Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007833.1 Hibiscus syriacus cultivar Beakdansim tig00110177_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: 816380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:247 original size:29 final size:29
Alignment explanation
Indices: 171--250 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
161 TCACATTTTC
171 AAACACTAATTTCACA-TTATCAAACTTG
1 AAACACTAATTTCACATTTATCAAACTTG
*** * *
199 AAACA--AGATGAAGACCTTTATCAAACTTT
1 AAACACTA-AT-TTCACATTTATCAAACTTG
228 AAACACTAATTTCACATTTATCA
1 AAACACTAATTTCACATTTATCA
251 TTCAGGTACA
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 7 0.18
29 25 0.66
30 2 0.05
31 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (29 bp):
AAACACTAATTTCACATTTATCAAACTTG
Found at i:831 original size:32 final size:32
Alignment explanation
Indices: 766--855 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
756 CCGGAACTCA
* **
766 GAAGGGGAAGATCGGCCGTA-GAAGTCATTAGG
1 GAAGGGGAAGATCGGCCG-ACGAAGTGACGAGG
*
798 GAAGGGGAAGATCGGCCGACGAAGTGGCGAGG
1 GAAGGGGAAGATCGGCCGACGAAGTGACGAGG
* * *
830 GAA-AGGAAGATCGACCGGCGAAGTGA
1 GAAGGGGAAGATCGGCCGACGAAGTGA
856 AGTCACCAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 20 0.41
32 29 0.59
ACGTcount: A:0.32, C:0.14, G:0.43, T:0.10
Consensus pattern (32 bp):
GAAGGGGAAGATCGGCCGACGAAGTGACGAGG
Found at i:1042 original size:39 final size:39
Alignment explanation
Indices: 969--1045 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
959 TAAACTCCTT
* * *
969 TATATATATTTTTAATTTAAATTAAATTTATTAATATTA
1 TATATATATTTATAATATAAAATAAATTTATTAATATTA
1008 TATATATATTTATAA-ATAAAATAATTATTT-TTAATATT
1 TATATATATTTATAATATAAAATAA--ATTTATTAATATT
1046 TATCGGGCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 7 0.21
39 22 0.67
40 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
TATATATATTTATAATATAAAATAAATTTATTAATATTA
Found at i:9361 original size:27 final size:27
Alignment explanation
Indices: 9331--9403 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
9321 AGATTGTAAT
*
9331 TTGCAATCTCTAACAAAACATGGATGG
1 TTGCAATCCCTAACAAAACATGGATGG
*
9358 TTGCAATCCCTAACAATACATGGATGG
1 TTGCAATCCCTAACAAAACATGGATGG
*
9385 TTGCAATCCCTGACAAAAC
1 TTGCAATCCCTAACAAAAC
9404 GTGATAGTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (27 bp):
TTGCAATCCCTAACAAAACATGGATGG
Found at i:9731 original size:76 final size:77
Alignment explanation
Indices: 9636--9785 Score: 221
Period size: 78 Copynumber: 1.9 Consensus size: 77
9626 TATACCGGAA
*** *
9636 ATTAAGTAGCGAAATTAACATTTTTGGTA-AAAAATAATGTTTTAGGTAACGCTTTACTAGAAAT
1 ATTAAGTAGCGAAATTAACATTTAAAGTAGAAAAATAATGTTTTAGGTAACGCTTTACCAGAAAT
9700 GTTAAAAACTTC
66 GTTAAAAACTTC
* * *
9712 ATTAGGTAGCGAAATTAACATTTAAAGTAGGAAAAATAATGTTTTAGGTAGCGTTTTACCAGAAA
1 ATTAAGTAGCGAAATTAACATTTAAAGTA-GAAAAATAATGTTTTAGGTAACGCTTTACCAGAAA
9777 TGTTAAAAA
65 TGTTAAAAA
9786 AATATTAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 25 0.38
78 40 0.62
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (77 bp):
ATTAAGTAGCGAAATTAACATTTAAAGTAGAAAAATAATGTTTTAGGTAACGCTTTACCAGAAAT
GTTAAAAACTTC
Found at i:10423 original size:31 final size:32
Alignment explanation
Indices: 10356--10439 Score: 134
Period size: 32 Copynumber: 2.6 Consensus size: 32
10346 CCTACTCTTT
*
10356 AATACATAAATGTAAATTTTATATTATCAAAA
1 AATACATAAATATAAATTTTATATTATCAAAA
*
10388 AATACGTAAATATAAATTTTATATTATC-AAA
1 AATACATAAATATAAATTTTATATTATCAAAA
10419 AATACATAAAATATAAATTTT
1 AATACAT-AAATATAAATTTT
10440 GCATATGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 9 0.19
32 39 0.81
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (32 bp):
AATACATAAATATAAATTTTATATTATCAAAA
Found at i:18247 original size:20 final size:20
Alignment explanation
Indices: 18222--18259 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18212 AACATGTTAA
*
18222 AGAATGCATTGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
18242 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
18260 TCAAGGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:22235 original size:15 final size:16
Alignment explanation
Indices: 22215--22249 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
22205 TTTGTAATTT
*
22215 TTAAAATTTTATTA-A
1 TTAAAATTTAATTATA
22230 TTAAAATTTAATTATA
1 TTAAAATTTAATTATA
22246 TTAA
1 TTAA
22250 GGGTTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAATTTAATTATA
Found at i:22525 original size:27 final size:26
Alignment explanation
Indices: 22495--22588 Score: 80
Period size: 26 Copynumber: 3.4 Consensus size: 26
22485 CAATTTAATC
*
22495 ATATTTTTAAATAAATTTTAAAATAAAATA
1 ATATTTTTAAATAAA-ATTAAAAT--AA-A
*
22525 TATATTTTTAAATGAAAATAAAAATAAA
1 -ATATTTTTAAAT-AAAATTAAAATAAA
* * *
22553 ATATTTTTAAATTAAGTTAATATAAA
1 ATATTTTTAAATAAAATTAAAATAAA
*
22579 ATATATTTAA
1 ATATTTTTAA
22589 TAAGTTAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.35
27 12 0.22
28 1 0.02
29 2 0.04
31 18 0.33
32 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATTTTTAAATAAAATTAAAATAAA
Found at i:22532 original size:31 final size:31
Alignment explanation
Indices: 22495--22556 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
22485 CAATTTAATC
* *
22495 ATATTTTTAAAT-AAATTTTAAAATAAAATAT
1 ATATTTTTAAATGAAA-ATAAAAATAAAATAT
22526 ATATTTTTAAATGAAAATAAAAATAAAATAT
1 ATATTTTTAAATGAAAATAAAAATAAAATAT
22557 TTTTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
ATATTTTTAAATGAAAATAAAAATAAAATAT
Found at i:22580 original size:31 final size:30
Alignment explanation
Indices: 22495--22581 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
22485 CAATTTAATC
* *
22495 ATATTTTTAAATAAATTTTAAAATAAAAT-AT
1 ATATTTTTAAATAAA--TTAATATAAAATAAA
*
22526 ATATTTTTAAATGAA--AATA-AAAATAAA
1 ATATTTTTAAATAAATTAATATAAAATAAA
*
22553 ATATTTTTAAATTAAGTTAATATAAAATA
1 ATATTTTTAAA-TAAATTAATATAAAATA
22582 TATTTAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
26 5 0.11
27 15 0.33
28 2 0.04
30 4 0.09
31 20 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
ATATTTTTAAATAAATTAATATAAAATAAA
Found at i:22592 original size:24 final size:24
Alignment explanation
Indices: 22548--22634 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 24
22538 GAAAATAAAA
*
22548 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATATTT-AA-TAAGTTAAT
22574 ATAAAATATATTTAATAAGTTAAT
1 ATAAAATATATTTAATAAGTTAAT
*
22598 ATAAAAATTATATTT--TAAGGTAAT
1 AT-AAAA-TATATTTAATAAGTTAAT
*
22622 ATATAAAAATATT
1 ATA-AAATATATT
22635 ATGAATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
23 6 0.11
24 24 0.44
25 6 0.11
26 19 0.35
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:26283 original size:54 final size:54
Alignment explanation
Indices: 26201--26309 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
26191 CATAAACAAT
26201 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
1 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
26255 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
1 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
26309 T
1 T
26310 TGCGGAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (54 bp):
TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
Found at i:28237 original size:15 final size:15
Alignment explanation
Indices: 28219--28274 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
28209 TAACCGGTTT
28219 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
28234 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
28251 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
28266 CGATTTTAA
1 CGGTTTTAA
28275 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:28247 original size:17 final size:17
Alignment explanation
Indices: 28222--28272 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
28212 CCGGTTTCGG
28222 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
28239 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
28254 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
28271 TT
1 TT
28273 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:28690 original size:13 final size:13
Alignment explanation
Indices: 28669--28723 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
28659 AAGTTCGATA
*
28669 AATTCAAATACTT
1 AATTGAAATACTT
28682 AATTGAAATACTT
1 AATTGAAATACTT
* *
28695 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
28709 AATTGAAATACTT
1 AATTGAAATACTT
28722 AA
1 AA
28724 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:28805 original size:32 final size:33
Alignment explanation
Indices: 28709--28807 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
28699 AACTCAACAT
* * *
28709 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
28742 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
28775 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
28807 A
1 A
28808 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:28826 original size:21 final size:21
Alignment explanation
Indices: 28802--28841 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28792 ACTTCAAGTT
28802 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
28823 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
28842 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:32947 original size:29 final size:29
