Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold552
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: 68056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:4318 original size:2 final size:2
Alignment explanation
Indices: 4311--4352 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4301 AACTAGGTTG
4311 AT AT AT 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 AT AT AT
4353 GTTATTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7002 original size:21 final size:21
Alignment explanation
Indices: 6962--7002 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6952 AGTAGAATAT
*
6962 AAAAAAATAAATTGATTATGA
1 AAAAAAATAAATTGAATATGA
6983 AAAAAAATTAAATT-AATATG
1 AAAAAAA-TAAATTGAATATG
7003 GCAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAAAATAAATTGAATATGA
Found at i:8643 original size:30 final size:29
Alignment explanation
Indices: 8609--8670 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
8599 ATAAGTTATT
* *
8609 AAAAAGTACAAGAATTTTTTTTAAGATGAA
1 AAAAAGCACAAGAATTTTTGTTAA-ATGAA
*
8639 AAAAAGCACAAGAATTTTTGTTCAATGAA
1 AAAAAGCACAAGAATTTTTGTTAAATGAA
8668 AAA
1 AAA
8671 TTTGAATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (29 bp):
AAAAAGCACAAGAATTTTTGTTAAATGAA
Found at i:9808 original size:2 final size:2
Alignment explanation
Indices: 9801--9834 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9791 TACTTTTTAA
9801 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
9835 TGGAACCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13657 original size:2 final size:2
Alignment explanation
Indices: 13650--13682 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
13640 TGCATTGCTC
13650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
13683 CTCATTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17630 original size:19 final size:19
Alignment explanation
Indices: 17592--17630 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17582 ATTGTATTAA
*
17592 AGTTTTTGACATTTGTTAT
1 AGTTTTTGACATTTGATAT
17611 AGTTTTTGAC-TTGTGATAT
1 AGTTTTTGACATT-TGATAT
17630 A
1 A
17631 AAGATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (19 bp):
AGTTTTTGACATTTGATAT
Found at i:18001 original size:20 final size:19
Alignment explanation
Indices: 17961--18022 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
17951 TATGAAAAAT
17961 AAAAATT-ACAAAAATTAAA
1 AAAAATTCA-AAAAATTAAA
*
17980 AATAATTCAAAAAATTAGAA
1 AAAAATTCAAAAAATTA-AA
**
18000 AAAAATTCTGAAAATTAAA
1 AAAAATTCAAAAAATTAAA
18019 AAAA
1 AAAA
18023 TATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAAATTCAAAAAATTAAA
Found at i:18022 original size:9 final size:9
Alignment explanation
Indices: 17961--18030 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
17951 TATGAAAAAT
*
17961 AAAAATTAC
1 AAAAATTAA
17970 AAAAATTAA
1 AAAAATTAA
*
17979 AAATAATTCA
1 AAA-AATTAA
17989 AAAAATTAGAA
1 AAAAATT--AA
**
18000 AAAAATTCT
1 AAAAATTAA
*
18009 GAAAATTAA
1 AAAAATTAA
18018 AAAAATATAA
1 AAAAAT-TAA
18028 AAA
1 AAA
18031 TAAATAATAC
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 26 0.54
10 14 0.29
11 8 0.17
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:19660 original size:31 final size:30
Alignment explanation
Indices: 19587--19648 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
19577 AGGTTTTTAT
*
19587 TTAA-TTTATTTATTTATAGTTATTTTTAAA
1 TTAATTTTATTTATTTATA-TTATGTTTAAA
19617 TTAATTTTATTTATTTAT-TTATGTTTAAA
1 TTAATTTTATTTATTTATATTATGTTTAAA
19646 TTA
1 TTA
19649 TTCATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 13 0.43
30 4 0.13
31 13 0.43
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (30 bp):
TTAATTTTATTTATTTATATTATGTTTAAA
Found at i:24348 original size:16 final size:17
Alignment explanation
Indices: 24317--24351 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
24307 AAGGAAGATG
*
24317 AAGAAGAAAGAAAGAAA
1 AAGAAGAAAAAAAGAAA
24334 AAGAA-AAAAAAAGAAA
1 AAGAAGAAAAAAAGAAA
24350 AA
1 AA
24352 ATATGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAGAAA
Found at i:24359 original size:10 final size:10
Alignment explanation
Indices: 24323--24352 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
24313 GATGAAGAAG
*
24323 AAAGAAAGAA
1 AAAGAAAAAA
24333 AAAGAAAAAA
1 AAAGAAAAAA
24343 AAAGAAAAAA
1 AAAGAAAAAA
24353 TATGAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:31132 original size:13 final size:13
Alignment explanation
