Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007313.1 Hibiscus syriacus cultivar Beakdansim tig00019483_pilon, 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: 89716
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4897 original size:21 final size:21
Alignment explanation
Indices: 4868--4911 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4858 ACTCCGAGAG
*
4868 CTAGTTCTTCACGAGCTTCTC
1 CTAGCTCTTCACGAGCTTCTC
* *
4889 CTAGCTCTTCTCGTGCTTCTC
1 CTAGCTCTTCACGAGCTTCTC
4910 CT
1 CT
4912 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.14, T:0.41
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTTCTC
Found at i:6103 original size:65 final size:64
Alignment explanation
Indices: 6017--6176 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 64
6007 GAATAAATTG
* * * **
6017 AACATCGAATGCATTTTATGCATTGATGCACACA-CCATGAATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-AGACATGAATCGATGCACTCAGGCAATTT-TG
6080 AA
64 -A
* * *
6082 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATTCACTCAGGCAATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGAATCGATGCACTCAGGCAATTTTGA
* *
6146 AACATCGAATGTACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
6177 TCTTACTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 30 0.36
65 50 0.60
66 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGACATGAATCGATGCACTCAGGCAATTTTGA
Found at i:13269 original size:10 final size:10
Alignment explanation
Indices: 13254--13289 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
13244 AATATGTTCA
13254 TTCATTTATG
1 TTCATTTATG
13264 TTCATTTATG
1 TTCATTTATG
*
13274 TTCGTTTATG
1 TTCATTTATG
*
13284 TGCATT
1 TTCATT
13290 CATTTATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58
Consensus pattern (10 bp):
TTCATTTATG
Found at i:13515 original size:23 final size:24
Alignment explanation
Indices: 13489--13548 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
13479 TTTACGTTCA
*
13489 TTTATTTTTC-TTTATTGTGTTGG
1 TTTATTGTTCGTTTATTGTGTTGG
*
13512 TTTA-TGTTCGTTTATTGTGTTTG
1 TTTATTGTTCGTTTATTGTGTTGG
13535 TTTA-TGTTCGTTTA
1 TTTATTGTTCGTTTA
13549 CATTCATTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (24 bp):
TTTATTGTTCGTTTATTGTGTTGG
Found at i:13582 original size:24 final size:23
Alignment explanation
Indices: 13502--13587 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 23
13492 ATTTTTCTTT
* * *
13502 ATTGTGTTGGTTTATGTTCGTTT
1 ATTGTTTTCGTTTATGTTCGTTC
13525 ATTGTGTTT-GTTTATGTTCGTTTAC
1 ATTGT-TTTCGTTTATGTTCG-TT-C
**
13550 ATT-CATTCGTTTATGTTCGTTC
1 ATTGTTTTCGTTTATGTTCGTTC
13572 ATTTGTTTTCGTTTAT
1 A-TTGTTTTCGTTTAT
13588 CATTTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
22 2 0.04
23 22 0.43
24 24 0.47
25 3 0.06
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.60
Consensus pattern (23 bp):
ATTGTTTTCGTTTATGTTCGTTC
Found at i:14590 original size:9 final size:8
Alignment explanation
Indices: 14575--14607 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
14565 TTCAAAGTAT
14575 GAAAAAAA
1 GAAAAAAA
14583 GAAAAAAA
1 GAAAAAAA
14591 GAAAAAAA
1 GAAAAAAA
14599 -AAACAAAA
1 GAAA-AAAA
14607 G
1 G
14608 GAAGAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 3 0.13
8 20 0.87
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:15576 original size:21 final size:21
Alignment explanation
Indices: 15550--15589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15540 AAAATTCTGT
* *
15550 ATCGATGCACTGTTACAGTGC
1 ATCGATACACTGCTACAGTGC
15571 ATCGATACACTGCTACAGT
1 ATCGATACACTGCTACAGT
15590 ATTTGTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
ATCGATACACTGCTACAGTGC
Found at i:16061 original size:46 final size:45
Alignment explanation
Indices: 15995--16098 Score: 147
Period size: 46 Copynumber: 2.3 Consensus size: 45
15985 AATCTTTTAT
* * *
15995 CATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
1 CATTTATACCATAAGCTCGTAAACTTATTTTACCAATACACTTAC
*
16040 CATTTAATACCATAAGCTCGTAAACTTATTTTACCAATACACTTGC
1 CATTT-ATACCATAAGCTCGTAAACTTATTTTACCAATACACTTAC
*
16086 CA-TTATTCCATAA
1 CATTTATACCATAA
16099 CCAAATACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 8 0.15
45 7 0.13
46 38 0.72
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.37
Consensus pattern (45 bp):
CATTTATACCATAAGCTCGTAAACTTATTTTACCAATACACTTAC
Found at i:16120 original size:20 final size:20
Alignment explanation
Indices: 16095--16150 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
16085 CCATTATTCC
*
16095 ATAACCAAATACCATAGAAA
1 ATAACCAAATACAATAGAAA
*
16115 ATAACCATAA-ACAATAGACA
1 ATAACCA-AATACAATAGAAA
16135 ATAACCCAATATACAA
1 ATAA-CCAA-ATACAA
16151 CCCTGAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 20 0.67
21 6 0.20
22 4 0.13
ACGTcount: A:0.59, C:0.21, G:0.04, T:0.16
Consensus pattern (20 bp):
ATAACCAAATACAATAGAAA
Found at i:16239 original size:40 final size:40
Alignment explanation
Indices: 16195--16356 Score: 243
Period size: 40 Copynumber: 4.0 Consensus size: 40
16185 ACCGTAGTGC
* *
16195 TACACATAAGGTTGTACCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCAAAGTGTAT
* *
16235 TACACATAAGGTCGTGCCCACTATATACACCAAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCAAAGTGTAT
**
16275 TACACATAAGGTCGTACTTACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCAAAGTGTAT
* * *
16315 TACACATAAGGTCGTGCCCACCATAGACACAAAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCAAAGTGTAT
16355 TA
1 TA
16357 TAAACCTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTACCCACCATATACACCAAAGTGTAT
Found at i:24417 original size:50 final size:50
Alignment explanation
Indices: 24356--24468 Score: 190
Period size: 50 Copynumber: 2.3 Consensus size: 50
24346 TGAAGGTGTT
* * *
24356 TGTGTTAGTTTATTTATTGTTCGTGAACATGTTCAAATAATGTTTGCTAA
1 TGTGTTCGTTTATTTATTGTTCGTAAACATGTTCAAATAATGTTCGCTAA
*
24406 TGTGTTCGTTTATTTATTGTTCGTAAACATGTTCATATAATGTTCGCTAA
1 TGTGTTCGTTTATTTATTGTTCGTAAACATGTTCAAATAATGTTCGCTAA
24456 TGTGTTCGTTTAT
1 TGTGTTCGTTTAT
24469 ATGTTTATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.50
Consensus pattern (50 bp):
TGTGTTCGTTTATTTATTGTTCGTAAACATGTTCAAATAATGTTCGCTAA
