Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold575
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: 120594
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.21
Warning! 41899 characters in sequence are not A, C, G, or T
Found at i:1436 original size:14 final size:14
Alignment explanation
Indices: 1409--1450 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1399 TATCTAACTT
*
1409 AAAAACTAAGAAATA
1 AAAAAATAA-AAATA
*
1424 AATAAATAAAAATA
1 AAAAAATAAAAATA
1438 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1451 CATTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:2278 original size:13 final size:13
Alignment explanation
Indices: 2262--2296 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2252 TTTAAACAAA
*
2262 TTAATTAACTTAT
1 TTAATTAACTAAT
2275 TTAATTAACTAAT
1 TTAATTAACTAAT
*
2288 TTAACTAAC
1 TTAATTAAC
2297 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:2827 original size:50 final size:52
Alignment explanation
Indices: 2702--2832 Score: 144
Period size: 50 Copynumber: 2.6 Consensus size: 52
2692 AAACTAAATG
* * * *
2702 AGTTACTTAATGCA-AGACTTAATTTAATGATGCTGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCTGACATAAACTAACATGGA
** *
2754 AGTTACATAATGCATGTCATTATTT-ATGATGCAT-ACAT-AACTAACATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGC-TGACATAAACTAACATGGA
*
2804 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
2833 CAGAACACGC
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
50 32 0.49
51 13 0.20
52 20 0.31
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCTGACATAAACTAACATGGA
Found at i:4559 original size:18 final size:18
Alignment explanation
Indices: 4510--4566 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
4500 TTACTCAATA
4510 TCTTTTCTCTCTTCAA-TT
1 TCTTTTCTCT-TTCAATTT
* * *
4528 TCAATCTCTTTTTCAATTT
1 TC-TTTTCTCTTTCAATTT
4547 TCTTTTCTCTTTCACATTT
1 TCTTTTCTCTTTCA-ATTT
4566 T
1 T
4567 TGTTTACTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTTTCTCTTTCAATTT
Found at i:6628 original size:20 final size:20
Alignment explanation
Indices: 6603--6648 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
6593 TTTCCAACAC
6603 TTTTTTTGAAGTTTCGTTTT
1 TTTTTTTGAAGTTTCGTTTT
* *
6623 TTTTTTTGAATTTTTGTTTT
1 TTTTTTTGAAGTTTCGTTTT
6643 TTTTTT
1 TTTTTT
6649 CAATACTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTTGAAGTTTCGTTTT
Found at i:8123 original size:52 final size:50
Alignment explanation
Indices: 8065--8181 Score: 146
Period size: 50 Copynumber: 2.3 Consensus size: 50
8055 CAAACTAAAT
* *
8065 GAGTTACTTAATGCAAG-CCTTAATTTAATGATGCAGACTTAAACTAACATGG
1 GAGTTACATAATGCAAGTCATT-ATTT-ATGATGCAGACTT-AACTAACATGG
* * *
8117 GAGTTACATAATGCATGTCATTATTTATGATGCATAGTTAACTAACATGG
1 GAGTTACATAATGCAAGTCATTATTTATGATGCAGACTTAACTAACATGG
*
8167 AAGTTACATAATGCA
1 GAGTTACATAATGCA
8182 TAACTTTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 25 0.43
51 11 0.19
52 19 0.33
53 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (50 bp):
GAGTTACATAATGCAAGTCATTATTTATGATGCAGACTTAACTAACATGG
Found at i:8191 original size:50 final size:52
Alignment explanation
Indices: 8087--8196 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 52
8077 GCAAGCCTTA
* **
8087 ATTTAATGATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGTCATT
1 ATTTAATGATGCAGACTTAAACTAACATGGAAGTTACATAATGCATAACATT
* * *
8139 ATTT-ATGATGCATAGTT-AACTAACATGGAAGTTACATAATGCATAACTTT
1 ATTTAATGATGCAGACTTAAACTAACATGGAAGTTACATAATGCATAACATT
*
8189 ATTAAATG
1 ATTTAATG
8197 CAGAACACAC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 32 0.64
51 14 0.28
52 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (52 bp):
ATTTAATGATGCAGACTTAAACTAACATGGAAGTTACATAATGCATAACATT
Found at i:13321 original size:16 final size:16
Alignment explanation
Indices: 13300--13333 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13290 TAGTAAGACA
13300 TAATTAAACACTTAAT
1 TAATTAAACACTTAAT
**
13316 TAATTAAGTACTTAAT
1 TAATTAAACACTTAAT
13332 TA
1 TA
13334 GGACATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
TAATTAAACACTTAAT
Found at i:13414 original size:17 final size:18
Alignment explanation
Indices: 13376--13419 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
13366 TCCAGGTTTT
*
13376 TTTAAC-AAATTAATTAA
1 TTTAACTAAATTAACTAA
*
13393 CTTAACTAAA-TAACTAA
1 TTTAACTAAATTAACTAA
13410 TTTAACTAAA
1 TTTAACTAAA
13420 GACAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAACTAAATTAACTAA
Found at i:13503 original size:10 final size:11
Alignment explanation
Indices: 13477--13505 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13467 AATCAAGCTC
13477 ATTGAGCTAAG
1 ATTGAGCTAAG
13488 ATTGAGCTAA-
1 ATTGAGCTAAG
13498 ATTGAGCT
1 ATTGAGCT
13506 TGAATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (11 bp):
ATTGAGCTAAG
Found at i:20038 original size:21 final size:21
Alignment explanation
Indices: 19986--20054 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
19976 AGGACCTTCC
19986 AGTCCACCTCCAAGAGGAGTT
1 AGTCCACCTCCAAGAGGAGTT
* *
20007 -GGCCCCACTCCAAGAGGAGTT
1 AGTCCAC-CTCCAAGAGGAGTT
* *
20028 AGTCTACCTCCAAG-GGAAGTC
1 AGTCCACCTCCAAGAGG-AGTT
20049 AGTCCA
1 AGTCCA
20055 ACTCGGATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 6 0.16
21 29 0.76
22 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (21 bp):
AGTCCACCTCCAAGAGGAGTT
Found at i:20341 original size:84 final size:84
Alignment explanation
Indices: 20236--20441 Score: 229
Period size: 84 Copynumber: 2.4 Consensus size: 84
20226 CCAAGAGGAG
* * * * *
20236 TCAGTCCAACTTCAAGGGTAGTTAGTCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATC
1 TCAGTTCAACTCCAAGGGTAGTAAGTCCAACTCAAATAAGAACATCCA-CATCATCGAGTCAATC
* *
20300 TCATAG-TTCGACTTCAGTTA
65 CCATAGCTT-AACTTCAGTTA
* * ** ** *
20320 TTAGTTCAACTCCAAGGGTAGTCAGTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCC
1 TCAGTTCAACTCCAAGGGTAGTAAGTCCAACTCAAATAAGAACATCCACATCATCGAGTCAATCC
20385 CATAGCTTAACTTCAGTTA
66 CATAGCTTAACTTCAGTTA
20404 TCAGTTCAACTCCAAGAGG-AGTAAGTCCAACTCCAAAT
1 TCAGTTCAACTCCAAG-GGTAGTAAGTCCAACT-CAAAT
20442 GTTATCATTT
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
83 2 0.02
84 92 0.91
85 7 0.07
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (84 bp):
TCAGTTCAACTCCAAGGGTAGTAAGTCCAACTCAAATAAGAACATCCACATCATCGAGTCAATCC
CATAGCTTAACTTCAGTTA
