Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014714.1 Kokia drynarioides strain JFW-HI SEQ_129753, whole genome shotgun sequence
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: 142710
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1231 original size:29 final size:27
Alignment explanation
Indices: 1197--1323 Score: 101
Period size: 27 Copynumber: 4.6 Consensus size: 27
1187 ATAAAATTAT
1197 GGGCAAAACTGTAAATTTTGAAAAGTAG
1 GGGCAAAACTGTAAATTTTGAAAA-TAG
* *
1225 GAGGCAAAATTGTAAAATTTGGAAAATAG
1 G-GGCAAAACTGT-AAATTTTGAAAATAG
* * *
1254 GGGAAAAACTATAAACTTTGAAAATAG
1 GGGCAAAACTGTAAATTTTGAAAATAG
* * * * * *
1281 TGGTAAAATTATAAAATCTGAAAACTAG
1 GGGCAAAACTGTAAATTTTGAAAA-TAG
* *
1309 GTGCAAAACTATAAA
1 GGGCAAAACTGTAAA
1324 ATCCCAAAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
27 32 0.40
28 23 0.29
29 14 0.17
30 11 0.14
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (27 bp):
GGGCAAAACTGTAAATTTTGAAAATAG
Found at i:1317 original size:55 final size:57
Alignment explanation
Indices: 1197--1323 Score: 152
Period size: 55 Copynumber: 2.3 Consensus size: 57
1187 ATAAAATTAT
* * * *
1197 GGGCAAAACTGTAAATTTTGAAAAGTAGGAGGCAAAATTGTAAAATTTGGAAAATAG
1 GGGCAAAACTATAAACTTTGAAAAGTAGGAGGCAAAATTATAAAATCTGGAAAATAG
* * *
1254 GGGAAAAACTATAAACTTTGAAAA-TA-GTGGTAAAATTATAAAATCT-GAAAACTAG
1 GGGCAAAACTATAAACTTTGAAAAGTAGGAGGCAAAATTATAAAATCTGGAAAA-TAG
*
1309 GTGCAAAACTATAAA
1 GGGCAAAACTATAAA
1324 ATCCCAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
54 5 0.08
55 32 0.53
56 2 0.03
57 21 0.35
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (57 bp):
GGGCAAAACTATAAACTTTGAAAAGTAGGAGGCAAAATTATAAAATCTGGAAAATAG
Found at i:1326 original size:28 final size:27
Alignment explanation
Indices: 1197--1325 Score: 123
Period size: 28 Copynumber: 4.6 Consensus size: 27
1187 ATAAAATTAT
* *
1197 GGGCAAAACTGTAAATTTTGAAAAGTAG
1 GGGCAAAACTATAAAATTTGAAAA-TAG
* *
1225 GAGGCAAAATTGTAAAATTTGGAAAATAG
1 G-GGCAAAACTATAAAATTT-GAAAATAG
* *
1254 GGGAAAAACTATAAACTTTGAAAATAG
1 GGGCAAAACTATAAAATTTGAAAATAG
* * * *
1281 TGGTAAAATTATAAAATCTGAAAACTAG
1 GGGCAAAACTATAAAATTTGAAAA-TAG
*
1309 GTGCAAAACTATAAAAT
1 GGGCAAAACTATAAAAT
1326 CCCAAAAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
27 27 0.33
28 31 0.37
29 20 0.24
30 5 0.06
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (27 bp):
GGGCAAAACTATAAAATTTGAAAATAG
Found at i:1373 original size:26 final size:26
Alignment explanation
Indices: 1332--1408 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 26
1322 AAATCCCAAA
* *
1332 AAAATAAAGGCAAAATTGTAAAATTT
1 AAAATATAGGGAAAATTGTAAAATTT
*
1358 GAAAATA-AGGGTAAATTTGTAAAATTT
1 -AAAATATAGGG-AAAATTGTAAAATTT
1385 AAAATATAGGGAAAATTGTAAAAT
1 AAAATATAGGGAAAATTGTAAAAT
1409 CTGGAAAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 21 0.47
27 24 0.53
ACGTcount: A:0.55, C:0.01, G:0.16, T:0.29
Consensus pattern (26 bp):
AAAATATAGGGAAAATTGTAAAATTT
Found at i:1873 original size:28 final size:28
Alignment explanation
Indices: 1805--1885 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
1795 ATAGGTTTGT
* * *
1805 CACAAAGGCTTTCCTTTCCGAGGTTCAC
1 CACAAAGGCTCTCCTTTCAGAGATTCAC
*
1833 CACAAAGGTTCTCCATTT-AGAGATTCAC
1 CACAAAGGCTCTCC-TTTCAGAGATTCAC
*
1861 CACAAAGGCTCTCTTTTCAGAGATT
1 CACAAAGGCTCTCCTTTCAGAGATT
1886 ATCATGAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.07
28 39 0.87
29 3 0.07
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (28 bp):
CACAAAGGCTCTCCTTTCAGAGATTCAC
Found at i:5492 original size:30 final size:29
Alignment explanation
Indices: 5417--5492 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
5407 TAAATTGAAG
*
5417 TTTTGGATCCCTTAAAAATTAGAAAAATTA
1 TTTTGGA-CCCTTAAAAATTAGAAAAATAA
* * *
5447 TTTTAGACCCATAAAAATTGGTAAAAA-AA
1 TTTTGGACCCTTAAAAATTAG-AAAAATAA
5476 TTTTGGACCCCTTAAAA
1 TTTTGGA-CCCTTAAAA
5493 GCTGGAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 19 0.50
30 19 0.50
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (29 bp):
TTTTGGACCCTTAAAAATTAGAAAAATAA
Found at i:7018 original size:21 final size:21
Alignment explanation
Indices: 6994--7043 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
6984 TGGGAAAGTT
6994 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
** * * *
7015 CTACTAATACAATTATTACTT
1 CTACCGATACAAGTATGACTA
7036 CTACCGAT
1 CTACCGAT
7044 GCAACAAACT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:12129 original size:36 final size:36
Alignment explanation
Indices: 12089--12161 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
12079 AACTCCAAAG
12089 TAAGAGCTTGTTTAATTGATGGTTTAAACGCAGGGA
1 TAAGAGCTTGTTTAATTGATGGTTTAAACGCAGGGA
*
12125 TAAGAGCTTGTTTAATTGATGGTTTAAATGCAGGGA
1 TAAGAGCTTGTTTAATTGATGGTTTAAACGCAGGGA
12161 T
1 T
12162 CGTCCTGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (36 bp):
TAAGAGCTTGTTTAATTGATGGTTTAAACGCAGGGA
Found at i:12847 original size:54 final size:54
Alignment explanation
Indices: 12765--12873 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
12755 AGCTGCCAGG
*
12765 GTCTTTCATCTTTGGTGGCAACTTATTTGTTAGCACAGCACTACACCTCTCTGT
1 GTCTTTCATCTTTGGTGGCAACTTATTTGTTAGCACAACACTACACCTCTCTGT
**
12819 GTCTTTCATCTTTGGTGGCAACTTATTTGTTAGCACAATGCTACACCTCTCTGT
1 GTCTTTCATCTTTGGTGGCAACTTATTTGTTAGCACAACACTACACCTCTCTGT
12873 G
