Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003526.1 Hibiscus syriacus cultivar Beakdansim tig00007448_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: 182817
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1288 original size:107 final size:105
Alignment explanation
Indices: 1098--1426 Score: 383
Period size: 108 Copynumber: 3.1 Consensus size: 105
1088 AAACGGTAAG
* * * * *
1098 AAAATAAG-TAATTACTTATTTTTTTTATTAATATTATCAACATATTAAGTAGCACCTAATATAT
1 AAAAT-AGTTAATTACTTA-TTTTGTTATTAATATTATCAACATATTAGGTAACGCCTAA-ATGT
* * *
1162 TATGAGAGTTTAAGCTGATGGGCCTTA-AATATTTGACGATAAC
63 TATCAAAGTTTAAGCTGATGGGCCTTAGAA-ATCTGACGATAAC
*
1205 AAAATATGTTAATTACTTATTTTGTTATTAATATTATCAACGTATTAGGTAACGCCTAGAATGTT
1 AAAATA-GTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCTA-AATGTT
* * * *
1270 ATCAAAGTTTAAGTTGATGGGCCCTTAGAAATCCGACAATAAT
64 ATCAAAGTTTAAGCTGATGGG-CCTTAGAAATCTGACGATAAC
* *
1313 AAAATAGATTAATTATTTATTTTGTTATTAATATTATCAACATATTAGGTACCGCCTAAAATGTT
1 AAAATAG-TTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCT-AAATGTT
* * * * *
1378 AACAAAGTTTAAGCTGATGAGCCTTATAAATCTCATGATAAC
64 ATCAAAGTTTAAGCTGATGGGCCTTAGAAATCTGACGATAAC
1420 AAAATAG
1 AAAATAG
1427 GTGTAATATA
Statistics
Matches: 190, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
106 1 0.01
107 85 0.45
108 101 0.53
109 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (105 bp):
AAAATAGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCTAAATGTTAT
CAAAGTTTAAGCTGATGGGCCTTAGAAATCTGACGATAAC
Found at i:2297 original size:99 final size:100
Alignment explanation
Indices: 2084--2297 Score: 292
Period size: 99 Copynumber: 2.1 Consensus size: 100
2074 TAAAAAAAAA
* * ** *
2084 TATTTCAAACGGTTAAGTTGTAAATATTTTACCGTTTACATTGTTCTTATACCTTTAAACAAATC
1 TATTTTAAACGGTTAAGTTGTAAATAATTTACCGTTTACATTAATATTATACCTTTAAACAAATC
*
2149 GGTAGTTAGTTTAACGTAATAGGTAGTGCTTATTT
66 GGTAGTTAGTTTAACGTAATAGGTAGCGCTTATTT
**
2184 TATTTT-AACTGGTTAAGTTGTAAATAATTTACTTTTTACATTAATATTATA-CTTTAAACAAA-
1 TATTTTAAAC-GGTTAAGTTGTAAATAATTTACCGTTTACATTAATATTATACCTTTAAACAAAT
*
2246 CTGGTA-TATAGTTTAACGTAATATGTAGCGCTTATTT
65 C-GGTAGT-TAGTTTAACGTAATAGGTAGCGCTTATTT
2283 TATTTTAAACGGTTA
1 TATTTTAAACGGTTA
2298 CATTATTTAT
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
98 2 0.02
99 56 0.55
100 43 0.43
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (100 bp):
TATTTTAAACGGTTAAGTTGTAAATAATTTACCGTTTACATTAATATTATACCTTTAAACAAATC
GGTAGTTAGTTTAACGTAATAGGTAGCGCTTATTT
Found at i:3303 original size:15 final size:15
Alignment explanation
Indices: 3283--3336 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3273 ACCGGGTATC
3283 GGTACCCGATTACCG
1 GGTACCCGATTACCG
**
3298 GGTACCCGCAAAATCCG
1 GGTACCCG-ATTA-CCG
*
3315 GATACCCGATTACCG
1 GGTACCCGATTACCG
3330 GGTACCC
1 GGTACCC
3337 ATAACATTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 10 0.32
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (15 bp):
GGTACCCGATTACCG
Found at i:3576 original size:65 final size:65
Alignment explanation
Indices: 3500--3621 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
3490 GCACGATTAG
*
3500 TGTTACCTTGGTATAAATAT-GAGCGGTGTCTAGGTGGGTCAGCTGAACCAAATAGCCTCAGATA
1 TGTTACCTTGGTATAAATATGGA-CGGTGTCTAGGTAGGTCAGCTGAACCAAATAGCCTCAGATA
3564 A
65 A
* * * * *
3565 TGTTATCTTGGTGTAGATATGGACGGTGTTTAGGTAGGTCAGTTGAACCAAATAGCC
1 TGTTACCTTGGTATAAATATGGACGGTGTCTAGGTAGGTCAGCTGAACCAAATAGCC
3622 ACAAATGACG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 48 0.96
66 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (65 bp):
TGTTACCTTGGTATAAATATGGACGGTGTCTAGGTAGGTCAGCTGAACCAAATAGCCTCAGATAA
Found at i:4026 original size:12 final size:11
Alignment explanation
Indices: 4005--4035 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
3995 TTTTTTAATT
4005 TTTAATTATTA
1 TTTAATTATTA
4016 TTTATATTATTA
1 TTTA-ATTATTA
4028 TTTAATTA
1 TTTAATTA
4036 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:12430 original size:24 final size:26
Alignment explanation
Indices: 12372--12433 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
12362 TTTTTCGGAT
*
12372 AAAAAACCGGTTTTTTATCCGGTTTGA
1 AAAAAACCGGTTTTTAATCCGG-TTGA
12399 AAAAAACCGGTTTTTAATCCGG-T-A
1 AAAAAACCGGTTTTTAATCCGGTTGA
12423 AAAAAACCGGT
1 AAAAAACCGGT
12434 CGTTCAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 12 0.35
25 1 0.03
27 21 0.62
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (26 bp):
AAAAAACCGGTTTTTAATCCGGTTGA
Found at i:15532 original size:27 final size:27
Alignment explanation
Indices: 15502--15562 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
15492 TATACTGAAC
15502 CATTTCAGGAATTGGATCATACGACGA
1 CATTTCAGGAATTGGATCATACGACGA
* * *
15529 CATTTCAGGAATTGTATTATAGGACGA
1 CATTTCAGGAATTGGATCATACGACGA
15556 CATTTCA
1 CATTTCA
15563 AAGTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (27 bp):
CATTTCAGGAATTGGATCATACGACGA
Found at i:15848 original size:17 final size:18
Alignment explanation
Indices: 15817--15850 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15807 CAAAACAACA
15817 TATCAACTAGAATCTTTT
1 TATCAACTAGAATCTTTT
*
15835 TATC-ACTAGCATCTTT
1 TATCAACTAGAATCTTT
15851 CACACCTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (18 bp):
TATCAACTAGAATCTTTT
Found at i:22025 original size:23 final size:23
Alignment explanation
Indices: 21999--22048 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
21989 TTCATAAAAT
21999 ATTGTGTCATATGTGAATTATCA
1 ATTGTGTCATATGTGAATTATCA
22022 ATTGTGTCATATGTGAATTATCA
1 ATTGTGTCATATGTGAATTATCA
22045 ATTG
1 ATTG
22049 GTTTATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (23 bp):
ATTGTGTCATATGTGAATTATCA
Found at i:25108 original size:18 final size:18
Alignment explanation
Indices: 25085--25136 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
25075 ACCGGTCAAC
25085 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
25103 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
25121 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
25137 TAACGGGTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:25130 original size:13 final size:13
Alignment explanation
Indices: 25114--25146 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
25104 GTCAACGGGT
25114 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
25127 CGGGTCGGGTTAA
1 CGGGTCGGGTCAA
25140 CGGGTCG
1 CGGGTCG
25147 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:25156 original size:31 final size:31