Indices: 31114--31139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31104 AATCCTAAAA
31114 AAAAAAAAAAACC
1 AAAAAAAAAAACC
31127 AAAAAAAAAAACC
1 AAAAAAAAAAACC
31140 TTTTCACCCT
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:32234 original size:27 final size:27
Alignment explanation
Indices: 32191--33032 Score: 1282
Period size: 27 Copynumber: 31.0 Consensus size: 27
32181 GTGGCATTTT
* *
32191 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
32219 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
32246 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
32274 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
32301 CTTTTAAAATCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
32329 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32356 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32383 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** *
32410 CTTTTAAGTCCACAACTCTATGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
32438 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32465 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
32492 CTTTTAAGTCCACAACTCTGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
32520 CTTTTAA-TACCACAACTCTGTGGCACC
1 CTTTTAAGT-CCACAACTCCGTGGCACC
*
32547 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
32574 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32601 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32628 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32655 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32682 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
32709 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
32737 CTGTTTAAGACCACAACTCCGTGGCACC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
* * **
32765 CTTTTAAGTCCATAACTTCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
32792 CTTTTAAGTCCACAACTCTGTGGCAACC
1 CTTTTAAGTCCACAACTCCGTGGC-ACC
* *
32820 TTTTTAAGTCCACAACTCCGGGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32847 CTTTTAAGT-CACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32873 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32900 CTTTTAAGTCCACAACTCCGT-GCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
32926 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
32954 C-TTTAAGTCCACAACT-CTTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
32979 CTTTTAAGTCCACAACTCC-TGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
33005 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
33032 C
1 C
33033 ATTTCAAAGC
Statistics
Matches: 752, Mismatches: 47, Indels: 31
0.91 0.06 0.04
Matches are distributed among these distances:
25 3 0.00
26 95 0.13
27 497 0.66
28 136 0.18
29 21 0.03
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:32535 original size:191 final size:189
Alignment explanation
Indices: 32191--33032 Score: 1309
Period size: 191 Copynumber: 4.4 Consensus size: 189
32181 GTGGCATTTT
* *
32191 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT-AAGT
* * *
32256 CCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCACAACTCC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCC
* *
32321 GTGGTACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
128 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
32383 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTATGGCATTCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CCCTTTTAAGTC
*
32448 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGT
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGT
* *
32513 GGCATTCCTTTTAA-TACCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
130 GGCA-CCCTTTTAAGT-CCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
32574 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
32639 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
*
32704 GCACCCTTTTAAGTCCACAACTCTGTGGCATCCCTGTTTAAGACCACAACTCCGTGGCACC
131 GCACCCTTTTAAGTCCACAACTCTGTGGCA-CCCT-TTTAAGTCCACAACTCCGTGGCACC
* * ** *
32765 CTTTTAAGTCCATAACTTCGTGGCATTCTTTTAAGTCCACAACTCTGTGGCAACCTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGC-ACCCTTTTAAGTC
*
32830 CACAACTCCGGGGCACCCTTTTAAGT-CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGT
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGT
*
32894 GGCACCCTTTTAAGTCCACAACTCCGT-GCACCCTTTTAAGTCCACAACTCCGTGGCATCC
130 GGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
