Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 86 of 187
Found at i:25564611 original size:37 final size:37
Alignment explanation
Indices: 25564561--25564635 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
25564551 CACTTGCTAA
* *
25564561 AGAGACTGGGTCTCATGATTGTATGGCCGGGGACGAC
1 AGAGACTAGGTCTCATGATTGCATGGCCGGGGACGAC
*
25564598 AGAGACTAGGTCTCATGATTGCATGGCTGGGGACGAC
1 AGAGACTAGGTCTCATGATTGCATGGCCGGGGACGAC
25564635 A
1 A
25564636 CCTTGTCCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (37 bp):
AGAGACTAGGTCTCATGATTGCATGGCCGGGGACGAC
Found at i:25579649 original size:43 final size:43
Alignment explanation
Indices: 25579576--25579673 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
25579566 ACTTAGTTCA
* * *
25579576 CCCATTGGTGAATACTATACAAAAGTAGACTTTATACTATTTG
1 CCCATTGGTGAATACTATACAAAAGAAGACTTCATACAATTTG
* * *
25579619 CCCGTTGGTGAATAGTATATC-GAAGAAGACTTCATACAATTTG
1 CCCATTGGTGAATACTATA-CAAAAGAAGACTTCATACAATTTG
25579662 CCCATTGGTGAA
1 CCCATTGGTGAA
25579674 ATTCCAAACT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (43 bp):
CCCATTGGTGAATACTATACAAAAGAAGACTTCATACAATTTG
Found at i:25581034 original size:21 final size:20
Alignment explanation
Indices: 25580989--25581034 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
25580979 TTGTTGGAAT
25580989 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
25581008 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
25581029 GGTTGA
1 GGTTGA
25581035 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:25588373 original size:21 final size:19
Alignment explanation
Indices: 25588347--25588398 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
25588337 AGATAAAAAT
25588347 GAAATAAGACTAAAAAAATAA
1 GAAATAA-AC-AAAAAAATAA
*
25588368 GAAATAAACATAAAAATAA
1 GAAATAAACAAAAAAATAA
25588387 -AAATAAAACAAA
1 GAAAT-AAACAAA
25588399 TGGATTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
19 15 0.54
20 2 0.07
21 7 0.25
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.13
Consensus pattern (19 bp):
GAAATAAACAAAAAAATAA
Found at i:25588380 original size:27 final size:25
Alignment explanation
Indices: 25588334--25588389 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
25588324 AATATAGTTT
* * * *
25588334 AAAAGATAAAAATGAAATAAGACTA
1 AAAAAATAAAAATAAAATAAAAATA
25588359 AAAAAATAAGAAATAAACATAAAAATA
1 AAAAAATAA-AAATAAA-ATAAAAATA
25588386 AAAA
1 AAAA
25588390 TAAAACAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 8 0.32
26 6 0.24
27 11 0.44
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAAAATAAAAATAAAATAAAAATA
Found at i:25588386 original size:6 final size:6
Alignment explanation
Indices: 25588360--25588394 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
25588350 ATAAGACTAA
*
25588360 AAAAAT AAGAAAT AAACAT AAAAAT AAAAAT AAAA
1 AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAA
25588395 CAAATGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:25589368 original size:9 final size:9
Alignment explanation
Indices: 25589354--25589378 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25589344 TGATAAAGAA
25589354 AAACCATAT
1 AAACCATAT
25589363 AAACCATAT
1 AAACCATAT
25589372 AAACCAT
1 AAACCAT
25589379 TAATTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (9 bp):
AAACCATAT
Found at i:25590429 original size:14 final size:13
Alignment explanation
Indices: 25590410--25590448 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
25590400 GAACCTATCG
*
25590410 AAGAAAATAAAAGA
1 AAGAAATTAAAA-A
25590424 AAGAAATTAAAAA
1 AAGAAATTAAAAA
25590437 ACAGAAATTAAA
1 A-AGAAATTAAA
25590449 CTAAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (13 bp):
AAGAAATTAAAAA
Found at i:25592240 original size:20 final size:20
Alignment explanation
Indices: 25592215--25592262 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
25592205 AGGGGCACCA
25592215 AAGTGCAATCAGGAGCAT-G
1 AAGTGCAATCAGGAGCATAG
*
25592234 AATGTGCAATCAGGGGCATAG
1 AA-GTGCAATCAGGAGCATAG
25592255 AAGTGCAA
1 AAGTGCAA
25592263 ATAGGGGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.17
Consensus pattern (20 bp):
AAGTGCAATCAGGAGCATAG
Found at i:25592289 original size:40 final size:40
Alignment explanation
Indices: 25592245--25592388 Score: 173
Period size: 40 Copynumber: 3.6 Consensus size: 40
25592235 ATGTGCAATC
* *
25592245 AGGGGCATAGAAGTGCAAAT-AGGGGTACCGAAGTACAAAT
1 AGGGGCACAGATGTGC-AATCAGGGGTACCGAAGTACAAAT
* * * *
25592285 AGGGGCACATATGTGCATTCAGGGGTACCGAACTACAAAC
1 AGGGGCACAGATGTGCAATCAGGGGTACCGAAGTACAAAT
* * *
25592325 AGGGGCACAGATGTGCATTCAAGGGTACTGAAGTACAAAT
1 AGGGGCACAGATGTGCAATCAGGGGTACCGAAGTACAAAT
* *
25592365 AGAGGCACAGATGTGCAAACAGGG
1 AGGGGCACAGATGTGCAATCAGGG
25592389 TCACTTCTTC
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.02
40 86 0.98
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (40 bp):
AGGGGCACAGATGTGCAATCAGGGGTACCGAAGTACAAAT
Found at i:25598815 original size:18 final size:18
Alignment explanation
Indices: 25598782--25598834 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
25598772 ATTCACCTAA
*
25598782 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
25598801 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
25598819 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
25598835 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:25598952 original size:9 final size:9
Alignment explanation
Indices: 25598938--25599013 Score: 109
Period size: 9 Copynumber: 8.4 Consensus size: 9
25598928 GTAGTGATTC
25598938 AATTCGGTT
1 AATTCGGTT
25598947 AATTCGGTT
1 AATTCGGTT
25598956 AATTCAGG-T
1 AATTC-GGTT
25598965 AATTCGGTT
1 AATTCGGTT
*
25598974 AATTCGGAT
1 AATTCGGTT
*
25598983 AATCCGGTT
1 AATTCGGTT
*
25598992 AATTCAGTT
1 AATTCGGTT
25599001 AATTCGGTT
1 AATTCGGTT
25599010 AATT
1 AATT
25599014 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
8 2 0.03
9 55 0.93
10 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:25612583 original size:14 final size:14
Alignment explanation
Indices: 25612566--25612593 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25612556 CCACAACGTG
25612566 GATGATGAAGAAAC
1 GATGATGAAGAAAC
25612580 GATGATGAAGAAAC
1 GATGATGAAGAAAC
25612594 TTGTAATGCA
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:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (14 bp):
GATGATGAAGAAAC
Found at i:25614603 original size:23 final size:23
Alignment explanation
Indices: 25614553--25614615 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
25614543 TAATATTGTT
25614553 TGTGAACATGTTCAATTATATAA
1 TGTGAACATGTTCAATTATATAA
* *
25614576 T-TGAACATGTTCATTTA-ATAT
1 TGTGAACATGTTCAATTATATAA
* *
25614597 TCGTGAATATGTTCGATTA
1 T-GTGAACATGTTCAATTA
25614616 AGTTAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 4 0.12
22 15 0.45
23 14 0.42
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (23 bp):
TGTGAACATGTTCAATTATATAA
Found at i:25618313 original size:13 final size:13
Alignment explanation
Indices: 25618297--25618336 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
25618287 ATTTGTTTAA
* *
25618297 CATTTCACGTCTT
1 CATTTCAAGTATT
25618310 CATTTCAAGTATT
1 CATTTCAAGTATT
*
25618323 CATTTCAATTATT
1 CATTTCAAGTATT
25618336 C
1 C
25618337 CTTTTCACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (13 bp):
CATTTCAAGTATT
Found at i:25631933 original size:2 final size:2
Alignment explanation
Indices: 25631926--25631964 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25631916 TGAAGATAGA
25631926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25631965 AACATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25632140 original size:21 final size:21
Alignment explanation
Indices: 25632114--25632177 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
25632104 GGATCCAATG
25632114 TTCGAAGATCTATCTCTTAGC
1 TTCGAAGATCTATCTCTTAGC
* **
25632135 TTCGAA-ATAC-ACCTCGAATG-
1 TTCGAAGAT-CTATCTCTTA-GC
25632155 TTCGAAGATCTATCTCTTAGC
1 TTCGAAGATCTATCTCTTAGC
25632176 TT
1 TT
25632178 TGAAATACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (21 bp):
TTCGAAGATCTATCTCTTAGC
Found at i:25632167 original size:41 final size:41
Alignment explanation
Indices: 25632110--25632194 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
25632100 GATGGGATCC
25632110 AATGTTCGAAGATCTATCTCTTAGCTTCGAAATACACCTCG
1 AATGTTCGAAGATCTATCTCTTAGCTTCGAAATACACCTCG
* *
25632151 AATGTTCGAAGATCTATCTCTTAGCTTTGAAATACATCTCG
1 AATGTTCGAAGATCTATCTCTTAGCTTCGAAATACACCTCG
25632192 AAT
1 AAT
25632195 CACTCAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (41 bp):
AATGTTCGAAGATCTATCTCTTAGCTTCGAAATACACCTCG
Found at i:25633325 original size:20 final size:20
Alignment explanation
Indices: 25633298--25633347 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
25633288 AACTAGAAAG
*
25633298 ATAAATAAAAACTCGTGCAAA
1 ATAAATAAAAACTCAT-CAAA
* *
25633319 A-AAATAAGACCTCATCAAA
1 ATAAATAAAAACTCATCAAA
25633338 ATAAATAAAA
1 ATAAATAAAA
25633348 TTATGTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.62, C:0.14, G:0.06, T:0.18