Alignment explanation
Indices: 25096--25157 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
25086 GTCAACGGGT
* *
25096 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCAACGGGTCGGGACCGGTCAA
* *
25127 CGGGTCGGGTTAACGGGTCGTGACCGGTCAA
1 CGGGTCGGGTCAACGGGTCGGGACCGGTCAA
25158 ACCGGTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.18
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGACCGGTCAA
Found at i:25169 original size:10 final size:10
Alignment explanation
Indices: 25149--25203 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
25139 ACGGGTCGTG
25149 ACCGGTC-AA
1 ACCGGTCAAA
25158 ACCGGTCAAA
1 ACCGGTCAAA
25168 ACCGGTTCAAA
1 ACCGG-TCAAA
*
25179 ACCGGT-TAA
1 ACCGGTCAAA
25188 ACCGGTCAAA
1 ACCGGTCAAA
25198 ACCGGT
1 ACCGGT
25204 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:25204 original size:19 final size:19
Alignment explanation
Indices: 25149--25204 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
25139 ACGGGTCGTG
*
25149 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
25168 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
25188 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
25205 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:32346 original size:13 final size:13
Alignment explanation
Indices: 32328--32366 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
32318 ACCGGTCAAC
32328 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32341 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32354 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32367 TGACCGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:32389 original size:10 final size:10
Alignment explanation
Indices: 32369--32424 Score: 96
Period size: 10 Copynumber: 5.6 Consensus size: 10
32359 ACGGGTCGTG
32369 ACCGGTC-AA
1 ACCGGTCAAA
32378 ACCGGTCAAA
1 ACCGGTCAAA
32388 ACCGGTTCAAA
1 ACCGG-TCAAA
32399 ACCGGTCAAA
1 ACCGGTCAAA
32409 ACCGGTCAAA
1 ACCGGTCAAA
32419 ACCGGT
1 ACCGGT
32425 TTCCAGCGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
9 7 0.16
10 28 0.62
11 10 0.22
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.12
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:32402 original size:21 final size:20
Alignment explanation
Indices: 32369--32424 Score: 96
Period size: 21 Copynumber: 2.8 Consensus size: 20
32359 ACGGGTCGTG
32369 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTCAAA
32388 ACCGGTTCAAAACCGGTCAAA
1 ACCGG-TCAAAACCGGTCAAA
32409 ACCGGTCAAAACCGGT
1 ACCGGTCAAAACCGGT
32425 TTCCAGCGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 17 0.49
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.12
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTCAAA
Found at i:35336 original size:20 final size:20
Alignment explanation
Indices: 35311--35384 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
35301 TTTTCCCAAT
*
35311 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
35331 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
35352 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
35372 TCGCAACGCGAAT
1 TCGCAACGCGAAT
35385 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:35354 original size:21 final size:21
Alignment explanation
Indices: 35328--35403 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
35318 GCGAATAAGT
35328 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
35349 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
35369 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* *
35390 AAATCACAATGCGA
1 AAATCGCAACGCGA
35404 TACTGACTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:35356 original size:41 final size:41
Alignment explanation
Indices: 35311--35403 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
35301 TTTTCCCAAT
35311 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
35352 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
35393 TCACAATGCGA
1 TCGCAATGCGA
35404 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:35421 original size:20 final size:20
Alignment explanation
Indices: 35400--35486 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
35390 AAATCACAAT
*
35400 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* * **
35420 GCGATAATAAAAAATCGCAAC
1 GCGATACT-GACTATCGCAAC
* * *
35441 GAGATACTTACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
35461 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
35481 GCGATA
1 GCGATA
35487 ATACATAATC
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 39 0.74
21 14 0.26
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:35434 original size:41 final size:41
Alignment explanation
Indices: 35389--35466 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
35379 GCGAATTGGG
* * *
35389 AAAATCACAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
35430 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATA
35467 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCACAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:35702 original size:22 final size:22
Alignment explanation
Indices: 35674--35717 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35664 CACTCTCTCA
35674 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
35696 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
35718 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:36006 original size:20 final size:20
Alignment explanation
Indices: 35981--36018 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35971 TGATTCTCTC
35981 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
36001 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
36019 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:37350 original size:18 final size:18
Alignment explanation
Indices: 37329--37374 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
37319 CTCCACTTCG
*
37329 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
*
37347 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
37365 AGAGCCATCA
1 AGAGCCATCA
37375 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:37838 original size:19 final size:20
Alignment explanation
Indices: 37784--37839 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
37774 TAGTTTACTT
* *
37784 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
37804 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
