Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000459.1 Hibiscus syriacus cultivar Beakdansim tig00000850_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: 55132
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:758 original size:163 final size:163
Alignment explanation
Indices: 488--819 Score: 601
Period size: 163 Copynumber: 2.0 Consensus size: 163
478 ATACGAGTCG
488 AATTTAATATTAGAATGTTCACTTTTATTCTAATGTCCTTGAACAGTTTATATTGTAATCTATGA
1 AATTTAATATTAGAATGTTCACTTTTATTCTAATGTCCTTGAACAGTTTATATTGTAATCTATGA
* *
553 GAACTAGACATGTATATAGGTCGGGTAAAGTTTTTAGTCGACTTTAACCCAATTCAAGTATTATA
66 GAACCAGACATGTATATAGGTCGGGTAAAGTTTTTAGTCGACTTGAACCCAATTCAAGTATTATA
618 AATCTTCCACCCATTATCACTTAATCCGGTTCA
131 AATCTTCCACCCATTATCACTTAATCCGGTTCA
* *
651 AATTTAATATTAGAATGTTCATTTTTATTCTAATGTCCTTGAACGGTTTATATTGTAATCTATGA
1 AATTTAATATTAGAATGTTCACTTTTATTCTAATGTCCTTGAACAGTTTATATTGTAATCTATGA
* * *
716 GAACCAGAGATGTATATAGGTCGGGTAATGTTTTTAGTCGACTTGAACCCAATTCGAGTATTATA
66 GAACCAGACATGTATATAGGTCGGGTAAAGTTTTTAGTCGACTTGAACCCAATTCAAGTATTATA
781 AATCTTCCACCCATTATCACTTAATCCGGTTCA
131 AATCTTCCACCCATTATCACTTAATCCGGTTCA
814 AATTTA
1 AATTTA
820 GGGAGACTCC
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (163 bp):
AATTTAATATTAGAATGTTCACTTTTATTCTAATGTCCTTGAACAGTTTATATTGTAATCTATGA
GAACCAGACATGTATATAGGTCGGGTAAAGTTTTTAGTCGACTTGAACCCAATTCAAGTATTATA
AATCTTCCACCCATTATCACTTAATCCGGTTCA
Found at i:1016 original size:2 final size:2
Alignment explanation
Indices: 1009--1038 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
999 GAAATTATTC
1009 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
1039 GATAATTTTG
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):
AT
Found at i:1878 original size:52 final size:52
Alignment explanation
Indices: 1821--1923 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
1811 TTAACAGAAA
* * * * * *
1821 AGCGCGCCCTCTGCACCGCGTTATATGCTGATTTGGTGCCACGTGGGTATAT
1 AGCGCGCCCCCTGCACCACGATATACGCTGATCTGGCGCCACGTGGGTATAT
* *
1873 AGCGCGCCCCCTGCCCCACGATATACGGTGATCTGGCGCCACGTGGGTATA
1 AGCGCGCCCCCTGCACCACGATATACGCTGATCTGGCGCCACGTGGGTATA
1924 GCGCCCCCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (52 bp):
AGCGCGCCCCCTGCACCACGATATACGCTGATCTGGCGCCACGTGGGTATAT
Found at i:5842 original size:6 final size:6
Alignment explanation
Indices: 5817--5870 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
5807 ACTCCTCGCT
* *
5817 GTCATC ATCATC GGCATC GTCATC GTCA-C --CATC GTCATC GTCATC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
*
5862 GTCGTC GTC
1 GTCATC GTC
5871 CTGAGCAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 1 0.03
6 36 0.90
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.30
Consensus pattern (6 bp):
GTCATC
Found at i:5855 original size:21 final size:21
Alignment explanation
Indices: 5825--5864 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5815 CTGTCATCAT
5825 CATCGGCATCGTCATCGTCAC
1 CATCGGCATCGTCATCGTCAC
*
5846 CATCGTCATCGTCATCGTC
1 CATCGGCATCGTCATCGTC
5865 GTCGTCCTGA
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:0.17, C:0.38, G:0.17, T:0.28
Consensus pattern (21 bp):
CATCGGCATCGTCATCGTCAC
Found at i:5867 original size:15 final size:15
Alignment explanation
Indices: 5831--5859 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5821 TCATCATCGG
5831 CATCGTCATCGTCAC
1 CATCGTCATCGTCAC
5846 CATCGTCATCGTCA
1 CATCGTCATCGTCA
5860 TCGTCGTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.28
Consensus pattern (15 bp):
CATCGTCATCGTCAC
Found at i:6242 original size:18 final size:18
Alignment explanation
Indices: 6219--6272 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
6209 GCGATGGCAT
6219 CATCATATATGGCTGCGG
1 CATCATATATGGCTGCGG
* *
6237 CATCATATATGGTTGTGG
1 CATCATATATGGCTGCGG
6255 CATCATATATGGCTGCGG
1 CATCATATATGGCTGCGG
6273 TGGCTGCTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (18 bp):
CATCATATATGGCTGCGG
Found at i:7893 original size:111 final size:111
Alignment explanation
Indices: 7754--7975 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
7744 ATTACAAAAA
* * *
7754 TTAATTCTTAATCTAATAATCATGCATTAAATGAATAAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
* *
7819 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
*
7865 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
7930 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
7976 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:8113 original size:12 final size:10
Alignment explanation
