Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1362
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: 84528
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:738 original size:2 final size:2
Alignment explanation
Indices: 731--776 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
721 TAAATAATAA
731 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
773 AG AG
1 AG AG
777 GATAATGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4310 original size:2 final size:2
Alignment explanation
Indices: 4303--4335 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4293 ATTCTGGAGA
*
4303 AT AT AT AT AA 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 AT AT A
4336 ATAAAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6948 original size:20 final size:20
Alignment explanation
Indices: 6923--6960 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6913 TCTTCCATTA
6923 ATTCTTTTGTTATTTATGAC
1 ATTCTTTTGTTATTTATGAC
6943 ATTCTTTTGTTATTTATG
1 ATTCTTTTGTTATTTATG
6961 GCCAATGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.63
Consensus pattern (20 bp):
ATTCTTTTGTTATTTATGAC
Found at i:9920 original size:17 final size:17
Alignment explanation
Indices: 9898--9930 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9888 TATTTATGAT
9898 TTTTTTTAAAAAATTAA
1 TTTTTTTAAAAAATTAA
*
9915 TTTTTTTTAAAAATTA
1 TTTTTTTAAAAAATTA
9931 TAAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTTTAAAAAATTAA
Found at i:10279 original size:7 final size:7
Alignment explanation
Indices: 10262--10296 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
10252 AAAAATAAAA
10262 AAATTTAT
1 AAATTT-T
*
10270 AAATATT
1 AAATTTT
10277 AAATTTT
1 AAATTTT
10284 AAATTTT
1 AAATTTT
10291 AAATTT
1 AAATTT
10297 ATCAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
AAATTTT
Found at i:10292 original size:14 final size:15
Alignment explanation
Indices: 10262--10307 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
10252 AAAAATAAAA
10262 AAATTTATAAATATT
1 AAATTTATAAATATT
*
10277 AAATTT-TAAATTTT
1 AAATTTATAAATATT
10291 AAATTTATCAAATATT
1 AAATTTAT-AAATATT
10307 A
1 A
10308 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 13 0.48
15 7 0.26
16 7 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTATAAATATT
Found at i:10676 original size:23 final size:23
Alignment explanation
Indices: 10639--10682 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
10629 AAAATTTTAT
10639 TAAAATTTAATTATAAAAATATA
1 TAAAATTTAATTATAAAAATATA
10662 TAAAATATTAA-TATAAAAATA
1 TAAAAT-TTAATTATAAAAATA
10683 GTTTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATTTAATTATAAAAATATA
Found at i:10761 original size:121 final size:121
Alignment explanation
Indices: 10619--10939 Score: 477
Period size: 121 Copynumber: 2.7 Consensus size: 121
10609 AAATTATTAT
**
10619 TTTAAA-AATAAAAATTTTATTAAAATTTAATTATAAAAATATATAAAATATTAATATAAAAATA
1 TTTAAATAATAAATTTTTTATTAAAATTTAATTATAAAAATATATAAAATATTAATATAAAAATA
* * * *
10683 GTTTTTATATTTTTGAATCATAGTTTAAATTATGA-CTCGACCATAAATATCTCTTG
66 ATTTTTATATTTTTGAATCATAGTTCAAATTATGAGC-CGACCATAAACATCTCTTA
10739 TTTAAATAATAAATTTTTTATTAAAATTTAATTATAAAAATATATAAAATATTAATATAAAAATA
1 TTTAAATAATAAATTTTTTATTAAAATTTAATTATAAAAATATATAAAATATTAATATAAAAATA
* *
10804 ATTTTTATATTTTTGAATCATAGTTCAAATTATGAGCCGGCCATAAACATCTTTTA
66 ATTTTTATATTTTTGAATCATAGTTCAAATTATGAGCCGACCATAAACATCTCTTA
* * **
10860 TTTAAATAATAAATTTTTTATTAAAAGTTAAATTATAAAAATATGT-AAATATTAATATAAAGTT
1 TTTAAATAATAAATTTTTTATTAAAA-TTTAATTATAAAAATATATAAAATATTAATATAAAAAT
*
10924 TATTTTTAATATTTTT
65 AATTTTT-ATATTTTT
10940 TAAATATTAA
Statistics
Matches: 184, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
120 6 0.03
121 152 0.83
122 26 0.14
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (121 bp):
TTTAAATAATAAATTTTTTATTAAAATTTAATTATAAAAATATATAAAATATTAATATAAAAATA
ATTTTTATATTTTTGAATCATAGTTCAAATTATGAGCCGACCATAAACATCTCTTA
Found at i:10787 original size:23 final size:23
Alignment explanation
Indices: 10760--10803 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
10750 AATTTTTTAT
10760 TAAAAT-TTAATTATAAAAATATA
1 TAAAATATTAA-TATAAAAATATA
10783 TAAAATATTAATATAAAAATA
