Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015519.1 Corchorus olitorius cultivar O-4 contig15552, 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: 91168
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2114 original size:16 final size:16
Alignment explanation
Indices: 2071--2114 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
2061 ATAACTAATC
2071 AAATCATGACTCCACT
1 AAATCATGACTCCACT
2087 -AA-CAAT-ACTCCACT
1 AAATC-ATGACTCCACT
2101 AAATCATGACTCCA
1 AAATCATGACTCCA
2115 ATATCAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 9 0.38
15 8 0.33
16 7 0.29
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATCATGACTCCACT
Found at i:2471 original size:147 final size:147
Alignment explanation
Indices: 2204--2500 Score: 567
Period size: 147 Copynumber: 2.0 Consensus size: 147
2194 ATGCATGGAA
*
2204 GTTTGCTCATATGCCAAGAGAGTGCAATGTTATTGTTGATGCTTTGGCTGAGCCAGTTGGTAAAA
1 GTTTGCTCATATGCCAAGAGAGTGCAATGTTATTGTTGATGCTTTGGCTGAACCAGTTGGTAAAA
*
2269 TTTTAATTGATTGGGAGAATGGGTTGTTTTTGATTTGTGGTTTTCTATTTCGACTGATGTGTTTT
66 TTTTAATTGATTGGGAGAATGGGTTGTTTTTGATTTGTGATTTTCTATTTCGACTGATGTGTTTT
2334 TTTTCATGGAAATTGTT
131 TTTTCATGGAAATTGTT
2351 GTTTGCTCATATGCCAAGAGAGTGCAATGTTATTGTTGATGCTTTGGCTGAACCAGTTGGTAAAA
1 GTTTGCTCATATGCCAAGAGAGTGCAATGTTATTGTTGATGCTTTGGCTGAACCAGTTGGTAAAA
*
2416 TTTTAATTGATTGGGAGAATGGGTTGTTTTTGATTTGTGATTTTCTATTTTGACTGATGTGTTTT
66 TTTTAATTGATTGGGAGAATGGGTTGTTTTTGATTTGTGATTTTCTATTTCGACTGATGTGTTTT
2481 TTTTCATGGAAATTGTT
131 TTTTCATGGAAATTGTT
2498 GTT
1 GTT
2501 CGGCTTTTAT
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.45
Consensus pattern (147 bp):
GTTTGCTCATATGCCAAGAGAGTGCAATGTTATTGTTGATGCTTTGGCTGAACCAGTTGGTAAAA
TTTTAATTGATTGGGAGAATGGGTTGTTTTTGATTTGTGATTTTCTATTTCGACTGATGTGTTTT
TTTTCATGGAAATTGTT
Found at i:4020 original size:6 final size:6
Alignment explanation
Indices: 4011--4039 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4001 GAATTTGCTG
4011 TTGCAT TTGCAT TTGCAT TTGCAT TTGCA
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCA
4040 GCCGAGCTTG
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:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
TTGCAT
Found at i:4844 original size:28 final size:29
Alignment explanation
Indices: 4811--4868 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
4801 GTTTGGAAGG
4811 ATTTAATTAGCC-AAATCG-AGTTTCAGAA
1 ATTTAATTAGCCAAAATCGAAG-TTCAGAA
*
4839 ATTTAATTGGCCAAAATCGAAGTTCAGAA
1 ATTTAATTAGCCAAAATCGAAGTTCAGAA
4868 A
1 A
4869 CTTATTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.41
29 14 0.52
30 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (29 bp):
ATTTAATTAGCCAAAATCGAAGTTCAGAA
Found at i:4914 original size:9 final size:9
Alignment explanation
Indices: 4900--4926 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4890 AATTTTCCAT
4900 TATCAAATA
1 TATCAAATA
4909 TATCAAATA
1 TATCAAATA
4918 TATCAAATA
1 TATCAAATA
4927 AGTTAGCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
TATCAAATA
Found at i:7165 original size:8 final size:8
Alignment explanation
Indices: 7152--7177 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
7142 TTAACCTATA
7152 TATCTTAC
1 TATCTTAC
7160 TATCTTAC
1 TATCTTAC
7168 TATCTTAC
1 TATCTTAC
7176 TA
1 TA
7178 CTATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (8 bp):
TATCTTAC
Found at i:8522 original size:15 final size:15
Alignment explanation
Indices: 8497--8576 Score: 55
Period size: 15 Copynumber: 5.6 Consensus size: 15
8487 ATATTAACCC
**
8497 TTATA-TTAATTTGT
1 TTATATTTAATTTAA
8511 TTATATTTAATTTAA
1 TTATATTTAATTTAA
*
8526 TTATCTTTAATTCATAA
1 TTATATTTAATT--TAA
