Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_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: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 21
Found at i:2100695 original size:2 final size:2
Alignment explanation
Indices: 2100688--2100712 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2100678 TTTTAAACAT
2100688 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2100713 GAAGAACATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2103962 original size:95 final size:93
Alignment explanation
Indices: 2103825--2104042 Score: 249
Period size: 95 Copynumber: 2.3 Consensus size: 93
2103815 GAATGAAAAT
* * * * *
2103825 TTAGACCCTATCATAATAATTCAAAATGGCAGTGAATATTTTCAGTGATATATCACTTCATTTCT
1 TTAGACCCTATCATAATAATTCAAAATGACAATGAATATTTTCAGTGATATATCACCTAATTTCA
* * * * *
2103890 GAAGTTTTTAGTACTACATTTTATGATTAA
66 GAACTTGTT-G-ACCACATTTAATAATTAA
* * * *
2103920 TTAGACACTATCATAATAATTAAAAATGACACAT-ATTCTTTTCAGTGATATATCACCTAATTTC
1 TTAGACCCTATCATAATAATTCAAAATGACA-ATGAATATTTTCAGTGATATATCACCTAATTTC
*
2103984 AGAACTTGTTGACCATATTTAATAATTAA
65 AGAACTTGTTGACCACATTTAATAATTAA
* *
2104013 TCAAACCCTATCATAATAATTCAAAATGAC
1 TTAGACCCTATCATAATAATTCAAAATGAC
2104043 TTTTCAGTGA
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
93 40 0.39
94 1 0.01
95 61 0.59
96 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (93 bp):
TTAGACCCTATCATAATAATTCAAAATGACAATGAATATTTTCAGTGATATATCACCTAATTTCA
GAACTTGTTGACCACATTTAATAATTAA
Found at i:2107096 original size:37 final size:35
Alignment explanation
Indices: 2107033--2107147 Score: 116
Period size: 30 Copynumber: 3.3 Consensus size: 35
2107023 ATCCCATTAT
* * *
2107033 CATTTTTC-AACAAGCATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAA
2107068 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
*
2107104 C-----CCAAAGAAACATTTACCAAACTTTGAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
2107134 CCATTTTTTCAAAG
1 -CA-TTTTTCAAAG
2107148 TTGGTTACCA
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
30 28 0.42
31 1 0.02
35 1 0.02
36 12 0.18
37 24 0.36
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (35 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
Found at i:2107110 original size:30 final size:30
Alignment explanation
Indices: 2107076--2107135 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2107066 AACTATTTTT
2107076 CAAAGAAACATTTACCAAACTTTGAAAACC
1 CAAAGAAACATTTACCAAACTTTGAAAACC
2107106 CAAAGAAACATTTACCAAACTTTGAAAACC
1 CAAAGAAACATTTACCAAACTTTGAAAACC
2107136 ATTTTTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (30 bp):
CAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:2111729 original size:36 final size:37
Alignment explanation
Indices: 2111652--2111736 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
2111642 ATCCCATTAT
*
2111652 CATTTTTC-AACAAACATCTACCAAACTTTGAAAGAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAGAC
* *
2111688 TATTTTTCAAAGAAACATTTACCAAACTTTGAAA-AC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAGAC
2111724 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
2111737 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 10 0.23
37 33 0.77
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAGAC
Found at i:2112647 original size:17 final size:17
Alignment explanation
Indices: 2112592--2112686 Score: 109
Period size: 17 Copynumber: 5.5 Consensus size: 17
2112582 TACGATGATT
**
2112592 TTAGAATCTGGGAATGAA
1 TTAGAATCTGTCAA-GAA
**
2112610 TTAGAATCTGGGAAGGAA
1 TTAGAATCTGTCAA-GAA
2112628 TTAGAATCTGTCAAGAA
1 TTAGAATCTGTCAAGAA
*
2112645 TTAGAATCTGTCAGGAA
1 TTAGAATCTGTCAAGAA
*
2112662 TTAGAATCTGTCAGGAA
1 TTAGAATCTGTCAAGAA
*
2112679 TTGGAATC
1 TTAGAATC
2112687 CAATTTCATA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
17 43 0.60
18 29 0.40
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.28
Consensus pattern (17 bp):
TTAGAATCTGTCAAGAA
Found at i:2112666 original size:34 final size:35
Alignment explanation
Indices: 2112592--2112686 Score: 120
Period size: 34 Copynumber: 2.7 Consensus size: 35
2112582 TACGATGATT
**
2112592 TTAGAATCTGGGAATGAATTAGAATCTGGGAAGGAA
1 TTAGAATCTGTCAA-GAATTAGAATCTGGGAAGGAA
**
2112628 TTAGAATCTGTCAAGAATTAGAATCT-GTCAGGAA
1 TTAGAATCTGTCAAGAATTAGAATCTGGGAAGGAA
* *
2112662 TTAGAATCTGTCAGGAATTGGAATC
1 TTAGAATCTGTCAAGAATTAGAATC
2112687 CAATTTCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 29 0.55
35 12 0.23
36 12 0.23
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.28
Consensus pattern (35 bp):
TTAGAATCTGTCAAGAATTAGAATCTGGGAAGGAA
Found at i:2113299 original size:33 final size:33
Alignment explanation
Indices: 2113257--2113377 Score: 163
Period size: 33 Copynumber: 3.5 Consensus size: 33
2113247 CCTAAACCCG
2113257 AACCTGACCCGACCCGAATATCACACTTTAAAA
1 AACCTGACCCGACCCGAATATCACACTTTAAAA
*
2113290 AACCTGACCCGACCCGAATATCACACTTAAAAAA
1 AACCTGACCCGACCCGAATATCACACTT-TAAAA
*
2113324 ACCCGACCTGACTCGACCCGAATATCACAC-TTAAAA
1 A----ACCTGACCCGACCCGAATATCACACTTTAAAA
*
2113360 AACCCGACCCGACCCGAA
1 AACCTGACCCGACCCGAA
2113378 CAAAATAAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
32 15 0.19
33 28 0.36
34 5 0.06
36 5 0.06
37 1 0.01
38 24 0.31
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.14
Consensus pattern (33 bp):
AACCTGACCCGACCCGAATATCACACTTTAAAA
Found at i:2114687 original size:75 final size:75
Alignment explanation
Indices: 2114591--2114737 Score: 195
Period size: 75 Copynumber: 2.0 Consensus size: 75
2114581 TTTAATCGGT
* * * * * * *
2114591 TAAAATAAAATTGGCGTTACCTATTATGTTAAACTACCTACCGGTTTGTCTGAATATTACTAATA
1 TAAAACAAAATAGGCGCTACCTATTATGTTAAACTACATACCGATTTGTCTAAAGATTACTAATA
2114656 ATGTAAACAG
66 ATGTAAACAG
* * * *
2114666 TAAAACAAAATAGGCGCTACCTATTATGTTAAACTATATACTGATTTGTTTAAAGGTTACTAATA
1 TAAAACAAAATAGGCGCTACCTATTATGTTAAACTACATACCGATTTGTCTAAAGATTACTAATA
2114731 ATGTAAA
66 ATGTAAA
2114738 TGATTACGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (75 bp):
TAAAACAAAATAGGCGCTACCTATTATGTTAAACTACATACCGATTTGTCTAAAGATTACTAATA
ATGTAAACAG
Found at i:2115054 original size:152 final size:153
Alignment explanation
Indices: 2114877--2115166 Score: 476
Period size: 153 Copynumber: 1.9 Consensus size: 153
2114867 AAAGGTTAAT
* * * *
2114877 AATAATGTAAACAGTAAAATATATACAACTTAATCGTTTG-ATTTTTTTTTTTAAATTCGAAAGT
1 AATAATGTAAACAGTAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTCGAAAGT
*
2114941 ATGAATATTTA-TTCTAAAAGTATGGATACTCTAAAAGTTAATAATAATGTATCCATACTTACTC