37824 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
37840 AAATCGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:37865 original size:33 final size:33
Alignment explanation
Indices: 37823--37915 Score: 161
Period size: 32 Copynumber: 2.8 Consensus size: 33
37813 GGAAATGGCT
37823 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
37856 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
37888 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
37916 CGATTTGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:37895 original size:14 final size:14
Alignment explanation
Indices: 37839--37896 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
37829 ATGCGAAATG
*
37839 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
37853 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
37869 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
37885 AAAATCGCAACG
1 AAAATCGCAACG
37897 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:37949 original size:14 final size:14
Alignment explanation
Indices: 37930--37987 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
37920 TTGTGTTTCG
37930 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
37944 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
37960 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
37976 CGTTGCGATTTT
1 CGTTGCGATTTT
37988 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:37964 original size:32 final size:33
Alignment explanation
Indices: 37925--38003 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
37915 GCGATTTGTG
37925 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
37957 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
37990 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
38004 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:38002 original size:19 final size:19
Alignment explanation
Indices: 37944--38061 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
37934 GCGATTTTGT
37944 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
37962 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
37976 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
37995 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
38015 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
38034 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
38054 TGTTGCGA
1 CGTTGCGA
38062 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:40069 original size:14 final size:14
Alignment explanation
Indices: 40049--40102 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
40039 CGAAATGGCT
40049 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
40063 TTCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
40082 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
40096 ATCGCAA
1 ATCGCAA
40103 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:40120 original size:33 final size:33
Alignment explanation
Indices: 40030--40107 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
40020 AAAACAGACT
* ***
40030 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
40063 TTCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
40096 ATCGCAATGCGA
1 ATCGCAATGCGA
40108 TTTTCATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:40172 original size:19 final size:19
Alignment explanation
Indices: 40128--40201 Score: 103
Period size: 19 Copynumber: 3.8 Consensus size: 19
40118 GCATTGCGAT
* * *
40128 TTTCTCGTTACGATAACCA
1 TTTCGCGTTGCGATAGCCA
40147 TTTTCGCGTTGCGATAGCCA
1 -TTTCGCGTTGCGATAGCCA
*
40167 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGCCA
40186 TTTCGCGTTGCGATAG
1 TTTCGCGTTGCGATAG
40202 TCAAATGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 34 0.68
20 16 0.32
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:40202 original size:19 final size:19
Alignment explanation
Indices: 40148--40204 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
40138 CGATAACCAT
*
40148 TTTCGCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
40167 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
40186 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
40205 AATGAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:41288 original size:24 final size:24
Alignment explanation
Indices: 41261--41314 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
41251 GTATTCGAAA
*
41261 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
41285 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
41309 TTTGAT
1 TTTGAT
41315 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:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:43847 original size:33 final size:33
Alignment explanation
Indices: 43805--43931 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
43795 GGAAATTACT
43805 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
43838 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
43870 TTTCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
43904 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
43932 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:43916 original size:66 final size:66
Alignment explanation
Indices: 43810--43938 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
43800 TTACTATCGC
*
43810 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
43875 T
66 T
*
43876 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
43939 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:43953 original size:19 final size:20
Alignment explanation
Indices: 43931--43973 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43921 AAATCGCAAC
43931 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
43950 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
43970 GCGA
1 GCGA
43974 TTATCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:43958 original size:14 final size:14
Alignment explanation
Indices: 43959--43992 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43949 TGCGATTTTC
43959 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
43973 ATTATCTCGTTGCG
1 ATTTTCGCGTTGCG
43987 ATTTTC
1 ATTTTC
43993 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:44133 original size:14 final size:14
Alignment explanation
Indices: 44114--44150 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44104 CATCAATTAA
44114 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
44128 ACAAATCACCTTTT
1 ACAAATCAACTTTT
