Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:1600610 original size:20 final size:20
Alignment explanation
Indices: 1600587--1600641 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1600577 CTGAAACTTT
1600587 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
1600607 AAATCGCAACACAAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1600627 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
1600642 TTTGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1601024 original size:22 final size:22
Alignment explanation
Indices: 1600994--1601053 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1600984 CCTCGGTGGT
*
1600994 TGATTTCGTCTGAGATGGAGAC
1 TGATTTCGTCAGAGATGGAGAC
* * *
1601016 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCAGAGATGGAGAC
1601038 TGATTTCGTCAGAGAT
1 TGATTTCGTCAGAGAT
1601054 AGGGACGGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.13, G:0.33, T:0.30
Consensus pattern (22 bp):
TGATTTCGTCAGAGATGGAGAC
Found at i:1601278 original size:20 final size:20
Alignment explanation
Indices: 1601255--1601363 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
1601245 CGATAGTCAG
1601255 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1601275 ATTCG---T--GATTTACGT
1 ATTCGCATTGCGATTTACGT
1601290 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1601310 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
1601331 ATTCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
1601351 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1601364 ATTAGGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
15 14 0.20
17 1 0.01
18 1 0.01
20 41 0.58
21 14 0.20
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1601286 original size:15 final size:15
Alignment explanation
Indices: 1601266--1601294 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1601256 TTCGCATTGC
1601266 GATTTACGTATTCGT
1 GATTTACGTATTCGT
1601281 GATTTACGTATTCG
1 GATTTACGTATTCG
1601295 CATTGCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (15 bp):
GATTTACGTATTCGT
Found at i:1601384 original size:21 final size:21
Alignment explanation
Indices: 1601360--1601405 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1601350 TATTCGCATT
1601360 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1601381 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1601402 GCGA
1 GCGA
1601406 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1602533 original size:21 final size:21
Alignment explanation
Indices: 1602509--1602551 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1602499 TATACAACTT
1602509 TAATGTGTATATGTATA-TATA
1 TAATGTGTATAT-TATAGTATA
1602530 TAATGTGTATATTATAGTATA
1 TAATGTGTATATTATAGTATA
1602551 T
1 T
1602552 TTGTTGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
TAATGTGTATATTATAGTATA
Found at i:1602708 original size:45 final size:47
Alignment explanation
Indices: 1602623--1602741 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 47
1602613 GAAAATGTAT
* *
1602623 ATATCTAATATATTATATATTTTTGAAAATATATAAATTTTGAAAAC
1 ATATCTAATATATTATATATTTTTGAAAACATACAAATTTTGAAAAC
* * * *
1602670 ATATTTAATATATT-TA-ATTTTTGAAAACATGCAGATTTTGAAAAT
1 ATATCTAATATATTATATATTTTTGAAAACATACAAATTTTGAAAAC
*
1602715 ATA-AT-ATATATTATATAGTTTTT-AAAA
1 ATATCTAATATATTATATA-TTTTTGAAAA
1602742 TTCTATAGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
43 7 0.11
44 3 0.05
45 32 0.52
46 7 0.11
47 13 0.21
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (47 bp):
ATATCTAATATATTATATATTTTTGAAAACATACAAATTTTGAAAAC
Found at i:1602765 original size:17 final size:17
Alignment explanation
Indices: 1602726--1602765 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1602716 TAATATATAT
* *
1602726 TATATAGTTTTTAAAAT
1 TATATAGCTTTTAAAAA
*
1602743 TCTATAGCTTTTAAAAA
1 TATATAGCTTTTAAAAA
1602760 TATATA
1 TATATA
1602766 TGTAGTATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (17 bp):
TATATAGCTTTTAAAAA
Found at i:1605870 original size:19 final size:19
Alignment explanation
Indices: 1605841--1605900 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
1605831 GATAACAAGT
1605841 AAATAAAATAAACAAAATAA
1 AAAT-AAATAAACAAAATAA
*
1605861 AAATAAATAAACAAAAAGAA
1 AAATAAATAAAC-AAAATAA
* *
1605881 AAATATATAAATAAAATAA
1 AAATAAATAAACAAAATAA
1605900 A
1 A
1605901 CGACATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (19 bp):
AAATAAATAAACAAAATAA
Found at i:1605936 original size:26 final size:26
Alignment explanation
Indices: 1605861--1605952 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 26
1605851 AACAAAATAA
* *
1605861 AAATAAATAAACAAAAAGAAAAATATAT
1 AAATAAATAAACGACAAGAAAAA-A-AT
*
1605889 AAATAAAATAAACGACATA-AAAAAGAT
1 AAAT-AAATAAACGACA-AGAAAAAAAT
1605916 AAATAAATAAA-GACAAGAAAAAAATT
1 AAATAAATAAACGACAAGAAAAAAA-T
*
1605942 GAATAAATAAA
1 AAATAAATAAA
1605953 ATACTGGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.02
25 10 0.18
26 18 0.33
27 6 0.11
28 4 0.07
29 15 0.27
30 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (26 bp):
AAATAAATAAACGACAAGAAAAAAAT
Found at i:1606052 original size:2 final size:2
Alignment explanation
Indices: 1606045--1606069 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1606035 GGTAAACAAA
1606045 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 A
1606070 AATACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1606141 original size:62 final size:63
Alignment explanation
Indices: 1606019--1606142 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 63
1606009 AAGAGAAAAA
* * *
1606019 AATAAAATAGATATAAGGTAAACAAAATATATATATATATATATATATATAAATACTAATATT
1 AATAAAATAGATATAAGGGAAACAAAATATATATATATATAAAAATATATAAATACTAATATT
* *
1606082 AATAAAATAGATA-AAGGGAAAGAAAATATATATTTATATACAAAATAT-TAAAATA-TAATAT
1 AATAAAATAGATATAAGGGAAACAAAATATATATATATATA-AAAATATAT-AAATACTAATAT
1606143 CTAAAATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 31 0.57
63 23 0.43
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.32
Consensus pattern (63 bp):
AATAAAATAGATATAAGGGAAACAAAATATATATATATATAAAAATATATAAATACTAATATT
Found at i:1608831 original size:84 final size:84
Alignment explanation
Indices: 1608750--1609442 Score: 636
Period size: 84 Copynumber: 8.4 Consensus size: 84
1608740 GTTTGCCTCT
* * * **
1608750 GAGCTGAGTGCAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTAGACTTAAACTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
1608815 TTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * * * *
1608834 GAGATAAGCGTAGTCAAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * * *
1608898 TTGTAAATGATGTTCCCTCG
66 CTGCAAATGATG-TGCCTTG
* * * * * * * *
1608918 AAGCTTAGTGTAATCGAACTCGAGGGTCTTTGG-T---AGATAGCCCTTATCGACTTAAGCTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
1608979 CTACAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * * * *
1608998 GAGCTGAGCATAGTTGAACTCGAAGGTATTTGCTTGGCAGATAACCCTTCTCGACTTAAGTTATA
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* *
1609063 CTGCAAATGATATGCCTTT
66 CTGCAAATGATGTGCCTTG
* * * * * * * *
1609082 GAGCCGAGCGTAGTCGAACTCGAAGGCCTTTAG-TGACATATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * * *
1609146 TTGTAAATGATGTGCCCTC
66 CTGCAAATGATGTGCCTTG
* * * * * * * *
1609165 GACGTTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGACAGCCCTTATCGACTTAAGCTAT
1 GA-GCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
1609226 GCTGCAAATGATGTGCCTTG
65 GCTGCAAATGATGTGCCTTG
* * *
1609246 GAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTT-GCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
1609310 CTGCAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
1609329 GAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-TGGCATATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
** * *
1609393 GCTATAAATGATATTCCTTG
65 GCTGCAAATGATGTGCCTTG
* * *
1609413 GAGCTAAGCGTAGTCAAACTCGAAGGTCTT
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTT
1609443 GGCTGACAGA
Statistics
Matches: 490, Mismatches: 106, Indels: 27
0.79 0.17 0.04
Matches are distributed among these distances:
80 50 0.10
81 70 0.14
82 2 0.00
83 150 0.31
84 218 0.44
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:1608996 original size:164 final size:164
Alignment explanation
Indices: 1608749--1609442 Score: 610
Period size: 164 Copynumber: 4.2 Consensus size: 164
1608739 GGTTTGCCTC
* * *
1608749 TGAGCTGAGTGCAATCGAACTCGAAGGTCTTCGGTTGG-CAGATAACCCTTCTAGACTTAAACTA
1 TGAGCTGAGCGTAATCGAACTCGAAGGTC-T---TTGGACAGATAACCCTTCTAGACTTAAGCTA
* * * *
1608813 TGTTGCAAATGATGTGCCTTGGAGATAAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAAC
62 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGGCAGATAAC
* * * * *
1608878 CCTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCCT
127 CCTTCTAGACTTAAGTTATGCTGCAAATGATATTCCCT
* * * * * * * *
1608916 CGAAGCTTAGTGTAATCGAACTCGAGGGTCTTTGG-TAGATAGCCCTTATCGACTTAAGCTATGC
1 TG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTAGACTTAAGCTATGC
* * ** * *
1608980 TACAAATGATGTGCCTTGGAGCTGAGCATAGTTGAACTCGAAGGTATTTGCTTGGCAGATAACCC
65 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTG-GTGGCAGATAACCC
* * * *
1609045 TTCTCGACTTAAGTTATACTGCAAATGATATGCCTT
129 TTCTAGACTTAAGTTATGCTGCAAATGATATTCCCT
* * * * * * *
1609081 TGAGCCGAGCGTAGTCGAACTCGAAGGCCTTTAGTGACATATAACCCTTCTAGCCTTGAGTTATG
1 TGAGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-GACAGATAACCCTTCTAGACTTAAGCTATG
* * * * * * * * * * *
1609146 TTGTAAATGATGTGCCCTCGACGTTGAGTGTAATCGAACTCGAGGGTC-TT--TGGCAGACAGCC
64 CTGCAAATGATGTGCCTTGGA-GCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGGCAGATAACC
* * * * *
1609208 CTTATCGACTTAAGCTATGCTGCAAATGAT-GTGCCT
128 CTTCTAGACTTAAGTTATGCTGCAAATGATATTCCCT
* * * * *
1609244 TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGCAGATAACCCTTCTCGACTTAAGTTAT
1 T-GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG--ACAGATAACCCTTCTAGACTTAAGCTAT
* *
1609309 GCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCATATAAC
63 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGGTGGCAGATAAC
* * **
1609374 CCTTCTAGCCTTGAGTTATGCTATAAATGATATT-CCT
127 CCTTCTAGACTTAAGTTATGCTGCAAATGATATTCCCT
* * *
1609411 TGGAGCTAAGCGTAGTCAAACTCGAAGGTCTT
1 T-GAGCTGAGCGTAATCGAACTCGAAGGTCTT
1609443 GGCTGACAGA
Statistics
Matches: 417, Mismatches: 96, Indels: 28
0.77 0.18 0.05
Matches are distributed among these distances:
162 1 0.00
163 25 0.06
164 199 0.48
165 43 0.10
166 1 0.00
167 104 0.25
168 44 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (164 bp):
TGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCT
GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGGCAGATAACCCTT
CTAGACTTAAGTTATGCTGCAAATGATATTCCCT
Found at i:1609188 original size:248 final size:248
Alignment explanation
Indices: 1608763--1609404 Score: 1000
Period size: 248 Copynumber: 2.6 Consensus size: 248