Indices: 8099--8140 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
8089 ACCTTAAAAA
*
8099 GAGAGTATTT
1 GAGAGAATTT
8109 GAGAGAAATTT
1 GAGAG-AATTT
8120 -AGAGAATTT
1 GAGAGAATTT
8129 GAGAGAATTT
1 GAGAGAATTT
8139 GA
1 GA
8141 TGTGATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.17
10 20 0.69
11 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:8378 original size:50 final size:50
Alignment explanation
Indices: 8275--8386 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
8265 AGCGCGGATT
* * * * * * * *
8275 AGGGGGCGCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGGC
1 AGGGGGCGCGCTATACCCACGTGACACCAAATCAACATATAACGCGAGAC
* *
8325 AGGGGGCGCTCTATACCCACGTGACACCAAATCAACATATAACGCGATAC
1 AGGGGGCGCGCTATACCCACGTGACACCAAATCAACATATAACGCGAGAC
8375 AGGGGGCGCGCT
1 AGGGGGCGCGCT
8387 TTCCTGCTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.14
Consensus pattern (50 bp):
AGGGGGCGCGCTATACCCACGTGACACCAAATCAACATATAACGCGAGAC
Found at i:11183 original size:39 final size:38
Alignment explanation
Indices: 11123--11232 Score: 91
Period size: 38 Copynumber: 2.8 Consensus size: 38
11113 TAAAAAACAT
* *
11123 AATAAAAGACTAATCTA-AAAAAGAAAAAAAA-TACAATA
1 AATAAAA-AC-AATATAGAAAAAGAAAAAAAAGTAAAATA
11161 CAATAAAATACAATATAGAAAAAATGAAAAAAATAAGTAAAATA
1 -AATAAAA-ACAATATAG-AAAAA-G-AAAAAA-AAGTAAAATA
* *
11205 AAT-AAAACAAAATAGAATAAGAAAAAAA
1 AATAAAAACAATATAGAAAAAGAAAAAAA
11233 TAAAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
37 1 0.02
38 11 0.18
39 10 0.17
40 9 0.15
41 9 0.15
42 9 0.15
43 5 0.08
44 6 0.10
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.15
Consensus pattern (38 bp):
AATAAAAACAATATAGAAAAAGAAAAAAAAGTAAAATA
Found at i:11237 original size:5 final size:5
Alignment explanation
Indices: 11141--11360 Score: 71
Period size: 5 Copynumber: 43.2 Consensus size: 5
11131 ACTAATCTAA
* * * * *
11141 AAAAG AAAA- AAAAT ACAAT ACAAT AAAAT ACAATAT AGAA- AAAAT GAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AA-AT AAAAT AAAAT AAAAT
* * * *
11190 AAAAT -AAGT AAAAT -AAAT AAAAC AAAAT AGAAT AAGAAA AAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT -AAAAT
* ** * * * * *
11240 AAAAAT AAGAAA AAAAT GGAAT TAAAT AAGATT AAAA- AACA- GAAAC
1 -AAAAT AA-AAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT
* * * *
11286 AAAAT AAAA- AAAAG AAAAC AAAA- AGAAT AGAAT AGAAAT AAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT -AAAAT
11336 ATATAAT AATAAT AATAAT AAAAT A
1 A-A-AAT AA-AAT AA-AAT AAAAT A
11361 TAGTATTAAT
Statistics
Matches: 166, Mismatches: 31, Indels: 36
0.71 0.13 0.15
Matches are distributed among these distances:
4 29 0.17
5 81 0.49
6 49 0.30
7 7 0.04
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:11243 original size:14 final size:15
Alignment explanation
Indices: 11199--11244 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
11189 AAAAATAAGT
*
11199 AAAATAAATAA-AAC
1 AAAATAAATAATAAA
*
11213 AAAATAGAATAAGAAA
1 AAAATA-AATAATAAA
11229 AAAATAAA-AATAAA
1 AAAATAAATAATAAA
11243 AA
1 AA
11245 TAAGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.46
15 7 0.25
16 8 0.29
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (15 bp):
AAAATAAATAATAAA
Found at i:11243 original size:41 final size:46
Alignment explanation
Indices: 11140--11243 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 46
11130 GACTAATCTA
* * *
11140 AAAAAGAAAAAAAATACAATACAATAAAATACAATATAGAAAAAATG
1 AAAAA-AATAAAAATAAAATACAATAAAATACAAAATAGAAAAAATG
* *
11187 AAAAAAAT--AAGTAAAATA-AAT-AAA-ACAAAATAG-AATAA-G
1 AAAAAAATAAAAATAAAATACAATAAAATACAAAATAGAAAAAATG
11226 AAAAAAATAAAAATAAAA
1 AAAAAAATAAAAATAAAA
11244 ATAAGAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
39 9 0.18
40 4 0.08
41 15 0.31
42 3 0.06
43 3 0.06
44 8 0.16
46 2 0.04
47 5 0.10
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (46 bp):
AAAAAAATAAAAATAAAATACAATAAAATACAAAATAGAAAAAATG
Found at i:11245 original size:12 final size:11
Alignment explanation
Indices: 11179--11256 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 11
11169 TACAATATAG
11179 AAAAAATGAAAA
1 AAAAAAT-AAAA
*
11191 AAATAAGTAAAA
1 AAA-AAATAAAA
11203 TAAATAAA-ACAAA
1 -AAA-AAATA-AAA
* * *
11216 ATAGAATAAGA
1 AAAAAATAAAA
11227 AAAAAATAAAA
1 AAAAAATAAAA
*
11238 ATAAAAATAAGA
1 A-AAAAATAAAA
11250 AAAAAAT
1 AAAAAAT
11257 GGAATTAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
11 19 0.37
12 21 0.40
13 12 0.23
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:11250 original size:23 final size:24
