Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011193.1 Kokia drynarioides strain JFW-HI SEQ_126169, 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: 172438
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1182 original size:12 final size:13
Alignment explanation
Indices: 1165--1193 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1155 AAATGGCATA
1165 AAAATAAAT-AAC
1 AAAATAAATAAAC
1177 AAAATAAATAAAC
1 AAAATAAATAAAC
1190 AAAA
1 AAAA
1194 ACAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAATAAATAAAC
Found at i:1211 original size:56 final size:55
Alignment explanation
Indices: 1107--1213 Score: 126
Period size: 56 Copynumber: 1.9 Consensus size: 55
1097 AAACAAAACA
* * * * * * *
1107 ATAACAATAAATGCAAATTAAATAAAAAGAATAAAAGAGATAACAATAAAATGGC
1 ATAAAAATAAATACAAAATAAATAAAAAAAACAAAAGAAATAAAAATAAAATGGC
1162 ATAAAAATAAATAACAAAATAAATAAACAAAAACAAAA-AAATAAAAATAAAA
1 ATAAAAATAAAT-ACAAAATAAATAAA-AAAAACAAAAGAAATAAAAATAAAA
1214 ATTAAATGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
55 11 0.26
56 24 0.56
57 8 0.19
ACGTcount: A:0.72, C:0.07, G:0.06, T:0.16
Consensus pattern (55 bp):
ATAAAAATAAATACAAAATAAATAAAAAAAACAAAAGAAATAAAAATAAAATGGC
Found at i:1305 original size:12 final size:12
Alignment explanation
Indices: 1267--1424 Score: 84
Period size: 12 Copynumber: 12.8 Consensus size: 12
1257 AAGTATGAAA
1267 AATAAATGACAAAT
1 AATAAAT-A-AAAT
1281 AAATAAATAAAAT
1 -AATAAATAAAAT
1294 AATAAACT-AAAT
1 AATAAA-TAAAAT
*
1306 ACAAAAATAAACA-
1 A-ATAAATAAA-AT
* *
1319 ACTAAACAATAAT
1 AATAAATAA-AAT
1332 AAT-AATAATAAT
1 AATAAATAA-AAT
*
1344 AA-CAATAATAAT
1 AATAAATAA-AAT
1356 AAT-AATAATAAT
1 AATAAATAA-AAT
1368 AAT-AATAATAAT
1 AATAAATAA-AAT
1380 AAT-AATAATAAT
1 AATAAATAA-AAT
1392 AAT-AATAATAAT
1 AATAAATAA-AAT
1404 AAT-AATAATAAT
1 AATAAATAA-AAT
1416 AAT-AATAAA
1 AATAAATAAA
1425 CGAATTCCAA
Statistics
Matches: 129, Mismatches: 6, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
11 1 0.01
12 104 0.81
13 15 0.12
14 2 0.02
15 7 0.05
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:1312 original size:20 final size:18
Alignment explanation
Indices: 1289--1336 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1279 ATAAATAAAT
1289 AAAATAATAAACTAAATACA
1 AAAATAATAAACT-AA-ACA
1309 AAAATAA-ACAACTAAACA
1 AAAATAATA-AACTAAACA
*
1327 ATAATAATAA
1 AAAATAATAA
1337 TAATAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 10 0.40
19 4 0.16
20 11 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATAATAAACTAAACA
Found at i:1334 original size:3 final size:3
Alignment explanation
Indices: 1326--1423 Score: 187
Period size: 3 Copynumber: 32.7 Consensus size: 3
1316 ACAACTAAAC
*
1326 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1374 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1422 AA
1 AA
1424 ACGAATTCCA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1641 original size:27 final size:24
Alignment explanation
Indices: 1603--1657 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1593 ACTTTGACTT
*
1603 TTCTTTAAATGTATGTCTCAAAAAAAA
1 TTCTTTAAATGT-TGTAT--AAAAAAA
*
1630 TTCTTTGAATGTTGTATAAAAAAA
1 TTCTTTAAATGTTGTATAAAAAAA
1654 TTCT
1 TTCT
1658 AAATCTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 11 0.42
26 4 0.15
27 11 0.42
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (24 bp):
TTCTTTAAATGTTGTATAAAAAAA
Found at i:5224 original size:49 final size:49
Alignment explanation
Indices: 5152--5278 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 49
5142 GTGGTATGAA
* * *
5152 ACTTGAACCCGTGATCGCATAACCATCGTCAACTGAGG-G-CCTGAGTTAT
1 ACTTGAACCCGTGATCGCATAACCACCATCAACTG-GGAGCCCT-AATTAT
* *
5201 ACTTGAACCTGTGATTGCATAACCACCATCAACTGGGAGCCCTAATTAT
1 ACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCTAATTAT
* * *
5250 ACTTGAACACGCGATCGTATAACCACCAT
1 ACTTGAACCCGTGATCGCATAACCACCAT
5279 GAATTAAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
48 2 0.03
49 61 0.92
50 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (49 bp):
ACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCTAATTAT
Found at i:8999 original size:89 final size:89
Alignment explanation
Indices: 8883--9097 Score: 258
Period size: 89 Copynumber: 2.4 Consensus size: 89
8873 TTTAATGGTG
* *
8883 TAAAAA-ACCC-TCAAATGTTTTCAAAAAAAGTAATTAAGTATCTACTTTTATTTTGCACTTATT
1 TAAAAAGACCCTTAAAAT-TTTTC-AAAAAAGTAATTAAGTATCTACTTTTATTTTGCACTTAAT
8946 TAGATAATTGAACTTTCAAAATGC-A
64 TAGATAATTGAACTTTCAAAATGCAA
* * * *
8971 TCAAAAATACCCTTAAAATTTTTCAAAAAAGCT-ATTAAGTCTCTGCTTTTATTTTGCGCTTAAT
1 T-AAAAAGACCCTTAAAATTTTTCAAAAAAG-TAATTAAGTATCTACTTTTATTTTGCACTTAAT
*
9035 TAGATACTTGAACTTTCAAAATGCAA
64 TAGATAATTGAACTTTCAAAATGCAA
* * ** *
9061 TAAAAAGACCTTTAAACTTTTTTTAAAAAGCAATTAA
1 TAAAAAGACCCTTAAAATTTTTCAAAAAAGTAATTAA
9098 ATACTTGATT
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
88 1 0.01
89 91 0.83
90 12 0.11
91 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (89 bp):
TAAAAAGACCCTTAAAATTTTTCAAAAAAGTAATTAAGTATCTACTTTTATTTTGCACTTAATTA
GATAATTGAACTTTCAAAATGCAA
Found at i:9252 original size:29 final size:27
Alignment explanation
Indices: 9220--9280 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
9210 TTTTTGAGGT
9220 ATTTTATAATTTTTTATATTTTTATTA-AA
1 ATTTTATAA-TTTTTAT-TTTTT-TTATAA
*
9249 ATTTAATAATTTTTATTTTTTTTATAA
1 ATTTTATAATTTTTATTTTTTTTATAA
9276 ATTTT
1 ATTTT
9281 TACCACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 11 0.38
28 7 0.24
29 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTATAATTTTTATTTTTTTTATAA
Found at i:9282 original size:29 final size:30
Alignment explanation
Indices: 9220--9280 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
9210 TTTTTGAGGT
9220 ATTTT-ATAATTTTTTATATTTTTATTAAA
1 ATTTTAATAATTTTTTATATTTTTATTAAA
9249 A-TTTAATAA-TTTTTAT-TTTTT-TTATAA
1 ATTTTAATAATTTTTTATATTTTTATTA-AA
9276 ATTTT
1 ATTTT
9281 TACCACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 3 0.10
27 8 0.28
28 13 0.45
29 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
ATTTTAATAATTTTTTATATTTTTATTAAA
Found at i:12457 original size:18 final size:18
Alignment explanation
Indices: 12391--12528 Score: 150
Period size: 18 Copynumber: 7.6 Consensus size: 18
12381 TGTCTCATTA
*
12391 GAGCATACTGTCTCGTTT
1 GAGCATACTGGCTCGTTT
* * *** *
12409 AAGCCTACAAACTCGTTA
1 GAGCATACTGGCTCGTTT
*
12427 GAGCATACAGGCTCGTTT
1 GAGCATACTGGCTCGTTT
12445 GAGCATACTGGCTCGTTT
1 GAGCATACTGGCTCGTTT
*
12463 GAGCATATTGGCTCGTTT
1 GAGCATACTGGCTCGTTT
* *
12481 GAGCATACTAGCTCGATT
1 GAGCATACTGGCTCGTTT
**
12499 GAGCATACTGGCTCGTAA
1 GAGCATACTGGCTCGTTT
12517 GAGCACTACTGG
1 GAGCA-TACTGG
12529 ATTGCAAATA
Statistics
Matches: 99, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
18 93 0.94
19 6 0.06
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (18 bp):
GAGCATACTGGCTCGTTT
Found at i:12588 original size:7 final size:7
Alignment explanation
Indices: 12578--12609 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12568 ATTGAATATT
12578 GAAGACG
1 GAAGACG
12585 GAAGACG
1 GAAGACG
12592 GAAGACG
1 GAAGACG
12599 GAAGACG
1 GAAGACG
12606 GAAG
1 GAAG
12610 GGATGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.44, T:0.00
Consensus pattern (7 bp):
GAAGACG
Found at i:14579 original size:20 final size:21
Alignment explanation
Indices: 14537--14580 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
14527 TTAACCTTTG
*
14537 ACCCAAACCCTTTTAAACTAA
1 ACCCAAACCCTTTTAAACCAA
* *
14558 ACCCAAA-CCTTTTGACCCAA
1 ACCCAAACCCTTTTAAACCAA
14578 ACC
1 ACC
14581 AACTGAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.39, C:0.39, G:0.02, T:0.20
Consensus pattern (21 bp):
ACCCAAACCCTTTTAAACCAA
Found at i:22187 original size:19 final size:19
Alignment explanation
Indices: 22165--22201 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22155 TTTTTAGTTT
22165 ATATAAGTTTTAAAATTTA
1 ATATAAGTTTTAAAATTTA
**
22184 ATATATTTTTTAAAATTT
1 ATATAAGTTTTAAAATTT
22202 TAGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATATAAGTTTTAAAATTTA
Found at i:22210 original size:19 final size:19
Alignment explanation
Indices: 22172--22213 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
22162 TTTATATAAG
* *
22172 TTTTAAAATTTAATATATT
1 TTTTAAAATTTAAGAAATT
*
22191 TTTTAAAATTTTAGAAATT
1 TTTTAAAATTTAAGAAATT
22210 TTTT
1 TTTT
22214 TAGTTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTAAAATTTAAGAAATT
Found at i:22212 original size:20 final size:19
Alignment explanation
Indices: 22172--22215 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
22162 TTTATATAAG
*
22172 TTTTAAAATTTAATATATT
1 TTTTAAAATTTAAAATATT
22191 TTTTAAAATTTTAGAAAT-TT
1 TTTTAAAA-TTTA-AAATATT
22211 TTTTA
1 TTTTA
22216 GTTTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 11 0.50
21 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTTAAAATATT
Found at i:22230 original size:19 final size:19
Alignment explanation
Indices: 22162--22235 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 19
22152 ATTTTTTTAG
*
22162 TTTATATAAG-TTTTAAAA
1 TTTATATAAGTTTTTTAAA
22180 TTTA-ATATA-TTTTTTAAAA
1 TTTATATA-AGTTTTTT-AAA
* * * *
22199 TTT-TAGAAATTTTTTTAG
1 TTTATATAAGTTTTTTAAA
22217 TTTATATAAG-TTTTTAAA
1 TTTATATAAGTTTTTTAAA
22235 T
1 T
22236 AATTATTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
17 3 0.07
18 21 0.50
19 18 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTATATAAGTTTTTTAAA
Found at i:24184 original size:41 final size:41
Alignment explanation
Indices: 24125--24343 Score: 285
Period size: 41 Copynumber: 5.3 Consensus size: 41
24115 CGTTTTTCAA
* * ** *
24125 ATAAGCGCCACTAATGCTCTGATGTTTAGCGGCACTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
* * * *
24166 ATAAGCACCGTTGTTGCTCTGACCTTTAGCGGCGGTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
* *
24207 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTGCTC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC-TTGCCC
* *
24249 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGACT
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
* **
24290 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
24331 ATAAGCGCCGCTA
1 ATAAGCGCCGCTA
24344 AATAAGTACC
Statistics
Matches: 153, Mismatches: 24, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
41 114 0.75
42 39 0.25
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (41 bp):
ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
Found at i:24269 original size:83 final size:82
Alignment explanation
Indices: 24125--24343 Score: 296
Period size: 83 Copynumber: 2.7 Consensus size: 82
24115 CGTTTTTCAA
* * * ** * * * *
24125 ATAAGCGCCACTAATGCTCTGATGTTTAGCGGCAC-TTGCCCATAAGCACCGTTGTTGCTCTGAC
1 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTG-CCATAAGCGCCGCTATTGCTCTGAC
* *
24189 CTTTAGCGGCGGTTGCCC
65 CTTTAGCGGCGCTTGACC
24207 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTGCTCATAAGCGCCGCTATTGCTCTGAC
1 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTGC-CATAAGCGCCGCTATTGCTCTGAC
*
24272 CTTTAGCGGCGCTTGACT
65 CTTTAGCGGCGCTTGACC
*
24290 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAGCGCCGCTA
1 ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTGCCATAAGCGCCGCTA
24344 AATAAGTACC
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
82 44 0.36
83 78 0.64
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (82 bp):
ATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTGCCATAAGCGCCGCTATTGCTCTGACC
TTTAGCGGCGCTTGACC
Found at i:24407 original size:42 final size:42
Alignment explanation
Indices: 24345--24501 Score: 196
Period size: 41 Copynumber: 3.8 Consensus size: 42
24335 GCGCCGCTAA
*
24345 ATAAGTACCGCTATTACTCTGACCTTTAGCGGCGCTTTGCTC
1 ATAAGCACCGCTATTACTCTGACCTTTAGCGGCGCTTTGCTC
* *
24387 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC-TTGACT-
1 ATAAGCACCGCTATTACTCTGACCTTTAGCGGCGCTTTG-CTC
* ** * *
24428 ATAAGTACCGCTATTGTTCTGACCTTTAGCGTCGCTTT-CCC
1 ATAAGCACCGCTATTACTCTGACCTTTAGCGGCGCTTTGCTC
*
24469 ATAAGCACCGCTATTACTCT-ACCTTTTGCGGCG
1 ATAAGCACCGCTATTACTCTGACCTTTAGCGGCG
24502 TTTATGTAGA
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 12 0.12
41 51 0.52
42 36 0.36
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.32
Consensus pattern (42 bp):
ATAAGCACCGCTATTACTCTGACCTTTAGCGGCGCTTTGCTC
Found at i:24422 original size:24 final size:24
Alignment explanation
Indices: 24353--24422 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
24343 AAATAAGTAC
*
24353 CGCTATTACTCTGACCTTTAGCGG
1 CGCTATTGCTCTGACCTTTAGCGG
* *
24377 CGCT-TTGCTC--A---TAAGCGC
1 CGCTATTGCTCTGACCTTTAGCGG
24395 CGCTATTGCTCTGACCTTTAGCGG
1 CGCTATTGCTCTGACCTTTAGCGG
24419 CGCT
1 CGCT
24423 TGACTATAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
18 9 0.26
19 6 0.17
21 2 0.06
23 5 0.14
24 13 0.37
ACGTcount: A:0.14, C:0.31, G:0.23, T:0.31
Consensus pattern (24 bp):
CGCTATTGCTCTGACCTTTAGCGG
Found at i:24432 original size:97 final size:96
Alignment explanation
Indices: 24256--24432 Score: 284
Period size: 97 Copynumber: 1.8 Consensus size: 96
24246 CTCATAAGCG
* *
24256 CCGCTATTGCTCTGACCTTTAGCGGCGCTTGACTATAAGCGTCGCTATTGCTCTGACCTTTAGCG
1 CCGCTATTACTCTGACCTTTAGCGGCGCTTGACTATAAGCGCCGCTATTGCTCTGACCTTTAGCG
**
24321 GCGCTTTTCCATAAGCGCCGCTAAATAAGTA
66 GCGCTTGACCATAAGCGCCGCTAAATAAGTA
24352 CCGCTATTACTCTGACCTTTAGCGGCGCTTTG-CTCATAAGCGCCGCTATTGCTCTGACCTTTAG
1 CCGCTATTACTCTGACCTTTAGCGGCGC-TTGACT-ATAAGCGCCGCTATTGCTCTGACCTTTAG
*
24416 CGGCGCTTGACTATAAG
64 CGGCGCTTGACCATAAG
24433 TACCGCTATT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
96 29 0.39
97 45 0.61
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.31
Consensus pattern (96 bp):
CCGCTATTACTCTGACCTTTAGCGGCGCTTGACTATAAGCGCCGCTATTGCTCTGACCTTTAGCG
GCGCTTGACCATAAGCGCCGCTAAATAAGTA
Found at i:24455 original size:138 final size:138
Alignment explanation
Indices: 24215--24481 Score: 462
Period size: 138 Copynumber: 1.9 Consensus size: 138
24205 CCATAAGCGT
*
24215 CGCTATTGCTCTGACCTTTAGCGGCGCTTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCG
1 CGCTATTACTCTGACCTTTAGCGGCGCTTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCG
** * *
24280 GCGCTTGACTATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAGCGCCGCTAA
66 GCGCTTGACTATAAGCACCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCTAA
24345 ATAAGTAC
131 ATAAGTAC
24353 CGCTATTACTCTGACCTTTAGCGGCGCTTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCG
1 CGCTATTACTCTGACCTTTAGCGGCGCTTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCG
* * *
24418 GCGCTTGACTATAAGTACCGCTATTGTTCTGACCTTTAGCGTCGCTTTCCCATAAGCACCGCTA
66 GCGCTTGACTATAAGCACCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCTA
24482 TTACTCTACC
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 121 1.00
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (138 bp):
CGCTATTACTCTGACCTTTAGCGGCGCTTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCG
GCGCTTGACTATAAGCACCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCACCGCTAA
ATAAGTAC
Found at i:30356 original size:14 final size:14
Alignment explanation
Indices: 30337--30367 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
30327 TATCCAAACA
30337 TTGATTGTGACATT
1 TTGATTGTGACATT
30351 TTGATTGTGACATT
1 TTGATTGTGACATT
30365 TTG
1 TTG
30368 TAACAGCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (14 bp):
TTGATTGTGACATT
Found at i:31100 original size:194 final size:194
Alignment explanation
Indices: 30771--31159 Score: 582
Period size: 194 Copynumber: 2.0 Consensus size: 194
30761 ATTCTTTTTG
* *
30771 CATTATGTTGGTCGTACTATAATTCATTTAAACTACTAATTAAATTTATTTACGTGTAGGTTAAT
1 CATTATGTTCGTCGTACTATAATTCATTTAAACTACTAATTAAATTTATTTACATGTAGGTTAAT
* *
30836 ATTAATTTAGAATTCATTTCTTTTGGGTATGATTTTCAGAGTACTTATCGACTCCGTACTATATT
66 ATTAATTTAGAATTCATTTCTTTTGGGTACGATTCTCAGAGTACTTATCGACTCCGTACTATATT
* * ** * *
30901 ACAATTTGATCTGTATATTTGCGTACACTACCTTTATTTCGTATTTTTAGTGACAATATTCACA
131 ACAATTTGACCTGTATATTTGCGGACACTACCTCAATTTCATATTTTTAGTAACAATATTCACA
* * * * *
30965 CATTATGTTCGTCTTACTATAATTTATTTAAACTATTAATTAGATTTATTTATATGTAGGTTAAT
1 CATTATGTTCGTCGTACTATAATTCATTTAAACTACTAATTAAATTTATTTACATGTAGGTTAAT
* * * * *
31030 ATTAATTTAGTATTCATATT-TTTTGGGTACGATTCTCGGAGTACTTGTCGACTTCGTACTGTAT
66 ATTAATTTAGAATTCAT-TTCTTTTGGGTACGATTCTCAGAGTACTTATCGACTCCGTACTATAT
31094 TACAATTTGACCTGTATATTTGCGGACACTACCTCAATTTCATATTTTTAGTAACAATATTCACA
130 TACAATTTGACCTGTATATTTGCGGACACTACCTCAATTTCATATTTTTAGTAACAATATTCACA
31159 C
1 C
31160 TCAGGTGATA
Statistics
Matches: 174, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
194 172 0.99
195 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (194 bp):
CATTATGTTCGTCGTACTATAATTCATTTAAACTACTAATTAAATTTATTTACATGTAGGTTAAT