32954 C-TTTAAGTCCACAACT-CTTGGCACCCTTTTAAGTCCACAACTC-CTGGCATCCTTTTAAATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
*
33016 ACAACTCTGTGGCACCC
66 ACAACTCCGTGGCACCC
33033 ATTTCAAAGC
Statistics
Matches: 602, Mismatches: 40, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
185 26 0.04
186 4 0.01
187 24 0.04
188 36 0.06
189 31 0.05
190 105 0.17
191 328 0.54
192 48 0.08
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (189 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
GCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:32570 original size:218 final size:216
Alignment explanation
Indices: 32191--33032 Score: 1320
Period size: 218 Copynumber: 3.9 Consensus size: 216
32181 GTGGCATTTT
* * *
32191 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
32256 CCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCACAACTCC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAATA-CCACAACTCC
* * *
32321 GTGGTACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTT
128 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTT
32386 TTAAGTCCACAACTCCGTGGCACC
193 TTAAGTCCACAACTCCGTGGCACC
** *
32410 CTTTTAAGTCCACAACTCTATGGCATTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
32475 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATTCCTTTTAATACCACAACTCTG
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CCCTTTTAATACCACAACTCCG
32540 TGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTT
129 TGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTT
32605 TAAGTCCACAACTCCGTGGCACC
194 TAAGTCCACAACTCCGTGGCACC
32628 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
32693 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCCCTGTTTAAGACCACAACTCCG
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CCCT-TTTAATACCACAACTCCG
* ** *
32758 TGGCACCCTTTTAAGTCCATAACT-TCGTGGCATTCTTTTAAGTCCACAACTCTGTGGCAACCTT
129 TGGCACCCTTTTAAGTCCACAACTCT-GTGGCACCCTTTTAAGTCCACAACTCTGTGGC-ACCCT
*
32822 TTTAAGTCCACAACTCCGGGGCACC
192 TTTAAGTCCACAACTCCGTGGCACC
32847 CTTTTAAGT-CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
32911 ACAACTCCGT-GCACCCTTTTAAGTCCACAACTCCGTGGCATCCC-TTTAAGT-CCACAACT-CT
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CCCTTTTAA-TACCACAACTCCG
* * *
32972 TGGCACCCTTTTAAGTCCACAACTC-CTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
129 TGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCC
33033 ATTTCAAAGC
Statistics
Matches: 588, Mismatches: 28, Indels: 21
0.92 0.04 0.03
Matches are distributed among these distances:
212 3 0.01
213 29 0.05
214 24 0.04
215 13 0.02
217 118 0.20
218 317 0.54
219 84 0.14
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (216 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAATACCACAACTCCGTG
GCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTA
AGTCCACAACTCCGTGGCACC
Found at i:33070 original size:32 final size:32
Alignment explanation
Indices: 33015--33424 Score: 662
Period size: 32 Copynumber: 12.8 Consensus size: 32
33005 CTTTTAAATC
* *
33015 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
33046 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
33078 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
33110 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
33142 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
33174 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
33206 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
33238 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
33270 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
33302 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
33334 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
33366 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
33398 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
33425 TCACCATTTT
Statistics
Matches: 355, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
31 15 0.04
32 337 0.95
33 3 0.01
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:34693 original size:17 final size:17
Alignment explanation
Indices: 34673--34708 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34663 AAGGAAGATG
* *
34673 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
34690 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
34707 AA
1 AA
34709 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:35091 original size:2 final size:2