1608753 CTGAGTGCAA
* * * ** * *
1608763 TCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTAGACTTAAACTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * * *
1608828 GCCTTGGAGATAAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGCCTTTGGTGACATATAACCCTTCTAGCCTTGAG
* * *
1608893 TTATGTTGTAAATGATGTTCCCTCGAAGCTTAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAG
131 TTATGTTGTAAATGATGTGCCCTCGAAGCTTAGTGTAATCGAACTCGAGGGTCTTTGGCAGACAG
1608958 CCCTTATCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCATAG
196 CCCTTATCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCATAG
* * *
1609011 TTGAACTCGAAGGTATTTGCTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATAT
1 TCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * * *
1609076 GCCTTTGAGCCGAGCGTAGTCGAACTCGAAGGCCTTTAGTGACATATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGCCTTTGGTGACATATAACCCTTCTAGCCTTGAG
*
1609141 TTATGTTGTAAATGATGTGCCCTCGACG-TTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGACA
131 TTATGTTGTAAATGATGTGCCCTCGAAGCTT-AGTGTAATCGAACTCGAGGGTCTTTGGCAGACA
* *
1609205 GCCCTTATCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
195 GCCCTTATCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCATAG
1609259 TCGAACTCGAAGGTATTTGGTT-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* *
1609323 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCATATAACCCTTCTAGCCTTGA
66 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGG-CCTTTGGTGACATATAACCCTTCTAGCCTTGA
* *
1609388 GTTATGCTATAAATGAT
130 GTTATGTTGTAAATGAT
1609405 ATTCCTTGGA
Statistics
Matches: 357, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
247 72 0.20
248 285 0.80
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
TCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGCCTTTGGTGACATATAACCCTTCTAGCCTTGAG
TTATGTTGTAAATGATGTGCCCTCGAAGCTTAGTGTAATCGAACTCGAGGGTCTTTGGCAGACAG
CCCTTATCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCATAG
Found at i:1612870 original size:17 final size:18
Alignment explanation
Indices: 1612840--1612877 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
1612830 ATACGAATGT
1612840 AAAAACATGGAAAATATAA
1 AAAAACAT-GAAAATATAA
1612859 AAAAACAT-AAAATATAA
1 AAAAACATGAAAATATAA
1612876 AA
1 AA
1612878 TGCAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAACATGAAAATATAA
Found at i:1616153 original size:24 final size:24
Alignment explanation
Indices: 1616122--1616188 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1616112 TAACAAGTAA
1616122 AAAAAAAACAAAATAAAAATAAAT
1 AAAAAAAACAAAATAAAAATAAAT
*
1616146 AAACAAAAACAAAA-ATAAATAAAT
1 AAA-AAAAACAAAATAAAAATAAAT
* * *
1616170 AAAATAAACGACATAAAAA
1 AAAAAAAACAAAATAAAAA
1616189 AGATAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 7 0.19
24 19 0.53
25 10 0.28
ACGTcount: A:0.79, C:0.07, G:0.01, T:0.12
Consensus pattern (24 bp):
AAAAAAAACAAAATAAAAATAAAT
Found at i:1616159 original size:20 final size:20
Alignment explanation
Indices: 1616127--1616173 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1616117 AGTAAAAAAA
*
1616127 AAAC-AAAATAAAAATAAAT
1 AAACAAAAACAAAAATAAAT
1616146 AAACAAAAACAAAAATAAAT
1 AAACAAAAACAAAAATAAAT
*
1616166 AAATAAAA
1 AAACAAAA
1616174 TAAACGACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (20 bp):
AAACAAAAACAAAAATAAAT
Found at i:1619152 original size:21 final size:21
Alignment explanation
Indices: 1619126--1619170 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1619116 CGCTAAACAA
*
1619126 TTACCTTAAACATT-ATTATTT
1 TTACCTAAAACATTAATT-TTT
*
1619147 TTACCTAAAATATTAATTTTT
1 TTACCTAAAACATTAATTTTT
1619168 TTA
1 TTA
1619171 ATATTTCCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (21 bp):
TTACCTAAAACATTAATTTTT
Found at i:1620343 original size:28 final size:29
Alignment explanation
Indices: 1620312--1620385 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 29
1620302 AAATACTATA
1620312 AATTTCAA-AAATAAATTTTAAACTGTCC
1 AATTTCAACAAATAAATTTTAAACTGTCC
* *
1620340 AA-TTGAACTAATAAATTTTAAACTGTCC
1 AATTTCAACAAATAAATTTTAAACTGTCC
* *
1620368 AA-TTGAACTAATAAATTT
1 AATTTCAACAAATAAATTT
1620386 ATCCACCATC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 4 0.09
28 39 0.91
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTTCAACAAATAAATTTTAAACTGTCC
Found at i:1622331 original size:23 final size:23
Alignment explanation
Indices: 1622288--1622331 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1622278 AGCATATATT
**
1622288 ATTATTATTATATAACTTCTATA
1 ATTATTATTATATAAAATCTATA
1622311 ATTATTATT-TAGTAAAATCTA
1 ATTATTATTATA-TAAAATCTA
1622332 GAGATTGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTATTATTATATAAAATCTATA
Found at i:1622644 original size:76 final size:73
Alignment explanation
Indices: 1622507--1622791 Score: 326
Period size: 75 Copynumber: 3.8 Consensus size: 73
1622497 TCGAAAATAT
** ** *
1622507 TTTTTGAAAACATATAATATATAGTTTTTAAAAATGAATTTGAAAACATATAATATATAGTTTTC
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGGTTTTTGAAAACATATAATATATAGTTTTA
1622572 AAAGACGG
66 AAAGACGG
1622580 TTTTTGAAAACATATAATATATATAGTTTTTAAAACGGTTTTTTGAAAACATATAATATATAGTT
1 TTTTTGAAAACATAT-A-ATATATAGTTTTTAAAACGG-TTTTTGAAAACATATAATATATAG-T
1622645 TTTAAAAGACGG
62 TTTAAAAGACGG
*
1622657 TTTTTGAAAACATATAATATATAGTTTTTAAAAAATGGTTTTTGAAAACATAT-ATAATATAGTT
1 TTTTTGAAAACATATAATATATAGTTTTT--AAAACGGTTTTTGAAAACATATAAT-ATATAGTT
* *
1622721 TTGAAA-AC-A
63 TTAAAAGACGG
* * * * *
1622730 TATTTTGAATATATATATATATATA-TATATATAACGGTTTTTGAAAACTTATATAATATATA
1 T-TTTTGAAAACATATA-ATATATAGTTTTTAAAACGGTTTTTGAAAAC--ATATAATATATA
1622792 TAATTTTTTA
Statistics
Matches: 186, Mismatches: 14, Indels: 23
0.83 0.06 0.10
Matches are distributed among these distances:
72 16 0.09
73 16 0.09
74 28 0.15
75 49 0.26
76 44 0.24
77 33 0.18
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (73 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAACGGTTTTTGAAAACATATAATATATAGTTTTA
AAAGACGG
Found at i:1622670 original size:38 final size:37
Alignment explanation
Indices: 1622507--1622791 Score: 314
Period size: 38 Copynumber: 7.6 Consensus size: 37
1622497 TCGAAAATAT
*
1622507 TTTTTGAAAACATATAATATATAGTTTTTAAAAA-TG
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAACGG
** * *
1622543 AATTTGAAAACATATAATATATAGTTTTCAAAGACGG
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAACGG
1622580 TTTTTGAAAACATATAATATATATAGTTTTT-AAAACGG
1 TTTTTGAAAACATAT-A-ATATATAGTTTTTAAAAACGG
1622618 TTTTTTGAAAACATATAATATATAGTTTTTAAAAGACGG
1 -TTTTTGAAAACATATAATATATAGTTTTTAAAA-ACGG
*
1622657 TTTTTGAAAACATATAATATATAGTTTTTAAAAAATGG
1 TTTTTGAAAACATATAATATATAGTTTTT-AAAAACGG
* *
1622695 TTTTTGAAAACATAT-ATAATATAG-TTTTGAAAAC-A
1 TTTTTGAAAACATATAAT-ATATAGTTTTTAAAAACGG
* * * * *
1622730 TATTTTGAATATATAT-ATATATA-TATATATATAACGG
1 T-TTTTGAAAACATATAATATATAGTTTTTA-AAAACGG
1622767 TTTTTGAAAACTTATATAATATATA
1 TTTTTGAAAAC--ATATAATATATA
1622792 TAATTTTTTA
Statistics
Matches: 212, Mismatches: 22, Indels: 27
0.81 0.08 0.10
Matches are distributed among these distances:
35 8 0.04
36 60 0.28
37 34 0.16
38 68 0.32
39 42 0.20
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (37 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAAACGG
Found at i:1622745 original size:2 final size:2
Alignment explanation
Indices: 1622738--1622762 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1622728 CATATTTTGA
1622738 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 A
1622763 ACGGTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1622798 original size:28 final size:30
Alignment explanation
Indices: 1622747--1622815 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 30
1622737 AATATATATA
1622747 TATATATATATATATAACGGTTTTTGAAAACT
1 TATATATATATATATAA--GTTTTTGAAAACT
* *
1622779 TATATA-ATATATATAA-TTTTTTAAAACA
1 TATATATATATATATAAGTTTTTGAAAACT
1622807 TAT-TATATA
1 TATATATATA
1622816 GTTTTTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 16 0.47
31 10 0.29
32 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATATATATATATAAGTTTTTGAAAACT
Found at i:1622908 original size:9 final size:9
Alignment explanation
Indices: 1622869--1622926 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 9
1622859 ATATATTACG
1622869 TATTATA-T
1 TATTATATT
1622877 TATATATTATT
1 TAT-TA-TATT
1622888 TATAGTACTATT
1 TAT--TA-TATT
1622900 TATTATATT
1 TATTATATT
1622909 TATTAT-TT
1 TATTATATT
1622917 TATTA-ATT
1 TATTATATT
1622925 TA
1 TA
1622927 CTTGCTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
8 14 0.33
9 12 0.28
10 4 0.09
11 4 0.09
12 9 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
TATTATATT
Found at i:1624290 original size:14 final size:15
Alignment explanation
Indices: 1624259--1624291 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1624249 CAATACGATC
*
1624259 TTTAATCATTTCTAA
1 TTTAATAATTTCTAA
1624274 TTTAATAATTT-TAA
1 TTTAATAATTTCTAA
1624288 TTTA
1 TTTA
1624292 GATTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATAATTTCTAA
Found at i:1624316 original size:31 final size:31
Alignment explanation
Indices: 1624279--1624340 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1624269 TCTAATTTAA
* *
1624279 TAATTTTAATTTAGATTTTATTTTA-TTTATT
1 TAATTTTAATTCAAATTTTA-TTTACTTTATT
*
1624310 TAATTTTACTTCAAATTTTATTTACTTTATT
1 TAATTTTAATTCAAATTTTATTTACTTTATT
1624341 CTAACCATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (31 bp):
TAATTTTAATTCAAATTTTATTTACTTTATT
Found at i:1632018 original size:16 final size:16
Alignment explanation
Indices: 1631997--1632027 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1631987 ACGGGTTCTC
1631997 AAGATACAACCAGATT
1 AAGATACAACCAGATT
*
1632013 AAGATACATCCAGAT
1 AAGATACAACCAGAT
1632028 GATATGGATA
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:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
AAGATACAACCAGATT
Found at i:1636233 original size:38 final size:37
Alignment explanation
Indices: 1636191--1636323 Score: 160
Period size: 37 Copynumber: 3.5 Consensus size: 37
1636181 AATTTATATA
*
1636191 GTTTTTGAAGATATATATATATATAGTTTTTAAAAATG
1 GTTTTTGAAAATATATA-ATATATAGTTTTTAAAAATG
*
1636229 G-TTTTGAAAATATATAATAAATAGTTTTTAAAAGATG
1 GTTTTTGAAAATATATAATATATAGTTTTTAAAA-ATG
* * * *
1636266 GTTTTTGAAAACATATAATATATTGGTTTAAAAAATG
1 GTTTTTGAAAATATATAATATATAGTTTTTAAAAATG
*
1636303 GTTTTTAAAAACGTATATAAT
1 GTTTTTGAAAA--TATATAAT
1636324 GTAGTTTTGA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
36 16 0.20
37 31 0.38
38 28 0.34
39 7 0.09
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.43
Consensus pattern (37 bp):
GTTTTTGAAAATATATAATATATAGTTTTTAAAAATG
Found at i:1636234 original size:37 final size:36
Alignment explanation
Indices: 1636193--1636312 Score: 150
Period size: 38 Copynumber: 3.2 Consensus size: 36
1636183 TTTATATAGT
*
1636193 TTTTGAAGATATATATATATATAGTTTTTAAAAATGG