1 TAAAATATTAATATAAAAATA
10804 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATATTAATATAAAAATATA
Found at i:13390 original size:50 final size:50
Alignment explanation
Indices: 13252--13560 Score: 395
Period size: 50 Copynumber: 6.2 Consensus size: 50
13242 AGTTACTTAA
* * *
13252 AGTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
* * *
13302 AGTCAACAACTA-TGCCACCTCTCTCAATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
* * * * * *
13351 CGTCAATAATTACAGCCACCTCTCTCGATTATCAAAGGTTTGTAAAAAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
** * * * * *
13401 AGTCAACAATTATTGCCACCTCTCTCAATTGTCAAAAGTTAGTAAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
* * *
13451 CGTCAACAATTATGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
* *
13501 AGTCAATAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
13551 AGTCAACAAT
1 AGTCAACAAT
13561 GGCAACACCT
Statistics
Matches: 227, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
49 43 0.19
50 184 0.81
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
Found at i:13462 original size:100 final size:99
Alignment explanation
Indices: 13253--13560 Score: 436
Period size: 100 Copynumber: 3.1 Consensus size: 99
13243 GTTACTTAAA
* * *
13253 GTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAACAACTATGCC
1 GTCAACAATTATGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAGTCAACAATTATGCC
*
13318 ACCTCTCTCAATTATCAAAGGTTGGTGAAGAATC
66 ACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATC
* ** * * *
13352 GTCAATAATTACAGCCACCTCTCTCGATTATCAAAGGTTTGTAAAAAATAGTCAACAATTATTGC
1 GTCAACAATTATGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAGTCAACAATTA-TGC
* * *
13417 CACCTCTCTCAATTGTCAAAAGTTAGTAAAGAATC
65 CACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATC
* * *
13452 GTCAACAATTATGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAATAATTACGGC
1 GTCAACAATTATGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAGTCAACAATTA-TGC
* *
13517 CACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATA
65 CACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATC
13552 GTCAACAAT
1 GTCAACAAT
13561 GGCAACACCT
Statistics
Matches: 180, Mismatches: 28, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
99 52 0.29
100 128 0.71
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (99 bp):
GTCAACAATTATGGCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAGTCAACAATTATGCC
ACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATC
Found at i:13522 original size:150 final size:149
Alignment explanation
Indices: 13252--13560 Score: 456
Period size: 150 Copynumber: 2.1 Consensus size: 149
13242 AGTTACTTAA
* * * * *
13252 AGTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAACAACTATGC
1 AGTCAACAATTATGGCCACCTCTCTCAATTATCAAAAGTTAGTAAAGAATAGTCAACAACTATGC
*
13317 CACCTCTCTCAATTATCAAAGGTTGGTGAAGAATCGTCAATAATTACAGCCACCTCTCTCGATTA
66 CACCTCTCTCAATTATCAAAGGTTGGTGAAGAATAGTCAATAATTACAGCCACCTCTCTCGATTA
*
13382 TCAAAGGTTTGTAAAAAAT
131 TCAAAGGTTGGTAAAAAAT
* * * *
13401 AGTCAACAATTATTGCCACCTCTCTCAATTGTCAAAAGTTAGTAAAGAATCGTCAACAATTATGG
1 AGTCAACAATTATGGCCACCTCTCTCAATTATCAAAAGTTAGTAAAGAATAGTCAACAACTAT-G
* * *
13466 CCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAATAATTACGGCCACCTCTCTCGATT
65 CCACCTCTCTCAATTATCAAAGGTTGGTGAAGAATAGTCAATAATTACAGCCACCTCTCTCGATT
* * *
13531 GTCAAAGGTTGGTGAAGAAT
130 ATCAAAGGTTGGTAAAAAAT
13551 AGTCAACAAT
1 AGTCAACAAT
13561 GGCAACACCT
Statistics
Matches: 142, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
149 54 0.38
150 88 0.62
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
AGTCAACAATTATGGCCACCTCTCTCAATTATCAAAAGTTAGTAAAGAATAGTCAACAACTATGC
CACCTCTCTCAATTATCAAAGGTTGGTGAAGAATAGTCAATAATTACAGCCACCTCTCTCGATTA
TCAAAGGTTGGTAAAAAAT
Found at i:18283 original size:49 final size:50
Alignment explanation
Indices: 18130--18390 Score: 174
Period size: 50 Copynumber: 5.3 Consensus size: 50
18120 TTGCTTAGAG
* ** * * * *
18130 TCAACAATTACGGTCAATTCTTTCTATTATCAAAGGTTTG-TGAAGAATAA
1 TCAACAATTACGATCACCTCTCTCAATTATCAAAAG-TTGATAAAGAATAA
* * * * **
18180 TCAACAATTATGGTCACCTCTCTCAATTGTCAAAAGTTGGTAAAGAATCG
