Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold185_ERROPOS720127
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: 99999
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:299 original size:22 final size:22
Alignment explanation
Indices: 273--317 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
263 TAAAGATTGA
273 ATGCTAATTGTTATCCTTGAAC
1 ATGCTAATTGTTATCCTTGAAC
295 ATGCTAATTGTTATCCTTGAAC
1 ATGCTAATTGTTATCCTTGAAC
317 A
1 A
318 CGATGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (22 bp):
ATGCTAATTGTTATCCTTGAAC
Found at i:875 original size:3 final size:3
Alignment explanation
Indices: 835--859 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
825 GCTCTTCCAA
835 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
860 AATATAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9197 original size:51 final size:50
Alignment explanation
Indices: 9122--9315 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 50
9112 CAGTGATGTT
* * * *
9122 CGGTTCACATAGTAGCATGTACATAGTACTACACATGTGACCGTTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCG-TACCATC
* * * * * *
9173 CGATACACGCAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCG-TACCATC
* * * *
9224 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCGTACCA-TC
*
9274 CGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC
9316 ATCACTTTCA
Statistics
Matches: 117, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 75 0.64
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCGTACCATC
Found at i:9305 original size:101 final size:101
Alignment explanation
Indices: 9129--9313 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
9119 GTTCGGTTCA
* * *
9129 CATAGTAGCATGTACATAGTACTACACATGTGACCGTTACCATCCGATACACGCAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCG-TACCATCCGATACACGCAGTAGCCTACA
9194 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
9231 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTACA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCGTACCA-TCCGATACACGCAGTAGCCTACA
*
9295 CATAGTACTACACATGTGA
65 CATAGTACTACACACGTGA
9314 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 32 0.43
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCGTACCATCCGATACACGCAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:11193 original size:27 final size:27
Alignment explanation
Indices: 11149--11215 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
11139 ATGGAATTAG
* *
11149 GACATATTAAAAAGGTGCAATAAGCTGA
1 GACAAATTAAAAAGGTGCAATAA-CTAA
* * *
11177 -ACAAATTAAATATGTGCACTAACTAA
1 GACAAATTAAAAAGGTGCAATAACTAA
11203 GACAAATTAAAAA
1 GACAAATTAAAAA
11216 CATGCATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.22
Consensus pattern (27 bp):
GACAAATTAAAAAGGTGCAATAACTAA
Found at i:14704 original size:17 final size:16
Alignment explanation
Indices: 14678--14713 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
14668 TGAGAGCTAA
*
14678 GAGAGTTGAGAGAGGAT
1 GAGAGATGAGA-AGGAT
14695 GAGAGATGAGAAGGAT
1 GAGAGATGAGAAGGAT
14711 GAG
1 GAG
14714 GGATAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.47, T:0.14
Consensus pattern (16 bp):
GAGAGATGAGAAGGAT
Found at i:21076 original size:49 final size:50
Alignment explanation
Indices: 20970--21151 Score: 172
Period size: 49 Copynumber: 3.7 Consensus size: 50
20960 TAATAGGTCC
** * * * **
20970 CATGTAAGACCATGTCTGGGACATGGTGTTGGTACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAACTCT
** *
21020 CCCGTAAGACCATGT-TGGGACATGGCATTGGCACTGATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAACTCT
* * * * * * *
21069 CATGTAAGACCGTATCTGGGATATGGCATTTGCAGT-ACAAGA-AACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAAC-TCT
*
21118 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
21152 TGTTATTATC
Statistics
Matches: 106, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
48 3 0.03
49 73 0.69
50 30 0.28
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAACTCT
Found at i:23208 original size:40 final size:40
Alignment explanation
Indices: 23125--23427 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
23115 TTGAATGCTG
* * * * * *
23125 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
23165 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