Alignment explanation
Indices: 35078--35108 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
35068 TTATTTTATT
*
35078 TA TA TG 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 TA TA T
35109 TTTGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41914 original size:22 final size:21
Alignment explanation
Indices: 41889--41932 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
41879 TCTCACTCAC
* *
41889 TAATAATTACTTTTAAATATAT
1 TAATAATTAATATTAAAT-TAT
*
41911 TAATATTTAATATTAAATTAT
1 TAATAATTAATATTAAATTAT
41932 T
1 T
41933 GATATTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATAATTAATATTAAATTAT
Found at i:41944 original size:22 final size:22
Alignment explanation
Indices: 41901--41950 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
41891 ATAATTACTT
*
41901 TTAAATATATTAATATTTAATA
1 TTAAATATATTAATATTAAATA
*
41923 TTAAAT-TATTGATATTGAAATA
1 TTAAATATATTAATATT-AAATA
*
41945 TAAAAT
1 TTAAAT
41951 CCAATCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TTAAATATATTAATATTAAATA
Found at i:42107 original size:50 final size:50
Alignment explanation
Indices: 42032--42240 Score: 330
Period size: 50 Copynumber: 4.2 Consensus size: 50
42022 AGTTGTTGCC
* * * *
42032 ATTGTTGACTATTTTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
42082 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
42132 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
42182 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
42232 ATTGTTGAC
1 ATTGTTGAC
42241 TCTAAGTATA
Statistics
Matches: 147, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 146 0.99
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:46701 original size:50 final size:50
Alignment explanation
Indices: 46632--46840 Score: 330
Period size: 50 Copynumber: 4.2 Consensus size: 50
46622 AGTTGTTGCC
* * ***
46632 ATTGTTGACTATTTTTCACCAACCTTTGACAATAGAGAGAGGTGGTTGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
46682 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
46732 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
46782 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
46832 ATTGTTGAC
1 ATTGTTGAC
46841 TCTAAGTATA
Statistics
Matches: 148, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 147 0.99
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:51211 original size:29 final size:30
Alignment explanation
Indices: 51179--51236 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
51169 TTAGTAAAAT
*
51179 TTTTAATTTATATTTAAAT-TATTTTTAAC
1 TTTTAATTTATATTTAAATAAATTTTTAAC
51208 TTTTAATTTATATTTAAATAAATTTTTAA
1 TTTTAATTTATATTTAAATAAATTTTTAA
51237 ATCAATCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAATTTATATTTAAATAAATTTTTAAC
Found at i:51504 original size:11 final size:11
Alignment explanation
Indices: 51490--51537 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
51480 ATATAACATA
51490 AAAAAATAATT
1 AAAAAATAATT
*
51501 AAAATATAA-T
1 AAAAAATAATT
*
51511 ATAAAAATAATA
1 A-AAAAATAATT
51523 AAAAAATAATAT
1 AAAAAATAAT-T
51535 AAA
1 AAA
51538 TAGATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 2 0.07
11 24 0.80
12 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAAAATAATT
Found at i:51508 original size:24 final size:26
Alignment explanation
Indices: 51467--51523 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 26
51457 TTAGAAATAG
*
51467 ATAATAATTTTAAATATAACATAAAA
1 ATAATAATTTAAAATATAACATAAAA
*
51493 A-AATAA-TTAAAATATAATATAAAA
1 ATAATAATTTAAAATATAACATAAAA
51517 ATAATAA
1 ATAATAA
51524 AAAAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 17 0.61
25 10 0.36
26 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATAATTTAAAATATAACATAAAA
Found at i:51519 original size:22 final size:22
Alignment explanation
Indices: 51491--51537 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
51481 TATAACATAA
* *
51491 AAAAATAATTAAAATATAATAT
1 AAAAATAATAAAAAAATAATAT
51513 AAAAATAATAAAAAAATAATAT
1 AAAAATAATAAAAAAATAATAT
51535 AAA
1 AAA
51538 TAGATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAATAATAAAAAAATAATAT
Found at i:51528 original size:24 final size:23
Alignment explanation
Indices: 51478--51537 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
51468 TAATAATTTT
* *
51478 AAATATAACATAAAAAAATAATTA
1 AAATATAATATAAAAAAAT-ATAA
51502 AAATATAATATAAAAATAATA-AA
1 AAATATAATATAAAAA-AATATAA
51525 AAA-ATAATATAAA