1 TTTTGAAAATATATA-ATATATAGTTTTTAAAAATGG
*
1636230 TTTTGAAAATATATAATAAATAGTTTTTAAAAGATGG
1 TTTTGAAAATATATAATATATAGTTTTTAAAA-ATGG
* * * *
1636267 TTTTTGAAAACATATAATATATTGGTTTAAAAAATGG
1 -TTTTGAAAATATATAATATATAGTTTTTAAAAATGG
*
1636304 TTTTTAAAA
1 TTTTGAAAA
1636313 ACGTATATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
36 24 0.33
37 22 0.30
38 27 0.37
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAAATGG
Found at i:1636419 original size:19 final size:21
Alignment explanation
Indices: 1636387--1636425 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1636377 AATATATAAT
*
1636387 TTTTGTAAACATATTATATAC
1 TTTTGTAAACATATAATATAC
1636408 TTTT-TAAA-ATATAATATA
1 TTTTGTAAACATATAATATA
1636426 TGTTATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTTGTAAACATATAATATAC
Found at i:1636449 original size:26 final size:28
Alignment explanation
Indices: 1636400--1636452 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1636390 TGTAAACATA
1636400 TTATATACTTTTTAAAATATAATATATG
1 TTATATACTTTTTAAAATATAATATATG
*
1636428 TTATATAGTTTTT-AAATA-AATATAT
1 TTATATACTTTTTAAAATATAATATAT
1636453 AGTATGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
27 5 0.21
28 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATATACTTTTTAAAATATAATATATG
Found at i:1636453 original size:28 final size:28
Alignment explanation
Indices: 1636400--1636459 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 28
1636390 TGTAAACATA
*
1636400 TTATATACTTTTTAAAATATAATATATG
1 TTATATACTTTTTAAAAAATAATATATG
*
1636428 TTATATAGTTTTTAAATAAATATATAGTATG
1 TTATATACTTTTTAAA-AAATA-ATA-TATG
1636459 T
1 T
1636460 ATTATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 15 0.56
29 4 0.15
30 3 0.11
31 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (28 bp):
TTATATACTTTTTAAAAAATAATATATG
Found at i:1636477 original size:12 final size:11
Alignment explanation
Indices: 1636448--1636505 Score: 64
Period size: 12 Copynumber: 5.1 Consensus size: 11
1636438 TTTAAATAAA
* *
1636448 TATATAGTATG
1 TATATATTATT
1636459 TATTATATTATAT
1 TA-TATATTAT-T
1636472 TATATATTATT
1 TATATATTATT
1636483 TATAGTATTATT
1 TATA-TATTATT
1636495 TAT-TATTATT
1 TATATATTATT
1636505 T
1 T
1636506 TATTCATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 25 0.60
13 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTATT
Found at i:1637878 original size:8 final size:9
Alignment explanation
Indices: 1637865--1637896 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
1637855 TAGATTTTCT
1637865 TTTATTT-A
1 TTTATTTAA
1637873 TTTATTTAA
1 TTTATTTAA
1637882 TTT-TTTAA
1 TTTATTTAA
1637890 TTTATTT
1 TTTATTT
1637897 TACTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTAA
Found at i:1639402 original size:43 final size:43
Alignment explanation
Indices: 1639329--1639454 Score: 127
Period size: 45 Copynumber: 2.9 Consensus size: 43
1639319 ATTTTACCCT
1639329 TTAATTTTCTTTAAT-TTAGTTTTTT-TCTTTATAATTGAAGTGCA
1 TTAATTTT-TTTAATCTTA-TTTTTTATCTTTATAATTGAAGT-CA
*
1639373 -T-ATTTTTTGTAATCTTATTTTTTATCTTTATAATTGAGGTCA
1 TTAATTTTTT-TAATCTTATTTTTTATCTTTATAATTGAAGTCA
* *
1639415 TTAATTTTTTTTAGTCTCATCTTTTTA-CATTTATAATTGA
1 TTAA-TTTTTTTAATCTTAT-TTTTTATC-TTTATAATTGA
1639455 TGATCCTAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
41 2 0.03
42 17 0.24
43 20 0.28
44 9 0.13
45 23 0.32
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.60
Consensus pattern (43 bp):
TTAATTTTTTTAATCTTATTTTTTATCTTTATAATTGAAGTCA
Found at i:1639485 original size:123 final size:121
Alignment explanation
Indices: 1639355--1639575 Score: 325
Period size: 123 Copynumber: 1.8 Consensus size: 121
1639345 TAGTTTTTTT
* * * *
1639355 CTTTATAATTGAAGTGCATATTTTTTGTAATCTTATTTTTTATCTTTATAATTGAGGTCATTAAT
1 CTTTATAATTGAAGTACATAATTTTTGTAATCTTACTTTTTATCTTTATAATTGAGGCCATTAA-
* * *
1639420 TTTTTTTAGTCTCATCTTTTTACATTTATAATTGATGATCCTAAGTTTTTCAATCCCA
65 -TTATTTAATCCCATCTTTTTACATTTATAATTGATGATCCTAAGTTTTTCAATCCCA
* * *
1639478 CTTTATAATTGAAGTACCTAATTTTTGTAATCTTACTTTTTATCTTTATGATTGAGGCCCTTAAT
1 CTTTATAATTGAAGTACATAATTTTTGTAATCTTACTTTTTATCTTTATAATTGAGGCCATTAAT
*
1639543 TATTTAATCCCATTTTTTTACATTTATAATTGA
66 TATTTAATCCCATCTTTTTACATTTATAATTGA
1639576 GGCACTAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
121 30 0.34
123 57 0.66
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.52
Consensus pattern (121 bp):
CTTTATAATTGAAGTACATAATTTTTGTAATCTTACTTTTTATCTTTATAATTGAGGCCATTAAT
TATTTAATCCCATCTTTTTACATTTATAATTGATGATCCTAAGTTTTTCAATCCCA
Found at i:1639598 original size:42 final size:43
Alignment explanation
Indices: 1639478--1639598 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 43
1639468 TTCAATCCCA
* *
1639478 CTTTATAATTGAAGTACCTAATTTTTGTAAT-C-TTACTTTTTAT
1 CTTTATAATTGAGGCA-CTAATTTTTGTAATCCATTA-TTTTTAT
* * *
1639521 CTTTATGATTGAGGCCCTTAATTATT-TAATCCCATT-TTTTTA-
1 CTTTATAATTGAGGCAC-TAATTTTTGTAAT-CCATTATTTTTAT
1639563 CATTTATAATTGAGGCACTAATTTTTGTAATCCATT
1 C-TTTATAATTGAGGCACTAATTTTTGTAATCCATT
1639599 CATTAAGAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
42 18 0.28
43 43 0.67
44 1 0.02
45 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (43 bp):
CTTTATAATTGAGGCACTAATTTTTGTAATCCATTATTTTTAT
Found at i:1645367 original size:13 final size:13
Alignment explanation
Indices: 1645349--1645375 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1645339 TTCGAACTAC
1645349 ATATTAGTATCGT
1 ATATTAGTATCGT
1645362 ATATTAGTATCGT
1 ATATTAGTATCGT
1645375 A
1 A
1645376 CTAACATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
ATATTAGTATCGT
Found at i:1654723 original size:21 final size:20
Alignment explanation
Indices: 1654698--1654736 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1654688 TATCAAGGTC
*
1654698 TTTGTTGAAGCCATTAAATCT
1 TTTGTCGAAGCCA-TAAATCT
*
1654719 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
1654737 TCCTACAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:1662722 original size:23 final size:23
Alignment explanation
Indices: 1662692--1662737 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1662682 TAAGCTAACA
* *
1662692 TAGGAATGTGTAGAACTTGGATC
1 TAGGAATGTATAGAACTCGGATC
1662715 TAGGAATGTATAGAACTCGGATC
1 TAGGAATGTATAGAACTCGGATC
1662738 AACCAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (23 bp):
TAGGAATGTATAGAACTCGGATC
Found at i:1670062 original size:21 final size:20
Alignment explanation
Indices: 1670018--1670073 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 20
1670008 GGTTGACTTG
* *
1670018 GTAGCTAACTAGGTAGGTGT
1 GTAGCTAGCTAGGTAAGTGT
1670038 GTAGCTAGCTAGGTAAGTGGT
1 GTAGCTAGCTAGGTAAGT-GT
1670059 GTAGCTAGCTAGGTA
1 GTAGCTAGCTAGGTA
1670074 GTTAAGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (20 bp):
GTAGCTAGCTAGGTAAGTGT
Found at i:1671788 original size:36 final size:36
Alignment explanation
Indices: 1671748--1671831 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
1671738 CTCCATACTT
* *
1671748 ATTTTCAACTCCTTTTTCTTTACTCTTATTCCTTGC
1 ATTTTCAACTCCTTTTTCCTTACTCCTATTCCTTGC
1671784 ATTTTCAACTCCTTTTTCCTTACTCCTATTCCTTGC
1 ATTTTCAACTCCTTTTTCCTTACTCCTATTCCTTGC
1671820 ATTTTCAACTCC
1 ATTTTCAACTCC
1671832 ATCGTTTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.15, C:0.31, G:0.02, T:0.51
Consensus pattern (36 bp):
ATTTTCAACTCCTTTTTCCTTACTCCTATTCCTTGC
Found at i:1674162 original size:21 final size:22
Alignment explanation
Indices: 1674138--1674194 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
1674128 AGATAGGTGT
* *
1674138 GTAGCTTGCTAGGTAAG-TGAG
1 GTAGCTAGCTAGGTAAGTTAAG
1674159 GTAGCTAGCTAGGT-AGTTAAG
1 GTAGCTAGCTAGGTAAGTTAAG
1674180 GTAGCTAGCTAGGTA
1 GTAGCTAGCTAGGTA
1674195 CCTAGTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.26, C:0.11, G:0.35, T:0.28
Consensus pattern (22 bp):
GTAGCTAGCTAGGTAAGTTAAG
Found at i:1676627 original size:20 final size:20
Alignment explanation
Indices: 1676599--1676647 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1676589 ATGCAAAGAA
*
1676599 TATCGATACT-ATAGGGTTGG
1 TATCGATACTCAT-GGGTTAG
*
1676619 TATCAATACTCATGGGTTAG
1 TATCGATACTCATGGGTTAG
1676639 TATCGATAC
1 TATCGATAC
1676648 CGGATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (20 bp):
TATCGATACTCATGGGTTAG
Found at i:1680823 original size:21 final size:20
Alignment explanation
Indices: 1680797--1680838 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1680787 TCTAGCCTAC
1680797 AGGTTTCAAAAACCCCCTCAA
1 AGGTTT-AAAAACCCCCTCAA
*
1680818 AGGTTTTAAAACCCCCTCAA
1 AGGTTTAAAAACCCCCTCAA
1680838 A
1 A
1680839 AATTTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (20 bp):
AGGTTTAAAAACCCCCTCAA
Found at i:1680844 original size:19 final size:20
Alignment explanation
Indices: 1680805--1680846 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1680795 ACAGGTTTCA
**
1680805 AAAACCCCCTCAAAGGTTTT
1 AAAACCCCCTCAAAGAATTT
1680825 AAAACCCCCTCAAA-AATTT
1 AAAACCCCCTCAAAGAATTT
1680844 AAA
1 AAA
1680847 TGAAGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.45, C:0.29, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAACCCCCTCAAAGAATTT
Found at i:1697360 original size:10 final size:10
Alignment explanation
Indices: 1697345--1697403 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
1697335 CATTTAATAA
1697345 ATAAACGAAC
1 ATAAACGAAC
1697355 ATAAACGAAC
1 ATAAACGAAC
** *
1697365 ACGAAC-ATAA
1 ATAAACGA-AC
1697375 ATGAACACGAAC
1 AT-AA-ACGAAC
1697387 ATAAACGAAC
1 ATAAACGAAC
1697397 ATAAACG
1 ATAAACG
1697404 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1697370 original size:16 final size:16
Alignment explanation
Indices: 1697349--1697397 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1697339 TAATAAATAA
1697349 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1697365 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1697381 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1697397 A
1 A
1697398 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1699157 original size:31 final size:31
Alignment explanation
Indices: 1699103--1699180 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1699093 TTTTTTCATT
*
1699103 TAAGTACCTAAAGTA-ATTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTTGGTCAAAA
* *
1699133 TAAGTATCTAAAGTATTTTTTTTGGTCAAGA
1 TAAGTACCTAAAGTATTTTTTTTGGTCAAAA
*
1699164 TAGGTACCTAAAGTATT
1 TAAGTACCTAAAGTATT
1699181 CAATTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 14 0.33
31 28 0.67
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (31 bp):
TAAGTACCTAAAGTATTTTTTTTGGTCAAAA
Found at i:1702408 original size:54 final size:54
Alignment explanation
Indices: 1702358--1702739 Score: 410
Period size: 54 Copynumber: 7.1 Consensus size: 54
1702348 TGTAGTGTCG
* * *
1702358 ATACTGTCGTTCATAAACACATTATGAATTTCGAT-GGTTGCACATTTAGTGCCT
1 ATACGGTCATTCATAAACACATTATGAATTTCG-TGGGTTGCACACTTAGTGCCT
** * * * *
1702412 ATACACTTGA-TCAAAAACACATTATGAATTCCGTGGGTTGCACAGTTAGTGCCT