Found at i:20460 original size:42 final size:42
Alignment explanation
Indices: 20400--20481 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
20390 CTTAACTTCA
*
20400 GTTATCAGTTCAACTCCAAGAGGAGT-AAGTCCAACTCCAAAT
1 GTTATCAGTTCAACTCCAAGAGGACTCAA-TCCAACTCCAAAT
* *
20442 GTTATCATTTCAATTCCAAGAGGACTCAATCCAACTCCAA
1 GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAA
20482 TCAGGATATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (42 bp):
GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAAAT
Found at i:20667 original size:21 final size:21
Alignment explanation
Indices: 20641--20688 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
20631 GTTATGGATT
20641 CAACTCCAAGAGG-AGCCAGTC
1 CAACTCCAAG-GGTAGCCAGTC
**
20662 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTAGCCAGTC
20683 CAACTC
1 CAACTC
20689 GGATGAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (21 bp):
CAACTCCAAGGGTAGCCAGTC
Found at i:20749 original size:84 final size:84
Alignment explanation
Indices: 20656--20856 Score: 278
Period size: 84 Copynumber: 2.4 Consensus size: 84
20646 CCAAGAGGAG
*
20656 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
1 CCAGTCCAACTCTAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
*
20721 CATAGCTCAACTTCAATTA
66 CATAGCTCAACCTCAATTA
* * * * * *
20740 CCAGTCCAACTCTAATGGTAGTTACTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCT
1 CCAGTCCAACTCTAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
*
20805 CATAGCTCAACCTCAGTTA
66 CATAGCTCAACCTCAATTA
* * *
20824 TCAGTTCAACTCTAAGAGG-AGTCAGTCCAACTC
1 CCAGTCCAACTCTAAG-GGTAGTTAGTCCAACTC
20857 CAAGGGTAGT
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
84 99 0.98
85 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (84 bp):
CCAGTCCAACTCTAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
CATAGCTCAACCTCAATTA
Found at i:20750 original size:105 final size:105
Alignment explanation
Indices: 20013--20751 Score: 567
Period size: 105 Copynumber: 7.0 Consensus size: 105
20003 AGTTGGCCCC
* * * * * * *
20013 ACTCCAAGAGGAGTTAGTCTACCTCCAAGGGAAGTCAGTCCAACTCGGATTAGGACATCCATCGC
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
* * * *
20078 ATCAAGTCAATCCCAAAACTCAACTTCAGTTTTCAGTTCA
66 ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* * * * *
20118 ACTCCAAGAGGAGTCATTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTC
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
* * * *
20183 ATCAAGTCAGTCCCATAGCTCAACTTCAGTTCTCATTTCA
66 ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* * * * ** * * *
20223 ACCCCAAGAGGAGTCAGTCCAACTTCAAGGGTAGTTAGTCCAATTCAAATAAGAACATCCAGCAT
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCA-CCT
* * * * *
20288 -ATTGAGTCAATCTCATAGTTCGACTTCAGTTATTAGTTCA
65 CATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* * * * *
20328 ACTCCAAG-GGTAGTCAGTCCAACTCGGATGGG-A-ACA-TCCACCTC--ATCGA-GTCAATCC-
1 ACTCCAAGAGG-AGTCAGTCCAACTC-CAAGGGTAGTCAGTCCAACTCGGAT-GAGGAC-ATCCA
* ** * * * * * ** * *
20385 CAT-AGCTTAACTTCAGT--TATCAGTTCAACTCCAAGAGGAGTAAGTCCA
62 CCTCA--TCGA-GTCAATCCCAT-AGCTCAACTTC-AG-TTA-TCAGTTCA
* * * * * * ** * *
20433 ACTCCAA-ATGTTA-TCATTTCAATTCCAAGAGG-ACTCAATCCAACTCCAATCAGGATATCCAC
1 ACTCCAAGA-G-GAGTCAGTCCAACTCCAAG-GGTAGTCAGTCCAACTCGGATGAGGACATCCAC
*
20495 CTCATCGAGTCAATCCCATAGCTCCACTTCAGTTATCAGTTCA
63 CTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* *
20538 ACTCCAAGAGG-GTTCAATCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCT
1 ACTCCAAGAGGAG-TCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCT
* *
20602 CATCGAGTCAATGCCATAGCTCAACTTCAGTTAT-GGATTCA
65 CATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAG-TTCA
* *
20643 ACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTC
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
* * *
20708 ATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCA
66 ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
20748 ACTC
1 ACTC
20752 TAATGGTAGT
Statistics
Matches: 498, Mismatches: 104, Indels: 64
0.75 0.16 0.10
Matches are distributed among these distances:
100 4 0.01
101 5 0.01
102 17 0.03
103 12 0.02
104 9 0.02
105 402 0.81
106 13 0.03
107 13 0.03
108 15 0.03
109 7 0.01
110 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (105 bp):
ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
Found at i:20781 original size:189 final size:189
Alignment explanation
Indices: 20555--21102 Score: 589
Period size: 189 Copynumber: 2.9 Consensus size: 189
20545 GAGGGTTCAA
*
20555 TCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATGC-CAT
1 TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAAT-CTCAT
* *
20619 AGCTCAACTTCAGTTAT-GGATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTC
65 AGCTCAACCTCAGTTATCAG-TTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTC
20683 CAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
129 CAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
* * * * *
20744 TCCAACTCTAATGGTAGTTACTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCTCATA
1 TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCTCATA
* *
20809 GCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGTCCA
66 GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCA
* * * **
20874 ACTCGGATGAGGACATCCACCTC-T--AG-CACAACCTCAGTTATCAATTCAACTCCAAGAGGAC
131 ACTCGGATGAGGACATCCACCTCATCGAGTCA-ATCC-CA--TAGC---TCAACTTC-A-ATTAC
*
20935 TTAG
187 -CAG
* *
20939 TCCAACTCCAAGGGTAGTTAGTCCAAATCGGATGAGG--AT--A--TC--C-A--C---CTC-TA
1 TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCTCATA
* ** ** * *
20989 GCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCTTCTCCAAGGGTAGTCAATCCA
66 GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCA
** *
21054 ACTCAAATGAGGACATCCACCTCATCTAGTCAATCCCATAGCTCAACTT
131 ACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTT
21103 TAGATATCAA
Statistics
Matches: 309, Mismatches: 34, Indels: 44
0.80 0.09 0.11
Matches are distributed among these distances:
177 6 0.02
180 84 0.27
181 4 0.01
182 2 0.01
183 5 0.02
184 3 0.01
185 2 0.01
186 6 0.02
187 3 0.01
188 2 0.01
189 144 0.47
190 1 0.00
191 1 0.00
192 7 0.02
193 2 0.01
194 3 0.01
195 34 0.11
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (189 bp):
TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCTCATA
GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCA
ACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
Found at i:20790 original size:420 final size:420
Alignment explanation
Indices: 20077--20859 Score: 1106
Period size: 420 Copynumber: 1.9 Consensus size: 420
20067 ACATCCATCG
* *
20077 CATCAAGTCAATCCCAAAACTCAACTTCAGTTTTCAGTTCAACTCCAAGAGGAGTCATTCCAACT
1 CATCAAGTCAATCCCAAAACTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAATCCAACT
*
20142 CCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAGTCCCATAGCTCAAC
66 CCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAAC
* * * *
20207 TTCAGTTCTCATTTCAACCCCAAGAGGAGTCAGTCCAACTTCAAGGGTAGTTAGTCCAATTCAAA
131 TTCAGTTATCATTTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAAA
* * * * * ** *
20272 TAAGAACATCCAGCATATTGAGTCAATCTCATAGTTCGACTTCAGTTATTAGTTCAACTCCAAGG
196 TAAGAACATCCAGCATATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCAAGG
* * *
20337 GTAGTCAGTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATAGCTTAACTTCAGT
261 GTAGTCACTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACCTCAGT
20402 TATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCAATTCCAAGAGGAC
326 TATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCAATTCCAAGAGGAC
20467 TCAATCCAACTCCAATCAGGATATCCACCT
391 TCAATCCAACTCCAATCAGGATATCCACCT
* * * *
20497 CATCGAGTCAATCCCATAGCTCCACTTCAGTTATCAGTTCAACTCCAAGAGG-GTTCAATCCAAC
1 CATCAAGTCAATCCCAAAACTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAG-TCAATCCAAC
* * * * * *
20561 TCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATGCCATAGCTCAA
65 TCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAA
* * *
20626 CTTCAGTTATGGA-TTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCG
130 CTTCAGTTAT-CATTTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCA
* * * * *
20690 GATGAGGACATCCA-CCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCTA
194 AATAAGAACATCCAGCAT-ATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCA
* * * * * *
20754 ATGGTAGTTACTCCAACTTGGATGAGG-ACGTCCACCTCATCTAGTCAATCTCATAGCTCAACCT
258 AGGGTAGTCACTCCAACTCGGATG-GGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACCT
* *
20818 CAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAA
322 CAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA
20860 GGGTAGTTAG
Statistics
Matches: 315, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
419 3 0.01
420 309 0.98
421 3 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (420 bp):
CATCAAGTCAATCCCAAAACTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAATCCAACT
CCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAAC
TTCAGTTATCATTTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAAA
TAAGAACATCCAGCATATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCAAGG
GTAGTCACTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACCTCAGT
TATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCAATTCCAAGAGGAC
TCAATCCAACTCCAATCAGGATATCCACCT
Found at i:20871 original size:21 final size:21
Alignment explanation
Indices: 20824--20877 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20814 ACCTCAGTTA
* *
20824 TCAGTTCAACTCTAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
20845 TCAGTCCAACTCCAAG-GGTAG
1 TCAGTCCAACTCCAAGAGG-AG
*
20866 TTAGTCCAACTC
1 TCAGTCCAACTC
20878 GGATGAGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:20910 original size:90 final size:90
Alignment explanation
Indices: 20807--21076 Score: 423
Period size: 90 Copynumber: 3.0 Consensus size: 90
20797 GTCAATCTCA
* * *
20807 TAGCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
20872 CAACTCGGATGAGGACATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
* *
20897 TAGCACAACCTCAGTTATCAATTCAACTCCAAGAGGACTTAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
* *
20962 CAAATCGGATGAGGATATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
** * *
20987 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCTTCTCCAAGGGTAGTCAATC
1 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
**
21052 CAACTCAAATGAGGACATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
21077 ATCTAGTCAA
Statistics
Matches: 163, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 163 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (90 bp):
TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
CAACTCGGATGAGGACATCCACCTC
Found at i:20946 original size:21 final size:21
Alignment explanation
Indices: 20920--20964 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
20910 GTTATCAATT
20920 CAACTCCAAGAGG-ACTTAGTC
1 CAACTCCAAG-GGTACTTAGTC
*
20941 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTACTTAGTC
20962 CAA
1 CAA
20965 ATCGGATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
CAACTCCAAGGGTACTTAGTC
Found at i:26399 original size:41 final size:41
Alignment explanation
Indices: 26311--26402 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
26301 TGACCTTTTG
* * * *
26311 GGGGCTTTAGTGGCGTTTTTAGAATATCGCCGCTAATGTTT
1 GGGGTTTTAGTGACGTTTTTAGAATATCGCCGCTAATGCTC
* *
26352 GGGGTTTTAGTGACGTTTTTAG-TTTTGCGCCGCTAATGCTC
1 GGGGTTTTAGTGACGTTTTTAGAATAT-CGCCGCTAATGCTC
*
26393 GTGGTTTTAG
1 GGGGTTTTAG
26403 CAGCATTTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.05
41 41 0.95
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.41
Consensus pattern (41 bp):
GGGGTTTTAGTGACGTTTTTAGAATATCGCCGCTAATGCTC
Found at i:27125 original size:21 final size:20
Alignment explanation
Indices: 27099--27146 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
27089 CTTGTATGGA
27099 TTTAGGGTTT-GGGATTTAAGG
1 TTTAGGGTTTAGGG--TTAAGG
27120 TTTAGGGTTTAGGGTTAAGG
1 TTTAGGGTTTAGGGTTAAGG
*
27140 GTTAGGG
1 TTTAGGG
27147 GTTAAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 10 0.40
22 3 0.12
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.40
Consensus pattern (20 bp):
TTTAGGGTTTAGGGTTAAGG
Found at i:27128 original size:7 final size:7
Alignment explanation
Indices: 27099--27146 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
27089 CTTGTATGGA
27099 TTTAGGG
1 TTTAGGG
27106 TTT-GGG
1 TTTAGGG
*
27112 ATTTAAGG
1 -TTTAGGG
27120 TTTAGGG
1 TTTAGGG
27127 TTTAGGG
1 TTTAGGG
*
27134 TTAAGGG
1 TTTAGGG
27141 -TTAGGG
1 TTTAGGG
27147 GTTAAAAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 8 0.23
7 25 0.71