44142 ACAAATCAA
1 ACAAATCAA
44151 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:45484 original size:21 final size:21
Alignment explanation
Indices: 45455--45535 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
45445 GAATGGTGGG
*
45455 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTCAACGATGAC
* * * *
45476 AGTGGCCTCTTGAACGGTGAG
1 AGGGGCCTCTTCAACGATGAC
* * * *
45497 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAC
45518 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
45536 AGGAGTGGAC
Statistics
Matches: 43, Mismatches: 15, Indels: 4
0.69 0.24 0.06
Matches are distributed among these distances:
20 3 0.07
21 36 0.84
22 4 0.09
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAC
Found at i:45525 original size:42 final size:42
Alignment explanation
Indices: 45479--45562 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
45469 CGATGACAGT
* *
45479 GGCCTCTTGAACGGT-GAGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAG-GAGGGGACTCTCGAGGAATGATAGG
* * *
45521 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
45563 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:47327 original size:20 final size:19
Alignment explanation
Indices: 47296--47436 Score: 77
Period size: 19 Copynumber: 7.8 Consensus size: 19
47286 TCTTTTGGTT
47296 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
47315 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
47336 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
47355 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
**
47369 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
47385 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
47402 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
47421 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
47437 TGCGATTTTG
Statistics
Matches: 92, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 16 0.17
15 1 0.01
16 3 0.03
17 4 0.04
18 1 0.01
19 36 0.39
20 29 0.32
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:47378 original size:33 final size:33
Alignment explanation
Indices: 47321--47419 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
47311 ACGAGATAAT
47321 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* * *
47355 GAGAATCGCAATGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
47388 GACAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
47420 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
33 43 0.77
34 13 0.23
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:47413 original size:19 final size:19
Alignment explanation
Indices: 47391--47441 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
47381 GCGACCAGAC
47391 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
47410 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
47429 AATCGCAATGCGA
1 AATCGCAACGCGA
47442 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:47470 original size:19 final size:19
Alignment explanation
Indices: 47437--47517 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
47427 AAAATCGCAA
**
47437 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
47456 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
47475 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
47489 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
47509 TGCGATTTT
1 TGCGATTTT
47518 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:48098 original size:21 final size:21
Alignment explanation
Indices: 48065--48165 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
48055 TGCGAAAGTA
* * *
48065 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
48086 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
48106 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
48128 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
48149 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
48166 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:48121 original size:20 final size:20
Alignment explanation
Indices: 48028--48121 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
48018 CGCTATGTAA
*
48028 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
48048 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
48068 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
48089 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
48109 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
48122 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:48140 original size:41 final size:41
Alignment explanation
Indices: 48049--48183 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
48039 AAAGTCAGTA
* * * ** *
48049 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
48089 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
48131 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
48172 TCGCGTTGCGAT
1 TCGCGTTGCGAT
48184 TTACTTATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:48154 original size:20 final size:20
Alignment explanation
Indices: 48110--48202 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
48100 ATAGTCAGTA
* **
48110 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
48131 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
48151 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
48172 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
*
48192 TTGCATTGCGA
1 TCGCATTGCGA
48203 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.54
21 26 0.46
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:48175 original size:21 final size:21
Alignment explanation
Indices: 48110--48185 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
48100 ATAGTCAGTA
48110 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
48131 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
48151 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
48172 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
48186 ACTTATTTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:48184 original size:41 final size:41
Alignment explanation
Indices: 48110--48202 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
48100 ATAGTCAGTA
48110 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
48151 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
48192 TTGCATTGCGA
1 TCGCATTGCGA
48203 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:62906 original size:34 final size:35
Alignment explanation