Alignment explanation
Indices: 32905--32962 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
32895 AGAGACACAT
32905 ATAACGAGAGAGTTTTCATAGTACAAAAA
1 ATAACGAGAGAGTTTTCATAGTACAAAAA
32934 ATAACGAGAGAGTTTTCATAGTACAAAAA
1 ATAACGAGAGAGTTTTCATAGTACAAAAA
32963 TAAAAAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.24
Consensus pattern (29 bp):
ATAACGAGAGAGTTTTCATAGTACAAAAA
Found at i:37271 original size:37 final size:37
Alignment explanation
Indices: 37221--37296 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
37211 GTGGCCGCTA
37221 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
1 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
37258 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
1 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
37295 GG
1 GG
37297 TGGCCGAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.16
Consensus pattern (37 bp):
GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
Found at i:38171 original size:19 final size:19
Alignment explanation
Indices: 38147--38184 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38137 TTAGGTATTT
*
38147 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAGGATTTAG
*
38166 TATTTTAATTAGGATTTAG
1 TATTTTAAATAGGATTTAG
38185 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
TATTTTAAATAGGATTTAG
Found at i:38184 original size:74 final size:75
Alignment explanation
Indices: 38031--38217 Score: 214
Period size: 74 Copynumber: 2.5 Consensus size: 75
38021 TAAACTCAAG
* * ** **
38031 TTTAGGATAATATTTTAAACATTATATTTTATTTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTATATTTTATATTTTATTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
*
38096 TCAATTAAGT
66 TCAATTAAGA
* *
38106 TTTAGGATATTATTTTATATTTTATA-TTTGTTTAGGTATTTTATTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTATATTTTATATTTTATTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
* *
38170 TTAATTAGGA
66 TCAATTAAGA
* * *
38180 TTTAGAATATTATATTATTTTTTAGATATTTTAGTTTA
1 TTTAGGATATTATTTTATATTTT--ATATTTTA-TTTA
38218 AATAGTTTTA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
74 61 0.66
75 22 0.24
76 3 0.03
77 3 0.03
78 4 0.04
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.57
Consensus pattern (75 bp):
TTTAGGATATTATTTTATATTTTATATTTTATTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
TCAATTAAGA
Found at i:38204 original size:64 final size:64
Alignment explanation
Indices: 38122--38247 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 64
38112 ATATTATTTT
* * *
38122 ATATTTTATATTTGTTTAGGTATTTTATTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAGA
1 ATATTATATATTTGTTTAGATATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTAGA
*
38186 ATATTATATTATTT-TTTAGATATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 ATATTATA-TATTTGTTTAGATATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
38248 AGATGTTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 5 0.09
64 46 0.82
65 5 0.09
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (64 bp):
ATATTATATATTTGTTTAGATATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGA
Found at i:38905 original size:16 final size:16
Alignment explanation
Indices: 38884--38914 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38874 AAACTCATTT
38884 TATTTATTACTATTAA
1 TATTTATTACTATTAA
*
38900 TATTTATTATTATTA
1 TATTTATTACTATTA
38915 TTTCCTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATTACTATTAA
Found at i:41851 original size:14 final size:14
Alignment explanation
Indices: 41827--41862 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
41817 CCCATTTTGT
*
41827 TTTATTTTCATTCTA
1 TTTA-TTTCATTCCA
41842 TTTATTTCATTCCA
1 TTTATTTCATTCCA
41856 TTTATTT
1 TTTATTT
41863 TAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTCATTCCA
Found at i:41886 original size:11 final size:11
Alignment explanation
Indices: 41856--41886 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
41846 TTTCATTCCA
*
41856 TTTATTTTAAT
1 TTTATTTTTAT
41867 TTTATTTTTAT
1 TTTATTTTTAT
41878 TTTATTTTT
1 TTTATTTTT
41887 CTCTGAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:44270 original size:22 final size:22
Alignment explanation
Indices: 44245--44320 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
44235 GTCCCATAGG
* *
44245 ACCATTATGTATGTCCCGAAGA
1 ACCACTATATATGTCCCGAAGA
*
44267 ACCACTGTATATGTCCCGAA-A
1 ACCACTATATATGTCCCGAAGA
* * *
44288 GACAACTGTATATGTCCCGAAGG
1 -ACCACTATATATGTCCCGAAGA
44311 ACCACTATAT
1 ACCACTATAT
44321 CCTGAAGGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (22 bp):
ACCACTATATATGTCCCGAAGA
Found at i:45563 original size:21 final size:21
Alignment explanation
Indices: 45533--45579 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45523 AGTGCCCAAT
* *
45533 AATAATAAAACTGATAGAAAA
1 AATAACAAAACCGATAGAAAA
* *
45554 AATAACAAAACCGGTAGAAAT
1 AATAACAAAACCGATAGAAAA
45575 AATAA
1 AATAA
45580 TGTTTCCGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.17
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:51723 original size:17 final size:17
Alignment explanation
Indices: 51697--51737 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
51687 AGCGTCAAAT
* *
51697 AATAACATTTTACTGAA
1 AATAATATTTTACCGAA
51714 AATAATATTTTACCGAA
1 AATAATATTTTACCGAA
*
51731 AGTAATA
1 AATAATA
51738 ACATTTCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (17 bp):
AATAATATTTTACCGAA
Found at i:52375 original size:28 final size:28
Alignment explanation
Indices: 52344--52432 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
52334 ATATTTTTTA
*
52344 TTTATGAATTATCATTAACACTTATTAG
1 TTTATGAATCATCATTAACACTTATTAG
* ** * * *
52372 TTTAATG-ACCGATTGTTATATATTTTTTA-
1 TTT-ATGAATC-ATCATTA-ACACTTATTAG
52401 TTTATGAATCATCATTAACACTTATTAG
1 TTTATGAATCATCATTAACACTTATTAG
52429 TTTA
1 TTTA
52433 ATGACGTGAT
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
27 7 0.16
28 16 0.37
29 13 0.30
30 7 0.16
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (28 bp):
TTTATGAATCATCATTAACACTTATTAG
Found at i:52392 original size:55 final size:57
Alignment explanation
Indices: 52326--52437 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
52316 CTTATATTAT
*
52326 CGATTG-T-TATATTTTTTATTTATGAATTATCATTAACACTTATTAGTTTAATGAC
1 CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
52381 CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
1 CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
52438 GTGATATATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 6 0.11
56 1 0.02
57 47 0.87
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (57 bp):
CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
Found at i:56446 original size:3 final size:3
Alignment explanation
Indices: 56432--56461 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
56422 TATTTTTTAA
*
56432 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56462 CCTTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:56639 original size:2 final size:2
Alignment explanation
Indices: 56632--56689 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
56622 ATTTGAGATA
56632 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
56674 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
56690 GAAGGAGTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58860 original size:16 final size:17
Alignment explanation
Indices: 58830--58861 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58820 ATATTTATTT
58830 ATATAAAATATAATATA
1 ATATAAAATATAATATA
58847 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
58862 TTTAATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:59011 original size:16 final size:17
Alignment explanation
Indices: 58990--59030 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
58980 CATAAGATTA
58990 TAAATAATTAAT-ATAT
1 TAAATAATTAATAATAT
59006 TAAAT-ATTAATAATAT
1 TAAATAATTAATAATAT
*
59022 AAAATAATT
1 TAAATAATT
59031 TTAAATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 13 0.59
17 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAATTAATAATAT
Found at i:60682 original size:29 final size:29
Alignment explanation
Indices: 60639--60721 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
60629 CTCACCTAAC
60639 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
60669 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
60698 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
60722 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:65434 original size:29 final size:29
Alignment explanation
Indices: 65391--65473 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
65381 CTCACCTAAC
65391 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
65421 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
65450 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
65474 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:74482 original size:29 final size:29
Alignment explanation
Indices: 74440--74572 Score: 115
Period size: 29 Copynumber: 4.4 Consensus size: 29
74430 ACCCAACCAT
*
74440 AGGTCGCCAAGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
***
74469 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* * * * *
74498 AGGTTGCCAAGCAATCCCGGCGACCAAGCTA