1 TCAACAATTACGATCACCTCTCTCAATTATCAAAAGTTGATAAAGAATAA
* *
18230 TCAACAATTACGATCACC-CTCTCGATTATCAAAAGTTGATGGAA-AATAA
1 TCAACAATTACGATCACCTCTCTCAATTATCAAAAGTTGAT-AAAGAATAA
* * * * * *
18279 TCAACAATTA-TAACTACCTCTCTCAATTATTAAAA-TTAATAAAAAATTA
1 TCAACAATTACGATC-ACCTCTCTCAATTATCAAAAGTTGATAAAGAATAA
* * * * * * *
18328 TCAATAATTAC-ATTTACCTCTTTTAATTATCAAAAATTGATAAAAAATGA
1 TCAACAATTACGA-TCACCTCTCTCAATTATCAAAAGTTGATAAAGAATAA
* *
18378 TTAATAATTACGA
1 TCAACAATTACGA
18391 ATTATTCTCT
Statistics
Matches: 168, Mismatches: 34, Indels: 17
0.77 0.16 0.08
Matches are distributed among these distances:
48 4 0.02
49 73 0.43
50 90 0.54
51 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (50 bp):
TCAACAATTACGATCACCTCTCTCAATTATCAAAAGTTGATAAAGAATAA
Found at i:18357 original size:99 final size:100
Alignment explanation
Indices: 18254--18435 Score: 235
Period size: 99 Copynumber: 1.8 Consensus size: 100
18244 CACCCTCTCG
* ** *
18254 ATTATCAAAAGTTGATGGAAAATAATCAACAATTA-TAACTAC-CTCTCTCAATTATT-AAAATT
1 ATTATCAAAAATTGATAAAAAATAATCAACAATTACGAACTACTCTCT-TC-ATTATTAAAAATT
*
18316 AATAAAAAATTATCAATAATTACATTTACCTCTTTTA
64 AATAAAAAATAATCAATAATTACATTTACCTCTTTTA
* * * * *
18353 ATTATCAAAAATTGATAAAAAATGATTAATAATTACGAATTATTCTCTTCATTATTAAAAATTAA
1 ATTATCAAAAATTGATAAAAAATAATCAACAATTACGAACTACTCTCTTCATTATTAAAAATTAA
18418 TAAAAAATAATCAATAAT
66 TAAAAAATAATCAATAAT
18436 AACAAGATCT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
99 35 0.50
100 31 0.44
101 4 0.06
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (100 bp):
ATTATCAAAAATTGATAAAAAATAATCAACAATTACGAACTACTCTCTTCATTATTAAAAATTAA
TAAAAAATAATCAATAATTACATTTACCTCTTTTA
Found at i:18385 original size:50 final size:50
Alignment explanation
Indices: 18272--18435 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
18262 AAGTTGATGG
* * * * *
18272 AAAATAATCAACAATTA-TAACTACCTCTCTCAATTATTAAAATTAATAA
1 AAAATAATCAATAATTACGAATTACCTCTCTTAATTATAAAAATTAATAA
* * * *
18321 AAAATTATCAATAATTAC-ATTTACCTCTTTTAATTATCAAAAATTGATAA
1 AAAATAATCAATAATTACGAATTACCTCTCTTAATTAT-AAAAATTAATAA
* * * *
18371 AAAATGATTAATAATTACGAATTA-TTCTCTTCATTATTAAAAATTAATAA
1 AAAATAATCAATAATTACGAATTACCTCTCTTAATTA-TAAAAATTAATAA
18421 AAAATAATCAATAAT
1 AAAATAATCAATAAT
18436 AACAAGATCT
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
49 30 0.32
50 59 0.63
51 5 0.05
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (50 bp):
AAAATAATCAATAATTACGAATTACCTCTCTTAATTATAAAAATTAATAA
Found at i:20439 original size:34 final size:34
Alignment explanation
Indices: 20396--20464 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
20386 TTGTAACAGA
20396 TAGATTTCTCCAATTTCATTTTTCATTTTCTTTC
1 TAGATTTCTCCAATTTCATTTTTCATTTTCTTTC
20430 TAGATTTCTCCAATTTCATTTTTCATTTTCTTTC
1 TAGATTTCTCCAATTTCATTTTTCATTTTCTTTC
20464 T
1 T
20465 TTGATTATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.20, G:0.03, T:0.59
Consensus pattern (34 bp):
TAGATTTCTCCAATTTCATTTTTCATTTTCTTTC
Found at i:21206 original size:2 final size:2
Alignment explanation
Indices: 21199--21234 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21189 TACTATTACA
21199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21235 CAAATTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25791 original size:15 final size:13
Alignment explanation
Indices: 25754--25806 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
25744 TAGAATAATG
25754 AATATTTTTTAAA
1 AATATTTTTTAAA
*
25767 AATTTATTTTTAGTAA
1 AATAT-TTTTTA--AA
25783 AATATTTTTTAAA
1 AATATTTTTTAAA
*
25796 ATAAATTTTTT
1 A-ATATTTTTT
25807 TAATGAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 7 0.21
14 14 0.42
15 6 0.18
16 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
AATATTTTTTAAA
Found at i:26021 original size:18 final size:19
Alignment explanation
Indices: 25998--26033 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25988 TATATTAATA
*
25998 TAATTT-AATTTTTTTAAG
1 TAATTTAAAATTTTTTAAG
26016 TAATTTAAAATTTTTTAA
1 TAATTTAAAATTTTTTAA
26034 AATCTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TAATTTAAAATTTTTTAAG
Found at i:29308 original size:17 final size:17
Alignment explanation