1 G
12874 AGCGTAATCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (54 bp):
GTCTTTCATCTTTGGTGGCAACTTATTTGTTAGCACAACACTACACCTCTCTGT
Found at i:13603 original size:17 final size:17
Alignment explanation
Indices: 13581--13632 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
13571 ACATTCGAGC
*
13581 TTATGACTGCATCTGGT
1 TTATGAATGCATCTGGT
*
13598 TTATGAATGCATCTGATT
1 TTATGAATGCATCTG-GT
* *
13616 TTTTGATTGCATCTGGT
1 TTATGAATGCATCTGGT
13633 CATGTGATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.46
Consensus pattern (17 bp):
TTATGAATGCATCTGGT
Found at i:16772 original size:120 final size:120
Alignment explanation
Indices: 16514--16772 Score: 365
Period size: 120 Copynumber: 2.2 Consensus size: 120
16504 AGAAAATAAT
* * * * * *
16514 CCAGCCATCAATATGGTATGCTATAATCTAGAATTTCATTCCCATGTCTGTATCGACTCTGTTAC
1 CCAGCCATCAATATAGTATGCTATAATCCAGAATTTCACTCCCATGTCTGTATCAACCCTATTAC
** * *
16579 CAGTATATGATGTTGCTCACACAAGTTGTCGAGGACTCACAACATATACGGTACC
66 CAGTATACCATGCTGCTCACACAAGCTGTCGAGGACTCACAACATATACGGTACC
* *
16634 CCAACCATCAATACAGTATGCTATAATCCAGAATTTCACTCCCATGTCTGTATCAACCCTATTAC
1 CCAGCCATCAATATAGTATGCTATAATCCAGAATTTCACTCCCATGTCTGTATCAACCCTATTAC
* * *
16699 CAGTATACCATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACC
66 CAGTATACCATGCTGCTCACACAAGCTGTCGAGGACTCACAACATATACGGTACC
* *
16754 CCAGTCATCGATATAGTAT
1 CCAGCCATCAATATAGTAT
16773 CTGTGCATAT
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (120 bp):
CCAGCCATCAATATAGTATGCTATAATCCAGAATTTCACTCCCATGTCTGTATCAACCCTATTAC
CAGTATACCATGCTGCTCACACAAGCTGTCGAGGACTCACAACATATACGGTACC
Found at i:25351 original size:58 final size:58
Alignment explanation
Indices: 25216--25357 Score: 154
Period size: 56 Copynumber: 2.5 Consensus size: 58
25206 ATATTATATA
* * *
25216 TTATGATTTTTATT-AATTCATATTT--TAA-TATATATTAAAAATGTTATTAAATTAT
1 TTATCATTTTTATTAAATT-ATATTTAATAATTATATATTAAAAATATAATTAAATTAT
* * *
25271 ATATCA--TTTATTAAATTGTATTTAATAATTAT-TATGTTAAAATATAATTAAATTAT
1 TTATCATTTTTATTAAATTATATTTAATAATTATATAT-TAAAAATATAATTAAATTAT
*
25327 TTATTATTTTTATTAAATTATATTTAATAAT
1 TTATCATTTTTATTAAATTATATTTAATAAT
25358 AATCTTATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
53 11 0.15
54 4 0.06
55 10 0.14
56 24 0.34
58 22 0.31
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (58 bp):
TTATCATTTTTATTAAATTATATTTAATAATTATATATTAAAAATATAATTAAATTAT
Found at i:25369 original size:58 final size:56
Alignment explanation
Indices: 25216--25376 Score: 152
Period size: 58 Copynumber: 2.9 Consensus size: 56
25206 ATATTATATA
* * * *
25216 TTATGATTTTTATT-AATTCATATTT--TAATATATATTAAAAATGTTATTAAATTAT
1 TTATCATTTTTATTAAATT-ATATTTAATAATATTTATT-AAAATATAATTAAATTAT
* * *
25271 ATATCA--TTTATTAAATTGTATTTAATAATTATTATGTTAAAATATAATTAAATTAT
1 TTATCATTTTTATTAAATTATATTTAATAA-TATT-TATTAAAATATAATTAAATTAT
* *
25327 TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAATTTAAT
1 TTATCATTTTTATTAAATTATATTTAATAAT-AT-TTATTAAAATATAAT
25377 AACAATAATC
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
53 11 0.13
54 4 0.05
55 7 0.08
56 23 0.27
57 4 0.05
58 35 0.41
59 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (56 bp):
TTATCATTTTTATTAAATTATATTTAATAATATTTATTAAAATATAATTAAATTAT
Found at i:27396 original size:30 final size:31
Alignment explanation
Indices: 27355--27428 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 31
27345 TAAATGATTT
27355 TAAAATTATTAAAATTATTTTTTAAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAAATAA
* **
27385 TAAAATCATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAAATAA
27416 TAAAATTATTAAA
1 TAAAATTATTAAA
27429 TAATTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 26 0.67
31 13 0.33
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTAAAAATAA
Found at i:28033 original size:3 final size:3
Alignment explanation
Indices: 28025--28059 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28015 AAATAAGCAA
28025 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28060 AGTATTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28299 original size:20 final size:21
Alignment explanation
Indices: 28259--28307 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
28249 AAAATTATTT
* *
28259 AATAATTTTATTATTTTTTAA
1 AATAATTTTAATATATTTTAA
28280 AATAATTTTAATA-ATTTTAA
1 AATAATTTTAATATATTTTAA
*
28300 AATCATTT
1 AATAATTT
28308 ACTGATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AATAATTTTAATATATTTTAA
Found at i:37750 original size:10 final size:10
Alignment explanation
Indices: 37729--37761 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
37719 TATTTCTTAC
*
37729 TTTTTAAATT
1 TTTTTCAATT
37739 TTTTTC-ATT
1 TTTTTCAATT
37748 TTTTTCAATT
1 TTTTTCAATT
37758 TTTT
1 TTTT
37762 AAAAATTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCAATT
Found at i:38816 original size:30 final size:30
Alignment explanation
Indices: 38780--39084 Score: 268
Period size: 30 Copynumber: 10.4 Consensus size: 30
38770 GTTTAAGGTT
* *
38780 AAATGTAATTTTGGAAAAGTTTAGGGGTAA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
* *
38810 AAATGTAATTTTAGGAAAGTTTA-GGGTTA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
* * *
38839 AAATGTGATTTTAGAGAAGTTT-GAGGTCA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
*
38868 AAATGTGATTTT-GAGAAAGTTT-GGTGGTCA