Found at i:24484 original size:12 final size:12
Alignment explanation
Indices: 24469--24498 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24459 GTTCGTTTAT
24469 ATGTTTATGAAC
1 ATGTTTATGAAC
*
24481 ATGTTTATGAAT
1 ATGTTTATGAAC
24493 ATGTTT
1 ATGTTT
24499 GTTTAGTGTT
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:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (12 bp):
ATGTTTATGAAC
Found at i:24509 original size:70 final size:70
Alignment explanation
Indices: 24435--24581 Score: 168
Period size: 70 Copynumber: 2.1 Consensus size: 70
24425 TTCGTAAACA
* * ** * ** * * * *
24435 TGTTCATATAATGTTCGCTAATGTGTTCGTTTATATGTTTATGAACATGTTTATGAATATGTTTG
1 TGTTCATATAATGTCCGCGAATGTGTTAATTTATATGTTCACAAACATGCTCATGAACATGTTCG
24500 TTTAG
66 TTTAG
* *
24505 TGTTCGTTTAATGTCCGCGAATGTGTTAATTTATATGTTCACAAACATGCTCATGAACATGTTCG
1 TGTTCATATAATGTCCGCGAATGTGTTAATTTATATGTTCACAAACATGCTCATGAACATGTTCG
24570 TTTAG
66 TTTAG
*
24575 TTTTCAT
1 TGTTCAT
24582 TTAGTGTTTG
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (70 bp):
TGTTCATATAATGTCCGCGAATGTGTTAATTTATATGTTCACAAACATGCTCATGAACATGTTCG
TTTAG
Found at i:27108 original size:22 final size:22
Alignment explanation
Indices: 27080--27128 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
27070 TGGAAGATAA
27080 TGATGATATAGGTGTGAAATGG
1 TGATGATATAGGTGTGAAATGG
27102 TGATGATATAGGTGTGAAATGG
1 TGATGATATAGGTGTGAAATGG
27124 TGATG
1 TGATG
27129 GAAGATGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.33
Consensus pattern (22 bp):
TGATGATATAGGTGTGAAATGG
Found at i:27138 original size:13 final size:14
Alignment explanation
Indices: 27120--27148 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27110 TAGGTGTGAA
27120 ATGGTGATGGA-AG
1 ATGGTGATGGACAG
27133 ATGGTGATGGACAG
1 ATGGTGATGGACAG
27147 AT
1 AT
27149 AGTATCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.03, G:0.41, T:0.24
Consensus pattern (14 bp):
ATGGTGATGGACAG
Found at i:31984 original size:16 final size:14
Alignment explanation
Indices: 31942--31992 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 14
31932 AGGATATGGT
31942 AATGAAATA-AAAA
1 AATGAAATATAAAA
*
31955 AATGAAAGATTAAAGA
1 AATGAAATA-TAAA-A
31971 AATGAAATAGTAAAA
1 AATGAAATA-TAAAA
31986 AAGTGAA
1 AA-TGAA
31993 GGTAACTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.26
15 6 0.19
16 17 0.55
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.18
Consensus pattern (14 bp):
AATGAAATATAAAA
Found at i:32234 original size:25 final size:23
Alignment explanation
Indices: 32189--32234 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
32179 GATGTAGGAG
32189 TCTTTTTATTTTCTTTTTGTTTT
1 TCTTTTTATTTTCTTTTTGTTTT
*
32212 TCTTCTTTCTTTTGCTTTTTGTT
1 TCTT-TTTATTTT-CTTTTTGTT
32235 GCAGCACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
25 9 0.45
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (23 bp):
TCTTTTTATTTTCTTTTTGTTTT
Found at i:32456 original size:6 final size:6
Alignment explanation
Indices: 32437--32496 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
32427 AATGAAAAGA
* *
32437 AAATGG AAACGG AAATGG AAATGG AAA--G AAAT-G AAAAGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
32482 AAATGG AAATGG AAA
1 AAATGG AAATGG AAA
32497 GAATTGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 40 0.83
ACGTcount: A:0.57, C:0.02, G:0.30, T:0.12
Consensus pattern (6 bp):
AAATGG
Found at i:32484 original size:33 final size:34
Alignment explanation
Indices: 32425--32509 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 34
32415 TGATAATTAA
*
32425 GAAATGAAAAGAAAATGGAAACGGAAATGGAAATG
1 GAAA-GAAATGAAAATGGAAACGGAAATGGAAATG
*
32460 GAAAGAAATGAAAA-GGAAATGGAAATGGAAATG
1 GAAAGAAATGAAAATGGAAACGGAAATGGAAATG
*
32493 GAAAGAATTG-AAATGGA
1 GAAAGAAATGAAAATGGA
32510 TAGAAAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 3 0.07
33 30 0.65
34 9 0.20
35 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.29, T:0.13
Consensus pattern (34 bp):
GAAAGAAATGAAAATGGAAACGGAAATGGAAATG
Found at i:32509 original size:27 final size:27
Alignment explanation
Indices: 32425--32490 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
32415 TGATAATTAA
* *
32425 GAAATGAAAAGAAAATGGAAACGGAAATG
1 GAAATGGAAAG-AAAT-GAAAAGGAAATG
32454 GAAATGGAAAGAAATGAAAAGGAAATG
1 GAAATGGAAAGAAATGAAAAGGAAATG
32481 GAAATGGAAA
1 GAAATGGAAA
32491 TGGAAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 21 0.60
28 4 0.11
29 10 0.29
ACGTcount: A:0.59, C:0.02, G:0.29, T:0.11
Consensus pattern (27 bp):
GAAATGGAAAGAAATGAAAAGGAAATG
Found at i:32686 original size:22 final size:22
Alignment explanation
Indices: 32655--32707 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
32645 TGGCTAAGGG
*
32655 ATGGTTATGATATAGACGTGAA
1 ATGGTGATGATATAGACGTGAA
*
32677 ATGGTGATGATATAGGCGTGAA
1 ATGGTGATGATATAGACGTGAA
32699 ATGGTGATG
1 ATGGTGATG
32708 GACAGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.04, G:0.34, T:0.30
Consensus pattern (22 bp):
ATGGTGATGATATAGACGTGAA
Found at i:34116 original size:15 final size:15
Alignment explanation
Indices: 34096--34130 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34086 ATGATAATAG
* *
34096 TGAGGTATTTTGGGT
1 TGAGGTATTTAGGGC
34111 TGAGGTATTTAGGGC
1 TGAGGTATTTAGGGC
34126 TGAGG
1 TGAGG
34131 GGATGTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.43, T:0.37
Consensus pattern (15 bp):
TGAGGTATTTAGGGC
Found at i:34411 original size:14 final size:14
Alignment explanation
Indices: 34392--34421 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
34382 GGAAGATTTA
34392 TAGCATTTATCGTT
1 TAGCATTTATCGTT
34406 TAGCATTTATCGTT
1 TAGCATTTATCGTT
34420 TA
1 TA
34422 AGTGTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (14 bp):
TAGCATTTATCGTT
Found at i:35739 original size:26 final size:26
Alignment explanation
Indices: 35710--35765 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
35700 GCTTGTATTG
*
35710 TAATGTAATGTAGGAGTTAATGTTTC
1 TAATGTAATGTAAGAGTTAATGTTTC
*
35736 TAATGTAATGTAAGAGTTAATGTTTT
1 TAATGTAATGTAAGAGTTAATGTTTC
35762 TAAT
1 TAAT
35766 ATGTGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.45
Consensus pattern (26 bp):
