Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1008
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: 28019
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6384 original size:20 final size:20
Alignment explanation
Indices: 6344--6394 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
6334 TTCTATGATT
6344 TGTATTGATATAACGAGTGAA
1 TGTATTGATATAAC-AGTGAA
6365 TGTATTGATATATA-AGTGAA
1 TGTATTGATATA-ACAGTGAA
*
6385 TGTATCGATA
1 TGTATTGATA
6395 CTGGACCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 15 0.54
21 12 0.43
22 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTATTGATATAACAGTGAA
Found at i:6512 original size:51 final size:51
Alignment explanation
Indices: 6433--6600 Score: 221
Period size: 51 Copynumber: 3.3 Consensus size: 51
6423 TATGGAAAGA
* * * *
6433 AAATATATCGATACA-TTTTTATTATATCGATACATTTTGGGTTTTGATCC
1 AAATATATTGATACACTCTTCATCATATCGATACATTTTGGGTTTTGATCC
* * *
6483 AAATTTATTGATACACTCTTTATCCTATCGATACATTTTGGGTTTTGATCC
1 AAATATATTGATACACTCTTCATCATATCGATACATTTTGGGTTTTGATCC
* * *
6534 AAATGTATTGATACATTCTTCATCATATCGATACATTTTGGGTTTTTTATCC
1 AAATATATTGATACACTCTTCATCATATCGATACATTTTGGG-TTTTGATCC
*
6586 AAATATATCGATACA
1 AAATATATTGATACA
6601 TCTATTAAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 13 0.12
51 70 0.67
52 21 0.20
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (51 bp):
AAATATATTGATACACTCTTCATCATATCGATACATTTTGGGTTTTGATCC
Found at i:9146 original size:98 final size:95
Alignment explanation
Indices: 8888--9146 Score: 234
Period size: 97 Copynumber: 2.7 Consensus size: 95
8878 AAAAATACCA
* * * * *
8888 AAATTGT-ATTCATCGAGGATACTCTAACCCCATTTTTTTGAGGGGATACTCCAATCTCGTTTTT
1 AAATTGTCA-TCATCGGGGATACTCAAACCTCATTCTTCTGA-GGGATACTCC-ATCTCGTTTTT
* *
8952 AAACTTATGAAGATTTAAATTTTATTCTCACCT
63 AAACTTATCAAGATTTAAATATTATTCTCACCT
* * * * * *
8985 AAATTGTTATCATTGGGGATACTTAAACCTCATTCTTCTGAGAGGATACTCCATCCCCATTTTTT
1 AAATTGTCATCATCGGGGATACTCAAACCTCATTCTTCTGAG-GGATACTCCAT-CTCGTTTTTA
* * * *
9050 AACTTGTCATGATTTAAATATTGTGT-TCGCCT
64 AACTTATCAAGATTTAAATATTAT-TCTCACCT
* * * *
9082 TAATTGTCATCGTCGGGGATACCTCCAACCTCGTTCTTCTGAAGGGATACTCCAGTCTCGTTTTT
1 AAATTGTCATCATCGGGGATA-CTCAAACCTCATTCTTCTG-AGGGATACTCCA-TCTCGTTTTT
9147 CAACCAAAGA
Statistics
Matches: 130, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
96 3 0.02
97 89 0.68
98 35 0.27
99 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (95 bp):
AAATTGTCATCATCGGGGATACTCAAACCTCATTCTTCTGAGGGATACTCCATCTCGTTTTTAAA
CTTATCAAGATTTAAATATTATTCTCACCT
Found at i:14348 original size:20 final size:20
Alignment explanation
Indices: 14323--14373 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
14313 CCACTGTTTG
*
14323 TATCGATACATGGT-ACATTA
1 TATCGATACATGATGA-ATTA
*
14343 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTA
14363 TATCGATACAT
1 TATCGATACAT
14374 TGCTTGTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGATGAATTA
Found at i:17802 original size:13 final size:13
Alignment explanation
Indices: 17784--17833 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
17774 ACATAAGTTT
17784 TGTATCGATACAA
1 TGTATCGATACAA
17797 TGTATCGATACATAA
1 TGTATCGATAC--AA
17812 GTTGTATCGATACAA
1 --TGTATCGATACAA
*
17827 AGTATCG
1 TGTATCG
17834 CTATGAAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 17 0.53
15 4 0.12
17 11 0.34
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:17819 original size:17 final size:16
Alignment explanation
Indices: 17765--17829 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 16
17755 ATTCAGTAAA
17765 TGTATCGATACATAAGTTT
1 TGTATCGATACA-AAG--T
17784 TGTATCGATAC-AA--
1 TGTATCGATACAAAGT
17797 TGTATCGATACATAAGT
1 TGTATCGATACA-AAGT
17814 TGTATCGATACAAAGT
1 TGTATCGATACAAAGT
17830 ATCGCTATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
16 4 0.10
17 14 0.33
19 11 0.26
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (16 bp):
TGTATCGATACAAAGT
Found at i:17819 original size:30 final size:31
Alignment explanation
Indices: 17763--17833 Score: 117
Period size: 30 Copynumber: 2.3 Consensus size: 31
17753 ACATTCAGTA
17763 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAG-TTTGTATCGATAC
17795 AATGTATCGATACATAAG-TTGTATCGATAC
1 AATGTATCGATACATAAGTTTGTATCGATAC
*
17825 AAAGTATCG
1 AATGTATCG
17834 CTATGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 20 0.53
32 18 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.34