66 ATGAATATTTACTT-TAAAAATATGGATACTCTAAAAGTTAATAATAATGTATCCATACTTACTC
2115005 TAAAAGTATGAATATTGTTTTGAC
130 TAAAAGTATGAATATTGTTTTGAC
*
2115029 AATAATGTAAACAGTAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTTGAAAGT
1 AATAATGTAAACAGTAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTCGAAAGT
* * *
2115094 ATGGATATTTACTTTAAAAATATGGATACTCTAAAGGTTAATAATAATGTATCCATACTTACTTT
66 ATGAATATTTACTTTAAAAATATGGATACTCTAAAAGTTAATAATAATGTATCCATACTTACTCT
2115159 AAAAGTAT
131 AAAAGTAT
2115167 TGATATTTGT
Statistics
Matches: 127, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
152 39 0.31
153 86 0.68
154 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (153 bp):
AATAATGTAAACAGTAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTCGAAAGT
ATGAATATTTACTTTAAAAATATGGATACTCTAAAAGTTAATAATAATGTATCCATACTTACTCT
AAAAGTATGAATATTGTTTTGAC
Found at i:2115642 original size:108 final size:106
Alignment explanation
Indices: 2115346--2115638 Score: 316
Period size: 108 Copynumber: 2.7 Consensus size: 106
2115336 TGCAATCTAC
* * ** * * *
2115346 TATGTTAATATTTATTTATAACAAAATAAGAAATTAACTTATTTTGTTGCTGTGGGATTTCGAAT
1 TATGTTAATA-ATA-TTATAACAAAATAAGTAATTAACTTATTTTGTTATTGTCGGATTTCTAAA
* *
2115411 GTCTCATCAGCTTAAACTTTAAAAACATTTTAGGTGTTACCTAA
64 GCCT-ATCAGCTTAAACTTTAAAAACATTTTAGGTGCTACCTAA
* * * *
2115455 TATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTATTATCGTCGGATTTCTAAAG
1 TATGTTAATAATATT-ATAACAAAATAAGTAATTAACTTATTTTGTTATTGTCGGATTTCTAAAG
* * * * * **
2115520 CACCATCAACTTAAACTTTGATAATATTTTAGGTGCTAGTTAA
65 C-CTATCAGCTTAAACTTTAAAAACATTTTAGGTGCTACCTAA
* * * *
2115563 TATGTTAATAATAGTTATAACAAATTAAGTAATTAACTTATTTTGTTATTATCGAATTTCTAAGG
1 TATGTTAATAATA-TTATAACAAAATAAGTAATTAACTTATTTTGTTATTGTCGGATTTCTAAAG
2115628 CCTATCAGCTT
65 CCTATCAGCTT
2115639 TAAAAAGACG
Statistics
Matches: 151, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
107 10 0.07
108 129 0.85
109 12 0.08
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (106 bp):
TATGTTAATAATATTATAACAAAATAAGTAATTAACTTATTTTGTTATTGTCGGATTTCTAAAGC
CTATCAGCTTAAACTTTAAAAACATTTTAGGTGCTACCTAA
Found at i:2116406 original size:24 final size:24
Alignment explanation
Indices: 2116379--2116430 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2116369 GAACGTTCAG
2116379 TTATATTCGTACGGTTATGTTCGT
1 TTATATTCGTACGGTTATGTTCGT
* *
2116403 TTATGTTCGTTCGGTTATGTTCGT
1 TTATATTCGTACGGTTATGTTCGT
2116427 TTAT
1 TTAT
2116431 TTTCATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.12, G:0.21, T:0.54
Consensus pattern (24 bp):
TTATATTCGTACGGTTATGTTCGT
Found at i:2116427 original size:14 final size:14
Alignment explanation
Indices: 2116372--2116427 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
2116362 CGTTTGTGAA
* *
2116372 CGTTCAGTTATATT
1 CGTTCGGTTATGTT
*
2116386 CGTACGGTTATGTT
1 CGTTCGGTTATGTT
2116400 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2116410 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2116424 CGTT
1 CGTT
2116428 TATTTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
14 24 0.71
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2116444 original size:24 final size:24
Alignment explanation
Indices: 2116392--2116447 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2116382 TATTCGTACG