TAATGTAATGTAAGAGTTAATGTTTC
Found at i:37247 original size:21 final size:21
Alignment explanation
Indices: 37222--37280 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
37212 GATTATTCAT
37222 TATTAATAATTTAATAAATAA
1 TATTAATAATTTAATAAATAA
** *
37243 TATT-ATAAAAATAATAAATTA
1 TATTAAT-AATTTAATAAATAA
*
37264 TATTAATTATATTAATA
1 TATTAATAAT-TTAATA
37281 CTTTATCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTAATAATTTAATAAATAA
Found at i:37807 original size:36 final size:36
Alignment explanation
Indices: 37765--37941 Score: 200
Period size: 36 Copynumber: 4.9 Consensus size: 36
37755 ATTTAATCAG
*
37765 TTTTTGAAAACATATATAATATGGTTTTGAAAAACC
1 TTTTTGAAAACATATATAATATAGTTTTGAAAAACC
* *
37801 TTTTTGAAAACATATA-ATATATAGTTTTGAAAGCACA
1 TTTTTGAAAACATATATA-ATATAGTTTTGAAA-AACC
*
37838 TTTTT-TAAA-ATATATAATATAGTTTTGAAAATACC
1 TTTTTGAAAACATATATAATATAGTTTTGAAAA-ACC
* * * **
37873 TTTTTGAAAACGTATA-ATATATAATTTTAAAAAAGG
1 TTTTTGAAAACATATATA-ATATAGTTTTGAAAAACC
*
37909 TTTTTGAAAACGTATATAATATAGTTTTGAAAA
1 TTTTTGAAAACATATATAATATAGTTTTGAAAA
37942 CATATATATA
Statistics
Matches: 119, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
35 27 0.23
36 67 0.56
37 25 0.21
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (36 bp):
TTTTTGAAAACATATATAATATAGTTTTGAAAAACC
Found at i:37939 original size:23 final size:20
Alignment explanation
Indices: 37910--37956 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
37900 TAAAAAAGGT
37910 TTTTGAAAACGTATATAATATAG
1 TTTTGAAAAC--ATAT-ATATAG
37933 TTTTGAAAACATATATATAG
1 TTTTGAAAACATATATATAG
37953 TTTT
1 TTTT
37957 TTAAAACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
23 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (20 bp):
TTTTGAAAACATATATATAG
Found at i:37957 original size:21 final size:23
Alignment explanation
Indices: 37908--37966 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 23
37898 TTTAAAAAAG
37908 GTTTTTGAAAACGTATATAATATA
1 GTTTTTGAAAACG-ATATAATATA
37932 G-TTTTGAAAAC-ATAT-ATATA
1 GTTTTTGAAAACGATATAATATA
*
37952 GTTTTTTAAAACGAT
1 GTTTTTGAAAACGAT
37967 TTTTGAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.19
21 13 0.41
22 2 0.06
23 10 0.31
24 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (23 bp):
GTTTTTGAAAACGATATAATATA
Found at i:37982 original size:57 final size:58
Alignment explanation
Indices: 37874--37988 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 58
37864 GAAAATACCT
* *
37874 TTTTGAAAACGTATAATATATAATTTTAAAAAAGGTTTTTGAAAACGTATATAATATAG
1 TTTTGAAAACG-ATAATATATAATTTTAAAAAAGATTTTTGAAAACATATATAATATAG
* * *
37933 TTTTGAAAAC-AT-ATATATAGTTTTTTAAAACGATTTTTGAAAACATATATAATATA
1 TTTTGAAAACGATAATATATA-ATTTTAAAAAAGATTTTTGAAAACATATATAATATA
37989 TATAATTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
56 7 0.14
57 33 0.66
59 10 0.20
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (58 bp):
TTTTGAAAACGATAATATATAATTTTAAAAAAGATTTTTGAAAACATATATAATATAG
Found at i:38028 original size:20 final size:21
Alignment explanation
Indices: 37983--38028 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
37973 AAACATATAT
37983 AATA-TATATAATTTTTGATCA
1 AATATTATATAATTTTTGA-CA
* *
38004 CATATTATATAGTTTTTGA-A
1 AATATTATATAATTTTTGACA
38024 AATAT
1 AATAT
38029 GTATGTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 13 0.62
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (21 bp):
AATATTATATAATTTTTGACA
Found at i:38055 original size:16 final size:16
Alignment explanation
Indices: 38034--38100 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
38024 AATATGTATG
*
38034 TTATATAGTT-TTTTTA
1 TTATATA-TTATTTATA
38050 TTATATATTATTTATA
1 TTATATATTATTTATA
38066 TTAT-TATT-TATTATTA
1 TTATATATTAT-TTA-TA
*
38082 TTTTATATT-TATTATA
1 TTATATATTAT-TTATA
38098 TTA
1 TTA
38101 GGTCAAAGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
16 25 0.57
17 9 0.20
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (16 bp):
TTATATATTATTTATA
Found at i:38922 original size:37 final size:36
Alignment explanation
Indices: 38879--39068 Score: 194
Period size: 37 Copynumber: 5.3 Consensus size: 36
38869 TGGTTTTTAA
* *
38879 AAACATAGATAATATGGTTTTGAAAACACTTTTTTGG
1 AAACATATATAATATAGTTTTGAAAACAC-TTTTTGG
*
38916 AAACATATA-ATATATAGTTTTAAAAACACATTTTT-G
1 AAACATATATA-ATATAGTTTTGAAAACAC-TTTTTGG
* *
38952 AAA-ATATATAATATGGTTTTGAAAACACCTTTTTGA
1 AAACATATATAATATAGTTTTGAAAACA-CTTTTTGG
* * * *
38988 AAACGTATA-ATATATAGTTTTAAAAACAGTTTTTGA
1 AAACATATATA-ATATAGTTTTGAAAACACTTTTTGG
* *
39024 AAACGTATATAATATAGTTTTGAAAATA-TTTTT-G
1 AAACATATATAATATAGTTTTGAAAACACTTTTTGG
39058 AAACATATATA
1 AAACATATATA
39069 TAGGTTTTTA
Statistics
Matches: 131, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
34 10 0.08
35 30 0.23
36 42 0.32
37 49 0.37
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACATATATAATATAGTTTTGAAAACACTTTTTGG
Found at i:38959 original size:35 final size:35
Alignment explanation
Indices: 38887--39068 Score: 167
Period size: 35 Copynumber: 5.1 Consensus size: 35
38877 AAAAACATAG
* * *
38887 ATAATATGGTTTTGAAAACACTTTTTTGGAAACATAT
1 ATAATATAGTTTTAAAAACACATTTTT-GAAA-ATAT
38924 A-ATATATAGTTTTAAAAACACATTTTTGAAAATAT
1 ATA-ATATAGTTTTAAAAACACATTTTTGAAAATAT
* * *
38959 ATAATATGGTTTTGAAAACACCTTTTTGAAAACGTAT
1 ATAATATAGTTTTAAAAACACATTTTTGAAAA--TAT
*
38996 A-ATATATAGTTTTAAAAACA-GTTTTTGAAAACGTAT
1 ATA-ATATAGTTTTAAAAACACATTTTTGAAAA--TAT
* *
39032 ATAATATAGTTTT-GAAA-ATATTTTTGAAACATAT
1 ATAATATAGTTTTAAAAACACATTTTTGAAA-ATAT
39066 ATA
1 ATA
39069 TAGGTTTTTA
Statistics
Matches: 126, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
34 7 0.06
35 43 0.34
36 34 0.27
37 42 0.33
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (35 bp):
ATAATATAGTTTTAAAAACACATTTTTGAAAATAT
Found at i:38977 original size:72 final size:71
Alignment explanation
Indices: 38872--39108 Score: 268
Period size: 72 Copynumber: 3.3 Consensus size: 71
38862 TTTAAATTGG
* *
38872 TTTTTAAAAACATAGATAATATGGTTTTGAAAACACTTTTTTGGAAACATATAATATATAGTTTT
1 TTTTTGAAAAC-TATATAATATGGTTTTGAAAACAC-TTTTTGGAAACATATAATATATAGTTTT
38937 AAAAACACA
64 AAAAACA-A
* *
38946 TTTTTGAAAA-TATATAATATGGTTTTGAAAACACCTTTTTGAAAACGTATAATATATAGTTTTA