1 AAATGTAATTTTAGA-AAAGTTTAGG-GGTCA
* * * * *
38898 AAATGTGATTTTACAGAAGTTTAGGAGTGA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
* * * *
38928 AAATATGATTTTAGAAAAGTTTAAGGGTTA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
* * * *
38958 AAATATGATTTTA-AAAATTTTAGGGGTTA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
*
38987 AAATGTAATTTT-GAAAAATTT-GGGGTCA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
* * * * *
39015 AAATGTAATTTTTG-GAAGTTTAAGTGTTA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTCA
*
39044 AAATATAATTTTAGAAAAGTTTTA-GGGTCA
1 AAATGTAATTTTAGAAAAG-TTTAGGGGTCA
39074 AAATGTAATTT
1 AAATGTAATTT
39085 CTATAAACTT
Statistics
Matches: 228, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
28 25 0.11
29 95 0.42
30 101 0.44
31 7 0.03
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
AAATGTAATTTTAGAAAAGTTTAGGGGTCA
Found at i:38849 original size:29 final size:29
Alignment explanation
Indices: 38744--39084 Score: 229
Period size: 29 Copynumber: 11.7 Consensus size: 29
38734 AAAGGAAAAA
38744 TAGGGTTTAAAATG-AAGTTTT--GAAGAGTT
1 TAGGG-TTAAAATGTAA-TTTTAGGAA-AGTT
*
38773 TAAGGTT-AAATGTAATTTT-GGAAAAGTT
1 TAGGGTTAAAATGTAATTTTAGG-AAAGTT
*
38801 TAGGGGTAAAAATGTAATTTTAGGAAAGTT
1 TA-GGGTTAAAATGTAATTTTAGGAAAGTT
*
38831 TAGGGTTAAAATGTGATTTTA-GAGAAGTT
1 TAGGGTTAAAATGTAATTTTAGGA-AAGTT
* *
38860 T-GAGGTCAAAATGTGATTTT-GAGAAAGTT
1 TAG-GGTTAAAATGTAATTTTAG-GAAAGTT
* * * *
38889 TGGTGGTCAAAATGTGATTTTA-CAGAAGTT
1 TAG-GGTTAAAATGTAATTTTAGGA-AAGTT
* * * *
38919 TAGGAGTGAAAATATGATTTTAGAAAAGTT
1 TAGG-GTTAAAATGTAATTTTAGGAAAGTT
* * * *
38949 TAAGGGTTAAAATATGATTTTA-AAAATTT
1 T-AGGGTTAAAATGTAATTTTAGGAAAGTT
* *
38978 TAGGGGTTAAAATGTAATTTT-GAAAAATT
1 TA-GGGTTAAAATGTAATTTTAGGAAAGTT
* * *
39007 TGGGGTCAAAATGTAATTTTTGG-AAGTT
1 TAGGGTTAAAATGTAATTTTAGGAAAGTT
* * *
39035 TAAGTGTTAAAATATAATTTTAGAAAAGTTT
1 T-AGGGTTAAAATGTAATTTTAGGAAAG-TT
*
39066 TAGGGTCAAAATGTAATTT
1 TAGGGTTAAAATGTAATTT
39085 CTATAAACTT
Statistics
Matches: 260, Mismatches: 30, Indels: 43
0.78 0.09 0.13
Matches are distributed among these distances:
27 9 0.03
28 37 0.14
29 103 0.40
30 102 0.39
31 9 0.03
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (29 bp):
TAGGGTTAAAATGTAATTTTAGGAAAGTT
Found at i:38859 original size:59 final size:59
Alignment explanation
Indices: 38744--39084 Score: 302
Period size: 59 Copynumber: 5.8 Consensus size: 59
38734 AAAGGAAAAA
* * * * * *
38744 TAGGGTTTAAAATG-AAGTTTT-GAAGAGTTTAAGGT-TAAATGTAATTTTGGAAAAGTT
1 TAGGGGTTAAAATGTAA-TTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTAGAGAAGTT
* * * *
38801 TAGGGGTAAAAATGTAATTTTAGGAAAGTTTAGGGTTAAAATGTGATTTTAGAGAAGTT
1 TAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTAGAGAAGTT
* * * * * *
38860 T-GAGGTCAAAATGTGATTTT-GAGAAAGTTTGGTGGTCAAAATGTGATTTTACAGAAGTT
1 TAGGGGTTAAAATGTAATTTTAGA-AAAGTTTAG-GGTCAAAATGTAATTTTAGAGAAGTT
* * * * * * * * *
38919 TAGGAGTGAAAATATGATTTTAGAAAAGTTTAAGGGTTAAAATATGATTTTA-AAAATTT
1 TAGGGGTTAAAATGTAATTTTAGAAAAGTTT-AGGGTCAAAATGTAATTTTAGAGAAGTT
* * *
38978 TAGGGGTTAAAATGTAATTTT-GAAAAATTTGGGGTCAAAATGTAATTTTTG-GAAGTT
1 TAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTAGAGAAGTT
* * *
39035 TAAGTGTTAAAATATAATTTTAGAAAAGTTTTAGGGTCAAAATGTAATTT
1 TAGGGGTTAAAATGTAATTTTAGAAAAG-TTTAGGGTCAAAATGTAATTT
39085 CTATAAACTT
Statistics
Matches: 231, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
57 54 0.23
58 50 0.22
59 86 0.37
60 38 0.16
61 3 0.01
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (59 bp):
TAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTAGAGAAGTT
Found at i:46320 original size:30 final size:29
Alignment explanation
Indices: 46285--46508 Score: 152
Period size: 30 Copynumber: 7.6 Consensus size: 29
46275 AAGAGTTTGA
46285 GGTCAAAATGTGATTTTGATAAAGTTT-AG
1 GGTCAAAATGTGATTTTGA-AAAGTTTAAG
*
46314 TGGTCAAAATGTGATTTTAGAGAAGTTTAAG
1 -GGTCAAAATGTGATTTT-GAAAAGTTTAAG
* *
46345 GGTGAAAATATGATTTTAGAAAAGTTT-AG
1 GGTCAAAATGTGATTTT-GAAAAGTTTAAG
* *
46374 GTGTCAAAATATGATTTT-ACAAAATTTAAG
1 G-GTCAAAATGTGATTTTGA-AAAGTTTAAG
* * *
46404 GGTTAAAATGTAATTTTGAGAAAG-TTATG
1 GGTCAAAATGTGATTTTGA-AAAGTTTAAG
* * * * *
46433 AGTTAAAATGT-ATTTTTTGGAACGTTTATG
1 GGTCAAAATGTGA--TTTTGAAAAGTTTAAG
* * * * *
46463 GGTTAAAATATAATTTTGGAGAAGTTTTAG
1 GGTCAAAATGTGATTTT-GAAAAGTTTAAG
*
46493 GGTCAAAATGTAATTT
1 GGTCAAAATGTGATTT
46509 CTATAAAGTC
Statistics
Matches: 159, Mismatches: 24, Indels: 22
0.78 0.12 0.11
Matches are distributed among these distances:
28 2 0.01
29 43 0.27
30 109 0.69
31 5 0.03
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
GGTCAAAATGTGATTTTGAAAAGTTTAAG
Found at i:46359 original size:60 final size:60
Alignment explanation
Indices: 46297--46508 Score: 188
Period size: 59 Copynumber: 3.6 Consensus size: 60
46287 TCAAAATGTG
* *
46297 ATTTT-GATAAAGTTTAGTG-GTCAAAATGTGATTTTAGAGAAGTTTAAGGGTGAAAATATG
1 ATTTTAGA-AAAGTTTAG-GAGTCAAAATGTGATTTTAGAGAAGTTTAAGGGTTAAAATATA
* * * * *
46357 ATTTTAGAAAAGTTTAGGTGTCAAAATATGATTTTACA-AAATTTAAGGGTTAAAATGTA
1 ATTTTAGAAAAGTTTAGGAGTCAAAATGTGATTTTAGAGAAGTTTAAGGGTTAAAATATA
* * * *
46416 ATTTT-GAGAAAG-TTATGAGTTAAAATGT-ATTTTTTG-GAACGTTTATGGGTTAAAATATA
1 ATTTTAGA-AAAGTTTAGGAGTCAAAATGTGA-TTTTAGAGAA-GTTTAAGGGTTAAAATATA
* * *
46475 ATTTTGGAGAAGTTTTAGG-GTCAAAATGTAATTT