Consensus pattern (20 bp):
ATAAATAAAAACTCATCAAA
Found at i:25639800 original size:23 final size:24
Alignment explanation
Indices: 25639753--25639808 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
25639743 GTTTTTTAGT
*
25639753 TTATT-TTATTAATATAGTTGTTA
1 TTATTATTATTAATATAGTTATTA
25639776 TTATTATTATT-ATATA-TTATATA
1 TTATTATTATTAATATAGTTAT-TA
*
25639799 TTTTTATTAT
1 TTATTATTAT
25639809 ACCTACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.10
23 21 0.72
24 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TTATTATTATTAATATAGTTATTA
Found at i:25645931 original size:12 final size:12
Alignment explanation
Indices: 25645910--25645965 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
25645900 GATTCAATCC
25645910 AAAAATAAAAAA-
1 AAAAA-AAAAAAG
* *
25645922 TAAAAAAAAAAC
1 AAAAAAAAAAAG
*
25645934 AAAAAAAAGAAG
1 AAAAAAAAAAAG
* *
25645946 AAAAAGAAGAAG
1 AAAAAAAAAAAG
25645958 AAAAAAAA
1 AAAAAAAA
25645966 CCCCCCGCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
11 6 0.16
12 31 0.84
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:25646477 original size:14 final size:14
Alignment explanation
Indices: 25646460--25646506 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
25646450 ATGATGTGAA
*
25646460 AAAAATGAAAAACT
1 AAAAATGAAAAAAT
25646474 AAAAAT-AAAAAAT
1 AAAAATGAAAAAAT
*
25646487 GAAAAATGGAAAAAGT
1 -AAAAAT-GAAAAAAT
25646503 AAAA
1 AAAA
25646507 TGGAGAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 12 0.43
15 4 0.14
16 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAAAT
Found at i:25647829 original size:88 final size:88
Alignment explanation
Indices: 25647709--25647882 Score: 258
Period size: 88 Copynumber: 2.0 Consensus size: 88
25647699 CGGTGAAACT
* * * *
25647709 CCAGCCTTGTCTCCCTGGGAAATAGTAGAGTAGGTTGAAAATGGTAGATCTTGCCTTCCTCTATT
1 CCAGCCTTGTCTCCCTAGGAAATAGTAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTCTACT
25647774 GACAGCGAAGCAGATCGAAGATA
66 GACAGCGAAGCAGATCGAAGATA
* * * * *
25647797 CCAGCCTTGTCTCCCTAGGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCTTGTACT
1 CCAGCCTTGTCTCCCTAGGAAATAGTAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTCTACT
*
25647862 GACAGTGAAGCAGATCGAAGA
66 GACAGCGAAGCAGATCGAAGA
25647883 CAACAGTCTT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 76 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (88 bp):
CCAGCCTTGTCTCCCTAGGAAATAGTAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTCTACT
GACAGCGAAGCAGATCGAAGATA
Found at i:25648158 original size:50 final size:49
Alignment explanation
Indices: 25648078--25648269 Score: 150
Period size: 50 Copynumber: 3.9 Consensus size: 49
25648068 AGCATTTCAG
* * * * * * *
25648078 TGGAAAAGATTGAAGCCGCAACAGCGGATCTTACTTCCCTGGCGGTGCAA
1 TGGAACAGATTGAAGCCACGACGGCAGATCTTATTTCCCTGGC-ATGCAA
* ** * *
25648128 TGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAA
1 TGGAACAGATTGAAGCCACGACGGCAGATCTTATTTCCCTGGCA-TGCAA
** * * ** *
25648178 TTAAAAAGATTGAAGCCACAACGGCAGATCTTATTTTTCTGGCATCGCAG
1 TGGAACAGATTGAAGCCACGACGGCAGATCTTATTTCCCTGGCAT-GCAA
* * * *
25648228 CGGAACAGATTGAAGCCAAGACGGCGGATCTTATCTCCCTGG
1 TGGAACAGATTGAAGCCACGACGGCAGATCTTATTTCCCTGG
25648270 TGTTAAGGCT
Statistics
Matches: 106, Mismatches: 34, Indels: 4
0.74 0.24 0.03
Matches are distributed among these distances:
49 1 0.01
50 105 0.99
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (49 bp):
TGGAACAGATTGAAGCCACGACGGCAGATCTTATTTCCCTGGCATGCAA
Found at i:25648407 original size:267 final size:267
Alignment explanation
Indices: 25647917--25648477 Score: 924
Period size: 267 Copynumber: 2.1 Consensus size: 267
25647907 GCAATGGAAT
** * * *
25647917 AGATTGAAGCCACAACGGTGGATCTTATTTTCCTGGCGTCGCAGCAGAGCAGATTGAAGCCACGA
1 AGATTGAAGCCACAACGGCAGATCTTATTTTCCTGGCATCGCAGCAGAACAGATTGAAGCCAAGA
*
25647982 TGGCAGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGATGAAGTGGAGTGGATTGAAGCTGTG
66 CGGCAGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGATGAAGTGGAGTGGATTGAAGCTGTG
* *
25648047 GGCAGCGAATCCTATCTCTTTAGCATTTCAGTGGAAAAGATTGAAGCCGCAACAGCGGATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACAGCGGATCTTAC
* *
25648112 TTCCCTGGCGGTGCAATGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCA
196 TTCCCTGGCGGTGCAATGGAACAGATTGAAGCTACGACAGCAGATCTGGTTCCCCCGACATTGCA
25648177 ATTAAAA
261 ATTAAAA
* *
25648184 AGATTGAAGCCACAACGGCAGATCTTATTTTTCTGGCATCGCAGCGGAACAGATTGAAGCCAAGA
1 AGATTGAAGCCACAACGGCAGATCTTATTTTCCTGGCATCGCAGCAGAACAGATTGAAGCCAAGA
*
25648249 CGGCGGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGATGAAGTGGAGTGGATTGAAGCTGTG
66 CGGCAGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGATGAAGTGGAGTGGATTGAAGCTGTG
* *
25648314 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGTTTGAAGCCACAACGGCGGATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACAGCGGATCTTAC
* * * * * * *
25648379 TTCCTTTGCGGTGTAGTGGAATAGATTGAAGCTACGACAGCGGATTTGGTTCCCCCGACATTGCA
196 TTCCCTGGCGGTGCAATGGAACAGATTGAAGCTACGACAGCAGATCTGGTTCCCCCGACATTGCA
25648444 ATTAAAA
261 ATTAAAA
25648451 AGATTGAAGCCACAACGGCAGATCTTA
1 AGATTGAAGCCACAACGGCAGATCTTA
25648478 CTTCCTTTGC
Statistics
Matches: 272, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
267 272 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (267 bp):
AGATTGAAGCCACAACGGCAGATCTTATTTTCCTGGCATCGCAGCAGAACAGATTGAAGCCAAGA
CGGCAGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGATGAAGTGGAGTGGATTGAAGCTGTG
GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACAGCGGATCTTAC
TTCCCTGGCGGTGCAATGGAACAGATTGAAGCTACGACAGCAGATCTGGTTCCCCCGACATTGCA
ATTAAAA
Found at i:25649702 original size:22 final size:20
Alignment explanation
Indices: 25649655--25649690 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
25649645 AATATAGTTG
25649655 TTAT-TATTATTATTATATA
1 TTATATATTATTATTATATA
25649674 TTATATATT-TTATTATA
1 TTATATATTATTATTATA
25649691 CCTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATATTATTATTATATA
Found at i:25652661 original size:13 final size:13
Alignment explanation
Indices: 25652643--25652685 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
25652633 AAATTTGAAT
25652643 TATTTAGTGATAA
1 TATTTAGTGATAA
25652656 TATTTAG-GAT--
1 TATTTAGTGATAA
25652666 TATTTAGTGATAA
1 TATTTAGTGATAA
25652679 TATTTAG
1 TATTTAG
25652686 GAAAAACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:25652667 original size:23 final size:23
Alignment explanation
Indices: 25652641--25652687 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
25652631 TAAAATTTGA
25652641 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
25652664 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
25652687 A
1 A
25652688 AAAACCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTAGG
Found at i:25654147 original size:37 final size:36
Alignment explanation
Indices: 25654064--25654140 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
25654054 AAAATTAAAG
25654064 TAAAAATTAAACATTTTTTATTTCTTGACAATATCT
1 TAAAAATTAAACATTTTTTATTTCTTGACAATATCT
25654100 TAAAAATTAAACATTTTTTATTTCTTGACAATATCT
1 TAAAAATTAAACATTTTTTATTTCTTGACAATATCT
25654136 TAAAA
1 TAAAA
25654141 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (36 bp):
TAAAAATTAAACATTTTTTATTTCTTGACAATATCT
Found at i:25658289 original size:42 final size:42
Alignment explanation
Indices: 25658231--25658526 Score: 301
Period size: 42 Copynumber: 7.0 Consensus size: 42
25658221 GCGTTTATAG
* * *
25658231 AAAAAAACGCAGCTAAAGGTCATGTTCTTTAGCGGCG-ATACA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-A
* *
25658273 AAAAAAACGCCGCTAAAGATCATGTCCTTTAGCGGCACTTAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
*
25658315 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTAGA
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-A
* *
25658359 AAAAAGACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* * * * * **
25658401 ACAAAAACACCGCTAAA-AGTAATGTTCTATAGCGGCTCTTGG
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAA
* * * *
25658443 TAAAAAACGCCGCTACAGATCATGTTCTTTAGTGGCGCTTTCA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAA
** * * *
25658486 CTACAAACGCCGCTAAA-AGTAATGTTCTTTAGCGGCACTTA
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTA
25658527 CTTCACAAAC
Statistics
Matches: 209, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.00
42 103 0.49
43 99 0.47
44 6 0.03
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
Found at i:25658319 original size:43 final size:43
Alignment explanation
Indices: 25658231--25658526 Score: 271
Period size: 43 Copynumber: 7.0 Consensus size: 43
25658221 GCGTTTATAG
* * *
25658231 AAAAAAACGCAGCTAAAGGTCATGTTCTTTAGCGGCGA--TACA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC-ACTTAAA
*
25658273 AAAAAAACGCCGCTAAAGATCATGTCCTTTAGCGGCACTTAAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTAAA
* * * *
25658316 AAAAAGACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTAGA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTAAA
* * *