1 ATAC-GGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCT
* * * * *
1702466 ATACAGTCAATCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCT
*
1702520 ATACGGTCATTCATAAACACATTATGAATTTTTGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCATTCATAAACACATTATGAA-TTTCGTGGGTTGCACACTTAGTGCCT
* * ** * * *
1702575 ATACGGTTATTCATCAACGTATGATGAA-TTCTATGGGTTTCACACTTAGTGCCT
1 ATACGGTCATTCATAAACACATTATGAATTTC-GTGGGTTGCACACTTAGTGCCT
* * *
1702629 ATATGGTCATTAATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCT
** * * * * * *
1702683 ATACGGTTGTTTATCAACATATGATGAATTACATGGGTTGCACACTTAGTGCCT
1 ATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCT
1702737 ATA
1 ATA
1702740 GTACACATAG
Statistics
Matches: 274, Mismatches: 48, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
53 5 0.02
54 218 0.80
55 51 0.19
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (54 bp):
ATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCT
Found at i:1702515 original size:108 final size:107
Alignment explanation
Indices: 1702367--1702739 Score: 471
Period size: 108 Copynumber: 3.4 Consensus size: 107
1702357 GATACTGTCG
* * * * ** *
1702367 TTCATAAACACATTATGAATTTCGAT-GGTTGCACATTTAGTGCCTATACACTTGATCAAAAACA
1 TTCATCAACATATGATGAATTTC-ATGGGTTGCACACTTAGTGCCTATAC-GGTCATCAAAAACA
* * * *
1702431 CATTATGAATTCCGTGGGTTGCACAGTTAGTGCCTATACAGTCA
64 CATTATGAATTACGTGGGTTGCACACTTAGTGCCTATACGGTTA
* * *
1702475 ATCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCATTCATAAACAC
1 TTCATCAACATATGATGAATTTCATGGGTTGCACACTTAGTGCCTATACGGTCA-TCAAAAACAC
**
1702540 ATTATGAATTTTTGTGGGTTGCACACTTAGTGCCTATACGGTTA
65 ATTATGAA-TTACGTGGGTTGCACACTTAGTGCCTATACGGTTA
* * * *
1702584 TTCATCAACGTATGATGAA-TTCTATGGGTTTCACACTTAGTGCCTATATGGTCATTAATAAACA
1 TTCATCAACATATGATGAATTTC-ATGGGTTGCACACTTAGTGCCTATACGGTCATCAA-AAACA
*
1702648 CATTATGAATTACGTGGGTTGCACACTTAGTGCCTATACGGTTG
64 CATTATGAATTACGTGGGTTGCACACTTAGTGCCTATACGGTTA
* *
1702692 TTTATCAACATATGATGAATTACATGGGTTGCACACTTAGTGCCTATA
1 TTCATCAACATATGATGAATTTCATGGGTTGCACACTTAGTGCCTATA
1702740 GTACACATAG
Statistics
Matches: 230, Mismatches: 29, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.01
108 136 0.59
109 91 0.40
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (107 bp):
TTCATCAACATATGATGAATTTCATGGGTTGCACACTTAGTGCCTATACGGTCATCAAAAACACA
TTATGAATTACGTGGGTTGCACACTTAGTGCCTATACGGTTA
Found at i:1708727 original size:18 final size:16
Alignment explanation
Indices: 1708677--1708729 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
1708667 CAAGGACTAA
1708677 ATTAAAAGGATACAAAT
1 ATTAAAAGGATA-AAAT
*
1708694 ATTAAAAGCAATTAAAAT
1 ATTAAAAG-GA-TAAAAT
1708712 ATATAAAAGGACTAAAAT
1 AT-TAAAAGGA-TAAAAT
1708730 TAAAGTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 8 0.27
18 14 0.47
19 8 0.27
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (16 bp):
ATTAAAAGGATAAAAT
Found at i:1708788 original size:14 final size:14
Alignment explanation
Indices: 1708771--1708806 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1708761 TAAAAATATT
*
1708771 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
1708785 AAATTAAAGGACTG
1 AAATTAAAGGAATG
1708799 AAATTAAA
1 AAATTAAA
1708807 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:1708993 original size:11 final size:11
Alignment explanation
Indices: 1708977--1709001 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1708967 TTCGAACATA
1708977 AAATAAATAAT
1 AAATAAATAAT
1708988 AAATAAATAAT
1 AAATAAATAAT
1708999 AAA
1 AAA
1709002 AATTAGCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:1710793 original size:139 final size:137
Alignment explanation
Indices: 1710637--1710958 Score: 480
Period size: 139 Copynumber: 2.4 Consensus size: 137
1710627 GAAGGAAAAG
*
1710637 AGCTAAGGTT-TAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCATCGAACGAGTTCTTCTC
1 AGCTAAGGTTAT-ACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAACGAGTTCTTCTC
* *
1710701 ATTATGAACTCTCTACTGGAATTGTTGATCCCTCGAGTGAGATGCTGCTGATTCAACTCTATATG
65 ATTATGAACTCTCTACTGGAATTGTTGAT-CCTCGAGTGAGATG-TGCTAATTCAACTCCATATG
1710766 TGATGAATCA
128 TGATGAATCA
* *
1710776 AGCTAAGGTTATACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCA
1 AGCTAAGGTTATACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAACGAGTTCTTCTCA
* *
1710841 TTATGAACTCTCTACTGGAATTGTTGATCCTCGAGTGAGGTGTGTTAATTCAACTCCATATGTGA
66 TTATGAACTCTCTACTGGAATTGTTGATCCTCGAGTGAGATGTGCTAATTCAACTCCATATGTGA
*
1710906 TGAATCG
131 TGAATCA
1710913 AGCTAAGGTTGA-ACAAG----T-TCATTATGAA-TTCTTCTCCCTCATCGAA
1 AGCTAAGGTT-ATACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAA
1710959 TGATTTCTCA
Statistics
Matches: 172, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
131 17 0.10
132 10 0.06
133 1 0.01
137 41 0.24
138 14 0.08
139 88 0.51
140 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (137 bp):
AGCTAAGGTTATACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAACGAGTTCTTCTCA
TTATGAACTCTCTACTGGAATTGTTGATCCTCGAGTGAGATGTGCTAATTCAACTCCATATGTGA
TGAATCA
Found at i:1711602 original size:96 final size:92
Alignment explanation
Indices: 1711367--1711745 Score: 270
Period size: 96 Copynumber: 3.9 Consensus size: 92
1711357 TTTTTTTTGT
* * * * * **
1711367 GAGTGAAACAATTTCAAAATTGTGTTTCAAGGGAAACTGCCTTTAAAAAAGACGAAATTGATTTT
1 GAGTGAAACAA-TTCCAAATTATGTTTCAAGGGAAATTGTC-TCAAGCAAGACGAAATT-A--TT
1711432 AAAAGAATTC-ATCTCAAGTGAGAT-AATAAAGTTTTT-
61 AAAA-AA--CAATCTCAAGTGAGATCAAT----TTTTTC
* * * *
1711468 GAGTGAAACAATTTCAAAAATTACGTTTCGAGGGAAATTATCTCAAGCAAGACGAAATTATTAAA
1 GAGTGAAACAA-TTC-CAAATTATGTTTCAAGGGAAATTGTCTCAAGCAAGACGAAATTATTAAA
1711533 AAACAATCTCAAGTGAGATCAATTTGGTTTC
64 AAACAATCTCAAGTGAGATCAATTT--TTTC
* * *
1711564 -AGGTGAAACAATTCCAAATTTATATTTCAAGGGAAAATTGTCTCAAGCGAA-ATGAAATTGGTT
1 GA-GTGAAACAATTCCAAA-TTATGTTTCAAGGG-AAATTGTCTCAAGC-AAGACGAAATT--AT
*
1711627 TGAGAAAAACAA--TCAAATGAGATCAATTTTTTC
60 T-A-AAAAACAATCTCAAGTGAGATCAATTTTTTC
* * * *
1711660 GAGTGAAACAATTTC-AATTGTGTTTCAAGGGAAACTGTCTCCAGCAAGACGAAATTTATTTTAA
1 GAGTGAAACAATTCCAAATTATGTTTCAAGGGAAATTGTCTCAAGCAAGACGAAA-TTA--TTAA
* *
1711724 GAAACAATCTCAAGTAAGATCA
63 AAAACAATCTCAAGTGAGATCA
1711746 GCTTTTGTCT
Statistics
Matches: 230, Mismatches: 27, Indels: 49
0.75 0.09 0.16
Matches are distributed among these distances:
92 9 0.04
93 20 0.09
94 30 0.13
95 21 0.09
96 59 0.26
97 8 0.03
98 24 0.10
99 1 0.00
100 9 0.04
101 29 0.13
102 20 0.09
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (92 bp):
GAGTGAAACAATTCCAAATTATGTTTCAAGGGAAATTGTCTCAAGCAAGACGAAATTATTAAAAA
ACAATCTCAAGTGAGATCAATTTTTTC
Found at i:1717878 original size:26 final size:27
Alignment explanation
Indices: 1717823--1717883 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1717813 AAATAATAGT
** *
1717823 AAATTAAAGTAATGAATTAAAGGACTG
1 AAATTAAAGTAAAAAATTAAAGGACAG
1717850 AAATTAAA-TAAAAAATTAAAGGGA-AG
1 AAATTAAAGTAAAAAATTAAA-GGACAG
1717876 AAATTAAA
1 AAATTAAA
1717884 ATGTGCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.23
Consensus pattern (27 bp):
AAATTAAAGTAAAAAATTAAAGGACAG
Found at i:1718098 original size:16 final size:16
Alignment explanation
Indices: 1718077--1718114 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1718067 AGTGGTTAGC
*
1718077 AGTTAGAAGTTAGAAA
1 AGTTAGAAATTAGAAA
*
1718093 AGTTAGAAATTATAAA
1 AGTTAGAAATTAGAAA
1718109 AGTTAG
1 AGTTAG
1718115 TTGTTAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (16 bp):
AGTTAGAAATTAGAAA
Found at i:1721739 original size:23 final size:23
Alignment explanation
Indices: 1721709--1721769 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
1721699 CATACTATCC
1721709 ATATTCGAATATCAACAAATCTG
1 ATATTCGAATATCAACAAATCTG
1721732 ATATTCGAATATCAACAAATCTG
1 ATATTCGAATATCAACAAATCTG
1721755 ATATTCGAATATCAA
1 ATATTCGAATATCAA
1721770 TATCTGCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (23 bp):
ATATTCGAATATCAACAAATCTG
Found at i:1728161 original size:3 final size:3
Alignment explanation
Indices: 1728153--1728177 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1728143 AAAAGCAGCT
1728153 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1728178 ATGATGATAA
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):
ATA
Found at i:1729471 original size:28 final size:28
Alignment explanation
Indices: 1729439--1729493 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1729429 TATCAGATTT
1729439 TTTTAATATTATGGAATAAGTATAAAGC
1 TTTTAATATTATGGAATAAGTATAAAGC
1729467 TTTTAATATTATGGAATAAGTATAAAG
1 TTTTAATATTATGGAATAAGTATAAAG
1729494 AAATATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.40
Consensus pattern (28 bp):
TTTTAATATTATGGAATAAGTATAAAGC
Found at i:1738948 original size:2 final size:2
Alignment explanation
Indices: 1738941--1738975 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1738931 TTAGTTATTA
1738941 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 A
1738976 AATGTGTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1740452 original size:2 final size:2
Alignment explanation
Indices: 1740445--1740493 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1740435 GTCAATCTAC
1740445 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
1740487 AT AT AT A
1 AT AT AT A
1740494 ATTTACGACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1741146 original size:18 final size:18
Alignment explanation
Indices: 1741123--1741191 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1741113 GAAAAATGCT
1741123 TGGGTATCGATACTCCCA
1 TGGGTATCGATACTCCCA
* *
1741141 TGGGTATTGATACTCTACCC
1 TGGGTATCGATACTC--CCA
* *
1741161 TAGGTATCGATACCCCCA
1 TGGGTATCGATACTCCCA
*
1741179 TGGGTATTGATAC
1 TGGGTATCGATAC
1741192 CAAATTTGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 27 0.66
20 14 0.34
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (18 bp):
TGGGTATCGATACTCCCA
Found at i:1747479 original size:16 final size:16
Alignment explanation
Indices: 1747458--1747500 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1747448 CAGTAATAAA
1747458 TACAATCAAATTATTT
1 TACAATCAAATTATTT
1747474 TACAATCAAATTATTT
1 TACAATCAAATTATTT
*
1747490 TACAACCAAAT
1 TACAATCAAAT
1747501 CAGAGCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (16 bp):
TACAATCAAATTATTT
Found at i:1757700 original size:12 final size:14
Alignment explanation
Indices: 1757678--1757732 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
1757668 ACAAAACGAA
1757678 ATAAT-ATAATTAT
1 ATAATAATAATTAT
1757691 -TAA-AATAATTAT
1 ATAATAATAATTAT
1757703 CATAATAATAATTAT
1 -ATAATAATAATTAT
*
1757718 A-ATATAATATTTAT
1 ATA-ATAATAATTAT
1757732 A
1 A
1757733 ACCCGACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 11 0.31
13 1 0.03
14 15 0.42
15 9 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATAATAATTAT
Found at i:1757971 original size:53 final size:53
Alignment explanation
Indices: 1757879--1758472 Score: 719