1 ATTTTAGAAAAG-TTTAGGAGTCAAAATGTGATTT
46509 CTATAAAGTC
Statistics
Matches: 124, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
57 1 0.01
58 20 0.16
59 51 0.41
60 45 0.36
61 7 0.06
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.39
Consensus pattern (60 bp):
ATTTTAGAAAAGTTTAGGAGTCAAAATGTGATTTTAGAGAAGTTTAAGGGTTAAAATATA
Found at i:48544 original size:123 final size:123
Alignment explanation
Indices: 48319--48564 Score: 440
Period size: 123 Copynumber: 2.0 Consensus size: 123
48309 GGATAACTGT
*
48319 AATATGCCCTATGATCGGTGTAAGAGATTGGATAGTTTTGATCTGCCCCATGATTGGGGTAAGAG
1 AATATGCCCTATGATCAGTGTAAGAGATTGGATAGTTTTGATCTGCCCCATGATTGGGGTAAGAG
*
48384 ATCGGATGATGCAATTTGCCCCTATCGCGGGGAAAGAGATTGGCTGACGGTGATCTGC
66 ATCGGATGATGCAATTTGCCCCTATCGCGAGGAAAGAGATTGGCTGACGGTGATCTGC
*
48442 AATATGCCCTATGATCAGTGTAAGAGATTGGATA-TTTGTGATCTGCCTCATGATTGGGGTAAGA
1 AATATGCCCTATGATCAGTGTAAGAGATTGGATAGTTT-TGATCTGCCCCATGATTGGGGTAAGA
*
48506 GATCGGATGATGCAATTTGCCCCTATCGCGAGGTAAGAGATTGGCTGACGGTGATCTGC
65 GATCGGATGATGCAATTTGCCCCTATCGCGAGGAAAGAGATTGGCTGACGGTGATCTGC
48565 CTCATGATCG
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
122 3 0.03
123 115 0.97
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (123 bp):
AATATGCCCTATGATCAGTGTAAGAGATTGGATAGTTTTGATCTGCCCCATGATTGGGGTAAGAG
ATCGGATGATGCAATTTGCCCCTATCGCGAGGAAAGAGATTGGCTGACGGTGATCTGC
Found at i:48602 original size:39 final size:38
Alignment explanation
Indices: 48559--49012 Score: 110
Period size: 39 Copynumber: 11.7 Consensus size: 38
48549 GCTGACGGTG
48559 ATCTGCCTCATGATCGGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCC-CATGATCGGGGTAAAAGATCGAATGGTTGCA
* * * * * ** * * **
48598 ATCTGCCCCTG-TCGCTGGTTAGAGATTGGCTGATGGTG
1 ATCTGCCCATGATCG-GGGTAAAAGATCGAATGGTTGCA
* * *
48636 ATTTGCCCCATGATTGGGGTAAAAGATCGAATGGTTACA
1 ATCTG-CCCATGATCGGGGTAAAAGATCGAATGGTTGCA
* * * ** *
48675 ATCTGCCCCT-ATCGTGGGGTAAGAGATTGGTTGACGGTG--
1 ATCTGCCCATGATC--GGGGTAAAAGATCGAATG--GTTGCA
*
48714 ATCTGCCCCATGATCGGGTTAAAAGATCGAATGGTTGCA
1 ATCTG-CCCATGATCGGGGTAAAAGATCGAATGGTTGCA
* * * * *
48753 ATCTACCCCA-GTCTCGGGGCAAGAGATTAGCAAATGG-TG--
1 ATCT-GCCCATG-ATCGGGGTAAAAGA-T--CGAATGGTTGCA
* * * *
48792 ATCTACCCCAAGCTCGGGGTAAAAAATCGAATGGTTGCA
1 ATCT-GCCCATGATCGGGGTAAAAGATCGAATGGTTGCA
* * * * *
48831 ATATGCCCCAGGCTCGGGGTAAGAGATTAGCCAATGG-TG--
1 ATCTG-CCCATGATCGGGGTAAAAGA-T--CGAATGGTTGCA
* * * * ** *
48870 ATCTGCCCCAAGCTCAGGGTAAAAGATCGGATGACTACA
1 ATCTG-CCCATGATCGGGGTAAAAGATCGAATGGTTGCA
* * * * *
48909 ATCTGCCCTAGGCT-AGGGTAAGAGATTGACCGATGG-TG--
1 ATCTGCCC-ATGATCGGGGTAAAAGATCGA---ATGGTTGCA
* *
48947 ATCTGCCCAAGGCTCGGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCCC-ATGATCGGGGTAAAAGATCGAATGGTTGCA
* * *
48986 ATCTGCCCTAGGCTCGGGGTAAGAGAT
1 ATCTGCCC-ATGATCGGGGTAAAAGAT
49013 TGGCTTATGG
Statistics
Matches: 303, Mismatches: 77, Indels: 70
0.67 0.17 0.16
Matches are distributed among these distances:
36 14 0.05
37 13 0.04
38 55 0.18
39 187 0.62
40 10 0.03
41 12 0.04
42 12 0.04
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (38 bp):
ATCTGCCCATGATCGGGGTAAAAGATCGAATGGTTGCA
Found at i:48726 original size:155 final size:156
Alignment explanation
Indices: 48461--49346 Score: 640
Period size: 155 Copynumber: 5.7 Consensus size: 156
48451 TATGATCAGT
* * * * * * * *
48461 GTAAGAGATTGG-ATATTTGTGATCTGCCTCATGATTGGGGTAAGAGATCGGAT-GATGCAATTT
1 GTAAGAGATTGGCAGA-TGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCT
* *
48524 GCCCCTATCG--CGAGGTAAGAGATTGGCTGACGGTGATCTGCCTCATGATCGGGGTAAAAGATC
65 GCCCCTA-CGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATC
*
48587 GAATGGTTGCAATCTGCCCCTGTCGCTG
129 GAATGGTTACAATCTGCCCCTGTCGCTG
* * * * *
48615 GTTAGAGATTGGCTGATGGTGATTTGCCCCATGATTGGGGTAAAAGATCGAATGGTTACAATCTG
1 GTAAGAGATTGGCAGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTG
* *
48680 CCCCTATCG-T-GGGGTAAGAGATTGGTTGACGGTGATCTGCCCCATGATCGGGTTAAAAGATCG
66 CCCCTA-CGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATCG
* * * * *
48743 AATGGTTGCAATCTACCCCAGTCTCGGG
130 AATGGTTACAATCTGCCCCTGTCGC-TG
* * * * * * * *
48771 GCAAGAGATTAGCAAATGGTGATCTACCCCAAGCTCGGGGTAAAAAATCGAATGGTTGCAATATG
1 GTAAGAGATTGGCAGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTG
* * ** * * * * *
48836 CCCC-AGGCTCGGGGTAAGAGATTAGCCAATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGG
66 CCCCTACGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATCGA
**
48900 ATGACTACAATCTG-CCCTAG--GCTAGG
131 ATGGTTACAATCTGCCCCT-GTCGCT--G
* * * * *
48926 GTAAGAGATTGACCGATGGTGATCTGCCCAAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCTG
1 GTAAGAGATTGGCAGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTG
* * * * * * *
48991 -CCCTAGGCTCGGGGTAAGAGATTGGCTTATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGA
66 CCCCTACGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATCGA
* *
49055 ATGGTTACAATATG--CCT-TAGGCTCG
131 ATGGTTACAATCTGCCCCTGT-CGCT-G
* *** * * * * * * * *
49080 AGATAAGAGATTAGTTTATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGGATAGCTGTAA-C
1 -G-TAAGAGATTGGCAGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATC
* * * ** * * * * * *
49144 TGTCTC-AGGCTTAGGGTAAGGGATTGG-TCGATGGTGATCTGCCTCAAGCTCGGGGTAAAACAT
64 TGCCCCTACGCTCGGGGTAAGAGATTGGCT-GACGGTGATCTGCCCCATGATCGGGGTAAAAGAT