1 AGGTCGCCATGCACTCCCAGCGACCTA-C-A
* *
74529 GTAGGTCGCCATGCACGCCCAGCGACCTTA-T
1 --AGGTCGCCATGCACTCCCAGCGACC-TACA
74560 AGGTCGCCATGCA
1 AGGTCGCCATGCA
74573 TGCCCGGCGT
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
29 59 0.74
33 20 0.25
34 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:74550 original size:62 final size:62
Alignment explanation
Indices: 74438--74586 Score: 175
Period size: 62 Copynumber: 2.5 Consensus size: 62
74428 CAACCCAACC
* * *
74438 ATAGGTCGCCAAGCACT-CCCAGCGACCTA-C-A--AGGTCGCCATGCACTCCCAGCGACCTT
1 ATAGGTCGCCAAGCA-TGCCCGGCGACCAAGCTAGTAGGTCGCCATGCACGCCCAGCGACCTT
* *
74496 GTAGGTTGCCAAGCAAT-CCCGGCGACCAAGCTAGTAGGTCGCCATGCACGCCCAGCGACCTT
1 ATAGGTCGCCAAGC-ATGCCCGGCGACCAAGCTAGTAGGTCGCCATGCACGCCCAGCGACCTT
* *
74558 ATAGGTCGCCATGCATGCCCGGCGTCCAA
1 ATAGGTCGCCAAGCATGCCCGGCGACCAA
74587 CGTTCTGCCG
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
58 23 0.30
59 2 0.03
60 1 0.01
61 2 0.03
62 48 0.63
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (62 bp):
ATAGGTCGCCAAGCATGCCCGGCGACCAAGCTAGTAGGTCGCCATGCACGCCCAGCGACCTT
Found at i:75124 original size:17 final size:17
Alignment explanation
Indices: 75090--75130 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
75080 TTGGCGAGAG
75090 AAAGAA-AATGAAAGGA
1 AAAGAAGAATGAAAGGA
75106 AAAGAAGAA-GAAGAGGA
1 AAAGAAGAATGAA-AGGA
*
75123 AATGAAGA
1 AAAGAAGA
75131 TAAAGGCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (17 bp):
AAAGAAGAATGAAAGGA
Found at i:75277 original size:21 final size:21
Alignment explanation
Indices: 75252--75295 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
75242 AATTTAGTTA
75252 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
75273 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
75294 AT
1 AT
75296 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:75309 original size:28 final size:28
Alignment explanation
Indices: 75272--75325 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
75262 TAGTATAAAT
*
75272 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
75300 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
75326 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:78229 original size:49 final size:49
Alignment explanation
Indices: 78172--78998 Score: 864
Period size: 49 Copynumber: 15.3 Consensus size: 49
78162 TTATAAGATT
* *
78172 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA
*
78230 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
78290 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78341 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78390 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78439 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78488 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
*
78546 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
* *
78606 TTTAGTAATGATTAGTAATAATGGAATTATTATTAATTTTTAATAATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78657 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
78715 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78766 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
* *
78824 TAGTAATGATTAGTAACAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
78882 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* *
78933 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
78981 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
78999 GATTTGATAG
Statistics
Matches: 702, Mismatches: 19, Indels: 103
0.85 0.02 0.12
Matches are distributed among these distances:
48 34 0.05
49 291 0.41
50 3 0.00
51 12 0.02
52 3 0.00
53 10 0.01
54 11 0.02
55 9 0.01
56 6 0.01
57 4 0.01
58 51 0.07
59 13 0.02
60 244 0.35
61 5 0.01
62 4 0.01
63 2 0.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:78239 original size:60 final size:59
Alignment explanation
Indices: 78171--78782 Score: 432
Period size: 60 Copynumber: 10.1 Consensus size: 59
78161 TTTATAAGAT
* *
78171 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
78230 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
78290 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* * * * * * * * *
78350 TTAGTAAT-AAT-GAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAG-TAATAATGA
1 TTAGTAATGATTAGTAATAATGA--AATTATTATTAATTT--T--TAATGATTTGATAGTAATG-
78412 AA
59 -A
* * * ** * * * * * ** * *
78414 TTATTATTAATTTTTAATGATTTGATAGTAATGATT-AGTAATAATGAAATT-ATTATTAAT--
1 TTAGTAATGATTAGTAAT-A-ATGA-AATTATTATTAATTTTTAATG-ATTTGA-TAGTAATGA
* * * * * * * ** *
78474 TT-TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGAT
1 TTAGTAATGATTAG-TAATAATGA--AATTATTAT-TAA-T-TT-TTAATGATT--TGA-TAG-T
* *
78538 AGTAA
55 AATGA
* *
78543 TGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 T----TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
*
78606 TTTAGTAATGATTAGTAATAATGGAATTATTATTAATTTTTAAT-A----AT--T--TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
78657 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
78715 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
78775 TTAGTAAT
1 TTAGTAAT
78783 AATGAAATTA
Statistics
Matches: 442, Mismatches: 65, Indels: 91
0.74 0.11 0.15
Matches are distributed among these distances:
49 41 0.09
50 1 0.00
51 3 0.01
53 1 0.00
54 2 0.00
55 2 0.00
56 1 0.00
57 7 0.02
58 8 0.02
59 47 0.11
60 218 0.49
61 2 0.00
62 12 0.03
63 17 0.04
64 19 0.04
65 6 0.01
66 8 0.02
67 16 0.04
68 3 0.01
69 2 0.00
70 2 0.00
71 6 0.01
73 9 0.02
74 9 0.02
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.47
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
Found at i:78245 original size:21 final size:21
Alignment explanation
Indices: 78168--78308 Score: 68
Period size: 21 Copynumber: 7.0 Consensus size: 21
78158 GTATTTATAA
78168 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
78189 GA--T-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* *
78207 -ATTTAATGATTTGA-TAGTAAT
1 GATTTAGT-A-ATGATTAGTAAT
78228 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * * *
78249 -A-AT-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
78267 -ATTTAATGATTTGA-TATTAAT
1 GATTTAGT-A-ATGATTAGTAAT
78288 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
78309 AATGAAATTA
Statistics
Matches: 85, Mismatches: 22, Indels: 26
0.64 0.17 0.20
Matches are distributed among these distances:
17 1 0.01
18 25 0.29
19 4 0.05
20 7 0.08
21 32 0.38
22 16 0.19
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
GATTTAGTAATGATTAGTAAT
Found at i:78346 original size:109 final size:108
Alignment explanation
Indices: 78232--78949 Score: 903
Period size: 109 Copynumber: 6.6 Consensus size: 108
78222 AGTAATGATT
* *
78232 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
78297 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
65 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78341 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* * * * * ** *
78406 T-AAT-GAAATTAT--TATTAATTTTTAATGATT--TGA-TAG-
66 TGATTAGTAATAATGAAATT-ATTATTAATTTTTAATGATTTGA
* *
78442 TAATGAT---TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* * * * * * *
78504 T-AAT-GAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TT--
66 TGATTAGTAATAATGA--AATTATTATTAATTT--T--TAATGATTTGA
* *
78548 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
* *
78613 ATGATTAGTAATAATGGAATTATTATTAATTTTTAATAATTTGA
65 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78657 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
78722 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
65 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
78766 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* *
78830 TGATTAGTAACAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
66 TGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
78882 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
78947 AAT
64 AAT
78950 AATAATTTAT
Statistics
Matches: 538, Mismatches: 39, Indels: 54
0.85 0.06 0.09
Matches are distributed among these distances:
98 67 0.12
101 10 0.02
102 5 0.01
103 4 0.01
104 3 0.01
105 11 0.02
106 16 0.03
107 42 0.08
108 12 0.02
109 265 0.49
110 21 0.04
111 3 0.01
112 8 0.01
114 3 0.01
116 3 0.01
118 58 0.11
119 7 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (108 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:78532 original size:35 final size:34
Alignment explanation
Indices: 78491--78593 Score: 89
Period size: 35 Copynumber: 3.2 Consensus size: 34
78481 GATTTGATAG
78491 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * * *
78526 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
78551 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
78586 TAATGATT
1 TAATGATT
78594 TGATATTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 8 0.16
27 3 0.06
28 2 0.04
29 7 0.14
30 2 0.04
31 7 0.14
32 2 0.04
33 3 0.06
35 16 0.32
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:78561 original size:21 final size:20
Alignment explanation
Indices: 78537--78625 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
78527 AATGATTTGA
78537 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
78558 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
78576 TATTAATATTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
