Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008230.1 Hibiscus syriacus cultivar Beakdansim tig00110866_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: 225826
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2374 original size:2 final size:2
Alignment explanation
Indices: 2363--2396 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2353 TAATAAAATG
2363 AT AT AT -T AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2397 TGTATTGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:17766 original size:6 final size:6
Alignment explanation
Indices: 17745--17780 Score: 51
Period size: 5 Copynumber: 6.5 Consensus size: 6
17735 TTATATTACT
17745 ATTTAA A-TTAA A-TTAA ATTTAA ATTT-A ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
17781 AATAATTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.54
6 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:17768 original size:11 final size:11
Alignment explanation
Indices: 17747--17782 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
17737 ATATTACTAT
17747 TTAAA-TTAAA
1 TTAAATTTAAA
17757 TTAAATTTAAA
1 TTAAATTTAAA
*
17768 TTTAATTTAAA
1 TTAAATTTAAA
17779 TTAA
1 TTAA
17783 TAATTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:17782 original size:16 final size:16
Alignment explanation
Indices: 17745--17780 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
17735 TTATATTACT
17745 ATTTAAATTAAATTAA
1 ATTTAAATTAAATTAA
*
17761 ATTTAAATTTAATTTAA
1 ATTTAAA-TTAAATTAA
17778 ATT
1 ATT
17781 AATAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAATTAAATTAA
Found at i:20398 original size:2 final size:2
Alignment explanation
Indices: 20391--20420 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20381 GCATAATGTG
20391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20421 CTTCATCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25943 original size:2 final size:2
Alignment explanation
Indices: 25936--25977 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
25926 GATCCTAACC
25936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25978 CAATTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26068 original size:15 final size:15
Alignment explanation
Indices: 26050--26086 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
26040 GAATTTGATC
26050 AATTTTAATTTTTAG
1 AATTTTAATTTTTAG
26065 AATTTTAATTTTTAG
1 AATTTTAATTTTTAG
26080 AATTTTA
1 AATTTTA
26087 TTCCCAACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (15 bp):
AATTTTAATTTTTAG
Found at i:30464 original size:21 final size:22
Alignment explanation
Indices: 30423--30465 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30413 TTATACAGGA
*
30423 ACCAAAGCATTTTCGAAATTGT
1 ACCAAAGCATCTTCGAAATTGT
30445 ACCAAAGCATCTTC-AAATTGT
1 ACCAAAGCATCTTCGAAATTGT
30466 CAATACGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (22 bp):
ACCAAAGCATCTTCGAAATTGT
Found at i:35640 original size:16 final size:18
Alignment explanation
Indices: 35599--35642 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
35589 TCACGGAATG
35599 TAAA-ATTATCAAGGGAA
1 TAAAGATTATCAAGGGAA
35616 TAAAAGATTATC-AGGGAA
1 T-AAAGATTATCAAGGGAA
35634 T-AAGATTAT
1 TAAAGATTAT
35643 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 10 0.40
19 6 0.24
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (18 bp):
TAAAGATTATCAAGGGAA
Found at i:35649 original size:15 final size:16
Alignment explanation
Indices: 35603--35642 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 16
35593 GGAATGTAAA
35603 ATTATCAAGGGAATAAAAG
1 ATTATC-AGGGAAT--AAG
35622 ATTATCAGGGAATAAG
1 ATTATCAGGGAATAAG
35638 ATTAT
1 ATTAT
35643 TGGGAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (16 bp):
ATTATCAGGGAATAAG
Found at i:37982 original size:23 final size:23
Alignment explanation
Indices: 37951--38011 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
37941 CACCACAGCT
* *
37951 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
37974 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
37997 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
38012 TAGTACCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:38163 original size:103 final size:103
Alignment explanation
Indices: 38038--38252 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 103
38028 TGTCCATAAG
* * * *
38038 GACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCATAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCAGAC
38103 CTCACACATATTCCAAAGAATACATATATGTCCCGAAT
66 CTCACACATATTCCAAAGAATACATATATGTCCCGAAT
38141 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCAGAC
*
38206 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
66 CTCACACATATTCCAAAGAATACATATATGTCCCGAAT
38244 GACCACATA
1 GACCACATA
38253 GACCCTCTAC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCAGAC
CTCACACATATTCCAAAGAATACATATATGTCCCGAAT
Found at i:44805 original size:23 final size:23
Alignment explanation
Indices: 44774--44842 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
44764 CACCACAGCT
* *
44774 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
44797 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
44820 CGTAGAATTGCATCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
44843 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:44990 original size:103 final size:103
Alignment explanation
Indices: 44858--45075 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
44848 TAATGTTCAT
* * *
44858 AAGGACCACATATCATTTCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTAGGTGTCTCACCA
44923 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
44961 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAATTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTAGGTGTCTCACCA
45026 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
45064 AAAGACCACATA
1 AAGGACCACATA
45076 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTAGGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:53854 original size:21 final size:21
Alignment explanation
Indices: 53803--53856 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
53793 ATTATTACTA
53803 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
***
53824 TCGTGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
53845 TCGCAATGCGAT
1 TCGCAATGCGAT
53857 ACTGACTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:53896 original size:62 final size:62
Alignment explanation
Indices: 53830--53994 Score: 190
Period size: 62 Copynumber: 2.7 Consensus size: 62
53820 AATTTCGTGT
** *
53830 TGCGATTTTCCCAATTCGCAATGCGATACTGACTATCGCAACACAATAATACAAAATTGCAA
1 TGCGATTTTGACAATTCGCAATGCGATACTGACTATCGCAACACAATAATACAAAATCGCAA
* * * *
53892 TGCGAATTTGGA-AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAA
1 TGCG-ATTTTGACAATTCGCAATGCGATACTGACTATCGCAACACAATAATACAAAATCGCAA
* ** * * *
53954 CGCGATACTGAC-TTTCGCAACGCGATACTGACTTTCGCAAC
1 TGCGATTTTGACAATTCGCAATGCGATACTGACTATCGCAAC
53995 GCGATTCTGA
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
61 29 0.34
62 53 0.62
63 4 0.05
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (62 bp):
TGCGATTTTGACAATTCGCAATGCGATACTGACTATCGCAACACAATAATACAAAATCGCAA
Found at i:53931 original size:20 final size:20
Alignment explanation
Indices: 53906--54020 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
53896 AATTTGGAAA
*
53906 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
53926 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
53947 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
53967 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
53987 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
54007 TTCGCAACGAGATA
1 ATCGCAACGCGATA
54021 ATACAGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:53950 original size:41 final size:41
Alignment explanation
Indices: 53903--54034 Score: 169
Period size: 41 Copynumber: 3.2 Consensus size: 41
53893 GCGAATTTGG
* *
53903 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
53944 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
53986 --TTTCGCAACGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
54025 AGAATCGCAA
1 AAAATCGCAA
54035 TGCGGTTTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.03
40 32 0.41
41 42 0.54
42 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:54783 original size:24 final size:24
Alignment explanation
Indices: 54756--54809 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
54746 GTATTCGAAA
*
54756 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
54780 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
54804 TTTGAT
1 TTTGAT
54810 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:57224 original size:19 final size:20
Alignment explanation
Indices: 57143--57225 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