* * * **
49207 CAAATGGTTGCAATCTGCCCCAAGCTCGGGG
128 CGAATGGTTACAATCTGCCCC-TG-TCGCTG
** * * * ** *
49238 GTAAGAGATTAGTTA-ATGGTGATCTTCCCCAGGCTCAAGGTAAAAGATCGAATGGCTGCAATCT
1 GTAAGAGATT-GGCAGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCT
* * * *
49302 G-CCTTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
65 GCCCCTACGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCA
49347 GGCTTAGGGT
Statistics
Matches: 589, Mismatches: 117, Indels: 49
0.78 0.15 0.06
Matches are distributed among these distances:
154 53 0.09
155 280 0.48
156 212 0.36
157 40 0.07
158 2 0.00
159 1 0.00
160 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (156 bp):
GTAAGAGATTGGCAGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTG
CCCCTACGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATCGA
ATGGTTACAATCTGCCCCTGTCGCTG
Found at i:48823 original size:233 final size:229
Alignment explanation
Indices: 48479--49346 Score: 819
Period size: 233 Copynumber: 3.7 Consensus size: 229
48469 TTGGATATTT
* * * * * * * * * * *
48479 GTGATCTGCCTCATGATTGGGGTAAGAGATCGGAT-GATGCAATTTGCCCCTATCGCGAGGTAAG
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCC-AGCTCGGGGTAAG
* * * * * * * *
48543 AGATTGGCTGACGGTGATCTGCCTCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCT
65 AGATTAGCTAATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATATG-CCCT
* * * * * * * *
48608 G-TCGCTGGTTAGAGATTGGCTGATGGTGATTTGCCCCATGATTGGGGTAAAAGATCGAATGGTT
129 GCTCG-TGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCT
* * *
48672 ACAATCTGCCCCTATCGTGGGGTAAGAGATTGGTTGACG
193 ACAATCTG-CCCTA-CGTAGGGTAAGAGATTGGTCGATG
* * * * *
48711 GTGATCTGCCCCATGATCGGGTTAAAAGATCGAATGGTTGCAATCTACCCCAGTCTCGGGGCAAG
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCAG-CTCGGGGTAAG
* * *
48776 AGATTAGCAAATGGTGATCTACCCCAAGCTCGGGGTAAAAAATCGAATGGTTGCAATATGCCCCA
65 AGATTAGCTAATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATATG-CCC-
* * ** * *
48841 GGCTCGGGGTAAGAGATTAGCCAATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGGATGACT
128 TGCTCGTGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCT
* **
48906 ACAATCTGCCCTAGGCTAGGGTAAGAGATTGACCGATG
193 ACAATCTGCCCTACG-TAGGGTAAGAGATTGGTCGATG
*
48944 GTGATCTG-CCCAAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCTAGGCTCGGGGTAA
1 GTGATCTGCCCCAA-GCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCA-GCTCGGGGTAA
* * * * *
49008 GAGATTGGCTTATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGAATGGTTACAATATGCCTT
64 GAGATTAGCTAATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATATGCCCT
* * * * * * * *
49073 AGGCTCGAGATAAGAGATTAGTTTATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGGATAGC
129 --GCTCGTGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGC
** * * *
49138 TGTAA-CTG-TCTCAGGCTTAGGGTAAGGGATTGGTCGATG
192 TACAATCTGCCCT-A--CGTAGGGTAAGAGATTGGTCGATG
* * *
49177 GTGATCTGCCTCAAGCTCGGGGTAAAACATCAAATGGTTGCAATCTGCCCCAAGCTCGGGGGTAA
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCC-AGCTC-GGGGTAA
* * ** * * *
49242 GAGATTAGTTAATGGTGATCTTCCCCAGGCTCAAGGTAAAAGATCGAATGGCTGCAATCTGCCTT
64 GAGATTAGCTAATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATATGCCCT
* *
49307 AGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
129 --GCTCGTGGTAAGAGATTAGCTGATGGTGATCTGCCCCA
49347 GGCTTAGGGT
Statistics
Matches: 525, Mismatches: 96, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
231 2 0.00
232 42 0.08
233 321 0.61
234 157 0.30
235 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (229 bp):
GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCAGCTCGGGGTAAGA
GATTAGCTAATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATATGCCCTGC
TCGTGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACA
ATCTGCCCTACGTAGGGTAAGAGATTGGTCGATG
Found at i:49341 original size:39 final size:39
Alignment explanation
Indices: 48690--49624 Score: 333
Period size: 39 Copynumber: 24.0 Consensus size: 39
48680 CCCCTATCGT
* * * *
48690 GGGGTAAGAGATTGGTTGACGGTGATCTGCCCCATGATC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * ** * * ** * *
48729 GGGTTAAAAGATCGAATGGTTGCAATCTACCCCAGTCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * ** * *
48768 GGGGCAAGAGATTAGCAAATGGTGATCTACCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * ** * * ** *
48807 GGGGTAAAAAATCGAATGGTTGCAATATGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* ** *
48846 GGGGTAAGAGATTAGCCAATGGTGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * * *** *
48885 AGGGTAAAAGATCGGATGACT-ACAATCTGCCCTAGGCT-
1 GGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAGGCTC
* * * *
48923 AGGGTAAGAGATTGACCGATGGTGATCTGCCCAAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * ** * * ** *
48962 GGGGTAAAAGATCGAATGGTTGCAATCTGCCCTAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * *
49001 GGGGTAAGAGATTGGCTTATGGTGATCTACCCTAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * ** * **** * **
49040 GGGGTAAAAGATCGAATGGTTACAATATGCCTTAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * * * * *
49079 GAGATAAGAGATTAGTTTATGGTGATCTACCCTAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * * * * * *
49118 GGGGTAAAAGATCGGAT-A-GCTGTAACTGTCTCAGGCTT
1 GGGGTAAGAGATTGGCTGATGGTG-ATCTGCCCCAGGCTC
* * * *