25658359 AAAAAGACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTAAA
* * * * * **
25658401 ACAAAAACACCGCTAAA-AGTAATGTTCTATAGCGGCTCTT-GG
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCACTTAAA
* * * * **
25658443 TAAAAAACGCCGCTACAGATCATGTTCTTTAGTGGCGCTTTCA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTAAA
** * *
25658486 CTACAAACGCCGCTAAA-AGTAATGTTCTTTAGCGGCACTTA
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCACTTA
25658527 CTTCACAAAC
Statistics
Matches: 209, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
41 2 0.01
42 96 0.46
43 111 0.53
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (43 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTAAA
Found at i:25658339 original size:85 final size:84
Alignment explanation
Indices: 25658231--25658521 Score: 289
Period size: 85 Copynumber: 3.4 Consensus size: 84
25658221 GCGTTTATAG
* * *
25658231 AAAAAAACGCAGCTAAAGGTCATGTTCTTTAGCGGCGATACAAAAAAAACGCCGCTAAAGATCAT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGATAGAAAAAAAACGCCGCTAAAGATCAT
*
25658296 GTCCTTTAGCGGCACTTAA
66 GTTCTTTAGCGGCACTTAA
* * * *
25658315 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTAGAAAAAAGACGTCGCTAAAGATC
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCG-ATAGAAAAAAAACGCCGCTAAAGATC
*
25658380 ATGTTCTTTAGCGGCGCTTAA
64 ATGTTCTTTAGCGGCACTTAA
* * * * ** * ** *
25658401 ACAAAAACACCGCTAAA-AGTAATGTTCTATAGCGGCTCTTGGTAAAAAACGCCGCTACAGATCA
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGATAGAAAAAAAACGCCGCTAAAGATCA
* * *
25658465 TGTTCTTTAGTGGCGCTTTCA
65 TGTTCTTTAGCGGCAC-TTAA
** * *
25658486 CTACAAACGCCGCTAAA-AGTAATGTTCTTTAGCGGC
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGC
25658522 ACTTACTTCA
Statistics
Matches: 174, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
84 42 0.24
85 86 0.49
86 46 0.26
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (84 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGATAGAAAAAAAACGCCGCTAAAGATCAT
GTTCTTTAGCGGCACTTAA
Found at i:25658580 original size:86 final size:85
Alignment explanation
Indices: 25658232--25658587 Score: 242
Period size: 85 Copynumber: 4.2 Consensus size: 85
25658222 CGTTTATAGA
* * * * * ** * *
25658232 AAAAAACGCAGCTAAAGGTCATGTTCTTTAGCGGCGA-TACAAAAAAAACGCCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGC-ACTTCGTAAAAAACGCCGCTACAGAACAT
* * *
25658296 G-TCCTTTAGCGGCAC-TTAAA
65 GCT-CTTTAGCGGCGCTTTTAT
* * * * * * * * *
25658316 AAAAAGACGCCGCT-AAAGATCATGTTCTTTAACGGCGCTTAGAAAAAAGACGTCGCTAAAGATC
1 AAAAA-ACGCCGCTAAAAG-TAATGTTCTATAGCGGCACTTCGTAAAAA-ACGCCGCTACAGAAC
* *
25658380 ATGTTCTTTAGCGGCGC--TTAA
63 ATGCTCTTTAGCGGCGCTTTTAT
* * * *
25658401 ACAAAAACACCGCTAAAAGTAATGTTCTATAGCGGCTCTTGGTAAAAAACGCCGCTACAGATCAT
1 A-AAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCACTTCGTAAAAAACGCCGCTACAGAACAT
* * *
25658466 GTTCTTTAGTGGCGCTTTCACT
65 GCTCTTTAGCGGCGCTTTTA-T
* * * * * *
25658488 -ACAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCACTTACTTCACAAACGCCGCTATAGAACAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCACTT-CGTAAAAAACGCCGCTACAGAACAT
25658552 GACT-TTTAGCGGCGCTTTTAT
65 G-CTCTTTAGCGGCGCTTTTAT
*
25658573 AAAAAACGCCACTAA
1 AAAAAACGCCGCTAA
25658588 TTTTGGGATT
Statistics
Matches: 222, Mismatches: 37, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
84 37 0.17
85 99 0.45
86 84 0.38
87 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (85 bp):
AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCACTTCGTAAAAAACGCCGCTACAGAACATG
CTCTTTAGCGGCGCTTTTAT
Found at i:25658975 original size:12 final size:12
Alignment explanation
Indices: 25658958--25658984 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25658948 TTTTGAACCT
25658958 CTGCTTCTCTCG
1 CTGCTTCTCTCG
25658970 CTGCTTCTCTCG
1 CTGCTTCTCTCG
25658982 CTG
1 CTG
25658985 TAGCCTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.19, T:0.41
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:25659010 original size:21 final size:21
Alignment explanation
Indices: 25658970--25659038 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
25658960 GCTTCTCTCG
* *
25658970 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCACTGCAGCCT
* *
25658991 TTGCTTCTCTCATTGCAGCCT
1 CTGCTTCTCTCACTGCAGCCT
* * *
25659012 CTGCTTCCCTCACTACCGCCT
1 CTGCTTCTCTCACTGCAGCCT
25659033 CTGCTT
1 CTGCTT
25659039 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.07, C:0.41, G:0.14, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCACTGCAGCCT
Found at i:25661647 original size:6 final size:6
Alignment explanation
Indices: 25661636--25661676 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
25661626 AGAGAGCGAT
* *
25661636 GGTGAC GGTGAC GGTGAC GGTGAC AGTGAC GGTGAC AGTGA
1 GGTGAC GGTGAC GGTGAC GGTGAC GGTGAC GGTGAC GGTGA
25661677 TGCAGTAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.22, C:0.15, G:0.46, T:0.17
Consensus pattern (6 bp):
GGTGAC
Found at i:25661653 original size:12 final size:12
Alignment explanation
Indices: 25661637--25661676 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
25661627 GAGAGCGATG
*
25661637 GTGACGGTGACG
1 GTGACGGTGACA
25661649 GTGACGGTGACA
1 GTGACGGTGACA
25661661 GTGACGGTGACA
1 GTGACGGTGACA
25661673 GTGA
1 GTGA
25661677 TGCAGTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.45, T:0.17
Consensus pattern (12 bp):
GTGACGGTGACA
Found at i:25663068 original size:22 final size:21
Alignment explanation
Indices: 25663006--25663070 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
25662996 TAAAGCGGCC
*
25663006 TAAACCCCAAACCCCAAACCT
1 TAAACCCCAAACCCAAAACCT
* *
25663027 TAAACCCCAAACTTCTAAACCT
1 TAAACCCCAAAC-CCAAAACCT
*
25663049 TAAACCCAAAACACCAAAACCT
1 TAAACCCCAAAC-CCAAAACCT
25663071 ACATCATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 12 0.32
22 25 0.68
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (21 bp):
TAAACCCCAAACCCAAAACCT
Found at i:25663343 original size:16 final size:17
Alignment explanation
Indices: 25663324--25663358 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25663314 CAAATATGAC
25663324 AAACTA-AATATATAAT
1 AAACTACAATATATAAT
*
25663340 AAACTACATTATATAAT
1 AAACTACAATATATAAT
25663357 AA
1 AA
25663359 CCTAGCGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (17 bp):
AAACTACAATATATAAT
Found at i:25663690 original size:114 final size:114
Alignment explanation
Indices: 25663485--25664150 Score: 825
Period size: 114 Copynumber: 5.9 Consensus size: 114
25663475 TTTGCGGCGC
* *
25663485 AATACTATGCATTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGGCCAAAC
1 AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAC
* * * *
25663550 GCCGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTGACGACGCGCCGCT
66 TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
* * * * ** *
25663599 AATACTATACATTAGTGGTGTTTTCGAATAAGTGCCACTAATTCTAATATACCTCAAGACCAAAC
1 AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAC
25663664 TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
66 TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
* * * *
25663713 AATACTATGCTTTAGCTGCATTTTCCAATAAGCGCCACTAATTCTAGTATACCTCAAGACCAAAC
1 AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAC
* * * * *
25663778 TCTGCGTTTTGGTTAAGATATGTTGCGGTGCTTTTGACGGCACACCACT
66 TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
* * *
25663827 AATACTATGCGTTAGCGGTGTTTTCCCATAAGTGCCACTAATTCTAATATACCTCAAGACCAAAC
1 AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAC
* * * * * **
25663892 TCTGCATTTTGGTTAATATATTTTGCGGCGCTTTTCACAAATCGCCGCT
66 TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
** * * *
25663941 AATACT-TGCTTTAGCGGCGTTTTTTCATATGCGCCACTAATTCTAATATACATAAAGACCAAAC
1 AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAC
* * * * *
25664005 TCTGCATTTTGGTTAAGATATGTTGCGGCGCGTTTGGCGA-TCGCCGTT
66 TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
* ** * * * * *
25664053 AATACT-TTCTTTAGCAACGTTTTCCTATAATCGCCACTAATTCTAGTATACATCTAGACCAAAA
1 AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACC-AAA
* * *
25664117 CGCTGCGTTTTGGTTAAGAGATTTTGCGGCGCTT
65 CTCTGCGTTTTGGTTAAGATATGTTGCGGCGCTT
25664151 GATAGTAAAC
Statistics
Matches: 477, Mismatches: 74, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
112 56 0.12
113 116 0.24
114 305 0.64
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (114 bp):
AATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAAC
TCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGCGCCGCT
Found at i:25665130 original size:31 final size:31
Alignment explanation
Indices: 25665095--25665155 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
25665085 GATTTCTATC
25665095 GGTAAGTGACATGCTTTACCAAAAACTAATT
1 GGTAAGTGACATGCTTTACCAAAAACTAATT
25665126 GGTAAGTGACATGCTTTACCAAAAACTAAT
1 GGTAAGTGACATGCTTTACCAAAAACTAAT
25665156 CAGTAAAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (31 bp):
GGTAAGTGACATGCTTTACCAAAAACTAATT
Found at i:25672109 original size:19 final size:19
Alignment explanation