*
8543 TGA-A-TTAA--TAA
1 TTATATTTAATTTAA
*
8554 TTATATTTGATTTAA
1 TTATATTTAATTTAA
8569 -TATATTTA
1 TTATATTTA
8577 TAATAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
11 5 0.10
12 1 0.02
13 3 0.06
14 12 0.24
15 25 0.49
17 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (15 bp):
TTATATTTAATTTAA
Found at i:10268 original size:44 final size:44
Alignment explanation
Indices: 10216--10405 Score: 193
Period size: 44 Copynumber: 4.3 Consensus size: 44
10206 TATATCGTGA
* * *
10216 TTATCAAAATTTCATAGGGAAATTATCAAAATTTCATACTAAGG
1 TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATAAGG
* * * * * * * *
10260 TTGTCAAAATTTCTTAGTGTGGTTATCAAAATTTCATATTATGG
1 TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATAAGG
* * *
10304 TTATCAAATTTTCATAGGGAGGTTATCGAAATTT-AGTAATGAGG
1 TTATCAAATTTTCATAGGGAGATTATCAAAATTTCA-TAATAAGG
* ** * *
10348 TTATCAAATTTTCACAGATAGATTATCGAAATTTCATAATGAGG
1 TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATAAGG
10392 TTATCAAATTTTCA
1 TTATCAAATTTTCA
10406 CAGTGTGATT
Statistics
Matches: 123, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.01
44 121 0.98
45 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (44 bp):
TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATAAGG
Found at i:10327 original size:22 final size:22
Alignment explanation
Indices: 10216--10410 Score: 162
Period size: 22 Copynumber: 8.9 Consensus size: 22
10206 TATATCGTGA
* **
10216 TTATCAAAATTTCATAGGGAAA
1 TTATCAAAATTTCATAGTGAGG
* *
10238 TTATCAAAATTTCATACTAAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
10260 TTGTCAAAATTTCTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
10282 TTATCAAAATTTCATA-TTATGG
1 TTATCAAAATTTCATAGTGA-GG
* *
10304 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
10326 TTATCGAAATTT-AGTAATGAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
10348 TTATCAAATTTTCACAGAT-AGA
1 TTATCAAAATTTCATAG-TGAGG
* *
10370 TTATCGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
10392 TTATCAAATTTTCACAGTG
1 TTATCAAAATTTCATAGTG
10411 TGATTGTCAA
Statistics
Matches: 132, Mismatches: 35, Indels: 12
0.74 0.20 0.07
Matches are distributed among these distances:
21 3 0.02
22 126 0.95
23 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:13921 original size:22 final size:22
Alignment explanation
Indices: 13893--14044 Score: 114
Period size: 22 Copynumber: 6.9 Consensus size: 22
13883 TGTCTCTGTG
13893 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
13915 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
13938 -GGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
13959 TGGTTACCAAAATTTCATATGGAA
1 TGGTTATCAAAATTTCATA-AG-A
** **
13983 AAGTTATCAAAATTTCATTGGA
1 TGGTTATCAAAATTTCATAAGA
*
14005 AGGTTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* *
14025 TGTGTTACCAAATTTTCATA
1 TG-GTTATCAAAATTTCATA
14045 GGATCAGGTT
Statistics
Matches: 103, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.02
21 15 0.15
22 65 0.63
23 5 0.05
24 16 0.16
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:13963 original size:44 final size:45
Alignment explanation
Indices: 13894--14023 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 45
13884 GTCTCTGTGT
** *
13894 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GG-A
1 GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCAT-ATGGAA
*
13938 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATATGGAAA
1 GGTTATCAAAATTTCATAAG-ATGGTTACCAAAATTTCATATGG-AA
* ** * *
13984 AGTTATCAAAATTTCATTGGAAGGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCATA
14024 GTGTGTTACC