Alignment explanation
Indices: 11187--11256 Score: 88
Period size: 23 Copynumber: 2.8 Consensus size: 24
11177 AGAAAAAATG
11187 AAAAAAATAAGTAAAATAAATAAAAC
1 AAAAAAATAAG-AAAA-AAATAAAAC
11213 AAAATAGAATAAGAAAAAAATAAAA-
1 AAAA-A-AATAAGAAAAAAATAAAAC
*
11238 ATAAAAATAAGAAAAAAAT
1 AAAAAAATAAGAAAAAAAT
11257 GGAATTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
23 14 0.34
24 1 0.02
25 3 0.07
26 12 0.29
27 5 0.12
28 6 0.15
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (24 bp):
AAAAAAATAAGAAAAAAATAAAAC
Found at i:11256 original size:39 final size:38
Alignment explanation
Indices: 11186--11261 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 38
11176 TAGAAAAAAT
* *
11186 GAAAAAAATAAGTAAAATAAATAAAACAAAATAGAATAA
1 GAAAAAAATAAG-AAAAAAAATAAAAAAAAATAGAATAA
*
11225 GAAAAAAATAA-AAATAAAAATAAGAAAAAAATGGAAT
1 GAAAAAAATAAGAAA-AAAAATAA-AAAAAAATAGAAT
11262 TAAATAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.09
38 7 0.22
39 22 0.69
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.14
Consensus pattern (38 bp):
GAAAAAAATAAGAAAAAAAATAAAAAAAAATAGAATAA
Found at i:11295 original size:18 final size:19
Alignment explanation
Indices: 11272--11308 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
11262 TAAATAAGAT
*
11272 TAAAAAACAG-AAACAAAA
1 TAAAAAAAAGAAAACAAAA
11290 TAAAAAAAAGAAAACAAAA
1 TAAAAAAAAGAAAACAAAA
11309 AGAATAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.81, C:0.08, G:0.05, T:0.05
Consensus pattern (19 bp):
TAAAAAAAAGAAAACAAAA
Found at i:11333 original size:57 final size:56
Alignment explanation
Indices: 11224--11334 Score: 129
Period size: 57 Copynumber: 2.0 Consensus size: 56
11214 AAATAGAATA
* * * *
11224 AGAAAAAAATAAAAATAAAAATAAGAAAAAAATGGAATTAAATAAGATTAAAAAAC
1 AGAAAAAAATAAAAATAAAAATAACAAAAAAATAGAATGAAATAAGAATAAAAAAC
11280 AGAAACAAAATAAAAA-AAAGAA-AACAAAAAGAATAGAATAGAAATAA-AATAAAAA
1 AGAAA-AAAATAAAAATAAA-AATAACAAAAA-AATAGAAT-GAAATAAGAATAAAAA
11335 TATATAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
56 15 0.32
57 26 0.55
58 6 0.13
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.13
Consensus pattern (56 bp):
AGAAAAAAATAAAAATAAAAATAACAAAAAAATAGAATGAAATAAGAATAAAAAAC
Found at i:11370 original size:22 final size:23
Alignment explanation
Indices: 11334--11385 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
11324 TAAAATAAAA
11334 ATATATAATAATAATAATAATAA
1 ATATATAATAATAATAATAATAA
* * *
11357 A-ATATAGTATTAATTA-AATAA
1 ATATATAATAATAATAATAATAA
*
11378 ATAAATAA
1 ATATATAA
11386 AAAGGATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
ATATATAATAATAATAATAATAA
Found at i:11380 original size:25 final size:24
Alignment explanation
Indices: 11316--11382 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 24
11306 AAAAGAATAG
11316 AATAGAAATAAAATAAAAATATATAAT
1 AATA-AAAT-AAAT-AAAATATATAAT
*
11343 AATAATAAT-AATAAAATATAGTATT
1 AATAA-AATAAATAAAATATA-TAAT
*
11368 AATTAAATAAATAAA
1 AATAAAATAAATAAA
11383 TAAAAAGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 11 0.31
25 16 0.46
26 1 0.03
27 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (24 bp):
AATAAAATAAATAAAATATATAAT
Found at i:11452 original size:22 final size:23
Alignment explanation
Indices: 11426--11476 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
11416 AGAACTAAAT
*
11426 TAAAATAAAAATAAAATAGAGGG
1 TAAAATAAAAAGAAAATAGAGGG
* * *
11449 -AAAATTAAAAGGAAATCGAGGG
1 TAAAATAAAAAGAAAATAGAGGG
11471 TAAAAT
1 TAAAAT
11477 TCGAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.18
Consensus pattern (23 bp):
TAAAATAAAAAGAAAATAGAGGG
Found at i:13738 original size:84 final size:85
Alignment explanation
Indices: 13516--13747 Score: 306
Period size: 85 Copynumber: 2.7 Consensus size: 85
13506 ATATGTTATC
* * * * *
13516 GAGCTCAATAGAATCGAACTCGAAAGTTTTTGTTGATAGATAACCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
13581 TGTAAATTTTATATGTCTTT
66 TGTAAATTTTATATGTCTTT
* * * *
13601 GAACTGAATGTAATCGAACTCGAAAGTTTTCGTTGACAGATATCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
13666 TGTAAATTTGT-TATGTC-TT
66 TGTAAATTT-TATATGTCTTT
* * * * * *
13685 GAGCTGAATGGAATCGAACTTGAAGGTTTTTGCTGAGAGATAGCCCTTGTCGCCTTGAGCTAT
1 GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
13748 ACAGTAATAG
Statistics
Matches: 128, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 56 0.44
85 71 0.55
86 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTTATATGTCTTT
Found at i:15437 original size:99 final size:99
Alignment explanation