57133 GGTAATCATT
*
57143 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
57163 TGACGT-TCGCAATCATC-CTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
57184 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
57204 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
57223 TGA
1 TGA
57226 AAATCGAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
19 8 0.16
20 27 0.55
21 13 0.27
22 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:57231 original size:19 final size:19
Alignment explanation
Indices: 57189--57300 Score: 75
Period size: 19 Copynumber: 6.4 Consensus size: 19
57179 CCTAATGTCT
* **
57189 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
57209 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
57228 ATCG-AA-ACG--A-GAGA
1 ATCGCAATGCGAAATGAAA
57242 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
57261 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
57275 ATCGC-ATCGCGAAATGAAA
1 ATCGCAAT-GCGAAATGAAA
57294 ATCGCAA
1 ATCGCAA
57301 CGAGGGAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
13 1 0.01
14 15 0.21
15 4 0.06
16 4 0.06
17 4 0.06
18 4 0.06
19 29 0.41
20 10 0.14
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:57251 original size:33 final size:33
Alignment explanation
Indices: 57209--57335 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
57199 GGAAATGACT
*
57209 ATCGCAATGCGAAATGAAAATCGAAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
57242 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
57275 ATCGC-ATCGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAAT-GCGAAATGAAAATCGCAACGAGAGA
* *
57308 ATTGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
57336 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
32 2 0.02
33 85 0.97
34 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:57338 original size:19 final size:18
Alignment explanation
Indices: 57189--57339 Score: 74
Period size: 19 Copynumber: 8.7 Consensus size: 18
57179 CCTAATGTCT
**
57189 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
57209 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
57228 ATCG-AAACG--A-GAGA
1 ATCGCAAGCGAAATGAAA
57242 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
57261 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
57275 ATCGCATCGCGAAATGAAA
1 ATCGCA-AGCGAAATGAAA
**
57294 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
57308 ATTGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
57327 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
57340 TTTAGTTTCG
Statistics
Matches: 98, Mismatches: 17, Indels: 33
0.66 0.11 0.22
Matches are distributed among these distances:
14 22 0.22
15 7 0.07
16 6 0.06
17 6 0.06
18 7 0.07
19 41 0.42
20 9 0.09
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:57387 original size:33 final size:33
Alignment explanation
Indices: 57345--57428 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
57335 GCGAATTTAG
* * *
57345 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCATTACGATTTTCA
*
57378 TTTCGCGTTGCGATTCTCTCATTACGATTTTCA
1 TTTCGCGTTGCGATTTTCTCATTACGATTTTCA
57411 TTTCGCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
57429 ATTTCGCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCATTACGATTTTCA
Found at i:57388 original size:19 final size:19
Alignment explanation
Indices: 57364--57435 Score: 82
Period size: 19 Copynumber: 4.1 Consensus size: 19
57354 GCGATTTTGT
57364 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
57383 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
* *
57397 CATTACGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
57416 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
57435 C
1 C
57436 ATTGAGATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
14 8 0.19
16 3 0.07
17 3 0.07
19 28 0.67
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:57449 original size:19 final size:19
Alignment explanation
Indices: 57408--57451 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
57398 ATTACGATTT
* * **
57408 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGAGATAG
57427 TCATTTCGCATTGAGATAG
1 TCATTTCGCATTGAGATAG
57446 TCATTT
1 TCATTT
57452 TTGCCTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGAGATAG
Found at i:57569 original size:14 final size:14
Alignment explanation
Indices: 57550--57583 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
57540 CATCAATTAA
57550 ACAAATAAACTTTT
1 ACAAATAAACTTTT
* *
57564 ACAAATCATCTTTT
1 ACAAATAAACTTTT
57578 ACAAAT
1 ACAAAT
57584 CAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:57584 original size:14 final size:14
Alignment explanation
Indices: 57559--57585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57549 AACAAATAAA
57559 CTTTTACAAATCAT
1 CTTTTACAAATCAT
57573 CTTTTACAAATCA
1 CTTTTACAAATCA
57586 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTTACAAATCAT
Found at i:58959 original size:21 final size:20
Alignment explanation
Indices: 58935--58995 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
58925 GTGAATCGGG
*
58935 CTCTTGAATGGTGAGAGGGAC
1 CTCTTGAACGGTGAGAGGG-C
* * *
58956 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGAGAG-GGC
*
58977 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGGTGAGAGGG
58996 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGAGAGGGC
Found at i:59020 original size:42 final size:42
Alignment explanation
Indices: 58974--59053 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
58964 CGATGACAGT
* * *
58974 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
59016 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
59054 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:59607 original size:94 final size:94
Alignment explanation
Indices: 59446--59750 Score: 512
Period size: 94 Copynumber: 3.3 Consensus size: 94
59436 GGATAGTTTC
*
59446 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
59511 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
59540 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
*
59605 ACAGTGTTAAAGAATACACAGTTTAGCAT
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
59634 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
*
59698 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* *
59724 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
59751 AAGCAATCTA
Statistics
Matches: 203, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
90 40 0.20
93 19 0.09
94 144 0.71
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:61464 original size:20 final size:20
Alignment explanation
Indices: 61439--61553 Score: 104
Period size: 20 Copynumber: 6.2 Consensus size: 20
61429 TTTTGGTTGA
61439 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
61459 AATGAAAATCGCAACGTG-G
1 AATGAAAATCGCAACGAGAG
**
61478 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
61497 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
**
61512 AATGACTATCGCAACGAGA-
1 AATGAAAATCGCAACGAGAG
61531 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
61551 AAT
1 AAT
61554 CGCAACGCGA
Statistics
Matches: 78, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.10
16 4 0.05
17 2 0.03
18 1 0.01
19 30 0.38
20 33 0.42
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:61481 original size:40 final size:39
Alignment explanation
Indices: 61437--61582 Score: 138
Period size: 33 Copynumber: 4.1 Consensus size: 39
61427 TCTTTTGGTT
** *
61437 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGTG
1 GAAATGACTATCGCAACGAGAGAATGAAAATCGCAACG-C
61477 GAAATGACTATCGCAAC--GAG-A-G--AATCGCAACGC
1 GAAATGACTATCGCAACGAGAGAATGAAAATCGCAACGC
61510 GAAATGACTATCGCAACGAGA-AATGAAAATCGCAA--C
1 GAAATGACTATCGCAACGAGAGAATGAAAATCGCAACGC
* * *
61546 GAGA-GA--ATCGCAACGCGA-AATGAAAATCGCAATGC
1 GAAATGACTATCGCAACGAGAGAATGAAAATCGCAACGC
61581 GA
1 GA
61583 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 5, Indels: 21
0.78 0.04 0.18
Matches are distributed among these distances:
33 42 0.45
34 10 0.11
35 8 0.09
36 6 0.06
37 1 0.01
38 11 0.12
40 15 0.16
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (39 bp):
GAAATGACTATCGCAACGAGAGAATGAAAATCGCAACGC
Found at i:61524 original size:19 final size:19
Alignment explanation
Indices: 61437--61582 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
61427 TCTTTTGGTT
*
61437 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
61456 GAGAATGAAAATCGCAACGTG
1 GA-AATGAAAATCGCAACG-C
**
61477 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
61494 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
61510 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGC
61529 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
61546 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