23205 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
23245 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
23285 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
23325 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
23365 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
23404 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
23428 TGAACGAGGA
Statistics
Matches: 239, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 35 0.15
40 196 0.82
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:31311 original size:39 final size:39
Alignment explanation
Indices: 31107--31329 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
31097 TTGAATGCTG
* * * * * *
31107 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
31147 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
31187 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
31227 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
31267 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
31306 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31330 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:31349 original size:79 final size:80
Alignment explanation
Indices: 31182--31364 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
31172 GTGCGAGATA
* * *
31182 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
31247 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
31262 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
31326 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
31341 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
31365 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:34555 original size:47 final size:47
Alignment explanation
Indices: 34501--34879 Score: 553
Period size: 47 Copynumber: 8.1 Consensus size: 47
34491 TTAGGATTTT
** * * **
34501 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGAAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
34548 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
34595 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
34642 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
34689 ATGTAATGAATGTGAACATGCATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
34736 ATGTGATGAATGTGAATATGCATATATGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
34783 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
34830 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
34877 ATG
1 ATG
34880 CGAAATGTGT
Statistics
Matches: 307, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 304 0.99
48 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:34742 original size:22 final size:22
Alignment explanation
Indices: 34715--34836 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 22
34705 CATGCATATG
34715 TGTGATAAGGCTGAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
* * *
34737 TGTGATGAATG-TGAATATGCATATA
1 TGTGAT-AAGGCTGAAT-GGC-CA-A
**
34762 TGTGATAAGGCCAAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
* *
34784 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCTG-A-ATGGC-CA-A
*
34809 TGTGATAAGGCAGAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
34831 TGTGAT
1 TGTGAT
34837 GAACGTGGAA
Statistics
Matches: 73, Mismatches: 15, Indels: 24
0.65 0.13 0.21
Matches are distributed among these distances:
22 25 0.34
23 15 0.21
24 15 0.21
25 18 0.25
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (22 bp):
TGTGATAAGGCTGAATGGCCAA
Found at i:34909 original size:46 final size:46
Alignment explanation
Indices: 34853--35035 Score: 267
Period size: 46 Copynumber: 4.0 Consensus size: 46
34843 GGAAGTGTAT
* *
34853 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
* *
34899 ATATGAGGTAAAGCTGAATGGCTAATGCGAAACGTGCATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
*
34945 ATATGAGGTAAAGCCGAATGGCTAATGCAAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
* * * * **
34991 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATG
35036 TGTATATATA
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 123 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
Found at i:37092 original size:28 final size:28
Alignment explanation
Indices: 37026--37153 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
37016 CATGAGATTG
* * **