Period size: 53 Copynumber: 11.2 Consensus size: 53
1757869 CCTCTTCTTT
*
1757879 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * *
1757932 GAACGATCTTTTGCCTACGGGTCCGCTCCCTCCTT-CTTCAAGGAGTAAAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCT-CTTGCTTCAGGGAGTAGAACTC
* * * ** * *
1757985 GAACAATCTTCTTCCTACGGGTTCTCTCCATCTTGCTTCAAAGAGTAAAAATC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * *
1758038 GAACAATCTTCTGCCTATGGGTTCACTCTCTCTTGCTTCATGGAGTATAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* ** *
1758091 GAACAATCTTTTGCCTACGGGTTCGCTCTTTCTTGCTTCA-AGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * * * *
1758143 AAACAATCTTCTACTTATGGGTTCGATCCCTCTTACTTCAAGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * *
1758196 GAACAATCTCCTACCTACGGGTTCGCTCCCTTTTTCTTCAGGGAGTAGAATTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * *
1758249 AAACAATCTTCTGCC-AGCGGGTTCGCCCCCTCTTGCTTCA-GGAGTAGAACTT
1 GAACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* *
1758301 GAATAATCTTCTGCCAACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * * *
1758354 GAACAATCTACTGCTTAAGTGTTCACTCTCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
*
1758407 AAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
*
1758460 GAATAATCTTCTG
1 GAACAATCTTCTG
1758473 GTGTGATTCT
Statistics
Matches: 458, Mismatches: 77, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
52 90 0.20
53 365 0.80
54 3 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (53 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
Found at i:1758235 original size:158 final size:158
Alignment explanation
Indices: 1757879--1758471 Score: 722
Period size: 158 Copynumber: 3.7 Consensus size: 158
1757869 CCTCTTCTTT
* * * * *
1757879 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTGGAACTCGAACGATCTTTT
1 GAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
* * *
1757944 GCCTACGGGTCCGCTCCCTCCTT-CTTCAAGGAGTAAAACTCGAACAATCTTCTTCCTACGGGTT
66 GCCTACGGGTTCGCTCCCT-CTTGCTTCAA-GAGTAGAACTCGAACAATCTTCTACCTACGGGTT
* * * * *
1758008 CTCTCCATCTTGCTTCAAAGAGTAAAAATC
129 CGCTCCCTCTTGCTTCAAGGAGTAGAACTC
* * * * * *
1758038 GAACAATCTTCTGCCTATGGGTTCACTCTCTCTTGCTTCATGGAGTATAACTCGAACAATCTTTT
1 GAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
** * * *
1758103 GCCTACGGGTTCGCTCTTTCTTGCTTCAAGAGTAGAACTCAAACAATCTTCTACTTATGGGTTCG
66 GCCTACGGGTTCGCTCCCTCTTGCTTCAAGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCG
* *
1758168 ATCCCTCTTACTTCAAGGAGTAGAACTC
131 CTCCCTCTTGCTTCAAGGAGTAGAACTC
* * * * * *
1758196 GAACAATCTCCTACCTACGGGTTCGCTCCCTTTTTCTTCAGGGAGTAGAATTCAAACAATCTTCT
1 GAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
* * * * * *
1758261 GCC-AGCGGGTTCGCCCCCTCTTGCTTCAGGAGTAGAACTTGAATAATCTTCTGCCAACGGGTTC
66 GCCTA-CGGGTTCGCTCCCTCTTGCTTCAAGAGTAGAACTCGAACAATCTTCTACCTACGGGTTC
*
1758325 GCTCCCTCTTGCTTCAGGGAGTAGAACTC
130 GCTCCCTCTTGCTTCAAGGAGTAGAACTC
* * * * *
1758354 GAACAATCTACTGCTTAAGTGTTCACTCTCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
1 GAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
* *
1758419 GCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCT
66 GCCTACGGGTTCGCTCCCTCTTGCTTCA-AGAGTAGAACTCGAACAATCTTCT
1758472 GGTGTGATTC
Statistics
Matches: 370, Mismatches: 60, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
157 1 0.00
158 265 0.72
159 104 0.28
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (158 bp):
GAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
GCCTACGGGTTCGCTCCCTCTTGCTTCAAGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCG
CTCCCTCTTGCTTCAAGGAGTAGAACTC
Found at i:1759127 original size:13 final size:13
Alignment explanation
Indices: 1759109--1759133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1759099 TGCTCGAAAG
1759109 ACTTACTGATGGT
1 ACTTACTGATGGT
1759122 ACTTACTGATGG
1 ACTTACTGATGG
1759134 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (13 bp):
ACTTACTGATGGT
Found at i:1759191 original size:135 final size:135
Alignment explanation
Indices: 1759022--1759434 Score: 637
Period size: 135 Copynumber: 3.1 Consensus size: 135
1759012 TCTTGCTCGA
* * * * *
1759022 AAGACTTATAAATGACCCGAAGGATTTAATCATCATGGTTGAAAGAATTACTGATGGCCCGAAGG
1 AAGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
*
1759087 AGTTCATCATCATGCTCGAAAGACTTACTGATGGTACTTACTGATGGATTTGCTTCACTACTCTT
66 ACTTCATCATCATGCTCGAAAGACTTACTGATGGTACTTACTGATGGATTTGCTTCACTACTCTT
1759152 CTGTG
131 CTGTG
* *
1759157 AAGACTTACAAATTACCCGAAGGATTTAATCATCAAGCTCGAAAGACTTACTGATGACCCGAAGG
1 AAGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
1759222 ATTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTACTCTT
66 ACTTCATCATCATGCTCGAAAGACTTACTGATGGTACTTACTGATGGATTTGCTTCACTACTCTT
1759287 CTGTG
131 CTGTG
* * ** * *
1759292 AAGACTTTCGAATTACCAAAAGAATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGG
1 AAGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * * *
1759357 ACTTCATCATCATGCTCCAAAAATTTACTGATGGTACTTACTGATGGATTTTCTTCACTACTCTT
66 ACTTCATCATCATGCTCGAAAGACTTACTGATGGTACTTACTGATGGATTTGCTTCACTACTCTT
*
1759422 CGGTG
131 CTGTG
1759427 AAGACTTA
1 AAGACTTA
1759435 ATATGGATTT
Statistics
Matches: 253, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 253 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (135 bp):
AAGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTCATCATCATGCTCGAAAGACTTACTGATGGTACTTACTGATGGATTTGCTTCACTACTCTT
CTGTG
Found at i:1759251 original size:42 final size:42
Alignment explanation
Indices: 1758991--1759254 Score: 221
Period size: 42 Copynumber: 6.1 Consensus size: 42
1758981 AGGTCTTATG
* * *
1758991 GATGACCTGAAGGACTT-ATCATCTTGCTCGAAAGACTTA-T
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * *
1759031 AAATGACCCGAAGGATTTAATCATCATGGTTGAAAGAATTACT
1 -GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* *
1759074 GATGGCCCGAAGGAGTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * *
1759116 GATGGTACTTACTGATGGATTTGCTTCA-CTACT-CTTCTGTGAAGACTTACA
1 GAT-G-AC---CCGAAGGATTT-CATCATC-A-TGC-TC-G-AAAGACTTACT
* * * *
1759167 AATTACCCGAAGGATTTAATCATCAAGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1759209 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1759251 GATG
1 GATG
1759255 GCACTTACTG
Statistics
Matches: 174, Mismatches: 34, Indels: 29
0.73 0.14 0.12
Matches are distributed among these distances:
41 14 0.08
42 107 0.61
43 3 0.02
44 3 0.02
45 5 0.03
46 10 0.06
47 9 0.05
48 6 0.03
49 5 0.03
50 1 0.01
51 11 0.06
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (42 bp):
GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
Found at i:1759262 original size:13 final size:13
Alignment explanation
Indices: 1759244--1759268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1759234 TGCTCGAAAG
1759244 ACTTACTGATGGC
1 ACTTACTGATGGC
1759257 ACTTACTGATGG
1 ACTTACTGATGG
1759269 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1759443 original size:37 final size:37
Alignment explanation
Indices: 1759399--1759514 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
1759389 GGTACTTACT
*
1759399 GATGGATTTTCTTCACTACTCTTCGGTGAAGACTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGACTTAA
* *
1759436 TATGGATTTGCTTCACTACTCTTCGGTGAAGACTTAG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGACTTAA
*
1759473 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGACTTAA
1759510 GATGG
1 GATGG
1759515 GTTCACTTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (37 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGACTTAA
Found at i:1764183 original size:6 final size:6
Alignment explanation
Indices: 1764172--1764223 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
1764162 AAATACATGG
* * *
1764172 AATGCA AATGCA AATGCA AATGCA AATGTA AATACA AATGCA AATACA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
1764220 AATG
1 AATG
1764224 TGTCATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (6 bp):
AATGCA
Found at i:1767726 original size:27 final size:27
Alignment explanation
Indices: 1767696--1767750 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1767686 AAATCAAATC
1767696 CAATAAAGTTCGGTTTATGGATCTTAA
1 CAATAAAGTTCGGTTTATGGATCTTAA
1767723 CAATAAAGTTCGGTTTATGGATCTTAA
1 CAATAAAGTTCGGTTTATGGATCTTAA
1767750 C
1 C
1767751 GAGATACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (27 bp):
CAATAAAGTTCGGTTTATGGATCTTAA
Found at i:1767866 original size:75 final size:75
Alignment explanation
Indices: 1767743--1767893 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
1767733 CGGTTTATGG
1767743 ATCTTAACGAGATACATCGAAGTTAGAAGGACCTCTCACGCCATTTCTCCTCCCAACGAAACA-G
1 ATCTTAACGAGATACATCGAAGTTAGAAGGACCTCTCACGCCATTTCTCCTCCCAACGAAACATG
1767807 GGGACCTTAAC
66 GGG-CCTTAAC
1767818 ATCTTAACGAGATACATCGAAGTTAGAAGGACCTCTCACGCCATTTCTCCTCCCAACGAAACATG
1 ATCTTAACGAGATACATCGAAGTTAGAAGGACCTCTCACGCCATTTCTCCTCCCAACGAAACATG
1767883 GGGCCTTAAC
66 GGGCCTTAAC
1767893 A
1 A
1767894 GGATGAAACG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
75 71 0.95
76 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (75 bp):
ATCTTAACGAGATACATCGAAGTTAGAAGGACCTCTCACGCCATTTCTCCTCCCAACGAAACATG
GGGCCTTAAC
Found at i:1768984 original size:118 final size:120
Alignment explanation
Indices: 1768775--1769007 Score: 402
Period size: 118 Copynumber: 1.9 Consensus size: 120
1768765 GGTCACTTGT
1768775 AATCGATCTGAACCAGTTGTACTGTTTGTAATTGGCTTCGTTTTTGGGCCTACAAAACGTAATAA
1 AATCGATCTGAACCAGTTGTACTGTTTGTAATTGGCTTCGTTTTTGGGCCTACAAAACGTAATAA
1768840 TATAATTGTTAAATAATTATC-ATAATAATAATAATATAATAGTAAAACTAGGTG
66 TATAATTGTTAAATAATTATCAATAATAATAATAATATAATAGTAAAACTAGGTG
1768894 AATCGATCTGAACCAGGTTGTA-TG-TTGTAATTGGCTTCGTTTTTGGGCCTACAAAA-GTAATA
1 AATCGATCTGAACCA-GTTGTACTGTTTGTAATTGGCTTCGTTTTTGGGCCTACAAAACGTAATA
1768956 ATATAATTGTTAAAATAATTATCATAATAATAATAATAATATAATAGTAAAA
65 ATATAATTGTT-AAATAATTATC--AATAATAATAATAATATAATAGTAAAA
1769008 TTATAATATA
Statistics
Matches: 109, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
117 17 0.16
118 43 0.39
119 17 0.16
120 6 0.06
121 26 0.24
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (120 bp):
AATCGATCTGAACCAGTTGTACTGTTTGTAATTGGCTTCGTTTTTGGGCCTACAAAACGTAATAA
TATAATTGTTAAATAATTATCAATAATAATAATAATATAATAGTAAAACTAGGTG
Found at i:1771387 original size:21 final size:21
Alignment explanation
Indices: 1771363--1771407 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1771353 GATTTTGAAA
* *
1771363 AAAATTGAAAGTTTAGGTACT
1 AAAACTGAAAGTTTAGATACT
*
1771384 AAAACTGATAGTTTAGATACT
1 AAAACTGAAAGTTTAGATACT
1771405 AAA
1 AAA
1771408 TGTATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.31
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGATACT
Found at i:1776526 original size:32 final size:31
Alignment explanation
Indices: 1776476--1776628 Score: 173
Period size: 32 Copynumber: 4.9 Consensus size: 31