*
78597 TATTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
78618 TAGTAATA
1 TAGTAATA
78626 ATGGAATTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
18 13 0.26
19 2 0.04
20 5 0.10
21 22 0.44
22 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:78702 original size:35 final size:35
Alignment explanation
Indices: 78660--78762 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
78650 AATTTGATAG
78660 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
* * * *
78695 TAATGATT--TGAT-A-GTAATGA-T-TT-A---G
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
78720 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
78755 TAATGATT
1 TAATGATT
78763 TGATAGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 8 0.16
27 3 0.06
28 2 0.04
29 7 0.14
30 2 0.04
31 7 0.14
32 2 0.04
33 3 0.06
35 16 0.32
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.48
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTTT
Found at i:78828 original size:58 final size:58
Alignment explanation
Indices: 78763--79002 Score: 329
Period size: 58 Copynumber: 4.2 Consensus size: 58
78753 TTTAATGATT
* *
78763 TGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAA
1 TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
*
78821 TGATAGTAATGATTAGTAACAATGAAATTATTATTAATATTTAATGATTTGATATTAA
1 TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
*
78879 TGATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--
1 TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
*
78930 TGATAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAA
1 TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
78987 TGATTTAGTAATGATT
1 TGA--TAGTAATGATT
79003 TGATAGTAAT
Statistics
Matches: 162, Mismatches: 7, Indels: 25
0.84 0.04 0.13
Matches are distributed among these distances:
48 13 0.08
49 23 0.14
51 4 0.02
52 1 0.01
53 5 0.03
55 5 0.03
56 1 0.01
57 4 0.02
58 58 0.36
59 14 0.09
60 34 0.21
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (58 bp):
TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
Found at i:78976 original size:48 final size:49
Alignment explanation
Indices: 78884--78998 Score: 187
Period size: 48 Copynumber: 2.3 Consensus size: 49
78874 ATTAATGATT
*
78884 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
78933 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
78981 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
78999 GATTTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 34 0.55
49 28 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:78986 original size:14 final size:14
Alignment explanation
Indices: 78970--79017 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
78960 TATTAATATT
*
78970 TAATGATTTGATAT
1 TAATGATTTGATAG
78984 TAATGA-TT--TAG
1 TAATGATTTGATAG
78995 TAATGATTTGATAG
1 TAATGATTTGATAG
79009 TAATGATTT
1 TAATGATTT
79018 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:81349 original size:22 final size:22
Alignment explanation
Indices: 81324--81372 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
81314 ACAACTAATA
*
81324 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
81346 AACTATTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
81368 AACTA
1 AACTA
81373 ATAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:81350 original size:30 final size:30
Alignment explanation
Indices: 81316--81441 Score: 103
Period size: 30 Copynumber: 4.4 Consensus size: 30
81306 TCCCTTAAAC
81316 AACTAATAAACTATTCTTTAATATAAC--T
1 AACTAATAAACTATTCTTTAATATAACTTT
*
81344 ---T--T-AACTATTCTTTAATATAACGTT
1 AACTAATAAACTATTCTTTAATATAACTTT
* *
81368 AACTAATAAACTATTCTTTAATATAAATTA
1 AACTAATAAACTATTCTTTAATATAACTTT
81398 AACTAATAAA-TGATT-TTTAATTATAA-TTT
1 AACTAATAAACT-ATTCTTTAA-TATAACTTT
*
81427 ACTACTAAAAAACTA
1 A--ACTAATAAACTA
81442 ATTAACTAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
22 19 0.24
23 1 0.01
24 1 0.01
25 1 0.01
27 1 0.01
29 10 0.12
30 37 0.46
31 9 0.11
32 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTT
Found at i:81719 original size:18 final size:18
Alignment explanation
Indices: 81666--81720 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
81656 TTGTTTTACC
*
81666 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
81684 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
81696 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
81713 CTAATTTA
1 CTAATTTA
81721 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:81779 original size:35 final size:37
Alignment explanation
Indices: 81740--81811 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
81730 TCTTTTATAT
81740 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
81775 AACTTAAACTACTAATAAACTAATTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATA
81812 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 18 0.55
39 8 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:81871 original size:27 final size:29
Alignment explanation
Indices: 81836--81900 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
81826 AAAATATAAC
*
81836 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
81863 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
81891 TTAATTATTT
1 TTAAATATTT
81901 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:82014 original size:9 final size:9
Alignment explanation
Indices: 81982--82019 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
81972 CTAACAAACT
81982 AATAATTTAA
1 AATAA-TTAA
81992 AATAA-TAA
1 AATAATTAA
*
82000 ACTAATTAA
1 AATAATTAA
82009 AATAATTAA
1 AATAATTAA
82018 AA
1 AA
82020 AAAACTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:82231 original size:11 final size:11
Alignment explanation
Indices: 82215--82250 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
82205 TTCACGGGCT
82215 GCAATAATGCA
1 GCAATAATGCA
*
82226 GCAATAAGTGCT
1 GCAATAA-TGCA
82238 GCAATAATGCA
1 GCAATAATGCA
82249 GC
1 GC
82251 TGATTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:82354 original size:29 final size:28
Alignment explanation
Indices: 82322--82405 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 28
82312 GAAGGCATAG
*
82322 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGCTGGGATCCC-TGGCGACCTACAAT
82351 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGCTGGGAT-CCCTGGCGACCTACAAT
*
82380 ATCGCTGGGATTCCCTGGCGACCTAC
1 GTCGCTGGGA-TCCCTGGCGACCTAC
82406 CCACGTTGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.24
Consensus pattern (28 bp):
GTCGCTGGGATCCCTGGCGACCTACAAT
Found at i:82509 original size:60 final size:60
Alignment explanation
Indices: 82437--82558 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
82427 CATGCTGCCA
82437 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
1 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
*
82497 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAGCCATGCAGAGACTCCAAGCTCGC
1 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
82557 CC
1 CC
82559 GGATGCCATG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.24, C:0.43, G:0.20, T:0.13
Consensus pattern (60 bp):
CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
Found at i:82568 original size:30 final size:28
Alignment explanation
Indices: 82533--82597 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
82523 GCCATGCACA
82533 GCCATGCAGAGACTCCAAGCTCGCCCGGAT
1 GCCATGC-GA-ACTCCAAGCTCGCCCGGAT
*
82563 GCCATGGCGACCTCCAAGCTCGCCCGGAT
1 GCCAT-GCGAACTCCAAGCTCGCCCGGAT
82592 GCCATG
1 GCCATG
82598 GCGACCTACG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 23 0.70
30 7 0.21
31 2 0.06
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (28 bp):
GCCATGCGAACTCCAAGCTCGCCCGGAT
Found at i:82579 original size:29 final size:29
Alignment explanation
Indices: 82545--82604 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
82535 CATGCAGAGA
82545 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
82574 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
82603 CT
1 CT
82605 ACGGCAACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.17, C:0.42, G:0.27, T:0.15
Consensus pattern (29 bp):
CTCCAAGCTCGCCCGGATGCCATGGCGAC
Found at i:93978 original size:12 final size:12
Alignment explanation
Indices: 93961--93985 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
93951 GAAATTAAAG
93961 AAATAGTACAAT
1 AAATAGTACAAT
93973 AAATAGTACAAT
1 AAATAGTACAAT
93985 A
1 A
93986 TACGAAACAA
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAATAGTACAAT
Found at i:96936 original size:3 final size:3
Alignment explanation
Indices: 96930--96975 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
96920 ATAATATATT
*
96930 TAA TAA TAA TAA TAA TAA TAA TAA TTTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
96976 AAACAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:97238 original size:76 final size:76
Alignment explanation
Indices: 97136--97922 Score: 1360
Period size: 76 Copynumber: 10.3 Consensus size: 76
97126 TCTTAAAAAT
* * *
97136 ATCATGCGCTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCTGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97201 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
97212 ATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97276 TTTTTGGAAAAAC