37026 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
37055 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
37083 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
37112 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
37140 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
37154 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:37115 original size:57 final size:57
Alignment explanation
Indices: 37026--37153 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
37016 CATGAGATTG
*
37026 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
37083 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
37140 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
37154 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:39812 original size:40 final size:40
Alignment explanation
Indices: 39757--40073 Score: 530
Period size: 40 Copynumber: 8.0 Consensus size: 40
39747 TGAGAGTTAT
39757 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
39797 ATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
39837 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
39877 ATATATCCGGGCTAAATTCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
39917 ATATATCCGGGATAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
39957 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
39997 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAATG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
40037 ATATATCCGGGCTAA-ACCTCGAAG-GCATTCATGCTAG
1 ATATATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCTAG
40074 AATTATGAGG
Statistics
Matches: 260, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 12 0.05
40 248 0.95
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Found at i:40169 original size:57 final size:57
Alignment explanation
Indices: 40079--40236 Score: 208
Period size: 57 Copynumber: 2.8 Consensus size: 57
40069 GCTAGAATTA
* * * * *
40079 TGAGGCACTGTGTGTGCAAGTTCTCCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCCAGATCAGTAAT
* * **
40136 TGAGGCACTATGTGTACGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCCAGATCAGTAAT
* * *
40193 TGAGGCACTATATGTGCGAGTTCTTTAATCGAGCGCTATGTGTG
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTG
40237 TGAAATCAGT
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 88 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCCAGATCAGTAAT
Found at i:40178 original size:28 final size:27
Alignment explanation
Indices: 40083--40236 Score: 110
Period size: 28 Copynumber: 5.4 Consensus size: 27
40073 GAATTATGAG
* * * *
40083 GCACTGTGTGTGCAAGTTCTCCAACCGA
1 GCACTATGTGTGCGAGTTCT-TAATCGA
* * * * *
40111 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
*
40139 GGCACTATGTGTACGAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
40168 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
*
40196 GGCACTATATGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
40225 GCGCTATGTGTG
1 GCACTATGTGTG
40237 TGAAATCAGT
Statistics
Matches: 96, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
28 52 0.54
29 44 0.46
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:40208 original size:29 final size:29
Alignment explanation
Indices: 40111--40212 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
40101 CTCCAACCGA
* * *
40111 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATTAGTAATTGAG
* ** *
40140 GCACTATGTGTACGAG-TTCTTCAATCGA-
1 GCACTATGTGTGCGAGATTAGT-AATTGAG
*
40168 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGATTAGTAATTGAG
*
40197 GCACTATATGTGCGAG
1 GCACTATGTGTGCGAG
40213 TTCTTTAATC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
28 22 0.38
29 36 0.62
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
GCACTATGTGTGCGAGATTAGTAATTGAG
Found at i:44159 original size:47 final size:47
Alignment explanation
Indices: 44046--44420 Score: 553
Period size: 46 Copynumber: 8.1 Consensus size: 47
44036 TTAGGATTTT
** * *
44046 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGG-CA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
44092 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
44139 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
44186 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
44233 ATGT-ATGAATGTGAACATGCATATGTGTGATAAGG-CGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