Consensus pattern (31 bp):
AATGTATCGATACATAAGTTTGTATCGATAC
Found at i:17876 original size:21 final size:21
Alignment explanation
Indices: 17850--17890 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17840 AGCTACTGCC
17850 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
17871 AAGGAAATGTATTGATACAT
1 AAGGAAATGTATCGATACAT
17891 CATATCGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:20293 original size:51 final size:52
Alignment explanation
Indices: 20238--20337 Score: 157
Period size: 51 Copynumber: 1.9 Consensus size: 52
20228 CAATTCTCCG
* * *
20238 TAATCGGGGATATTTCAAATCCGATTTTATTTTC-AAAACACCAATTTTCTA
1 TAATCGGGGATACTCCAAATCCGATTTTATTTCCAAAAACACCAATTTTCTA
*
20289 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTT
1 TAATCGGGGATACTCCAAATCCGATTTTATTTCCAAAAACACCAATTTT
20338 TCACAATCGA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 30 0.68
52 14 0.32
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (52 bp):
TAATCGGGGATACTCCAAATCCGATTTTATTTCCAAAAACACCAATTTTCTA
Found at i:20354 original size:52 final size:51
Alignment explanation
Indices: 20257--20359 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
20247 ATATTTCAAA
* * * *
20257 TCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAAC
1 TCCGATTTTATTTCCAAAACACCAATTTTCTACAATCGAGAATACTCCAAC
20308 TCCGATTTTATTTCCAAAAACACCAATTTT-TCACAATCGAGAATACTCCAAC
1 TCCGATTTTATTTCC-AAAACACCAATTTTCT-ACAATCGAGAATACTCCAAC
20360 CCCGTTAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 15 0.33
52 31 0.67
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (51 bp):
TCCGATTTTATTTCCAAAACACCAATTTTCTACAATCGAGAATACTCCAAC
Found at i:20432 original size:78 final size:79
Alignment explanation
Indices: 20291--20441 Score: 225
Period size: 78 Copynumber: 1.9 Consensus size: 79
20281 ATTTTCTATA
20291 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTC
20356 CAACCCCGTTAATC
66 CAACCCCGTTAATC
* * * * * *
20370 ATCGGGGATACTCCAAC-CTCGGTTTTATTT-CTAAAACACTAATTTTTCATAATCGGGGATACT
1 ATCGGGGATACTCCAACTC-CGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACT
20433 CCAACCCCG
65 CCAACCCCG
20442 GTTTTATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 38 0.58
79 27 0.42
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (79 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTC
CAACCCCGTTAATC
Found at i:20444 original size:51 final size:51
Alignment explanation
Indices: 20370--20544 Score: 235
Period size: 51 Copynumber: 3.4 Consensus size: 51
20360 CCCGTTAATC
*
20370 ATCGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTTCATA
1 ATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCATA
* * *
20421 ATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCCTTTA
1 ATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACTAATTTTTC-ATA
* * * * * *
20473 ATCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTTACA
1 ATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCATA
20524 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
20545 TTATTTTCGA
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.01
51 63 0.59
52 42 0.40
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
ATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCATA
Found at i:20542 original size:181 final size:181
Alignment explanation
Indices: 20238--20569 Score: 506
Period size: 181 Copynumber: 1.8 Consensus size: 181
20228 CAATTCTCCG
* * * *
20238 TAATCGGGGATATTTCAAATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
1 TAATCGGGGATACTCCAAACCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACT
20303 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCGTTAA
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCGTT-A
20368 TCATC-GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTTCA
130 TCATCAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTTCA
* * *
20419 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATAC
1 TAATCGGGGATACTCCAAACCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGAGGATAC
* * * *
20484 TCCAACTCCGATTTTATTTCC-AAAACACTAATTTTTTACAATCGGGGATACTCCAACCCCGTTA
65 TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCGTTA
**
20548 TTTTCGAGGGGATACTCCAACC
130 TCATC-AGGGGATACTCCAACC
20570 CCGTTATTTC
Statistics
Matches: 135, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
180 4 0.03
181 81 0.60
182 50 0.37
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (181 bp):
TAATCGGGGATACTCCAAACCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCGTTAT
CATCAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTTCA
Found at i:20567 original size:28 final size:28
Alignment explanation
Indices: 20527--20600 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
20517 TTTTACAATC
20527 GGGGATACTCCAACCCCGTTATTT-TCGA
1 GGGGATACTCCAACCCCGTTATTTCT-GA
20555 GGGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTATTTCTGA
*
20583 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
20601 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCTGA
Found at i:20624 original size:107 final size:108
Alignment explanation
Indices: 20478--20680 Score: 273
Period size: 107 Copynumber: 1.9 Consensus size: 108
20468 CTTTAATCGA
* * * *
20478 GGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTTACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAACCC
* *
20543 CGTT-ATTTTCGAGGGGATACTCCAACCCCGTTATTTCTGAGG
66 CGTTAATCTCCGAGGGGATACTCCAACCCCGTTATTTCTGAGG
* * * * * *
20585 GGATACTCTAACCCCGACTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATATTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAACCC
* *
20650 TGTTAATCTCCGAGGGGATATTCCAACCCCG
66 CGTTAATCTCCGAGGGGATACTCCAACCCCG
20681 GTTTTATTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
107 58 0.72
108 23 0.28
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (108 bp):
GGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAACCC
CGTTAATCTCCGAGGGGATACTCCAACCCCGTTATTTCTGAGG
Found at i:20646 original size:79 final size:77
Alignment explanation
Indices: 20555--20789 Score: 206
Period size: 80 Copynumber: 2.9 Consensus size: 77
20545 TTATTTTCGA
*
20555 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCG--TTTATTTCTAAAATATT
20620 AATTTCTCATAATC
64 AATTTCTCATAATC
* * * * * *
20634 GGGGATATTCCAACCCTGTTAATCTCCGAGGGGATATTCCAACCCCGGTTTTATTT-TCAAATCA
1 GGGGATACTCCAACCCCGTT-ATTTCTGAGGGGATACTCCAACCCC-G-TTTATTTCTAAAAT-A
* * *
20698 TCGAGTTT-TCACAATC
62 T-TAATTTCTCATAATC
* * * * * *
20714 GAGGATACTCAAACCCCGTTATTT-TCAAGGGGATACACCAACCCCGTTACTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCGTT--TATTTCTAAAATAT
20778 TAAATTTCTCAT
63 T-AATTTCTCAT
20790 CGGGAAATAT
Statistics
Matches: 120, Mismatches: 26, Indels: 19
0.73 0.16 0.12
Matches are distributed among these distances:
77 2 0.02
78 1 0.01
79 52 0.43
80 60 0.50
81 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGTTTATTTCTAAAATATTAA
TTTCTCATAATC
Found at i:22749 original size:1 final size:1
Alignment explanation
Indices: 22743--22817 Score: 105
Period size: 1 Copynumber: 75.0 Consensus size: 1
22733 AAAGTGTTTG
*** *
22743 AAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
22808 AAAATAAAAA
1 AAAAAAAAAA
22818 TTTAAATGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.93, C:0.00, G:0.01, T:0.05
Consensus pattern (1 bp):
A
Found at i:22774 original size:25 final size:25
Alignment explanation
Indices: 22740--22812 Score: 116
Period size: 25 Copynumber: 3.0 Consensus size: 25
22730 GATAAAGTGT
22740 TTGAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAA
22765 TTGAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAA
*
22790 ---AAAAAAAAAAAAAAAATAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAA
22812 T
1 T
22813 AAAAATTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 21 0.46
25 25 0.54
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (25 bp):
TTGAAAAAAAAAAAAAAAAAAAAAA
Found at i:22816 original size:25 final size:24
Alignment explanation
Indices: 22743--22817 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
22733 AAAGTGTTTG
*
22743 AAAAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAAAATA
*
22767 GAAAAAAAAAAAAAAAAAAAAA-A
1 AAAAAAAAAAAAAAAAAAAAAATA
*
22790 AAAAAAAAAAAAAAAATAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAATA
22814 AAAA
1 AAAA
22818 TTTAAATGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 20 0.43
24 26 0.57
ACGTcount: A:0.93, C:0.00, G:0.01, T:0.05
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAAAAAATA
Found at i:22846 original size:21 final size:21
Alignment explanation
Indices: 22822--22878 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
22812 TAAAAATTTA
22822 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
22843 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
22864 AATGTATCGATACAT