1 TTTTTGAAAACTATATAATATGGTTTTGAAAACA-CTTTTTGGAAACATATAATATATAGTTTTA
*
39010 AAAACAG
65 AAAACAA
* * * *
39017 TTTTTGAAAACGTATATAATATAGTTTTGAAAATA-TTTTT-GAAACATAT-ATATA-GGTTTTT
1 TTTTTGAAAAC-TATATAATATGGTTTTGAAAACACTTTTTGGAAACATATAATATATAGTTTTA
**
39078 AAAATGA
65 AAAACAA
39085 TTTTTGAAAAAACATATATAATAT
1 TTTTTG--AAAAC-TATATAATAT
39109 ATACAATTTT
Statistics
Matches: 143, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
68 15 0.10
69 5 0.03
70 22 0.15
71 15 0.10
72 55 0.38
73 22 0.15
74 9 0.06
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (71 bp):
TTTTTGAAAACTATATAATATGGTTTTGAAAACACTTTTTGGAAACATATAATATATAGTTTTAA
AAACAA
Found at i:39093 original size:33 final size:32
Alignment explanation
Indices: 38887--39093 Score: 137
Period size: 37 Copynumber: 5.9 Consensus size: 32
38877 AAAAACATAG
* *
38887 ATAATATGGTTTTGAAAACACTTTTTTGGAAACAT
1 ATAATATAGTTTTGAAAATA--TTTTT-GAAACAT
* * *
38922 ATAATATATAGTTTTAAAAACACATTTTTGAAAATAT
1 AT-A-ATATAGTTTT-GAAA-ATATTTTTG-AAACAT
* * *
38959 ATAATATGGTTTTGAAAACACCTTTTTGAAAACGT
1 ATAATATAGTTTTGAAAATA--TTTTTG-AAACAT
* *
38994 ATAATATATAGTTTTAAAAACAGTTTTTGAAAACGTAT
1 AT-A-ATATAGTTTTGAAAATA-TTTTTG-AAAC--AT
39032 ATAATATAGTTTTGAAAATATTTTTGAAACAT
1 ATAATATAGTTTTGAAAATATTTTTGAAACAT
*
39064 AT-ATATAGGTTTTTAAAATGATTTTTGAAA
1 ATAATATA-GTTTTGAAAAT-ATTTTTGAAA
39094 AAACATATAT
Statistics
Matches: 145, Mismatches: 14, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
31 5 0.03
32 14 0.10
33 13 0.09
34 7 0.05
35 30 0.21
36 30 0.21
37 37 0.26
38 6 0.04
39 3 0.02
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (32 bp):
ATAATATAGTTTTGAAAATATTTTTGAAACAT
Found at i:39102 original size:32 final size:31
Alignment explanation
Indices: 39035--39102 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
39025 AACGTATATA
* *
39035 ATATAGTTTTGAAAATATTTTTGAAACATAT
1 ATATAGTTTTGAAAATATTTTTGAAACAAAC
*
39066 ATATAGGTTTTTAAAATGATTTTTGAAA-AAAC
1 ATATA-GTTTTGAAAAT-ATTTTTGAAACAAAC
39098 ATATA
1 ATATA
39103 TAATATATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 5 0.16
32 17 0.53
33 10 0.31
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (31 bp):
ATATAGTTTTGAAAATATTTTTGAAACAAAC
Found at i:39134 original size:24 final size:22
Alignment explanation
Indices: 39108--39165 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
39098 ATATATAATA
*
39108 TATACAATTTTTGAAAACATAT
1 TATATAATTTTTGAAAACATAT
* *
39130 TATATAGTTTTTGAAAATATATGT
1 TATATAATTTTTGAAAACATA--T
*
39154 TATATAGTTTTT
1 TATATAATTTTT
39166 TTATTATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 18 0.58
24 13 0.42
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (22 bp):
TATATAATTTTTGAAAACATAT
Found at i:39157 original size:22 final size:22
Alignment explanation
Indices: 39115--39165 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 22
39105 ATATATACAA
39115 TTTTTGAAAACATATTATATAG
1 TTTTTGAAAACATATTATATAG
*
39137 TTTTTGAAAATATATGTTATATAG
1 TTTTTGAAAACATA--TTATATAG
39161 TTTTT
1 TTTTT
39166 TTATTATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 13 0.50
24 13 0.50
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (22 bp):
TTTTTGAAAACATATTATATAG
Found at i:39173 original size:23 final size:24
Alignment explanation
Indices: 39115--39182 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 24
39105 ATATATACAA
*
39115 TTTTTGAAAACAT--ATTATATAG
1 TTTTTGAAAATATACATTATATAG
**
39137 TTTTTGAAAATATATGTTATATAG
1 TTTTTGAAAATATACATTATATAG
** *
39161 TTTTT-TTATTATACATTATATA
1 TTTTTGAAAATATACATTATATA
39183 TTATTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 12 0.32
23 12 0.32
24 13 0.35
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (24 bp):
TTTTTGAAAATATACATTATATAG
Found at i:39187 original size:3 final size:3
Alignment explanation
Indices: 39175--39231 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
39165 TTTATTATAC
*
39175 ATT ATAT ATT ATT ATT -TT ATA ATT ATT A-T ATT A-T ATT A-T ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39217 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
39232 TAATGTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 36 0.77
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:39192 original size:27 final size:28
Alignment explanation
Indices: 39153--39230 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
39143 AAAATATATG
*
39153 TTATA-TAGTTTTTTTATTATACATTATA
1 TTATATTA-TTTTATTATTATACATTATA
* *
39181 -TATTATTATTTTATAATTATTATATTATA
1 TTA-TATTATTTTATTATTA-TACATTATA
39210 TTATATTATTATTATTATTAT
1 TTATATTATT-TTATTATTAT
39231 TTAATGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.05
28 11 0.27
29 18 0.44
30 10 0.24
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TTATATTATTTTATTATTATACATTATA
Found at i:39240 original size:27 final size:26
Alignment explanation
Indices: 39179--39230 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
39169 TTATACATTA
39179 TATATTATTATTTTATAATTATTATAT
1 TATATTA-TATTTTATAATTATTATAT
*
39206 TATATTATATTATTATTATTATTAT
1 TATATTATATT-TTATAATTATTAT
39231 TTAATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TATATTATATTTTATAATTATTATAT
Found at i:49684 original size:15 final size:15
Alignment explanation
Indices: 49656--49690 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49646 AACAACATCC
* *
49656 CCTCAGCCCTAAATA
1 CCTCAACCCAAAATA
49671 CCTCAACCCAAAATA
1 CCTCAACCCAAAATA
49686 CCTCA
1 CCTCA
49691 CTATTATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.43, G:0.03, T:0.17
Consensus pattern (15 bp):
CCTCAACCCAAAATA
Found at i:52922 original size:35 final size:35
Alignment explanation
Indices: 52867--52995 Score: 141
Period size: 35 Copynumber: 3.6 Consensus size: 35
52857 CAAAAATCGG
52867 TTTTTGAAAACATATATAATATGGTTTTGAAAACACC
1 TTTTT-AAAA-ATATATAATATGGTTTTGAAAACACC
* * **
52904 TTTTTAAAAATGTATAATATATAGTTTTGAAAACATA
1 TTTTTAAAAATATAT-A-ATATGGTTTTGAAAACACC
* *
52941 TTTTTGAAAATATATAATATGGTTTTGAAAATACC
1 TTTTTAAAAATATATAATATGGTTTTGAAAACACC
* **
52976 TTTTTGAAAATGCATAATAT
1 TTTTTAAAAATATATAATAT
52996 AAAACAGATT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