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 3 0.04
44 34 0.47
46 34 0.47
47 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCATATGGAA
Found at i:14073 original size:67 final size:68
Alignment explanation
Indices: 13890--14113 Score: 262
Period size: 67 Copynumber: 3.3 Consensus size: 68
13880 TCTTGTCTCT
* * * *
13890 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGATAGGTTATTAAAATTTCATTAGGAAGGTTATCAAAATTTC
13953 ATA
66 ATA
* * *
13956 GTGTGGTTACCAAAATTTCATATGGAAAAGTTATCAAAATTTCATT-GGAAGGTTATCAAAATTT
1 GTGTGGTTACCAAAATTTCATA-GGATAGGTTATTAAAATTTCATTAGGAAGGTTATCAAAATTT
14020 CATA
65 CATA
* * * **
14024 GTGT-GTTACCAAATTTTCATAGGATCAGGTTATTAAAAATTC-TTAGGAAGGTTGTTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGGAT-AGGTTATTAAAATTTCATTAGGAAGGTTATCAAAATTT
14087 CATA
65 CATA
*
14091 GTGTGGTTATCACAAATTT-ATAG
1 GTGTGGTTACCA-AAATTTCATAG
14114 AAAGGTAATC
Statistics
Matches: 134, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
66 26 0.19
67 56 0.42
68 47 0.35
69 5 0.04
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (68 bp):
GTGTGGTTACCAAAATTTCATAGGATAGGTTATTAAAATTTCATTAGGAAGGTTATCAAAATTTC
ATA
Found at i:14186 original size:22 final size:22
Alignment explanation
Indices: 14161--14276 Score: 101
Period size: 22 Copynumber: 5.3 Consensus size: 22
14151 TGTTTTTAAG
* *
14161 AATTTCATAGTGTGTTTAACAA
1 AATTTCATAGTGTGGTTATCAA
* *
14183 AATTTCATAAG-GAGATTA-CTAA
1 AATTTCAT-AGTGTGGTTATC-AA
* * * *
14205 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
*
14227 AATTTCATAGTATGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
**
14249 AATTTTTTAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
14271 AATTTC
1 AATTTC
14277 TTTTTTTTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.03
22 71 0.93
23 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:14408 original size:22 final size:22
Alignment explanation
Indices: 14356--14588 Score: 181
Period size: 22 Copynumber: 10.6 Consensus size: 22
14346 TAAGGAGTGC
* *
14356 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAGAGAGATTAT
* *
14377 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGAGATTAT
*
14398 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGA---GATTAT
14423 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAG-AGATTAT
* * *
14444 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGAGATTAT
* *
14466 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GAGATTAT
* * *
14488 CAAAATTTCATAGAGGGATCAA
1 CAAAATTTCATAGAGAGATTAT
* *
14510 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGATTAT
* *
14532 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGAGATTAT
* * * *
14554 CAAATTTTCA-AAATGTGATTAC
1 CAAAATTTCATAGA-GAGATTAT
14576 CAAAATTTCATAG
1 CAAAATTTCATAG
14589 TGGTATTTCT
Statistics
Matches: 169, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
20 10 0.06
21 24 0.14
22 113 0.67
23 4 0.02
24 5 0.03
25 13 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGATTAT
Found at i:14569 original size:88 final size:87
Alignment explanation
Indices: 14356--14588 Score: 251
Period size: 88 Copynumber: 2.6 Consensus size: 87
14346 TAAGGAGTGC
* * * * *
14356 CAAAATTTGATAGA-AGGTTATCAAATCTCATAGA-GTGATTATCGAAATTTCATAGAGATCGGA
1 CAAAATTTCATAAAGAGGTTATCAAATTTCA-AAATGTGATTATCAAAATTTCATAGAGA--GGA
* *
14419 TTATCAAAATTTATAGGAAGATTAT
63 TCAACAAAATTTATAGGAAGATTAT
* * *
14444 CAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAG-GGAT
1 CAAAATTTCATAA-AGAGGTTATC-AAATTTCAAAATGTGATTATCAAAATTTCATAGAGAGGAT
*
14507 CAACAAAATTTTATA-GAGAGGTTAT
64 CAACAAAA-TTTATAGGA-AGATTAT
*