ATTAATTTAGAATTCATTTCTTTTGGGTACGATTCTCAGAGTACTTATCGACTCCGTACTATATT
ACAATTTGACCTGTATATTTGCGGACACTACCTCAATTTCATATTTTTAGTAACAATATTCACA
Found at i:31435 original size:30 final size:31
Alignment explanation
Indices: 31399--31470 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
31389 ATCACATTTA
*
31399 ATAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ATAAAACAGTCACTAAACTTATCGAAAA-GTG
* *
31429 ATAAAACAATCACTAAAGTTATCGAAAAGTG
1 ATAAAACAGTCACTAAACTTATCGAAAAGTG
*
31460 ATAAAATAGTC
1 ATAAAACAGTC
31471 CTCTTGTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (31 bp):
ATAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:34487 original size:7 final size:7
Alignment explanation
Indices: 34475--34501 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34465 TTTAATTAAA
34475 TAAATTT
1 TAAATTT
34482 TAAATTT
1 TAAATTT
34489 TAAATTT
1 TAAATTT
34496 TAAATT
1 TAAATT
34502 AATTACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TAAATTT
Found at i:35449 original size:10 final size:10
Alignment explanation
Indices: 35414--35476 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
35404 AATATAAAAT
35414 TAAAAATTT-
1 TAAAAATTTA
*
35423 TAAAAAATTA
1 TAAAAATTTA
*
35433 AAAAAATTTA
1 TAAAAATTTA
*
35443 TAAAAATGTA
1 TAAAAATTTA
*
35453 T-ACAATTTA
1 TAAAAATTTA
*
35462 -AAATATGTTA
1 TAAAAAT-TTA
35472 TAAAA
1 TAAAA
35477 TAATAATAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
9 17 0.43
10 20 0.50
11 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:35777 original size:15 final size:15
Alignment explanation
Indices: 35743--35776 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35733 ATGCCTAATT
*
35743 AAAAACCTTACTAGG
1 AAAAACCCTACTAGG
35758 AAAAACCCTA-TAGG
1 AAAAACCCTACTAGG
35772 AAAAA
1 AAAAA
35777 AACCTAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.15
Consensus pattern (15 bp):
AAAAACCCTACTAGG
Found at i:38030 original size:17 final size:17
Alignment explanation
Indices: 38008--38041 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
37998 CAATAGACAA
38008 CTTAAAATTATCCCAAC
1 CTTAAAATTATCCCAAC
38025 CTTAAAATTATCCCAAC
1 CTTAAAATTATCCCAAC
38042 TAAAACTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (17 bp):
CTTAAAATTATCCCAAC
Found at i:48596 original size:30 final size:30
Alignment explanation
Indices: 48562--48831 Score: 243
Period size: 30 Copynumber: 9.0 Consensus size: 30
48552 ATTAAAATAT
*
48562 GGTCAAACTTGAATTTTTGGAAAGTTCAAG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * *
48592 GGTCAAATTTGAATGTTTAGAAAGTTAAAG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * ** *
48622 GGTCAAATTGGATTTTTTGGAAAGTTTTAT
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * ** * *
48652 GGTTAAATTTAAAAATTTGGAAAGTTTAGG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * *
48682 GGTTAAATTTGAATTCTTGGAAAGTTCGAG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * *
48712 GCTCAAATTTAAATTTTTGGAAAGTTCGAGG
1 GGTCAAATTTGAATTTTTGGAAAGTTC-AAG
* * *
48743 GGTCAAATTTGAATTTTTGGAAAATTCGAT
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * * ***
48773 GGTAAAATTTGGATTTTTGGAAAATTTGGG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* *
48803 GGTAAAATTTGGATTTTTGGAAAGTTCAA
1 GGTCAAATTTGAATTTTTGGAAAGTTCAA
48832 AGGCAAAACA
Statistics
Matches: 191, Mismatches: 48, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
30 166 0.87
31 25 0.13
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (30 bp):
GGTCAAATTTGAATTTTTGGAAAGTTCAAG
Found at i:49487 original size:13 final size:13
Alignment explanation
Indices: 49469--49498 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49459 TTTTTCATAT
49469 ATTTCCTTTGAAA
1 ATTTCCTTTGAAA
*
49482 ATTTCCTTTGTAA
1 ATTTCCTTTGAAA
49495 ATTT
1 ATTT
49499 TTTTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (13 bp):
ATTTCCTTTGAAA
Found at i:50755 original size:50 final size:50
Alignment explanation
Indices: 50711--50914 Score: 282
Period size: 50 Copynumber: 4.1 Consensus size: 50
50701 AGCTTCAAAA
* * * *
50711 GTATAAGATTTTCCCTTGCAGCTTCAATCTGCCCCTCTACAGCTTTAGGT
1 GTATGAGATTTGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGT
* * * *
50761 GAATGAGATTTGCCATTGCGGCTTCAATATACCCCTCTACAGCGTTAGGT
1 GTATGAGATTTGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGT
*
50811 GTATGAGATTTGCCATTGCGGCTTCAATCTGCCCCTCTACAACTTTAGGT
1 GTATGAGATTTGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGT
* * ** *
50861 GTATGAGATTTTCCATTGCGGCTTCAATCCGTTCCTCTACAGCTTTAGGG
1 GTATGAGATTTGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGT
50911 GTAT
1 GTAT
50915 ATGATTCGTC
Statistics
Matches: 135, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 135 1.00
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (50 bp):
GTATGAGATTTGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGT
Found at i:50964 original size:21 final size:21
Alignment explanation
Indices: 50915--50958 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
50905 TTAGGGGTAT
*
50915 ATGATTCGTCATTCTATCGCC
1 ATGATTTGTCATTCTATCGCC
50936 ATGATTTGTCATTCTATCGCC
1 ATGATTTGTCATTCTATCGCC
50957 AT
1 AT
50959 TCTTTGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (21 bp):
ATGATTTGTCATTCTATCGCC
Found at i:51915 original size:83 final size:83
Alignment explanation
Indices: 51769--51929 Score: 250
Period size: 83 Copynumber: 1.9 Consensus size: 83
51759 AAACTGTCAT
* * *
51769 GTGTAAATTAATATTGCTGTAGCATGTGCAAGTGTACACAACGTTCAAGTAATAAAATAATAAGT
1 GTGTAAAATAATATTGCTATAGCATGTGAAAGTGTACACAACGTTCAAGTAATAAAATAATAAGT