Indices: 25672085--25672121 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
25672075 CAAATCCATC
25672085 ATCCTTATATCAAGCTTAT
1 ATCCTTATATCAAGCTTAT
25672104 ATCCTTATATCAAGCTTA
1 ATCCTTATATCAAGCTTA
25672122 CCAAAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (19 bp):
ATCCTTATATCAAGCTTAT
Found at i:25673806 original size:70 final size:70
Alignment explanation
Indices: 25673690--25673827 Score: 258
Period size: 70 Copynumber: 2.0 Consensus size: 70
25673680 AACAAGGCCA
* *
25673690 AACCAACTTGTTCTTTTTCTTTATTTTTCTTTTGTATTTTCGGCAAAGATGATGAACTTTTTGCA
1 AACCAACTTGTTCTTTTTCTTTATTTTTCTTTTGTATTTTCAGCAAAGATAATGAACTTTTTGCA
25673755 TGTCG
66 TGTCG
25673760 AACCAACTTGTTCTTTTTCTTTATTTTTCTTTTGTATTTTCAGCAAAGATAATGAACTTTTTGCA
1 AACCAACTTGTTCTTTTTCTTTATTTTTCTTTTGTATTTTCAGCAAAGATAATGAACTTTTTGCA
25673825 TGT
66 TGT
25673828 TTTATATTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (70 bp):
AACCAACTTGTTCTTTTTCTTTATTTTTCTTTTGTATTTTCAGCAAAGATAATGAACTTTTTGCA
TGTCG
Found at i:25678309 original size:15 final size:15
Alignment explanation
Indices: 25678289--25678318 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25678279 AAACATTTAT
25678289 TTATTTATAAAATTA
1 TTATTTATAAAATTA
*
25678304 TTATTTTTAAAATTA
1 TTATTTATAAAATTA
25678319 AATTTTATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTTATAAAATTA
Found at i:25687275 original size:32 final size:32
Alignment explanation
Indices: 25687234--25687297 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
25687224 TTAAAAGTAC
25687234 ATCTTCAATATTGATGGAAGTCTGCTTCAGAG
1 ATCTTCAATATTGATGGAAGTCTGCTTCAGAG
25687266 ATCTTCAATATTGATGGAAGTCTGCTTCAGAG
1 ATCTTCAATATTGATGGAAGTCTGCTTCAGAG
25687298 TTGGCTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (32 bp):
ATCTTCAATATTGATGGAAGTCTGCTTCAGAG
Found at i:25688852 original size:16 final size:16
Alignment explanation
Indices: 25688827--25688864 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
25688817 GTCCTAAAGT
*
25688827 ATAAATCTCACAATGC
1 ATAAACCTCACAATGC
25688843 ATAAACCTCACAATGC
1 ATAAACCTCACAATGC
25688859 ATAAAC
1 ATAAAC
25688865 ATCCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.21
Consensus pattern (16 bp):
ATAAACCTCACAATGC
Found at i:25700923 original size:52 final size:51
Alignment explanation
Indices: 25700827--25700925 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 51
25700817 AAAATTGTGA
* * * * **
25700827 AAATATGAAAAATGTATGTATGTATGTATGTATACATATTTTAAAATTATT
1 AAATATAAAAAATGTAAGTATGTATATATATATACATAAATTAAAATTATT
*
25700878 AAATATAAAAATATGTAAGTATGTATATATATATAGATAAATTAAAAT
1 AAATATAAAAA-ATGTAAGTATGTATATATATATACATAAATTAAAAT
25700926 ATGCATATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 10 0.25
52 30 0.75
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (51 bp):
AAATATAAAAAATGTAAGTATGTATATATATATACATAAATTAAAATTATT
Found at i:25701240 original size:20 final size:22
Alignment explanation
Indices: 25701203--25701244 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25701193 CATGTACGTA
25701203 TATGCATATATTATAAAAAATG
1 TATGCATATATTATAAAAAATG
*
25701225 TATGTATATA-TA-AAAAAATG
1 TATGCATATATTATAAAAAATG
25701245 AAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGCATATATTATAAAAAATG
Found at i:25716365 original size:22 final size:23
Alignment explanation
Indices: 25716328--25716403 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
25716318 AACTAATCCT
* *
25716328 CTCTCAAATTTTCTCTTAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
25716351 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
*
25716373 CTCTCAAATTTCTTC-CAAATTT-
1 CTCTCAAATTTCCTCTC-AATTTC
25716395 CTCTCAAAT
1 CTCTCAAAT
25716404 CCATATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 29 0.62
23 18 0.38
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.46
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:25716402 original size:11 final size:11
Alignment explanation
Indices: 25716327--25716403 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
25716317 AAACTAATCC
25716327 TCTCTCAAATT
1 TCTCTCAAATT
*
25716338 T-TCTCTTAATT
1 TCTCTC-AAATT
25716349 TC-CTCTAAATT
1 TCTCTC-AAATT
25716360 TCCTCTC-AATT
1 T-CTCTCAAATT
25716371 TGCTCTCAAATT
1 T-CTCTCAAATT
25716383 TCT-TCCAAATT
1 TCTCT-CAAATT
25716394 TCTCTCAAAT
1 TCTCTCAAAT
25716404 CCATATTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 5 0.09
11 41 0.73
12 7 0.12
13 3 0.05
ACGTcount: A:0.25, C:0.27, G:0.01, T:0.47
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:25716420 original size:51 final size:50
Alignment explanation
Indices: 25716363--25716462 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
25716353 CTAAATTTCC
25716363 TCTCAATTTGCTCTCAAATT-TCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCTCTT--AAATTTCTCTCAAATCCATATTTAA
* * *
25716414 TCTCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATT-CTCTTAAATTTCTCTCAAATCCATATTT
25716463 TTAAATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 40 0.91
53 4 0.09
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (50 bp):
TCTCAATTTGCTCTCAAATTCTCTTAAATTTCTCTCAAATCCATATTTAA
Found at i:25717000 original size:124 final size:126
Alignment explanation
Indices: 25716759--25717011 Score: 402
Period size: 124 Copynumber: 2.0 Consensus size: 126
25716749 GAACTACCTA
* *
25716759 CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCTA
1 CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATATCTTCCAGGACCTA
* * * * *
25716824 CTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
66 CTATAGCAAAAGCGCGTACACGAGGGCGCGACTTCACAAATCCTTCTAATAAAGCATCCTG
*
25716885 CTTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATAT-TTCCAGGACCTA
1 CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATATCTTCCAGGACCTA
* *
25716948 CTATAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATCCTTCTAATAAAGCATCCTG
66 CTATAGCAAAAGCGCGTACACGAGGGCGCGACTTCACAAATCCTTCTAATAAAGCATCCTG
25717009 CTT
1 CTT
25717012 TGATTTTATC
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
124 68 0.58
125 40 0.34
126 9 0.08
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (126 bp):
CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATATCTTCCAGGACCTA
CTATAGCAAAAGCGCGTACACGAGGGCGCGACTTCACAAATCCTTCTAATAAAGCATCCTG
Found at i:25719717 original size:64 final size:64
Alignment explanation
Indices: 25719560--25719699 Score: 212
Period size: 64 Copynumber: 2.2 Consensus size: 64
25719550 ATAAACATAC
* * ** *
25719560 AAAAA-ACAA-ACAATTAATTTATTTATTTTTTAATAAAATGTAAATAAGTATATTATTGATGT
1 AAAAATACAATACAAATAATTTATTCATTTTTTGGTAAAATGTAAATAAGTAGATTATTGATGT
25719622 AAAAATACAATACAAATAATTTATTCATTTTTTGGTAAAATGTAAATAAGTAGATTATTGATGT
1 AAAAATACAATACAAATAATTTATTCATTTTTTGGTAAAATGTAAATAAGTAGATTATTGATGT
*
25719686 AACAATACAATACA
1 AAAAATACAATACA
25719700 TTTTTTGTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
62 5 0.07
63 4 0.06
64 61 0.87
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (64 bp):
AAAAATACAATACAAATAATTTATTCATTTTTTGGTAAAATGTAAATAAGTAGATTATTGATGT
Found at i:25722979 original size:23 final size:23
Alignment explanation
Indices: 25722948--25722999 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
25722938 ACCTACTTTC
* *
25722948 TTACTGTAGTAATTTTTGAGG-TA
1 TTACAGTAGTAATTTTCG-GGATA
25722971 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
25722994 TTACAG
1 TTACAG
25723000 AAATATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:25724046 original size:30 final size:31
Alignment explanation
Indices: 25724012--25724082 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
25724002 TTGCCCAGGA
* * *
25724012 GTAAATATTTAAAATTTGAGGGGTTAA-AGT
1 GTAAATATTTAAAAGTTGAAGGATTAACAGT
** *
25724042 GTAAATATGAAAAAGTTGAAGGATTAACTGT
1 GTAAATATTTAAAAGTTGAAGGATTAACAGT
25724073 GTAAATATTT
1 GTAAATATTT
25724083 TAAGTGTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.35
Consensus pattern (31 bp):
GTAAATATTTAAAAGTTGAAGGATTAACAGT
Found at i:25729359 original size:99 final size:98
Alignment explanation
Indices: 25729232--25729415 Score: 323
Period size: 99 Copynumber: 1.9 Consensus size: 98
25729222 CCTTTACAGG
*
25729232 GCACATTAAAGAAAATGATAACCTATCTTCTCGCTTTTATATTTGATAACATATAAATTTAAGGG
1 GCACATTAAAGAAAATGATAACCTATCTTCTCGCTTTTATATTTGATAACATATAAATTTAAAGG
25729297 GGTAAAAAGAAAATGGCATTTTCTTTAAAGGCGA
66 GGT-AAAAGAAAATGGCATTTTCTTTAAAGGCGA
* * *
25729331 GCACTTTAAAGAAAATGATAACTTATCTTCTCTCTTTTATATTTGATAACATATAAATTTAAAGG
1 GCACATTAAAGAAAATGATAACCTATCTTCTCGCTTTTATATTTGATAACATATAAATTTAAAGG
25729396 GGTAAAAGAAAATGGCATTT
66 GGTAAAAGAAAATGGCATTT
25729416 GCATTTGCCA
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 17 0.21
99 64 0.79
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (98 bp):
GCACATTAAAGAAAATGATAACCTATCTTCTCGCTTTTATATTTGATAACATATAAATTTAAAGG
GGTAAAAGAAAATGGCATTTTCTTTAAAGGCGA
Found at i:25730456 original size:42 final size:42
Alignment explanation
Indices: 25730375--25730457 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
25730365 GACTAATGGG
* * *