14532 CAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCATAG
1 CAAAATTTCATAAAGAGGTTATCAAA-TTTCAAAATGTGATTATCAAAATTTCATAG
14589 TGGTATTTCT
Statistics
Matches: 122, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
87 16 0.13
88 67 0.55
89 11 0.09
90 28 0.23
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (87 bp):
CAAAATTTCATAAAGAGGTTATCAAATTTCAAAATGTGATTATCAAAATTTCATAGAGAGGATCA
ACAAAATTTATAGGAAGATTAT
Found at i:14780 original size:22 final size:22
Alignment explanation
Indices: 14667--15046 Score: 185
Period size: 22 Copynumber: 17.5 Consensus size: 22
14657 TTGTGGAGTA
* *
14667 ATCAAAAATTCAT--GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
14687 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* **
14709 TTCAAAATTTCATA-AAAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
14731 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
14753 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
14775 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
14797 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
14819 ATCAAAATTT--TA-TGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * * * *
14839 ATCATAATTTTATTGGAACGTTT
1 ATCAAAATTTCATAGGGA-GGTT
*
14862 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
14884 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
14906 AACAAAA--TCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
14926 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * *
14948 ATCAACATCTCAT-GGTGTTGGTT
1 ATCAAAATTTCATAGG-G-AGGTT
* * *
14971 ATCAAAATTTCATTGGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
14993 ATCAAAATTTCATAGTGAGATCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
15016 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
15037 AACAAAATTT
1 ATCAAAATTT
15047 TATAAGGTTA
Statistics
Matches: 269, Mismatches: 69, Indels: 42
0.71 0.18 0.11
Matches are distributed among these distances:
19 5 0.02
20 42 0.16
21 7 0.03
22 175 0.65
23 37 0.14
24 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:14840 original size:20 final size:22
Alignment explanation
Indices: 14812--14893 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
14802 AAAATCATAG
14812 GGAGG-TTATCAAAATTTTA-T
1 GGAGGTTTATCAAAATTTTATT
*
14832 -GAGGTTTATCATAATTTTATT
1 GGAGGTTTATCAAAATTTTATT
* * *
14853 GGAACGTTTATCAAAATTTCATA
1 GG-AGGTTTATCAAAATTTTATT
*
14876 GCGAGG-TTATCACAATTT
1 G-GAGGTTTATCAAAATTT
14894 CATAGTGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.08
20 13 0.26
21 1 0.02
22 12 0.24
23 19 0.38
24 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (22 bp):
GGAGGTTTATCAAAATTTTATT
Found at i:14871 original size:131 final size:131
Alignment explanation
Indices: 14680--15051 Score: 309
Period size: 131 Copynumber: 2.8 Consensus size: 131
14670 AAAAATTCAT
* * * * *
14680 GGAGGATATCAAAATTTCATAGT-TTAGTTTTCAAAATTTCA-T-AAAAGGGTTATCAAAATTTC
1 GGAGGTTATCAAAATCTCATGGTGTT-GTTATCAAAATTTCATTGGAAA--GTTATCAAAATTTC
*
14742 ATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTA-TCAAAAAA
63 ATAG-ATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGATTACT-AAAAAA
14806 TCATAG
126 TCATAG
* * * * *
14812 GGAGGTTATCAAAATTTTATGAG-G-T-TTATCATAATTTTATTGGAACGTTTATCAAAATTTCA
1 GGAGGTTATCAAAATCTCATG-GTGTTGTTATCAAAATTTCATTGGAAAG-TTATCAAAATTTCA
* * * * * * * * *
14874 TAGCGAGGT-TATCACAATTTCATAGTGTGATTAACAAAA--TCATAGTGTGATTACTAACAATT
64 TA--GATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGATTACTAAAAAAT
*
14936 CATAT
127 CATAG
*
14941 GGAGGTTATCAACATCTCATGGTGTTGGTTATCAAAATTTCATTGGAAAGTTATCAAAATTTCAT
1 GGAGGTTATCAAAATCTCATGGTGTT-GTTATCAAAATTTCATTGGAAAGTTATCAAAATTTCAT