1 AAATATAATATAAA
51538 TAGATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.30
23 4 0.12
24 16 0.48
25 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
AAATATAATATAAAAAAATATAA
Found at i:51601 original size:8 final size:7
Alignment explanation
Indices: 51590--51648 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 7
51580 AATTAAAATT
51590 TATATAA
1 TATATAA
51597 CTATATAA
1 -TATATAA
51605 TATATTAA
1 TATA-TAA
*
51613 -ATAAAA
1 TATATAA
51619 T-TATAA
1 TATATAA
51625 TATATAA
1 TATATAA
*
51632 -AAATAA
1 TATATAA
51638 TATA-AA
1 TATATAA
51644 TATAT
1 TATAT
51649 CATAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
6 18 0.43
7 14 0.33
8 10 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (7 bp):
TATATAA
Found at i:51639 original size:60 final size:57
Alignment explanation
Indices: 51501--51656 Score: 124
Period size: 60 Copynumber: 2.7 Consensus size: 57
51491 AAAAATAATT
*
51501 AAAAT-ATAATATAAAAATAATAAAAAAATAATATAAATAGATAAATATATTAAAATC
1 AAAATAAT-ATATAAAAATAATAAAAAAATAATATAAATAGATAAATATATTAAAATA
* * * * * *
51558 TAAATAATAT-TAATTATTAATAAATTAAAATTTATATAACTATAT-AATATATT-AAATA
1 AAAATAATATATAA-AAATAATAAA--AAAA-TAATATAAATAGATAAATATATTAAAATA
* *
51616 AAATTATAATATATAAAAATAATATAAATAT-ATCATAAATA
1 AAA--ATAATATATAAAAATAATAAAAAAATAAT-ATAAATA
51657 TTTTAATTAT
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
56 5 0.06
57 21 0.27
58 11 0.14
59 12 0.16
60 25 0.32
61 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (57 bp):
AAAATAATATATAAAAATAATAAAAAAATAATATAAATAGATAAATATATTAAAATA
Found at i:51647 original size:24 final size:24
Alignment explanation
Indices: 51477--51647 Score: 69
Period size: 22 Copynumber: 7.3 Consensus size: 24
51467 ATAATAATTT
* *
51477 TAAATATAACATAAAAAAATAAT-
1 TAAATATAATATATAAAAATAATA
51500 TAAA-AT-ATAATATAAAAATAATA
1 TAAATATAAT-ATATAAAAATAATA
* *
51523 -AAA-A-AATA-ATATAAAT-AGA
1 TAAATATAATATATAAAAATAATA
* * **
51542 TAAATATATTAAAATCTAAATAATA
1 TAAATATAAT-ATATAAAAATAATA
* * * *
51567 TTAATTATTAATAAATTAAAATTTATA
1 -TAAATA-TAATATA-TAAAAATAATA
*
51594 TAACTATATAATATAT-TAAAT-A-A
1 TAA--ATATAATATATAAAAATAATA
*
51617 -AATTATAATATATAAAAATAATA
1 TAAATATAATATATAAAAATAATA
51640 TAAATATA
1 TAAATATA
51648 TCATAAATAT
Statistics
Matches: 110, Mismatches: 20, Indels: 35
0.67 0.12 0.21
Matches are distributed among these distances:
19 2 0.02
20 20 0.18
21 7 0.06
22 25 0.23
23 7 0.06
24 14 0.13
25 5 0.05
26 12 0.11
27 16 0.15
28 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.35
Consensus pattern (24 bp):
TAAATATAATATATAAAAATAATA
Found at i:53966 original size:20 final size:19
Alignment explanation
Indices: 53943--54008 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 19
53933 TTAGAGGCCA
53943 AAGGTTAGGGTTAGGAGTTC
1 AAGGTTAGGGTTAGG-GTTC
*
53963 AAGGTTAAGGTTAAGGGTTC
1 AAGGTTAGGGTT-AGGGTTC
53983 AAGGTTAAGGGTTTAGGGTT-
1 AAGGTT-AGGG-TTAGGGTTC
54003 AAGGTT
1 AAGGTT
54009 TAAAGGTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 27 0.66
21 12 0.29
22 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.38, T:0.32
Consensus pattern (19 bp):
AAGGTTAGGGTTAGGGTTC
Found at i:53988 original size:7 final size:6
Alignment explanation
Indices: 53943--54029 Score: 66
Period size: 6 Copynumber: 13.0 Consensus size: 6
53933 TTAGAGGCCA
* *
53943 AAGGTT AGGGTT AGGAGTT CAAGGTT AAGGTT AAGGGTT CAAGGTT AAGGGTTT
1 AAGGTT AAGGTT AAG-GTT -AAGGTT AAGGTT AA-GGTT -AAGGTT AA-GG-TT
*
53997 AGGGTT AAGGTTT AAAGGTT AAGGTTT AAGGTT
1 AAGGTT AAGG-TT -AAGGTT AAGG-TT AAGGTT
54030 TAAGATTTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
6 29 0.43
7 28 0.41
8 11 0.16
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (6 bp):
AAGGTT
Found at i:54313 original size:21 final size:20
Alignment explanation
Indices: 54280--54339 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
54270 TGTGGCTTAG
*
54280 GGCTTAAGATTTAAGGTTTA
1 GGCTTAAGGTTTAAGGTTTA
*
54300 GGTTTAAGGCTTT-AGGTTATA
1 GGCTTAAGG-TTTAAGGTT-TA
* *
54321 GGCTTCATGTTTAAGGTTT
1 GGCTTAAGGTTTAAGGTTT
54340 TTAAGATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (20 bp):
GGCTTAAGGTTTAAGGTTTA
Found at i:54555 original size:41 final size:41
Alignment explanation
Indices: 54505--54680 Score: 153
Period size: 41 Copynumber: 4.3 Consensus size: 41
54495 AGGGATTAGA
**
54505 GTTTAAGGTTTAGGTTTAAAGTTTAAAGTTTAAGATCTAAG
1 GTTTAAGGTTTAGGTTTGGAGTTTAAAGTTTAAGATCTAAG
* * *