49156 AGGGTAAGGGATTGG-TCGATGGTGATCTGCCTCAAGCTC
1 GGGGTAAGAGATTGGCT-GATGGTGATCTGCCCCAGGCTC
* * ** *
49195 GGGGTAAAACA-T--CAAATGGTTGCAATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGGCTC
* * * *
49234 GGGGGTAAGAGATTAGTTAATGGTGATCTTCCCCAGGCTC
1 -GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
** * **
49274 AAGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCTTAGGCTC
1 GGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCCAGGCTC
* *
49313 GAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTT
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * ** *
49352 AGGGTAAGAGATTTGCTGATGATGATCTGCCTTAGGCTT
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * * * *
49391 GGGGTAAGAGA-T--CAGATGGCTGTAATTTGCCTCATGATT
1 GGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGGCTC
* * * * *
49430 GGGGTAAGAGATTGGCTAATAGTGATTTGCCCGATGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* ** * * * *
49469 GGGGTAAGAGATCGAATGGCT-GTAATTTGCCTCAGGCTC
1 GGGGTAAGAGATTGGCT-GATGGTGATCTGCCCCAGGCTC
** *
49508 AAGGTAAAAGATTGGCTGATGGTGATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * *
49547 GGGGTAAGAGATT-G--AATGGCTACAATCTGCCCCAGGCTT
1 GGGGTAAGAGATTGGCTGATGG-T--GATCTGCCCCAGGCTC
* *
49586 GGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
49625 AAGGTAAAGG
Statistics
Matches: 633, Mismatches: 226, Indels: 74
0.68 0.24 0.08
Matches are distributed among these distances:
36 17 0.03
37 12 0.02
38 54 0.09
39 493 0.78
40 30 0.05
41 6 0.01
42 15 0.02
43 6 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
Found at i:49358 original size:78 final size:78
Alignment explanation
Indices: 48537--49350 Score: 800
Period size: 78 Copynumber: 10.5 Consensus size: 78
48527 CCTATCGCGA
* * * *
48537 GGTAAGAGATTGGCTGACGGTGATCTGCCTCATGATCGGGGTAAAAGATCGAATGGTTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
*
48602 GCCCCT--G-TCGCT
66 G-CCCTAGGCTCG-G
* * * * * *
48614 GGTTAGAGATTGGCTGATGGTGATTTGCCCCATGATTGGGGTAAAAGATCGAATGGTTACAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
*
48679 GCCCCTA-TCGT-GG
66 G-CCCTAGGC-TCGG
* * * * *
48692 GGTAAGAGATTGGTTGACGGTGATCTGCCCCATGATCGGGTTAAAAGATCGAATGGTTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
* * *
48757 ACCCCAGTCTCGG
66 GCCCTAGGCTCGG
* * ** * * * *
48770 GGCAAGAGATTAGCAAATGGTGATCTACCCCAAGCTCGGGGTAAAAAATCGAATGGTTGCAATAT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
*
48835 GCCCCAGGCTCGG
66 GCCCTAGGCTCGG
* ** * * * ** *
48848 GGTAAGAGATTAGCCAATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGGATGACTACAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
*
48913 GCCCTAGGCT-AG
66 GCCCTAGGCTCGG
* * *
48925 GGTAAGAGATTGACCGATGGTGATCTGCCCAAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
48990 GCCCTAGGCTCGG
66 GCCCTAGGCTCGG
* * * * *
49003 GGTAAGAGATTGGCTTATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGAATGGTTACAATAT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
* *
49068 GCCTTAGGCTCGA
66 GCCCTAGGCTCGG
* * * * * * * * * *
49081 GATAAGAGATTAGTTTATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGGATAGCTGTAA-CT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
* **
49145 G-TCTCAGGCTTAG
66 GCCCT-AGGCTCGG
* * * * *
49158 GGTAAGGGATTGG-TCGATGGTGATCTGCCTCAAGCTCGGGGTAAAACATCAAATGGTTGCAATC
1 GGTAAGAGATTGGCT-GATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATC
* *
49222 TGCCCCAAGCTCGGG
65 TGCCCTAGGCTC-GG
* * * * ** *
49237 GGTAAGAGATTAGTTAATGGTGATCTTCCCCAGGCTCAAGGTAAAAGATCGAATGGCTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
* *
49302 GCCTTAGGCTCGA
66 GCCCTAGGCTCGG
49315 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCT
49351 TAGGGTAAGA
Statistics
Matches: 610, Mismatches: 115, Indels: 23
0.82 0.15 0.03
Matches are distributed among these distances:
76 2 0.00
77 189 0.31
78 354 0.58
79 63 0.10
80 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (78 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
GCCCTAGGCTCGG
Found at i:50593 original size:106 final size:106
Alignment explanation
Indices: 50405--50595 Score: 240
Period size: 106 Copynumber: 1.8 Consensus size: 106
50395 ATTAACCATC
* * *
50405 ATTTCAATGCAAAAATGATTGAACAAGATTGTGAGGTGGATAAAATTGAATTTTATTGGAGCCAG
1 ATTTCAATGCAAAAATGATTGAACAAGATTGTAAGGTGGATAAAATTAAATTTTATTGGAGCCAA
* **
50470 AGCTCGCGTGAACGAAAAGAATTATTAGTCCACTAACTGTT
66 AACTCGCACGAACGAAAAGAATTATTAGTCCACTAACTGTT
** * * **
50511 ATTTCAATGCAAATGTGCTTGAACAAGGTTGTAAGGTGGATAAAATTAAATTTTATTAGG-GGTA
1 ATTTCAATGCAAAAATGATTGAACAAGATTGTAAGGTGGATAAAATTAAATTTTATT-GGAGCCA
* *
50575 AAACTCGTACGAATGAAAAGA
65 AAACTCGCACGAACGAAAAGA
50596 TTAAAATAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
106 68 0.97
107 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (106 bp):
ATTTCAATGCAAAAATGATTGAACAAGATTGTAAGGTGGATAAAATTAAATTTTATTGGAGCCAA
AACTCGCACGAACGAAAAGAATTATTAGTCCACTAACTGTT
Found at i:57831 original size:30 final size:30
Alignment explanation
Indices: 57799--58096 Score: 213
Period size: 29 Copynumber: 10.1 Consensus size: 30
57789 TTAAAACATA
* * *
57799 ATTTTAGAAAATTTTAGGGGTAAAAATGTA
1 ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
57829 ATTTTA-AGAAAGTTTA-GGGTCAAAATGTG
1 ATTTTAGA-AAAGTTTAGGGGTCAAAATGTG
* * * *
57858 ATTTTATAGAAGTTT-GAGGTTAAAATGTG