66 TTTTTGG--AAAC
* * * * *
97289 ATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97354 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
97365 ATCATGAACTGTAGGACTTACAGATGACTCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97430 TTTTTGGAAAC
66 TTTTTGGAAAC
*
97441 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97506 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
97517 ATCATGTACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97582 TTTTTGGAAAC
66 TTTTTGGAAAC
*
97593 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97658 TTTTTGGAAAC
66 TTTTTGGAAAC
97669 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97734 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
97745 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97810 TTTTTGGAAAC
66 TTTTTGGAAAC
*
97821 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
97886 TTTTTGGAAAC
66 TTTTTGGAAAC
97897 ATCATGCACTGCAGGACTTACAGATG
1 ATCATGCACTGCAGGACTTACAGATG
97923 TGGGAAATAG
Statistics
Matches: 681, Mismatches: 27, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
75 35 0.05
76 576 0.85
77 35 0.05
78 35 0.05
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:98172 original size:184 final size:185
Alignment explanation
Indices: 97863--98232 Score: 697
Period size: 184 Copynumber: 2.0 Consensus size: 185
97853 AGGCTTTAAA
*
97863 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGGA
97928 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGCTTTCTTACTTTTCAACAATTTCA-TTTTAG
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGCTTTCTTACTTTTCAACAATTTCATTTTTAG
*
97992 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAATAAC
98047 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGGA
*
98112 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGCTTTCTTACTTTTCAACAATTTCATTTTTAG
*
98177 AAAAGATAAAATGAGAAACTATGGAAATCATTTTCTTATTATTTTTCAAAATAAC
131 AAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAATAAC
98232 A
1 A
98233 TGTTGATTGG
Statistics
Matches: 181, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
184 121 0.67
185 60 0.33
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (185 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGGA
AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGCTTTCTTACTTTTCAACAATTTCATTTTTAG
AAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAATAAC
Found at i:98809 original size:22 final size:22
Alignment explanation
Indices: 98784--98838 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
98774 CATAAAGCTT
98784 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
98806 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
98828 TCATCTTTGAA
1 TCATCTTTGAA
98839 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:101450 original size:115 final size:114
Alignment explanation
Indices: 101287--101507 Score: 343
Period size: 115 Copynumber: 1.9 Consensus size: 114
101277 GATCATGCAG
* * * * *
101287 TTCATCTTTTAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
101352 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGAGGATATTGGGCCTCCTTATTTCTACTATGAGCAAA
*
101401 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
101466 AACACTTCTAGAAGAGGATATTGGGTCTCCTTATTTCTACTA
65 AACACTTCCAGAAGAGGATATTGGGCCTCCTTATTTCTACTA
101508 CGAGAACGTG
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 22 0.23
115 74 0.77
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGAGGATATTGGGCCTCCTTATTTCTACTATGAGCAAA
Found at i:103787 original size:13 final size:14
Alignment explanation
Indices: 103769--103798 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
103759 AATTTTCCTT
103769 TTTTTTCTTT-TTC
1 TTTTTTCTTTCTTC
103782 TTTTTTCTTTCTTC
1 TTTTTTCTTTCTTC
103796 TTT
1 TTT
103799 CTTTGCTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTCTTC
Found at i:114635 original size:20 final size:21
Alignment explanation
Indices: 114610--114651 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
114600 CCAACTTACA
114610 ATGCATTATG-AACCATTATT
1 ATGCATTATGCAACCATTATT
*
114630 ATGCATTATGCAACTATTATT
1 ATGCATTATGCAACCATTATT
114651 A
1 A
114652 GTTGCATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGCATTATGCAACCATTATT
Found at i:121355 original size:15 final size:16
Alignment explanation
Indices: 121335--121375 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
121325 CTCTCTCTCT
121335 CTCTTCTTCTTC-TTC
1 CTCTTCTTCTTCTTTC
121350 CTCTTCTTCTTCTTTC
1 CTCTTCTTCTTCTTTC
121366 CTC-TCTTCTT
1 CTCTTCTTCTT
121376 TTCTTGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTTCTTCTTCTTTC
Found at i:124008 original size:42 final size:42
Alignment explanation
Indices: 123961--124042 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
123951 ACTCATCGTA
123961 AATGTAATAACATTAACTTGTTA-TTTCATATCCATGTAATGT
1 AATGTAATAACATTAACTTG-TAGTTTCATATCCATGTAATGT
*
124003 AATGTAATGACATTAACTTGTAGTTTCATATCCATGTAAT
1 AATGTAATAACATTAACTTGTAGTTTCATATCCATGTAAT
124043 TTGATCTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (42 bp):
AATGTAATAACATTAACTTGTAGTTTCATATCCATGTAATGT
Found at i:141593 original size:21 final size:21
Alignment explanation
Indices: 141552--141594 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
141542 TTCTGGGTTG
*
141552 TGTGCATCGATGTATCTTCAA
1 TGTGCATCGATGCATCTTCAA
141573 TGTGCATCGATGCA-CTCTCAA
1 TGTGCATCGATGCATCT-TCAA
141594 T
1 T
141595 TAAACAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:142659 original size:23 final size:23
Alignment explanation
Indices: 142568--142651 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
142558 CATTATTATA
142568 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
142591 CGGCACTACGATGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
142614 TGGCACTTCTGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
142637 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
142652 TTTATACGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:146711 original size:31 final size:31
Alignment explanation
Indices: 146673--146738 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
146663 GTCAAAGAAC
**
146673 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
* *
146704 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
146735 TACC
1 TACC
146739 GAGGATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:146770 original size:30 final size:30
Alignment explanation
Indices: 146726--146940 Score: 394
Period size: 30 Copynumber: 7.1 Consensus size: 30
146716 AAGGAACATA
146726 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
146757 TGGACAGTTACCGAAGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
146787 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
146817 TGGACAGTTACTGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
146847 TGGACAGTTACCTAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
146877 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
146907 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
146937 TGGA
1 TGGA
146941 TAGGTTCTTC
Statistics
Matches: 178, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 171 0.96
31 7 0.04
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:149382 original size:21 final size:21
Alignment explanation
Indices: 149358--149400 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
149348 TTTTGGGTTG
149358 TGTGCATCGATGCA-TCTTCAA
1 TGTGCATCGATGCACTC-TCAA
149379 TGTGCATCGATGCACTCTCAA
1 TGTGCATCGATGCACTCTCAA
149400 T
1 T
149401 TAAACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATGCACTCTCAA
Found at i:150465 original size:23 final size:23
Alignment explanation
Indices: 150374--150457 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
150364 CATTATTATA
150374 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
150397 CGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
150420 TGGCACTTCTGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
150443 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
150458 TTTATACGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:154316 original size:19 final size:19
Alignment explanation
Indices: 154292--154328 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
154282 AGATACAATG
154292 GGCGTTCGAAGTTTGATTC
1 GGCGTTCGAAGTTTGATTC
154311 GGCGTTCGAAGTTTGATT
1 GGCGTTCGAAGTTTGATT
154329 TTACTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.32, T:0.38
Consensus pattern (19 bp):
GGCGTTCGAAGTTTGATTC
Found at i:161037 original size:105 final size:105
Alignment explanation
Indices: 160854--161066 Score: 336
Period size: 105 Copynumber: 2.0 Consensus size: 105
160844 ATCTCCTCCT
* * *
160854 GGCGTGGTGCCCACCCGTTTTGATACTTCAACAAGCGCACATGGAAACCATGATAGCGCACATGA
1 GGCGTGGTGCCCACCCGTTTTGACAATTCAACAAGCACACATGGAAACCATGATAGCGCACATGA
*
160919 ATTAAGGGCCACACATGAGTTAAATCCCATTCATATTGAA
66 ATTAAGGGCCACACATGAGTTAAATCCCACTCATATTGAA
* * *
160959 GGCGTGGTGCCCACCCGTTTTGACAATTCAACAAGTACACATGGAAATCATGATGGCGCACATGA
1 GGCGTGGTGCCCACCCGTTTTGACAATTCAACAAGCACACATGGAAACCATGATAGCGCACATGA
** *
161024 ATTGGGGGGCACACATGAGTTAAATCCCACTCATATTGAA
66 ATTAAGGGCCACACATGAGTTAAATCCCACTCATATTGAA
161064 GGC
1 GGC
161067 ACATGTGAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (105 bp):