8 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:28712 original size:336 final size:332
Alignment explanation
Indices: 27830--28944 Score: 1162
Period size: 337 Copynumber: 3.3 Consensus size: 332
27820 ACCGTTTGGT
* * * * *
27830 TTAAGTAAAATAATTTTTAGTGGCATGTTTAAA-AAAATGCCAGAACTGTGCATTGAAGCTTAAT
1 TTAAGCAAATTAATTTTTACTGGCAT-TTTAAAGAAAATGCCAGAAATGTGCATTAAAGCTTAAT
* * * *
27894 AAAACGGCG-CAGTTTCCGATTAGAACTTTAACA-ATTAGTGGTGTTTTTGTTA-AAAACGCCGC
65 AAAACGGCGTC-GTTTCGGATTAGAACTTTAA-ATTTTAGTGGCG-CTTT-TTAGAAAACGCCGC
* * ** *
27956 TACTGTTGAAGCAATAGCGGCGTTTGTAC-AAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTT
126 AAATGTACAAGCAATAGCGGCGTTTGT-CTAAGAAACGCCGCAAAAGTGTCTTAAAATTTT-GTT
* * * *
28020 GAACGACGCCGTTTCTGTCCACAATTTTTAACTTAGCATTTTCTCTATATTAATTAAAC-GGTGC
189 AAACGACGCCGTTTCTGTACAC-GTTTTTAACTTAGCATTTTCTCTATATTAATTCAACGGGT-C
* * * * *
28084 CGTTTATGTTAATTTTTAGTGGCGTTTGTTCAGGAAACGCCGCAAAAGTGACTTGAAATATTGGC
252 CATTTCTGTTAATTTTT-GTGGCGTTT-TTCACGAAACGCCGCAAAAGTGACTTAAAATATTGCC
* * * *
28149 TAAAAGTCGAT-GTCTAAC
315 TAAACGAC-ATCGTTTAGC
* * * *
28167 TTAAGCAAATTAATTTTTAGTGGCATTTTAAAGGAAAAGGCCAGAAATGTGCATTAAATCTTAAC
1 TTAAGCAAATTAATTTTTACTGGCATTTTAAA-GAAAATGCCAGAAATGTGCATTAAAGCTTAAT
* * *
28232 AAAACGGTGTCGTTTCGGATTAGAACCTT-AATTCTTTGTGGCGCTTCTTTAG-AAACGCCGCAA
65 AAAACGGCGTCGTTTCGGATTAGAACTTTAAATT-TTAGTGGCGCTT-TTTAGAAAACGCCGCAA
* * * * * *
28295 ATATACAAGCTATAGCAGCGTTTGT-TCAATAAACGCCACAAAAGTGTCTTAAAATTTTTGGTAA
128 ATGTACAAGCAATAGCGGCGTTTGTCT-AAGAAACGCCGCAAAAGTGTCTTAAAA-TTTTGTTAA
* *
28359 ACGACGCCGTCTCTGTACACGCTTTTATACTTAGCATTTTCTCTATATTAATTCAACGGGTCCAT
191 ACGACGCCGTTTCTGTACACGTTTTTA-ACTTAGCATTTTCTCTATATTAATTCAACGGGTCCAT
* ** * *
28424 TTCTGTTAATTTCTTGTGGCATTTTTACATAAAACACCGCAAAAGTGACATAAAATATTGCCTAA
255 TTCTGTTAATTT-TTGTGGCGTTTTT-CACGAAACGCCGCAAAAGTGACTTAAAATATTGCCTAA
*
28489 ACGACTTCGTTTAGC
318 ACGACATCGTTTAGC
* *
28504 TTAAGCAAATTAATTTTTACTGGCGTTTTAGAAGAAAATGCCAAAAATGTG-ATTAAAGCTTAAT
1 TTAAGCAAATTAATTTTTACTGGCATTTTA-AAGAAAATGCCAGAAATGTGCATTAAAGCTTAAT
* *
28568 AAAATGGCGTCGTTTTGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGCAAAT
65 AAAACGGCGTCGTTTCGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGCAAAT
* ** * *
28633 GTACAAGCAATAGCGGCGTTTGTCTAGGATTCACCGCAAAATTGTCTTAAAATTTTGTCTAAACG
130 GTACAAGCAATAGCGGCGTTTGTCTAAGAAACGCCGCAAAAGTGTCTTAAAATTTTGT-TAAACG
* * * **
28698 ACGCCATTTCTGTACTA-GTTTTTTAACTTAGCATTTTCTCTAAATTAATCCAACGGCACCATTT
194 ACGCCGTTTCTGTAC-ACG-TTTTTAACTTAGCATTTTCTCTATATTAATTCAACGGGTCCATTT
* * * *
28762 CTCTTAATTTATAGTGGCGTTTTTGCACGAAACGCTGCAAAA-TGACTTAAAAATATTGTCT-AA
257 CTGTTAATTT-TTGTGGCGTTTTT-CACGAAACGCCGCAAAAGTGACTT-AAAATATTGCCTAAA
** *
28825 CGACCCCGTTTTGC
319 CGACATCGTTTAGC
* * * * *
28839 TTAAGAAAATTAATTTTTACTGGCGTTTTTACAGAAAATGCCAGAACTGTGCAATAAAGCTTAAT
1 TTAAGCAAATTAATTTTTACTGGC-ATTTTAAAGAAAATGCCAGAAATGTGCATTAAAGCTTAAT
* * * * *
28904 TAAACGGCGCCGTTTCAG-TTTGAACTTTAATTTTTAGTGGC
65 AAAACGGCGTCGTTTCGGATTAGAACTTTAAATTTTAGTGGC
28945 ATTTTTTGCA
Statistics
Matches: 652, Mismatches: 101, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
335 89 0.14
336 244 0.37
337 249 0.38
338 69 0.11
339 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (332 bp):
TTAAGCAAATTAATTTTTACTGGCATTTTAAAGAAAATGCCAGAAATGTGCATTAAAGCTTAATA
AAACGGCGTCGTTTCGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGCAAATG
TACAAGCAATAGCGGCGTTTGTCTAAGAAACGCCGCAAAAGTGTCTTAAAATTTTGTTAAACGAC
GCCGTTTCTGTACACGTTTTTAACTTAGCATTTTCTCTATATTAATTCAACGGGTCCATTTCTGT
TAATTTTTGTGGCGTTTTTCACGAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACATC
GTTTAGC
Found at i:28987 original size:63 final size:63
Alignment explanation
Indices: 28888--29080 Score: 379
Period size: 63 Copynumber: 3.1 Consensus size: 63
28878 GCCAGAACTG
28888 TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCATTTTT
1 TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCATTTTT
28951 TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCATTTTT
1 TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCATTTTT
29014 TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCA-TTTT
1 TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCATTTTT
29076 TGCAA
1 TGCAA
29081 AAAACACCGC
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 9 0.07
63 121 0.93
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (63 bp):
TGCAATAAAGCTTAATTAAACGGCGCCGTTTCAGTTTGAACTTTAATTTTTAGTGGCATTTTT
Found at i:29239 original size:13 final size:13
Alignment explanation
Indices: 29195--29246 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
29185 GAAACAGAAC
*
29195 AAAGGAGAAAACG
1 AAAGGAAAAAACG
*
29208 AAAGGGGTAAAAACG
1 AAA--GGAAAAAACG
29223 AAAGAGAAAAAAC-
1 AAAG-GAAAAAACG
29236 AAAGGAAAAAA
1 AAAGGAAAAAA
29247 GGGAGAGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.21
13 8 0.24
14 7 0.21
15 11 0.33
ACGTcount: A:0.67, C:0.06, G:0.25, T:0.02
Consensus pattern (13 bp):
AAAGGAAAAAACG
Found at i:29409 original size:117 final size:118
Alignment explanation
Indices: 29260--29496 Score: 449
Period size: 117 Copynumber: 2.0 Consensus size: 118
29250 AGAGGAGAAC
29260 TCAGAAATCATCAGAAACGAAGCATAACGTACGAGTCAATCTTGAGAGGATACTATCAAAGCTAG
1 TCAGAAATCA-CAGAAACGAAGCATAACGTACGAGTCAATCTTGAGAGGATACTATCAAAGCTAG
29325 AAAATTTGTGGCTAAAAGGTAAGCTTTTTTTCTTTTGAAACACTGTATCTTGAT
65 AAAATTTGTGGCTAAAAGGTAAGCTTTTTTTCTTTTGAAACACTGTATCTTGAT
29379 TCAGAAATCA-AGAAACGAAGCATAACGTACGAGTCAATCTTGAGAGGATACTATCAAAGCTAGA
1 TCAGAAATCACAGAAACGAAGCATAACGTACGAGTCAATCTTGAGAGGATACTATCAAAGCTAGA
*
29443 AAATTTGTGGCTAAAAGGTAAGCTTTTTTTTTTTTGAAACACTGTATCTTGAT
66 AAATTTGTGGCTAAAAGGTAAGCTTTTTTTCTTTTGAAACACTGTATCTTGAT
29496 T
1 T
29497 TAGGGTTTTG
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
117 107 0.91
119 10 0.09
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (118 bp):
TCAGAAATCACAGAAACGAAGCATAACGTACGAGTCAATCTTGAGAGGATACTATCAAAGCTAGA
AAATTTGTGGCTAAAAGGTAAGCTTTTTTTCTTTTGAAACACTGTATCTTGAT
Found at i:29806 original size:22 final size:22
Alignment explanation
Indices: 29776--29819 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29766 TTTGGTATTT
29776 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
29798 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
29820 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:30678 original size:30 final size:30
Alignment explanation