44278 ATGTGATGAATGTGAATATGCATATATGTGATAAGGCC-AATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
44324 ATGTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
44371 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGTCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
44418 ATG
1 ATG
44421 CGAAATAAGT
Statistics
Matches: 305, Mismatches: 19, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
45 14 0.05
46 144 0.47
47 144 0.47
48 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:44192 original size:22 final size:22
Alignment explanation
Indices: 44121--44192 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
44111 GCATATATGA
44121 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
44143 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
44168 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
44190 GAT
1 GAT
44193 GAATGTGAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:44461 original size:46 final size:46
Alignment explanation
Indices: 44394--44576 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
44384 GGAAGTGTAT
* * * *
44394 ATATGTGGTAAAGTCGAATGGCTAATGCGAAATAAGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
* *
44440 ATATGAGGTAAAGCTGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
*
44486 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
* * * * *
44532 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATG
44577 TGTATATATA
Statistics
Matches: 124, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 124 1.00
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:46017 original size:27 final size:28
Alignment explanation
Indices: 45987--46125 Score: 85
Period size: 27 Copynumber: 5.1 Consensus size: 28
45977 CCTCACATAG
*
45987 GGGCCAAAT-AGTCAATTTACCATGTAA
1 GGGCCAAATCAGTCAATTTACCATATAA
** *
46014 GGG-CATTTCAGTCATTTTACCATATAA
1 GGGCCAAATCAGTCAATTTACCATATAA
* * * *
46041 GGG-CAAAACAATCATTTTACC-TCAGAA
1 GGGCCAAATCAGTCAATTTACCAT-ATAA
* * * *
46068 GGG-CAAAACAATCATTTTACCACATAA
1 GGGCCAAATCAGTCAATTTACCATATAA
* *
46095 GGG-CAGAA-CAGTCATTTTACCACATAA
1 GGGCCA-AATCAGTCAATTTACCATATAA
46122 GGGC
1 GGGC
46126 AAAACAATTG
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.04
27 89 0.94
28 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (28 bp):
GGGCCAAATCAGTCAATTTACCATATAA
Found at i:46126 original size:27 final size:27
Alignment explanation
Indices: 46025--46165 Score: 192
Period size: 27 Copynumber: 5.2 Consensus size: 27
46015 GGCATTTCAG
*
46025 TCATTTTACCATATAAGGGCAAAACAA
1 TCATTTTACCACATAAGGGCAAAACAA
* *
46052 TCATTTTACCTCAGAAGGGCAAAACAA
1 TCATTTTACCACATAAGGGCAAAACAA
* *
46079 TCATTTTACCACATAAGGGCAGAACAG
1 TCATTTTACCACATAAGGGCAAAACAA
46106 TCATTTTACCACATAAGGGCAAAACAA
1 TCATTTTACCACATAAGGGCAAAACAA
** * * *
46133 TTGTTTCACCTCATAAGGGCAAAACAG
1 TCATTTTACCACATAAGGGCAAAACAA
46160 TCATTT
1 TCATTT
46166 CATCAAATTG
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (27 bp):
TCATTTTACCACATAAGGGCAAAACAA
Found at i:49042 original size:42 final size:42
Alignment explanation
Indices: 48949--49097 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 42
48939 AATGTCAACG
* * * * *
48949 TCCCAGACGTGGTCTTACATGTAATCAAATATTGATGCCACTG
1 TCCCAGACATGGTCTTACACGAAATCAATTATTGATGCCA-TA
*
48992 TCCCAGACAGGGTCTTACACGAAATCAATTA-TGATGCCGATA
1 TCCCAGACATGGTCTTACACGAAATCAATTATTGATGCC-ATA
* * *
49034 TCCAAGACATGGTCTTACATGTAAATC-ATAAGTTGATGCCAATA
1 TCCCAGACATGGTCTTACACG-AAATCAATTA-TTGATGCC-ATA
49078 TCCCAGACATGGTCTTACAC
1 TCCCAGACATGGTCTTACAC
49098 AAAAACACAT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 29 0.33
43 32 0.36
44 28 0.31
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAATCAATTATTGATGCCATA
Found at i:52452 original size:40 final size:39
Alignment explanation
Indices: 52376--52453 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
52366 TACTTTAGTT
*
52376 TGTGTCTTTAATTATGTCTTAGTTTGAACATAATTAATA
1 TGTGTCTTTAATTATGTCTTACTTTGAACATAATTAATA
*
52415 TGTGT-TTTAATTATGTGTCTTAACTTTG-ACATCATTAAT
1 TGTGTCTTTAATTA--TGTCTT-ACTTTGAACATAATTAAT
52454 GTTTGTCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 8 0.24
39 5 0.15
40 16 0.47
41 5 0.15
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (39 bp):