Indices: 15265--15466 Score: 305
Period size: 99 Copynumber: 2.0 Consensus size: 99
15255 GGACAACTCA
* *
15265 ATATTATAACCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACGAATT
1 ATATTATAACCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
* *
15330 GCTTTAGAGGGATAACTCAAGCTTTATTATATAG
66 GCTCTAGAGGGACAACTCAAGCTTTATTATATAG
* * * * *
15364 ATATTATAATCACCTTTATTAGGCTAGCTGCATCTTATCCATAAAGTCAGGGTGTTTAACCAATT
1 ATATTATAACCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
* *
15429 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
66 GCTCTAGAGGGACAACTCAAGCTTTATTATATAG
15463 ATAT
1 ATAT
15467 AATATTATAA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (99 bp):
ATATTATAACCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTATATAG
Found at i:19772 original size:20 final size:20
Alignment explanation
Indices: 19747--19808 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 20
19737 AAAATGCTAA
19747 AGTGTACTGATACACCCTGC
1 AGTGTACTGATACACCCTGC
* *
19767 AGTGTA-T-ATATACACTG-
1 AGTGTACTGATACACCCTGC
*
19784 -GTGTACCGATACACCCTGC
1 AGTGTACTGATACACCCTGC
19803 AGTGTA
1 AGTGTA
19809 TCCATACACC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
18 16 0.48
19 1 0.03
20 11 0.33
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (20 bp):
AGTGTACTGATACACCCTGC
Found at i:19815 original size:20 final size:20
Alignment explanation
Indices: 19756--19818 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 20
19746 AAGTGTACTG
19756 ATACACCCTGCAGTGTAT--
1 ATACACCCTGCAGTGTATCC
* *
19774 ATATACACTG--GTGTA-CC
1 ATACACCCTGCAGTGTATCC
19791 GATACACCCTGCAGTGTATCC
1 -ATACACCCTGCAGTGTATCC
19812 ATACACC
1 ATACACC
19819 TATGACTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 5 0.14
18 16 0.46
20 12 0.34
21 2 0.06
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (20 bp):
ATACACCCTGCAGTGTATCC
Found at i:19816 original size:36 final size:36
Alignment explanation
Indices: 19748--19817 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
19738 AAATGCTAAA
* *
19748 GTGTACTGATACACCCTGCAGTGTATATATACACTG
1 GTGTACCGATACACCCTGCAGTGTATACATACACTG
*
19784 GTGTACCGATACACCCTGCAGTGTATCCATACAC
1 GTGTACCGATACACCCTGCAGTGTATACATACAC
19818 CTATGACTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (36 bp):
GTGTACCGATACACCCTGCAGTGTATACATACACTG
Found at i:21376 original size:2 final size:2
Alignment explanation
Indices: 21369--21419 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
21359 TGCACCTTTC
21369 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
21411 AT AT AT AT A
1 AT AT AT AT A
21420 CACACATATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21755 original size:30 final size:30
Alignment explanation
Indices: 21699--21797 Score: 164
Period size: 30 Copynumber: 3.3 Consensus size: 30
21689 AAAGGACCTA
* *
21699 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
21728 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
21758 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
21788 TCCATAGGTC
1 TCCAGAGGTC
21798 CCGAAGAACC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 16 0.24
30 50 0.76
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:21814 original size:60 final size:60
Alignment explanation
Indices: 21699--21822 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
21689 AAAGGACCTA
* * *
21699 TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
* * * * *
21758 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
21819 TCCA
1 TCCA
21823 TATGTTCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 16 0.29
60 30 0.55
61 9 0.16
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.20
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
Found at i:21893 original size:63 final size:61
Alignment explanation
Indices: 21780--21908 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
21770 AAAGATCCTC
* *
21780 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
21841 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
21904 GGTAA
1 GGTAA
21909 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:21903 original size:32 final size:31
Alignment explanation
Indices: 21783--21910 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
21773 GATCCTCGGT
* * * *
21783 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
21814 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
21845 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
21877 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