1776466 GAGTCGAGAG
*
1776476 TTACTTATGTCTTTCGGGACATATGGACAATA
1 TTACCTATGTCTTTCGGGACATATGGAC-ATA
* * *
1776508 TTACCTATATCTTTCGGGATATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-TA
* *
1776540 TTACCTATGTATTTAGGGACATATGGACATGA
1 TTACCTATGTCTTTCGGGACATATGGACAT-A
* * *
1776572 TTACCGATGTCTTTCGGGATATATGGACA-G
1 TTACCTATGTCTTTCGGGACATATGGACATA
* *
1776602 TTACCTTTGTCTTTTGGGACATATGGA
1 TTACCTATGTCTTTCGGGACATATGGA
1776629 TAGGTCATTC
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
30 23 0.23
31 1 0.01
32 77 0.76
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACATA
Found at i:1776560 original size:64 final size:62
Alignment explanation
Indices: 1776474--1776628 Score: 213
Period size: 64 Copynumber: 2.5 Consensus size: 62
1776464 AAGAGTCGAG
* * *
1776474 AGTTACTTATGTCTTTCGGGACATATGGACAAT-ATTACCTATATCTTTCGGGATATATGGAC
1 AGTTACCTATGTCTTTAGGGACATATGGAC-ATGATTACCGATATCTTTCGGGATATATGGAC
* *
1776536 AGGATTACCTATGTATTTAGGGACATATGGACATGATTACCGATGTCTTTCGGGATATATGGAC
1 A-G-TTACCTATGTCTTTAGGGACATATGGACATGATTACCGATATCTTTCGGGATATATGGAC
* *
1776600 AGTTACCTTTGTCTTTTGGGACATATGGA
1 AGTTACCTATGTCTTTAGGGACATATGGA
1776629 TAGGTCATTC
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
62 25 0.30
63 4 0.05
64 53 0.65
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (62 bp):
AGTTACCTATGTCTTTAGGGACATATGGACATGATTACCGATATCTTTCGGGATATATGGAC
Found at i:1777253 original size:22 final size:22
Alignment explanation
Indices: 1777228--1777270 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1777218 ATTGTTTACG
*
1777228 GTACTGTTCATTAATATTCACA
1 GTACTGATCATTAATATTCACA
*
1777250 GTACTGATCATTACTATTCAC
1 GTACTGATCATTAATATTCAC
1777271 GGCACTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (22 bp):
GTACTGATCATTAATATTCACA
Found at i:1777282 original size:22 final size:22
Alignment explanation
Indices: 1777225--1777282 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1777215 AGTATTGTTT
*
1777225 ACGGTACTGTTCATTAATATTC
1 ACGGTACTATTCATTAATATTC
* *
1777247 ACAGTACTGA-TCATTACTATTC
1 ACGGTACT-ATTCATTAATATTC
*
1777269 ACGGCACTATTCAT
1 ACGGTACTATTCAT
1777283 ACAGTATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (22 bp):
ACGGTACTATTCATTAATATTC
Found at i:1781225 original size:19 final size:20
Alignment explanation
Indices: 1781201--1781250 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1781191 GGCCAAGAGG
*
1781201 ATGTATCTTCATT-AAAATC
1 ATGTATTTTCATTAAAAATC
1781220 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATTAAAAATC
1781240 ATGTATTTTCA
1 ATGTATTTTCA
1781251 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATC
Found at i:1782099 original size:31 final size:30
Alignment explanation
Indices: 1782045--1782104 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
1782035 ATTTGGAGTA
*
1782045 CAAAAAGAAAAGAAAAGAAAAGAAGAAATTT
1 CAAAAACAAAAGAAAAGAAAAGAA-AAATTT
* **
1782076 CAAAAACAAAAGTAAAGTGAAGAAAAATT
1 CAAAAACAAAAGAAAAGAAAAGAAAAATT
1782105 GCAATTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (30 bp):
CAAAAACAAAAGAAAAGAAAAGAAAAATTT
Found at i:1785292 original size:19 final size:20
Alignment explanation
Indices: 1785268--1785311 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1785258 AGCATGTATC
1785268 TTCATT-AAAATCATATATT
1 TTCATTAAAAATCATATATT
*
1785287 TTCATTAAAAAATCATGTATT
1 TTCATT-AAAAATCATATATT
1785308 TTCA
1 TTCA
1785312 AAGGGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
21 16 0.73
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (20 bp):
TTCATTAAAAATCATATATT
Found at i:1789968 original size:21 final size:20
Alignment explanation
Indices: 1789944--1790007 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1789934 AACTTTGAAA
1789944 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1789965 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1789979 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1790000 AAATGTTT
1 AAATGTTT
1790008 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1789982 original size:35 final size:36
Alignment explanation
Indices: 1789936--1790057 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
1789926 TGGTAATCAA
1789936 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
1789973 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1790008 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
1790045 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
1790058 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1790055 original size:72 final size:69
Alignment explanation
Indices: 1789909--1790052 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 69
1789899 TGAAAGTATT
1789909 AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTTC
1 AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTTC
*
1789974 TTTG
66 GTTG
*** * *
1789978 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATG
1 AAAATGGTTTTC-AAGTTTGGT-AAT-CAACTTTGAAAAAAT-GATTTTCAAAGTTTGGTAAATG
1790042 TTT-GTTG
62 TTTCGTTG
1790049 AAAA
1 AAAA
1790053 ATGATAATGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 12 0.18
70 9 0.14
71 16 0.25
72 28 0.43
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTTC
GTTG
Found at i:1790481 original size:16 final size:17
Alignment explanation
Indices: 1790460--1790491 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1790450 TTACTATTCA
1790460 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
1790476 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1790492 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:1794591 original size:21 final size:20
Alignment explanation
Indices: 1794567--1794630 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1794557 AACTTTGAAA
1794567 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1794588 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1794602 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1794623 AAATGTTT
1 AAATGTTT
1794631 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1794605 original size:35 final size:36
Alignment explanation
Indices: 1794559--1794680 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
1794549 TGGTAACCAA
1794559 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
1794596 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1794631 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
1794668 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
1794681 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1796180 original size:87 final size:87
Alignment explanation
Indices: 1796089--1796459 Score: 243
Period size: 87 Copynumber: 4.2 Consensus size: 87
1796079 GTCCCATTGT
* * * * *
1796089 TTGTCCAACGCCATATCTAATACCCTT-TCCATTTCCATTGCCAACTCCAATGCCATATCCAAAG
1 TTGTCCAACGCCATACCCAA-AACCTTCTCCATCTCCATTGCCAACTCCAATACCATATCCAAAG
***
1796153 TTGTTTCCTGACTGACCTC-CTGA
65 CCATTTCCTGACTGACCTCTC-GA
* * * *
1796176 TTGTCCAATGCCATACCCAAAACCTTCTCCATCTCCATTGCCAATTCCGATACCATATCCAACGC
1 TTGTCCAACGCCATACCCAAAACCTTCTCCATCTCCATTGCCAACTCCAATACCATATCCAAAGC
*
1796241 CATTTCCTGATTGACCTCTCGA
66 CATTTCCTGACTGACCTCTCGA
* * * * * ** *
1796263 TTGTCCAACACCATACCCAATA-CTATTTCCCGA-CTGACCCCTT--TATTGTCCAACACCATAT
1 TTGTCCAACGCCATACCCAAAACCT-TCT-CC-ATCT---CCATTGCCA-ACTCCAATACCATAT
* * * * *
1796324 CCAATA-CTATTTCTTGATTGACCCCTCGG
59 CCAA-AGCCATTTCCTGACTGACCTCTCGA
* * * * ** * **
1796353 TTGTCCAACACCATATCCAACACCTTCTCCTTCTCCGCTGCCAATTCCAATACCATATCCATCGC
1 TTGTCCAACGCCATACCCAAAACCTTCTCCATCTCCATTGCCAACTCCAATACCATATCCAAAGC
* * *
1796418 CGTTTCTTGACTGACCTCCCGA
66 CATTTCCTGACTGACCTCTCGA
* *
1796440 TTGTCCTACTCCATACCCAA
1 TTGTCCAACGCCATACCCAA
1796460 TACTATTTCC
Statistics
Matches: 220, Mismatches: 49, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
86 10 0.05
87 136 0.62
88 6 0.03
89 6 0.03
90 56 0.25
91 6 0.03
ACGTcount: A:0.24, C:0.36, G:0.09, T:0.30
Consensus pattern (87 bp):
TTGTCCAACGCCATACCCAAAACCTTCTCCATCTCCATTGCCAACTCCAATACCATATCCAAAGC
CATTTCCTGACTGACCTCTCGA
Found at i:1796292 original size:45 final size:45
Alignment explanation
Indices: 1796242--1796549 Score: 252
Period size: 45 Copynumber: 6.9 Consensus size: 45
1796232 ATCCAACGCC
1796242 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATACT
1 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATACT
* * * ** *
1796287 ATTTCCCGACTGACCCCTTTATTGTCCAACACCATATCCAATACT
1 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATACT
* * * * *
1796332 ATTTCTTGATTGACCCCTCGGTTGTCCAACACCATATCCAACACCT
1 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATA-CT
* * * * * * * *
1796378 -TCTCCT--TCT--CCGCTGCCAAT-TCCAATACCATATCC-ATCGCC
1 ATTTCCTGAT-TGACCTCT-CGATTGTCCAACACCATACCCAAT-ACT
* * * * * *
1796419 GTTTCTTGACTGACCTCCCGATTGTCCTACTCCATACCCAATACT
1 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATACT
* * *
1796464 ATTTCCTGATTGGCCTCCCGATTGTCCGACACCATACCCAATACT
1 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATACT
* * *
1796509 ATTTCCTGATTGACCTCCCGATTGTCCGATACCATACCCAA
1 ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAA
1796550 CACCTTCTCC
Statistics
Matches: 208, Mismatches: 44, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.01
42 22 0.11
43 4 0.02
44 4 0.02
45 172 0.83
46 4 0.02
ACGTcount: A:0.23, C:0.36, G:0.10, T:0.31
Consensus pattern (45 bp):
ATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATACT
Found at i:1796397 original size:177 final size:177
Alignment explanation
Indices: 1796156--1796656 Score: 592
Period size: 177 Copynumber: 2.8 Consensus size: 177
1796146 TCCAAAGTTG
* * * *
1796156 TTTCCTGACTGACCTCCTGATTGTCCAATGCCATACCCAAAACCTTCTCCATCTCCATTGCCAAT
1 TTTCCTGATTGACCTCCCGATTGTCCAATACCATACCCAACACCTTCTCCATCTCCATTGCCAAT
* * *
1796221 TCCGATACCATATCCAACGCCATTTCCTGATTGACCTCTCGATTGTCCAACACCATACCCAATAC
66 TCCAATACCATATCCAACGCCATTTCCTGACTGACCTCCCGATTGTCCAACACCATACCCAATAC
** *
1796286 TATTTCCCGACTGACC-CCTTTATTGTCCAACACCATATCCAATACTA
131 TATTTCCCGACTGACCTCC-CGATTGTCCAACACCATACCCAATACTA
* * * * * **
1796333 TTTCTTGATTGACC-CCTCGGTTGTCCAACACCATATCCAACACCTTCTCCTTCTCCGCTGCCAA
1 TTTCCTGATTGACCTCC-CGATTGTCCAATACCATACCCAACACCTTCTCCATCTCCATTGCCAA
* * * * *
1796397 TTCCAATACCATATCCATCGCCGTTTCTTGACTGACCTCCCGATTGTCCTACTCCATACCCAATA
65 TTCCAATACCATATCCAACGCCATTTCCTGACTGACCTCCCGATTGTCCAACACCATACCCAATA
* * * *
1796462 CTATTTCCTGATTGGCCTCCCGATTGTCCGACACCATACCCAATACTA
130 CTATTTCCCGACTGACCTCCCGATTGTCCAACACCATACCCAATACTA
* *
1796510 TTTCCTGATTGACCTCCCGATTGTCCGATACCATACCCAACACCTTCTCCATCTCCATTGTCAAT
1 TTTCCTGATTGACCTCCCGATTGTCCAATACCATACCCAACACCTTCTCCATCTCCATTGCCAAT
* *** * * * * * *
1796575 TCCAATACCATATCAAACGTTGTTTCGTGCCTGACCCCCCCGATTATCCAACACCATATCTAATA
66 TCCAATACCATATCCAACGCCATTTCCTGACTGA-CCTCCCGATTGTCCAACACCATACCCAATA
* * *
1796640 TTATTTCCTGATTGACC
130 CTATTTCCCGACTGACC
1796657 CCCTAATTTT
Statistics
Matches: 271, Mismatches: 49, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