GGCGTGGTGCCCACCCGTTTTGACAATTCAACAAGCACACATGGAAACCATGATAGCGCACATGA
ATTAAGGGCCACACATGAGTTAAATCCCACTCATATTGAA
Found at i:179747 original size:120 final size:118
Alignment explanation
Indices: 179588--180427 Score: 659
Period size: 120 Copynumber: 7.0 Consensus size: 118
179578 ATTCTTGTGA
* * * * * *
179588 TCCCTGAAAACTACCTCCTGAACTGGTTCAGTAGCAGTTATGCTGATATCTTCAAATTGCATTAA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTAA
* *
179653 ATTTTGATCCTCTAGTGC-AGCACTTATGTCTTCTTTAACTTCAATTTTGTCACTT
66 ATTTTGATCCTCT-GAGCAAG-ACTTA-GTCCTCTTTAACTTCAATTTTGTCACTT
** * * * *
179708 TCCCAGAAAACTTGCTCCTGAGCTGGTTCAGCAGCAGTTATCTCGGTATCTTCTAAGTGTATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATT-A
* * * * * *
179773 ACTGTGGTATCCT-TGAGCAAGAATCGTA-ACCTCTTTAACTTC-ATCTTTTTCACTT
65 AATTTTG-ATCCTCTGAGCAAG-A-CTTAGTCCTCTTTAACTTCAAT-TTTGTCACTT
* * ** * * * * *
179828 TCCCAGTAAACTACCTGCTGGGCTGGTTCAGCAGCAATTGTGTTGGTATCTTCTAATTGCAGTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTAA
* * * * * * * *
179893 AGTCTGATCCTCTTCAACAAGACGTGAGTACTCCTTAACTTCAATTTTGTCACTG
66 ATTTTGATCCTC-TGAGCAAGAC-TTAGTCCTCTTTAACTTCAATTTTGTCACTT
* * *
179948 TCCCAGACAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTACATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTAA
* * * * *
180013 ACTGTGATCCTTTGGAGCAAGATTTATGTCCTCTTTAACTTCCATTTTGTCACTT
66 ATTTTGATCCTCT-GAGCAAGACTTA-GTCCTCTTTAACTTCAATTTTGTCACTT
* * * * * * * *
180068 TCCCAGATACCTAACTCCTGAACTGATCCAGCAGCAGTCATGTTGGTATCTTCTATGTGCATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTAA
* * * * * *
180133 ACTCTGATCCTCTGGAGCAAGATTTGTGTCCTCTTTAACGTCCATTTT-TCCACTT
66 ATTTTGATCCTCT-GAGCAAGACTT-AGTCCTCTTTAACTTCAATTTTGT-CACTT
* * * * * * * **
180188 TCCCGGATAAGTAACTCCTGAACTGATCCAGCAGCAGTCATGTTGGTATCTTCTAAGTGCATGGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTAA
* * * * * * *
180253 ATTCTGATCCTCTTGAGCAGGACATGTA-ACCCCTTTAACATCCATTTTATCACTT
66 ATTTTGATCCTC-TGAGCAAGAC-T-TAGTCCTCTTTAACTTCAATTTTGTCACTT
** ** * * *
180308 TCCTGGATGACTACCTTCTGAACTGGTTCAGTC-GCAGTTATGTCGGTATCTTCTAAGTGCATTG
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAG-CAGCAGTTATGTTGGTATCTTCTAAGTGCATTA
* * * * *
180372 AACTATGATCCTCTGGAACAAGACTTGAGACCTCTTTACCTTCAATTTTGTCACTT
65 AATTTTGATCCTCT-GAGCAAGACTT-AGTCCTCTTTAACTTCAATTTTGTCACTT
180428 GTATAGTTAA
Statistics
Matches: 586, Mismatches: 112, Indels: 44
0.79 0.15 0.06
Matches are distributed among these distances:
118 7 0.01
119 13 0.02
120 542 0.92
121 15 0.03
122 9 0.02
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (118 bp):
TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTAA
ATTTTGATCCTCTGAGCAAGACTTAGTCCTCTTTAACTTCAATTTTGTCACTT
Found at i:180018 original size:240 final size:236
Alignment explanation
Indices: 179596--180427 Score: 820
Period size: 240 Copynumber: 3.5 Consensus size: 236
179586 GATCCCTGAA
* * * * * * *
179596 AACTACCTCCTGAACTGGTTCAGTAGCAGTTATGCTGATATCTTCAAATTGCATTAAATTTTGAT
1 AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAATTGCATTGAACTCTGAT
* ** **
179661 CCTCTAGTGC-AGCACTT-ATGT-CTTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTTGC
66 CCTCTGGAACAAG-ACTTGA-GTAC-TCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTAAC
* * * *
179723 TCCTGAGCTGGTTCAGCAGCAGTTATCTCGGTATCTTCTAAGTGTATTGAACTGTGGTATCCTTG
128 TCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGT-G-ATCCTTG
*
179788 AGCAAGAATCGTAACCTCTTTAACTTCATCTTTTTCACTTTCCCAG-T
191 AGCAAGAAT-GTAACCTCTTTAACTTCAT-TTTATCACTTTCCCAGAT
* ** * * * *
179835 AAACTACCTGCTGGGCTGGTTCAGCAGCAATTGTGTTGGTATCTTCTAATTGCAGTGAAGTCTGA
1 -AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAATTGCATTGAACTCTGA
** * * * * *
179900 TCCTCTTCAACAAGACGTGAGTACTCCTTAACTTCAATTTTGTCACTGTCCCAGACAACTACCTC
65 TCCTCTGGAACAAGACTTGAGTACTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTAACTC
*
179965 CTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTACATTGAACTGTGATCCTTTGGAG
130 CTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTGATCC-TT-GAG
*
180030 CAAGATTTATGT--CCTCTTTAACTTCCATTTTGTCACTTTCCCAGAT
193 CAAGA---ATGTAACCTCTTTAACTT-CATTTTATCACTTTCCCAGAT
* * * * *
180076 ACCTAACTCCTGAACTGATCCAGCAGCAGTCATGTTGGTATCTTCT-ATGTGCATTGAACTCTGA
1 AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAT-TGCATTGAACTCTGA
* * * * * * * * *
180140 TCCTCTGGAGCAAGATTTGTGTCCTCTTTAACGTCCATTTT-TCCACTTTCCCGGATAAGTAACT
65 TCCTCTGGAACAAGACTTGAGTACTCTTTAACTTCAATTTTGT-CACTTTCCCAGAAAACTAACT
* * * * * *
180204 CCTGAACTGATCCAGCAGCAGTCATGTTGGTATCTTCTAAGTGCATGGAATTCTGATCCTCTTGA
129 CCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTGAT-C-CTTGA
* * * **
180269 GCAGGACATGTAACCCCTTTAACATCCATTTTATCACTTTCCTGGAT
192 GCAAGA-ATGTAACCTCTTTAAC-TTCATTTTATCACTTTCCCAGAT
* * * * *
180316 GACTACCTTCTGAACTGGTTCAGTC-GCAGTTATGTCGGTATCTTCTAAGTGCATTGAACTATGA
1 AACTACCTCCTGAACTGGTTCAG-CAGCAGTTATGTTGGTATCTTCTAATTGCATTGAACTCTGA
*
180380 TCCTCTGGAACAAGACTTGAG-ACCTCTTTACCTTCAATTTTGTCACTT
65 TCCTCTGGAACAAGACTTGAGTA-CTCTTTAACTTCAATTTTGTCACTT
180428 GTATAGTTAA
Statistics
Matches: 484, Mismatches: 87, Indels: 42
0.79 0.14 0.07
Matches are distributed among these distances:
238 8 0.02
239 6 0.01
240 450 0.93
241 15 0.03
242 3 0.01
243 2 0.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (236 bp):
AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAATTGCATTGAACTCTGAT
CCTCTGGAACAAGACTTGAGTACTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTAACTCC
TGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTGATCCTTGAGCAA
GAATGTAACCTCTTTAACTTCATTTTATCACTTTCCCAGAT
Found at i:180118 original size:360 final size:360
Alignment explanation
Indices: 179596--180427 Score: 901
Period size: 360 Copynumber: 2.3 Consensus size: 360
179586 GATCCCTGAA
* * * * * * * *
179596 AACTACCTCCTGAACTGGTTCAGTAGCAGTTATGCTGATATCTTCAAATTGCATTAAATTTTGAT
1 AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTATGAT
* * * * **
179661 CCTCTAGTGC-AGCACTTATGTCTTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTTGCTC
66 CCTCTGGAGCAAG-ATTTATGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTAACTC
* * * * * *
179725 CTGAGCTGGTTCAGCAGCAGTTATCTCGGTATCTTCTAAGTGTATTGAACTGTGGTATCCT-T-G
130 CTGAACTGATCCAGCAGCAGTCATCTCGGTATCTTCTAAGTGCATTGAACTCT-G-ATCCTCTGG
* * * * * **
179788 AGCAAGAATCGTAACCTCTTTAAC-TTCATCTTTTTCACTTTCCCAG-TAAACTACCTGCTGGGC
193 AGCAAGAATCGTAACCTCTTTAACGTCCAT-TTTTCCACTTTCCCGGAT-AACTAACTCCTGAAC
* * ** *
179851 TGGTTCAGCAGCAATTGTGTTGGTATCTTCTAATTGCA-GTGAAGTCTGATCCTCTTCAACAAGA
256 TGATCCAGCAGCAATCATGTTGGTATCTTCTAAGTGCATG-GAAGTCTGATCCTCTTCAACAAGA
* * * *
179915 CGTG-AGTACTCC-TTAACTTCAATTTTGTCACTGTCCCAGAC
320 CATGTA--ACCCCTTTAACATCAATTTTATCACTGTCCCAGAC
* *
179956 AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTACATTGAACTGTGAT
1 AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTATGAT
* * * *
180021 CCTTTGGAGCAAGATTTATGTCCTCTTTAACTTCCATTTTGTCACTTTCCCAGATACCTAACTCC
66 CCTCTGGAGCAAGATTTATGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTAACTCC
* * *
180086 TGAACTGATCCAGCAGCAGTCATGTTGGTATCTTCTATGTGCATTGAACTCTGATCCTCTGGAGC
131 TGAACTGATCCAGCAGCAGTCATCTCGGTATCTTCTAAGTGCATTGAACTCTGATCCTCTGGAGC
* * ** *
180151 AAGATTTGTGTCCTCTTTAACGTCCATTTTTCCACTTTCCCGGATAAGTAACTCCTGAACTGATC
196 AAGAATCGTAACCTCTTTAACGTCCATTTTTCCACTTTCCCGGATAACTAACTCCTGAACTGATC
* * * * *
180216 CAGCAGCAGTCATGTTGGTATCTTCTAAGTGCATGGAATTCTGATCCTCTTGAGCAGGACATGTA
261 CAGCAGCAATCATGTTGGTATCTTCTAAGTGCATGGAAGTCTGATCCTCTTCAACAAGACATGTA
* * ** *
180281 ACCCCTTTAACATCCATTTTATCACTTTCCTGGAT
326 ACCCCTTTAACATCAATTTTATCACTGTCCCAGAC
* * *
180316 GACTACCTTCTGAACTGGTTCAGTC-GCAGTTATGTCGGTATCTTCTAAGTGCATTGAACTATGA
1 AACTACCTCCTGAACTGGTTCAG-CAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTATGA
* * * *
180380 TCCTCTGGAACAAGACTTGA-GACCTCTTTACCTTCAATTTTGTCACTT
65 TCCTCTGGAGCAAGA-TTTATGTCCTCTTTAACTTCAATTTTGTCACTT
180428 GTATAGTTAA
Statistics
Matches: 392, Mismatches: 70, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
358 5 0.01
359 6 0.02
360 368 0.94
361 13 0.03
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (360 bp):
AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTATGAT
CCTCTGGAGCAAGATTTATGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAGAAAACTAACTCC
TGAACTGATCCAGCAGCAGTCATCTCGGTATCTTCTAAGTGCATTGAACTCTGATCCTCTGGAGC
AAGAATCGTAACCTCTTTAACGTCCATTTTTCCACTTTCCCGGATAACTAACTCCTGAACTGATC
CAGCAGCAATCATGTTGGTATCTTCTAAGTGCATGGAAGTCTGATCCTCTTCAACAAGACATGTA
ACCCCTTTAACATCAATTTTATCACTGTCCCAGAC
Found at i:186692 original size:24 final size:24
Alignment explanation
Indices: 186659--186711 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
186649 CGTTCGGTAA
*
186659 TATGTTCATTTATATTCGTTCATT
1 TATGTCCATTTATATTCGTTCATT
* *
186683 TATGTCCATTTATATTCTTTCGTT
1 TATGTCCATTTATATTCGTTCATT
186707 TATGT
1 TATGT
186712 GCGTTCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.58
Consensus pattern (24 bp):
TATGTCCATTTATATTCGTTCATT
Found at i:186724 original size:14 final size:14
Alignment explanation
Indices: 186662--186726 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
186652 TCGGTAATAT
*
186662 GTTCATTTATATTC
1 GTTCATTTATGTTC
186676 GTTCATTTATG-TC
1 GTTCATTTATGTTC
*
186689 ---CATTTATATTC
1 GTTCATTTATGTTC
* * *