61562 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
61581 GA
1 GA
61583 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 4 0.04
17 2 0.02
18 2 0.02
19 41 0.41
20 28 0.28
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:61544 original size:52 final size:53
Alignment explanation
Indices: 61445--61577 Score: 196
Period size: 52 Copynumber: 2.5 Consensus size: 53
61435 TTGAAATGAA
* * **
61445 AATCGCAACGAGAGAATGAAAATCGCAACGTGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGTAGAAATGAAAATCGCAACGAGAG
**
61499 AATCGCAACGCGAAATGACTATCGCAACG-AGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGTAGAAATGAAAATCGCAACGAGAG
61551 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
61578 TGCGATTTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 45 0.63
53 14 0.20
54 12 0.17
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCGCAACGTAGAAATGAAAATCGCAACGAGAG
Found at i:61641 original size:19 final size:19
Alignment explanation
Indices: 61605--61644 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
61595 GTTGCAATTA
**
61605 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATAGTCATT
61624 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATAGTCATT
61643 TC
1 TC
61645 CGCGTTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TCTCGTTGCGATAGTCATT
Found at i:62227 original size:20 final size:20
Alignment explanation
Indices: 62204--62297 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
62194 CGATAGTCAG
62204 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
62224 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
62244 AATTCGCATTACGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
62265 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
62285 ATTCACATTGCGA
1 ATTCGCATTGCGA
62298 ATTATGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 44 0.72
21 17 0.28
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:62328 original size:20 final size:21
Alignment explanation
Indices: 62294--62347 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
62284 TATTCACATT
62294 GCGAATTATGAAAATCGCAAC
1 GCGAATTATGAAAATCGCAAC
* *
62315 GCGAA-TATGTAAATCGCAAT
1 GCGAATTATGAAAATCGCAAC
*
62335 ACGAATTA-GAAAA
1 GCGAATTATGAAAA
62348 ATTGCGTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (21 bp):
GCGAATTATGAAAATCGCAAC
Found at i:81797 original size:65 final size:63
Alignment explanation
Indices: 81724--81883 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
81714 AATCAAATTG
* * *
81724 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATTGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-
81788 A
63 A
* * *
81789 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGA
* *
81853 AACATTGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
81884 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 50 0.59
66 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGA
Found at i:81883 original size:17 final size:19
Alignment explanation
Indices: 81861--81903 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
81851 GAAACATTGA
*
81861 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
81878 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
81897 ATGCACT
1 ATGCACT
81904 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:82844 original size:18 final size:18
Alignment explanation
Indices: 82821--82886 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
82811 GGGTCTACGC
82821 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
* *
82839 GGTCCTTCGAGACACAGT
1 GGTCCTTCGGGACATAGT
*
82857 GGTCATTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
* *
82875 GGCCCTACGGGA
1 GGTCCTTCGGGA
82887 TAAATTCTAC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:88475 original size:21 final size:21
Alignment explanation
Indices: 88451--88493 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
88441 ACAATCAAAT
88451 ATAAACAACATCAATAATTTA
1 ATAAACAACATCAATAATTTA
88472 ATAAACAACATCAATAATTTA
1 ATAAACAACATCAATAATTTA
88493 A
1 A
88494 ATATGTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAACAACATCAATAATTTA
Found at i:94517 original size:46 final size:46
Alignment explanation
Indices: 94464--94557 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
94454 TATTCAAAGA
94464 TAGTCTCCGATATGGTATATGATATGTCTTCTTTTGTTCTACATGT
1 TAGTCTCCGATATGGTATATGATATGTCTTCTTTTGTTCTACATGT
94510 TAGTCTCCGATATGGTATATGATATGTCTTCTTTTGTTCTACATGT
1 TAGTCTCCGATATGGTATATGATATGTCTTCTTTTGTTCTACATGT
94556 TA
1 TA
94558 TTAAAAACCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (46 bp):
TAGTCTCCGATATGGTATATGATATGTCTTCTTTTGTTCTACATGT
Found at i:102625 original size:16 final size:14
Alignment explanation
Indices: 102604--102663 Score: 59
Period size: 16 Copynumber: 4.0 Consensus size: 14
102594 TTAGGAATTA
102604 TTTAGGGATTTGAATG
1 TTTAGGGATTT-AA-G
102620 TTTA-GGATTTTAAAG
1 TTTAGGGA-TTT-AAG
*
102635 ATTTAAGGATTTAAG
1 -TTTAGGGATTTAAG
102650 TTTAGGGATTTAAG
1 TTTAGGGATTTAAG
102664 GGAGTGGGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.33
15 7 0.18
16 16 0.41
17 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (14 bp):
TTTAGGGATTTAAG
Found at i:102975 original size:38 final size:38
Alignment explanation
Indices: 102933--103007 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
102923 AATGTCACAC
*
102933 AAATTATTAATAAAATAAATTAGAGTGATTAGAACATA
1 AAATTATTAATAAAATAAATTAGAGTGATTAAAACATA
102971 AAATTATTAATAAAATAAATTAGAGTGATTAAAACAT
1 AAATTATTAATAAAATAAATTAGAGTGATTAAAACAT
103008 GAGTAATTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (38 bp):
AAATTATTAATAAAATAAATTAGAGTGATTAAAACATA
Found at i:103001 original size:22 final size:22
Alignment explanation
Indices: 102938--103002 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
102928 CACACAAATT
102938 ATTAATAAAATAAATTAGAGTG
1 ATTAATAAAATAAATTAGAGTG
* * *
102960 ATT-AGAACAT-AA--A-A-TT
1 ATTAATAAAATAAATTAGAGTG
102976 ATTAATAAAATAAATTAGAGTG
1 ATTAATAAAATAAATTAGAGTG
102998 ATTAA
1 ATTAA
103003 AACATGAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 3 0.10
20 3 0.10
21 6 0.19
22 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (22 bp):
ATTAATAAAATAAATTAGAGTG
Found at i:106431 original size:37 final size:37
Alignment explanation
Indices: 106338--106433 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
106328 CTTTTCATCC
106338 TACTAGGATTCAAACTCCTAAAAATAGGATAACATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAACATTT
* *
106375 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA-GTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATA-ACATTT
* * *
106412 TACTAAGATTTAAATTCCTAAA
1 TACTAGGATTCAAACTCCTAAA
106434 GATAAGATCC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 51 0.98
38 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAACATTT
Found at i:106834 original size:2 final size:2
Alignment explanation
Indices: 106827--106857 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
106817 ATTATGTTAT
106827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
106858 TTCTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:107336 original size:9 final size:9
Alignment explanation
Indices: 107315--107348 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
107305 TTTTTTTTCC
107315 TTTATCTTA-
1 TTTAT-TTAT
107324 TTTATTTAT
1 TTTATTTAT
107333 TTTATTTAT
1 TTTATTTAT
107342 TTTATTT
1 TTTATTT
107349 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:107337 original size:13 final size:14
Alignment explanation
Indices: 107315--107349 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
107305 TTTTTTTTCC
*
107315 TTTATCTTATTTA-
1 TTTATTTTATTTAT
107328 TTTATTTTATTTAT
1 TTTATTTTATTTAT
107342 TTTATTTT
1 TTTATTTT
107350 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:110470 original size:16 final size:17
Alignment explanation
Indices: 110445--110481 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
110435 AAAACAAAGA
110445 AAAAGAGAAACAAGAAC
1 AAAAGAGAAACAAGAAC
*
110462 AAAAG-GAAACAAGAGC
1 AAAAGAGAAACAAGAAC
110478 AAAA
1 AAAA
110482 ATCAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.70, C:0.11, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAACAAGAAC
Found at i:111160 original size:22 final size:22
Alignment explanation
Indices: 111132--111182 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
111122 CCCCATCAAT
111132 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
111154 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
111176 CCTTTGA
1 CCTTTGA
111183 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:112083 original size:36 final size:35
Alignment explanation
Indices: 112043--112448 Score: 380
Period size: 36 Copynumber: 11.5 Consensus size: 35
112033 ACTCATGATT
* * * *