25730375 TTCCATTGATGCAGAAGGCATCAGTGATGGCATGGCCATTGA
1 TTCCATTGATGCAGAAGACATCAGTGATCGCATGACCATTGA
* * * *
25730417 TTCCATTGATGGAGAAGATATTAGTGATCGCGTGACCATTG
1 TTCCATTGATGCAGAAGACATCAGTGATCGCATGACCATTG
25730458 TAGGTTGACT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
TTCCATTGATGCAGAAGACATCAGTGATCGCATGACCATTGA
Found at i:25744412 original size:16 final size:17
Alignment explanation
Indices: 25744351--25744415 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
25744341 TCTTTTAATT
*
25744351 AATAAAACATAAAATAA
1 AATAAAACATAATATAA
**
25744368 AATAAAAGGTTAATATAA
1 AATAAAA-CATAATATAA
25744386 TAATGAAAACATAATA-AA
1 -AAT-AAAACATAATATAA
25744404 AATAAAACATAA
1 AATAAAACATAA
25744416 GTGAATATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.22
17 10 0.25
18 9 0.22
19 8 0.20
20 4 0.10
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.22
Consensus pattern (17 bp):
AATAAAACATAATATAA
Found at i:25750627 original size:27 final size:27
Alignment explanation
Indices: 25750576--25750627 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
25750566 CAGTAATATG
* *
25750576 AAAAATAAAGAACTCAATTTTTAAAAA
1 AAAAATAAAGAACTCAAATTCTAAAAA
25750603 AAAAATATAAGAACT-AAATTCTAAA
1 AAAAATA-AAGAACTCAAATTCTAAA
25750628 TTTACGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAATAAAGAACTCAAATTCTAAAAA
Found at i:25762843 original size:168 final size:168
Alignment explanation
Indices: 25762563--25762901 Score: 633
Period size: 168 Copynumber: 2.0 Consensus size: 168
25762553 TGCTTAATTA
25762563 CATAACTTATCAAAAATCATCACATGGTTAGGTAAATCTCATAATCATAATACATATGATATCAT
1 CATAACTTATCAAAAATCATCACATGGTTAGGTAAATCTCATAATCATAATACATATGATATCAT
*
25762628 ACTTTTCATAACATGGCTGTATATACTTTGTTCATCAATACTTCATACCTTTCCATAATTTTATA
66 ACTTTTCATAACATGGCTGTACATACTTTGTTCATCAATACTTCATACCTTTCCATAATTTTATA
*
25762693 GTGTATTCAATCGGAACCCTTTCCAGTTCATCCATTTT
131 GTGTATTCAATCGAAACCCTTTCCAGTTCATCCATTTT
*
25762731 CATAACTTATCAAAAATCATCACATGGTTAGGTAAATCTTATAATCATAATACATATGATATCAT
1 CATAACTTATCAAAAATCATCACATGGTTAGGTAAATCTCATAATCATAATACATATGATATCAT
*
25762796 ACTTTTCATAACATGGCTGTACATACTTTGTTCATCAATAGTTCATACCTTTCCATAATTTTATA
66 ACTTTTCATAACATGGCTGTACATACTTTGTTCATCAATACTTCATACCTTTCCATAATTTTATA
*
25762861 GTGTATTCAATCGAAACCCTTTCCAGTTCATCCCTTTT
131 GTGTATTCAATCGAAACCCTTTCCAGTTCATCCATTTT
25762899 CAT
1 CAT
25762902 GCCAATTGAA
Statistics
Matches: 166, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
168 166 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (168 bp):
CATAACTTATCAAAAATCATCACATGGTTAGGTAAATCTCATAATCATAATACATATGATATCAT
ACTTTTCATAACATGGCTGTACATACTTTGTTCATCAATACTTCATACCTTTCCATAATTTTATA
GTGTATTCAATCGAAACCCTTTCCAGTTCATCCATTTT
Found at i:25766322 original size:20 final size:20
Alignment explanation
Indices: 25766297--25766338 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
25766287 ACACAGACGA
25766297 TAGAGATTCATTTTGTGTGT
1 TAGAGATTCATTTTGTGTGT
25766317 TAGAGATTCATTTTGTGTGT
1 TAGAGATTCATTTTGTGTGT
25766337 TA
1 TA
25766339 TCTGTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (20 bp):
TAGAGATTCATTTTGTGTGT
Found at i:25786227 original size:16 final size:17
Alignment explanation
Indices: 25786206--25786238 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25786196 TTTTCAAATA
25786206 TAACATT-CAATTTAAT
1 TAACATTACAATTTAAT
*
25786222 TAACATTATAATTTAAT
1 TAACATTACAATTTAAT
25786239 CCATGATACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
TAACATTACAATTTAAT
Found at i:25788140 original size:24 final size:24
Alignment explanation
Indices: 25788108--25788155 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
25788098 CTAAATTCTA
25788108 AGTTAGTTACTGACCATGTGTATG
1 AGTTAGTTACTGACCATGTGTATG
*
25788132 AGTTAGTTACTGACTATGTGTATG
1 AGTTAGTTACTGACCATGTGTATG
25788156 TAACTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (24 bp):
AGTTAGTTACTGACCATGTGTATG
Found at i:25800846 original size:12 final size:12
Alignment explanation
Indices: 25800829--25800905 Score: 56
Period size: 12 Copynumber: 6.7 Consensus size: 12
25800819 TTTGAACGAG
25800829 TTTTATAATAAT
1 TTTTATAATAAT
* *
25800841 TTTTATATTTAT
1 TTTTATAATAAT
* *
25800853 GTATATATATAA-
1 TTTTATA-ATAAT
25800865 TTTT-T-AT-AT
1 TTTTATAATAAT
25800874 TTTTATAATAAAT
1 TTTTATAAT-AAT
25800887 TTTT-TAATAAT
1 TTTTATAATAAT
*
25800898 TGTTATAA
1 TTTTATAA
25800906 GTGTTTATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
8 1 0.02
9 6 0.12
10 1 0.02
11 9 0.18
12 24 0.49
13 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTATAATAAT
Found at i:25800864 original size:25 final size:23
Alignment explanation
Indices: 25800832--25800890 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
25800822 GAACGAGTTT
25800832 TATA-ATAATTTTTATATTTATGTA
1 TATATATAATTTTTATATTT-T-TA
25800856 TATATATAATTTTTATATTTTTA
1 TATATATAATTTTTATATTTTTA
25800879 TA-ATA-AATTTTT
1 TATATATAATTTTT
25800891 TAATAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 4 0.12
24 5 0.15
25 15 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATATATAATTTTTATATTTTTA
Found at i:25801006 original size:8 final size:9
Alignment explanation
Indices: 25800860--25801009 Score: 54
Period size: 9 Copynumber: 15.3 Consensus size: 9
25800850 TATGTATATA
25800860 TATAATTTT
1 TATAATTTT
*
25800869 TATATTTTT
1 TATAATTTT
25800878 ATAATAAATTTTT
1 -T-AT-AA-TTTT
*
25800891 TAATAATTGT
1 T-ATAATTTT
*
25800901 TATAAGTGTT
1 TATAA-TTTT
25800911 TAT-ATTTT
1 TATAATTTT
25800919 TATAAGTTATT
1 TATAA-TT-TT
*
25800930 TAT-ATGCTTA
1 TATAAT--TTT
*
25800940 TATAAAATTT
1 TAT-AATTTT
25800950 TA-ATATTTT
1 TATA-ATTTT
*
25800959 TATCATTTT
1 TATAATTTT
* **
25800968 TATCATACT
1 TATAATTTT
*
25800977 TACAATTTTTTT
1 TATAA---TTTT
25800989 TATAATTTT
1 TATAATTTT
25800998 TATAATTTT
1 TATAATTTT
25801007 TAT
1 TAT
25801010 TAGAAATGTA
Statistics
Matches: 106, Mismatches: 18, Indels: 34
0.67 0.11 0.22
Matches are distributed among these distances:
8 7 0.07
9 52 0.49
10 21 0.20
11 10 0.09
12 12 0.11
13 4 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (9 bp):
TATAATTTT
Found at i:25802092 original size:18 final size:18
Alignment explanation
Indices: 25802061--25802095 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25802051 CTCACATAAA
* *
25802061 TTTTTTTATTTTTTTTTG
1 TTTTTGTATCTTTTTTTG
25802079 TTTTTGTATCTTTTTTT
1 TTTTTGTATCTTTTTTT
25802096 ATCACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.86
Consensus pattern (18 bp):
TTTTTGTATCTTTTTTTG
Found at i:25803263 original size:19 final size:19
Alignment explanation
Indices: 25803217--25803272 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
25803207 AATCTTCAAG
*
25803217 GATATGCAATCTTAGATAT
1 GATATGCAATCTTGGATAT
25803236 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTGGATAT
25803257 GATATGCAATCTTGGA
1 GATATGCAATCTTGGA
25803273 AGGTATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTGGATAT
Found at i:25810324 original size:88 final size:88
Alignment explanation
Indices: 25810181--25811057 Score: 1127
Period size: 88 Copynumber: 10.0 Consensus size: 88
25810171 GAAATCACAA
* * * * * * *
25810181 AGCCTTGCCTTCCC-GGTTTGCAGCGTAGCAGGTTGAAAATAACAAATCTTGCCTTCCTGTACTG
1 AGCCTTGCC-TCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTG
* * *
25810245 ACGGCGAAGCAAATCGAAGATACC
65 ACAGTGAAGCAGATCGAAGATACC
* * ** *
25810269 AGCCTTGCCTCACTGGGTTGTTGTGGAGCAGGTTGAAGATAGCAGATCTCACCTTCCTGCA-TCG
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACT-G
*
25810333 ACAGCGAAGCAGATCGAAGATACC
65 ACAGTGAAGCAGATCGAAGATACC
* *
25810357 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGTAGATCTTGCCTTCCTGCA-TCG
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACT-G
*
25810421 ACAGCGAAGCAGATCGAAGATACC
65 ACAGTGAAGCAGATCGAAGATACC
* * *
25810445 AGCCTTGCCTCCTTGGGTTGTAGTGGAGCATGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
* *
25810510 TAGTGAAGCAGATCAAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * *
25810533 AGCCTTGCCTCTCTGGGTCGTAGTGGAGCAGGTTGAAGATAGTAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
25810598 CAGTGAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * *
25810621 AGCCTTGCCTCCCTGGGTTGTAGTAGAGCAGGTTGAAGATAGCAGATCTTGCCTCCCTGCA-TCG
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACT-G
*
25810685 AGAGTGAAGCAGATCGAAGATACC
65 ACAGTGAAGCAGATCGAAGATACC
* * *
25810709 AGCCTTGCCTCCCTGGGTTGTAGTGGAGTAGGTTGAAGATAGCAGATCTTGCTTTCCTGTA-TCA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACT-G
*
25810773 ACAGTGAAACAGATCGAAGATACC
65 ACAGTGAAGCAGATCGAAGATACC
* * * *
25810797 AGCCTTGCCTCCCTGGGTCGTAGTGGAGCTGGTTGAAGATAGCAGATCTTACCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
25810862 CAGTGAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * *
25810885 AGCCTTGCCTCCCTGGGTTGTAATGGAGCAGATAGAAGATAGCAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
* * *
25810950 AAGTGAAGCAAATCAAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * * * * * * * * *
25810973 AGCCTTGCCTCCTTGGGTTGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
* *