* *
51834 ACAGTATTGTACTATCAC
66 AAAGTATCGTACTATCAC
* * *
51852 GTGTAAAATAATATTGCTATAGCATGTGAAAGTGTACATAACGTTCAAGTAATAAAGTGATAAGT
1 GTGTAAAATAATATTGCTATAGCATGTGAAAGTGTACACAACGTTCAAGTAATAAAATAATAAGT
51917 AAAGTATCGTACT
66 AAAGTATCGTACT
51930 CACAGAGAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (83 bp):
GTGTAAAATAATATTGCTATAGCATGTGAAAGTGTACACAACGTTCAAGTAATAAAATAATAAGT
AAAGTATCGTACTATCAC
Found at i:60486 original size:19 final size:19
Alignment explanation
Indices: 60449--60490 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
60439 CTGCATTAAC
*
60449 CATTTGGCATTCTTCAACA
1 CATTTGGCATACTTCAACA
*
60468 TCATTT-GCATACTTTAACA
1 -CATTTGGCATACTTCAACA
60487 CATT
1 CATT
60491 AAACACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (19 bp):
CATTTGGCATACTTCAACA
Found at i:61401 original size:17 final size:17
Alignment explanation
Indices: 61379--61411 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
61369 TTAAATAGCT
61379 TTGCAATGCTC-TATTCC
1 TTGCAAT-CTCGTATTCC
61396 TTGCAATCTCGTATTC
1 TTGCAATCTCGTATTC
61412 TCAGTATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.42
Consensus pattern (17 bp):
TTGCAATCTCGTATTCC
Found at i:65861 original size:17 final size:17
Alignment explanation
Indices: 65826--65878 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
65816 TACAAATAAA
65826 AATGAAAATGCAACTAC
1 AATGAAAATGCAACTAC
*
65843 AATGCAAATG-AACTAAC
1 AATGAAAATGCAACT-AC
*
65860 AA-GTAAAATGCAACGAC
1 AATG-AAAATGCAACTAC
65877 AA
1 AA
65879 CTAAAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 5 0.17
17 22 0.73
18 3 0.10
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (17 bp):
AATGAAAATGCAACTAC
Found at i:67723 original size:29 final size:29
Alignment explanation
Indices: 67686--67936 Score: 292
Period size: 29 Copynumber: 8.6 Consensus size: 29
67676 ATTGAGGTTA
*
67686 AAAAATGGAATTTTTAGACA-TTCGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGT
* * *
67715 AAAAGTGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT
**
67745 AAAAATGGAATTTTTGGAAGTTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* *
67774 AAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
67803 AAAAATGGAATTTTTTGAAGTTTC-GGGGT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT
* *
67832 CAAAAATAGG-ATTTTTAGAAGTTTGGGGGT
1 -AAAAAT-GGAATTTTTGGAAGTTCGGGGGT
* * *
67862 AAAAATGGAATTTTTGGAAGTTTTGAGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT
*
67892 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
67921 AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
67937 AATAGTTTAG
Statistics
Matches: 190, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.02
29 109 0.57
30 76 0.40
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:67749 original size:59 final size:58
Alignment explanation
Indices: 67686--67936 Score: 317
Period size: 59 Copynumber: 4.3 Consensus size: 58
67676 ATTGAGGTTA
* * * * * *
67686 AAAAATGGAATTTTTAGACA-TTCGGGGGTAAAAGTGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGGATTTTTGGAAG-TTCGGGGGT
* *
67745 AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
67803 AAAAATGGAATTTTTTGAAGTTTCG-GGGTCAAAAATAGGATTTTTAGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
67862 AAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
67921 AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
67937 AATAGTTTAG
Statistics
Matches: 168, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
58 30 0.18
59 135 0.80
60 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:67778 original size:88 final size:88
Alignment explanation
Indices: 67686--67936 Score: 319
Period size: 88 Copynumber: 2.9 Consensus size: 88
67676 ATTGAGGTTA
* * * *
67686 AAAAATGGAATTTTTAGACA-TTCGGGGGTAAAAGTGGAATTTTTGGAAGTTTTGGGGTTAAAAA
1 AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAA
67750 TGGAATTTTTGGAAGTTCAAGGGT
65 TGGAATTTTTGGAAGTTCAAGGGT
* * *
67774 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTGAAGTTTCGGGGTCAAAAAT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAAT
* ***
67839 AGG-ATTTTTAGAAGTTTGGGGGT
66 -GGAATTTTTGGAAGTTCAAGGGT
* * * *
67862 AAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAG-TTCGGGGGTAAAAA
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAA
67926 TGGAATTTTTG
65 TGGAATTTTTG
67937 AATAGTTTAG
Statistics
Matches: 140, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
87 3 0.02
88 110 0.79
89 27 0.19
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (88 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAAT
GGAATTTTTGGAAGTTCAAGGGT
Found at i:69042 original size:15 final size:15
Alignment explanation
Indices: 69022--69050 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
69012 TTTTTTATTA
69022 ATTATTAATAATAAT
1 ATTATTAATAATAAT
69037 ATTATTAATAATAA
1 ATTATTAATAATAA
69051 AACATTTATT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATTAATAATAAT
Found at i:69081 original size:21 final size:21
Alignment explanation
Indices: 69057--69112 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
69047 ATAAAACATT
69057 TATTATTAATGCCTTTATTAA
1 TATTATTAATGCCTTTATTAA
* ***
69078 TATTAATAATAATTTTATTAA
1 TATTATTAATGCCTTTATTAA
*
69099 TACCTATTAATGCC
1 TA-TTATTAATGCC
69113 AATATTTATT
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.48
Consensus pattern (21 bp):
TATTATTAATGCCTTTATTAA
Found at i:69824 original size:17 final size:17
Alignment explanation
Indices: 69799--69850 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
69789 TAACTGGACC
*
69799 TTTTCAATTAATTTAAA