54546 GTTTTAGGTTTAGTGGTTTGGAGTTTGAGGTTTAA-A-CTTAAG
1 GTTTAAGGTTTA--GGTTTGGAGTTTAAAGTTTAAGATC-TAAG
* * * *
54588 ATTTAGGGTTCAAGGTTT-GAGTTT-AAGTTTAAGATTTAAG
1 GTTTAAGGTT-TAGGTTTGGAGTTTAAAGTTTAAGATCTAAG
* * * * * *
54628 GTTTGAGATTTAGGCTTGGGGTTTAAAGTTTAAGGTTTAAG
1 GTTTAAGGTTTAGGTTTGGAGTTTAAAGTTTAAGATCTAAG
54669 GTTTAAGGTTTA
1 GTTTAAGGTTTA
54681 AAGTTTAAGA
Statistics
Matches: 106, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
39 12 0.11
40 22 0.21
41 42 0.40
42 12 0.11
43 18 0.17
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.43
Consensus pattern (41 bp):
GTTTAAGGTTTAGGTTTGGAGTTTAAAGTTTAAGATCTAAG
Found at i:54907 original size:7 final size:7
Alignment explanation
Indices: 53963--54904 Score: 206
Period size: 7 Copynumber: 135.0 Consensus size: 7
53953 TTAGGAGTTC
53963 AAGG-TT
1 AAGGTTT
53969 AAGG-TT
1 AAGGTTT
*
53975 AAGGGTTC
1 AA-GGTTT
53983 AAGG-TT
1 AAGGTTT
53989 AAGGGTTT
1 AA-GGTTT
*
53997 -AGGGTT
1 AAGGTTT
54003 AAGGTTT
1 AAGGTTT
54010 AAAGG-TT
1 -AAGGTTT
54017 AAGGTTT
1 AAGGTTT
54024 AAGGTTT
1 AAGGTTT
*
54031 AAGATTT
1 AAGGTTT
*
54038 AAAAG-TT
1 -AAGGTTT
*
54045 ATGG-TT
1 AAGGTTT
*
54051 AAGGATT
1 AAGGTTT
*
54058 AAAG-TT
1 AAGGTTT
54064 -AGAGTTT
1 AAG-GTTT
*
54071 AAAGTTT
1 AAGGTTT
54078 AAAGG-TT
1 -AAGGTTT
*
54085 -AGAATTT
1 AAG-GTTT
54092 AAGGTTT
1 AAGGTTT
54099 AAGGTTT
1 AAGGTTT
54106 -AGGTTTT
1 AAGG-TTT
*
54113 AAGGTTC
1 AAGGTTT
* *
54120 GAGGTTC
1 AAGGTTT
* *
54127 ATGGTCT
1 AAGGTTT
*
54134 AAAGTTT
1 AAGGTTT
54141 AAGGTTT
1 AAGGTTT
*
54148 AGGGGTTT
1 A-AGGTTT
*
54156 -TGAGTTT
1 AAG-GTTT
*
54163 AAAGTTT
1 AAGGTTT
*
54170 AAGCTTT
1 AAGGTTT
54177 -AGGATTAT
1 AAGG-TT-T
*
54185 AAGGTTCA
1 AAGGTT-T
*
54193 AAAGTTT
1 AAGGTTT
54200 AAGGTTT
1 AAGGTTT
* *
54207 CGAGTTTT
1 -AAGGTTT
54215 AA-GTTT
1 AAGGTTT
54221 AAGGTTT
1 AAGGTTT
54228 --GGATTT
1 AAGG-TTT
* *
54234 -TGGGTT
1 AAGGTTT
*
54240 AAGGTTG
1 AAGGTTT
54247 AA-GTTT
1 AAGGTTT
*
54253 --GGGTT
1 AAGGTTT
*
54258 -AGGGTT
1 AAGGTTT
*
54264 AAGGTAT
1 AAGGTTT
** *
54271 GTGGCTT
1 AAGGTTT
* *
54278 AGGGCTT
1 AAGGTTT
*
54285 AAGATTT
1 AAGGTTT
54292 AAGGTTT
1 AAGGTTT
54299 -AGGTTT
1 AAGGTTT
54305 AAGGCTTT
1 AAGG-TTT
54313 -AGG-TT
1 AAGGTTT
*
54318 ATAGGCTT
1 A-AGGTTT
* *
54326 CATGTTT
1 AAGGTTT
54333 AAGGTTTTT
1 AAGG--TTT
*
54342 AAGATTT
1 AAGGTTT
*
54349 AAGATTT
1 AAGGTTT
*
54356 ATA-ATTT
1 A-AGGTTT
*
54363 AAGATTT
1 AAGGTTT
54370 AAGGTTT
1 AAGGTTT
*
54377 AAGATTT
1 AAGGTTT
*
54384 AAGATTT
1 AAGGTTT
*
54391 AAGATTT
1 AAGGTTT
*
54398 TAGGTTT
1 AAGGTTT
*
54405 AAAGTTT
1 AAGGTTT
*
54412 AAGATTT
1 AAGGTTT
*
54419 AAGATTT
1 AAGGTTT
**
54426 AAAATTT
1 AAGGTTT
* *
54433 GA-GATT
1 AAGGTTT
* *
54439 AAAGATT
1 AAGGTTT
54446 AAGG-TT
1 AAGGTTT
* *
54452 AGAAGATT
1 A-AGGTTT
*
54460 AAGGATT
1 AAGGTTT
* *
54467 -GGAGATT
1 AAG-GTTT
*
54474 AGGGTTT
1 AAGGTTT
*
54481 AGGGTTT
1 AAGGTTT
*
54488 AAAG-TT
1 AAGGTTT
*
54494 AAGGGATT
1 AA-GGTTT
54502 -AGAGTTT
1 AAG-GTTT
54509 AAGGTTT
1 AAGGTTT
54516 -AGGTTT
1 AAGGTTT
*
54522 AAAGTTT
1 AAGGTTT
*
54529 AAAGTTT
1 AAGGTTT
* *
54536 AAGATCT
1 AAGGTTT
54543 AAGGTTT
1 AAGGTTT
*
54550 TAGGTTT
1 AAGGTTT
*
54557 AGTGGTTT
1 A-AGGTTT
*
54565 -GGAGTTT
1 AAG-GTTT
*
54572 GAGGTTT
1 AAGGTTT
**
54579 AA-ACTT
1 AAGGTTT
*
54585 AAGATTT
1 AAGGTTT
* *
54592 AGGGTTC
1 AAGGTTT
54599 AAGGTTT
1 AAGGTTT
*
54606 GA-GTTT
1 AAGGTTT
54612 AA-GTTT
1 AAGGTTT
*
54618 AAGATTT
1 AAGGTTT
54625 AAGGTTT
1 AAGGTTT
* *
54632 GAGATTT
1 AAGGTTT
*
54639 -AGGCTT
1 AAGGTTT
**
54645 GGGGTTT
1 AAGGTTT
*
54652 AAAGTTT
1 AAGGTTT
54659 AAGGTTT
1 AAGGTTT
54666 AAGGTTT
1 AAGGTTT
54673 AAGGTTT
1 AAGGTTT
*
54680 AAAGTTT
1 AAGGTTT
*
54687 AAGATTT
1 AAGGTTT
*
54694 GAGGTTTT
1 AAGG-TTT
*
54702 AAAGTTT
1 AAGGTTT
*
54709 AGGGTTT
1 AAGGTTT
*
54716 AAAGTTTT
1 -AAGGTTT
*
54724 AAGATTTT
1 AAG-GTTT
*
54732 AAGGTTAG
1 AAGGTT-T
*
54740 AAAGTTT
1 AAGGTTT
*
54747 AA-GCTT
1 AAGGTTT
54753 AAGGGTTT
1 AA-GGTTT
*
54761 AAGATTT
1 AAGGTTT
**
54768 AAATATTT
1 -AAGGTTT
54776 AAAAGG-TT
1 --AAGGTTT
*
54784 AATGTTT
1 AAGGTTT
54791 AAGGTTT
1 AAGGTTT
54798 -AGGATTT
1 AAGG-TTT
54805 -AGAGTTT
1 AAG-GTTT
* **
54812 GACATTT
1 AAGGTTT
*
54819 AA-ATTT
1 AAGGTTT
54825 -AGGTTT
1 AAGGTTT
*
54831 TAGAGTTT
1 AAG-GTTT
*
54839 TAGGTTT
1 AAGGTTT
*
54846 AAGATTT
1 AAGGTTT
*
54853 AGAGATTTT
1 A-AG-GTTT
*
54862 AAAAGTTT
1 -AAGGTTT
54870 AAGGTTT
1 AAGGTTT
*
54877 AAAGTTT
1 AAGGTTT
* *
54884 GAGATTT
1 AAGGTTT
*
54891 AAAGTTT
1 AAGGTTT
*
54898 GAGGTTT