25811038 C-GTGAAGTAGATCAAAGATA
66 CAGTGAAGCAGATCGAAGATA
25811058 GCAGATTTTG
Statistics
Matches: 702, Mismatches: 82, Indels: 11
0.88 0.10 0.01
Matches are distributed among these distances:
87 21 0.03
88 681 0.97
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (88 bp):
AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
CAGTGAAGCAGATCGAAGATACC
Found at i:25811061 original size:44 final size:44
Alignment explanation
Indices: 25810994--25811336 Score: 386
Period size: 44 Copynumber: 7.8 Consensus size: 44
25810984 CTTGGGTTGT
25810994 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * *
25811038 CGTGAAGTAGATCAAAGATAGCAGATTTTGTCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * * *** *
25811082 CATTAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
*
25811126 TGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
1 -CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * *** *
25811171 CGTGAAGTAGATCGAATG-TAGTAGATCTTGTCTTCCCATACTGG
1 CGTGAAGTAGATCGAA-GAAAGCAGATCTTGTCTTCATGTATTGG
* *
25811215 TGGTGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGG
1 -CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* *
25811260 C--GAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATCGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * ** ** *
25811302 CATGAAATAGATTAAAGGTAGCAGATCTTATCTTC
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
25811337 CCATACTGGT
Statistics
Matches: 250, Mismatches: 43, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
42 39 0.16
44 138 0.55
45 73 0.29
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (44 bp):
CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
Found at i:25811164 original size:89 final size:88
Alignment explanation
Indices: 25810996--25811292 Score: 420
Period size: 89 Copynumber: 3.4 Consensus size: 88
25810986 TGGGTTGTCG
*** * * * *
25810996 TGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAGC
1 TGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGC
*
25811060 AGATTTTGTCTTCATGTATTGGC
66 AGATCTTGTCTTCATGTATTGGC
* *
25811083 ATTAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAG
1 -TGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAG
25811148 CAGATCTTGTCTTCATGTATTGGC
65 CAGATCTTGTCTTCATGTATTGGC
* *
25811172 GTGAAGTAGATCGAATG-TAGTAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAA
1 -TGAAGTAGATCGAA-GAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAA
*
25811236 GTAGATCTTGTCTTCATGTATTGGC
64 GCAGATCTTGTCTTCATGTATTGGC
*
25811261 -GAAGTAGATCGAAGAAAGCAGATATTGTCTTC
1 TGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
25811293 ATGTATCGGC
Statistics
Matches: 189, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 27 0.14
88 36 0.19
89 124 0.66
90 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (88 bp):
TGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGC
AGATCTTGTCTTCATGTATTGGC
Found at i:25811328 original size:131 final size:133
Alignment explanation
Indices: 25810997--25811364 Score: 481
Period size: 131 Copynumber: 2.8 Consensus size: 133
25810987 GGGTTGTCGT
*
25810997 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTAGCAG
* *** * ** * * *
25811062 ATTTTGTCTTCATGTATTGG-CATTAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGG
66 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT-CCATACTAG
*
25811126 TGGT
130 TGGC
* * *
25811130 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATGTAGTAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTAGCAG
* * *
25811195 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGTAGATCTTGTCTT-CAT-GTATT
66 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCATACTAGT
25811258 GGC
131 GGC
* * * * *
25811261 GAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATCGGCATGAAATAGATTAAAGGTAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTAGCAG
* *
25811326 ATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
66 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
25811365 TACAAGTCTT
Statistics
Matches: 206, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
131 98 0.48
132 3 0.01
133 76 0.37
134 29 0.14
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (133 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTAGCAG
ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCATACTAGT
GGC
Found at i:25811783 original size:19 final size:19
Alignment explanation
Indices: 25811709--25811780 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
25811699 AATCTTCAAG
25811709 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
25811728 GGTATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
25811747 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
25811768 GATATGCAATCTT
1 GATATGCAATCTT
25811781 GGAATATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 31 0.65
21 17 0.35
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:25821882 original size:6 final size:6
Alignment explanation
Indices: 25821871--25821943 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
25821861 TTTTTCCTTA
25821871 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
25821919 ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT A
25821944 ACTCATTTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:25822859 original size:25 final size:25
Alignment explanation
Indices: 25822806--25822859 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
25822796 TTTTCTTTTC
** *
25822806 TTTTTCTTTTCATTTTTAATTTAGG
1 TTTTTCTTTTCATTTTTAAAGTAGA
25822831 TTTTCTCTTTTC-TTTTTAAAGTAGA
1 TTTT-TCTTTTCATTTTTAAAGTAGA
25822856 TTTT
1 TTTT
25822860 ATTCTTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.17, C:0.09, G:0.07, T:0.67
Consensus pattern (25 bp):
TTTTTCTTTTCATTTTTAAAGTAGA
Found at i:25822865 original size:26 final size:26
Alignment explanation
Indices: 25822806--25822867 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
25822796 TTTTCTTTTC
** *
25822806 TTTTTCTTTTCATTTTTAATTTAGGT
1 TTTTTCTTTTCATTTTTAAAGTAGAT
*
25822832 TTTCTCTTTTC-TTTTTAAAGTAGAT
1 TTTTTCTTTTCATTTTTAAAGTAGAT
25822857 TTTATTCTTTT
1 TTT-TTCTTTT
25822868 AGTTTCTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (26 bp):
TTTTTCTTTTCATTTTTAAAGTAGAT
Found at i:25825766 original size:12 final size:12
Alignment explanation
Indices: 25825749--25825774 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25825739 GTAATGGACA
25825749 TTGGACATTTAT
1 TTGGACATTTAT
25825761 TTGGACATTTAT
1 TTGGACATTTAT
25825773 TT
1 TT
25825775 TGGTGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGGACATTTAT
Found at i:25835530 original size:3 final size:3
Alignment explanation
Indices: 25835522--25835593 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
25835512 TTTTAGTTAG
* *
25835522 TAT TAT TAT TTT TAT TAT TAT T-T CCATT TAT TAT TAT T-T TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT TAT TAT TAT
* * *
25835566 TAT TAT TACT TAG TCT TAT TAA TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT
25835594 GATGTATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
2 5 0.09
3 43 0.81
4 4 0.08
5 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:25835553 original size:16 final size:15
Alignment explanation
Indices: 25835532--25835573 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
25835522 TATTATTATT
25835532 TTTATTATTATTTCCA
1 TTTATTATTATTT-CA
*
25835548 TTTATTATTATTTTA
1 TTTATTATTATTTCA
25835563 TATTATTATTA
1 T-TTATTATTA
25835574 CTTAGTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTATTATTTCA
Found at i:25845034 original size:12 final size:11
Alignment explanation
Indices: 25845006--25845065 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 11
25844996 TTATCTCTTC
* *
25845006 AAAAAAAAAAA
1 AAAAAAGAAAG
25845017 AAAGAAAGAAAG
1 AAA-AAAGAAAG
25845029 AAAGAAAGAAAG
1 AAA-AAAGAAAG
*
25845041 -AAAAACAAAG
1 AAAAAAGAAAG
25845051 AAAAAAGAAA-
1 AAAAAAGAAAG
25845061 AAAAA
1 AAAAA
25845066 GAGAGCATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
10 12 0.28
11 13 0.30
12 18 0.42
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:25845799 original size:10 final size:11
Alignment explanation
Indices: 25845761--25845802 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
25845751 TAACATGTTG
25845761 AATTTTGATTA
1 AATTTTGATTA
25845772 AATTTT-ATAATA
1 AATTTTGAT--TA
25845784 AATTTTGATT-
1 AATTTTGATTA
25845794 AATTTTGAT
1 AATTTTGAT
25845803 CATTTTCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 11 0.39
11 7 0.25
12 8 0.29
13 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (11 bp):
AATTTTGATTA
Found at i:25845962 original size:22 final size:22
Alignment explanation
Indices: 25845937--25845979 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
25845927 TATGAATATT
*
25845937 AATTCATAATCTAA-TTATTTTA
1 AATT-ATAATCCAATTTATTTTA
*
25845959 AATTTTAATCCAATTTATTTT
1 AATTATAATCCAATTTATTTT
25845980 TGGTTAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTATAATCCAATTTATTTTA
Found at i:25860895 original size:24 final size:24