Indices: 29285--29319 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29275 ATTTAATTAA
*
29285 AAAAAATAAACAAATAAT
1 AAAAATTAAA-AAATAAT
29303 AAAAATTAAAAAATAAT
1 AAAAATTAAAAAATAAT
29320 TTATTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAATTAAAAAATAAT
Found at i:29980 original size:23 final size:25
Alignment explanation
Indices: 29934--29980 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
29924 TGAATCATAC
29934 TTTTAAATAAAATAACATTAAATTA
1 TTTTAAATAAAATAACATTAAATTA
*
29959 TTTTAAA-AAATTAA-ATTAAATT
1 TTTTAAATAAAATAACATTAAATT
29981 CATATAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTAAATAAAATAACATTAAATTA
Found at i:30225 original size:21 final size:21
Alignment explanation
Indices: 30195--30234 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30185 ATTTGTGACT
*
30195 TTTTTTTAATTTAA-ATTTTTA
1 TTTTTATAA-TTAAGATTTTTA
30216 TTTTTATAATTAAGATTTT
1 TTTTTATAATTAAGATTTT
30235 AAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTTATAATTAAGATTTTTA
Found at i:30304 original size:30 final size:27
Alignment explanation
Indices: 30251--30311 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 27
30241 ATATATAATA
30251 AAATAAAATAAATTAAATTAATTTTAT
1 AAATAAAATAAATTAAATTAATTTTAT
* *
30278 AAATAAAAATATATTAAATTTTAATTTTTT
1 AAAT-AAAATAAATTAAA--TTAATTTTAT
30308 AAAT
1 AAAT
30312 TACTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.14
28 12 0.41
30 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATAAAATAAATTAAATTAATTTTAT
Found at i:30455 original size:9 final size:9
Alignment explanation
Indices: 30441--30473 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
30431 TTAATATATT
30441 ATTTATTAA
1 ATTTATTAA
30450 ATTTATTAA
1 ATTTATTAA
30459 ATTTAATT-A
1 ATTT-ATTAA
30468 ATTTAT
1 ATTTAT
30474 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 18 0.78
10 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTTATTAA
Found at i:30533 original size:13 final size:13
Alignment explanation
Indices: 30515--30553 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
30505 ATTTTTAATA
30515 TAAAAAATTATTT
1 TAAAAAATTATTT
*
30528 TAAAAAA-TATGT
1 TAAAAAATTATTT
30540 TAAAAAATATATTT
1 TAAAAAAT-TATTT
30554 ATGAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAAAAAATTATTT
Found at i:30866 original size:22 final size:21
Alignment explanation
Indices: 30841--30881 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30831 TATTTATAAT
* *
30841 TTTTTTTAATTTAATTTTTTTA
1 TTTTTATAA-TTAATATTTTTA
30863 TTTTTATAATTAATATTTT
1 TTTTTATAATTAATATTTT
30882 AGATTTATAT
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTATAATTAATATTTTTA
Found at i:30872 original size:17 final size:16
Alignment explanation
Indices: 30831--30873 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
30821 AGGTAAAATA
30831 TATTTATAATTTTTTT
1 TATTTATAATTTTTTT
*
30847 TAATT-TAATTTTTTT
1 TATTTATAATTTTTTT
*
30862 ATTTTTATAATT
1 -TATTTATAATT
30874 AATATTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 10 0.45
16 7 0.32
17 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTATAATTTTTTT
Found at i:30918 original size:24 final size:25
Alignment explanation
Indices: 30891--30955 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
30881 TAGATTTATA
30891 TATAATAAAATAAA-AAATAAATTT
1 TATAATAAAATAAATAAATAAATTT
*
30915 TAT-A-AAAATAAATTAAATTAATTT
1 TATAATAAAATAAA-TAAATAAATTT
30939 TATAAATAAAAATAAAT
1 TAT-AAT-AAAATAAAT
30956 TTAATTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 8 0.24
23 1 0.03
24 15 0.44
26 1 0.03
27 1 0.03
28 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TATAATAAAATAAATAAATAAATTT
Found at i:30977 original size:28 final size:31
Alignment explanation
Indices: 30946--31012 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
30936 TTTTATAAAT
* *
30946 AAAAATAAATTTAATTTA-A-AATT-ATTTA
1 AAAAATAAATTAAATTTATATAATTAAATTA
30974 AAAAATTAAATTAAATTTATATAATTAAATTA
1 AAAAA-TAAATTAAATTTATATAATTAAATTA
31006 AAAAATA
1 AAAAATA
31013 TTTTAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 5 0.15
29 12 0.36
30 1 0.03
31 6 0.18
32 9 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
AAAAATAAATTAAATTTATATAATTAAATTA