1 TTTTAAATTAATTTAAA
*
69816 TTTTAAATTCAAATTAAA
1 TTTTAAATT-AATTTAAA
69834 -TTTAAACTTAATTTAAA
1 TTTTAAA-TTAATTTAAA
69851 CTTAAACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAATTAATTTAAA
Found at i:69855 original size:17 final size:17
Alignment explanation
Indices: 69806--69868 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
69796 ACCTTTTCAA
*
69806 TTAATTTAAATTTTAAA-
1 TTAATTTAAA-CTTAAAC
* *
69823 TTCAAATTAAATTTAAAC
1 TT-AATTTAAACTTAAAC
69841 TTAATTTAAACTTAAAC
1 TTAATTTAAACTTAAAC
*
69858 TAAATTTAAAC
1 TTAATTTAAAC
69869 CCAAAATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
17 31 0.77
18 9 0.22
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTTAAACTTAAAC
Found at i:69867 original size:6 final size:6
Alignment explanation
Indices: 69808--69867 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
69798 CTTTTCAATT
* * *
69808 AATTTA AATTTTA AATTCA AA-TTA AATTTA AACTT- AATTTA AACTTA
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
69855 AA-CTA AATTTA AA
1 AATTTA AATTTA AA
69868 CCCAAAATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.28
6 25 0.58
7 6 0.14
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:73986 original size:15 final size:15
Alignment explanation
Indices: 73966--73999 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
73956 ATTATAATTT
73966 TTTTCTTTTTCTTTC
1 TTTTCTTTTTCTTTC
73981 TTTTCTTTTTCTTTC
1 TTTTCTTTTTCTTTC
73996 TTTT
1 TTTT
74000 TATGTGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTCTTTC
Found at i:95485 original size:24 final size:24
Alignment explanation
Indices: 95437--95483 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
95427 AAGAGTTAAT
95437 TTGTCAACGCAAATATAAAATAAA
1 TTGTCAACGCAAATATAAAATAAA
*
95461 TTGTCAGA-GCAAAT-TAAGATAAA
1 TTGTCA-ACGCAAATATAAAATAAA
95484 ATGAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.26
Consensus pattern (24 bp):
TTGTCAACGCAAATATAAAATAAA
Found at i:99771 original size:50 final size:51
Alignment explanation
Indices: 99691--99801 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
99681 CTAGCTTTAG
* * * *
99691 TGCAACTTCATGAAGATAATATTTGCTTTCT-TAACTTCAATCCAATCCAT
1 TGCAACTTCAAGAAGATAAGATTTGCTTTCTGTAACTTCAATCCAACCCAC
* * *
99741 TGCAACTTCAAGGAGATCAAGATTTG-TTTCTGTAGCTTCAGTCCAACCCAC
1 TGCAACTTCAAGAAGAT-AAGATTTGCTTTCTGTAACTTCAATCCAACCCAC
*
99792 TACAACTTCA
1 TGCAACTTCA
99802 TGAGTATAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 20 0.39
51 31 0.61
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
TGCAACTTCAAGAAGATAAGATTTGCTTTCTGTAACTTCAATCCAACCCAC
Found at i:104415 original size:27 final size:27
Alignment explanation
Indices: 104380--104435 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
104370 AAATTTAACA
104380 GGTCAAAGTAAACAAGTCGGGTCAACG
1 GGTCAAAGTAAACAAGTCGGGTCAACG
* * * *
104407 GGTCTAAGTCAACGAGTTGGGTCAACG
1 GGTCAAAGTAAACAAGTCGGGTCAACG
104434 GG
1 GG
104436 CAGGTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.34, T:0.18
Consensus pattern (27 bp):
GGTCAAAGTAAACAAGTCGGGTCAACG
Found at i:105224 original size:20 final size:20
Alignment explanation
Indices: 105199--105239 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
105189 CCATAAAGTT
105199 TTAATTAAAGCACAACTTCA
1 TTAATTAAAGCACAACTTCA
105219 TTAATTAAAGCACAACTTCA
1 TTAATTAAAGCACAACTTCA
105239 T
1 T
105240 CCCTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (20 bp):
TTAATTAAAGCACAACTTCA
Found at i:125282 original size:40 final size:40
Alignment explanation
Indices: 125236--125355 Score: 186
Period size: 40 Copynumber: 3.0 Consensus size: 40
125226 TAGAGATTAA
*
125236 CAGGCTTTGAGTCGGTGATGTAATTCAAGCTACGGCTTAG
1 CAGGCTTTGAGTCGGTGATGTAATTCAAGCTACGACTTAG
* *
125276 TAGGCTTTGAGACGGTGATGTAATTCAAGCTACGACTTAG
1 CAGGCTTTGAGTCGGTGATGTAATTCAAGCTACGACTTAG
* * *
125316 CAGGCTTTGAGTCAGTGATGTGATTCAAGCTATGACTTAG
1 CAGGCTTTGAGTCGGTGATGTAATTCAAGCTACGACTTAG
125356 AAAGTTTTGA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (40 bp):
CAGGCTTTGAGTCGGTGATGTAATTCAAGCTACGACTTAG
Found at i:125365 original size:40 final size:40
Alignment explanation
Indices: 125237--125374 Score: 177
Period size: 40 Copynumber: 3.5 Consensus size: 40
125227 AGAGATTAAC
* * *
125237 AGGCTTTGAGTCGGTGATGTAATTCAAGCTACGGCTTAGT
1 AGGCTTTGAGTCAGTGATGTAATTCAAGCTACGACTTAGA
* * *
125277 AGGCTTTGAGACGGTGATGTAATTCAAGCTACGACTTAGC
1 AGGCTTTGAGTCAGTGATGTAATTCAAGCTACGACTTAGA
* *
125317 AGGCTTTGAGTCAGTGATGTGATTCAAGCTATGACTTAGA
1 AGGCTTTGAGTCAGTGATGTAATTCAAGCTACGACTTAGA
* * *
125357 AAGTTTTGAGCCAGTGAT
1 AGGCTTTGAGTCAGTGAT
125375 ATGATTGAGC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.31
Consensus pattern (40 bp):
AGGCTTTGAGTCAGTGATGTAATTCAAGCTACGACTTAGA
Found at i:125384 original size:17 final size:17
Alignment explanation
Indices: 125362--125397 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
125352 TTAGAAAGTT
*
125362 TTGAGCCAGTGATATGA
1 TTGAGCCAATGATATGA
*
125379 TTGAGCCAATGATGTGA
1 TTGAGCCAATGATATGA
125396 TT
1 TT
125398 CAAGCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (17 bp):
TTGAGCCAATGATATGA
Found at i:125412 original size:57 final size:57
Alignment explanation
Indices: 125322--125437 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
125312 TTAGCAGGCT
* * * *
125322 TTGAGTCAGTGATGTGATTCAAGCTATGACTTAGAAAGTTTTGAGCCAGTGATATGA
1 TTGAGCCAATGATGTGATTCAAGCTACGACTTAGAAAGCTTTGAGCCAGTGATATGA
* * * * *
125379 TTGAGCCAATGATGTGATTCAAGCTACGGCTTAGCAAGCTTTGAGTCGGTGATTTGA
1 TTGAGCCAATGATGTGATTCAAGCTACGACTTAGAAAGCTTTGAGCCAGTGATATGA
125436 TT
1 TT