Indices: 30620--30678 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
30610 TTGAAAATGT
* *
30620 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
30650 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
30679 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:31857 original size:13 final size:13
Alignment explanation
Indices: 31835--31898 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
31825 CGCTATATAT
*
31835 TACATAACTTAAA
1 TACATTACTTAAA
31848 TACATTACTTACTAA
1 TACATTACTTA--AA
31863 -A-ATTTACTTAAA
1 TACA-TTACTTAAA
*
31875 TATATTACTTAAA
1 TACATTACTTAAA
*
31888 TACATGACTTA
1 TACATTACTTA
31899 CTAAAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.05
13 30 0.70
14 9 0.21
15 2 0.05
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (13 bp):
TACATTACTTAAA
Found at i:31898 original size:40 final size:37
Alignment explanation
Indices: 31841--32033 Score: 167
Period size: 39 Copynumber: 5.0 Consensus size: 37
31831 ATATTACATA
31841 ACTTAAATACATTACTTACTAAAATTTACTTAAATATATT
1 ACTTAAATACATTACTTACTAAAATTTA--T-AATATATT
*
31881 ACTTAAATACATGACTTACTAAAATTTA-AGTATATATT
1 ACTTAAATACATTACTTACTAAAATTTATA--ATATATT
*** * *
31919 ACATTGCTTACATTACTTACTAAAA--TATATTACATT
1 AC-TTAAATACATTACTTACTAAAATTTATAATATATT
* *
31955 ACTTAAATATATTACTTACTAAAATTTATAACTTACATT
1 ACTTAAATACATTACTTACTAAAATTTATAA--TATATT
* **
31994 TCTTAAATGTATTACATTACTTAAAATTTATATATATATT
1 ACTTAAATACATTAC-TTAC-TAAAATTTATA-ATATATT
32034 TAAAATTTTG
Statistics
Matches: 127, Mismatches: 15, Indels: 22
0.77 0.09 0.13
Matches are distributed among these distances:
35 18 0.14
36 8 0.06
37 6 0.05
38 10 0.08
39 37 0.29
40 36 0.28
41 11 0.09
42 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (37 bp):
ACTTAAATACATTACTTACTAAAATTTATAATATATT
Found at i:31942 original size:39 final size:39
Alignment explanation
Indices: 31841--31982 Score: 150
Period size: 40 Copynumber: 3.7 Consensus size: 39
31831 ATATTACATA
**
31841 ACTTAAATACATTACTTACTAAAATTTACTTAAATATATT
1 ACTTAAATACATTACTTACTAAAATTTAAGT-AATATATT
*
31881 ACTTAAATACATGACTTACTAAAATTTAAGT-ATATATT
1 ACTTAAATACATTACTTACTAAAATTTAAGTAATATATT
*** * *
31919 ACATTGCTTACATTACTTACTAAAA--T-A-TATTACATT
1 AC-TTAAATACATTACTTACTAAAATTTAAGTAATATATT
*
31955 ACTTAAATATATTACTTACTAAAATTTA
1 ACTTAAATACATTACTTACTAAAATTTA
31983 TAACTTACAT
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
35 19 0.23
36 8 0.10
37 2 0.02
38 9 0.11
39 18 0.21
40 28 0.33
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.42
Consensus pattern (39 bp):
ACTTAAATACATTACTTACTAAAATTTAAGTAATATATT
Found at i:31956 original size:18 final size:18
Alignment explanation
Indices: 31930--32020 Score: 87
Period size: 18 Copynumber: 4.9 Consensus size: 18
31920 CATTGCTTAC
31930 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
31947 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
31965 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTAAAA--TAT
* * *
31984 AACTTACATTTCTTAAATGT
1 -A-TTACATTACTAAAATAT
32004 ATTACATTACTTAAAAT
1 ATTACATTAC-TAAAAT
32021 TTATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.22
18 24 0.40
19 9 0.15
20 3 0.05
21 4 0.07
22 7 0.12
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.44
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:31970 original size:31 final size:31
Alignment explanation
Indices: 31866--31970 Score: 89
Period size: 31 Copynumber: 3.6 Consensus size: 31
31856 TTACTAAAAT
* * *
31866 TTACTTAAATATATTACTTAAATACATGAC-
1 TTACTTAAATATATTACTAAAATATATTACA
**
31896 TTAC-TAAA-AT-TTA--AGTATATATTACA
1 TTACTTAAATATATTACTAAAATATATTACA
* *
31922 TTGCTTACAT-TACTTACTAAAATATATTACA
1 TTACTTAAATATA-TTACTAAAATATATTACA
31953 TTACTTAAATATATTACT
1 TTACTTAAATATATTACT
31971 TACTAAAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 15
0.68 0.13 0.18
Matches are distributed among these distances:
25 7 0.12
26 3 0.05
27 7 0.12
28 2 0.04
29 7 0.12
30 4 0.07
31 24 0.43
32 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (31 bp):
TTACTTAAATATATTACTAAAATATATTACA
Found at i:31973 original size:22 final size:22
Alignment explanation
Indices: 31925--32013 Score: 57
Period size: 22 Copynumber: 4.2 Consensus size: 22
31915 TATTACATTG
*
31925 CTTACATTACTTACTAAAATA-TA
1 CTTACATTACTTA--AATATATTA
31948 -TTACATTACTTAAATATATTA
1 CTTACATTACTTAAATATATTA
* *
31969 CTTAC--TA---AAATTTATAA
1 CTTACATTACTTAAATATATTA
* *
31986 CTTACATTTCTTAAATGTATTA
1 CTTACATTACTTAAATATATTA
32008 CATTAC
1 C-TTAC
32014 TTAAAATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
17 13 0.25
19 1 0.02
20 7 0.13
21 2 0.04
22 25 0.48
23 4 0.08
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (22 bp):
CTTACATTACTTAAATATATTA
Found at i:31979 original size:17 final size:17
Alignment explanation
Indices: 31930--31990 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
31920 CATTGCTTAC
31930 ATTACTTACTAAAATAT
1 ATTACTTACTAAAATAT
*
31947 ATTACATTACTTAAATAT
1 ATTAC-TTACTAAAATAT
*
31965 ATTACTTACTAAAATTT
1 ATTACTTACTAAAATAT
*
31982 ATAACTTAC
1 ATTACTTAC
31991 ATTTCTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 23 0.59
18 16 0.41
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTACTTACTAAAATAT
Found at i:32458 original size:44 final size:44
Alignment explanation
Indices: 32395--32637 Score: 459
Period size: 44 Copynumber: 5.5 Consensus size: 44
32385 TAACATTTCT
* *
32395 TACATAACTTACATAATACATAATACACAACTTAATTAATATTA
1 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
32439 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
1 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
32483 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
1 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
32527 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
1 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
32571 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
1 TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
*
32615 TACATAACGTACCTAATACATAA
1 TACATAACGTACATAATACATAA
32638 ATATATATCA
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 196 1.00
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (44 bp):
TACATAACGTACATAATACATAATACAAAACTTAATTAATATTA
Found at i:32840 original size:25 final size:25
Alignment explanation
Indices: 32812--32868 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