1 ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
57887 ATTTT-GAGAAAGTTT-GGTGGTCAAAATGTG
1 ATTTTAGA-AAAGTTTAGG-GGTCAAAATGTG
* * *
57917 ATTTTAGAGAAGTTTAGGGGTGAAAATATG
1 ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
*
57947 ATTTTAG-AAAGTTT-GAGGGTCAAAATATG
1 ATTTTAGAAAAGTTTAG-GGGTCAAAATGTG
* * * *
57976 ATTTTA-AAAAATTTAAGGGTTAAAATGTA
1 ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
* *
58005 ATTTT-GAAAAAGTTT-GGGGTTAAAATGTA
1 ATTTTAG-AAAAGTTTAGGGGTCAAAATGTG
* * * * * * *
58034 ATTTTTGGAAAGATTAAGGGTTAAAATATA
1 ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
* ** * *
58064 ATTTTGGAGTAGTTTTGGGGTC-AAATGTA
1 ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
58093 ATTT
1 ATTT
58097 CTATAAAGTT
Statistics
Matches: 219, Mismatches: 35, Indels: 29
0.77 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 126 0.58
30 87 0.40
31 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (30 bp):
ATTTTAGAAAAGTTTAGGGGTCAAAATGTG
Found at i:57847 original size:88 final size:89
Alignment explanation
Indices: 57755--58068 Score: 263
Period size: 88 Copynumber: 3.6 Consensus size: 89
57745 AAAGGAAAAA
** * * *
57755 TAGGGTCGAAAATGAAG-TTTCGGAGAGTTTGA-GGTTAAAACATAATTTTAGAAAATTTTAGGG
1 TAGGGT-GAAAATGAAGATTTTAGAAAGTTTGAGGGTTAAAATATAATTTTAGAAAAATTTAGGG
57818 GTAAAAATGTAATTTTAAGAAAGTT
65 GTAAAAATGTAATTTTAAGAAAGTT
* * * * * *
57843 TAGGGTCAAAATG-TGATTTTATAGAAGTTTGA-GGTTAAAATGTGATTTT-GAGAAAGTTT-GG
1 TAGGGTGAAAATGAAGATTTTAGA-AAGTTTGAGGGTTAAAATATAATTTTAGA-AAAATTTAGG
* *
57904 TGGTCAAAATGTGATTTT-AGAGAAGTT
64 -GGTAAAAATGTAATTTTAAGA-AAGTT
* * * *
57931 TAGGGGTGAAAAT-ATGATTTTAGAAAGTTTGAGGGTCAAAATATGATTTTA-AAAAATTTAAGG
1 TA-GGGTGAAAATGAAGATTTTAGAAAGTTTGAGGGTTAAAATATAATTTTAGAAAAATTTAGGG
*
57994 GTTAAAATGTAATTTTGAA-AAAGTT
65 GTAAAAATGTAATTTT-AAGAAAGTT
* * * * * *
58019 TGGGGTTAAAATGTAA-TTTTTGGAAAGATTAAGGGTTAAAATATAATTTT
1 TAGGGTGAAAATG-AAGATTTTAGAAAGTTTGAGGGTTAAAATATAATTTT
58069 GGAGTAGTTT
Statistics
Matches: 183, Mismatches: 29, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
86 1 0.01
87 26 0.14
88 118 0.64
89 37 0.20
90 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (89 bp):
TAGGGTGAAAATGAAGATTTTAGAAAGTTTGAGGGTTAAAATATAATTTTAGAAAAATTTAGGGG
TAAAAATGTAATTTTAAGAAAGTT
Found at i:57863 original size:59 final size:59
Alignment explanation
Indices: 57799--58068 Score: 278
Period size: 59 Copynumber: 4.6 Consensus size: 59
57789 TTAAAACATA
* *
57799 ATTTTAGAAAATTTTAGGGGTAAAAATGTAATTTTAAGAAAGTTTAGGGTCAAAATGTG
1 ATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAGAAAGTTTAGGGTCAAAATGTG
* * * * * *
57858 ATTTTATAGAAGTTT-GAGGTTAAAATGTGATTTTGAGAAAGTTTGGTGGTCAAAATGTG
1 ATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAGAAAGTTTAG-GGTCAAAATGTG
* * * * *
57917 ATTTTAGAGAAGTTTAGGGGTGAAAATATGATTTT-AGAAAGTTTGAGGGTCAAAATATG
1 ATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAGAAAGTTT-AGGGTCAAAATGTG
* * * * *
57976 ATTTTA-AAAAATTTAAGGGTTAAAATGTAATTTTGAA-AAAGTTTGGGGTTAAAATGTA
1 ATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTT-AAGAAAGTTTAGGGTCAAAATGTG
* * * * *
58034 ATTTTTGGAAAGATTAAGGGTTAAAATATAATTTT
1 ATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTT
58069 GGAGTAGTTT
Statistics
Matches: 176, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
58 63 0.36
59 95 0.54
60 18 0.10
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (59 bp):
ATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAGAAAGTTTAGGGTCAAAATGTG
Found at i:58069 original size:59 final size:59
Alignment explanation
Indices: 57800--58111 Score: 260
Period size: 59 Copynumber: 5.3 Consensus size: 59
57790 TAAAACATAA
* * * * *
57800 TTTTAGAAAATTTTAGGGGTAAAAATGTAATTTT-AAGAAAGTTTAGGGTCAAAATGTGAT
1 TTTTAG-AAAGTTTAAGGGTTAAAATGTAATTTTGAA-AAAGTTTGGGGTCAAAATGTAAT
* * * *
57860 TTTATAG-AAGTTTGA-GGTTAAAATGTGATTTTGAGAAAGTTTGGTGGTCAAAATGTGA-
1 TTT-TAGAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAGTTTGG-GGTCAAAATGTAAT
* * * * * * *
57918 TTTTAGAGAAGTTTAGGGGTGAAAATATGATTTT-AGAAAGTTTGAGGGTCAAAATATGA-
1 TTTTAGA-AAGTTTAAGGGTTAAAATGTAATTTTGAAAAAGTTTG-GGGTCAAAATGTAAT
* * *
57977 TTTTAAAAAATTTAAGGGTTAAAATGTAATTTTGAAAAAGTTTGGGGTTAAAATGTAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAGTTTGGGGTCAAAATGTAAT
* * * * **
58036 TTTTGGAAAGATTAAGGGTTAAAATATAATTTTGGAGTAGTTTTGGGGTC-AAATGTAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAG-TTTGGGGTCAAAATGTAAT
* * *
58095 TTCTATAAAGTTCAAGG
1 TTTTAGAAAGTTTAAGG
58112 ACCTATTAAA
Statistics
Matches: 206, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
57 3 0.01
58 58 0.28
59 115 0.56
60 27 0.13
61 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (59 bp):
TTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAGTTTGGGGTCAAAATGTAAT
Found at i:59073 original size:23 final size:23
Alignment explanation
Indices: 59047--59090 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
59037 TTTGAATCTG
59047 TTTTTT-TGTTCTTTTTATTGAT
1 TTTTTTGTGTTCTTTTTATTGAT
* *
59069 TTTTTTGTGTTTTTTTTTTTGA
1 TTTTTTGTGTTCTTTTTATTGA
59091 AAATTTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.07, C:0.02, G:0.11, T:0.80
Consensus pattern (23 bp):
TTTTTTGTGTTCTTTTTATTGAT
Found at i:62517 original size:13 final size:13
Alignment explanation