* * * *
15006 AG-TG-AGATCTTCAAAATTCCTTAGGGAGGTTAACAAAATTTTATAA
65 AGATGTAGA---TCAAAATTTCATAGGGAGATTAACAAAATTTCATAA
15052 GGTTAAAAAA
Statistics
Matches: 187, Mismatches: 35, Indels: 35
0.73 0.14 0.14
Matches are distributed among these distances:
128 3 0.02
129 40 0.21
130 14 0.07
131 81 0.43
132 43 0.23
133 6 0.03
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (131 bp):
GGAGGTTATCAAAATCTCATGGTGTTGTTATCAAAATTTCATTGGAAAGTTATCAAAATTTCATA
GATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGATTACTAAAAAATCATA
G
Found at i:15068 original size:19 final size:19
Alignment explanation
Indices: 15032--15070 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
15022 TTCCTTAGGG
* **
15032 AGGTTAACAAAATTTTATA
1 AGGTTAAAAAAAAGTTATA
15051 AGGTTAAAAAAAAGTTATA
1 AGGTTAAAAAAAAGTTATA
15070 A
1 A
15071 AAAGGTTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (19 bp):
AGGTTAAAAAAAAGTTATA
Found at i:17473 original size:29 final size:29
Alignment explanation
Indices: 17431--17488 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
17421 ATCATTTTCC
17431 AAATTTTTAACCAATCATAGTGATAAAAT
1 AAATTTTTAACCAATCATAGTGATAAAAT
17460 AAATTTTTAACCAATCATAGTGATAAAAT
1 AAATTTTTAACCAATCATAGTGATAAAAT
17489 TACTGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (29 bp):
AAATTTTTAACCAATCATAGTGATAAAAT
Found at i:20885 original size:33 final size:33
Alignment explanation
Indices: 20848--20914 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
20838 ATGGGATAAA
20848 TTGTCCTGATTTTAGTTTAGGGGACATTGTACT
1 TTGTCCTGATTTTAGTTTAGGGGACATTGTACT
20881 TTGTCCTGATTTTAGTTTAGGGGACATTGTACT
1 TTGTCCTGATTTTAGTTTAGGGGACATTGTACT
20914 T
1 T
20915 AGCCCTACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.46
Consensus pattern (33 bp):
TTGTCCTGATTTTAGTTTAGGGGACATTGTACT
Found at i:24020 original size:29 final size:31
Alignment explanation
Indices: 23988--24062 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
23978 TGATACGTAT
* *
23988 TTTTTGTG-CACGTCGCATGCCATGTGTCAT
1 TTTTTGTGACACATCGCATGCCATGTGTCAC
** *
24018 TTTTTGAAACACATGGCATGCCATGTGTCAC
1 TTTTTGTGACACATCGCATGCCATGTGTCAC
24049 TTTTTG-GTACACAT
1 TTTTTGTG-ACACAT
24063 GGTGTGATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 6 0.16
31 31 0.84
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (31 bp):
TTTTTGTGACACATCGCATGCCATGTGTCAC
Found at i:24037 original size:31 final size:31
Alignment explanation
Indices: 24002--24064 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
23992 TGTGCACGTC
*
24002 GCATGCCATGTGTCATTTTTTGAAACACATG
1 GCATGCCATGTGTCACTTTTTGAAACACATG
**
24033 GCATGCCATGTGTCACTTTTTGGTACACATG
1 GCATGCCATGTGTCACTTTTTGAAACACATG
24064 G
1 G
24065 TGTGATACGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (31 bp):
GCATGCCATGTGTCACTTTTTGAAACACATG
Found at i:24077 original size:31 final size:32
Alignment explanation
Indices: 24042--24130 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 32
24032 GGCATGCCAT
*
24042 GTGTCACTTTTTGGTACACA-TGGTGTGATAC
1 GTGTCACTTTTTGGTACACATTGGCGTGATAC
*
24073 GTGTCACTTTTTGGTACA-ATTGGCGTGATAT
1 GTGTCACTTTTTGGTACACATTGGCGTGATAC
* * *
24104 GTGTCGCTTTTTAGTACACGTT-GCGTG
1 GTGTCACTTTTTGGTACACATTGGCGTG
24131 CCACGTCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 1 0.02
31 48 0.94
32 2 0.04
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40
Consensus pattern (32 bp):
GTGTCACTTTTTGGTACACATTGGCGTGATAC
Found at i:26589 original size:29 final size:29
Alignment explanation
Indices: 26544--26599 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
26534 TAGAGTTTGA
*
26544 ACGTTTTGTCCGCTGAATTTCAATTTTAG