32802 ACAACTTATG
32812 TAACTTAAATAACGT-ACATAATACA
1 TAACTTAAATAAC-TAACATAATACA
** *
32837 TAACTTTGATAACTAACATTATACA
1 TAACTTAAATAACTAACATAATACA
*
32862 CAACTTA
1 TAACTTA
32869 CATACTACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.32
Consensus pattern (25 bp):
TAACTTAAATAACTAACATAATACA
Found at i:32950 original size:44 final size:44
Alignment explanation
Indices: 32883--32986 Score: 154
Period size: 44 Copynumber: 2.3 Consensus size: 44
32873 CTACAATTCT
* *
32883 TACATAACTTACATTATACACAACTTAAATAATATTATACATAATG
1 TACATAA--TACATAATACACAACTTAAATAATATTATACATAACG
*
32929 TACATAATACATAATACACAACTTAATTAATATTATACATAACG
1 TACATAATACATAATACACAACTTAAATAATATTATACATAACG
*
32973 TACCTAATACATAA
1 TACATAATACATAA
32987 ATATATATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 47 0.87
46 7 0.13
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (44 bp):
TACATAATACATAATACACAACTTAAATAATATTATACATAACG
Found at i:52178 original size:21 final size:21
Alignment explanation
Indices: 52152--52197 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
52142 CTACAACTTA
* *
52152 AAGCAGAGGCTGTAACGAGGG
1 AAGCAGAGGCAGTAACGAGAG
*
52173 AAGCAGAGGCAGTAGCGAGAG
1 AAGCAGAGGCAGTAACGAGAG
52194 AAGC
1 AAGC
52198 TGGGGTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.41, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCAGTAACGAGAG
Found at i:52630 original size:43 final size:43
Alignment explanation
Indices: 52572--52987 Score: 468
Period size: 43 Copynumber: 9.7 Consensus size: 43
52562 ATAAAAAAAT
** ** * *
52572 GCCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
* * *
52615 GCCACTAAAGATCCTGATCTATAGCGGCGTTT-T-TAAAAAGGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAA-GC
* * * * ** *
52657 GCCGCTAAA-AGTCCTGATCTATAACAGCGTTTTTAAAAAAAGT
1 GCCGCTAAAGA-CCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
** * * **
52700 GCCGCTAAAGGTCCTGATCTATAGTGGCATTTG-CAAAAGAAGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAA-AAGC
* *
52743 GTCGCTAAAGACCCTGATCTATAGCGGCGTTTGT-AAAAAAGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
* *
52785 ACCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
* * *
52828 GACGCTAAAGACACT-ACTCTATAGCGGCGTTTGTGG-AGAAGC
1 GCCGCTAAAGACCCTGA-TCTATAGCGGCGTTTGTGGAAAAAGC
*
52870 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAGAAAGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
*
52913 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAGAAAGC
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
52956 GCCGCTAAAGACCCTGATCTATAGCGGCGTTT
1 GCCGCTAAAGACCCTGATCTATAGCGGCGTTT
52988 TTTTCTATAA
Statistics
Matches: 325, Mismatches: 37, Indels: 22
0.85 0.10 0.06
Matches are distributed among these distances:
41 6 0.02
42 108 0.33
43 206 0.63
44 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAAAAAGC
Found at i:52663 original size:85 final size:85
Alignment explanation
Indices: 52555--52989 Score: 462
Period size: 85 Copynumber: 5.1 Consensus size: 85
52545 TAAAATTAGT
* ** * ** * * *
52555 GGCGTTTATAAAAAAATGCCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGCGCCAC
1 GGCGTTTTTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
*
52620 TAAAGATCCTGATCTATAGC
66 TAAAGACCCTGATCTATAGC
* * * * * * ** *
52640 GGCGTTTTTAAAAAGGCGCCGCTAAAAGTCCTGATCTATAACAGCGTTTTTAAAAAAAGTGCCGC
1 GGCGTTTTTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
** *
52705 TAAAGGTCCTGATCTATAGT
66 TAAAGACCCTGATCTATAGC
* ** * * * *
52725 GGCATTTGCAAAAGAAGCGTCGCTAAAGACCCTGATCTATAGCGGCGTTTGT-AAAAAAGCACCG
1 GGCGTTTTTAAAA-AAGCGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCG
52789 CTAAAGACCCTGATCTATAGC
65 CTAAAGACCCTGATCTATAGC
* * * * *
52810 GGCGTTTGTAGAAAAAGCGACGCTAAAGACACT-ACTCTATAGCGGCGTTTGTGG-AGAAGCGCC
1 GGCGTTTTTA-AAAAAGCGCCGCTAAAGGCCCTGA-TCTATAGCGGCGTTTGTGGAAAAAGCGCC
52873 GCTAAAGACCCTGATCTATAGC
64 GCTAAAGACCCTGATCTATAGC
** * * *
52895 GGCGTTTGTGGAGAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCGTTTGTGGAGAAAGCGCCG
1 GGCGTTT-TTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCG
52960 CTAAAGACCCTGATCTATAGC
65 CTAAAGACCCTGATCTATAGC
52981 GGCGTTTTT
1 GGCGTTTTT
52990 TTCTATAAAT
Statistics
Matches: 293, Mismatches: 50, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.00
85 222 0.76
86 70 0.24
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (85 bp):
GGCGTTTTTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
TAAAGACCCTGATCTATAGC
Found at i:52987 original size:128 final size:127
Alignment explanation
Indices: 52555--52983 Score: 486
Period size: 128 Copynumber: 3.4 Consensus size: 127
52545 TAAAATTAGT
* ** ** ** * * *
52555 GGCGTTTATA-AAAAAATGCCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGCGCCA
1 GGCGTTTGTAGAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTGG-AGAAGCGCCG
* * * * *
52619 CTAAAGATCCTGATCTATAGCGGCGTTTTTAAAAAGGCGCCGCTAAA-AGTCCTGATCTATAAC
65 CTAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGA-CCCTGATCTATAGC
* * * * ** * *** *
52682 AGCGTTTTTAAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGTGGCATTTGCAAAAGAAGCGTCG
1 GGCGTTTGTAGAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTG-TGGAGAAGCGCCG
*
52747 CTAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAGCACCGCTAAAGACCCTGATCTATAGC
65 CTAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* * *
52810 GGCGTTTGTAGAAAAAGCGACGCTAAAGACACT-ACTCTATAGCGGCGTTTGTGGAGAAGCGCCG
1 GGCGTTTGTAGAAAAAGCGCCGCTAAAGACCCTGA-TCTATAGCGGCATTTGTGGAGAAGCGCCG
* *
52874 CTAAAGACCCTGATCTATAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCCTGATCTATAGC
65 CTAAAGACCCTGATCTATAGCGGCGTTTGT-AAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
* *
52938 GGCGTTTGTGGAGAAAGCGCCGCTAAAGACCCTGATCTATAGCGGC
1 GGCGTTTGTAGAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGC
52984 GTTTTTTTCT
Statistics
Matches: 258, Mismatches: 38, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
127 48 0.19
128 208 0.81
129 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (127 bp):
GGCGTTTGTAGAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTGGAGAAGCGCCGC
TAAAGACCCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGC
Found at i:53866 original size:131 final size:132
Alignment explanation
Indices: 53632--53895 Score: 521
Period size: 131 Copynumber: 2.0 Consensus size: 132