Found at i:30991 original size:19 final size:19
Alignment explanation
Indices: 30969--31007 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
30959 ATTTAAAATT
30969 ATTTAAAAAATTAAATTAA
1 ATTTAAAAAATTAAATTAA
* *
30988 ATTTATATAATTAAATTAA
1 ATTTAAAAAATTAAATTAA
31007 A
1 A
31008 AAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAAAAAATTAAATTAA
Found at i:33596 original size:3 final size:3
Alignment explanation
Indices: 33588--33619 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33578 ATTTGGTGGG
33588 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
33620 TGACCACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34005 original size:18 final size:18
Alignment explanation
Indices: 33984--34064 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 18
33974 AAAAATAATT
*
33984 AAAATATAATATTATTTA
1 AAAATATAATATTATATA
*
34002 AAAATATAAATATAATATA
1 AAAATAT-AATATTATATA
34021 AAAA-ATAA-A-TATATA
1 AAAATATAATATTATATA
* *
34036 AAAAT-TTATATAATATA
1 AAAATATAATATTATATA
* *
34053 AATATACAATAT
1 AAAATATAATAT
34065 AGAATGTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
15 11 0.22
16 2 0.04
17 11 0.22
18 13 0.26
19 13 0.26
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATAATATTATATA
Found at i:34030 original size:24 final size:24
Alignment explanation
Indices: 33969--34033 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
33959 CGAATTTAAT
*
33969 ATATAAAAAATAATTA-AAATATA
1 ATATAAAAAATAAATATAAATATA
***
33992 ATATTATTTAA-AAATATAAATATA
1 ATA-TAAAAAATAAATATAAATATA
34016 ATATAAAAAATAAATATA
1 ATATAAAAAATAAATATA
34034 TAAAAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
ATATAAAAAATAAATATAAATATA
Found at i:34033 original size:13 final size:15
Alignment explanation
Indices: 33965--34065 Score: 55
Period size: 16 Copynumber: 6.5 Consensus size: 15
33955 TATACGAATT
33965 TAATATATAAAAA-A
1 TAATATATAAAAATA
*
33979 TAAT-TA-AAATATAA
1 TAATATATAAAAAT-A
* *
33993 TATTATTTAAAAATA
1 TAATATATAAAAATA
*
34008 TAAATATAATATAAAAAA
1 T-AATAT-ATA-AAAATA
*
34026 TAAATATATAAAAATT
1 T-AATATATAAAAATA
*
34042 TATATAATATAAATATA
1 TA-AT-ATATAAAAATA
*
34059 CAATATA
1 TAATATA
34066 GAATGTATCG
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
12 4 0.06
13 2 0.03
14 8 0.12
15 7 0.11
16 18 0.27
17 15 0.23
18 12 0.18
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATATATAAAAATA
Found at i:37397 original size:34 final size:35
Alignment explanation
Indices: 37358--37440 Score: 84
Period size: 34 Copynumber: 2.4 Consensus size: 35
37348 ATTTGATCGG
37358 ATTAAAATTTAAA-AATATATT-TTTTATTTATTT-A
1 ATTAAAATTTAAATAA-ATATTATTTTA-TTATTTAA
* *
37392 ATT-AAATATAAATTAAATTTTATTTTATTATTTAA
1 ATTAAAATTTAAA-TAAATATTATTTTATTATTTAA
*
37427 ATAAAAATTTAAAT
1 ATTAAAATTTAAAT
37441 TATTAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
33 8 0.20
34 13 0.32
35 11 0.28
36 8 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
ATTAAAATTTAAATAAATATTATTTTATTATTTAA
Found at i:37413 original size:30 final size:31
Alignment explanation
Indices: 37379--37441 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
37369 AAAATATATT
*
37379 TTTTA-TTTATTTAATTAAATATAAA-TTAAA
1 TTTTATTTTA-TTAATTAAATAAAAATTTAAA
*
37409 TTTTATTTTATTATTTAAATAAAAATTTAAA
1 TTTTATTTTATTAATTAAATAAAAATTTAAA
37440 TT
1 TT
37442 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTTATTTTATTAATTAAATAAAAATTTAAA
Found at i:38412 original size:5 final size:5
Alignment explanation
Indices: 38402--38453 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
38392 AAAAATTTGG
* *
38402 TAAAA TAAAA TAAAA TAAAA T--AA TAAATT TAAAA TAAAA TAAAA TTAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA-A TAAAA TAAAA TAAAA TAAAA
38451 TAA
1 TAA
38454 TAAATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.08
5 33 0.82
6 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:38417 original size:29 final size:28
Alignment explanation
Indices: 38402--38464 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
38392 AAAAATTTGG
38402 TAAAATAAAATAAAATAAAATAATAAATT
1 TAAAATAAAATAAAAT-AAATAATAAATT
38431 TAAAATAAAATAAAATTAAATAATAAATT
1 TAAAATAAAATAAAA-TAAATAATAAATT
