTCCTACC
65749 TTAACTTAAAAATATAT
1 TTAACTTAAAAATATAT
65766 ATTTTACTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
118 17 0.15
119 60 0.52
120 36 0.31
121 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (118 bp):
TTAACTTAAAAATATATTTTATTTTTCTTAACTTATTGAGTATATTATATTCTAACTTTAAATAA
AAAATATATATTATAGTCCTATCTTAAATTATAAAATATATATTATTCCTACC
Found at i:65785 original size:25 final size:28
Alignment explanation
Indices: 65599--65793 Score: 116
Period size: 30 Copynumber: 6.9 Consensus size: 28
65589 TTAGTCCTAT
* * *
65599 CTTAATTTATAAAATATATATTATTCCTA
1 CTTAAATTATTAAATATATA-TATTCTTA
* * * *
65628 CCTTAACTTA-AAAATATATTTTATTTTTA
1 -CTTAAATTATTAAATATA-TATATTCTTA
* * **
65657 TCTTAACTTGTTACGTATATTATATTCTTAA
1 -CTTAAATTATTAAATATA-TATATTCTT-A
65688 CTTAAATTATTAAATATATTATATTCTTA
1 CTTAAATTATTAAATATA-TATATTCTTA
*
65717 CATTAAATTATTAAATATTATTTATTCTTA
1 C-TTAAATTATTAAATA-TATATATTCTTA
*
65747 TCTTAACTTA--AAA-ATATATATT-TTA
1 -CTTAAATTATTAAATATATATATTCTTA
* *
65772 CTTTAATT-TTAAA-ATGTATATT
1 CTTAAATTATTAAATATATATATT
65794 TTTATTTTTA
Statistics
Matches: 136, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
24 6 0.04
25 14 0.10
26 7 0.05
27 1 0.01
28 3 0.02
29 24 0.18
30 77 0.57
31 4 0.03
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (28 bp):
CTTAAATTATTAAATATATATATTCTTA
Found at i:72366 original size:19 final size:19
Alignment explanation
Indices: 72344--72382 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
72334 TCAAAATGCA
72344 AAATTTTTGTTAAAAATAT
1 AAATTTTTGTTAAAAATAT
72363 AAATTTTTGTTAAAAATAT
1 AAATTTTTGTTAAAAATAT
72382 A
1 A
72383 TTAACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTTTGTTAAAAATAT
Found at i:73357 original size:6 final size:6
Alignment explanation
Indices: 73348--73376 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
73338 AACTCAAACG
73348 GAAAGA GAAAGA GAAAGA GAAAGA GAAAG
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAG
73377 GGAGGGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:76826 original size:123 final size:123
Alignment explanation
Indices: 76663--76910 Score: 433
Period size: 123 Copynumber: 2.0 Consensus size: 123
76653 GAGCTAGTTT
* *
76663 GATCAAATGTGGGATAGAATCTTTTCCGATACATTATCTTGGGTTACCGTTGGATCATCGTCGCA
1 GATCAAATGTGGGATAGAATCTTTTCCGACACATTATCTTGGGTTACCGTTGGATCATCGTCACA
* * *
76728 ACTCCAAAGTAATGTGGCAGCTTATTATTGAGAAAGTTCAGTCTAGGCTCCATGGATG
66 ACTCCAAAGTAACGTGACAGCTTATTATCGAGAAAGTTCAGTCTAGGCTCCATGGATG
* *
76786 GATCAAATGTGGGGTAGAATCTTTTCCGACACATTATCTTGGGTTACCGTTGGGTCATCGTCACA
1 GATCAAATGTGGGATAGAATCTTTTCCGACACATTATCTTGGGTTACCGTTGGATCATCGTCACA
76851 ACTCCAAAGTAACGTGACAGCTTATTATCGAGAAAGTTCAGTCTAGGCTCCATGGATG
66 ACTCCAAAGTAACGTGACAGCTTATTATCGAGAAAGTTCAGTCTAGGCTCCATGGATG
76909 GA
1 GA
76911 AATGAAAATT
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (123 bp):
GATCAAATGTGGGATAGAATCTTTTCCGACACATTATCTTGGGTTACCGTTGGATCATCGTCACA
ACTCCAAAGTAACGTGACAGCTTATTATCGAGAAAGTTCAGTCTAGGCTCCATGGATG
Found at i:85941 original size:9 final size:9
Alignment explanation
Indices: 85927--85951 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
85917 GAAATCGGTT
85927 AATTAACCG
1 AATTAACCG
85936 AATTAACCG
1 AATTAACCG
85945 AATTAAC
1 AATTAAC
85952 ATTTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:86076 original size:17 final size:17
Alignment explanation
Indices: 86054--86092 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
86044 TGAATCAAAT
86054 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
86071 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
86088 -AATTA
1 TAATTA
86093 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:94260 original size:20 final size:20
Alignment explanation
Indices: 94212--94260 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
94202 CGTCCGTTGT
* *
94212 TCGCCGCCATCGTCCGCCAC
1 TCGCCGCCGTCGTACGCCAC
* *
94232 CCGCCGCCGTCTTACGCCAC
1 TCGCCGCCGTCGTACGCCAC
94252 TCGCCGCCG
1 TCGCCGCCG
94261 CCGACAGCCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.08, C:0.55, G:0.22, T:0.14
Consensus pattern (20 bp):
TCGCCGCCGTCGTACGCCAC
Found at i:100373 original size:19 final size:18
Alignment explanation
Indices: 100341--100376 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
100331 TAATTTTTGA
*
100341 ATCAATCAACTTTAATTT
1 ATCAATCAAATTTAATTT
100359 ATCACATCAAATTTAATT
1 ATCA-ATCAAATTTAATT
100377 ATTTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCAATCAAATTTAATTT
Found at i:100465 original size:20 final size:20
Alignment explanation
Indices: 100440--100484 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
100430 TGTATTATCA
100440 ATATATTAAATGATAATTTT
1 ATATATTAAATGATAATTTT
*
100460 ATATATTAAATGATACTTTT
1 ATATATTAAATGATAATTTT
100480 ATATA
1 ATATA
100485 ATTTAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
ATATATTAAATGATAATTTT
Found at i:100594 original size:18 final size:18
Alignment explanation
Indices: 100573--100607 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
100563 ATAAATTATG
100573 TGATAATAAGATAATATT
1 TGATAATAAGATAATATT
100591 TGATAATAAGATAATAT
1 TGATAATAAGATAATAT
100608 ATTTACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
TGATAATAAGATAATATT
Done.