53622 TATCTAGCAT
53632 AGCTAGTGGCGTCTACCTTCTTTCTTTGAACTTATCACTCAACCCCGAGTGTGGCGTTCACCCCA
1 AGCTAGTGGCGTCTACCTTCTTTCTTTGAACTTATCACTCAACCCCGAGTGTGGCGTTCACCCCA
53697 GTTATACCTTTGGTTCTTACTTGACTAAGTAACGGGTCAAGGTTCTATCCTATCCA-TCCGTAAA
66 GTTATACCTTTGGTTCTTACTTGACTAAGTAACGGGTCAAGGTTCTATCCTATCCATTCCGTAAA
53761 CC
131 CC
53763 AGCTAGTGGCGTCTACCTTCTTTCTTTGAACTTATCACTCAACCCCGAGTGTGGCGTTCACCCCA
1 AGCTAGTGGCGTCTACCTTCTTTCTTTGAACTTATCACTCAACCCCGAGTGTGGCGTTCACCCCA
53828 GTTATACCTTTGGTTCTTACTTGACTAAGTAACGGGTCAAGGTTCTATCCTATCCATTCCGTAAA
66 GTTATACCTTTGGTTCTTACTTGACTAAGTAACGGGTCAAGGTTCTATCCTATCCATTCCGTAAA
53893 CC
131 CC
53895 A
1 A
53896 TCGTAAGGTC
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 121 0.92
132 11 0.08
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (132 bp):
AGCTAGTGGCGTCTACCTTCTTTCTTTGAACTTATCACTCAACCCCGAGTGTGGCGTTCACCCCA
GTTATACCTTTGGTTCTTACTTGACTAAGTAACGGGTCAAGGTTCTATCCTATCCATTCCGTAAA
CC
Found at i:56087 original size:10 final size:11
Alignment explanation
Indices: 56067--56112 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
56057 TAGTAGTTTC
56067 TTTGAAAAAAA
1 TTTGAAAAAAA
56078 TTTGAAAAAAAA
1 TTTG-AAAAAAA
*
56090 TTCGAAAAAAA
1 TTTGAAAAAAA
* *
56101 ATTAAAAAAAA
1 TTTGAAAAAAA
56112 T
1 T
56113 ATTTCCATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (11 bp):
TTTGAAAAAAA
Found at i:56088 original size:12 final size:12
Alignment explanation
Indices: 56067--56112 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
56057 TAGTAGTTTC
56067 TTTG-AAAAAAA
1 TTTGAAAAAAAA
56078 TTTGAAAAAAAA
1 TTTGAAAAAAAA
*
56090 TTCGAAAAAAAA
1 TTTGAAAAAAAA
56102 -TT-AAAAAAAA
1 TTTGAAAAAAAA
56112 T
1 T
56113 ATTTCCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.26
11 5 0.16
12 18 0.58
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (12 bp):
TTTGAAAAAAAA
Found at i:56650 original size:216 final size:217
Alignment explanation
Indices: 56276--56708 Score: 859
Period size: 216 Copynumber: 2.0 Consensus size: 217
56266 CAACCCTTTT
56276 CATTTCTTTGTTTCAAGCCTACCTTTCTTGTCCTACAATATCCTAACCAAGCCCAAACATCAAAT
1 CATTTCTTTGTTTCAAGCCTACCTTTCTTGTCCTACAATATCCTAACCAAGCCCAAACATCAAAT
56341 TTGTAAGCCGACCCACAACAACTGCCTTTTAAGTTTAAATAATTCCTAAGAACTTAGAGAGGAGG
66 TTGTAAGCCGACCCACAACAACTGCCTTTTAAGTTTAAATAATTCCTAAGAACTTAGAGAGGAGG
56406 AGTGAGTGGAAAGAGGCAAGAGAGTAGTAAGACTAATCGAGAGTATAAAAGCCAAGTGTGTGATA
131 AGTGAGTGGAAAGAGGCAAGAGAGTAGTAAGACTAATCGAGAGTATAAAAGCCAAGTGTGTGATA
56471 TTTCTTTGTGA-TGGATAGTGA
196 TTTCTTTGTGAGTGGATAGTGA
56492 CATTTCTTTGTTTCAAGCCTACCTTTCTTGTCCTACAATATCCTAACCAAGCCCAAACATCAAAT
1 CATTTCTTTGTTTCAAGCCTACCTTTCTTGTCCTACAATATCCTAACCAAGCCCAAACATCAAAT
56557 TTGTAAGCCGACCCACAACAACTGCCTTTTAAGTTTAAATAATTCCTAAGAACTTAGAGAGGAGG
66 TTGTAAGCCGACCCACAACAACTGCCTTTTAAGTTTAAATAATTCCTAAGAACTTAGAGAGGAGG
56622 AGTGAGTGGAAAGAGGCAAGAGAGTAGTAAGACTAATCGAGAGTATAAAAGCCAAGTGTGTGATA
131 AGTGAGTGGAAAGAGGCAAGAGAGTAGTAAGACTAATCGAGAGTATAAAAGCCAAGTGTGTGATA
56687 TTTCTTTGTGAGTGGATAGTGA
196 TTTCTTTGTGAGTGGATAGTGA
56709 GGTTCTTTGT
Statistics
Matches: 216, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
216 206 0.95
217 10 0.05
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (217 bp):
CATTTCTTTGTTTCAAGCCTACCTTTCTTGTCCTACAATATCCTAACCAAGCCCAAACATCAAAT
TTGTAAGCCGACCCACAACAACTGCCTTTTAAGTTTAAATAATTCCTAAGAACTTAGAGAGGAGG
AGTGAGTGGAAAGAGGCAAGAGAGTAGTAAGACTAATCGAGAGTATAAAAGCCAAGTGTGTGATA
TTTCTTTGTGAGTGGATAGTGA
Found at i:58155 original size:20 final size:20
Alignment explanation
Indices: 58130--58176 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
58120 AGCTCGTTTC
58130 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * *
58150 CAGCTCATTCGAGTTCAATT
1 CAGCTCACTCGAGCTCAAGT
58170 CAGCTCA
1 CAGCTCA
58177 ACCTCAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:59598 original size:29 final size:27
Alignment explanation
Indices: 59565--59619 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
59555 GTTATTAAAT
59565 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
59594 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
59620 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:62247 original size:20 final size:20
Alignment explanation
Indices: 62224--62262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62214 TTGAGCTAAA
*
62224 ATTGAGCTGAATTGAGCTTG
1 ATTGAGCTGAATCGAGCTTG
*
62244 ATTGAGCTGGATCGAGCTT
1 ATTGAGCTGAATCGAGCTT
62263 TATTTTGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (20 bp):
ATTGAGCTGAATCGAGCTTG
Found at i:65696 original size:19 final size:20
Alignment explanation
Indices: 65672--65709 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
65662 GAGCTGGTTA
65672 GAGCTGAAA-CGAGCTAAAG
1 GAGCTGAAATCGAGCTAAAG
65691 GAGCTGAAATCGAGCTAAA
1 GAGCTGAAATCGAGCTAAA
65710 ATCAACTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.16, G:0.29, T:0.13
Consensus pattern (20 bp):
GAGCTGAAATCGAGCTAAAG
Found at i:66009 original size:19 final size:20
Alignment explanation
Indices: 65977--66014 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
65967 CAAGCTGATT
65977 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
65997 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
66015 AACCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:66218 original size:15 final size:15
Alignment explanation
Indices: 66208--66247 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
66198 AATTTAATAG
66208 CTATGTTTTTAATTAA
1 CTATGTTTTTAATT-A
* *
66224 TTATTTTTTTAATTA
1 CTATGTTTTTAATTA
66239 CTATGTTTT
1 CTATGTTTT
66248 GTTGCTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
CTATGTTTTTAATTA
Found at i:66443 original size:16 final size:16
Alignment explanation
Indices: 66422--66463 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
66412 TTAAGGATGA
66422 TACATGAATGGTTCAT
1 TACATGAATGGTTCAT
66438 TACATGAATGGTTCAT
1 TACATGAATGGTTCAT
66454 TACATTGAAT
1 TACA-TGAAT
66464 AGGAGAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (16 bp):
TACATGAATGGTTCAT
Found at i:96277 original size:15 final size:15
Alignment explanation
Indices: 96257--96287 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
96247 CCTATAGTAG
96257 TTCTCAAAAGCAGAA
1 TTCTCAAAAGCAGAA
*
96272 TTCTCACAAGCAGAA
1 TTCTCAAAAGCAGAA
96287 T
1 T
96288 AAATTTCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TTCTCAAAAGCAGAA