*
38460 AAAAA
1 TAAAA
38465 CATTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAAATAAAATAAAATAAATAATAAATT
Found at i:38427 original size:34 final size:31
Alignment explanation
Indices: 38374--38457 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 31
38364 AAAGAAAGAG
*
38374 AAATAAATAAAAAATAATAAAAATTTGGTAAAATA
1 AAATAAA-ATAAAATAATAAAAA-TT--TAAAATA
38409 AAATAAAATAAAATAAT--AAATTTAAAATA
1 AAATAAAATAAAATAATAAAAATTTAAAATA
*
38438 AAATAAAATTAAATAATAAA
1 AAATAAAATAAAATAATAAA
38458 TTAAAAACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 23 0.51
31 3 0.07
32 3 0.07
34 9 0.20
35 7 0.16
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (31 bp):
AAATAAAATAAAATAATAAAAATTTAAAATA
Found at i:38628 original size:21 final size:20
Alignment explanation
Indices: 38580--38637 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
38570 GTCAATTATA
*
38580 AAAAATAAAAA-TATTT-TT
1 AAAAATAAAAATTATTTAAT
38598 AAAAATTAAAAATTATTTAAAT
1 AAAAA-TAAAAATTATTT-AAT
38620 AAAAATAAAAATTATTTA
1 AAAAATAAAAATTATTTA
38638 TATTTATTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 5 0.14
19 6 0.17
20 6 0.17
21 12 0.34
22 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATAAAAATTATTTAAT
Found at i:45440 original size:22 final size:22
Alignment explanation
Indices: 45415--45456 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45405 TATAATTAAA
*
45415 TTTAAATAAATAATATTTTATT
1 TTTAAATAAATAATAATTTATT
*
45437 TTTAATTAAATAATAATTTA
1 TTTAAATAAATAATAATTTA
45457 AACAGCCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAATAAATAATAATTTATT
Found at i:46356 original size:2 final size:2
Alignment explanation
Indices: 46345--46375 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
46335 ATCTTCTTAT
46345 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46376 GCACTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47896 original size:23 final size:23
Alignment explanation
Indices: 47866--47915 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
47856 CTTGGAATGG
47866 AATTTATAATTCAA-AACTAGAAA
1 AATTTATAATTCAAGAA-TAGAAA
*
47889 AATTTATAATTCAAGAATGGAAA
1 AATTTATAATTCAAGAATAGAAA
47912 AATT
1 AATT
47916 AGCATATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (23 bp):
AATTTATAATTCAAGAATAGAAA
Found at i:54028 original size:2 final size:2
Alignment explanation
Indices: 54016--54052 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
54006 ATTGATACTG
54016 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54053 CGTTATCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59334 original size:15 final size:15
Alignment explanation
Indices: 59314--59345 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
59304 CTATAATTAA
59314 TGTACAAAATCAGAG
1 TGTACAAAATCAGAG
59329 TGTACAAAATCAGAG
1 TGTACAAAATCAGAG
59344 TG
1 TG
59346 ATGTAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (15 bp):
TGTACAAAATCAGAG
Found at i:61868 original size:19 final size:18
Alignment explanation
Indices: 61846--61967 Score: 52
Period size: 19 Copynumber: 7.1 Consensus size: 18
61836 AAGATATTTA
61846 AAATATTAAAAATTAATAT
1 AAATATTAAAAATT-ATAT
*
61865 AAATA-TAATATAAATATAT
1 AAATATTAA-A-AATTATAT
*
61884 AAATATATTAAAATT-TAT
1 AAATAT-TAAAAATTATAT
61902 ATAATA-T--AAA-TATA-
1 A-AATATTAAAAATTATAT
* *
61916 AAATTATTAAAATTTATGT
1 AAA-TATTAAAAATTATAT
61935 -AATA-TAAATAATTA-AT
1 AAATATTAAA-AATTATAT
*
61951 --ATATTAAAATTTATAT
1 AAATATTAAAAATTATAT
61967 A
1 A
61968 TTGTAAATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 34
0.65 0.07 0.28
Matches are distributed among these distances:
13 2 0.03
14 4 0.05
15 13 0.16
16 11 0.14
17 9 0.11
18 12 0.15
19 22 0.28
20 4 0.05
21 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
AAATATTAAAAATTATAT
Found at i:61875 original size:11 final size:11
Alignment explanation
Indices: 61855--61916 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
61845 AAAATATTAA
61855 AAAT-TAATAT
1 AAATATAATAT
61865 AAATATAATAT
1 AAATATAATAT
61876 AAATAT-ATA-
1 AAATATAATAT
*
61885 AATATATTAAAAT
1 AA-ATA-TAATAT
**
61898 TTATATAATAT
1 AAATATAATAT
61909 AAATATAA
1 AAATATAA
61917 AATTATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