TGTGTCTTTAATTATGTCTTACTTTGAACATAATTAATA
Found at i:53932 original size:21 final size:21
Alignment explanation
Indices: 53908--53948 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53898 GTGTTTTTTG
53908 ATGTCTAATGGTAGAAAATAT
1 ATGTCTAATGGTAGAAAATAT
* *
53929 ATGTTTGATGGTAGAAAATA
1 ATGTCTAATGGTAGAAAATA
53949 GGGACCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (21 bp):
ATGTCTAATGGTAGAAAATAT
Found at i:61292 original size:20 final size:20
Alignment explanation
Indices: 61267--61307 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
61257 TTGCAATTTG
61267 TGCATTACTAGGACGAGCAA
1 TGCATTACTAGGACGAGCAA
61287 TGCATTACTAGGACGAGCAA
1 TGCATTACTAGGACGAGCAA
61307 T
1 T
61308 AAATTAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (20 bp):
TGCATTACTAGGACGAGCAA
Found at i:61313 original size:20 final size:20
Alignment explanation
Indices: 61270--61313 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
61260 CAATTTGTGC
**
61270 ATTACTAGGACGAGCAATGC
1 ATTACTAGGACGAGCAATAA
61290 ATTACTAGGACGAGCAATAA
1 ATTACTAGGACGAGCAATAA
61310 ATTA
1 ATTA
61314 GCATTACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (20 bp):
ATTACTAGGACGAGCAATAA
Found at i:61317 original size:26 final size:26
Alignment explanation
Indices: 61288--61339 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
61278 GACGAGCAAT
61288 GCATTACTAGGACGAGCAATAAATTA
1 GCATTACTAGGACGAGCAATAAATTA
61314 GCATTACTAGGACGAGCAATAAATTA
1 GCATTACTAGGACGAGCAATAAATTA
61340 AGTTTGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (26 bp):
GCATTACTAGGACGAGCAATAAATTA
Found at i:63697 original size:35 final size:35
Alignment explanation
Indices: 63639--63706 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
63629 ATACTCTAAT
* *
63639 AGGTGACACTGTGAAAATGGTTTACAAGTCCTTTA
1 AGGTGACACCGTGAAAATAGTTTACAAGTCCTTTA
* * *
63674 AGGTGACACCGTGTAAATAGTTTATAGGTCCTT
1 AGGTGACACCGTGAAAATAGTTTACAAGTCCTT
63707 CGAGATGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (35 bp):
AGGTGACACCGTGAAAATAGTTTACAAGTCCTTTA
Found at i:66797 original size:60 final size:59
Alignment explanation
Indices: 66732--66933 Score: 194
Period size: 60 Copynumber: 3.4 Consensus size: 59
66722 AGTGACGACC
*
66732 ATCAAATTATGAAAAGGGATGGCTGTGGCTATCGATCTATGAAAAGGGATGGCTTCTGCT
1 ATCAAATTATGAAAAGGGATGGCTGTGGCTATCGAACTATGAAAAGGGATGGCTT-TGCT
* * * * * *
66792 ATCAAATCATGAAAAAGGGATGG-TG-GCAACTATCAAACAATGAAAAGGGATGG-TGATGACA
1 ATCAAATTATG-AAAAGGGATGGCTGTG--GCTATCGAACTATGAAAAGGGATGGCT-TTG-CT
* * ** *
66853 ATCAAATTATGAAAAGGGATAGCTTTGGCTATCGAACTATGAAAAGGGATAACTTTGGTT
1 ATCAAATTATGAAAAGGGATGGCTGTGGCTATCGAACTATGAAAAGGGATGGCTTT-GCT
* *
66913 ATCGAATTACGAAAAGGGATG
1 ATCAAATTATGAAAAGGGATG
66934 TGAGAACCAT
Statistics
Matches: 112, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
59 1 0.01
60 64 0.57
61 46 0.41
62 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (59 bp):
ATCAAATTATGAAAAGGGATGGCTGTGGCTATCGAACTATGAAAAGGGATGGCTTTGCT
Found at i:66835 original size:91 final size:89
Alignment explanation
Indices: 66681--66903 Score: 238
Period size: 91 Copynumber: 2.5 Consensus size: 89
66671 TCATTGACGA
* * * * **
66681 ATGAAAAGGGATAACTTCGGCTATCAATTATGAAAAGGGATAGTGACGACCATCAAATTATGAAA
1 ATGAAAAGGGATAGCTTCTGCTATCAATCATGAAAAGGGATAGTGACAACCATCAAACAATGAAA
* * *
66746 AGGGATGGCTG-TGGCTATC-GATCT
66 AGGGATGG-TGATGACAATCAAAT-T
* * * *
66770 ATGAAAAGGGATGGCTTCTGCTATCAAATCATGAAAAAGGGATGGTGGCAACTATCAAACAATGA
1 ATGAAAAGGGATAGCTTCTGCTATC-AATCATG-AAAAGGGATAGTGACAACCATCAAACAATGA
66835 AAAGGGATGGTGATGACAATCAAATT
64 AAAGGGATGGTGATGACAATCAAATT
66861 ATGAAAAGGGATAGCTT-TGGCTATCGAA-CTATGAAAAGGGATA
1 ATGAAAAGGGATAGCTTCT-GCTATC-AATC-ATGAAAAGGGATA
66904 ACTTTGGTTA
Statistics
Matches: 112, Mismatches: 16, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
89 22 0.20
90 19 0.17
91 69 0.62
92 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (89 bp):
ATGAAAAGGGATAGCTTCTGCTATCAATCATGAAAAGGGATAGTGACAACCATCAAACAATGAAA
AGGGATGGTGATGACAATCAAATT
Found at i:66857 original size:61 final size:60
Alignment explanation
Indices: 66710--66902 Score: 185
Period size: 60 Copynumber: 3.2 Consensus size: 60
66700 GCTATCAATT
* * * * * * *
66710 ATGAAAAGGGATAGTGACGACCATCAAATTATGAAAAGGGATGGCTGTGGCTATCGATCT
1 ATGAAAAGGGATGGTGATGACAATCAAATTATGAAAAGGGATGGCTGTGACTATCAAACA