Found at i:97897 original size:18 final size:18
Alignment explanation
Indices: 97876--97934 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 18
97866 TCTTTTCTCA
97876 TTTTCTTTTCGCTTTCTT
1 TTTTCTTTTCGCTTTCTT
*
97894 TTTTATTTTCGCTTTCTTT
1 TTTTCTTTTCGCTTTC-TT
* *
97913 TTTTCATTTGGCTTTTCTT
1 TTTTCTTTTCGC-TTTCTT
97932 TTT
1 TTT
97935 CATTTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.43
19 16 0.46
20 4 0.11
ACGTcount: A:0.03, C:0.17, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTCTTTTCGCTTTCTT
Found at i:97909 original size:24 final size:24
Alignment explanation
Indices: 97864--97909 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
97854 TTTTCTTATT
*
97864 TTTCTTTTCTCATTTTCTTTTCGC
1 TTTCTTTTCTCATTTTCCTTTCGC
*
97888 TTTCTTTT-TTATTTTCGCTTTC
1 TTTCTTTTCTCATTTTC-CTTTC
97910 TTTTTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTCTTTTCTCATTTTCCTTTCGC
Found at i:97910 original size:37 final size:38
Alignment explanation
Indices: 97869--97940 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
97859 TTATTTTTCT
* *
97869 TTTCTCATTTTCTTTTCGC-TTTCTTTTTTATTTTCGC
1 TTTCTCATTTTCATTTCGCTTTTCTTTTTCATTTTCGC
** *
97906 TTTCTTTTTTTCATTTGGCTTTTCTTTTTCATTTT
1 TTTCTCATTTTCATTTCGCTTTTCTTTTTCATTTT
97941 TTTCTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 15 0.52
38 14 0.48
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.71
Consensus pattern (38 bp):
TTTCTCATTTTCATTTCGCTTTTCTTTTTCATTTTCGC
Found at i:97916 original size:19 final size:19
Alignment explanation
Indices: 97876--97934 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
97866 TCTTTTCTCA
*
97876 TTTTCTTTTCGCTTTC-TT
1 TTTTATTTTCGCTTTCTTT
97894 TTTTATTTTCGCTTTCTTT
1 TTTTATTTTCGCTTTCTTT
*
97913 TTTTCA-TTTGGCTTTTCTTT
1 TTTT-ATTTTCGC-TTTCTTT
97933 TT
1 TT
97935 CATTTTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.42
19 11 0.31
20 10 0.28
ACGTcount: A:0.03, C:0.17, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTATTTTCGCTTTCTTT
Found at i:97952 original size:38 final size:37
Alignment explanation
Indices: 97854--97953 Score: 87
Period size: 38 Copynumber: 2.6 Consensus size: 37
97844 TTTTTTTATA
* *
97854 TTTTC-TTATTTTTCTTTTCTCATTTTCTTTTCGCTTTCT
1 TTTTCATT-TTTTTCTTTT-T-TTTTTCATTTCGCTTTCT
* ** *
97893 TTTTTA-TTTTCGCTTTCTTTTTTTCATTTGGCTTTTCT
1 TTTTCATTTTTTTCTTT-TTTTTTTCATTTCGC-TTTCT
97931 TTTTCATTTTTTTCTTTTTTTTT
1 TTTTCATTTTTTTCTTTTTTTTT
97954 CGATTGAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
37 10 0.21
38 24 0.50
39 14 0.29
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.75
Consensus pattern (37 bp):
TTTTCATTTTTTTCTTTTTTTTTTCATTTCGCTTTCT
Found at i:100393 original size:16 final size:16
Alignment explanation
Indices: 100372--100410 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
100362 CACTTCACTC
**
100372 TTTTTTTTACTTCGTA
1 TTTTTTTTACTTCAAA
100388 TTTTTTTTACTTCAAA
1 TTTTTTTTACTTCAAA
100404 TTTTTTT
1 TTTTTTT
100411 CAATTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTTTTACTTCAAA
Found at i:103779 original size:25 final size:26
Alignment explanation
Indices: 103714--103783 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
103704 CAAAGGAGAG
103714 CATTCAAGGAAGCATGCATGAACGGA
1 CATTCAAGGAAGCATGCATGAACGGA
* *
103740 -ATTAAAAGAAGCATGCATGAAC-GA
1 CATTCAAGGAAGCATGCATGAACGGA
*
103764 CATTCAAGGAAACATGCATG
1 CATTCAAGGAAGCATGCATG
103784 CTGATTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.95
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (26 bp):
CATTCAAGGAAGCATGCATGAACGGA
Found at i:109744 original size:18 final size:19
Alignment explanation
Indices: 109699--109747 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
109689 GAATATTTAC
*
109699 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
109719 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
109737 ATAAAAATAAA
1 ATAAAAATAAA
109748 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:111944 original size:150 final size:150
Alignment explanation
Indices: 111673--112187 Score: 1030
Period size: 150 Copynumber: 3.4 Consensus size: 150
111663 ATTTCGTTTT
111673 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
1 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
111738 AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
66 AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
111803 GTCCTATTCCAACACCTTTA
131 GTCCTATTCCAACACCTTTA
111823 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
1 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
111888 AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
66 AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
111953 GTCCTATTCCAACACCTTTA
131 GTCCTATTCCAACACCTTTA
111973 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
1 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
112038 AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
66 AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
112103 GTCCTATTCCAACACCTTTA
131 GTCCTATTCCAACACCTTTA
112123 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
1 AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
112188 TTTGAAGCTA
Statistics
Matches: 365, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 365 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (150 bp):
AGACTCAAGCTGACTTATCTAGCATACCTAGTGGTGTCTACCATGTTTCTTTGAACTTATCACTC
AATCTCGAGTGTGGCGTTCACCCTATTATACCTTTGGTTCATACTTAACTAAGTATTGGGTCAAG
GTCCTATTCCAACACCTTTA
Found at i:113551 original size:22 final size:22
Alignment explanation
Indices: 113499--113563 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
113489 TATTTGGGAA
* *
113499 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
113521 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
113543 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
113564 TTCAAAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.37, C:0.06, G:0.32, T:0.25
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:114433 original size:10 final size:10
Alignment explanation
Indices: 114418--114459 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
114408 TTTGCAAGTT
114418 TTGAGCTAAA
1 TTGAGCTAAA
* *
114428 TTGAGCTGAT
1 TTGAGCTAAA
*
114438 TTGAGCT-CA
1 TTGAGCTAAA
114447 TTGAGCTAAA
1 TTGAGCTAAA
114457 TTG
1 TTG
114460 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Done.