Alignment explanation
Indices: 25860855--25860901 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
25860845 AAAGGGAAAT
*
25860855 AAGAGAAAGTGATGGAAAATGTTG
1 AAGAGAAAGTGAAGGAAAATGTTG
*
25860879 AAGAGAAAG-GAAAGGAAAGTGTT
1 AAGAGAAAGTG-AAGGAAAATGTT
25860902 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
AAGAGAAAGTGAAGGAAAATGTTG
Found at i:25862364 original size:26 final size:25
Alignment explanation
Indices: 25862322--25862370 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
25862312 TCTCCTCTAT
25862322 ATTTTACCCTAGCAAAATTTTGAAG
1 ATTTTACCCTAGCAAAATTTTGAAG
* *
25862347 ATTTTACCCCTGGTAAAATTTTGA
1 ATTTTA-CCCTAGCAAAATTTTGA
25862371 GAAAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (25 bp):
ATTTTACCCTAGCAAAATTTTGAAG
Found at i:25862608 original size:10 final size:10
Alignment explanation
Indices: 25862583--25862611 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
25862573 CATTTTTCGT
25862583 TTTCTATTCA
1 TTTCTATTCA
25862593 -TTCTATTCA
1 TTTCTATTCA
25862602 TTTCTATTCA
1 TTTCTATTCA
25862612 AACATGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:25889822 original size:15 final size:15
Alignment explanation
Indices: 25889804--25889845 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25889794 TAAAATATTT
25889804 AAAAATTAGAATTAA
1 AAAAATTAGAATTAA
25889819 AAAAATTAG-ATT-A
1 AAAAATTAGAATTAA
* *
25889832 AGAAATTAAAATTA
1 AAAAATTAGAATTA
25889846 GGTGTCTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (15 bp):
AAAAATTAGAATTAA
Found at i:25898286 original size:38 final size:38
Alignment explanation
Indices: 25898152--25898286 Score: 101
Period size: 38 Copynumber: 3.4 Consensus size: 38
25898142 TTCCAACATG
* * * * *
25898152 TATTATGTTCAATTTAATTTCTCTTTAAAATAATCAAA
1 TATTATCTTCAATTTAATTACTATTCAAAATAATAAAA
* * * * *
25898190 TATAATCTTCAATTCAATTCCTGTCCAAAATAATCCCCAATAAA
1 TATTATCTTCAATTTAATTACTATTCAAAATAAT-----A-AAA
*
25898234 TTTTAT-TTGCAATTTAATTACTATTCAAAATAATAAAA
1 TATTATCTT-CAATTTAATTACTATTCAAAATAATAAAA
25898272 TATTATCTTCAATTT
1 TATTATCTTCAATTT
25898287 CATTCCCCTA
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
38 41 0.55
39 3 0.04
43 2 0.03
44 28 0.38
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (38 bp):
TATTATCTTCAATTTAATTACTATTCAAAATAATAAAA
Found at i:25899551 original size:13 final size:11
Alignment explanation
Indices: 25899523--25899565 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
25899513 AGTTAAATAT
25899523 TATTTTATTAA
1 TATTTTATTAA
25899534 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
25899547 TA-TTTATTAT
1 TATTTTATTAA
25899557 TATTTTATT
1 TATTTTATT
25899566 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:25899552 original size:23 final size:23
Alignment explanation
Indices: 25899526--25899569 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25899516 TAAATATTAT
25899526 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
25899549 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
25899570 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:25900883 original size:2 final size:2
Alignment explanation
Indices: 25900876--25900930 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
25900866 AGGAGGAGGA
25900876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25900918 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
25900931 GTAGATAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25903021 original size:17 final size:18
Alignment explanation
Indices: 25902999--25903033 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25902989 CAAAATTTAT
25902999 TTAAAA-TTTAAAAAAAA
1 TTAAAATTTTAAAAAAAA
25903016 TTAAAATTTTAAAAAAAA
1 TTAAAATTTTAAAAAAAA
25903034 ATTGCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAATTTTAAAAAAAA
Found at i:25903355 original size:17 final size:18
Alignment explanation
Indices: 25903319--25903372 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
25903309 ATGCAAACTC
* * *
25903319 TTTTTACATAATTTTAAA
1 TTTTTATATTATTTTTAA
25903337 TTCTTTA-ATT-TTTTTAA
1 TT-TTTATATTATTTTTAA
25903354 TTTTTATATTATTTTTAA
1 TTTTTATATTATTTTTAA
25903372 T
1 T
25903373 AAGGTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 4 0.13
17 11 0.35
18 12 0.39
19 4 0.13
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATATTATTTTTAA
Found at i:25903407 original size:7 final size:7
Alignment explanation
Indices: 25903395--25903432 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
25903385 TTTTATAATT
25903395 ATTTTAA
1 ATTTTAA
25903402 ATTTTAA
1 ATTTTAA
25903409 ATTTTAA
1 ATTTTAA
25903416 ATTTTAA
1 ATTTTAA
25903423 ATTTTTAA
1 A-TTTTAA
25903431 AT
1 AT
25903433 ATTTTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTTAA
Found at i:25903430 original size:8 final size:8
Alignment explanation
Indices: 25903330--25903437 Score: 60
Period size: 7 Copynumber: 12.5 Consensus size: 8
25903320 TTTTACATAA
25903330 TTTTAAAT
1 TTTTAAAT
*
25903338 TCTTTAATT
1 T-TTTAAAT
*
25903347 TTTTTAAT
1 TTTTAAAT
25903355 TTTTATATTAT
1 TTTTA-A--AT
*
25903366 TTTTAATAAG
1 TTTT-A-AAT
*
25903376 GTTTAATAT
1 TTTTAA-AT
25903385 TTTTATAATT
1 TTTTA-AA-T
25903395 ATTTTAAA-
1 -TTTTAAAT
25903403 TTTTAAA-
1 TTTTAAAT
25903410 TTTTAAA-
1 TTTTAAAT
25903417 TTTTAAAT
1 TTTTAAAT
25903425 TTTTAAAT
1 TTTTAAAT
25903433 ATTTT
1 -TTTT
25903438 TCTATTATTT
Statistics
Matches: 81, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
7 21 0.26
8 19 0.23
9 19 0.23
10 8 0.10
11 11 0.14
12 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (8 bp):
TTTTAAAT
Found at i:25905348 original size:17 final size:17
Alignment explanation
Indices: 25905326--25905359 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25905316 CCCATTAGTG
*
25905326 AAATAAACCAAATAAAA
1 AAATAAACAAAATAAAA
*
25905343 AAATAAATAAAATAAAA
1 AAATAAACAAAATAAAA
25905360 CCAAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAATAAACAAAATAAAA
Found at i:25905363 original size:27 final size:26
Alignment explanation
Indices: 25905326--25905376 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
25905316 CCCATTAGTG
25905326 AAATAAACCAAATAAAAAAATAAATA
1 AAATAAACCAAATAAAAAAATAAATA
* *
25905352 AAATAAAACCAAATTAAAAATTAAA
1 AAAT-AAACCAAATAAAAAAATAAA
25905377 GGTCCACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATAAACCAAATAAAAAAATAAATA
Found at i:25907324 original size:3 final size:3
Alignment explanation
Indices: 25907316--25907340 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25907306 AGGTTTTTTA
25907316 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
25907341 GGGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25919622 original size:17 final size:17
Alignment explanation
Indices: 25919600--25919633 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25919590 CACATTAGTG
*
25919600 AAATAAACCAAATAAAA
1 AAATAAACAAAATAAAA
*
25919617 AAATAAATAAAATAAAA
1 AAATAAACAAAATAAAA
25919634 CCAAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAATAAACAAAATAAAA
Found at i:25919637 original size:27 final size:26
Alignment explanation
Indices: 25919600--25919650 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
25919590 CACATTAGTG
25919600 AAATAAACCAAATAAAAAAATAAATA
1 AAATAAACCAAATAAAAAAATAAATA
* *
25919626 AAATAAAACCAAATTAAAAATTAAA
1 AAAT-AAACCAAATAAAAAAATAAA
25919651 GGTCCACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATAAACCAAATAAAAAAATAAATA
Found at i:25920008 original size:5 final size:5
Alignment explanation
Indices: 25919998--25920026 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
25919988 TTTGGATTTC
25919998 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
25920027 TATTCTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:25921611 original size:3 final size:3
Alignment explanation
Indices: 25921603--25921627 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25921593 AGGTTTTTTA
25921603 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
25921628 GGGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25923150 original size:9 final size:9
Alignment explanation
Indices: 25923121--25923150 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25923111 TGAATTTTAC
25923121 AATTCGAAT
1 AATTCGAAT
*
25923130 AACTCGAAT
1 AATTCGAAT
25923139 AATTCGAAT
1 AATTCGAAT
25923148 AAT
1 AAT
25923151 AGATTGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:25923253 original size:19 final size:19
Alignment explanation
Indices: 25923229--25923298 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
25923219 AAAATTATAA
*
25923229 AAAATTCAAATTAATTTTC
1 AAAATTCAAAATAATTTTC
*
25923248 AAAATTTTAAAATAATTTTTC
1 AAAA-TTCAAAATAA-TTTTC
*
25923269 -AAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TC
25923287 AAAATTCAAAAT
1 AAAATTCAAAAT
25923299 TTTATATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 22 0.51
20 11 0.26
21 5 0.12
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:25923302 original size:18 final size:19
Alignment explanation