** * *
66770 ATGAAAAGGGATGGCTTCTG-CTATCAAATCATGAAAAAGGGATGG-TG-GCAACTATCAAACA
1 ATGAAAAGGGATGG-TGATGACAATCAAATTATG-AAAAGGGATGGCTGTG--ACTATCAAACA
* * * * *
66831 ATGAAAAGGGATGGTGATGACAATCAAATTATGAAAAGGGATAGCTTTGGCTATCGAACT
1 ATGAAAAGGGATGGTGATGACAATCAAATTATGAAAAGGGATGGCTGTGACTATCAAACA
66891 ATGAAAAGGGAT
1 ATGAAAAGGGAT
66903 AACTTTGGTT
Statistics
Matches: 107, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
59 1 0.01
60 59 0.55
61 46 0.43
62 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (60 bp):
ATGAAAAGGGATGGTGATGACAATCAAATTATGAAAAGGGATGGCTGTGACTATCAAACA
Found at i:66894 original size:30 final size:30
Alignment explanation
Indices: 66681--66932 Score: 160
Period size: 30 Copynumber: 8.4 Consensus size: 30
66671 TCATTGACGA
* *
66681 ATGAAAAGGGATAACTTCGGCTATC-AATT
1 ATGAAAAGGGATAGCTTTGGCTATCAAATT
** * *
66710 ATGAAAAGGGATAG-TGACGACCATCAAATT
1 ATGAAAAGGGATAGCT-TTGGCTATCAAATT
* * *
66740 ATGAAAAGGGATGGCTGTGGCTATC-GATCT
1 ATGAAAAGGGATAGCTTTGGCTATCAAAT-T
* *
66770 ATGAAAAGGGATGGCTTCT-GCTATCAAATC
1 ATGAAAAGGGATAGCTT-TGGCTATCAAATT
* **
66800 ATGAAAAAGGGAT-G--GTGGCAACTATCAAACA
1 ATG-AAAAGGGATAGCTTTGG---CTATCAAATT
* * * *
66831 ATGAAAAGGGAT-GGTGATGACAATCAAATT
1 ATGAAAAGGGATAGCT-TTGGCTATCAAATT
* *
66861 ATGAAAAGGGATAGCTTTGGCTATCGAACT
1 ATGAAAAGGGATAGCTTTGGCTATCAAATT
* * *
66891 ATGAAAAGGGATAACTTTGGTTATCGAATT
1 ATGAAAAGGGATAGCTTTGGCTATCAAATT
*
66921 ACGAAAAGGGAT
1 ATGAAAAGGGAT
66933 GTGAGAACCA
Statistics
Matches: 177, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.01
28 2 0.01
29 21 0.12
30 125 0.71
31 26 0.15
33 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTTGGCTATCAAATT
Found at i:66927 original size:121 final size:120
Alignment explanation
Indices: 66710--66933 Score: 315
Period size: 121 Copynumber: 1.9 Consensus size: 120
66700 GCTATCAATT
* * *
66710 ATGAAAAGGGATAGTGACGACCATCAAATTATGAAAAGGGATGGCTGTGGCTATCGATCTATGAA
1 ATGAAAAGGGATAGTGACGACAATCAAATTATGAAAAGGGATAGCTGTGGCTATCGAACTATGAA
** *
66775 AAGGGATGGCTTCTGCTATCAAATCATGAAAAAGGGATGGTGGCAACTATCAAACA
66 AAGGGATAACTTCTGCTATCAAATCACG-AAAAGGGATGGTGGCAACTATCAAACA
* * *
66831 ATGAAAAGGGATGGTGATGACAATCAAATTATGAAAAGGGATAGCTTTGGCTATCGAACTATGAA
1 ATGAAAAGGGATAGTGACGACAATCAAATTATGAAAAGGGATAGCTGTGGCTATCGAACTATGAA
* * *
66896 AAGGGATAACTT-TGGTTATCGAATTACGAAAAGGGATG
66 AAGGGATAACTTCT-GCTATCAAATCACGAAAAGGGATG
66934 TGAGAACCAT
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
120 11 0.12
121 79 0.88
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.24
Consensus pattern (120 bp):
ATGAAAAGGGATAGTGACGACAATCAAATTATGAAAAGGGATAGCTGTGGCTATCGAACTATGAA
AAGGGATAACTTCTGCTATCAAATCACGAAAAGGGATGGTGGCAACTATCAAACA
Found at i:68391 original size:29 final size:30
Alignment explanation
Indices: 68344--68400 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
68334 ATTTCGAGCA
* *
68344 TAGGGGCAAAATGGTCATTTTGCCAAAGTT
1 TAGGGGCAAAATGATCATTTTACCAAAGTT
68374 TAGGGGC-AAATGATCATTTTACCAAAG
1 TAGGGGCAAAATGATCATTTTACCAAAG
68401 ATGTGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGATCATTTTACCAAAGTT
Found at i:68876 original size:46 final size:46
Alignment explanation
Indices: 68772--68898 Score: 166
Period size: 46 Copynumber: 2.7 Consensus size: 46
68762 CCACATTATG
* *
68772 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACT
1 AGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTGAGACT
* * *
68820 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTTGAGATGT
1 AGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGA-CT
*
68867 A-AGCCAGTGTAAGACATGTTTGGGACATGCAT
1 AGAGCCAGTGTAAGACATGTCTGGGACATGCAT
68899 TGGCTACAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
46 42 0.59
47 15 0.21
48 14 0.20
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
AGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGACT
Found at i:68987 original size:140 final size:140
Alignment explanation
Indices: 68732--68995 Score: 331
Period size: 140 Copynumber: 1.9 Consensus size: 140
68722 TTCGTGTGCT
**
68732 AGTGTAAGACATGTTTAGGACATGCATTGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTAG
1 AGTGTAAGACATGTTTAGGACATGCATTGGCCACAAAAT-AGAGCCAGTGTAAGACCATGTCTAG
* *
68797 GACATGGCATCGGCATTGAGACTAGAGCTAGTGTAAGACATGTCTGGGACATG-CATCGACCTTG