21908 AAC
1 AAC
21911 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:26453 original size:2 final size:2
Alignment explanation
Indices: 26446--26517 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
26436 TGCACCTTTC
26446 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
*
26488 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26518 CCACGCATAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26845 original size:30 final size:30
Alignment explanation
Indices: 26789--26887 Score: 164
Period size: 30 Copynumber: 3.3 Consensus size: 30
26779 AAAGGACCTA
* *
26789 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
26818 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
26848 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
26878 TCCATAGGTC
1 TCCAGAGGTC
26888 CCGAAGAACC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 16 0.24
30 50 0.76
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:26904 original size:60 final size:60
Alignment explanation
Indices: 26789--26912 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
26779 AAAGGACCTA
* * *
26789 TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
* * * * *
26848 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
26909 TCCA
1 TCCA
26913 TATGTTCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 16 0.29
60 30 0.55
61 9 0.16
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.20
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
Found at i:26989 original size:63 final size:61
Alignment explanation
Indices: 26870--26998 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 61
26860 AAAGATCCTC
* * *
26870 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATA
* *
26931 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTATCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTATCCATATGTTCCGTAGAACATA
26994 GGTAA
1 GGTAA
26999 ACCCTCGACT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.42
63 30 0.50
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATA
Found at i:26993 original size:32 final size:31
Alignment explanation
Indices: 26873--27000 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
26863 GATCCTCGGT
* * * *
26873 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
26904 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
26935 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
*
26967 AACTATCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
26998 AAC
1 AAC
27001 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.63
32 22 0.27
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:29904 original size:15 final size:14
Alignment explanation
Indices: 29884--29999 Score: 55
Period size: 13 Copynumber: 7.9 Consensus size: 14
29874 AATAATAGCT
29884 AAATAATAATAAATA
1 AAATAA-AATAAATA
29899 AAAT-AAA-AAATA
1 AAATAAAATAAATA
*
29911 ATAATAAAAGACTAATCTCA
1 A-AAT-AAA-A-TAA-AT-A
*
29931 AAAAAAACAATAAAT-
1 AAATAAA-A-TAAATA
29946 AAA-AAAATGAAA-A
1 AAATAAAAT-AAATA
29959 AAATAAAA-AAATA
1 AAATAAAATAAATA
29972 AAATAAAATAGAATA
1 AAATAAAATA-AATA
*
29987 AGATAAAAATAAA
1 AAAT-AAAATAAA
30000 AATAAGGAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 30
0.69 0.05 0.26
Matches are distributed among these distances:
12 10 0.12
13 21 0.26
14 9 0.11
15 18 0.22
16 7 0.09
17 1 0.01
18 9 0.11
19 3 0.04
20 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.18
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:29910 original size:19 final size:18
Alignment explanation
Indices: 29883--29919 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29873 AAATAATAGC
*
29883 TAAATAATAATAAATAAAA
1 TAAAAAATAAT-AATAAAA
29902 TAAAAAATAATAATAAAA
1 TAAAAAATAATAATAAAA
29920 GACTAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAAATAATAATAAAA
Found at i:29913 original size:25 final size:23
Alignment explanation
Indices: 29884--30000 Score: 92
Period size: 26 Copynumber: 4.7 Consensus size: 23
29874 AATAATAGCT
29884 AAATAATAATAAATAAAATAAAAA
1 AAATAATAA-AAATAAAATAAAAA
**
29908 ATAATAATAAAAGACTAATCTCAAAAA
1 A-AATAATAAAA-A-TAAAAT-AAAAA
* * *
29935 AAACAATAAATAAAAAAATGAAAA
1 AAATAATAAA-AATAAAATAAAAA
29959 AAATAA-AAAAATAAAATAAAATA
1 AAATAATAAAAATAAAATAAAA-A
*
29982 GAATAAGATAAAAATAAAA
1 AAAT-A-ATAAAAATAAAA
30001 ATAAGGAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
22 10 0.14
23 7 0.10
24 13 0.18
25 13 0.18
26 23 0.32
27 7 0.10
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.18
Consensus pattern (23 bp):