112043 GTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACC
1 GTTTCTCTTGAAACAAT-TTTGTCTCTCTTGAGACA
* * * * *
112079 GTTTTCACTAG-AAGAGTTTTTTCTCTCTTGAGACA
1 G-TTTCTCTTGAAACAATTTTGTCTCTCTTGAGACA
*
112114 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AATTTTGTCTCTCTTGAGACA
*
112150 GTTTCTCTTGAAACAAATTTTTTTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AA-TTTTGTCTCTCTTGAGACA
*
112187 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AATTTTGTCTCTCTTGAGACA
*
112223 GTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTGAAACAATTTT-GTCTCTCTTGAGACA
* *
112259 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAA-CAATTTTGTCTCTCTTGAGACA
* ** * *
112295 GTTTCCCTTGAAACAA-----AATAT-TTGA-ATA
1 GTTTCTCTTGAAACAATTTTGTCTCTCTTGAGACA
** *
112323 TGTTT-TCTTTGAAACAAATTCCGTCTCCCTTGAGACA
1 -GTTTCTC-TTGAAAC-AATTTTGTCTCTCTTGAGACA
* *
112360 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AA-TTTTGTCTCTCTTGAGACA
*
112397 GTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTGAAACAATTTT-GTCTCTCTTGAGACA
*
112433 GTTTCCCTTGAAACAA
1 GTTTCTCTTGAAACAA
112449 AACCTTTGAA
Statistics
Matches: 307, Mismatches: 44, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.01
29 15 0.05
30 4 0.01
34 7 0.02
35 31 0.10
36 171 0.56
37 76 0.25
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (35 bp):
GTTTCTCTTGAAACAATTTTGTCTCTCTTGAGACA
Found at i:112199 original size:73 final size:73
Alignment explanation
Indices: 112095--112449 Score: 428
Period size: 73 Copynumber: 5.0 Consensus size: 73
112085 ACTAGAAGAG
112095 TTTTT-TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
1 TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
112159 GAAACAAA
66 GAAACAAA
*
112167 TTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
1 TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
112232 GAAAC-AA
66 GAAACAAA
* * * *
112239 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
112304 GAAACAAA
66 GAAACAAA
* * * * * ** * *
112312 -------ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTT
1 TTTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* *
112368 TGGAACTAA
65 TGAAACAAA
* * * *
112377 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCT
1 TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCTCT
112441 TGAAACAAA
65 TGAAACAAA
112450 ACCTTTGAAT
Statistics
Matches: 239, Mismatches: 31, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.01
65 47 0.20
66 3 0.01
72 78 0.33
73 107 0.45
74 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
GAAACAAA
Found at i:112511 original size:174 final size:174
Alignment explanation
Indices: 112101--112512 Score: 452
Period size: 174 Copynumber: 2.4 Consensus size: 174
112091 AGAGTTTTTT
*
112101 CTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 CTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC-C-CTTGAGATAG-TTCTCTTGAAACAA
*** *
112166 ATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT
63 ATTTCCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* *
112231 TGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGT
128 TGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA---T-A
* * *
112282 CTCTCTTGAGACAGTTTCCCTTGAAACAAA--ATAT---TTGA-ATATGTTTTCTTTGAAACAAA
1 CTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCCCTTGAGATA-GTTCTC-TTGAAACAAA
** * *
112341 -TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
64 TTTCCGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCT
112405 TGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA-A
128 TGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATA
* * *
112451 C-CT-TTGA-ATTTA-TTTCCCCTAAAACAAATTTTGTCGCCCTTGAGATAGTTACTCTTGAAAC
1 CTCTCTTGAGA--CAGTTTCCCTTGAAACAAATTTTGT--CCCTTGAGATAGTT-CTCTTGAAAC
112512 A
61 A
112513 CAAAATCTTC
Statistics
Matches: 197, Mismatches: 20, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
166 1 0.01
167 18 0.09
168 3 0.02
169 3 0.02
173 32 0.16
174 103 0.52
175 5 0.03
179 2 0.01
181 30 0.15
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (174 bp):
CTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCCCTTGAGATAGTTCTCTTGAAACAAATT
TCCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
AACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATA
Found at i:113554 original size:105 final size:104
Alignment explanation
Indices: 113186--114053 Score: 1230
Period size: 105 Copynumber: 8.3 Consensus size: 104
113176 GCCATCCGCG
* * * * * *
113186 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
113251 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAAC-AACAACTTCCCAA-TTCAGAGCCA
*
113295 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
113360 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAA-CAACAA-CTTCCCAA-TTCAGAGCCA
113402 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
113467 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
113507 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
113572 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
113612 ATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
113677 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
113712 ATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
113777 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
113817 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
113882 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * * *
113917 ATTTCAAATTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
113982 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGGTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
114023 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
114054 TGGAACAATG
Statistics
Matches: 695, Mismatches: 50, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
100 167 0.24
101 8 0.01
102 6 0.01
103 7 0.01
104 8 0.01
105 287 0.41
106 92 0.13
107 99 0.14
109 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:113795 original size:205 final size:210
Alignment explanation
Indices: 113186--114053 Score: 1265
Period size: 205 Copynumber: 4.1 Consensus size: 210
113176 GCCATCCGCG
* * * * * *
113186 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
113251 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGG
63 GGGACCGCTGCTTGTCAAC-AACAACTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
*
113316 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACA
* *
113381 ATTTTCCCAATTTCAGAGCCA
190 ACTTTCCCAATCTCAGAGCCA
113402 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
113467 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAACAACTTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
113532 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTT
113597 -CCAATCTCAGAGCCA
195 CCCAATCTCAGAGCCA
*
113612 ATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
113677 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCAATTTTAACTTCACAGCGAAGGATATT
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* *
113738 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAAC-TTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTC
*
113802 CCAATCCCAGAGCCA
196 CCAATCTCAGAGCCA
*
113817 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
** *
113882 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTCAATTTCAAATTCACAACGAAGGATATT
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * * *
113943 GGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTT
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTT
**
114007 CCCGGT-TCCAGAGCCA
195 CCCAATCT-CAGAGCCA
* *
114023 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
114054 TGGAACAATG
Statistics
Matches: 608, Mismatches: 39, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
204 2 0.00
205 276 0.45
206 49 0.08
207 1 0.00
208 2 0.00
209 2 0.00
210 95 0.16
211 9 0.01
212 98 0.16
213 49 0.08
214 3 0.00
216 22 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (210 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTC
CCAATCTCAGAGCCA
Found at i:113800 original size:310 final size:312
Alignment explanation
Indices: 113186--114053 Score: 1277
Period size: 310 Copynumber: 2.8 Consensus size: 312
113176 GCCATCCGCG
* * * * * *
113186 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
113251 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
63 GGGACCGCTGCTTGTCAAC-AACAACTTTC-CAA-TTCAGAGCCAATTTCAACTTCACAACGAAG
*
113315 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
125 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAAC
*
113380 AATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
189 AA-TTT-CCAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
113445 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
251 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCCCAGAGCCA
*