1 AATGTATCGATACAT
22879 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:22958 original size:19 final size:19
Alignment explanation
Indices: 22934--23001 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
22924 AATTCAACAA
22934 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
22953 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
22968 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
22985 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
23002 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:22973 original size:13 final size:13
Alignment explanation
Indices: 22955--22979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22945 ACATAAGTTT
22955 TGTATCGATACAA
1 TGTATCGATACAA
22968 TGTATCGATACA
1 TGTATCGATACA
22980 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:22977 original size:32 final size:32
Alignment explanation
Indices: 22936--22998 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
22926 TTCAACAATT
*
22936 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
22968 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
22999 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:23059 original size:13 final size:13
Alignment explanation
Indices: 23041--23066 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23031 CATTTTTCTG
23041 TGTATCGATACAT
1 TGTATCGATACAT
23054 TGTATCGATACAT
1 TGTATCGATACAT
23067 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23063 original size:33 final size:33
Alignment explanation
Indices: 23021--23087 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
23011 GCCAAGGAAA
***
23021 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
23054 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
23087 T
1 T
23088 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:25627 original size:52 final size:51
Alignment explanation
Indices: 25554--25723 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 51
25544 TTATTTTCGA
*
25554 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT--TTCAAAACACCAATTTTTCCACAATC
* **
25606 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTA-TTTCAAAACACCAATTTTTCC-ACAATC
* *
25658 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTT-C-AAAACACCAATTTTTCCACAATC
*
25710 GAGGATACTCCAAC
1 GGGGATACTCCAAC
25724 CTCGTTATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
51 14 0.14
52 69 0.69
53 13 0.13
54 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATTTCAAAACACCAATTTTTCCACAATC
Found at i:25743 original size:28 final size:28
Alignment explanation
Indices: 25707--25783 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
25697 ATTTTTCACA
* * *
25707 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
25735 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
25763 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
25784 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:25824 original size:212 final size:213
Alignment explanation
Indices: 25436--25830 Score: 528
Period size: 212 Copynumber: 1.8 Consensus size: 213
25426 AATTCTCCAC
* *
25436 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAAAAACACCAATTTCTTCACAATCGG
1 AATCGAGGATACTCCAACTCCGATTTTATTTCC-----AAAAAACACCAATTTCTTCACAATCGA
* *
25501 GGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCA
61 GGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCA
* * ** * *
25566 ACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTAT
126 ACCCCGGCTTTATCGCCAAAACACTAATTTCTCCACAATAGGGGATACTCCAATCCTGGTTTTAT
25631 TTTCAAAACGCCAATTTTCCTTT
191 TTTCAAAACGCCAATTTTCCTTT
* *
25654 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATA
1 AATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATA
* *
25717 CTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCC
66 CTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCC
* * * *
25782 CGGCTTTATTC-CCAAAATATTGATTTCT-CATAATTAGGGGATACTCCAA
130 CGGCTTTA-TCGCCAAAACACTAATTTCTCCACAA-TAGGGGATACTCCAA
25831 CCTCGTATTA
Statistics
Matches: 156, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
211 32 0.21
212 91 0.58
213 2 0.01
218 31 0.20
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (213 bp):
AATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATA
CTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCC
GGCTTTATCGCCAAAACACTAATTTCTCCACAATAGGGGATACTCCAATCCTGGTTTTATTTTCA
AAACGCCAATTTTCCTTT
Done.