125438 CAAGCTACAG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (57 bp):
TTGAGCCAATGATGTGATTCAAGCTACGACTTAGAAAGCTTTGAGCCAGTGATATGA
Found at i:125437 original size:40 final size:40
Alignment explanation
Indices: 125387--125492 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
125377 GATTGAGCCA
**
125387 ATGATGTGATTCAAGCTACGGCTTAGCAAGCTTTGAGTCG
1 ATGATGTGATTCAAGCTACGGCTTAGCAAGCTTTGAACCG
* * * ** *
125427 GTGATTTGATTCAAGCTACAGCTTAATAGGCTTTGAACCG
1 ATGATGTGATTCAAGCTACGGCTTAGCAAGCTTTGAACCG
*
125467 ATGATGTGATTCAAGCTATGGCTTAG
1 ATGATGTGATTCAAGCTACGGCTTAG
125493 TGGAACGATG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (40 bp):
ATGATGTGATTCAAGCTACGGCTTAGCAAGCTTTGAACCG
Found at i:127113 original size:15 final size:15
Alignment explanation
Indices: 127093--127133 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
127083 TAGCTTTAAC
127093 TTAGATTATATCAGT
1 TTAGATTATATCAGT
*
127108 TTAGATTA-AT-ATT
1 TTAGATTATATCAGT
127121 TTAGATTAATATC
1 TTAGATT-ATATC
127134 CTTCACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 9 0.41
14 3 0.14
15 10 0.45
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (15 bp):
TTAGATTATATCAGT
Found at i:127125 original size:13 final size:13
Alignment explanation
Indices: 127093--127132 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
127083 TAGCTTTAAC
*
127093 TTAGATTATATCAGT
1 TTAGATTA-AT-ATT
127108 TTAGATTAATATT
1 TTAGATTAATATT
127121 TTAGATTAATAT
1 TTAGATTAATAT
127133 CCTTCACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 14 0.58
14 2 0.08
15 8 0.33
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (13 bp):
TTAGATTAATATT
Found at i:143741 original size:13 final size:13
Alignment explanation
Indices: 143723--143748 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
143713 TTAAATGATT
143723 TTTGTGTTGGTAG
1 TTTGTGTTGGTAG
143736 TTTGTGTTGGTAG
1 TTTGTGTTGGTAG
143749 AGATGGTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (13 bp):
TTTGTGTTGGTAG
Found at i:145489 original size:38 final size:38
Alignment explanation
Indices: 145447--145524 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
145437 CCCATTATAG
145447 TTAAAACATAAGAAAATATTGTGTCTTTTGGGGTCATC
1 TTAAAACATAAGAAAATATTGTGTCTTTTGGGGTCATC
145485 TTAAAACATAAGAAAATATTGTGTCTTTTGGGGTCATC
1 TTAAAACATAAGAAAATATTGTGTCTTTTGGGGTCATC
145523 TT
1 TT
145525 CTTCCATCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (38 bp):
TTAAAACATAAGAAAATATTGTGTCTTTTGGGGTCATC
Found at i:146607 original size:40 final size:40
Alignment explanation
Indices: 146562--146935 Score: 437
Period size: 40 Copynumber: 9.4 Consensus size: 40
146552 ATATTGGCAG
* * *
146562 GCTTTGAGCC-AGTGATGTAATTCAAGCTATGACTTAGCAA
1 GCTTTGAGCCGA-TGATGTGATTCAAGCTACGGCTTAGCAA
* * * *
146602 GCTTTGAGCCGGTGATGTAATTCACGCTACGGCTTAGCAG
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
** * * *
146642 GCTTTGAGTTGATGATGTAATTCAAGTTACAGCTTAGCAA
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
*
146682 GCATTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
* * *
146722 GCATTGAGCCGATGATGTGATTCAAGCTACGACTTAACAA
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
* * *
146762 -CTTTGAGTCGATGATGTGATTCAAGCTACGGCTTAGTAG
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
* * * *
146801 GCTTTGAGCCGGTGATGTGCTTCAAGCTACGGCTTAGTAG
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
* * *
146841 GCTTTGAGCCGGTGATGTGCTTCAAGCTACGGCTTAGCAG
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
* * * *
146881 GCTTTGATCCGATGATTTGATTCAAGCTACGGCTTTGCAG
1 GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
* *
146921 GCTTTAAGTCGATGA
1 GCTTTGAGCCGATGA
146936 GAAGATTTAG
Statistics
Matches: 294, Mismatches: 38, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
39 33 0.11
40 261 0.89
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
GCTTTGAGCCGATGATGTGATTCAAGCTACGGCTTAGCAA
Found at i:146817 original size:159 final size:160
Alignment explanation
Indices: 146565--146911 Score: 455
Period size: 159 Copynumber: 2.2 Consensus size: 160
146555 TTGGCAGGCT
* * * * *
146565 TTGAGCC-AGTGATGTAATTCAAGCTATGACTTAGCAAGCTTTGAGCCGGTGATGTAATTCACGC
1 TTGAGCCGA-TGATGTGATTCAAGCTACGACTTAACAAGCTTTGAGCCGATGATGTAATTCAAGC
** *
146629 TACGGCTTAGCAGGCTTTGAGTTGATGATGTAATTCAAGTTACAGCTTAGCAAGCATTGAGCCGA
65 TACGGCTTAGCAGGCTTTGAGCCGATGATGTAATTCAAGCTACAGCTTAGCAAGCATTGAGCCGA
146694 TGATGTGATTCAAGCTACGGCTTAGCAAGCA
130 TGATGTGATTCAAGCTACGGCTTAGCAAGCA
* *
146725 TTGAGCCGATGATGTGATTCAAGCTACGACTTAACAA-CTTTGAGTCGATGATGTGATTCAAGCT
1 TTGAGCCGATGATGTGATTCAAGCTACGACTTAACAAGCTTTGAGCCGATGATGTAATTCAAGCT
* * ** * * * * *
146789 ACGGCTTAGTAGGCTTTGAGCCGGTGATGTGCTTCAAGCTACGGCTTAGTAGGCTTTGAGCCGGT
66 ACGGCTTAGCAGGCTTTGAGCCGATGATGTAATTCAAGCTACAGCTTAGCAAGCATTGAGCCGAT
* * *
146854 GATGTGCTTCAAGCTACGGCTTAGCAGGCT
131 GATGTGATTCAAGCTACGGCTTAGCAAGCA
* *
146884 TTGATCCGATGATTTGATTCAAGCTACG
1 TTGAGCCGATGATGTGATTCAAGCTACG
146912 GCTTTGCAGG
Statistics
Matches: 162, Mismatches: 24, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
159 129 0.80
160 32 0.20
161 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (160 bp):
TTGAGCCGATGATGTGATTCAAGCTACGACTTAACAAGCTTTGAGCCGATGATGTAATTCAAGCT
ACGGCTTAGCAGGCTTTGAGCCGATGATGTAATTCAAGCTACAGCTTAGCAAGCATTGAGCCGAT
GATGTGATTCAAGCTACGGCTTAGCAAGCA
Found at i:146975 original size:159 final size:159
Alignment explanation
Indices: 146565--146975 Score: 391
Period size: 159 Copynumber: 2.6 Consensus size: 159
146555 TTGGCAGGCT
* * * * * * *
146565 TTGAGCC-AGTGATGTAATTCAAGCTATGACTTAGCAAGCTTTGAGCCGGTGATGTA-ATTCACG