9 2 0.05
10 10 0.24
11 24 0.59
12 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATATAATAT
Found at i:61924 original size:31 final size:33
Alignment explanation
Indices: 61867--62005 Score: 178
Period size: 32 Copynumber: 4.3 Consensus size: 33
61857 ATTAATATAA
61867 ATATAATATAAATATATAAATATATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
61900 ATATAATATAAATATA-AAAT-TATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
* *
61931 ATGTAATATAAATA-ATTAATATATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
* * * * *
61963 ATATATTGTAAAT-TATTAATGTATAAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
61995 ATATAAATATA
1 ATAT-AATATA
62006 TAAAATTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
30 1 0.01
31 27 0.29
32 45 0.48
33 20 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAATTT
Found at i:62396 original size:25 final size:26
Alignment explanation
Indices: 62329--62403 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
62319 AAATAAATTT
* **
62329 ATTTGATAATAAATAATAAATTTTAAA
1 ATTT-ATAATAAATTATTTATTTTAAA
62356 ATTTATAATAAATTATTTATTTTAAA
1 ATTTATAATAAATTATTTATTTTAAA
62382 ATTT-TAAT---TT-TTTATTTTAAA
1 ATTTATAATAAATTATTTATTTTAAA
62403 A
1 A
62404 CTAAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.27
22 2 0.04
25 4 0.09
26 23 0.51
27 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
ATTTATAATAAATTATTTATTTTAAA
Found at i:65446 original size:2 final size:2
Alignment explanation
Indices: 65439--65467 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
65429 AGTTTTTACA
65439 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
65468 AGATTTATTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:67060 original size:3 final size:3
Alignment explanation
Indices: 67052--67077 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
67042 GGACGTTTGG
67052 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
67078 GCAGAAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:67323 original size:2 final size:2
Alignment explanation
Indices: 67316--67342 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67306 CTTAATAATG
67316 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
67343 GCATACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69934 original size:2 final size:2
Alignment explanation
Indices: 69927--69964 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
69917 CACTGGGGAC
69927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69965 GCAAGAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70645 original size:25 final size:27
Alignment explanation
Indices: 70617--70667 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
70607 AAAAAACATT
*
70617 TTTATTTTA-CTTAAAAAT-TTATAAC
1 TTTATTATATCTTAAAAATATTATAAC
70642 TTTATTATATCTTAAAAATATTATAA
1 TTTATTATATCTTAAAAATATTATAA
70668 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 9 0.39
27 6 0.26
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTATTATATCTTAAAAATATTATAAC
Found at i:71629 original size:17 final size:17
Alignment explanation
Indices: 71596--71648 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
71586 CAATTTCAAT
* *
71596 TAATAAATGAATAAAAA
1 TAATAAATTATTAAAAA
* *
71613 TATTTAATTATTAAAAA
1 TAATAAATTATTAAAAA
*
71630 AAATAAATTATTAAAAA
1 TAATAAATTATTAAAAA
71647 TA
1 TA
71649 CTTATTTTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TAATAAATTATTAAAAA
Found at i:72688 original size:14 final size:14
Alignment explanation
Indices: 72652--72693 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
72642 AATTAAATAA
*
72652 AAAATTATAAATATT
1 AAAATTTTAAA-ATT
72667 AAAA--TTAAAATT
1 AAAATTTTAAAATT
72679 AAAATTTTAAAATT
1 AAAATTTTAAAATT
72693 A
1 A
72694 CTATATAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
14 9 0.38
15 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTTTAAAATT
Found at i:72688 original size:20 final size:21
Alignment explanation
Indices: 72652--72693 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
72642 AATTAAATAA
72652 AAAATTATAAATATTAAAATT
1 AAAATTATAAATATTAAAATT
*
72673 AAAATTA-AAATTTTAAAATT
1 AAAATTATAAATATTAAAATT