Indices: 62863--62964 Score: 170
Period size: 34 Copynumber: 2.9 Consensus size: 35
62853 TTTCGTCCTA
62863 TTAGGATTCAAACTCCTAAAAATAGGATAGAA-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
62897 TTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
62932 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
62965 GTTATACTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 31 0.49
35 3 0.05
37 29 0.46
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (35 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:63395 original size:18 final size:17
Alignment explanation
Indices: 63356--63398 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
63346 ATTATATGGA
63356 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
63372 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
63390 TATTATTAT
1 TATTATTAT
63399 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:63707 original size:24 final size:24
Alignment explanation
Indices: 63662--63709 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
63652 ACTTTATATA
* *
63662 TATTTTTTATTATTTTCGTTTTTT
1 TATTTATTATTATTTTCATTTTTT
63686 TATTTATTATTATTATT-ATTTTTT
1 TATTTATTATTATT-TTCATTTTTT
63710 AAAAAATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (24 bp):
TATTTATTATTATTTTCATTTTTT
Found at i:66643 original size:2 final size:2
Alignment explanation
Indices: 66638--66670 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66628 TTTAACATTT
66638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66671 TTTATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66860 original size:2 final size:2
Alignment explanation
Indices: 66855--66890 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
66845 TATTTTTTAT
*
66855 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66891 CACGTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:70966 original size:21 final size:21
Alignment explanation
Indices: 70920--70976 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
70910 ACTTTGATGA
*
70920 AGAAGATAAAGCTAAAAAGAT
1 AGAAGATAAAGATAAAAAGAT
* *
70941 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAAGA-T
*
70962 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
70977 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAGAT
Found at i:78050 original size:23 final size:23
Alignment explanation
Indices: 78020--78065 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
78010 CAAGGCTCAT
78020 GCACATGCTTGAGATGGTTGAGG
1 GCACATGCTTGAGATGGTTGAGG
78043 GCACATGCTTGAGATGGTTGAGG
1 GCACATGCTTGAGATGGTTGAGG
78066 AGCATCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.26
Consensus pattern (23 bp):
GCACATGCTTGAGATGGTTGAGG
Found at i:78465 original size:105 final size:105
Alignment explanation
Indices: 78283--78951 Score: 1081
Period size: 105 Copynumber: 6.4 Consensus size: 105
78273 AGGTTTTACC
78283 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
78348 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
78388 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
78453 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
78493 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
78558 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
78598 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACTTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
78663 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
78703 CAGAGCCAATTCCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
78768 ACGAAGGGACCGCTGGTTGTCAACAATA-ATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAA-ACATTTCTCAATTT
* * ***
78808 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* ** ** * *
78873 ACGAAGGGGCCGCTGACTGTCAACCGACGATTTC-CCAGTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
78913 CTAGAACCAATTTCAACTTCACAGCGGAGGATATTGGAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
78952 GCGGAACAAT
Statistics
Matches: 532, Mismatches: 28, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
104 1 0.00
105 492 0.92
106 39 0.07
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:80726 original size:2 final size:2
Alignment explanation
Indices: 80721--80754 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
80711 TATTTTTTAT
*
80721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80755 CACGTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:83583 original size:20 final size:20
Alignment explanation
Indices: 83517--83582 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
83507 CAAAAAGGGC
*
83517 AAAAAGAAAAAAAAGAAGCAA
1 AAAAAGAAAAACAAGAA-CAA
*
83538 AAAAGGAAAAACAAGAACAA
1 AAAAAGAAAAACAAGAACAA
* *
83558 AAAAAGAAAGAACAAAAATAA
1 AAAAAGAAA-AACAAGAACAA
83579 AAAA
1 AAAA
83583 GGGAACAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.28
21 28 0.72
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAACAAGAACAA
Found at i:85101 original size:36 final size:36
Alignment explanation
Indices: 85061--85182 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
85051 ACTCATGATT
* * *
85061 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
* * * * *
85097 GTTT-TCACTAGAA-GAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAGATTTGTCTCCCTTGAGACA
* *
85132 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAGA-TTTGTCTCCCTTGAGACA
*
85168 GTTTCTCTTGAAACA
1 GTTTCTCTTAAAACA
85183 TAAACATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 27 0.40
36 41 0.60
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
Found at i:85245 original size:36 final size:36
Alignment explanation
Indices: 85198--85460 Score: 272
Period size: 36 Copynumber: 7.4 Consensus size: 36
85188 ATTGAAAACA
* *
85198 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
85234 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
85271 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
85307 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * *
85336 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
85372 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
85409 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAA
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
85445 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
85461 ATCTTTGAAT
Statistics
Matches: 189, Mismatches: 27, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 2 0.01
35 1 0.01
36 99 0.52
37 66 0.35