65 GACATGGCATCGGCATCGAGACTAGAGCTAGTGTAAGACATGTCTAGGACATGTCATCGACCTTG
68861 AGATGTAAGCC
130 AGATGTAAGCC
* * * * * *
68872 AGTGTAAGACATGTTTGGGACATGCATTGGCTACAAAAT-GTG-TAGTGTAAGACCGTGTCTGGG
1 AGTGTAAGACATGTTTAGGACATGCATTGGCCACAAAATAGAGCCAGTGTAAGACCATGTCTAGG
* *
68935 ACATGGCATCGGCA-CGAATATGTGAGAG-TCAGTGTAAGACCATGTCTAGGACATGTCATCG
66 ACATGGCATCGGCATCG-AGA-CT-AGAGCT-AGTGTAAGA-CATGTCTAGGACATGTCATCG
68996 GTATTATACT
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
136 1 0.01
137 34 0.32
138 4 0.04
139 13 0.12
140 49 0.46
141 5 0.05
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (140 bp):
AGTGTAAGACATGTTTAGGACATGCATTGGCCACAAAATAGAGCCAGTGTAAGACCATGTCTAGG
ACATGGCATCGGCATCGAGACTAGAGCTAGTGTAAGACATGTCTAGGACATGTCATCGACCTTGA
GATGTAAGCC
Found at i:71157 original size:39 final size:40
Alignment explanation
Indices: 71112--71334 Score: 242
Period size: 39 Copynumber: 5.7 Consensus size: 40
71102 GCTCCTCGTT
* * * *
71112 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
71152 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
71191 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
71230 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
71269 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
71310 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
71335 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
38 14 0.09
39 76 0.48
40 56 0.36
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:71343 original size:41 final size:41
Alignment explanation
Indices: 71266--71343 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
71256 TTTGTATCTC
* * *
71266 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
71307 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
71344 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:78718 original size:39 final size:40
Alignment explanation
Indices: 78673--78895 Score: 242
Period size: 39 Copynumber: 5.7 Consensus size: 40
78663 GCTCCTCGTT
* * * *
78673 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
78713 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
78752 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
78791 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
78830 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
78871 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
78896 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
38 14 0.09
39 76 0.48
40 56 0.36
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:78904 original size:41 final size:41
Alignment explanation
Indices: 78827--78904 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
78817 TTTGTATCTC
* * *
78827 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
78868 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
78905 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:82320 original size:19 final size:21
Alignment explanation
Indices: 82296--82339 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
82286 CAAGCTAGAT
82296 AAATAAATA-AAA-AAAAAAA
1 AAATAAATAGAAATAAAAAAA
82315 AAATAAATAGGAAATAAAAAAA
1 AAATAAATA-GAAATAAAAAAA
82337 AAA
1 AAA
82340 GATATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (21 bp):
AAATAAATAGAAATAAAAAAA
Found at i:82402 original size:19 final size:18
Alignment explanation
Indices: 82369--82404 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
82359 AAGATATGAA
82369 ATAAAAAAAAAAAATAAT
1 ATAAAAAAAAAAAATAAT
*
82387 ATAAACAAATAAAAATAA
1 ATAAA-AAAAAAAAATAA
82405 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAAAAAAAAATAAT
Found at i:82411 original size:40 final size:41
Alignment explanation
Indices: 82326--82414 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
82316 AATAAATAGG
* * * * **
82326 AAATAAAAAAAAAAGATATTTTTAATCAAATAAAAGATATG
1 AAATAAAAAAAAAAAATATATATAAACAAATAAAAGATAAA
82367 AAATAAAAAAAAAAAATA-ATATAAACAAATAAAA-ATAAAA
1 AAATAAAAAAAAAAAATATATATAAACAAATAAAAGAT-AAA
82407 AAATAAAA
1 AAATAAAA
82415 TTAAATTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.05
40 22 0.54
41 17 0.41
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.20
Consensus pattern (41 bp):
AAATAAAAAAAAAAAATATATATAAACAAATAAAAGATAAA
Found at i:93886 original size:37 final size:36
Alignment explanation
Indices: 93841--94014 Score: 189