Indices: 62491--62530 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
62481 ATAATCACAC
62491 AAATAT-ATTAAA
1 AAATATAATTAAA
62503 AAATTATAATTAAA
1 AAA-TATAATTAAA
62517 AAATATAATTAAA
1 AAATATAATTAAA
62530 A
1 A
62531 TATGCAACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.12
13 14 0.54
14 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATAATTAAA
Found at i:74703 original size:18 final size:20
Alignment explanation
Indices: 74680--74720 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
74670 GAATTTCCTT
74680 ATTGTGTGA-ATTAAA-TTG
1 ATTGTGTGATATTAAATTTG
*
74698 ATTGTGTGATTTTAAATTTG
1 ATTGTGTGATATTAAATTTG
74718 ATT
1 ATT
74721 AAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (20 bp):
ATTGTGTGATATTAAATTTG
Found at i:77303 original size:25 final size:26
Alignment explanation
Indices: 77257--77308 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
77247 TTTTATATAC
77257 ACATTATTTTAAATTATATATTTTAT
1 ACATTATTTTAAATTATATATTTTAT
*
77283 ACATT-TTTTATA-TATACTATTTTAT
1 ACATTATTTTAAATTATA-TATTTTAT
77308 A
1 A
77309 TATATACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (26 bp):
ACATTATTTTAAATTATATATTTTAT
Found at i:77406 original size:55 final size:55
Alignment explanation
Indices: 77291--77406 Score: 121
Period size: 55 Copynumber: 2.1 Consensus size: 55
77281 ATACATTTTT
* * *
77291 TATATATACTATTTTATATATATACAATCTTATATCTACATTTTATATATATACA
1 TATATACACTATTTTATATATATACAATATTATATCTACATTATATATATATACA
* * * *
77346 CATATACACTATTTTATAT-T-TACACATATTATTTTTACA-TATATACTGATCTACA
1 TATATACACTATTTTATATATATACA-ATATTATATCTACATTATATA-T-ATATACA
77401 TATATA
1 TATATA
77407 TATATACTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
53 9 0.18
54 13 0.26
55 28 0.56
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.47
Consensus pattern (55 bp):
TATATACACTATTTTATATATATACAATATTATATCTACATTATATATATATACA
Found at i:80190 original size:27 final size:27
Alignment explanation
Indices: 80159--80213 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
80149 AGGTTTTAGG
80159 TAGAAACCTTAAGGGGTAGTGGTTCTA
1 TAGAAACCTTAAGGGGTAGTGGTTCTA
80186 TAGAAACCTTAAGGGGTAGTGGTTCTA
1 TAGAAACCTTAAGGGGTAGTGGTTCTA
80213 T
1 T
80214 CTTACCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (27 bp):
TAGAAACCTTAAGGGGTAGTGGTTCTA
Found at i:82926 original size:22 final size:22
Alignment explanation
Indices: 82877--82926 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
82867 TTTACAAGAA
*
82877 AAGGTAAGAAAGAATCAAGCTC
1 AAGGTTAGAAAGAATCAAGCTC
82899 AAGGTTAGAAAGAATCAAGCTC
1 AAGGTTAGAAAGAATCAAGCTC
82921 AAGGTT
1 AAGGTT
82927 GTTTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.18
Consensus pattern (22 bp):
AAGGTTAGAAAGAATCAAGCTC
Found at i:89740 original size:31 final size:32
Alignment explanation
Indices: 89705--89765 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
89695 ACCTAATATA
*
89705 ATAAGG-AAAATAACTAAAACTAAAACTCTTG
1 ATAAGGCAAAATAAATAAAACTAAAACTCTTG
** *
89736 ATAAGGCAAGTTAAATAAATCTAAAACTCT
1 ATAAGGCAAAATAAATAAAACTAAAACTCT
89766 AATTGCAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (32 bp):
ATAAGGCAAAATAAATAAAACTAAAACTCTTG
Found at i:114338 original size:11 final size:12
Alignment explanation
Indices: 114314--114343 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
114304 ATAAACTTAT
*
114314 AAAAATTATAAA
1 AAAAATCATAAA
114326 AAAAATCATAAA
1 AAAAATCATAAA
114338 AAAAAT
1 AAAAAT
114344 TAAACTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAATCATAAA
Found at i:114743 original size:11 final size:11
Alignment explanation
Indices: 114727--114751 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
114717 ATCCGACAAG
114727 TTTTTATAATT
1 TTTTTATAATT
114738 TTTTTATAATT
1 TTTTTATAATT
114749 TTT
1 TTT
114752 ATAGGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:114877 original size:20 final size:19
Alignment explanation
Indices: 114818--114878 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
114808 TAAAACGTTC
114818 TTTTATAAAA-TTTTAAAA
1 TTTTATAAAATTTTTAAAA
* *
114836 TTTTA-AATATTTTTTTACAA
1 TTTTATAA-A-ATTTTTAAAA
114856 TTTTATAAAATTTTTAATAA
1 TTTTATAAAATTTTTAA-AA
114876 TTT
1 TTT
114879 ATTAGAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.06
18 6 0.18
19 6 0.18
20 18 0.53
21 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTATAAAATTTTTAAAA
Found at i:123550 original size:30 final size:30
Alignment explanation
Indices: 123515--123604 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
123505 AAAACCATCC
123515 TACAACCACTTGGAAATGTGGGGGGTGTCT
1 TACAACCACTTGGAAATGTGGGGGGTGTCT
* * *
123545 TACAACCACTTGGAAATGTGAGGGATGTCC
1 TACAACCACTTGGAAATGTGGGGGGTGTCT
*
123575 TACAACCACTT-GAAATGTGGAGGGTGTCT
1 TACAACCACTTGGAAATGTGGGGGGTGTCT
123604 T
1 T
123605 GCTAAATGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 15 0.28
30 38 0.72
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (30 bp):
TACAACCACTTGGAAATGTGGGGGGTGTCT
Found at i:138284 original size:14 final size:15
Alignment explanation
Indices: 138252--138291 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
138242 AAGGACGAAC
138252 AAAGAAAGAAAAGAA
1 AAAGAAAGAAAAGAA
138267 AAAGAAA-AAATA-AA
1 AAAGAAAGAAA-AGAA
138281 AAAGAAAGAAA
1 AAAGAAAGAAA
138292 GAACGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Done.