35 38 0.49
36 6 0.08
37 34 0.44
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTTTAAAAATATATAATATGGTTTTGAAAACACC
Found at i:52931 original size:37 final size:37
Alignment explanation
Indices: 52867--52996 Score: 149
Period size: 37 Copynumber: 3.6 Consensus size: 37
52857 CAAAAATCGG
**
52867 TTTTTGAAAACATAT-ATAATATGGTTTTGAAAACACC
1 TTTTTGAAAATGTATAAT-ATATGGTTTTGAAAACACC
* * **
52904 TTTTTAAAAATGTATAATATATAGTTTTGAAAACATA
1 TTTTTGAAAATGTATAATATATGGTTTTGAAAACACC
* *
52941 TTTTTGAAAATATAT-A-ATATGGTTTTGAAAATACC
1 TTTTTGAAAATGTATAATATATGGTTTTGAAAACACC
*
52976 TTTTTGAAAATGCATAATATA
1 TTTTTGAAAATGTATAATATA
52997 AAACAGATTT
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
35 28 0.37
36 2 0.03
37 44 0.58
38 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (37 bp):
TTTTTGAAAATGTATAATATATGGTTTTGAAAACACC
Found at i:53066 original size:33 final size:31
Alignment explanation
Indices: 53028--53120 Score: 102
Period size: 33 Copynumber: 3.0 Consensus size: 31
53018 TATAACTTAG
53028 TTTTGAAAACATATATATAGTTTTTAAAACGAT
1 TTTTGAAAACATATATATAGTTTTTAAAA--AT
* * *
53061 TTTTGAAAACATATATA-A-TATAT-ATAAT
1 TTTTGAAAACATATATATAGTTTTTAAAAAT
*
53089 TTTTGAAAACATATTATATAGTTTTTGAAAAT
1 TTTTGAAAACATA-TATATAGTTTTTAAAAAT
53121 ATATATGTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
28 15 0.30
29 4 0.08
30 3 0.06
31 6 0.12
32 5 0.10
33 17 0.34
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTGAAAACATATATATAGTTTTTAAAAAT
Found at i:53106 original size:22 final size:22
Alignment explanation
Indices: 53081--53124 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
53071 ATATATAATA
53081 TATATAATTTTTGAAAACATAT
1 TATATAATTTTTGAAAACATAT
* *
53103 TATATAGTTTTTGAAAATATAT
1 TATATAATTTTTGAAAACATAT
53125 ATGTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (22 bp):
TATATAATTTTTGAAAACATAT
Found at i:53131 original size:26 final size:24
Alignment explanation
Indices: 53060--53140 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 24
53050 TTTAAAACGA
*
53060 TTTTTGAAAACATATATAATATATATAA
1 TTTTTGAAAA-ATATAT--T-TATATAG
*
53088 TTTTTG-AAAACATA-TTATATAG
1 TTTTTGAAAAATATATTTATATAG
53110 TTTTTGAAAATATATATGTTATATAG
1 TTTTTGAAAA-ATATAT-TTATATAG
53136 TTTTT
1 TTTTT
53141 TATTATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 12 0.26
23 4 0.09
24 4 0.09
26 17 0.37
27 3 0.07
28 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
TTTTTGAAAAATATATTTATATAG
Found at i:53148 original size:26 final size:26
Alignment explanation
Indices: 53102--53176 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
53092 TGAAAACATA
* **
53102 TTATATAGTTTTTGAAAATATA-TAT
1 TTATATAGTTTTTTATTATATATTAT
53127 GTTATATAGTTTTTTATTATATATTAT
1 -TTATATAGTTTTTTATTATATATTAT
*
53154 TTATATTA-TTATTTATTAT-TATT
1 TTATA-TAGTTTTTTATTATATATT
53177 TTATATTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 4 0.09
26 34 0.79
27 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (26 bp):
TTATATAGTTTTTTATTATATATTAT
Found at i:53182 original size:32 final size:35
Alignment explanation
Indices: 53139--53220 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 35
53129 TATATAGTTT
* *
53139 TTTATTATATA-TTATTTATATTA-TTAT-TTATTA
1 TTTATTTTATATTTA-TCATATTAGTTATATTATTA
53172 -TTATTTTATATTTATCATATTAGGTTATATTATTA
1 TTTATTTTATATTTATCATATTA-GTTATATTATTA
53207 TTTATTTTAT-TTTA
1 TTTATTTTATATTTA
53221 ACAGGTCCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 16 0.38
33 3 0.07
34 4 0.10
35 10 0.24
36 9 0.21
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (35 bp):
TTTATTTTATATTTATCATATTAGTTATATTATTA
Found at i:53183 original size:29 final size:30
Alignment explanation
Indices: 53140--53216 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
53130 ATATAGTTTT
*
53140 TTATTATATATTATTTAT-ATTATTA-TT-TA
1 TTATTATTTA-TATTTATCA-TATTAGTTATA
53169 TTATTATTTTATATTTATCATATTAGGTTATA
1 TTATTA-TTTATATTTATCATATTA-GTTATA
53201 TTATTATTTAT-TTTAT
1 TTATTATTTATATTTAT
53217 TTTAACAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
29 18 0.43
30 9 0.21
31 7 0.17
32 8 0.19
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (30 bp):
TTATTATTTATATTTATCATATTAGTTATA
Found at i:53218 original size:9 final size:10
Alignment explanation
Indices: 53140--53218 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 10
53130 ATATAGTTTT
*
53140 TTATTATATA
1 TTATTATTTA
*
53150 TTATT-TATA
1 TTATTATTTA
53159 TTATTATTTA
1 TTATTATTTA
53169 TTATTA-TT-
1 TTATTATTTA
53177 TTA-TATTTA
1 TTATTATTTA
53186 TCATATTAGGTTATA
1 T--TATTA--TT-TA
53201 TTATTATTTA
1 TTATTATTTA
53211 TT-TTATTT
1 TTATTATTT
53219 TAACAGGTCC
Statistics
Matches: 59, Mismatches: 1, Indels: 19
0.75 0.01 0.24
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 18 0.31
10 18 0.31
11 4 0.07
12 2 0.03
13 5 0.08
14 2 0.03
15 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (10 bp):
TTATTATTTA
Found at i:55903 original size:31 final size:31
Alignment explanation
Indices: 55867--55930 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
55857 TGTGATCGAA
* * *
55867 AATTTAATAAAATATTTAATAAAGTCGGTTT
1 AATTTAATAAAATACTTAACAAAGTCGATTT
55898 AATTTAATAAAATACTTAACAAAGTCGATTT
1 AATTTAATAAAATACTTAACAAAGTCGATTT
55929 AA
1 AA
55931 CGGTACCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (31 bp):
AATTTAATAAAATACTTAACAAAGTCGATTT
Found at i:56343 original size:20 final size:20
Alignment explanation
Indices: 56318--56374 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
56308 AACATGTTAA
56318 AGTTTGACAAAACCGGTTTC
1 AGTTTGACAAAACCGGTTTC
56338 AGTTTGACAAAACCGGTTTC
1 AGTTTGACAAAACCGGTTTC
*
56358 AGTTTGACAAAAACGGT
1 AGTTTGACAAAACCGGT
56375 AGAGATACCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
AGTTTGACAAAACCGGTTTC
Found at i:62267 original size:13 final size:13
Alignment explanation
Indices: 62249--62273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62239 GTTTCATCAT
62249 TATTAAAAAATAA
1 TATTAAAAAATAA
62262 TATTAAAAAATA
1 TATTAAAAAATA
62274 TTACTCTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATTAAAAAATAA
Found at i:62319 original size:9 final size:10
Alignment explanation