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:85346 original size:102 final size:102
Alignment explanation
Indices: 85240--85424 Score: 291
Period size: 102 Copynumber: 1.8 Consensus size: 102
85230 ATAGTTTCCC
* *
85240 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGA
1 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGA
85304 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
** * *
85342 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
*
85407 AGTTTCTCTTGAAACAAA
66 AGTTTCCCTTGAAACAAA
85425 TTTCGTCTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
101 27 0.36
102 48 0.64
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (102 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
Found at i:85366 original size:138 final size:138
Alignment explanation
Indices: 85113--85523 Score: 563
Period size: 138 Copynumber: 3.0 Consensus size: 138
85103 ACTAGAAGAG
* *
85113 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * * *
85178 AAACATAAACA-TTGAAAACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTT
66 AAACA-AAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTT
85242 GAAACAAAA
130 GAAACAAAA
*
85251 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
85316 AAACAAAATATTTGAATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
66 AAACAAAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTG
* * *
85381 GAACTAAG
131 AAACAAAA
* * * *
85389 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAATTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
85454 AAACAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTG
66 AAACAAAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTG
85519 AAACA
131 AAACA
85524 CAAAATCTTC
Statistics
Matches: 238, Mismatches: 34, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
137 4 0.02
138 234 0.98
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (138 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTG
AAACAAAA
Found at i:85522 original size:65 final size:65
Alignment explanation
Indices: 85418--85592 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
85408 GTTTCTCTTG
* ** * **
85418 AAACAAATTTCGTCTATCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
*
85483 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
85548 TA
64 TA
* ** *
85550 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAA
85593 CAGATATCTT
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
65 32 0.33
66 6 0.06
67 31 0.32
68 27 0.28
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:86416 original size:105 final size:105
Alignment explanation
Indices: 86196--86960 Score: 1069
Period size: 105 Copynumber: 7.3 Consensus size: 105
86186 GCCATCTGCG
* * * * * *
86196 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
86261 TGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
86305 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
86370 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
86410 ATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
86474 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
86514 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
86579 ACTGCTACTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
86619 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
86684 ACCGCTGCTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
86724 ATTTCAAATTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
86789 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
86824 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
86889 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
86930 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
86961 TGGAACAATG
Statistics
Matches: 597, Mismatches: 50, Indels: 21
0.89 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 78 0.13
101 3 0.01
102 3 0.01
103 4 0.01
104 103 0.17
105 300 0.50
106 78 0.13
107 5 0.01
109 21 0.04
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:87532 original size:33 final size:35
Alignment explanation
Indices: 87495--87595 Score: 161
Period size: 37 Copynumber: 2.9 Consensus size: 35
87485 TTTCGTCCTA
87495 TTAGGATTCAAACTCCT-AAAATAGGATAGAA-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
87528 TTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
87563 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
87596 GTTATACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 17 0.27
34 13 0.21
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (35 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:88026 original size:18 final size:17
Alignment explanation
Indices: 87987--88029 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
87977 ATTATATGGA
87987 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
88003 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
88021 TATTATTAT
1 TATTATTAT
88030 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:88040 original size:2 final size:2
Alignment explanation
Indices: 88027--88126 Score: 68
Period size: 2 Copynumber: 51.5 Consensus size: 2
88017 TTATTATTAT
* * *
88027 TA TA TG TA TA TA TA TA TA TA TA TA TA TA T- TA AA T- TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
88066 TCA TT TA T- TT TT TA CTA TA T- TT TA CTA T- TA TA TA TA TA TA
1 T-A TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA
88106 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
88127 TCTTTAATAT
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
1 6 0.08
2 69 0.86
3 5 0.06
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (2 bp):
TA
Found at i:92088 original size:2 final size:2
Alignment explanation
Indices: 92083--92118 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
92073 ATGACAGTAT
92083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92119 ATTTCTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:103819 original size:14 final size:14
Alignment explanation
Indices: 103800--103828 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
103790 TAGCACTTCT
103800 ACCTATTCTTCAGA
1 ACCTATTCTTCAGA
103814 ACCTATTCTTCAGA
1 ACCTATTCTTCAGA
103828 A
1 A
103829 GGCTTATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (14 bp):
ACCTATTCTTCAGA
Found at i:104406 original size:90 final size:90
Alignment explanation
Indices: 104245--104513 Score: 407
Period size: 90 Copynumber: 3.0 Consensus size: 90
104235 ATATTCGTCG
* * * *