176 2 0.01
177 226 0.83
178 43 0.16
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.31
Consensus pattern (177 bp):
TTTCCTGATTGACCTCCCGATTGTCCAATACCATACCCAACACCTTCTCCATCTCCATTGCCAAT
TCCAATACCATATCCAACGCCATTTCCTGACTGACCTCCCGATTGTCCAACACCATACCCAATAC
TATTTCCCGACTGACCTCCCGATTGTCCAACACCATACCCAATACTA
Found at i:1799737 original size:21 final size:22
Alignment explanation
Indices: 1799712--1799763 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1799702 AAAAAAATAC
*
1799712 CTAAAATATTATTA-TTTTTAG
1 CTAAAACATTATTATTTTTTAG
1799733 CTAAAACATTATTATTTTTTAG
1 CTAAAACATTATTATTTTTTAG
1799755 CTAAAACAT
1 CTAAAACAT
1799764 CAATTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (22 bp):
CTAAAACATTATTATTTTTTAG
Found at i:1799772 original size:22 final size:22
Alignment explanation
Indices: 1799712--1799772 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1799702 AAAAAAATAC
* *
1799712 CTAAAATATTATTA-TTTTTAG
1 CTAAAACATAATTATTTTTTAG
*
1799733 CTAAAACATTATTATTTTTTAG
1 CTAAAACATAATTATTTTTTAG
1799755 CTAAAACATCAATT-TTTT
1 CTAAAACAT-AATTATTTT
1799773 GTAACATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 13 0.36
22 20 0.56
23 3 0.08
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (22 bp):
CTAAAACATAATTATTTTTTAG
Found at i:1800775 original size:45 final size:45
Alignment explanation
Indices: 1800712--1801040 Score: 262
Period size: 45 Copynumber: 7.3 Consensus size: 45
1800702 TCAAACATTG
* * *
1800712 TTTCCTGATTGACCCCCTGATTGTCCGATGCCGTACCCAATGCTA
1 TTTCCTGATTGTCCCCCTGATTGCCCAATGCCGTACCCAATGCTA
* * *
1800757 TTTCTTG-TCTGTCCCCCTGATTGCCCAATGTCGTACCCAATACT-
1 TTTCCTGAT-TGTCCCCCTGATTGCCCAATGCCGTACCCAATGCTA
* * * *
1800801 TTCTTCTGACTG-CCCTCCTGATTGTCCAATGCCATACCCAA-GACT-
1 TT-TCCTGATTGTCCC-CCTGATTGCCCAATGCCGTACCCAATG-CTA
* * ** * *
1800846 TTCTCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTA
1 TT-TCCTGATTGTCCCCCTGATTGCCCAATGCCGTACCCAATGCTA
* * ** * *
1800892 TTTCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTA
1 TTTCCTGATTGTCCCCCTGATTGCCCAATGCCGTACCCAATGCTA
* *
1800937 TTTCCTGATTGTCCCCCTGATT-CGCCAATGCCGTACCCGATACT-
1 TTTCCTGATTGTCCCCCTGATTGC-CCAATGCCGTACCCAATGCTA
* * * *
1800981 TTCTCCTGACTGTCCCCCTGATTGTCCAATACCATACCCAA-GACT-
1 TT-TCCTGATTGTCCCCCTGATTGCCCAATGCCGTACCCAATG-CTA
1801026 TTCTCCTGATTGTCC
1 TT-TCCTGATTGTCC
1801041 AACACCATAC
Statistics
Matches: 234, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
44 9 0.04
45 220 0.94
46 5 0.02
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.36
Consensus pattern (45 bp):
TTTCCTGATTGTCCCCCTGATTGCCCAATGCCGTACCCAATGCTA
Found at i:1800887 original size:90 final size:90
Alignment explanation
Indices: 1800727--1801040 Score: 295
Period size: 90 Copynumber: 3.5 Consensus size: 90
1800717 TGATTGACCC
* * *
1800727 CCTGATTGTCCGATGCCGTACCCAATGCTATT-TCTTG-TCTGTCCCCCTGATTGCCCAATGTCG
1 CCTGATTGTCCAATGCCATACCCAATGCT-TTCTCCTGAT-TGTCCCCCTGATTGCCCAATGTCG
1800790 TACCCAATACTTTCTTCTGACTGCCCT
64 TACCCAATACTTTCTTCTGACTGCCCT
* * *
1800817 CCTGATTGTCCAATGCCATACCCAA-GACTTTCTCCTGATTGTCCTCTTGATTGCCCAATGTTGT
1 CCTGATTGTCCAATGCCATACCCAATG-CTTTCTCCTGATTGTCCCCCTGATTGCCCAATGTCGT
* * * *
1800881 ATCCAAT-GTTAT-TTCCTGATTGTCCT
65 ACCCAATACTT-TCTT-CTGACTGCCCT
* * *** * * *
1800907 CTTGATTGCCCAATGTTGTATCCAATG-TTATTTCCTGATTGTCCCCCTGATT-CGCCAATGCCG
1 CCTGATTGTCCAATGCCATACCCAATGCTT-TCTCCTGATTGTCCCCCTGATTGC-CCAATGTCG
* *
1800970 TACCCGATACTTTCTCCTGACTGTCCC-
64 TACCCAATACTTTCTTCTGACTG-CCCT
*
1800997 CCTGATTGTCCAATACCATACCCAA-GACTTTCTCCTGATTGTCC
1 CCTGATTGTCCAATGCCATACCCAATG-CTTTCTCCTGATTGTCC
1801041 AACACCATAC
Statistics
Matches: 176, Mismatches: 35, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
89 11 0.06
90 156 0.89
91 9 0.05
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.36
Consensus pattern (90 bp):
CCTGATTGTCCAATGCCATACCCAATGCTTTCTCCTGATTGTCCCCCTGATTGCCCAATGTCGTA
CCCAATACTTTCTTCTGACTGCCCT
Found at i:1800932 original size:135 final size:135
Alignment explanation
Indices: 1800714--1801010 Score: 316
Period size: 135 Copynumber: 2.2 Consensus size: 135
1800704 AAACATTGTT
* * * * ** * *
1800714 TCCTGATTGACCCCCTGATTGTCCGATGCCGTACCCAATGCTATTTCTTGTCTGTCCCCCTGATT
1 TCCTGACTGTCCCCCTGATTGCCCAATGTTGTATCCAATGCTATTTCCTGTCTGTCCCCCTGATT
1800779 GCCCAATGTCGTACCCAATACTT-TCTT-CTGACTG-CCCTCCTGATT-GTCCAATGCCATACCC
66 GCCCAATGTCGTACCCAAT-CTTAT-TTCCTGACTGTCCC-CCTGATTCG-CCAATGCCATACCC
1800840 AAGACTTTC
127 AAGACTTTC
* * * * * *
1800849 TCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTATTTCCTGAT-TGTCCTCTTGAT
1 TCCTGACTGTCCCCCTGATTGCCCAATGTTGTATCCAATGCTATTTCCTG-TCTGTCCCCCTGAT
* * * * * * *
1800913 TGCCCAATGTTGTATCCAATGTTATTTCCTGATTGTCCCCCTGATTCGCCAATGCCGTACCCGAT
65 TGCCCAATGTCGTACCCAATCTTATTTCCTGACTGTCCCCCTGATTCGCCAATGCCATACCCAAG
1800978 ACTTTC
130 ACTTTC
*
1800984 TCCTGACTGTCCCCCTGATTGTCCAAT
1 TCCTGACTGTCCCCCTGATTGCCCAAT
1801011 ACCATACCCA
Statistics
Matches: 134, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
134 4 0.03
135 125 0.93
136 5 0.04
ACGTcount: A:0.17, C:0.32, G:0.15, T:0.36
Consensus pattern (135 bp):
TCCTGACTGTCCCCCTGATTGCCCAATGTTGTATCCAATGCTATTTCCTGTCTGTCCCCCTGATT
GCCCAATGTCGTACCCAATCTTATTTCCTGACTGTCCCCCTGATTCGCCAATGCCATACCCAAGA
CTTTC
Found at i:1801018 original size:180 final size:180
Alignment explanation
Indices: 1800712--1801040 Score: 484
Period size: 180 Copynumber: 1.8 Consensus size: 180
1800702 TCAAACATTG
* * *
1800712 TTTCCTGATTGACCCCCTGATTGTCCGATGCCGTACCCAATGCTATTTCTTGTCTGTCCCCCTGA
1 TTTCCTGATTGACCCCCTGATTGCCCAATGCCGTACCCAATGCTATTTCCTGTCTGTCCCCCTGA
* * *
1800777 TTGCCCAATGTCGTACCCAATACTTTCTTCTGACTGCCCTCCTGATTGTCCAATGCCATACCCAA
66 TTGCCCAATGCCGTACCCAATACTTTCTCCTGACTGCCCTCCTGATTGTCCAATACCATACCCAA
1800842 GACTTTCTCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTA
131 GACTTTCTCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTA
* * * ** * *
1800892 TTTCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTATTTCCTGAT-TGTCCCCCTG
1 TTTCCTGATTGACCCCCTGATTGCCCAATGCCGTACCCAATGCTATTTCCTG-TCTGTCCCCCTG
*
1800956 ATT-CGCCAATGCCGTACCCGATACTTTCTCCTGACTGTCCC-CCTGATTGTCCAATACCATACC
65 ATTGC-CCAATGCCGTACCCAATACTTTCTCCTGACTG-CCCTCCTGATTGTCCAATACCATACC
1801019 CAAGACTTTCTCCTGATTGTCC
128 CAAGACTTTCTCCTGATTGTCC
1801041 AACACCATAC
Statistics
Matches: 132, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
179 1 0.01
180 127 0.96
181 4 0.03
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.36
Consensus pattern (180 bp):
TTTCCTGATTGACCCCCTGATTGCCCAATGCCGTACCCAATGCTATTTCCTGTCTGTCCCCCTGA
TTGCCCAATGCCGTACCCAATACTTTCTCCTGACTGCCCTCCTGATTGTCCAATACCATACCCAA
GACTTTCTCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATGTTA
Found at i:1801039 original size:33 final size:33
Alignment explanation
Indices: 1800997--1801073 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
1800987 TGACTGTCCC
* *
1800997 CCTGATTGTCCAATACCATACCCAAGACTTTCT
1 CCTGATTGTCCAACACCATACCCAAGACCTTCT
*
1801030 CCTGATTGTCCAACACCATACCCAATACCTTCT
1 CCTGATTGTCCAACACCATACCCAAGACCTTCT
1801063 CCTGATTGTCC
1 CCTGATTGTCC
1801074 CCATGATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.25, C:0.36, G:0.09, T:0.30
Consensus pattern (33 bp):
CCTGATTGTCCAACACCATACCCAAGACCTTCT
Found at i:1801055 original size:90 final size:87
Alignment explanation
Indices: 1800714--1801097 Score: 226
Period size: 90 Copynumber: 4.4 Consensus size: 87
1800704 AAACATTGTT
* * * * *
1800714 TCCTGATTGACCCCCTGATTGTCCGATGCCGTACCCAATG-CTATT-TCTTG-TCTGTCCCCCTG
1 TCCTGACTGTCCCCCTGATTGTCCAATGCCATACCCAA-GACT-TTCTCCTGAT-TGTCCCCC--
*
1800776 ATTGCCCAATGTCGTACCCAATACTTTC
61 A-TACCCAATGTCGTACCCAATACTTTC
* **
1800804 TTCTGACTG-CCCTCCTGATTGTCCAATGCCATACCCAAGACTTTCTCCTGATTGTCCTCTTGAT
1 TCCTGACTGTCCC-CCTGATTGTCCAATGCCATACCCAAGACTTTCTCCTGATTGTCC-C-CCA-
* * * * *
1800868 TGCCCAATGTTGTATCCAAT-GTTATT
62 TACCCAATGTCGTACCCAATACTT-TC
* * * * *** * *
1800894 TCCTGATTGTCCTCTTGATTGCCCAATGTTGTATCCAATG--TTATTTCCTGATTGTCCCCCTGA
1 TCCTGACTGTCCCCCTGATTGTCCAATGCCATACCCAA-GACTT-TCTCCTGATTGTCCCCC--A
* * *
1800957 TTCGCCAATGCCGTACCCGATACTTTC
62 TAC-CCAATGTCGTACCCAATACTTTC
*
1800984 TCCTGACTGTCCCCCTGATTGTCCAATACCATACCCAAGACTTTCTCCTGATTGT---CCA-ACA
1 TCCTGACTGTCCCCCTGATTGTCCAATGCCATACCCAAGACTTTCTCCTGATTGTCCCCCATAC-
*
1801045 CC-A-----TACCCAATACCTTC
65 CCAATGTCGTACCCAATACTTTC
* *
1801062 TCCTGATTGTCCCCATGATTGTCCAATGCCATACCC
1 TCCTGACTGTCCCCCTGATTGTCCAATGCCATACCC
1801098 GATACCATTT
Statistics
Matches: 231, Mismatches: 47, Indels: 44
0.72 0.15 0.14
Matches are distributed among these distances:
78 45 0.19
83 1 0.00
84 3 0.01
85 1 0.00
87 2 0.01
89 14 0.06
90 156 0.68
91 9 0.04
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.34
Consensus pattern (87 bp):
TCCTGACTGTCCCCCTGATTGTCCAATGCCATACCCAAGACTTTCTCCTGATTGTCCCCCATACC
CAATGTCGTACCCAATACTTTC
Found at i:1801831 original size:32 final size:32
Alignment explanation
Indices: 1801790--1801854 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1801780 ACAATGTTTG
*
1801790 ATAGTCATTAAATATTGAATCGAACTCGAATT
1 ATAGTCATTAAATATTGAATCAAACTCGAATT
1801822 ATAGTCATTAAATATTGAATCAAACTCGAATT
1 ATAGTCATTAAATATTGAATCAAACTCGAATT
1801854 A
1 A
1801855 AATATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (32 bp):
ATAGTCATTAAATATTGAATCAAACTCGAATT
Found at i:1804022 original size:13 final size:13
Alignment explanation
Indices: 1804004--1804029 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1803994 TGCTCTCGGT
1804004 TCTTTTTTTGTTG
1 TCTTTTTTTGTTG
1804017 TCTTTTTTTGTTG
1 TCTTTTTTTGTTG
1804030 ATGATGGGTA
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:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (13 bp):
TCTTTTTTTGTTG
Found at i:1804680 original size:2 final size:2
Alignment explanation
Indices: 1804673--1804702 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1804663 TACTTAATGC
1804673 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
1804703 GTTAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1805019 original size:55 final size:55
Alignment explanation
Indices: 1804959--1805093 Score: 164
Period size: 55 Copynumber: 2.5 Consensus size: 55
1804949 TTCTTTAGGA
* * * * *
1804959 AGTATGAAACTTGAAGAATTTTCAACCATCATATCTGCTCTCTATTCCTTCAGAG
1 AGTATGAAACTCGAACAATCTTCAACAATCATATCTGCTCCCTATTCCTTCAGAG
* * * *
1805014 AGTATGAGACTCGAACAGTCTTCAACAATCATGTCTGCTCCCTATTTCTTCAGAG
1 AGTATGAAACTCGAACAATCTTCAACAATCATATCTGCTCCCTATTCCTTCAGAG
*
1805069 AGTAT-AAGACTCGAACATTCTTCAA
1 AGTATGAA-ACTCGAACAATCTTCAA
1805094 ACGGGTTCGC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 1 0.01
55 67 0.99
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (55 bp):
AGTATGAAACTCGAACAATCTTCAACAATCATATCTGCTCCCTATTCCTTCAGAG
Found at i:1805163 original size:51 final size:52
Alignment explanation
Indices: 1805050--1805559 Score: 535
Period size: 51 Copynumber: 9.8 Consensus size: 52