186700 TTTCGTTTATGTGC
1 GTTCATTTATGTTC
186714 GTTCATTTATGTT
1 GTTCATTTATGTT
186727 TAGTCCAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
13 2 0.05
14 28 0.72
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:186913 original size:10 final size:10
Alignment explanation
Indices: 186891--186938 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
186881 AAAAAATATT
*
186891 TTCATTTATG
1 TTCATTTACG
*
186901 TTCGTTTACG
1 TTCATTTACG
*
186911 TTCATTTATG
1 TTCATTTACG
**
186921 TTTGTTTACG
1 TTCATTTACG
186931 TTCATTTA
1 TTCATTTA
186939 TTGTGTTCGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (10 bp):
TTCATTTACG
Found at i:186916 original size:20 final size:20
Alignment explanation
Indices: 186891--186986 Score: 102
Period size: 20 Copynumber: 4.5 Consensus size: 20
186881 AAAAAATATT
186891 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
*
186911 TTCATTTATGTTTGTTTACG
1 TTCATTTATGTTCGTTTACG
*
186931 TTCATTTATTGTGTTCGTTTGCGTTTG
1 TTCATTTA---TGTTCGTTTAC----G
*
186958 TTCATTTGTGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
186978 TTCATTTAT
1 TTCATTTAT
186987 TGTGTTCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
20 36 0.57
23 9 0.14
24 10 0.16
27 8 0.13
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCGTTTACG
Found at i:186950 original size:23 final size:23
Alignment explanation
Indices: 186899--186999 Score: 136
Period size: 23 Copynumber: 4.5 Consensus size: 23
186889 TTTTCATTTA
186899 TGTTCGTTTACGTTCATTTA-TG
1 TGTTCGTTTACGTTCATTTATTG
186921 T-TT-GTTTACGTTCATTTATTG
1 TGTTCGTTTACGTTCATTTATTG
* ** *
186942 TGTTCGTTTGCGTTTGTTCATTTG
1 TGTTCGTTTACGTTCATTTA-TTG
186966 TGTTCGTTTACGTTCATTTATTG
1 TGTTCGTTTACGTTCATTTATTG
186989 TGTTCGTTTAC
1 TGTTCGTTTAC
187000 ATCCGTTCGT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
20 15 0.22
21 5 0.07
22 3 0.04
23 25 0.37
24 19 0.28
ACGTcount: A:0.11, C:0.13, G:0.19, T:0.57
Consensus pattern (23 bp):
TGTTCGTTTACGTTCATTTATTG
Found at i:187017 original size:47 final size:47
Alignment explanation
Indices: 186909--187020 Score: 161
Period size: 47 Copynumber: 2.4 Consensus size: 47
186899 TGTTCGTTTA
* * * *
186909 CGTTCATTTATGTTTGTTTACGTTCATTTATTGTGTTCGTTTGCGTT
1 CGTTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACATC
* *
186956 TGTTCATTTGTGTTCGTTTACGTTCATTTATTGTGTTCGTTTACATC
1 CGTTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACATC
*
187003 CGTTCGTTTATGTTCGTT
1 CGTTCATTTATGTTCGTT
187021 CATTTGTGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.11, C:0.14, G:0.19, T:0.56
Consensus pattern (47 bp):
CGTTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACATC
Found at i:191239 original size:31 final size:31
Alignment explanation
Indices: 191169--191283 Score: 169
Period size: 31 Copynumber: 3.7 Consensus size: 31
191159 GTCGAGGGAT
*
191169 TTACCTATG-TCTTACAGGACATATGGACAGGA
1 TTACCTATGTTCTT-CGGGACATATGGACA-GA
* *
191201 TTACCTATGTTCTTTGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
191232 TTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
191263 TTATCTATGTTCTTCGGGACA
1 TTACCTATGTTCTTCGGGACA
191284 ACATAAGTGT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
31 50 0.66
32 22 0.29
33 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:192729 original size:67 final size:67
Alignment explanation
Indices: 192649--192799 Score: 225
Period size: 67 Copynumber: 2.3 Consensus size: 67
192639 ACCCATTCAA
* *
192649 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGG-GGAATCGATACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAG-GGAGGAACCGATA-CCCC
192713 A-GG
64 AGGG
* *
192716 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGGGAGGAACCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGGGAGGAACCGATACCCCAG
192781 GG
66 GG
*
192783 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
192800 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
66 7 0.09
67 70 0.91
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGGGAGGAACCGATACCCCAG
GG
Found at i:193545 original size:149 final size:149
Alignment explanation
Indices: 193275--193578 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
193265 GGGTAGAGGG
193275 TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
193340 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
193405 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
193424 TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
193489 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
193554 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
193573 TCTACG
1 TCTACG
193579 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:193601 original size:23 final size:23
Alignment explanation
Indices: 193557--193601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
193547 ATCATTATAT
*
193557 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
193580 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
193602 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:199747 original size:47 final size:47
Alignment explanation
Indices: 199678--199788 Score: 186
Period size: 47 Copynumber: 2.4 Consensus size: 47
199668 TACCCATTCA
*
199678 AGGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATGCTAG
1 AGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAG
* *
199725 AGGGGAATCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAG
1 AGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAG
*
199772 GGGGGAACCGATACCCC
1 AGGGGAACCGATACCCC
199789 AGGGGGGGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.17
Consensus pattern (47 bp):
AGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAG
Found at i:199810 original size:21 final size:20
Alignment explanation
Indices: 199771--199808 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
199761 CAGAATGCTA
199771 GGGGGGAACCGATACCCCAG
1 GGGGGGAACCGATACCCCAG
*
199791 GGGGGGAACCGATTCCCC
1 GGGGGGAACCGATACCCC
199809 CATGAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.32, G:0.39, T:0.08
Consensus pattern (20 bp):
GGGGGGAACCGATACCCCAG
Found at i:200465 original size:23 final size:23
Alignment explanation
Indices: 200421--200465 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
200411 ATCATTATAT
*
200421 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
200444 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
200466 AGCTGTGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:201212 original size:22 final size:22
Alignment explanation
Indices: 201184--201240 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
201174 TTTTAGCATT
201184 CGGTATTGTTCATCACTGTTCA
1 CGGTATTGTTCATCACTGTTCA
* * *
201206 CGGTATTGTTTATTATTGTTCA
1 CGGTATTGTTCATCACTGTTCA
* *
201228 CGGCACTGTTCAT
1 CGGTATTGTTCAT
201241 ACCGTATAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (22 bp):
CGGTATTGTTCATCACTGTTCA
Found at i:204117 original size:29 final size:31
Alignment explanation
Indices: 204081--204143 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
204071 AAAAAATGTA
204081 AAATAAAATATAAGGATTAAATT-AAA-AAT
1 AAATAAAATATAAGGATTAAATTGAAATAAT
* *
204110 AAATAAAATTTATGGATTAAATTGAAATAAT
1 AAATAAAATATAAGGATTAAATTGAAATAAT
204141 AAA
1 AAA
204144 CCAAAACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.70
30 3 0.10
31 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (31 bp):
AAATAAAATATAAGGATTAAATTGAAATAAT
Found at i:204311 original size:22 final size:22
Alignment explanation
Indices: 204286--204328 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
204276 CCTCTCCCCA
204286 CAAAATTCTCAAATTCTCTCAC
1 CAAAATTCTCAAATTCTCTCAC
204308 CAAAATTCTCAAATTCTCTCA
1 CAAAATTCTCAAATTCTCTCA
204329 ACTCACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (22 bp):
CAAAATTCTCAAATTCTCTCAC
Found at i:205490 original size:2 final size:2
Alignment explanation
Indices: 205485--205524 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
205475 TAAATAAAAC
*
205485 TA TA TA TA TA TT TA -A 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 TA TA TA TA TA T
205525 TTCAAAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:205491 original size:21 final size:23
Alignment explanation
Indices: 205467--205518 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
205457 AAAATATAAC
205467 ATATAT-TTTAA-ATA-AAACTAT
1 ATATATATTTAATATATAAA-TAT
*
205488 ATATATATTTAATATATATATAT
1 ATATATATTTAATATATAAATAT
205511 ATATATAT
1 ATATATAT
205519 ATATATTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 5 0.19
23 14 0.52
24 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATATTTAATATATAAATAT
Found at i:207799 original size:13 final size:13
Alignment explanation
Indices: 207781--207812 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
207771 GACAACGAGT
207781 CTCCTTGTCTCAC
1 CTCCTTGTCTCAC
207794 CTCCTTGTCTCAC
1 CTCCTTGTCTCAC
207807 CTCCTT
1 CTCCTT
207813 CTTACCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.47, G:0.06, T:0.41
Consensus pattern (13 bp):
CTCCTTGTCTCAC
Found at i:208147 original size:31 final size:31
Alignment explanation
Indices: 208112--208170 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
208102 GTAAATAAAT
**
208112 TAATTAAAAAATTTATTTTAAAAATTTTCAA
1 TAATTAAAAAATGAATTTTAAAAATTTTCAA