AAATAATAAAAATAAAATAAAAA
Found at i:29950 original size:17 final size:17
Alignment explanation
Indices: 29930--29978 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
29920 GACTAATCTC
*
29930 AAAAAAA-ACAATAAAT
1 AAAAAAATAAAATAAAT
29946 AAAAAAATGAAAA-AAAT
1 AAAAAAAT-AAAATAAAT
29963 AAAAAAATAAAATAAA
1 AAAAAAATAAAATAAA
29979 ATAGAATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.38
17 15 0.52
18 3 0.10
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAAATAAAT
Found at i:29958 original size:8 final size:8
Alignment explanation
Indices: 29942--29974 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
29932 AAAAAACAAT
29942 AAATAAAA
1 AAATAAAA
29950 AAATGAAAA
1 AAAT-AAAA
29959 AAATAAAA
1 AAATAAAA
29967 AAATAAAA
1 AAATAAAA
29975 TAAAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:29977 original size:34 final size:33
Alignment explanation
Indices: 29930--30001 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
29920 GACTAATCTC
*
29930 AAAAAAAACAAT-AAATAAAAAAATGAAAAAAAT
1 AAAAAAAAAAATAAAATAAAAAAA-GAAAAAAAT
* * *
29963 AAAAAAATAAAATAAAATAGAATAAGATAAAAAT
1 AAAAAAA-AAAATAAAATAAAAAAAGAAAAAAAT
29997 AAAAA
1 AAAAA
30002 TAAGGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.21
34 17 0.52
35 9 0.27
ACGTcount: A:0.81, C:0.01, G:0.04, T:0.14
Consensus pattern (33 bp):
AAAAAAAAAAATAAAATAAAAAAAGAAAAAAAT
Found at i:30005 original size:17 final size:17
Alignment explanation
Indices: 29942--30005 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
29932 AAAAAACAAT
*
29942 AAATAAAAA-AATGAAAA
1 AAATAAAAATAA-GATAA
*
29959 AAATAAAAAAATAAAAT-A
1 AAAT--AAAAATAAGATAA
*
29977 AAAT-AGAATAAGATAA
1 AAATAAAAATAAGATAA
29993 AAATAAAAATAAG
1 AAATAAAAATAAG
30006 GAAAAATGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
15 8 0.22
16 5 0.14
17 11 0.30
18 5 0.14
19 6 0.16
20 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (17 bp):
AAATAAAAATAAGATAA
Found at i:30052 original size:5 final size:5
Alignment explanation
Indices: 30042--30087 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
30032 AAACAGAAAC
* *
30042 AAAAG AAAAG AAAAAG AAAAG AAAAAG AATAG AAAAG AATAG AAAA
1 AAAAG AAAAG -AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA
30088 AAGAATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:30066 original size:10 final size:11
Alignment explanation
Indices: 30042--30088 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
30032 AAACAGAAAC
30042 AAAAGAAAAGA
1 AAAAGAAAAGA
30053 AAAAGAAAAGA
1 AAAAGAAAAGA
*
30064 AAAAGAATAG-
1 AAAAGAAAAGA
*
30074 AAAAGAATAGA
1 AAAAGAAAAGA
30085 AAAA
1 AAAA
30089 AGAATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 10 0.29
11 24 0.71
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:30089 original size:22 final size:22
Alignment explanation
Indices: 30042--30094 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
30032 AAACAGAAAC
*
30042 AAAAGAAAAGAAAAAGAAAAGA
1 AAAAGAATAGAAAAAGAAAAGA
*
30064 AAAAGAATAG-AAAAGAATAGAA
1 AAAAGAATAGAAAAAGAAAAG-A
30086 AAAAGAATA
1 AAAAGAATA
30095 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAAGAATAGAAAAAGAAAAGA
Found at i:30173 original size:28 final size:30
Alignment explanation
Indices: 30135--30205 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 30
30125 ATTAATTAAA
* *
30135 TAAATATAAAAATAAAAATA-AAAAAGGAT
1 TAAATAAAAAAATAAAAATATAAAAAGGAC
* *
30164 TAAA-ACAAAAAT-AAACTATAAAAAGGAC
1 TAAATAAAAAAATAAAAATATAAAAAGGAC
30192 TAAATAAAAAAATA
1 TAAATAAAAAAATA
30206 TGGCAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.14
28 19 0.54
29 11 0.31
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (30 bp):
TAAATAAAAAAATAAAAATATAAAAAGGAC
Found at i:32305 original size:7 final size:7
Alignment explanation
Indices: 32293--32317 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32283 AAGGTCAAAC
32293 ATATTAA
1 ATATTAA
32300 ATATTAA
1 ATATTAA
32307 ATATTAA
1 ATATTAA
32314 ATAT
1 ATAT
32318 AATTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATTAA
Found at i:33821 original size:60 final size:60
Alignment explanation
Indices: 33702--33870 Score: 177
Period size: 60 Copynumber: 2.8 Consensus size: 60
33692 ACACTCGTTT
* * * * *
33702 TAAATTGGTCCTTAAACATTTAAATATTTCAATTTCATCTCTAA-TCTATGGTTATCATTC
1 TAAATTGGTCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAGT-TATGGTTATCATTC
* *
33762 TTAATTAGTCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAGTTAT-GTCT-TGCATTC