1 ACGTTTTGTCCGCTGAACTTCAATTTTAG
*
26573 ACGTTTTG-CCTCATGAACTTCAATTTT
1 ACGTTTTGTCCGC-TGAACTTCAATTTT
26600 GAGTCCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (29 bp):
ACGTTTTGTCCGCTGAACTTCAATTTTAG
Found at i:36586 original size:3 final size:3
Alignment explanation
Indices: 36573--36645 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
36563 TAAACTCAAA
36573 TAT TA- TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36619 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
36646 AGCAATTAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:47269 original size:35 final size:35
Alignment explanation
Indices: 47230--47299 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
47220 TGATCCTATA
47230 GACTCGAGTTTGTCAATCTGTGGCTAATCAACAGT
1 GACTCGAGTTTGTCAATCTGTGGCTAATCAACAGT
47265 GACTCGAGTTTGTCAATCTGTGGCTAATCAACAGT
1 GACTCGAGTTTGTCAATCTGTGGCTAATCAACAGT
47300 TCAAGGATCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (35 bp):
GACTCGAGTTTGTCAATCTGTGGCTAATCAACAGT
Found at i:48828 original size:28 final size:26
Alignment explanation
Indices: 48796--48848 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
48786 AGTTTCTAAC
48796 CCAATCCAAAATAAAAATCAAACAAAAA
1 CCAAT-CAAAATAAAAATCAAA-AAAAA
* *
48824 CCAATGAAAATAAAAATTAAAAAAA
1 CCAATCAAAATAAAAATCAAAAAAA
48849 GGAATATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 14 0.61
28 5 0.22
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (26 bp):
CCAATCAAAATAAAAATCAAAAAAAA
Found at i:49960 original size:80 final size:75
Alignment explanation
Indices: 49857--50003 Score: 213
Period size: 80 Copynumber: 1.9 Consensus size: 75
49847 AAATAACATG
*
49857 GTTTGATACAAATCTAAGTCTGACCGACATGACTATAAAGGTAGTATATGAAAATAGTTAGAAAA
1 GTTTGATACAAATCTAAGTCTGACCGACATGAC--TAAA-G--GTATACGAAAATAGTTAGAAAA
*
49922 TATTGAATGAATCTT
61 AATTGAATGAATCTT
* *
49937 GTTTGATACATATCTGAGTCTGACCGACATGACTAAAGGTATACGAAAATAGTTAGAAAAAATTG
1 GTTTGATACAAATCTAAGTCTGACCGACATGACTAAAGGTATACGAAAATAGTTAGAAAAAATTG
50002 AA
66 AA
50004 CGGATCCATG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
75 27 0.43
77 1 0.02
78 4 0.06
80 31 0.49
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.29
Consensus pattern (75 bp):
GTTTGATACAAATCTAAGTCTGACCGACATGACTAAAGGTATACGAAAATAGTTAGAAAAAATTG
AATGAATCTT
Found at i:53504 original size:34 final size:34
Alignment explanation
Indices: 53431--53521 Score: 168
Period size: 33 Copynumber: 2.7 Consensus size: 34
53421 AAGAGTGGTG
53431 ATAAAA-TTTTTTCATTTCTGATCTATGAACATC
1 ATAAAATTTTTTTCATTTCTGATCTATGAACATC
53464 AT-AAATTTTTTTCATTTCTGATCTATGAACATC
1 ATAAAATTTTTTTCATTTCTGATCTATGAACATC
53497 ATAAAATTTTTTTCATTTCTGATCT
1 ATAAAATTTTTTTCATTTCTGATCT
53522 CTAATTTGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
32 3 0.05
33 31 0.55
34 22 0.39
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.49
Consensus pattern (34 bp):
ATAAAATTTTTTTCATTTCTGATCTATGAACATC
Found at i:55471 original size:2 final size:2
Alignment explanation
Indices: 55466--55502 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
55456 TAATGGCACT
*
55466 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55503 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:66542 original size:19 final size:19
Alignment explanation
Indices: 66526--66563 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
66516 GCAGGAAATG
66526 GAAAAAAGAAAAAGAAAAA
1 GAAAAAAGAAAAAGAAAAA
*
66545 GAAAAAGGAAAAAGGAAAA
1 GAAAAAAGAAAAA-GAAAA
66564 CTCACCCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAAAAGAAAAAGAAAAA
Found at i:66543 original size:5 final size:6
Alignment explanation