113507 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
113572 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAATGATAT
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
113637 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AATTT-
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAATTTC
* *
113700 C-ATTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
195 CAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
113764 TCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
260 TCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCCCAGAGCCA
*
113817 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
** *
113882 ACCGCTGCTTGTCAACAA-AA-TTT-C-ATTCAGATTCAATTTCAAATTCACAACGAAGGATATT
66 ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * * *
113943 GGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAATTT-
** *
114008 CCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACT
194 CCAATT-CAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACT
114054 TGGAACAATG
Statistics
Matches: 506, Mismatches: 32, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
305 81 0.16
306 4 0.01
307 6 0.01
308 3 0.01
309 3 0.01
310 194 0.38
311 36 0.07
312 1 0.00
314 3 0.01
315 2 0.00
316 3 0.01
317 95 0.19
318 50 0.10
319 3 0.01
321 22 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (312 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAATTTCC
AATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCCCAGAGCCA
Found at i:114691 original size:37 final size:37
Alignment explanation
Indices: 114597--114701 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
114587 CCTTTTCGTC
114597 CTACTAGGATTCAAACTCCTAAAAATAGGATAACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAACATT
* * *
114634 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGA-GTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA-ACATT
* * * *
114671 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
114702 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 57 0.98
38 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAACATT
Found at i:115079 original size:14 final size:13
Alignment explanation
Indices: 115060--115098 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
115050 TATATGGATA
115060 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
115074 TTTTATTATTTAT
1 TTTTATTATTTAT
115087 GTTATTATTATT
1 -TT-TTATTATT
115099 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:115097 original size:18 final size:17
Alignment explanation
Indices: 115058--115100 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
115048 ATTATATGGA
115058 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
115074 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
115092 TATTATTAT
1 TATTATTAT
115101 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:115308 original size:2 final size:2
Alignment explanation
Indices: 115303--115327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
115293 CTTATAACTT
115303 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
115328 TTCGTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115604 original size:9 final size:9
Alignment explanation
Indices: 115583--115616 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
115573 TTTTTTTTCC
115583 TTTATCTTA-
1 TTTAT-TTAT
115592 TTTATTTAT
1 TTTATTTAT
115601 TTTATTTAT
1 TTTATTTAT
115610 TTTATTT
1 TTTATTT
115617 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:115605 original size:13 final size:14
Alignment explanation
Indices: 115583--115617 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
115573 TTTTTTTTCC
*
115583 TTTATCTTATTTA-
1 TTTATTTTATTTAT
115596 TTTATTTTATTTAT
1 TTTATTTTATTTAT
115610 TTTATTTT
1 TTTATTTT
115618 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:117962 original size:3 final size:3
Alignment explanation
Indices: 117954--117980 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
117944 TTATCTGATA
117954 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
117981 TTTGTGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:127877 original size:12 final size:12
Alignment explanation
Indices: 127860--127884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
127850 TGCACAGAGG
127860 TTTATTAGGTTA
1 TTTATTAGGTTA
127872 TTTATTAGGTTA
1 TTTATTAGGTTA
127884 T
1 T
127885 GTTGTTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TTTATTAGGTTA
Found at i:129052 original size:36 final size:36
Alignment explanation
Indices: 129005--129129 Score: 214
Period size: 36 Copynumber: 3.5 Consensus size: 36
128995 TCCCCAACCC
*
129005 AGATAATTACTATAATGTTCCTCTATATATATTTAG
1 AGATAAATACTATAATGTTCCTCTATATATATTTAG
129041 AGATAAATACTATAATGTTCCTCTATATATATTTAG
1 AGATAAATACTATAATGTTCCTCTATATATATTTAG
* * *
129077 AGATAAATATTATAATGTTCCTCTCTAAATATTTAG
1 AGATAAATACTATAATGTTCCTCTATATATATTTAG
129113 AGATAAATACTATAATG
1 AGATAAATACTATAATG
129130 CCCTATATCA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (36 bp):
AGATAAATACTATAATGTTCCTCTATATATATTTAG
Found at i:132565 original size:19 final size:19
Alignment explanation
Indices: 132537--132576 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
132527 ATTTTATATC
132537 AATATATTATATCAAGGAA
1 AATATATTATATCAAGGAA
*
132556 AATATTTTATATCAAGGAA
1 AATATATTATATCAAGGAA
132575 AA
1 AA
132577 GTTGTCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
AATATATTATATCAAGGAA
Found at i:140480 original size:21 final size:21
Alignment explanation
Indices: 140454--140500 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
140444 CCCTCAACCA
*
140454 TGCTCTCATGTCATTGTTGCT
1 TGCTCTCATGTCATTGCTGCT
140475 TGCTCTCATGTCATTGCTGCT
1 TGCTCTCATGTCATTGCTGCT
140496 TGCTC
1 TGCTC
140501 ACATTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.28, G:0.19, T:0.45
Consensus pattern (21 bp):
TGCTCTCATGTCATTGCTGCT
Found at i:145123 original size:47 final size:47
Alignment explanation
Indices: 145065--145159 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 47
145055 GATTGTGTTG
*
145065 CAGCTAAGTGGTATACC-GAGATGGCTT-GAATAAGGTTCTGGTAGTTT
1 CAGCTAAGTGGT-TACCGGAGATGG-TTAGAATAAGATTCTGGTAGTTT
* *
145112 CAGCTATGTGGTTTCCGGAGATGGTTAGAATAAGATTCTGGTAGTTT
1 CAGCTAAGTGGTTACCGGAGATGGTTAGAATAAGATTCTGGTAGTTT
145159 C
1 C
145160 TTGGTCACTG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
46 5 0.12
47 38 0.88
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (47 bp):
CAGCTAAGTGGTTACCGGAGATGGTTAGAATAAGATTCTGGTAGTTT
Found at i:145862 original size:6 final size:6
Alignment explanation
Indices: 145828--145859 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
145818 TGGCTCTCTC
*
145828 TGGCAA TGGCAA TGGCAA TGGCAA TGTCAA TG
1 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA TG
145860 TCATCCTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (6 bp):
TGGCAA
Found at i:151251 original size:55 final size:55
Alignment explanation
Indices: 151194--151510 Score: 377
Period size: 55 Copynumber: 5.9 Consensus size: 55
151184 TGACGAGCCT
* * * *
151194 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATA-AAATGTGTCT
1 GCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCA-ACAAACGGGTCC
*
151249 GCTCTCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
151304 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * **
151359 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACGAACTTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * * **
151414 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * *
151465 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
151511 AGTTTGCTTC
Statistics
Matches: 244, Mismatches: 15, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
51 64 0.26
54 1 0.00
55 177 0.73
56 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (55 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
Found at i:152921 original size:14 final size:14
Alignment explanation
Indices: 152904--153034 Score: 56
Period size: 14 Copynumber: 8.9 Consensus size: 14
152894 TCATTTTCCA
152904 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
*
152918 TTTTCTT-TTCGTTT
1 TTTT-TTCTTCTTTT
* *
152932 TTTTTCCATCATTTT
1 TTTTTTCTTC-TTTT
152947 CCTTTTTTC-TCATTTT
1 --TTTTTTCTTC-TTTT
152963 TTTTTTCTT-TTTCT
1 TTTTTTCTTCTTT-T
* *
152977 TCTTCTCATT-TTTAT
1 TTTTTTC-TTCTTT-T
*
152992 TATTATTTTTTCATTTT
1 T-TT-TTTCTTC-TTTT
153009 TTCTTTT-TTCTTTT
1 TT-TTTTCTTCTTTT
*
153023 TTATTTCTTCTT
1 TTTTTTCTTCTT
153035 CAAGCGAAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 28
0.69 0.09 0.21
Matches are distributed among these distances:
13 7 0.08
14 40 0.44
15 16 0.18
16 14 0.15
17 11 0.12
18 3 0.03
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTCTTTT
Found at i:152986 original size:42 final size:42
Alignment explanation