1805040 AATCATGTCT
* * *
1805050 GCTCCCTATTTCTTCA-GAGAGTATA-AGACTCGAACATTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGA-AGTATAGA-ACTCGAATAATCTTCAAACGGGTTC
* * *
1805102 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAA-AATCTTCAAACGGGCTC
1 GCTCCCTCTTTCTTC-AGGAAGTATAGAACTCGAATAATCTTCAAACGGGTTC
* * * * *** *
1805153 ACTCCTTCTTTC-TCTAGGGAGTATGGAACTTTTA-AATCTTTAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGAAGTATAGAACTCGAATAATCTTCAAACGGGTTC
**
1805204 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GA-ATAATCTTCAAACGGGTTC
* *
1805258 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAATAA-CTTCACACGGGTTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCAAACGGGTTC
* * **
1805309 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGAAGTATAGAACTCG-A-ATAATCTTCAAACGGGTTC
**
1805363 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GA-ATAATCTTCAAACGGGTTC
* *
1805417 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAATAA-CTTCACAA-TGGTTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCA-AACGGGTTC
* *
1805468 GCTCCCTCTTTC-TCTAGGGAA-TATGGAACTCGAA-CATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-A-GGAAGTATAGAACTCGAATAATCTTCAAACGGGTTC
*
1805519 GCTCCCTCTTTCTTCAGAAAGTATAGAACTCGAAT-ATCTTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTC
1805560 TTCCTCTTCA
Statistics
Matches: 393, Mismatches: 44, Indels: 43
0.82 0.09 0.09
Matches are distributed among these distances:
50 10 0.03
51 198 0.50
52 39 0.10
53 7 0.02
54 136 0.35
55 3 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (52 bp):
GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCAAACGGGTTC
Found at i:1805312 original size:105 final size:104
Alignment explanation
Indices: 1805069--1805562 Score: 535
Period size: 105 Copynumber: 4.7 Consensus size: 104
1805059 TTCTTCAGAG
* * *
1805069 AGTATA-AGACTCGAACATTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACT
1 AGTATAGA-ACTCGAATA-TCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAACT
* * * * *
1805132 CGAAA--ATCTTCAAACGGGCTCACTCCTTCTTTCTCTAGGG
63 CGAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGA
* ** *
1805172 AGTATGGAACTTTTAA-ATCTTTAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCG
1 AGTATAGAAC-TCGAATATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-
*
1805236 GACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGA
64 GAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGA
* * * * *
1805277 AGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCG
1 AGTATAGAACTCGAATATCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAACTCG
1805341 AACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGA
65 AA-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGA
*
1805382 AGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
1 AGTATAGAACTC-GA-AT-ATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
* ** *
1805447 C-CAAT-AACTTCACAA-TGGTTCGCTCCCTCTTTCTCTAGGGA
63 CGAAATCTTCTTCA-AACGGGTTCGCTCCCTCTTTCTCTA-GGA
* * *
1805488 A-TATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAAAGTATAGAACTCGA
1 AGTATAGAACTCGAATATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGA
1805552 ATATCTTCTTC
66 A-ATCTTCTTC
1805563 CTCTTCACTA
Statistics
Matches: 333, Mismatches: 38, Indels: 38
0.81 0.09 0.09
Matches are distributed among these distances:
102 85 0.26
103 15 0.05
104 16 0.05
105 163 0.49
106 10 0.03
107 3 0.01
108 39 0.12
109 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (104 bp):
AGTATAGAACTCGAATATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGA
AATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGA
Found at i:1805426 original size:159 final size:158
Alignment explanation
Indices: 1805050--1805562 Score: 742
Period size: 159 Copynumber: 3.3 Consensus size: 158
1805040 AATCATGTCT
*
1805050 GCTCCCTATTTCTTCA-GAGAGTATA-AGACTCGAACA--TTCTTCAAACGGGTTCGCTCCCTCT
1 GCTCCCTCTTTCTTCAGGA-AGTATAGA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCT
* * * * * * *
1805111 TTC-TCTAGGGAGTATGGAACTCGAA-AATCTTCAAACGGGCTCACTCCTTCTTTCTCTAGGGAG
64 TTCTTC-AGGAAGTATAGAACTCCAATAA-CTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAG
**
1805174 TATGGAACTTTTAA-ATCT-TT-AAACGGGTTC
127 TATGGAAC-TCGAACATCTCTTCAAACGGGTTC
*
1805204 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1805269 CTTCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG
66 CTTCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG
1805334 GAACTCGAACATCTTCTTCAAACGGGTTC
131 GAACTCGAACATC-TCTTCAAACGGGTTC
*
1805363 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
** *
1805428 CTTCAGGAAGTATAGAACTCCAATAACTTCACAATGGTTCGCTCCCTCTTTCTCTAGGGAATATG
66 CTTCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG
1805493 GAACTCGAACA--TCTTCAAACGGGTTC
131 GAACTCGAACATCTCTTCAAACGGGTTC
* *
1805519 GCTCCCTCTTTCTTCAGAAAGTATAGAACTCGAATATCTTCTTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTC
1805563 CTCTTCACTA
Statistics
Matches: 332, Mismatches: 17, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
154 29 0.09
155 6 0.02
156 142 0.43
157 5 0.02
158 2 0.01
159 148 0.45
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (158 bp):
GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
CTTCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG
GAACTCGAACATCTCTTCAAACGGGTTC
Found at i:1806853 original size:1 final size:1
Alignment explanation
Indices: 1806847--1806906 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
1806837 TGAACCCTCC
* * * * * * *
1806847 TTTTTTTCTTTTTTTTGTTCTTTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1806907 CATTGTTTTC
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.02, C:0.03, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:1806891 original size:19 final size:18
Alignment explanation
Indices: 1806847--1806906 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
1806837 TGAACCCTCC
*
1806847 TTTTTTTCTTTTTTTTGTT
1 TTTTTTTGTTTTTTTT-TT
*
1806866 CTTTTTTGTTTTTTTTTT
1 TTTTTTTGTTTTTTTTTT
1806884 GTTTTTTTGTTTTTTATTTT
1 -TTTTTTTGTTTTTT-TTTT
1806904 TTT
1 TTT
1806907 CATTGTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 2 0.06
19 30 0.83
20 4 0.11
ACGTcount: A:0.02, C:0.03, G:0.07, T:0.88
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTTTT
Found at i:1806912 original size:19 final size:17
Alignment explanation
Indices: 1806847--1806915 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
1806837 TGAACCCTCC
1806847 TTTTTTTCTT-TTTTTT
1 TTTTTTTCTTGTTTTTT
*
1806863 GTTCTTTT-TTGTTTTTTT
1 -TTTTTTTCTTG-TTTTTT
*
1806881 TTTGTTTTTTTGTTTTTT
1 TTT-TTTTCTTGTTTTTT
1806899 ATTTTTTTCATTGTTTT
1 -TTTTTTTC-TTGTTTT
1806916 CATCTTCAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.05
17 8 0.19
18 20 0.47
19 13 0.30
ACGTcount: A:0.03, C:0.04, G:0.07, T:0.86
Consensus pattern (17 bp):
TTTTTTTCTTGTTTTTT
Found at i:1806912 original size:27 final size:27
Alignment explanation
Indices: 1806847--1806915 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
1806837 TGAACCCTCC
* *
1806847 TTTTTTTCTTTTTTTTGTTCTTTTTTG
1 TTTTTTTCTTGTTTTTGTTCTTTTTTA
* *
1806874 TTTTTTTTTTGTTTTT-TTGTTTTTTA
1 TTTTTTTCTTGTTTTTGTTCTTTTTTA
1806900 TTTTTTTCATTGTTTT
1 TTTTTTTC-TTGTTTT
1806916 CATCTTCAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.03, C:0.04, G:0.07, T:0.86
Consensus pattern (27 bp):
TTTTTTTCTTGTTTTTGTTCTTTTTTA
Found at i:1815246 original size:35 final size:35
Alignment explanation
Indices: 1815162--1815255 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
1815152 AAAAATTCAA
* * * *
1815162 GAGCTCGATTGAAGCTCGAGACTCTAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGA-ACTCAAACTCGAATTT
* * *
1815198 GAACTCGAGTCAAGCTCGAACTCAAACTTGAATTT
1 GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTT
1815233 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTCAAGCTCGAACTC
1815256 GATTCAAGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 33 0.67
36 16 0.33
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (35 bp):
GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTT
Found at i:1815258 original size:17 final size:17
Alignment explanation
Indices: 1815236--1815289 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
1815226 TGAATTTGAG
1815236 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
1815253 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
*
1815270 CTCGATTTAAGCTCGAA
1 CTCGATTCAAGCTCGAA
1815287 CTC
1 CTC
1815290 AAACCTACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:1819105 original size:21 final size:21
Alignment explanation
Indices: 1819079--1819283 Score: 104
Period size: 21 Copynumber: 9.8 Consensus size: 21
1819069 AACTTAAACC
1819079 TAAACCTTAAACCCTAATATA
1 TAAACCTTAAACCCTAATATA
* *
1819100 TAAACCCTAAACCCTAA-ACTC
1 TAAACCTTAAACCCTAATA-TA
* * *
1819121 TAAACCTTAAATCAT-ATCACA
1 TAAACCTTAAACCCTAAT-ATA
* *
1819142 -AAAACTCTAAACTCTAATATA
1 TAAACCT-TAAACCCTAATATA
* *
1819163 TAAACCCTAAACCATAA-ACTA
1 TAAACCTTAAACCCTAATA-TA
* * * *
1819184 AAAACCTTAAATCAT-ATCACA
1 TAAACCTTAAACCCTAAT-ATA
* * *
1819205 TAAACCTTAAATCTTAA-ACTC
1 TAAACCTTAAACCCTAATA-TA
*
1819226 TAAA-CTCTAACCCCTAATATA
1 TAAACCT-TAAACCCTAATATA
1819247 TAAACAC-TAAACCCTAA-ACTA
1 TAAAC-CTTAAACCCTAATA-TA
*
1819268 TAAACCTTAAATCCTA
1 TAAACCTTAAACCCTA
1819284 TCACATAAAC
Statistics
Matches: 137, Mismatches: 30, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
20 14 0.10
21 112 0.82
22 10 0.07
23 1 0.01
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCTTAAACCCTAATATA
Found at i:1819117 original size:14 final size:14
Alignment explanation
Indices: 1819071--1819131 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
1819061 ATGCGTATAA
1819071 CTTAAA-CCTAAAC
1 CTTAAACCCTAAAC
1819084 CTTAAACCCTAATA-
1 CTTAAACCCTAA-AC
1819098 -TATAAACCCTAAAC
1 CT-TAAACCCTAAAC
* *
1819112 CCTAAACTCTAAAC
1 CTTAAACCCTAAAC
1819126 CTTAAA
1 CTTAAA
1819132 TCATATCACA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.20
14 31 0.77
15 1 0.03
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
CTTAAACCCTAAAC
Found at i:1819187 original size:42 final size:42
Alignment explanation
Indices: 1819141--1819272 Score: 117
Period size: 42 Copynumber: 3.1 Consensus size: 42
1819131 ATCATATCAC
1819141 AAAAACTCTAAACTCTAATATATAAACCCTAAACCATAAACT
1 AAAAACTCTAAACTCTAATATATAAACCCTAAACCATAAACT
* * * *
1819183 AAAAAC-CTTAAA-TC-ATATCACATAAACCTTAAATCTTAAACT
1 AAAAACTC-TAAACTCTA-AT-ATATAAACCCTAAACCATAAACT
** * * * *
1819225 CTAAACTCTAACCCCTAATATATAAACACTAAACCCTAAACT
1 AAAAACTCTAAACTCTAATATATAAACCCTAAACCATAAACT
*
1819267 ATAAAC
1 AAAAAC
1819273 CTTAAATCCT
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.01
41 5 0.07
42 59 0.84
43 4 0.06
44 1 0.01
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (42 bp):
AAAAACTCTAAACTCTAATATATAAACCCTAAACCATAAACT
Done.