104245 GCACCTGGTTGCTTGAGGATTTCTTGTACCATTGTGCAGCAGAAACTGGAGGAAAATCAGAAGAG
1 GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGCAGCAGAAACTGGAGGAAAATCAGAAGCG
* *
104310 AGTGGTTCA-AGGTATCCATTCATCA
66 AATGGTTCAGA-GTATCCACTCATCA
*
104335 GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGCAGCCGAAACTGGAGGAAAATCAGAAGCG
1 GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGCAGCAGAAACTGGAGGAAAATCAGAAGCG
* *
104400 AATGGTTCTGAGTATCCACTCGTCA
66 AATGGTTCAGAGTATCCACTCATCA
104425 GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGCAGCAGAAACTGGAGGAAAATCAGAAGCG
1 GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGCAGCAGAAACTGGAGGAAAATCAGAAGCG
* **
104490 GATGGTTTTGAGTATCCAC-CATCA
66 AATGGTTCAGAGTATCCACTCATCA
104514 TGGAGATTTG
Statistics
Matches: 165, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
89 4 0.02
90 160 0.97
91 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (90 bp):
GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGCAGCAGAAACTGGAGGAAAATCAGAAGCG
AATGGTTCAGAGTATCCACTCATCA
Found at i:107417 original size:234 final size:234
Alignment explanation
Indices: 107008--107480 Score: 937
Period size: 234 Copynumber: 2.0 Consensus size: 234
106998 ATGACGAAAC
107008 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
1 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
107073 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
66 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
107138 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
131 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
107203 ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
196 ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
107242 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
1 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
107307 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
66 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
107372 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
131 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
*
107437 ACATGCTAAAGACTGTAGCCAGTGATGTTTGTAGAATGA
196 ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
107476 AGTTG
1 AGTTG
107481 ACTGTTTATG
Statistics
Matches: 238, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 238 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (234 bp):
AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
Found at i:121643 original size:12 final size:13
Alignment explanation
Indices: 121620--121644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
121610 ATATTATTTA
121620 AACTTAAAAAAAC
1 AACTTAAAAAAAC
121633 AACTTAAAAAAA
1 AACTTAAAAAAA
121645 TAAAAAAGTA
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:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AACTTAAAAAAAC
Found at i:125666 original size:3 final size:3
Alignment explanation
Indices: 125658--125695 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
125648 TTAGTTCCCT
125658 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
125696 TATTCCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:135515 original size:35 final size:36
Alignment explanation
Indices: 135476--135543 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
135466 TTTTTATATT
*
135476 TTTAATTTTGTAAA-AAATTATATAAATATTTTGAA
1 TTTAATTTTGTAAAGAAAATATATAAATATTTTGAA
*
135511 TTTAATTTTTTAAAGAAAATATATAAATATTTT
1 TTTAATTTTGTAAAGAAAATATATAAATATTTT
135544 ACAATTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (36 bp):
TTTAATTTTGTAAAGAAAATATATAAATATTTTGAA
Found at i:139828 original size:19 final size:18
Alignment explanation
Indices: 139796--139834 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
139786 AAGAAAGTAA
*
139796 AAAAAAAACAAAAATCAT
1 AAAAAAAACAAAAATAAT
*
139814 AAAAATAACAAAAAATAAT
1 AAAAAAAAC-AAAAATAAT
139833 AA
1 AA
139835 TATGTAACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAAAAACAAAAATAAT
Found at i:140879 original size:25 final size:24
Alignment explanation
Indices: 140851--140902 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
140841 CAATTTTTTC
140851 AAATAAAAGTCATAATTATTTTT-AA
1 AAATAAAA-T-ATAATTATTTTTCAA
* *
140876 AAATAATATTTAATTATTTTTCAA
1 AAATAAAATATAATTATTTTTCAA
140900 AAA
1 AAA
140903 AATGTTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.46
24 6 0.25
25 7 0.29
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
AAATAAAATATAATTATTTTTCAA
Found at i:141116 original size:20 final size:19
Alignment explanation
Indices: 141068--141118 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
141058 AAATGACCAA
* *
141068 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCAAACT
141087 CAAATTCGCAACGCAAACT
1 CAAATTCGCAACGCAAACT
*
141106 CCAATTTCGCAAC
1 -CAAATTCGCAAC
141119 ACAGGTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (19 bp):
CAAATTCGCAACGCAAACT
Found at i:141191 original size:20 final size:20
Alignment explanation
Indices: 141148--141219 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
141138 TACGATTTTC
* *
141148 TAAATTCGCAACAAGAATAGG
1 TAAA-TCGCAACGAGAATATG
* *
141169 TAAATCGTAACGATAATATG
1 TAAATCGCAACGAGAATATG
* *
141189 TAAATCGCAACGGGAATATA
1 TAAATCGCAACGAGAATATG
141209 TAAATCGCAAC
1 TAAATCGCAAC
141220 ACATAAGTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 39 0.91
21 4 0.09
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGAGAATATG
Found at i:141421 original size:20 final size:20
Alignment explanation
Indices: 141398--141435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
141388 TGGAGAATCG
*
141398 CGTTGCGATTTACATATTAT
1 CGTTGCAATTTACATATTAT
*
141418 CGTTGCAATTTACCTATT
1 CGTTGCAATTTACATATT
141436 CGCAATACTA
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:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (20 bp):
CGTTGCAATTTACATATTAT
Found at i:141539 original size:104 final size:104
Alignment explanation
Indices: 141330--141542 Score: 293
Period size: 104 Copynumber: 2.0 Consensus size: 104
141320 GAATTTCATT
* * * *
141330 TTCGCAACATTAATTACCTATATCGATAATTAGCGTTGCGAAATTTGAGTTGCGAATTTGGAGAA
1 TTCGCAACACTAATTACCTATATCGATAATTAACGTTGCAAAATTCGAGTTGCGAATTTGGAGAA
* *
141395 TCGCGTTGCGATTTACATATTATCGTTGCAATTTACCTA
66 TCGCGTTGCGAATTACATATTATCGTTGCAATTTAACTA
* * * *
141434 TTCGCAATACTAATTACCTATATCGGTAATTAACGTTGTAAAATTCGAGTTGTGAATTTGGAGAA
1 TTCGCAACACTAATTACCTATATCGATAATTAACGTTGCAAAATTCGAGTTGCGAATTTGGAGAA