Indices: 152863--152988 Score: 114
Period size: 42 Copynumber: 2.9 Consensus size: 42
152853 CCTCCTTTTA
* *
152863 TTTCTCTTTTTTTCTTCATTTTTCTCTTTTTTCATTTTCCATTT
1 TTTCTCTTTTTTTTTTCA-TTTT-TCTTTTCTCATTTTCCATTT
* *
152907 TTTCTTCTTTTTTTTCTTTTCGTTTTT-TTTCCATCATTTTCC-TTT
1 TTTC-TC--TTTTTT-TTTTCATTTTTCTTTTC-TCATTTTCCATTT
152952 TTTCTCATTTTTTTTTTC-TTTTTCTTCTTCTCATTTT
1 TTTCTC-TTTTTTTTTTCATTTTTCTT-TTCTCATTTT
152989 TATTATTATT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
41 5 0.07
42 14 0.20
43 8 0.12
44 6 0.09
45 12 0.17
46 10 0.14
47 10 0.14
48 4 0.06
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.74
Consensus pattern (42 bp):
TTTCTCTTTTTTTTTTCATTTTTCTTTTCTCATTTTCCATTT
Found at i:153000 original size:54 final size:56
Alignment explanation
Indices: 152890--153035 Score: 130
Period size: 56 Copynumber: 2.7 Consensus size: 56
152880 ATTTTTCTCT
* * * * *
152890 TTTTTCA--TTTTC-CA-TTTTTTCTTCTTTTTTTTCTTTTCGTTTTTTTTCCATCA
1 TTTTTCATTTTTTCTCATTTTTTTTTTCTTTTTCTTCTTCTCATTTTTATT-CATCA
* *
152943 -TTTTCCTTTTTTCTCATTTTTTTTTTCTTTTTCTTCTTCTCATTTTTATT-ATTA
1 TTTTTCATTTTTTCTCATTTTTTTTTTCTTTTTCTTCTTCTCATTTTTATTCATCA
*
152997 TTTTTTCATTTTTTCT--TTTTTCTTTTT-TATTTCTTCTTC
1 -TTTTTCATTTTTTCTCATTTTT-TTTTTCTTTTTCTTCTTC
153036 AAGCGAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
52 5 0.06
54 24 0.31
55 7 0.09
56 41 0.53
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.75
Consensus pattern (56 bp):
TTTTTCATTTTTTCTCATTTTTTTTTTCTTTTTCTTCTTCTCATTTTTATTCATCA
Found at i:153017 original size:15 final size:14
Alignment explanation
Indices: 152863--153034 Score: 61
Period size: 15 Copynumber: 11.9 Consensus size: 14
152853 CCTCCTTTTA
*
152863 TTTCTCTTTT-TTT
1 TTTCTTTTTTCTTT
*
152876 CTTCATTTTTCTCTTT
1 TTTC-TTTTT-TCTTT
* *
152892 TTTCATTTTCCATTT
1 TTTCTTTTTTC-TTT
*
152907 TTTC-TTCTT-TTT
1 TTTCTTTTTTCTTT
152919 TTTCTTTTCGTT-TTT
1 TTTCTTTT--TTCTTT
*
152934 TTTCCATCATTTTCCTTT
1 TTT-C-T--TTTTTCTTT
*
152952 TTTCTCATTTT-TTT
1 TTTCT-TTTTTCTTT
152966 TTTC-TTTTTCTTCT
1 TTTCTTTTTTCTT-T
* * *
152980 TCTCATTTTT-ATT
1 TTTCTTTTTTCTTT
* *
152993 ATTATTTTTTCATTT
1 TTTCTTTTTTC-TTT
153008 TTTCTTTTTTCTTT
1 TTTCTTTTTTCTTT
* *
153022 TTTATTTCTTCTT
1 TTTCTTTTTTCTT
153035 CAAGCGAAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 33
0.67 0.14 0.19
Matches are distributed among these distances:
12 11 0.09
13 14 0.12
14 34 0.29
15 39 0.33
16 8 0.07
17 3 0.03
18 6 0.05
19 3 0.03
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (14 bp):
TTTCTTTTTTCTTT
Found at i:153022 original size:21 final size:20
Alignment explanation
Indices: 152863--153023 Score: 59
Period size: 21 Copynumber: 7.8 Consensus size: 20
152853 CCTCCTTTTA
*
152863 TTTCTCTTTTT-TTCTTCATTT
1 TTTCT-TTTTTCTTTTTC-TTT
*
152884 TTCTCTTTTTTCATTTTCCATTT
1 TT-TCTTTTTTC-TTTTTC-TTT
*
152907 TTTCTTCTTT-TTTTTC--T
1 TTTCTTTTTTCTTTTTCTTT
** *
152924 TTTCGTTTTTT-TTCCATCATT
1 TTTC-TTTTTTCTT-TTTCTTT
*
152945 TTCCTTTTTTCTCATTTT-TTT
1 TTTCTTTTTTCT--TTTTCTTT
*
152966 TTTC-TTTTTCTTCTTCTCATT
1 TTTCTTTTTTCTT-TT-TCTTT
* *
152987 TTTATTATTAT-TTTTTCATTT
1 TTTCTT-TTTTCTTTTTC-TTT
153008 TTTCTTTTTTCTTTTT
1 TTTCTTTTTTCTTTTT
153024 TATTTCTTCT
Statistics
Matches: 105, Mismatches: 18, Indels: 34
0.67 0.11 0.22
Matches are distributed among these distances:
17 5 0.05
18 8 0.08
19 4 0.04
20 24 0.23
21 36 0.34
22 14 0.13
23 14 0.13
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTCTTT
Found at i:167279 original size:20 final size:20
Alignment explanation
Indices: 167250--167302 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
167240 ATTCCACCAC
*
167250 ATGCAACTATATGCTACTAA
1 ATGCATCTATATGCTACTAA
167270 ATGCATCTATATGCTACTAA
1 ATGCATCTATATGCTACTAA
167290 ATGCATCTATATG
1 ATGCATCTATATG
167303 TTCCTATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGCATCTATATGCTACTAA
Found at i:173444 original size:18 final size:18
Alignment explanation
Indices: 173421--173467 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
173411 GAAATAAGTG
173421 CAAGTATACACAATCGAA
1 CAAGTATACACAATCGAA
173439 CAAGTATACACAATCGAA
1 CAAGTATACACAATCGAA
173457 CAAGTAATACA
1 CAAGT-ATACA
173468 GTGATAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (18 bp):
CAAGTATACACAATCGAA
Found at i:185027 original size:36 final size:36
Alignment explanation
Indices: 184980--185104 Score: 223
Period size: 36 Copynumber: 3.5 Consensus size: 36
184970 TCCCCAACCC
*
184980 AGATAATTACTATAATGTTCCTCTCTATATATTTAG
1 AGATAAATACTATAATGTTCCTCTCTATATATTTAG
*
185016 AGATAAATACTATAATGTTCCTCTATATATATTTAG
1 AGATAAATACTATAATGTTCCTCTCTATATATTTAG
*
185052 AGATAAATACTATAATGTTCCTCTCTAAATATTTAG
1 AGATAAATACTATAATGTTCCTCTCTATATATTTAG
185088 AGATAAATACTATAATG
1 AGATAAATACTATAATG
185105 CCCTATATCA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 85 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (36 bp):
AGATAAATACTATAATGTTCCTCTCTATATATTTAG
Found at i:194065 original size:20 final size:20
Alignment explanation
Indices: 194042--194093 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
194032 AACGCGATCC
194042 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
194062 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
194082 CCAAAATCGCAA
1 CCAGAATCGCAA
194094 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:194110 original size:21 final size:20
Alignment explanation
Indices: 194083--194181 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
194073 AATCAGTTTC
194083 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
194104 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
194125 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
194145 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
194166 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
194182 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:194210 original size:20 final size:20
Alignment explanation
Indices: 194148--194341 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
194138 CGATTTTCCA
* ** *
194148 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
194168 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
194188 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
194208 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
194228 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
194248 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
194268 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
194288 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
194308 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
194329 AAATCGCAACGCG
1 AAATCGCAACGCG
194342 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:194232 original size:60 final size:60
Alignment explanation
Indices: 194148--194341 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
194138 CGATTTTCCA
* ** * *
194148 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
194208 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
194268 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
194329 AAATCGCAACGCG
1 AAATCGCAACGCG
194342 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:194759 original size:33 final size:33
Alignment explanation
Indices: 194722--194792 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
194712 TTCATTTAGA
*
194722 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
194755 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
194788 TTTCA
1 TTTCA
194793 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:194932 original size:14 final size:14
Alignment explanation
Indices: 194913--194967 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
194903 AGAATGACTG
194913 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
194927 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
194946 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
194960 TCGCAACG
1 TCGCAACG
194968 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:194980 original size:33 final size:33
Alignment explanation
Indices: 194913--194983 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
194903 AGAATGACTG
***
194913 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
194946 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
194979 TCGCA
1 TCGCA
194984 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:195001 original size:19 final size:19
Alignment explanation
Indices: 194979--195076 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
194969 GAAACCAAAA
*
194979 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
194998 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
195012 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
195031 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
195045 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