1 TAAATTGGTCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAGTTATGGT-TAT-CATTC
* *
33822 TAAATTGGT-CTCCAAACTTTTTGAACATTCCAATTTCA-CCCCAAGTTAT
1 TAAATTGGTCCT-CAAAC-TTTTGAATATTTCAATTTCATCCCCAAGTTAT
33871 ATTATTATAT
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
59 5 0.05
60 69 0.74
61 19 0.20
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.42
Consensus pattern (60 bp):
TAAATTGGTCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAGTTATGGTTATCATTC
Found at i:34045 original size:59 final size:60
Alignment explanation
Indices: 33977--34113 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
33967 AGAGTTTAGG
** * * * *
33977 GACTAATTTAGAAA-GAGGGTCATA-TTTTAGGGATGAAACTAGAAT-TTCAAAAGTTTAAA
1 GACTAATTTA-AAATGAGAATCATAGTTTGA-GGATAAAACTAAAATATTCAAAAATTTAAA
* *
34036 GATTAATTTAAAATGAGAATCATAGTTTGAGGATAAAATTAAAATATTCAAAAATTTAAA
1 GACTAATTTAAAATGAGAATCATAGTTTGAGGATAAAACTAAAATATTCAAAAATTTAAA
34096 GACTAATTTAAAATGAGA
1 GACTAATTTAAAATGAGA
34114 GTTATTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
58 3 0.05
59 29 0.44
60 34 0.52
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.31
Consensus pattern (60 bp):
GACTAATTTAAAATGAGAATCATAGTTTGAGGATAAAACTAAAATATTCAAAAATTTAAA
Found at i:34530 original size:19 final size:19
Alignment explanation
Indices: 34506--34636 Score: 100
Period size: 19 Copynumber: 6.5 Consensus size: 19
34496 TCTACAGTTG
34506 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
34525 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
** * *
34544 TCGTTGCGATAGTCTATAGTT
1 TCGTTGCGATTTTCCA-A-AT
* *
34565 GTTGTTGCGATAGTTTACAAAT
1 -TCGTTGCGAT--TTTCCAAAT
* * **
34587 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
34608 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
34628 TCGTTGCGA
1 TCGTTGCGA
34637 AAATTCGTTG
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
19 41 0.47
20 6 0.07
21 18 0.20
22 20 0.23
23 1 0.01
24 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:34557 original size:60 final size:61
Alignment explanation
Indices: 34467--34596 Score: 183
Period size: 60 Copynumber: 2.1 Consensus size: 61
34457 GAAAATCGCA
* *
34467 TTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT-TTTCCAAATTCG
1 TTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGTCGTTGCGATATTTACAAATTCG
* *
34528 TTGCGATTTTCCAAATT-CGTTGCGATAGTCTATAGTTGTTGTTGCGATAGTTTACAAATTCG
1 TTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTGTCGTTGCGATA-TTTACAAATTCG
34590 TTGCGAT
1 TTGCGAT
34597 AGTCTACAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
60 29 0.47
61 12 0.19
62 21 0.34
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.42
Consensus pattern (61 bp):
TTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGTCGTTGCGATATTTACAAATTCG
Found at i:34589 original size:43 final size:41
Alignment explanation
Indices: 34525--34636 Score: 179
Period size: 43 Copynumber: 2.7 Consensus size: 41
34515 TTTTCCAAAT
*
34525 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTATAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
* *
34566 TTGTTGCGATAGTTTACAAATTCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGAT--TTTCCAAATTCGTTGCGATAGTCTACAGTTG
34609 TCGTTGCGATTTTCCAAATTCGTTGCGA
1 TCGTTGCGATTTTCCAAATTCGTTGCGA
34637 AAATTCGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 26 0.41
43 38 0.59
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
Found at i:34743 original size:6 final size:6
Alignment explanation
Indices: 34732--34776 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
34722 GACACGTATT
*
34732 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG GCCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
34777 CGAGACGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.31, C:0.51, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:35816 original size:41 final size:41
Alignment explanation
Indices: 35759--35853 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
35749 TCTTTTTTTT
35759 ACTATCGCAACGAATTTGGAAA-ATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAACATCGCAACGACAACT-TAG
*
35800 ACTATCGCAACGAATTTGGAAACTATCGCAACGACAACTTGG
1 ACTATCGCAACGAATTTGGAAAC-ATCGCAACGACAACTTAG
*
35842 ACTATCGTAACG
1 ACTATCGCAACG
35854 CGAAATGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
41 22 0.44
42 13 0.26
43 15 0.30
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAACATCGCAACGACAACTTAG
Found at i:35826 original size:21 final size:21
Alignment explanation