72693 A
1 A
72694 CTATATAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTATAAATATTAAAATT
Found at i:73142 original size:18 final size:18
Alignment explanation
Indices: 73116--73155 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
73106 TTTACTTAAT
* *
73116 AATATTAAATATGATATA
1 AATAATAAATATAATATA
73134 AATAATAAATATAATATA
1 AATAATAAATATAATATA
73152 AATA
1 AATA
73156 TTTCAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATAATAAATATAATATA
Found at i:75741 original size:2 final size:2
Alignment explanation
Indices: 75734--75776 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
75724 CTTTTCAAAT
75734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75776 T
1 T
75777 TCTCGACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76423 original size:33 final size:31
Alignment explanation
Indices: 76354--76435 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 31
76344 ACATATAGCT
* *
76354 ATATTATTATATATAATTTCATTAAACATATAA
1 ATATT-TTATAT-TAATATCATTAAAAATATAA
*
76387 ATATTTTATATTAATATCATTAAATAAATATTA
1 ATATTTTATATTAATATCATT-AA-AAATATAA
*
76420 ATATTATAT-TTAATAT
1 ATATTTTATATTAATAT
76436 TTAATAAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
31 9 0.21
32 15 0.35
33 19 0.44
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATTTTATATTAATATCATTAAAAATATAA
Found at i:76427 original size:31 final size:29
Alignment explanation
Indices: 76358--76435 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 29
76348 ATAGCTATAT
* *
76358 TATTATATATAATTTCATTAAACATATAAA
1 TATTATAT-TAATATCATTAAAAATATAAA
*
76388 TATTTTATATTAATATCATTAAATAAATATTAA
1 TA--TTATATTAATATCATT-AA-AAATATAAA
76421 TATTATATTTAATAT
1 TATTATA-TTAATAT
76436 TTAATAAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 2 0.05
31 14 0.35
32 15 0.38
33 9 0.22
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTATATTAATATCATTAAAAATATAAA
Found at i:77429 original size:11 final size:10
Alignment explanation
Indices: 77398--77435 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
77388 ATTTGATAAA
77398 TTTATATATT
1 TTTATATATT
77408 TTTAT-TATT
1 TTTATATATT
77417 TTTATGATATT
1 TTTAT-ATATT
77428 TTT-TATAT
1 TTTATATAT
77436 CATATCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.50
10 6 0.23
11 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTATATATT
Found at i:81034 original size:6 final size:6
Alignment explanation
Indices: 81026--81079 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
81016 CTATCTAATA
* *
81026 TATATA TATATG TATATG TATTATG --TATG TATATG TATATG --CATG
1 TATATG TATATG TATATG TA-TATG TATATG TATATG TATATG TATATG
81071 TATATG TAT
1 TATATG TAT
81080 GTATGTGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
4 7 0.17
6 29 0.73
7 4 0.10
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:81041 original size:10 final size:10
Alignment explanation
Indices: 81023--81083 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
81013 TTCCTATCTA
*
81023 ATATATATAT
1 ATATGTATAT
81033 ATATGTATATGT
1 ATATGTATA--T
*
81045 ATTATGTATGT
1 A-TATGTATAT
81056 ATATGTATAT
1 ATATGTATAT
**
81066 GCATGTATAT
1 ATATGTATAT
*
81076 GTATGTAT
1 ATATGTAT
81084 GTGTTGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 31 0.74
11 2 0.05
12 2 0.05
13 7 0.17
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (10 bp):
ATATGTATAT
Found at i:81056 original size:11 final size:10
Alignment explanation
Indices: 81032--81083 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
81022 AATATATATA
*
81032 TATATGTATA
1 TATATGTATG
*
81042 TGTAT-TATG
1 TATATGTATG
* *
81051 TATGTATATG
1 TATATGTATG
*
81061 TATATGCATG
1 TATATGTATG
81071 TATATGTATG
1 TATATGTATG
81081 TAT
1 TAT
81084 GTGTTGAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 6 0.18
10 27 0.82
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (10 bp):
TATATGTATG
Found at i:83236 original size:3 final size:3
Alignment explanation
Indices: 83228--83254 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
83218 ATGTCAGCTG
83228 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
83255 GAGTAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Done.