1 TTGAGCCGA-TGATGTGATTCAAGCTACGACTTAACAA-CTTTAAGTCGATGATG-AGATTCAAG
* * * ** ** *
146628 CTACGGCTTAGCAGGCTTTGAG-TTGATGATGTAATTCAAGTTACAGCTTAGCAAGCATTGAGCC
63 CTACGACCTAGTAGGCTTTGAGCCAG-TGATGTGCTTCAAGCTACAGCTTAGCAAGCATTGAGCC
146692 GATGATGTGATTCAAGCTACGGCTTAGCAAGCA
127 GATGATGTGATTCAAGCTACGGCTTAGCAAGCA
* *
146725 TTGAGCCGATGATGTGATTCAAGCTACGACTTAACAACTTTGAGTCGATGATGTGATTCAAGCTA
1 TTGAGCCGATGATGTGATTCAAGCTACGACTTAACAACTTTAAGTCGATGATGAGATTCAAGCTA
* * * * * * * *
146790 CGGCTTAGTAGGCTTTGAGCCGGTGATGTGCTTCAAGCTACGGCTTAGTAGGCTTTGAGCCGGTG
66 CGACCTAGTAGGCTTTGAGCCAGTGATGTGCTTCAAGCTACAGCTTAGCAAGCATTGAGCCGATG
* * *
146855 ATGTGCTTCAAGCTACGGCTTAGCAGGCT
131 ATGTGATTCAAGCTACGGCTTAGCAAGCA
* * * ** * * * *
146884 TTGATCCGATGATTTGATTCAAGCTACGGCTTTGCAGGCTTTAAGTCGATGA-GAAGATTTAGGT
1 TTGAGCCGATGATGTGATTCAAGCTACGACTTAACA-ACTTTAAGTCGATGATG-AGATTCAAGC
*
146948 TATGACCTAGTAGGCTTT-AGCCAGTGAT
64 TACGACCTAGTAGGCTTTGAGCCAGTGAT
146976 TTTGTATAAT
Statistics
Matches: 210, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
159 142 0.68
160 67 0.32
161 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (159 bp):
TTGAGCCGATGATGTGATTCAAGCTACGACTTAACAACTTTAAGTCGATGATGAGATTCAAGCTA
CGACCTAGTAGGCTTTGAGCCAGTGATGTGCTTCAAGCTACAGCTTAGCAAGCATTGAGCCGATG
ATGTGATTCAAGCTACGGCTTAGCAAGCA
Found at i:148862 original size:36 final size:37
Alignment explanation
Indices: 148801--148870 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
148791 AAAAATAATA
148801 TTATTTTAATAGTTAATATTAAATTTAAT-TTAATCC
1 TTATTTTAATAGTTAATATTAAATTTAATATTAATCC
**
148837 TTATTTTAATAGTATTTTATT-AATTTAATATTAA
1 TTATTTTAATAGT-TAATATTAAATTTAATATTAA
148871 AGTGATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 21 0.70
37 9 0.30
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (37 bp):
TTATTTTAATAGTTAATATTAAATTTAATATTAATCC
Found at i:148868 original size:11 final size:11
Alignment explanation
Indices: 148796--148870 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
148786 ATTTCAAAAA
*
148796 TAATATTATTT
1 TAATATTAATT
148807 TAATAGTTAATAT
1 TAATA-TTAAT-T
148820 TAA-ATTTAATT
1 TAATA-TTAATT
* *
148831 TAATCCTTATTT
1 TAAT-ATTAATT
*
148843 TAATAGT-ATT
1 TAATATTAATT
148853 T--TATTAATT
1 TAATATTAATT
148862 TAATATTAA
1 TAATATTAA
148871 AGTGATTATC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 16 0.33
12 19 0.39
13 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:148878 original size:20 final size:18
Alignment explanation
Indices: 148797--148902 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
148787 TTTCAAAAAT
*
148797 AATATTATTTTAATAGTT-
1 AATATTAATTTAATA-TTA
148815 AATATTAAATTTAAT-TT-
1 AATATT-AATTTAATATTA
* * *
148832 AATCCTTATTTTAATAGTA
1 AAT-ATTAATTTAATATTA
**
148851 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
148870 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
148890 AAT-TTAATTTAAT
1 AATATTAATTTAAT
148903 GTTTATCTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
17 19 0.28
18 11 0.16
19 23 0.34
20 15 0.22
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:154113 original size:18 final size:18
Alignment explanation
Indices: 154090--154128 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
154080 GATCATTTTC
154090 CTACAACTCACGAATTCA
1 CTACAACTCACGAATTCA
154108 CTACAACTCACGAATTCA
1 CTACAACTCACGAATTCA
154126 CTA
1 CTA
154129 TAGAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.23
Consensus pattern (18 bp):
CTACAACTCACGAATTCA
Found at i:162177 original size:15 final size:15
Alignment explanation
Indices: 162159--162190 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
162149 TAACCATTGT
162159 AACCCAAACCCTTTA
1 AACCCAAACCCTTTA
162174 AACCCAAACCCTTTA
1 AACCCAAACCCTTTA
162189 AA
1 AA
162191 AACCAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCAAACCCTTTA
Found at i:162198 original size:16 final size:15
Alignment explanation
Indices: 162162--162199 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
162152 CCATTGTAAC
*
162162 CCAAACCCTTTAAAC
1 CCAAACCCTTTAAAA
162177 CCAAACCCTTTAAAAA
1 CCAAACCCTTT-AAAA
162193 CCAAACC
1 CCAAACC
162200 AAACCCAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (15 bp):
CCAAACCCTTTAAAA
Found at i:168536 original size:44 final size:39
Alignment explanation
Indices: 168485--168616 Score: 147
Period size: 40 Copynumber: 3.2 Consensus size: 39
168475 AGAATGTGAT
*
168485 AAAGGAAGACTTATGACTCGAAAGGAGCGTGAGAATATTGTTAA
1 AAAGGAAGACTTATGACTCGAAA--AGC---AGAAGATTGTTAA
* *
168529 AAAGGAAGACTTATGACTCGGTAAAGCATAAGATTGTTAA
1 AAAGGAAGACTTATGACTC-GAAAAGCAGAAGATTGTTAA
* * *
168569 AAAGGAAGACTTATGACTCGGTAGAGCATAAGATTGTTAA
1 AAAGGAAGACTTATGACTC-GAAAAGCAGAAGATTGTTAA
168609 AAAGGAAG
1 AAAGGAAG
168617 TCACATGAAC
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
40 58 0.70
43 3 0.04
44 19 0.23
45 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.26, T:0.23
Consensus pattern (39 bp):
AAAGGAAGACTTATGACTCGAAAAGCAGAAGATTGTTAA
Found at i:168576 original size:40 final size:40
Alignment explanation
Indices: 168521--168616 Score: 183
Period size: 40 Copynumber: 2.4 Consensus size: 40
168511 GCGTGAGAAT
168521 ATTGTTAAAAAGGAAGACTTATGACTCGGTAAAGCATAAG
1 ATTGTTAAAAAGGAAGACTTATGACTCGGTAAAGCATAAG
*
168561 ATTGTTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAG
1 ATTGTTAAAAAGGAAGACTTATGACTCGGTAAAGCATAAG
168601 ATTGTTAAAAAGGAAG
1 ATTGTTAAAAAGGAAG
168617 TCACATGAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.25
Consensus pattern (40 bp):
ATTGTTAAAAAGGAAGACTTATGACTCGGTAAAGCATAAG
Done.