* * *
141499 TTTGCGTTGTGAATTACATATTATCGTTGCGA-TTAACTA
66 -TCGCGTTGCGAATTACATATTATCGTTGCAATTTAACTA
141538 TTCGC
1 TTCGC
141543 GTTGCGAATT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 68 0.72
105 27 0.28
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (104 bp):
TTCGCAACACTAATTACCTATATCGATAATTAACGTTGCAAAATTCGAGTTGCGAATTTGGAGAA
TCGCGTTGCGAATTACATATTATCGTTGCAATTTAACTA
Found at i:141704 original size:186 final size:187
Alignment explanation
Indices: 141434--141794 Score: 553
Period size: 186 Copynumber: 1.9 Consensus size: 187
141424 AATTTACCTA
* * * **
141434 TTCGCAATACTAATTACCTATATCGGTAATTAACGTTGTAAAATTCGAGTTGTGAATTTGGAGAA
1 TTCGCAACACTAATTACCTATATCGGGAATTAACGTTGCAAAATTCGAGTTGCAAATTTGGAGAA
* * *
141499 TTTGCGTTGTGAATTACATATTATCGTTGCGA-TTAACTATTCGCGTTGCGAATTTGGAAAATCG
66 TTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACTATTCGCGTTGCGAATTTAGAAAATCG
*
141563 CAACGCGAATTTCGTTTTCGCAACGCGATTCTCCAAAATCGCAACATGAATTTCATT
131 CAACGCGAATTTCGTTTTCGCAACGCAATTCTCCAAAATCGCAACATGAATTTCATT
* ** *
141620 TTCGCAACGCTAATTACCTATATCGGGAATTCGCGTTGCGAAATTCGAGTTGCAAATTTGGAGAA
1 TTCGCAACACTAATTACCTATATCGGGAATTAACGTTGCAAAATTCGAGTTGCAAATTTGGAGAA
* * *
141685 TTCGCGTTGCGATTTACATATTATCGTTGTGATTTACCTATTCGCGTTGCGAATTTAGAAAATCG
66 TTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACTATTCGCGTTGCGAATTTAGAAAATCG
* *
141750 CAACGCGAATTTCGTTTTCGCAATGCAATTCTCCAAATTCGCAAC
131 CAACGCGAATTTCGTTTTCGCAACGCAATTCTCCAAAATCGCAAC
141795 TCGGCTTTCG
Statistics
Matches: 156, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
186 84 0.54
187 72 0.46
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (187 bp):
TTCGCAACACTAATTACCTATATCGGGAATTAACGTTGCAAAATTCGAGTTGCAAATTTGGAGAA
TTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACTATTCGCGTTGCGAATTTAGAAAATCG
CAACGCGAATTTCGTTTTCGCAACGCAATTCTCCAAAATCGCAACATGAATTTCATT
Found at i:141718 original size:20 final size:20
Alignment explanation
Indices: 141689--141741 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
141679 GGAGAATTCG
141689 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* * **
141709 CGTTGTGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
141729 CGTTGCGAATTTA
1 CGTTGCG-ATTTA
141742 GAAAATCGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:142008 original size:20 final size:20
Alignment explanation
Indices: 141983--142044 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
141973 GCATTGTGAT
141983 TTACATATTATCGTTGCGAA
1 TTACATATTATCGTTGCGAA
*
142003 TTACATATTATCGTTGCGAT
1 TTACATATTATCGTTGCGAA
**
142023 TTA-ACTATTCGCGTTGCGAA
1 TTACA-TATTATCGTTGCGAA
142043 TT
1 TT
142045 TGATTTTCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TTACATATTATCGTTGCGAA
Found at i:149147 original size:20 final size:20
Alignment explanation
Indices: 149122--149172 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
149112 CACGTTAAGG
149122 GATGCATCGATACACGGTAA
1 GATGCATCGATACACGGTAA
149142 GATGCATCGATACACGGTAA
1 GATGCATCGATACACGGTAA
149162 GATGCATCGAT
1 GATGCATCGAT
149173 GCACTTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (20 bp):
GATGCATCGATACACGGTAA
Found at i:150225 original size:5 final size:5
Alignment explanation
Indices: 150215--150247 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
150205 GTGTGATAGC
150215 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
150248 TTCATGCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
ATGAT
Found at i:170689 original size:20 final size:20
Alignment explanation
Indices: 170651--170690 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
170641 GGATGTAACC
*
170651 GAACATAAACGAACGTAAAT
1 GAACATAAACGAACATAAAT
* *
170671 GAACGTAAACGTACATAAAT
1 GAACATAAACGAACATAAAT
170691 AAAAATATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (20 bp):
GAACATAAACGAACATAAAT
Found at i:174441 original size:29 final size:29
Alignment explanation
Indices: 174395--174451 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
174385 AGTGTTGGCC
*
174395 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCACCATGCACTCCGGGCGACCTT
* *
174424 GTAGGTCATCATGTACTCCGGGCGACCT
1 GTAGGTCACCATGCACTCCGGGCGACCT
174452 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.23
Consensus pattern (29 bp):
GTAGGTCACCATGCACTCCGGGCGACCTT
Found at i:174589 original size:33 final size:33
Alignment explanation
Indices: 174552--174636 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
174542 GCGACCTACC
*
174552 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATCCCCTCGCATAG
174585 CTCGCTCGGTTGCCCTCGGATCCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATCCCCTCGCATAG
* * *
174618 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
174637 TCGGATGACC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.08, C:0.40, G:0.26, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATCCCCTCGCATAG
Found at i:174662 original size:20 final size:20
Alignment explanation
Indices: 174637--174690 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
174627 ATGGCCTCGG
*
174637 TCGGATGACCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
* *
174657 TCGGATGGCGTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
174677 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
174691 TCGGATGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:174696 original size:14 final size:14
Alignment explanation
Indices: 174677--174704 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
174667 TCGGATGCTT
174677 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
174691 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
174705 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:177335 original size:18 final size:19
Alignment explanation
Indices: 177294--177335 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
177284 TAGTCTTAAA
177294 ATTTTATATTTTAACATTT
1 ATTTTATATTTTAACATTT
*
177313 TTTTTA-ATTTTAATC-TTT
1 ATTTTATATTTTAA-CATTT
177331 ATTTT
1 ATTTT
177336 TCTCATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTATATTTTAACATTT
Found at i:177717 original size:20 final size:19
Alignment explanation
Indices: 177692--177730 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
177682 CTAAATGACC
177692 TAAATTCAATTTTTTAATAA
1 TAAATT-AATTTTTTAATAA
* *
177712 TAAATTATTTTTTTTATAA
1 TAAATTAATTTTTTAATAA
177731 CTGAATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAATTAATTTTTTAATAA
Done.