195064 TCGCGTTGCGATT
1 TCGCGTTGCGATT
195077 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:195020 original size:14 final size:14
Alignment explanation
Indices: 195001--195090 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
194991 TTTCATTTCG
195001 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
195015 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
195034 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
195048 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
195065 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
195081 CGTTGCGATT
1 CGTTGCGATT
195091 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:195026 original size:33 final size:33
Alignment explanation
Indices: 194984--195098 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
194974 CAAAATCGCA
194984 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
195017 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
195050 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
195083 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
195099 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:197082 original size:93 final size:93
Alignment explanation
Indices: 196880--197252 Score: 739
Period size: 93 Copynumber: 4.0 Consensus size: 93
196870 TGTCTTTTGG
196880 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTGTCT
1 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
196944 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
66 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
196972 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
1 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
197037 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
66 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
197065 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
1 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
197130 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
66 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
197158 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
1 TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
197223 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
66 TTGTTTTGTCTTTTGGTTGAAAGTAAAT
197251 TT
1 TT
197253 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 55 0.20
93 225 0.80
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCT
TTGTTTTGTCTTTTGGTTGAAAGTAAAT
Found at i:197336 original size:19 final size:19
Alignment explanation
Indices: 197296--197423 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
197286 TAGTTTACTT
* *
197296 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
197316 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
197335 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
197354 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
197368 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
197387 TCGCAA--TG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
197401 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
197419 TCGCA
1 TCGCA
197424 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 9 0.10
19 38 0.44
20 13 0.15
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:197375 original size:33 final size:32
Alignment explanation
Indices: 197332--197423 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
197322 CGCGAAACCA
**
197332 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
197364 AGAATCGCAACGCGAAACCAAAATCGCAATGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
197397 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
197424 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 10 0.18
33 45 0.82
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:197446 original size:19 final size:19
Alignment explanation
Indices: 197419--197553 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
197409 CGAAACCAAA
*
197419 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
197438 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
197454 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
197471 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
197487 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
197504 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
197523 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
197543 TCGTGTTGCGA
1 TCGCGTTGCGA
197554 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:197460 original size:14 final size:14
Alignment explanation
Indices: 197441--197497 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
197431 TTTCATTTCG
197441 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
197455 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
197472 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
197488 CGTTGCGATT
1 CGTTGCGATT
197498 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:197466 original size:33 final size:33
Alignment explanation
Indices: 197424--197516 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
197414 CCAAATCGCA
*
197424 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
197457 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
197490 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
197517 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:199473 original size:14 final size:14
Alignment explanation
Indices: 199454--199489 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
199444 ATTGTTTAAT
199454 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
199468 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
199482 TGATTTGT
1 TGATTTGT
199490 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:199612 original size:19 final size:19
Alignment explanation
Indices: 199596--199697 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
199586 AAAAATGACT
199596 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
199615 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
199634 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
199648 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
199667 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
199687 ATCGCAATGCG
1 ATCGCAATGCG
199698 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:199746 original size:33 final size:33
Alignment explanation
Indices: 199704--199889 Score: 127
Period size: 33 Copynumber: 5.5 Consensus size: 33
199694 TGCGTTTATA
199704 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
199737 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
199773 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTATGTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
** * * *
199810 GGTTCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
199841 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
199874 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
199890 TTCATTTCGC
Statistics
Matches: 127, Mismatches: 11, Indels: 30
0.76 0.07 0.18
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 77 0.61
35 9 0.07
36 9 0.07
37 4 0.03
38 10 0.08
39 1 0.01
40 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:199766 original size:52 final size:52
Alignment explanation
Indices: 199726--199947 Score: 252
Period size: 52 Copynumber: 4.2 Consensus size: 52
199716 GATTATCTCG
** *
199726 TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCATTTCG-ATTTGC-ATT-TCGCA
* ** *
199778 TTGCGATTTTCATTTCGCATTGCGATTATGTCGGTTCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCATTTCGATTTGCATTTCGCA
* * * *
199830 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCATTTCGATTTGCATTTCGCA
* * * *
199882 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCATTTCGATTTGCATTT-CGCA
199935 TTGCGATTTTCAT
1 TTGCGATTTTCAT
199948 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
52 125 0.80
53 22 0.14
54 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCATTTCGATTTGCATTTCGCA
Found at i:199818 original size:85 final size:83
Alignment explanation
Indices: 199704--199975 Score: 354
Period size: 85 Copynumber: 3.2 Consensus size: 83
199694 TGCGTTTATA
199704 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTAT-TCGTT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
199769 ATTCTTTCGTTGCGATTTTC
64 ATTCTTTCGTTGCGATTTTC
199789 ATTTCGCATTGCGATTATGTCGGTTCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTAT-TC-GTTCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
199854 ATTCTCTCGTTGCGATTTTC
64 ATTCTTTCGTTGCGATTTTC
* * * *
199874 ATTTCGCATTGCGATT-TTCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATT
1 ATTTCGCATTGCGATTATTC-GTTCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTT-CGCATT
*
199937 GCGA-T-TTTCATGTTGGGATTTTC
61 GCGATTCTTTC--GTTGCGATTTTC
*
199960 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