1 AAGGTTT
54905 GAGTTGAGGG
Statistics
Matches: 697, Mismatches: 164, Indels: 149
0.69 0.16 0.15
Matches are distributed among these distances:
5 11 0.02
6 116 0.17
7 445 0.64
8 108 0.15
9 16 0.02
10 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (7 bp):
AAGGTTT
Found at i:54964 original size:14 final size:13
Alignment explanation
Indices: 54934--54986 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
54924 AGGTGATAGG
*
54934 GTTTGATATTTGAA
1 GTTTGAGATTTG-A
54948 GTTTGAGATTTAGA
1 GTTTGAGATTT-GA
*
54962 GTTTAAGATTTGA
1 GTTTGAGATTTGA
*
54975 GATTTGAAATTT
1 G-TTTGAGATTT
54987 AAGGTTAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 29 0.88
15 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (13 bp):
GTTTGAGATTTGA
Found at i:54987 original size:21 final size:20
Alignment explanation
Indices: 54935--54989 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
54925 GGTGATAGGG
*
54935 TTTGATATTTGAAGTTTGAGA
1 TTTGAAATTT-AAGTTTGAGA
*
54956 TTT-AGAGTTTAAGATTTGAGA
1 TTTGA-AATTTAAG-TTTGAGA
54977 TTTGAAATTTAAG
1 TTTGAAATTTAAG
54990 GTTAGGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
21 23 0.82
22 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTGAAATTTAAGTTTGAGA
Found at i:56252 original size:47 final size:47
Alignment explanation
Indices: 56183--56272 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
56173 TTTTTAAATT
* *
56183 AAACTTTAATAGTTAACGTTTAATACTTTTAGTAAATAAATAAGTTG
1 AAACTTTAATAGCTAAAGTTTAATACTTTTAGTAAATAAATAAGTTG
56230 AAACTTTAATAGCTAAAGTTTAATACTTTTAGTAAATAAATAA
1 AAACTTTAATAGCTAAAGTTTAATACTTTTAGTAAATAAATAA
56273 ATAAATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (47 bp):
AAACTTTAATAGCTAAAGTTTAATACTTTTAGTAAATAAATAAGTTG
Found at i:58902 original size:69 final size:69
Alignment explanation
Indices: 58749--58886 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
58739 GCACGATATG
* * **
58749 GCATTTCTATGGAATACACACTATATTAACCTGAATACTTTCTCAACATGCCTAAATACCCACTC
1 GCATTTCTATGGAATACACACTATATCAACCTGAATACTTTCTCAAAACACCTAAATACCCACTC
58814 CCAC
66 CCAC
* * *
58818 GCATTTCTATGGAATACACATTATATCAACCTGAATATTTTCTCAAAACACCTAAATACCCATTC
1 GCATTTCTATGGAATACACACTATATCAACCTGAATACTTTCTCAAAACACCTAAATACCCACTC
58883 CCAC
66 CCAC
58887 TATAATATCT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.30
Consensus pattern (69 bp):
GCATTTCTATGGAATACACACTATATCAACCTGAATACTTTCTCAAAACACCTAAATACCCACTC
CCAC
Found at i:61159 original size:2 final size:2
Alignment explanation
Indices: 61154--61178 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61144 ACACACACAT
61154 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 T
61179 TTGGGTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:63883 original size:16 final size:15
Alignment explanation
Indices: 63856--63885 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
63846 ATGTTAATTT
63856 TATATTCTATTCTAC
1 TATATTCTATTCTAC
63871 TATATTACTATTCTA
1 TATATT-CTATTCTA
63886 AGTGTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:64526 original size:7 final size:7
Alignment explanation
Indices: 64509--64611 Score: 75
Period size: 7 Copynumber: 14.6 Consensus size: 7
64499 CCACCTTTAC
*
64509 TTAAACC
1 TTAAACT
*
64516 TTAATCT
1 TTAAACT
64523 TTAAACT
1 TTAAACT
*
64530 TTAAACC
1 TTAAACT
64537 TTAAA-T
1 TTAAACT
*
64543 TCTAAACC
1 T-TAAACT
64551 TTAAACT
1 TTAAACT
* *
64558 TTAAGCC
1 TTAAACT
*
64565 ATAAACT
1 TTAAACT
64572 TTAAA-T
1 TTAAACT
*
64578 CTTAAATT
1 -TTAAACT
*
64586 TTAAACC
1 TTAAACT
64593 TTAAACT
1 TTAAACT
*
64600 GTAAACT
1 TTAAACT
64607 CTTAA
1 -TTAA
64612 CCTTAAATCC
Statistics
Matches: 73, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
6 2 0.03
7 66 0.90
8 5 0.07
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (7 bp):
TTAAACT
Found at i:64528 original size:14 final size:14
Alignment explanation
Indices: 64508--64701 Score: 114
Period size: 14 Copynumber: 14.0 Consensus size: 14
64498 GCCACCTTTA
* *
64508 CTTAAACCTTAATC
1 CTTAAACTTTAAAC
*
64522 TTTAAACTTTAAAC
1 CTTAAACTTTAAAC
64536 CTTAAA-TTCTAAAC
1 CTTAAACTT-TAAAC
*
64550 CTTAAACTTTAAGC
1 CTTAAACTTTAAAC
* *
64564 CATAAACTTTAAAT
1 CTTAAACTTTAAAC
*
64578 CTTAAATTTTAAAC
1 CTTAAACTTTAAAC
*
64592 CTTAAACTGTAAAC
1 CTTAAACTTTAAAC
*
64606 TCTT-AACCTTAAATC
1 -CTTAAACTTTAAA-C
* *
64621 C-TAACCATTAAAC
1 CTTAAACTTTAAAC
** **
64634 CAAAAACCCTAAA-
1 CTTAAACTTTAAAC
* *
64647 CTTGAACCTTAAAC
1 CTTAAACTTTAAAC
*