Indices: 62294--62332 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
62284 ACGAATCTAT
62294 ATAATTTTTA
1 ATAATTTTTA
62304 ATAATTTTTA
1 ATAATTTTTA
62314 AT-ATTTTT-
1 ATAATTTTTA
*
62322 ATAATTATTA
1 ATAATTTTTA
62332 A
1 A
62333 AATAATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 2 0.08
9 11 0.42
10 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:62325 original size:18 final size:19
Alignment explanation
Indices: 62297--62332 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62287 AATCTATATA
*
62297 ATTTTTAATAATTTTTAAT
1 ATTTTTAATAATTATTAAT
62316 ATTTTT-ATAATTATTAA
1 ATTTTTAATAATTATTAA
62333 AATAATTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTAATAATTATTAAT
Found at i:66931 original size:28 final size:29
Alignment explanation
Indices: 66891--66965 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
66881 ATTTTCATTT
* * *
66891 AAGTATCTCAAATATTTTTTTATTAAAA-
1 AAGTATTTAAAATATTTTTTTATCAAAAC
* *
66919 AAGTATTTAAAATTATATTTTTGTCAAAAC
1 AAGTATTTAAAA-TATTTTTTTATCAAAAC
* *
66949 AAATATTTAAAGTATTT
1 AAGTATTTAAAATATTT
66966 AATTTTTTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 10 0.27
29 17 0.46
30 10 0.27
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Consensus pattern (29 bp):
AAGTATTTAAAATATTTTTTTATCAAAAC
Found at i:67115 original size:30 final size:28
Alignment explanation
Indices: 67047--67135 Score: 115
Period size: 30 Copynumber: 3.1 Consensus size: 28
67037 AAAATGATTG
* *
67047 AATATCTATTTTGGTAAAAAATATTTTA
1 AATATCTATTTTGATAAAAAATACTTTA
*
67075 AATAACTATTTTGATAAGAAAATAACTTTA
1 AATATCTATTTTGATAA-AAAAT-ACTTTA
*
67105 GATATCTATTTTGATAAAAAGATACTTTA
1 AATATCTATTTTGATAAAAA-ATACTTTA
67134 AA
1 AA
67136 CTTAAATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
28 15 0.29
29 15 0.29
30 22 0.42
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (28 bp):
AATATCTATTTTGATAAAAAATACTTTA
Found at i:73838 original size:18 final size:18
Alignment explanation
Indices: 73804--73843 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
73794 TTAATTGCGA
*
73804 AAATTTAAATTTAAATTG
1 AAATTTAAATTTAAATTC
73822 AAATTTAAAATTT-AATTC
1 AAATTT-AAATTTAAATTC
73840 AAAT
1 AAAT
73844 AATTACCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATTTAAATTTAAATTC
Found at i:76122 original size:12 final size:12
Alignment explanation
Indices: 76105--76159 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
76095 AGTGGGGTGC
76105 AAAAATATTAAT
1 AAAAATATTAAT
76117 AAAAATATTAAT
1 AAAAATATTAAT
*
76129 -AAAATAATAAT
1 AAAAATATTAAT
*
76140 AATAAT-TTATAT
1 AAAAATATTA-AT
*
76152 AAATATAT
1 AAAAATAT
76160 ATTTGTATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 12 0.34
12 22 0.63
13 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAAATATTAAT
Found at i:76139 original size:23 final size:23
Alignment explanation
Indices: 76106--76154 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
76096 GTGGGGTGCA
*
76106 AAAATATTAATAAAAATATTA-AT
1 AAAATAATAATAAAAAT-TTATAT
*
76129 AAAATAATAATAATAATTTATAT
1 AAAATAATAATAAAAATTTATAT
76152 AAA
1 AAA
76155 TATATATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAATAATAATAAAAATTTATAT
Found at i:76849 original size:116 final size:116
Alignment explanation
Indices: 76696--77179 Score: 385
Period size: 110 Copynumber: 4.0 Consensus size: 116
76686 CAATCTAAAG
* *
76696 ATGAATGTTACTAGTGAGCACG-TTTCCCTTCGTCGTGAAGTTGAAACCGTAGAT-GACCCATTC
1 ATGAATGTTGCT-GTGAGCACGATAT-CCTTCGTCGTGAAGTTGAAACCGTAGATGGACCCATTC
*
76759 GTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCA
64 GTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * *
76812 ATGAATGTTGCTGGTGAGCACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCGGCCCT
1 ATGAATGTTGCT-GTGAGCACGATAT-CCTTCGTCGTGAAGTTGAAACCGTAGAT-G--GACCCA
* * * * *
76876 TTCATGGTGAAATTAAGCCTTGAATTGGGTATCCTTCGTCGTGAAGTTGAAATCCAA
61 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCC-A
* * *
76933 TATGAAGATTAATGTTGCTTTGAGTC-CAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAT
1 -AT---G---AATGTTGCTGTGAG-CACGATATCCTTCGTCGTGAAGTTGAAA----C-C-G--T
* * ** *
76997 GAAACTGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTG
50 -AGA-T-GG-A-CCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTG
77062 AAATCCA
110 AAATCCA
** * * * * *
77069 ATCTA-G-AG-TTTGA--ACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGG-CCCATTCGT
1 ATGAATGTTGCTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAACCGTAGATGGACCCATTCGT
* *
77128 TGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCA
66 TGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
77179 A
1 A
77180 GCTTGTATTG
Statistics
Matches: 300, Mismatches: 40, Indels: 62
0.75 0.10 0.15
Matches are distributed among these distances:
110 55 0.18
113 2 0.01
114 1 0.00
115 1 0.00
116 50 0.17
117 1 0.00
118 1 0.00
119 1 0.00
120 53 0.18
121 1 0.00
122 2 0.01
124 23 0.08
125 1 0.00
126 5 0.02
127 27 0.09
128 12 0.04
129 1 0.00
131 1 0.00
132 1 0.00
133 1 0.00
135 4 0.01
136 2 0.01
137 54 0.18
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (116 bp):
ATGAATGTTGCTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAACCGTAGATGGACCCATTCGT
TGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
Found at i:76932 original size:120 final size:116
Alignment explanation
Indices: 76696--76933 Score: 332
Period size: 120 Copynumber: 2.0 Consensus size: 116
76686 CAATCTAAAG
* *
76696 ATGAATGTTACTAGTGAGCACGTTTCCCTTCGTCGTGAAGTTGAAACCGTAGATGACCCATTCGT
1 ATGAATGTTACTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTAGATGACCCATTCAT
* * * *
76761 TGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCA
66 GGTGAAATTAAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
* * * * *
76812 ATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCGGCCCTT
1 ATGAATGTTACTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTAGAT----GACCCAT
*
76877 TCATGGTGAAATTAAGCCTTGAATTGGGTATCCTTCGTCGTGAAGTTGAAATCCA
62 TCATGGTGAAATTAAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
76932 AT
1 AT
76934 ATGAAGATTA
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
116 50 0.47