Indices: 25923269--25923304 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25923259 ATAATTTTTC
25923269 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTATAA
25923288 AAATTCAAAAT-TTTATA
1 AAATTCAAAATATTTATA
25923305 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTCAAAATATTTATAA
Found at i:25923319 original size:20 final size:20
Alignment explanation
Indices: 25923307--25923375 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
25923297 ATTTTATATT
25923307 TTTTAAAAAAATTATAATAA
1 TTTTAAAAAAATTATAATAA
25923327 TTTTAAAAAAATTATAAATAA
1 TTTTAAAAAAATTAT-AATAA
* ** *
25923348 TATATAAAGGAATTTTAA-AA
1 T-TTTAAAAAAATTATAATAA
25923368 TTTTAAAA
1 TTTTAAAA
25923376 TTTTCTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 5 0.12
20 18 0.44
21 8 0.20
22 10 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TTTTAAAAAAATTATAATAA
Found at i:25923497 original size:16 final size:16
Alignment explanation
Indices: 25923478--25923508 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25923468 TTGAAAAAAT
25923478 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
25923494 TTTCAAATTTATATG
1 TTTCAAATATATATG
25923509 CTCTAACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:25925905 original size:4 final size:4
Alignment explanation
Indices: 25925889--25925961 Score: 103
Period size: 4 Copynumber: 18.0 Consensus size: 4
25925879 ATCATAAATT
*
25925889 CATA CAAA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
25925937 CATA CATC CA-A CATCA CATAA CATA
1 CATA CATA CATA CAT-A CAT-A CATA
25925962 ATTCATACTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
3 2 0.03
4 52 0.84
5 8 0.13
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:25935986 original size:30 final size:30
Alignment explanation
Indices: 25935905--25935986 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 30
25935895 AATGTGCATG
*
25935905 ATTAAATCAAAATTAAAGTTTCGAGTATACA
1 ATTAAA-CCAAATTAAAGTTTCGAGTATACA
* * *
25935936 TTTAAACCACAATTAGAGTTTC-ATGTATATA
1 ATTAAACCA-AATTAAAGTTTCGA-GTATACA
**
25935967 ATTGCACCAAATTAAAGTTT
1 ATTAAACCAAATTAAAGTTT
25935987 ATTTATACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
30 13 0.32
31 28 0.68
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (30 bp):
ATTAAACCAAATTAAAGTTTCGAGTATACA
Found at i:25937016 original size:40 final size:40
Alignment explanation
Indices: 25936961--25937126 Score: 206
Period size: 40 Copynumber: 4.2 Consensus size: 40
25936951 AAATGAAGAA
25936961 GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCT
1 GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCT
* * ** * *
25937001 GTGCCATTGTTTGTACTTTGGCGCACCTGAATGCACATAT
1 GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCT
* * *
25937041 GTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCT
1 GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCT
* * * * *
25937081 ATGTCCTTGTTTGTACTTCGGTAACCCTAAATGCACATTT
1 GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCT
25937121 GTGCCC
1 GTGCCC
25937127 CTAATTGCAC
Statistics
Matches: 101, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (40 bp):
GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCT
Found at i:25937094 original size:80 final size:80
Alignment explanation
Indices: 25936961--25937158 Score: 240
Period size: 80 Copynumber: 2.5 Consensus size: 80
25936951 AAATGAAGAA
* * * * * *
25936961 GTGCCCTTGTTTGTACTTCGGTACCCCTGAATGCACATCTGTGCCATTGTTTGTACTTTGGCGCA
1 GTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTATGCCATTGTTTGTACTTCGG-GAA
*
25937026 -CCTGAATGCACATAT
65 CCCTAAATGCACATAT
*
25937041 GTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTATGTCC-TTGTTTGTACTTCGGTAA
1 GTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTATG-CCATTGTTTGTACTTCGGGAA
*
25937105 CCCTAAATGCACATTT
65 CCCTAAATGCACATAT
* * *
25937121 GTGCCCCTAATTGCACTTCAGTGCCCCTG-ATCGCACAT
1 GTGCCCCTATTTGTACTTCAGTACCCCTGAAT-GCACAT
25937159 TCATGCTCCT
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 3 0.03
80 98 0.95
81 2 0.02
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (80 bp):
GTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTATGCCATTGTTTGTACTTCGGGAAC
CCTAAATGCACATAT
Found at i:25937139 original size:40 final size:40
Alignment explanation
Indices: 25937030--25937142 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 40
25937020 GGCGCACCTG
* *
25937030 AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTG
1 AATGCACATATGTGCCCCTATTTGTACTTCAGTAACCCTA
* * * * * *
25937070 AATGCACATCTATGTCCTTGTTTGTACTTCGGTAACCCTA
1 AATGCACATATGTGCCCCTATTTGTACTTCAGTAACCCTA
* * *
25937110 AATGCACATTTGTGCCCCTAATTGCACTTCAGT
1 AATGCACATATGTGCCCCTATTTGTACTTCAGT
25937143 GCCCCTGATC
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (40 bp):
AATGCACATATGTGCCCCTATTTGTACTTCAGTAACCCTA
Found at i:25937144 original size:20 final size:21
Alignment explanation
Indices: 25937112--25937178 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
25937102 TAACCCTAAA
* *
25937112 TGCACATT-TGTGCCCCTAAT
1 TGCACATTCAGTGCCCCTGAT
25937132 TGCAC-TTCAGTGCCCCTGAT
1 TGCACATTCAGTGCCCCTGAT
* *
25937152 CGCACATTCA-TGCTCCTGAT
1 TGCACATTCAGTGCCCCTGAT
25937172 TGCACAT
1 TGCACAT
25937179 GAGTATAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 34 0.85
21 4 0.10
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.31
Consensus pattern (21 bp):
TGCACATTCAGTGCCCCTGAT
Found at i:25937578 original size:20 final size:20
Alignment explanation
Indices: 25937553--25937618 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
25937543 AGAAACATTT
25937553 GTGCCCTTGATTGCACTTCG
1 GTGCCCTTGATTGCACTTCG
* * *
25937573 GTGCCCCTGATCT-CACATCC
1 GTGCCCTTGAT-TGCACTTCG
* *
25937593 GTGCTCTTGATTGCACTTTG
1 GTGCCCTTGATTGCACTTCG
25937613 GTGCCC
1 GTGCCC
25937619 CTATTATGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.11, C:0.33, G:0.23, T:0.33
Consensus pattern (20 bp):
GTGCCCTTGATTGCACTTCG
Found at i:25938436 original size:15 final size:15
Alignment explanation
Indices: 25938416--25938449 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
25938406 TAAGCATTTT
25938416 TGGCTAAGGTTATAA
1 TGGCTAAGGTTATAA
25938431 TGGCTAAGGTTATAA
1 TGGCTAAGGTTATAA
25938446 TGGC
1 TGGC
25938450 ATGTATTGGT
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:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (15 bp):
TGGCTAAGGTTATAA
Found at i:25942443 original size:19 final size:16
Alignment explanation
Indices: 25942400--25942446 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
25942390 ATTGAGCTTT
25942400 GAATGCTCCTTTTGAA
1 GAATGCTCCTTTTGAA
25942416 -AAT-CTCCTTTTACGTAA
1 GAATGCTCCTTTT--G-AA
25942433 GAATGCTCCTTTTG
1 GAATGCTCCTTTTG
25942447 TTGGACTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 1 0.04
17 3 0.12
18 3 0.12
19 8 0.31
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (16 bp):
GAATGCTCCTTTTGAA
Found at i:25942502 original size:16 final size:17
Alignment explanation
Indices: 25942481--25942514 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25942471 CTTTGAAAAG
25942481 CTCAAG-TCTGTTCTGA
1 CTCAAGCTCTGTTCTGA
25942497 CTCAAGCTTCTGTTCTGA
1 CTCAAGC-TCTGTTCTGA
25942515 TACAGCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (17 bp):
CTCAAGCTCTGTTCTGA
Found at i:25948489 original size:17 final size:17
Alignment explanation
Indices: 25948469--25948519 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
25948459 CACATGGCCG
25948469 TGTGCCCCACACGGTCA
1 TGTGCCCCACACGGTCA
*
25948486 TGTG----ACACGGTCG
1 TGTGCCCCACACGGTCA
*
25948499 TGTACCCCACACGGTCA
1 TGTGCCCCACACGGTCA
25948516 TGTG
1 TGTG
25948520 GCACGGCCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 11 0.42
17 15 0.58
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (17 bp):
TGTGCCCCACACGGTCA
Found at i:25948507 original size:30 final size:30
Alignment explanation
Indices: 25948464--25948531 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
25948454 GCTACCACAT
*
25948464 GGCCGTGTGCCCCACACGGTCATGTGACAC
1 GGCCGTGTACCCCACACGGTCATGTGACAC
* *
25948494 GGTCGTGTACCCCACACGGTCATGTGGCAC
1 GGCCGTGTACCCCACACGGTCATGTGACAC
25948524 GGCCGTGT
1 GGCCGTGT
25948532 GATTCTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.19
Consensus pattern (30 bp):
GGCCGTGTACCCCACACGGTCATGTGACAC
Found at i:25950936 original size:19 final size:18
Alignment explanation
Indices: 25950909--25950944 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25950899 CAGCTCAAAG
*
25950909 TAAATAAATTATTAAAAAA
1 TAAAAAAATTA-TAAAAAA
25950928 TAAAAAAATTATAAAAA
1 TAAAAAAATTATAAAAA
25950945 CCAAATCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAAATTATAAAAAA
Found at i:25961179 original size:19 final size:19
Alignment explanation
Indices: 25961144--25961181 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25961134 ATATGAAACA
**
25961144 TTGAGTTCTAAGTTATTTT
1 TTGAGTTCTAAAATATTTT
25961163 TTGAGTTCTAAAATATTTT
1 TTGAGTTCTAAAATATTTT
25961182 CTTTTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (19 bp):
TTGAGTTCTAAAATATTTT
Done.