Indices: 66528--66563 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
66518 AGGAAATGGA
66528 AAAAAG AAAAAG AAAAAG AAAAAGG AAAAAGG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA-G AAAA
66564 CTCACCCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:67392 original size:19 final size:20
Alignment explanation
Indices: 67368--67425 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
67358 CTGTTTGGCA
67368 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* * *
67387 ACTGTACATATTAGATTATGT
1 ACTGTACAGATGAGATTA-GC
*
67408 ACTCTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
67426 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:67423 original size:21 final size:20
Alignment explanation
Indices: 67372--67426 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
67362 TTGGCAACTG
*
67372 TACAGATGAGATTA-CACTG
1 TACAGATGAGATTATCACTC
* * *
67391 TACATATTAGATTATGTACTC
1 TACAGATGAGATTAT-CACTC
67412 TACAGATGAGATTAT
1 TACAGATGAGATTAT
67427 TAGAGCAGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (20 bp):
TACAGATGAGATTATCACTC
Found at i:67500 original size:19 final size:19
Alignment explanation
Indices: 67476--67514 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
67466 TTTGGTCCCA
67476 AAACGGTGATGAAACGATT
1 AAACGGTGATGAAACGATT
*
67495 AAACGGTGGTGAAACGATT
1 AAACGGTGATGAAACGATT
67514 A
1 A
67515 CAGATAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (19 bp):
AAACGGTGATGAAACGATT
Found at i:67862 original size:30 final size:33
Alignment explanation
Indices: 67803--67868 Score: 111
Period size: 30 Copynumber: 2.1 Consensus size: 33
67793 GATTATGATT
67803 TTTGATAATATAGAGAAGGAATAAAAAAAGATG
1 TTTGATAATATAGAGAAGGAATAAAAAAAGATG
67836 TTTGAT-A-ATAGAGAAGGAAT-AAAAAAGATG
1 TTTGATAATATAGAGAAGGAATAAAAAAAGATG
67866 TTT
1 TTT
67869 TTATAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 13 0.39
31 13 0.39
32 1 0.03
33 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (33 bp):
TTTGATAATATAGAGAAGGAATAAAAAAAGATG
Found at i:68997 original size:101 final size:107
Alignment explanation
Indices: 68880--69090 Score: 308
Period size: 112 Copynumber: 2.0 Consensus size: 107
68870 AATTTGCCAC
*
68880 ATATATAAATTTAAGGATTAATATTTGATG-T-ATA-GT-T-TT-CATACACTATCAGTAAATCA
1 ATATATAAATTTAAGGATTAATATTTGATGCTGACAGGTATATTCCATACACTATCAGTAAATCA
*
68939 TAGGTTGCGACATCATAGAAAAATAATTATTAAAAATTATTA
66 TAGGTTGCCACATCATAGAAAAATAATTATTAAAAATTATTA
68981 ATATATAAATTTAAGGATTAATATTTGATGCACTGACAGTGTATAGCTTCCATACACTATCAGTA
1 ATATATAAATTTAAGGATTAATATTTGATG--CTGACAG-GTATA--TTCCATACACTATCAGTA
*
69046 AATCATAGGTTGCCACATCATAGAAAAATAATTTTTAAAAATTAT
61 AATCATAGGTTGCCACATCATAGAAAAATAATTATTAAAAATTAT
69091 GATATGGCAA
Statistics
Matches: 96, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
101 30 0.31
104 1 0.01
105 2 0.02
107 2 0.02
108 1 0.01
111 2 0.02
112 58 0.60
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (107 bp):
ATATATAAATTTAAGGATTAATATTTGATGCTGACAGGTATATTCCATACACTATCAGTAAATCA
TAGGTTGCCACATCATAGAAAAATAATTATTAAAAATTATTA
Found at i:70161 original size:20 final size:20
Alignment explanation
Indices: 70138--70190 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
70128 TTTTTTTTCG
*
70138 TTTTTGTATTTTTTTATAGTTT
1 TTTTTATATTTTTTTATA--TT
70160 TTTTTATATTCTTTTTATA-T
1 TTTTTATATT-TTTTTATATT
70180 TTTTTATATTT
1 TTTTTATATTT
70191 ATTACTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
22 9 0.31
23 8 0.28
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (20 bp):
TTTTTATATTTTTTTATATT
Found at i:70163 original size:12 final size:11
Alignment explanation