120 56 0.53
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (116 bp):
ATGAATGTTACTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTAGATGACCCATTCAT
GGTGAAATTAAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
Found at i:77274 original size:240 final size:243
Alignment explanation
Indices: 76756--77355 Score: 766
Period size: 240 Copynumber: 2.4 Consensus size: 243
76746 AGATGACCCA
* * * ** *
76756 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGAATGTT
1 TTCGTCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA-G-A
* * *
76821 GCTGGTGAGCACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCGGCCCTTTCATGGTG
64 G-T-TTGA-CACGATAT-CCTTCGTCGTGAAGTTGAAATCGTGGAT----GGCCCATTCATGGTG
** *
76885 AAATTAAGCCTTGAATTGGGTATCCTTCGTCGTGAAGTTGAAATCCAATATGAAGATTAATGTTG
121 AAATTAAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCC---A--AAGATTAATATTG
*
76950 CTTTGAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCC
181 CTTTGAGTCCAATATCCTTCGCCGTGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAGCCCC
*
77013 TTCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGT
1 TTCGTCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGT
* * * * *
77078 TTGA-ACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCC
66 TTGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCATGGTGAAATTAAGCC
* * *
77142 TTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCC-AAGCTT-GTATTG-TTTCGAGTCCAATA
131 TTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAAAGATTAATATTGCTTT-GAGTCCAATA
77204 TCCTTCGCCGTGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAGCCCC
195 TCCTTCGCCGTGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAGCCCC
* *
77253 TTCGTCGTGAAGTTGAGCTTTGAATTGGATATCCTTCATCGT---GTTGAAATCCAATCTAGAGA
1 TTCGTCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGT
* *
77315 TGGACACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATG
66 TTGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
77356 TGTGGGCATG
Statistics
Matches: 312, Mismatches: 28, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
237 22 0.07
238 34 0.11
239 3 0.01
240 102 0.33
241 5 0.02
247 53 0.17
251 31 0.10
252 1 0.00
253 3 0.01
254 1 0.00
255 1 0.00
256 1 0.00
257 55 0.18
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (243 bp):
TTCGTCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGT
TTGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCATGGTGAAATTAAGCC
TTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAAAGATTAATATTGCTTTGAGTCCAATAT
CCTTCGCCGTGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAGCCCC
Found at i:77378 original size:43 final size:43
Alignment explanation
Indices: 77314--77441 Score: 184
Period size: 43 Copynumber: 3.0 Consensus size: 43
77304 CAATCTAGAG
* * * *
77314 ATGGACACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGT
1 ATGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGT
* * *
77357 GTGGGCATGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTT
1 ATGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGT
*
77400 ATGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
1 ATGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
77442 GCCCATTCGT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (43 bp):
ATGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGT
Found at i:81293 original size:5 final size:5
Alignment explanation
Indices: 81283--81322 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
81273 TAAGAAAAAA
* * *
81283 TAAAT TAAAT TAAAT TAAAA TAAAT AAAAA TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
81323 AAAAAGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
TAAAT
Found at i:81296 original size:10 final size:10
Alignment explanation
Indices: 81279--81325 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
81269 AATGTAAGAA
81279 AAAATAAATT
1 AAAATAAATT
*
81289 AAATTAAATT
1 AAAATAAATT
*
81299 AAAATAAATA
1 AAAATAAATT
81309 AAAATAAATT
1 AAAATAAATT
81319 -AAATAAA
1 AAAATAAA
81326 AAGATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
9 7 0.21
10 26 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATAAATT
Found at i:81327 original size:15 final size:15
Alignment explanation
Indices: 81278--81327 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
81268 AAATGTAAGA
81278 AAAAATAAATTAAAT
1 AAAAATAAATTAAAT
* * *
81293 TAAATTAAAATAAAT
1 AAAAATAAATTAAAT
81308 AAAAATAAATTAAAT
1 AAAAATAAATTAAAT
81323 AAAAA
1 AAAAA
81328 GATAAAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAAATTAAAT
Found at i:81341 original size:30 final size:30
Alignment explanation
Indices: 81278--81346 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
81268 AAATGTAAGA
* **
81278 AAAAATAAATTAAATTAAATTAAAATAAAT
1 AAAAATAAATTAAATAAAAAGAAAATAAAT
*
81308 AAAAATAAATTAAATAAAAAGATAAA-AAGT
1 AAAAATAAATTAAATAAAAAGA-AAATAAAT
81338 AAAAATAAA
1 AAAAATAAA
81347 ATAGTAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (30 bp):
AAAAATAAATTAAATAAAAAGAAAATAAAT
Found at i:81697 original size:23 final size:23
Alignment explanation
Indices: 81671--81714 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
81661 GGTAATACCT
* *
81671 ATATATATGTATATATAATAATG
1 ATATAAATATATATATAATAATG
*
81694 ATATAAATATATGTATAATAA
1 ATATAAATATATATATAATAA
81715 AAAATATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
ATATAAATATATATATAATAATG
Found at i:81725 original size:23 final size:27
Alignment explanation
Indices: 81673--81750 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
81663 TAATACCTAT
*
81673 ATATATGTATATATAATAATGATATAA
1 ATATATGTATATATAATAATAATATAA
81700 ATATATGTATA-ATAA-AA-AATAT-A
1 ATATATGTATATATAATAATAATATAA
* * *
81723 ATATA-ATATAAATAATAAAAATA-AA
1 ATATATGTATATATAATAATAATATAA
81748 ATA
1 ATA
81751 GAAAAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 4 0.09
23 10 0.22
24 6 0.13
25 10 0.22
26 4 0.09
27 11 0.24
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
ATATATGTATATATAATAATAATATAA
Found at i:81763 original size:23 final size:24
Alignment explanation
Indices: 81710--81764 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