* * *
208143 TAATTTAAGAATGAATTTTAAATATTTT
1 TAATTAAAAAATGAATTTTAAAAATTTT
208171 TATAGATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
TAATTAAAAAATGAATTTTAAAAATTTTCAA
Found at i:211628 original size:18 final size:17
Alignment explanation
Indices: 211605--211641 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
211595 AAACAAAAAC
*
211605 AAAAACAAAAGATTTATA
1 AAAAACAAAA-ATATATA
211623 AAAAACAAAAATATATA
1 AAAAACAAAAATATATA
211640 AA
1 AA
211642 TAAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAACAAAAATATATA
Found at i:216263 original size:6 final size:6
Alignment explanation
Indices: 216254--216317 Score: 87
Period size: 6 Copynumber: 11.0 Consensus size: 6
216244 TCCCCGTCTT
* *
216254 CGTATC CGTATC CGTATC CGTATC CGT-CC CGTATC CGTATC CATATC
1 CGTATC CGTATC CGTATC CGTATC CGTATC CGTATC CGTATC CGTATC
*
216301 CGT-CC CGTATC CGTATC
1 CGTATC CGTATC CGTATC
216318 AGTGCAACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 8 0.16
6 42 0.84
ACGTcount: A:0.16, C:0.38, G:0.16, T:0.31
Consensus pattern (6 bp):
CGTATC
Found at i:216289 original size:23 final size:23
Alignment explanation
Indices: 216259--216317 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
216249 GTCTTCGTAT
*
216259 CCGTATCCGTATCCGTATCCGTC
1 CCGTATCCGTATCCATATCCGTC
216282 CCGTATCCGTATCCATATCCGTC
1 CCGTATCCGTATCCATATCCGTC
216305 CCGTATCCGTATC
1 CCGTATCCGTATC
216318 AGTGCAACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.15, C:0.39, G:0.15, T:0.31
Consensus pattern (23 bp):
CCGTATCCGTATCCATATCCGTC
Found at i:216314 original size:29 final size:29
Alignment explanation
Indices: 216254--216317 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
216244 TCCCCGTCTT
* *
216254 CGTATCCGTATCCGTATCCGTATCCGTCC
1 CGTATCCGTATCCATATCCGTACCCGTCC
*
216283 CGTATCCGTATCCATATCCGT-CCCGTATC
1 CGTATCCGTATCCATATCCGTACCCGT-CC
216312 CGTATC
1 CGTATC
216318 AGTGCAACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.16, C:0.38, G:0.16, T:0.31
Consensus pattern (29 bp):
CGTATCCGTATCCATATCCGTACCCGTCC
Found at i:218346 original size:17 final size:17
Alignment explanation
Indices: 218316--218351 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
218306 TTTTTTTTAT
* *
218316 ATTTTTTATTTCTTAAA
1 ATTTTGTATCTCTTAAA
218333 ATTTTGTATCTCTTAAA
1 ATTTTGTATCTCTTAAA
218350 AT
1 AT
218352 ATCTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTGTATCTCTTAAA
Found at i:223551 original size:22 final size:22
Alignment explanation
Indices: 223494--223552 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
223484 ACGCGATTCT
*
223494 GACTATCGCATTGCTATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
223516 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
223537 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
223553 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:223566 original size:20 final size:20
Alignment explanation
Indices: 223541--223675 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
223531 TTTTCCGACT
223541 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
* *
223561 ATCGCAATGCGAGTATGACT
1 ATCGCAATGCGAATATGACA
* *
223581 ATCACAACGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
* *
223601 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGAATATGACA
* * *
223621 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
* * * *
223641 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
*
223661 GTCGCAATGCTGAAT
1 ATCGCAATGC-GAAT
223676 CTCAAATTCG
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.02
20 90 0.94
21 4 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGACA
Found at i:223645 original size:40 final size:40
Alignment explanation
Indices: 223537--223675 Score: 172
Period size: 40 Copynumber: 3.5 Consensus size: 40
223527 GCGATTTTCC
*
223537 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* *
223577 GACTATCACAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* * * * *
223617 GACTATCGCAATGCGATTCTG-ACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTAT
*
223657 GACTGTCGCAATGCTGAAT
1 GACTATCGCAATGC-GAAT
223676 CTCAAATTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 81 0.95
41 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:223666 original size:60 final size:60
Alignment explanation
Indices: 223537--223675 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
223527 GCGATTTTCC
223537 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCACAACGCGAATAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCACAACGCGAATAT
* * * * * * * *
223597 GTA-AATCGCAATGCGATTATG-ACTATCGCAATGCGATTCTGACTATCGCAACGCGATTCT
1 G-ACTATCGCAATGCGAATATGTA-AATCGCAATGCGAGTATGACTATCACAACGCGAATAT
*
223657 GACTGTCGCAATGCTGAAT
1 GACTATCGCAATGC-GAAT
223676 CTCAAATTCG
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
59 2 0.03
60 58 0.91
61 4 0.06
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (60 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCACAACGCGAATAT
Found at i:224520 original size:24 final size:24
Alignment explanation
Indices: 224488--224541 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
224478 GTATTCAAAA
224488 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
224512 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
224536 TTTGAT
1 TTTGAT
224542 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:226826 original size:18 final size:18
Alignment explanation
Indices: 226803--226837 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
226793 AGAAAAAGGC
*
226803 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
226821 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
226838 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:227040 original size:20 final size:20
Alignment explanation
Indices: 227015--227295 Score: 230
Period size: 20 Copynumber: 14.7 Consensus size: 20
227005 CACATTCATT
*
227015 TGACTATCGCAACGTGAATA
1 TGACTATCGCAACGCGAATA
*
227035 TGACTATCACAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
227055 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* * *
227075 TGAATATCGTAACG-GGATA
1 TGACTATCGCAACGCGAATA
* *
227094 --A-TA--GCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
227109 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
227129 TGAGTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
227149 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
227169 TGACTATCGCAACTCGAATT
1 TGACTATCGCAACGCGAATA
* * * *
227189 TAACTATCACAACACGAATT
1 TGACTATCGCAACGCGAATA
*
227209 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
227226 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
227242 TGACTATCGCAACACGAATT
1 TGACTATCGCAACGCGAATA
* *
227262 TGATTATCGCAACG-GAAATT
1 TGACTATCGCAACGCG-AATA
227282 TGACTATCGCAACG
1 TGACTATCGCAACG
227296 AGAAAATCGC
Statistics
Matches: 210, Mismatches: 37, Indels: 28
0.76 0.13 0.10
Matches are distributed among these distances:
14 11 0.05
15 3 0.01
16 7 0.03
17 6 0.03
18 4 0.02
19 16 0.08
20 163 0.78
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:227282 original size:73 final size:73
Alignment explanation
Indices: 227154--227339 Score: 230
Period size: 73 Copynumber: 2.5 Consensus size: 73
227144 GAAAATGACT
* * * *
227154 ATCGCAATGCGAAAATGACTATCGCAACTCGAATTTAACTATCACAACACGAATTTGACTATCGC
1 ATCGCAAAGCG-AAATGACTATCGCAACACGAATTTGATTATCACAACACGAATTTGACTATCGC
*
227219 AACGAGATA
65 AACGAGAAA
* * *
227228 ATCGCAACGCGAAATGACTATCGCAACACGAATTTGATTATCGCAAC-GGAAATTTGACTATCGC
1 ATCGCAAAGCGAAATGACTATCGCAACACGAATTTGATTATCACAACACG-AATTTGACTATCGC
227292 AACGAGAAA
65 AACGAGAAA
* * * *
227301 ATCGCAAAGTGTATTAGACTATCGCAACACGAATATGAT
1 ATCGCAAAGCGAAAT-GACTATCGCAACACGAATTTGAT
227340 GCAGATTGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
72 1 0.01
73 65 0.66
74 32 0.33
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.23
Consensus pattern (73 bp):
ATCGCAAAGCGAAATGACTATCGCAACACGAATTTGATTATCACAACACGAATTTGACTATCGCA
ACGAGAAA
Found at i:228474 original size:18 final size:18
Alignment explanation
Indices: 228451--228487 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
228441 TAATTTCTTT
228451 TCTTTTGTTTATGTACAC
1 TCTTTTGTTTATGTACAC
228469 TCTTTTGTTTATGTACAC
1 TCTTTTGTTTATGTACAC
228487 T
1 T
228488 AACTTATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (18 bp):
TCTTTTGTTTATGTACAC
Found at i:229217 original size:15 final size:13
Alignment explanation
Indices: 229189--229213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229179 CATGATATTA
229189 AGAAAAAAATAAT
1 AGAAAAAAATAAT
229202 AGAAAAAAATAA
1 AGAAAAAAATAA
229214 AATAAAGTAA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:229217 original size:18 final size:18
Alignment explanation
Indices: 229194--229258 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
229184 TATTAAGAAA
229194 AAAATAATAGAAAAAAAT
1 AAAATAATAGAAAAAAAT
*
229212 AAAATAA-AG-TAAAAAT
1 AAAATAATAGAAAAAAAT
* * *
229228 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAAAAAAT
*
229247 AAAAAAATAGAA
1 AAAATAATAGAA
229259 TATTAAGAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
16 11 0.31
17 3 0.08
18 13 0.36
19 9 0.25
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAATAATAGAAAAAAAT
Done.