Period size: 37 Copynumber: 4.8 Consensus size: 36
93831 TCCTCGTTCA
* *
93841 AATGCCTTCGGGAC-ATAGCCGG-TTTAGTAACTCACAC
1 AATGCCTTCGGGACTA-ACCCGGATTTA--AACTCGCAC
93878 AATGCCTTCGGGACTAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTAACCCGGATTT-A-AACTCGCAC
*
93916 GATGCCTTCGGGACTTAACCCGGATTTAAACTCGCAC
1 AATGCCTTCGGGAC-TAACCCGGATTTAAACTCGCAC
*
93953 AATGCCTTC-GGACTTAA-CCGGATTTATACTCGCAC
1 AATGCCTTCGGGAC-TAACCCGGATTTAAACTCGCAC
93988 GAATG-CTTC-GGACTTAACCCGGATTTA
1 -AATGCCTTCGGGAC-TAACCCGGATTTA
94015 GTATCTCGCA
Statistics
Matches: 125, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
35 29 0.23
36 21 0.17
37 36 0.29
38 26 0.21
39 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (36 bp):
AATGCCTTCGGGACTAACCCGGATTTAAACTCGCAC
Found at i:93948 original size:75 final size:74
Alignment explanation
Indices: 93841--94015 Score: 220
Period size: 75 Copynumber: 2.4 Consensus size: 74
93831 TCCTCGTTCA
* *
93841 AATGCCTTCGGGACAT-AGCCGG-TTTAGTAACTCACACAATGCCTTCGGGAC-TAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAG-AACTCACACAATGCCTTC-GGACTTAA-CCGGATT
93903 TAACAACTCGCACG
63 T-A-AACTCGCACG
* *
93917 -ATGCCTTCGGGACTTAACCCGGATTTA-AACTCGCACAATGCCTTCGGACTTAACCGGATTTAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGAACTCACACAATGCCTTCGGACTTAACCGGATTTAA
93980 ACTCGCACG
66 ACTCGCACG
93989 AATG-CTTC-GGACTTAACCCGGATTTAG
1 AATGCCTTCGGGACTTAACCCGGATTTAG
94016 TATCTCGCAC
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
71 18 0.20
72 13 0.14
73 4 0.04
74 12 0.13
75 34 0.38
76 5 0.06
77 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (74 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGAACTCACACAATGCCTTCGGACTTAACCGGATTTAA
ACTCGCACG
Found at i:94048 original size:38 final size:35
Alignment explanation
Indices: 93921--94049 Score: 134
Period size: 35 Copynumber: 3.5 Consensus size: 35
93911 CGCACGATGC
* * *
93921 CTTCGGGACTTAACCCGGATTTAAACTCGCACAATGC
1 CTTC-GGACTTAA-CCGGATTTATACTCGCACAAAGG
* *
93958 CTTCGGACTTAACCGGATTTATACTCGCACGAATG
1 CTTCGGACTTAACCGGATTTATACTCGCACAAAGG
93993 CTTCGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CTTCGGACTTAA-CCGGATTTA-TA-CTCGCACAAAGG
*
94031 -TCTCGGATCTTATCCGGAT
1 CT-TCGGA-CTTAACCGGAT
94050 ATATTCACTA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
35 30 0.38
36 17 0.22
37 7 0.09
38 21 0.27
39 4 0.05
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (35 bp):
CTTCGGACTTAACCGGATTTATACTCGCACAAAGG
Found at i:96445 original size:39 final size:36
Alignment explanation
Indices: 96371--96587 Score: 188
Period size: 39 Copynumber: 5.7 Consensus size: 36
96361 CTGTCCGGGC
* * * *
96371 TAAGTCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGA
1 TAAGTCCGAAGGCATTCGTGC-GAGT--ATAAATCCGGT
* *
96409 TAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTCGTGCGAG-TA-TAAATCC-GGT
96449 TAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGT
1 TAAGTCCGAAGGCATTCGTGCGAG-TA-TAAATCCGGT
96487 TAAGTCCGAAGGCATTCGTGCGAGTATAAATCCGGGT
1 TAAGTCCGAAGGCATTCGTGCGAGTATAAATCC-GGT
* *
96524 TAAGTCCCGAAGGCA-GCGTGCGAGTTGTTAAATCCGGGT
1 TAAGT-CCGAAGGCATTCGTGCGAG-T-ATAAATCC-GGT
* *
96563 TATGTCCCGAAGGCATT-GTGTGAGT
1 TAAGT-CCGAAGGCATTCGTGCGAGT
96588 TACTAAAACC
Statistics
Matches: 157, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.04
37 18 0.11
38 43 0.27
39 75 0.48
40 14 0.09
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (36 bp):
TAAGTCCGAAGGCATTCGTGCGAGTATAAATCCGGT
Found at i:96588 original size:39 final size:40
Alignment explanation
Indices: 96415--96618 Score: 251
Period size: 39 Copynumber: 5.3 Consensus size: 40
96405 CGGATAAGAT
* * * *
96415 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGT-
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
96454 CCGAAGGCATTCGTGCGAGTTATTAAATCC-GGTTAAGT-
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
96492 CCGAAGGCATTCGTGCGAG-TA-TAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * *
96530 CCGAAGGCA-GCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
96569 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
96608 CCGAAGGCATT
1 CCGAAGGCATT
96619 TGAACGAGGA
Statistics
Matches: 147, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
36 7 0.05
37 18 0.12
38 37 0.25
39 85 0.58
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Done.