Indices: 70146--70184 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
70136 CGTTTTTGTA
70146 TTTTTTTATAGT
1 TTTTTTTATA-T
70158 TTTTTTTATAT
1 TTTTTTTATAT
*
70169 TCTTTTTATAT
1 TTTTTTTATAT
70180 TTTTT
1 TTTTT
70185 ATATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:70169 original size:22 final size:22
Alignment explanation
Indices: 70138--70184 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
70128 TTTTTTTTCG
*
70138 TTTTTGTATT-TTTTTATAGTTT
1 TTTTTATATTCTTTTTATA-TTT
70160 TTTTTATATTCTTTTTATATTT
1 TTTTTATATTCTTTTTATATTT
70182 TTT
1 TTT
70185 ATATTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTATATTCTTTTTATATTT
Found at i:78657 original size:16 final size:16
Alignment explanation
Indices: 78636--78666 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
78626 AGGGTGATGA
78636 AAATTAAAAGACAAGG
1 AAATTAAAAGACAAGG
78652 AAATTAAAAGACAAG
1 AAATTAAAAGACAAG
78667 TAAAGGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.13
Consensus pattern (16 bp):
AAATTAAAAGACAAGG
Found at i:83784 original size:15 final size:14
Alignment explanation
Indices: 83758--83807 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
83748 CAATTCATCA
83758 TGATGAAAGCGTCC
1 TGATGAAAGCGTCC
83772 TGATGATAAGCGTCC
1 TGATGA-AAGCGTCC
*
83787 TGATGGAAAGTCGCCC
1 TGAT-GAAAG-CGTCC
83803 TGATG
1 TGATG
83808 GTGTGATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 6 0.19
15 16 0.50
16 10 0.31
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (14 bp):
TGATGAAAGCGTCC
Found at i:85280 original size:21 final size:22
Alignment explanation
Indices: 85256--85296 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
85246 GTTTATAATA
*
85256 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
85277 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
85297 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:86037 original size:49 final size:49
Alignment explanation
Indices: 85984--86081 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
85974 AGATTGGGTC
85984 AAATCCTATGAGCTGCTTGGTAGTCCATTAGGATTATCATAGAATAATT
1 AAATCCTATGAGCTGCTTGGTAGTCCATTAGGATTATCATAGAATAATT
** * *
86033 AAATCCTATGAGCTTTTTGGTAGTCCATTAGGATTGTTATAGAATAATT
1 AAATCCTATGAGCTGCTTGGTAGTCCATTAGGATTATCATAGAATAATT
86082 TGAAAGTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (49 bp):
AAATCCTATGAGCTGCTTGGTAGTCCATTAGGATTATCATAGAATAATT
Found at i:86721 original size:18 final size:18
Alignment explanation
Indices: 86698--86732 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
86688 AACTTTTTCA
*
86698 AAACTAAACCTCAATCCC
1 AAACTAAACCTAAATCCC
86716 AAACTAAACCTAAATCC
1 AAACTAAACCTAAATCC
86733 TCTACTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (18 bp):
AAACTAAACCTAAATCCC
Found at i:87461 original size:17 final size:18
Alignment explanation
Indices: 87439--87472 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
87429 CTTTTATCTT
87439 TTAATTACATT-AATTAA
1 TTAATTACATTCAATTAA
*
87456 TTAATTATATTCAATTA
1 TTAATTACATTCAATTA
87473 GTACTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTACATTCAATTAA
Found at i:90919 original size:28 final size:28
Alignment explanation
Indices: 90888--90962 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
90878 TTAAGATATC
* *
90888 AAAATTACTGTTTTGCCCTTGGTCAGCT
1 AAAATTACAGTTTTGCCCTTGGTCAACT
* * *
90916 AAAATTACCA-TTTTACCCCTGGTTAACT
1 AAAATTA-CAGTTTTGCCCTTGGTCAACT
90944 -AAATTACAGTTTTGCCCTT
1 AAAATTACAGTTTTGCCCTT
90963 AAATGCCGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.05
27 14 0.37
28 21 0.55
29 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (28 bp):
AAAATTACAGTTTTGCCCTTGGTCAACT
Done.