64661 C-TAAACCTTAAA-
1 CTTAAACTTTAAAC
* *
64673 CTT-CACATTCAAAC
1 CTTAAAC-TTTAAAC
64687 CTTAAAACTTTAAAC
1 CTT-AAACTTTAAAC
64702 TTGAACCCTA
Statistics
Matches: 137, Mismatches: 31, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
12 3 0.02
13 29 0.21
14 91 0.66
15 12 0.09
16 2 0.01
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.32
Consensus pattern (14 bp):
CTTAAACTTTAAAC
Found at i:64604 original size:21 final size:21
Alignment explanation
Indices: 64508--64598 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
64498 GCCACCTTTA
64508 CTTAAACCTT-AATCTTTAAAC
1 CTTAAACCTTAAAT-TTTAAAC
* *
64529 TTTAAACCTTAAATTCTAAAC
1 CTTAAACCTTAAATTTTAAAC
* ****
64550 CTTAAACTTTAAGCCATAAAC
1 CTTAAACCTTAAATTTTAAAC
* *
64571 TTTAAATCTTAAATTTTAAAC
1 CTTAAACCTTAAATTTTAAAC
64592 CTTAAAC
1 CTTAAAC
64599 TGTAAACTCT
Statistics
Matches: 52, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
21 49 0.94
22 3 0.06
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (21 bp):
CTTAAACCTTAAATTTTAAAC
Found at i:64647 original size:7 final size:7
Alignment explanation
Indices: 64623--64810 Score: 52
Period size: 7 Copynumber: 27.3 Consensus size: 7
64613 CTTAAATCCT
64623 AACCATTA
1 AACC-TTA
**
64631 AACCAAA
1 AACCTTA
*
64638 AACCCTA
1 AACCTTA
*
64645 AA-CTTG
1 AACCTTA
64651 AACCTTA
1 AACCTTA
64658 AACC-TA
1 AACCTTA
64664 AACCTTA
1 AACCTTA
64671 AA-CTT-
1 AACCTTA
* *
64676 CACATTCA
1 AACCTT-A
64684 AACCTTAA
1 AACCTT-A
*
64692 AACTTTA
1 AACCTTA
*
64699 AA-CTTG
1 AACCTTA
*
64705 AACCCTA
1 AACCTTA
*
64712 AACC-CA
1 AACCTTA
*
64718 AA-CTCTG
1 AACCT-TA
64725 AACCTTA
1 AACCTTA
* *
64732 AAACTCA
1 AACCTTA
*
64739 AACCTTT
1 AACCTTA
**
64746 AA-CTCG
1 AACCTTA
**
64752 AATGTCT-
1 AACCT-TA
64759 AACCTTA
1 AACCTTA
*
64766 AACCCTA
1 AACCTTA
*
64773 ACCCTTA
1 AACCTTA
*
64780 AACTTTA
1 AACCTTA
*
64787 AACCCATA
1 AA-CCTTA
*
64795 AACCTAA
1 AACCTTA
64802 AACCTTA
1 AACCTTA
64809 AA
1 AA
64811 TCATAACCTT
Statistics
Matches: 125, Mismatches: 42, Indels: 27
0.64 0.22 0.14
Matches are distributed among these distances:
5 2 0.02
6 27 0.22
7 75 0.60
8 21 0.17
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24
Consensus pattern (7 bp):
AACCTTA
Found at i:64815 original size:21 final size:21
Alignment explanation
Indices: 64759--64816 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
64749 TCGAATGTCT
* * *
64759 AACCTTAAACCCTAACCCTTA
1 AACCTTAAACCATAAACCTAA
*
64780 AACTTTAAACCCATAAACCTAA
1 AACCTTAAA-CCATAAACCTAA
*
64802 AACCTTAAATCATAA
1 AACCTTAAACCATAA
64817 CCTTTCAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCTTAAACCATAAACCTAA
Found at i:64902 original size:2 final size:2
Alignment explanation
Indices: 64895--65044 Score: 187
Period size: 2 Copynumber: 75.0 Consensus size: 2
64885 AATTTAACCA
* * *
64895 TG TG TG TG TG TG TG TG TG TG TG TG TG TC TG TG TC TG TG TC TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * **
64937 TG TG TC TG TG TG TC TG TG TG AA TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
64979 TG TG TG CG TG TG TG TG TAG -G TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG T-G TG TG TG TG TG TG TG TG TG TG TG TG
*
65021 TG TAG -G GG TG TG TG TG TG TG TG TG
1 TG T-G TG TG TG TG TG TG TG TG TG TG
65045 AAAGGTTTAT
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
1 2 0.02
2 123 0.97
3 2 0.02
ACGTcount: A:0.03, C:0.04, G:0.47, T:0.47
Consensus pattern (2 bp):
TG
Found at i:66756 original size:85 final size:85
Alignment explanation
Indices: 66591--66803 Score: 259
Period size: 85 Copynumber: 2.5 Consensus size: 85
66581 CAATCAATTG
* * *
66591 TTCTATTTTGTTTCATTCTTATTTTCTCTTT-ATTTTAGTTTTAAACTTTTTCCTTATTTACCAA
1 TTCTAATTTGTTTCATT-TTTTTTTCT-TTTCATTTTAG--TTAAACTTTTTCCTTATTCACCAA
* * * *
66655 TATCTTTAAAATGCATAATTTCAA
62 AATCTATAAAACGCATAATGTCAA
*
66679 CTT-TTATTTGTTTCATTTTTTTTTCTTTTCATTTTAGTTAAACTTTTTCCTTATTCACCAAAAT
1 -TTCTAATTTGTTTCATTTTTTTTTCTTTTCATTTTAGTTAAACTTTTTCCTTATTCACCAAAAT
*
66743 CTATAATACGCATAATGTCAA
65 CTATAAAACGCATAATGTCAA
* *
66764 TTCTAATTTGTTTCATTTTTATTTTCTCTACATTTTAGTT
1 TTCTAATTTGTTTCATTTTT-TTTTCTTTTCATTTTAGTT
66804 TTTTTTTTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
84 2 0.02
85 58 0.53
86 20 0.18
87 15 0.14
88 12 0.11
89 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.57
Consensus pattern (85 bp):
TTCTAATTTGTTTCATTTTTTTTTCTTTTCATTTTAGTTAAACTTTTTCCTTATTCACCAAAATC
TATAAAACGCATAATGTCAA
Done.