Indices: 35759--35833 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
35749 TCTTTTTTTT
35759 ACTATCGCAACGAATTTGGAA
1 ACTATCGCAACGAATTTGGAA
** * *
35780 A--ATCGCAACGACAACTGTAG
1 ACTATCGCAACGA-ATTTGGAA
35800 ACTATCGCAACGAATTTGGAA
1 ACTATCGCAACGAATTTGGAA
35821 ACTATCGCAACGA
1 ACTATCGCAACGA
35834 CAACTTGGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 10 0.23
20 5 0.12
21 18 0.42
22 10 0.23
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGAATTTGGAA
Found at i:35845 original size:21 final size:19
Alignment explanation
Indices: 35759--35853 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 19
35749 TCTTTTTTTT
*
35759 ACTATCGCAACGAATTTGG
1 ACTATCGCAACGAACTTGG
** *
35778 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACG--AACT-TGG
*
35800 ACTATCGCAACGAATTTGG
1 ACTATCGCAACGAACTTGG
35819 AAACTATCGCAACGACAACTTGG
1 --ACTATCGCAACG--AACTTGG
*
35842 ACTATCGTAACG
1 ACTATCGCAACG
35854 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 12 0.20
20 3 0.05
21 26 0.44
22 12 0.20
23 6 0.10
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (19 bp):
ACTATCGCAACGAACTTGG
Found at i:36665 original size:17 final size:18
Alignment explanation
Indices: 36643--36677 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
36633 ATATTCATAG
36643 TTTTTAAAAAAT-TAAAT
1 TTTTTAAAAAATATAAAT
36660 TTTTTAAAAAATATAAAT
1 TTTTTAAAAAATATAAAT
36678 GTGACACGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTTAAAAAATATAAAT
Found at i:46626 original size:149 final size:147
Alignment explanation
Indices: 46444--46795 Score: 380
Period size: 149 Copynumber: 2.4 Consensus size: 147
46434 TCCATTAGAT
* * *
46444 AAAAACAGCTGAA-AATGCAAGATAAAAAGTGAAA-GAGACTATTTTCCTG-GAAAATTCAATGC
1 AAAAACAGCTGAAGAA-GCAAGAGAAAAAGTGAAAGGA-ACTATCTTCCTGAGAAAA-TC-ATGA
* * * * *
46506 TT-GTGAAAACA-CTCAGT-TGATACAATTTTTCTCATTATCCAAACAC-TCCCAA-ATATATAT
62 TTGGGGAAAACATC-CA-TCTGATACAAGTTTTCTCACTATCCAAACACACCCCAAGATACA-AT
*
46566 TTTTTAACACCCCGATTGATTTTAAAA
124 TTTTTAACACCCCAATTGA---TAAAA
46593 AAAAACAGCTGAAGAAGCAAGAGAAAATA-TGAAAGGAACTATCTTCCTGAGAAAATCATGATTG
1 AAAAACAGCTGAAGAAGCAAGAGAAAA-AGTGAAAGGAACTATCTTCCTGAGAAAATCATGATTG
** *
46657 GGGAAAGTATCCATCTGATACAAGTTTTCTCACTATCCAAACACACCCCAAGATGCAATTTTTTA
65 GGGAAAACATCCATCTGATACAAGTTTTCTCACTATCCAAACACACCCCAAGATACAATTTTTTA
46722 ACACCCCAATTGATAAAA
130 ACACCCCAATTGATAAAA
* * * * * *
46740 AAAAGCAGCTGAAGAAGCAATAGAAAAAGAGGAAGGAACTGTTTTCCTGAGAAAAT
1 AAAAACAGCTGAAGAAGCAAGAGAAAAAGTGAAAGGAACTATCTTCCTGAGAAAAT
46796 TAAAACTTGG
Statistics
Matches: 175, Mismatches: 18, Indels: 22
0.81 0.08 0.10
Matches are distributed among these distances:
146 1 0.01
147 53 0.30
148 6 0.03
149 76 0.43
150 36 0.21
151 3 0.02
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (147 bp):
AAAAACAGCTGAAGAAGCAAGAGAAAAAGTGAAAGGAACTATCTTCCTGAGAAAATCATGATTGG
GGAAAACATCCATCTGATACAAGTTTTCTCACTATCCAAACACACCCCAAGATACAATTTTTTAA
CACCCCAATTGATAAAA
Found at i:46788 original size:147 final size:147
Alignment explanation
Indices: 46523--46795 Score: 374
Period size: 147 Copynumber: 1.8 Consensus size: 147
46513 AACACTCAGT
* * * * *
46523 TGATACAATTTTTCTCATTATCCAAACACTCCCAAATATATATTTTTTAACACCCCGATTGATTT
1 TGATACAAGTTTTCTCACTATCCAAACACCCCCAAATACATATTTTTTAACACCCCAATTGA--T
46588 TAAAAAAAAACAGCTGAAGAAGCAAGAGAAAATATGAAAGGAACTATCTTCCTGAGAAAATCATG
64 TAAAAAAAAACAGCTGAAGAAGCAAGAGAAAATATGAAAGGAACTATCTTCCTGAGAAAATCATG
46653 ATTGGGGAAAGTATCCATC
129 ATTGGGGAAAGTATCCATC
*
46672 TGATACAAGTTTTCTCACTATCCAAACACACCCCAAGATGCA-ATTTTTTAACACCCCAATTGA-
1 TGATACAAGTTTTCTCACTATCCAAACAC-CCCCAA-ATACATATTTTTTAACACCCCAATTGAT
* * * *
46735 TAAAAAAAAGCAGCTGAAGAAGCAATAGAAAA-A-GAGGAAGGAACTGTTTTCCTGAGAAAAT
64 TAAAAAAAAACAGCTGAAGAAGCAAGAGAAAATATGA--AAGGAACTATCTTCCTGAGAAAAT
46796 TAAAACTTGG
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
145 2 0.02
146 1 0.01
147 52 0.47
149 27 0.25
150 25 0.23
151 3 0.03
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (147 bp):
TGATACAAGTTTTCTCACTATCCAAACACCCCCAAATACATATTTTTTAACACCCCAATTGATTA
AAAAAAAACAGCTGAAGAAGCAAGAGAAAATATGAAAGGAACTATCTTCCTGAGAAAATCATGAT
TGGGGAAAGTATCCATC
Found at i:49485 original size:22 final size:22
Alignment explanation
Indices: 49455--49505 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
49445 CGGGACATAT
*
49455 ACAATATACAAAGGTCCTTCGGG
1 ACAA-ATACAAAGGTCATTCGGG
*
49478 ACAAATACATAGGTCATTCGGG
1 ACAAATACAAAGGTCATTCGGG
49500 ACAAAT
1 ACAAAT
49506 TTCATATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (22 bp):
ACAAATACAAAGGTCATTCGGG
Done.