199976 GTATTTTCCG
Statistics
Matches: 170, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
83 9 0.05
84 8 0.05
85 114 0.67
86 39 0.23
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (83 bp):
ATTTCGCATTGCGATTATTCGTTCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
TCTTTCGTTGCGATTTTC
Found at i:199919 original size:33 final size:33
Alignment explanation
Indices: 199745--199975 Score: 220
Period size: 33 Copynumber: 6.8 Consensus size: 33
199735 TCATTTCGCA
*
199745 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
199778 TTGCGATTTTCATTTCGCATTGCGATTATGTCGG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-G
*
199812 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
199847 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
199882 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
199915 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
199949 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
199976 GTATTTTCCG
Statistics
Matches: 165, Mismatches: 18, Indels: 30
0.77 0.08 0.14
Matches are distributed among these distances:
31 9 0.05
32 5 0.03
33 89 0.54
34 32 0.19
35 6 0.04
36 3 0.02
37 4 0.02
38 5 0.03
39 3 0.02
40 9 0.05
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:202510 original size:24 final size:24
Alignment explanation
Indices: 202476--202522 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
202466 CTGAAACATC
202476 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
202500 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
202523 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:203223 original size:20 final size:20
Alignment explanation
Indices: 203195--203563 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
203185 AAATTTCAGT
* * * *
203195 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
203215 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
203235 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
203255 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
203275 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
203295 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
203315 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
203335 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
203355 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
203375 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
203395 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
203415 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
203435 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
203455 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
203475 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
203495 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
203515 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
203535 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
203555 GTTGCGATT
1 GTTGCGATT
203564 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:204141 original size:38 final size:38
Alignment explanation
Indices: 204085--204167 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
204075 TTCACCCTAA
204085 ACCCGAACCCAACCCGAATATCACACTTAACAAAACCCG
1 ACCCGAACCCAACCCGAATATCACACTTAA-AAAACCCG
*
204124 ACCCG-ACCCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGAACCCAACCCGAATATCACACTTAAAAAACCCG
204161 A-CCGAAC
1 ACCCGAAC
204168 AAAATAAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 3 0.07
37 11 0.26
38 23 0.55
39 5 0.12
ACGTcount: A:0.40, C:0.41, G:0.10, T:0.10
Consensus pattern (38 bp):
ACCCGAACCCAACCCGAATATCACACTTAAAAAACCCG
Found at i:208276 original size:34 final size:34
Alignment explanation
Indices: 208233--208309 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
208223 TTTATTTATA
208233 TATATATTTAGATATAATTACTATAATTGA-CTTC
1 TATATATTTAGATATAATTACTATAATTGATC-TC
*
208267 TATATATTTAGATATAATTACTATAATTTATCTC
1 TATATATTTAGATATAATTACTATAATTGATCTC
208301 TATATATTT
1 TATATATTT
208310 TTTAATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 40 0.98
35 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (34 bp):
TATATATTTAGATATAATTACTATAATTGATCTC
Found at i:214236 original size:29 final size:31
Alignment explanation
Indices: 214176--214236 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
214166 ATTAAAAGAA
*
214176 TGATAAAAAATGATATTAATAATTTAATGAT
1 TGATAAAAAATGATATTAATAATTTAAGGAT
* *
214207 TGATATAAAAT-ATTTTAA-AATTTAAGGAT
1 TGATAAAAAATGATATTAATAATTTAAGGAT
214236 T
1 T
214237 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 11 0.41
30 6 0.22
31 10 0.37
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (31 bp):
TGATAAAAAATGATATTAATAATTTAAGGAT
Found at i:215117 original size:12 final size:12
Alignment explanation
Indices: 215100--215128 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
215090 AATTCCCTCT
215100 TAAACATCTCAA
1 TAAACATCTCAA
215112 TAAACATCTCAA
1 TAAACATCTCAA
215124 TAAAC
1 TAAAC
215129 CAAAAGCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAACATCTCAA
Found at i:218081 original size:12 final size:12
Alignment explanation
Indices: 218064--218088 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
218054 GAGGAGATTT
218064 TCAATTTTATCA
1 TCAATTTTATCA
218076 TCAATTTTATCA
1 TCAATTTTATCA
218088 T
1 T
218089 GGTAGTTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TCAATTTTATCA
Found at i:220340 original size:83 final size:83
Alignment explanation
Indices: 220227--220391 Score: 244
Period size: 83 Copynumber: 2.0 Consensus size: 83
220217 ATATCAAATT
* * *
220227 ATTCCAATAAAAACTTGAGTATATAGTTTAAAAATGATT-AAATTTAGGGATCAATTTGTAATAT
1 ATTCCAATAAAAACTTGAGTATATAATTT-AAAATCATTAAAATTTAGGGATCAATTTGTAATAC
220291 CAAGCCAAGTGTATATATC
65 CAAGCCAAGTGTATATATC
* *
220310 ATTCCAATAAATACTTGAGTATCA-AATTTAAAATCTTTAAAATTTAGGGATCAATTTGTAATAC
1 ATTCCAATAAAAACTTGAGTAT-ATAATTTAAAATCATTAAAATTTAGGGATCAATTTGTAATAC
*
220374 CAAGCCTAGTGTATATAT
65 CAAGCCAAGTGTATATAT
220392 ATCATTCGCC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
82 7 0.09
83 66 0.89
84 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (83 bp):
ATTCCAATAAAAACTTGAGTATATAATTTAAAATCATTAAAATTTAGGGATCAATTTGTAATACC
AAGCCAAGTGTATATATC
Found at i:223139 original size:29 final size:29
Alignment explanation
Indices: 223106--223189 Score: 109
Period size: 28 Copynumber: 2.9 Consensus size: 29
223096 TCCCAACACA
223106 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
***
223135 TAGGTCGCCATG-CCGGAGGGC-ATCCTTG
1 TAGGTCGCCATGCCCTCCGGGCGA-CCTTG
*
223163 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
223190 ACCCTCGCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.02
28 23 0.51
29 20 0.44
30 1 0.02
ACGTcount: A:0.13, C:0.35, G:0.32, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:223241 original size:23 final size:23
Alignment explanation
Indices: 223207--223289 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
223197 CTCGGCTTCT
223207 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
*
223230 CTCGGTTGCCCTCGGATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
223253 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
223276 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
223290 GTCGGATGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 2 0.04
23 52 0.96
ACGTcount: A:0.10, C:0.36, G:0.28, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:223316 original size:20 final size:20
Alignment explanation
Indices: 223291--223344 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
223281 ATGGCCTCGG
*
223291 TCGGATGGCATCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
223311 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
223331 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
223345 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.28, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:223350 original size:14 final size:14
Alignment explanation
Indices: 223331--223358 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
223321 TCGGATGCTC
223331 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
223345 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
223359 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:223361 original size:10 final size:10
Alignment explanation
Indices: 223291--223344 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
223281 ATGGCCTCGG
*
223291 TCGGATGGCA
1 TCGGATGGCC
223301 TCGGAT-GCTC
1 TCGGATGGC-C
223311 TCGGATGGCC
1 TCGGATGGCC
223321 TCGGAT-GCTC
1 TCGGATGGC-C
223331 TCGGATGGCC
1 TCGGATGGCC
223341 TCGG
1 TCGG
223345 TCGGATGGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.10
10 31 0.79
11 4 0.10
ACGTcount: A:0.11, C:0.28, G:0.37, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Done.