81700 ATATATGTAT
* * *
81710 AATA-AAAAATATAATATAATATA
1 AATATAAAAATAAAATAGAATAAA
81733 AATAATAAAAATAAAATAGAA-AAA
1 AAT-ATAAAAATAAAATAGAATAAA
81757 AATATAAA
1 AATATAAA
81765 TATATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.30
24 6 0.22
25 13 0.48
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AATATAAAAATAAAATAGAATAAA
Found at i:83471 original size:12 final size:13
Alignment explanation
Indices: 83443--83475 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
83433 TGGTGAACGT
83443 AATTGAGAAAGAA
1 AATTGAGAAAGAA
83456 AATTGAGAAA-AA
1 AATTGAGAAAGAA
83468 AATTGAGA
1 AATTGAGA
83476 GAATGCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (13 bp):
AATTGAGAAAGAA
Found at i:83763 original size:182 final size:182
Alignment explanation
Indices: 83456--83823 Score: 736
Period size: 182 Copynumber: 2.0 Consensus size: 182
83446 TGAGAAAGAA
83456 AATTGAGAAAAAAATTGAGAGAATGCAAAGGGAGTATTCGGCCATGCATGCTTGGATTTCAAGCT
1 AATTGAGAAAAAAATTGAGAGAATGCAAAGGGAGTATTCGGCCATGCATGCTTGGATTTCAAGCT
83521 TAGATTACTAAAGAATTCACCTAGCCTACAATTAATCCTTTCCCTTTATTTCCTTTCGAAATTTT
66 TAGATTACTAAAGAATTCACCTAGCCTACAATTAATCCTTTCCCTTTATTTCCTTTCGAAATTTT
83586 AAGAGTTTAATTGAGTTGATCCTTTAGAAATTATAAGTTTGATTATGGATAT
131 AAGAGTTTAATTGAGTTGATCCTTTAGAAATTATAAGTTTGATTATGGATAT
83638 AATTGAGAAAAAAATTGAGAGAATGCAAAGGGAGTATTCGGCCATGCATGCTTGGATTTCAAGCT
1 AATTGAGAAAAAAATTGAGAGAATGCAAAGGGAGTATTCGGCCATGCATGCTTGGATTTCAAGCT
83703 TAGATTACTAAAGAATTCACCTAGCCTACAATTAATCCTTTCCCTTTATTTCCTTTCGAAATTTT
66 TAGATTACTAAAGAATTCACCTAGCCTACAATTAATCCTTTCCCTTTATTTCCTTTCGAAATTTT
83768 AAGAGTTTAATTGAGTTGATCCTTTAGAAATTATAAGTTTGATTATGGATAT
131 AAGAGTTTAATTGAGTTGATCCTTTAGAAATTATAAGTTTGATTATGGATAT
83820 AATT
1 AATT
83824 TCAATTGTTG
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 186 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (182 bp):
AATTGAGAAAAAAATTGAGAGAATGCAAAGGGAGTATTCGGCCATGCATGCTTGGATTTCAAGCT
TAGATTACTAAAGAATTCACCTAGCCTACAATTAATCCTTTCCCTTTATTTCCTTTCGAAATTTT
AAGAGTTTAATTGAGTTGATCCTTTAGAAATTATAAGTTTGATTATGGATAT
Found at i:86040 original size:49 final size:49
Alignment explanation
Indices: 85895--86042 Score: 121
Period size: 49 Copynumber: 3.1 Consensus size: 49
85885 AGGCTGTTGG
**
85895 GAATTGTTTAATCCGATTGCCATATAGATTGCATGAATACATATGTGGT
1 GAATTGTTTAATCCGATTGCCATATAGATAACATGAATACATATGTGGT
* * * * * * * ** *
85944 GAATT-TCT--TCTTG-TT-CGA-ATAGAGAA-AAGAATGTCGTACATGTT
1 GAATTGTTTAATC-CGATTGCCATATAGATAACATGAAT-ACATATGTGGT
85988 GAATTGTTTAATCCGATTGCCATATAGATAACATGAATACATATGTGGT
1 GAATTGTTTAATCCGATTGCCATATAGATAACATGAATACATATGTGGT
86037 GAATTG
1 GAATTG
86043 CTTCTTGTTC
Statistics
Matches: 68, Mismatches: 22, Indels: 18
0.63 0.20 0.17
Matches are distributed among these distances:
43 5 0.07
44 16 0.24
45 4 0.06
46 5 0.07
47 5 0.07
48 4 0.06
49 24 0.35
50 5 0.07
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (49 bp):
GAATTGTTTAATCCGATTGCCATATAGATAACATGAATACATATGTGGT
Found at i:86123 original size:97 final size:93
Alignment explanation
Indices: 85895--86163 Score: 387
Period size: 97 Copynumber: 2.8 Consensus size: 93
85885 AGGCTGTTGG
*
85895 GAATTGTTTAATCCGATTGCCATATAGATTGCATGAATACATATGTGGTGAATTTCTTCTTGTTC
1 GAATTGTTTAATCCGATTGCCATATAGATTGCATGAATACATATGTGGTGAATTGCTTCTTGTTC
*
85960 GAATAGAGAAAAGAATGTCGTACATGTT
66 GAATAGAGAAAAGAATGTCATACATGTT
**
85988 GAATTGTTTAATCCGATTGCCATATAGATAACATGAATACATATGTGGTGAATTGCTTCTTGTTC
1 GAATTGTTTAATCCGATTGCCATATAGATTGCATGAATACATATGTGGTGAATTGCTTCTTGTTC
*
86053 GAATAGAATAGAGGAAATAATGT-ATACATGTT
66 GAATAG---AGA--AAAGAATGTCATACATGTT
* * * *
86085 GAATCGTTTAATCTGAATGCCATATAGATTGCATGAATACATATGTGGTGAATTGTTTCTTGTTC
1 GAATTGTTTAATCCGATTGCCATATAGATTGCATGAATACATATGTGGTGAATTGCTTCTTGTTC
* *
86150 GAATGGAGGAAAGA
66 GAATAGAGAAAAGA
86164 TTGAAATGCA
Statistics
Matches: 157, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
92 4 0.03
93 68 0.43
94 2 0.01
96 3 0.02
97 72 0.46
98 8 0.05
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (93 bp):
GAATTGTTTAATCCGATTGCCATATAGATTGCATGAATACATATGTGGTGAATTGCTTCTTGTTC
GAATAGAGAAAAGAATGTCATACATGTT
Found at i:88997 original size:237 final size:243
Alignment explanation
Indices: 88507--89051 Score: 626
Period size: 237 Copynumber: 2.3 Consensus size: 243
88497 AACCTTTGTT
** * * * * * **
88507 GTGAAGTTGAAATCTAACTCGGAATCTGGGCTAGAAAGTAGCTCCTCATTATTGAGTTAAGCTAA
1 GTGAAGTTGAAATCTAACTCAAAATCTAGGTTGGGAAGTAGCTCCTCGTCGTTGAGTTAAGCTAA
* * * * **
88572 ACCGTAGTCAATTTTGAGTCTCCTTCTAGTTCAATGTCCCTCGTTGCGAGGTTAAATTTCGACTT
66 ACCATAGTCAATCTTGAGTCTCCTTATAGTTCAATATCCCTCGTCACGAGGTTAAATTTCGACTT
* *
88637 AAAAACCTTAGTTGAAAAATAACTTCTTGTTGTTGAGTTAAACAATGTTGCAGATAACTCCTCCA
131 AAAAACCTTAGTTGAAAAATAACTTCTTGCTGTTAAGTTAAACAATGTTGCAGATAACTCCTCCA
** * * * * * *
88702 TTGTGGTTTAATTTGACCCTAGGCGACTCGAGCTTGATATCATTCTTC
196 TAATGGTTAAAGTCGACCCTAAGCGACTCGAGCTTGATATCACTCATC
88750 GTGAAGTTGAAATCTAACTCAAAATCTAGGTTGGGAAGTAGC-CC-CGTCGTTGAGTTAAGCTAA
1 GTGAAGTTGAAATCTAACTCAAAATCTAGGTTGGGAAGTAGCTCCTCGTCGTTGAGTTAAGCTAA
* *
88813 ATCATAGTCAATCTT-A-TCTCCTTATAG-TCTAATATCCCTCGTCACGAGGTTGAATTT-GACT
66 ACCATAGTCAATCTTGAGTCTCCTTATAGTTC-AATATCCCTCGTCACGAGGTTAAATTTCGACT
* * *** **
88874 TGAAAA-CTTAGTTGAAAAAT-AGTTCTTCGCTGTTAAGTTAAGTTTATGTTGTGGATAACTCCT
130 TAAAAACCTTAGTTGAAAAATAACTTCTT-GCTGTTAAGTTAA-ACAATGTTGCAGATAACTCCT
* * *
88937 CCATAATGAG-TAAAGTCGATCTTAAGCGATTCGAGCTTGATATC-CTCATC
193 CCATAATG-GTTAAAGTCGACCCTAAGCGACTCGAGCTTGATATCACTCATC
*
88987 GTGAAGTTGAAATCTAACTCAAAATCTA-GTCTGGGAAATAGCTCCTCGTCGTTGAGTTAAGCTA
1 GTGAAGTTGAAATCTAACTCAAAATCTAGGT-TGGGAAGTAGCTCCTCGTCGTTGAGTTAAGCTA
89051 A
65 A
89052 CTTGTCATAA
Statistics
Matches: 257, Mismatches: 38, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
236 8 0.03
237 67 0.26
238 62 0.24
239 53 0.21
240 1 0.00
241 28 0.11
242 2 0.01
243 36 0.14
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (243 bp):
GTGAAGTTGAAATCTAACTCAAAATCTAGGTTGGGAAGTAGCTCCTCGTCGTTGAGTTAAGCTAA
ACCATAGTCAATCTTGAGTCTCCTTATAGTTCAATATCCCTCGTCACGAGGTTAAATTTCGACTT
AAAAACCTTAGTTGAAAAATAACTTCTTGCTGTTAAGTTAAACAATGTTGCAGATAACTCCTCCA
TAATGGTTAAAGTCGACCCTAAGCGACTCGAGCTTGATATCACTCATC
Done.