* *
2116392 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
*
2116416 GTTATGTTCGTTTATTTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
2116440 TTTATGTT
1 GTTATGTT
2116448 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:2117553 original size:16 final size:16
Alignment explanation
Indices: 2117522--2117582 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
2117512 GGGTATCCAA
2117522 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* * *
2117538 CATTTATATTCATGTT
1 CGTTTATGTTCGTGTT
2117554 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
2117570 CGTTTATGTTCGT
1 CGTTTATGTTCGT
2117583 TTATTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:2121682 original size:14 final size:15
Alignment explanation
Indices: 2121663--2121692 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2121653 ATTTTTTATC
2121663 TTTT-AAAATTATTT
1 TTTTAAAAATTATTT
2121677 TTTTAAAAATTATTT
1 TTTTAAAAATTATTT
2121692 T
1 T
2121693 AAAAGGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAAAAATTATTT
Found at i:2127773 original size:23 final size:22
Alignment explanation
Indices: 2127725--2127772 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
2127715 TTGGTGCTGG
*
2127725 AAACAAGATAAGAAATGAGATTA
1 AAACAAGATAAGAAA-GAGATAA
2127748 AAACAAGATAAAGAAA-AGATAA
1 AAACAAGAT-AAGAAAGAGATAA
2127770 AAA
1 AAA
2127773 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.69, C:0.04, G:0.15, T:0.12
Consensus pattern (22 bp):
AAACAAGATAAGAAAGAGATAA
Found at i:2127774 original size:24 final size:23
Alignment explanation
Indices: 2127725--2127774 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
2127715 TTGGTGCTGG
* **
2127725 AAACAAGATAAGAAATGAGATTA
1 AAACAAGATAAGAAAAGAGAAAA
*
2127748 AAACAAGATAAAGAAAAGATAAAA
1 AAACAAGAT-AAGAAAAGAGAAAA
2127772 AAA
1 AAA
2127775 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.70, C:0.04, G:0.14, T:0.12
Consensus pattern (23 bp):
AAACAAGATAAGAAAAGAGAAAA
Found at i:2132104 original size:11 final size:11
Alignment explanation
Indices: 2132090--2132132 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2132080 GAAATTTTTG
2132090 TTTTTTTG-TT
1 TTTTTTTGTTT
**
2132100 TTTTTTTGCCT
1 TTTTTTTGTTT
2132111 TTTTTTTGTTT
1 TTTTTTTGTTT
2132122 TTTTTTTGTTT
1 TTTTTTTGTTT
2132133 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:2135436 original size:19 final size:19
Alignment explanation
Indices: 2135401--2135449 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2135391 TATGCAAGCA
*
2135401 GTATCGATACCGAAAGG-GG
1 GTATCGATA-CGAAAGGAAG
*
2135420 GTATCGATACTATAAGGAAG
1 GTATCGATACGA-AAGGAAG
2135440 GTATCGATAC
1 GTATCGATAC
2135450 CATTGATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (19 bp):
GTATCGATACGAAAGGAAG
Found at i:2135953 original size:54 final size:54
Alignment explanation
Indices: 2135871--2136099 Score: 341
Period size: 54 Copynumber: 4.2 Consensus size: 54
2135861 CCAAATAGGA
* * * **
2135871 ACTAAGTGTGCAATTCATGAAATTCATCATATGTTGATGAAAAACCGTTTTGAT
1 ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
*
2135925 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
1 ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
** *
2135979 ACTAAGTGTGCAATTCATGGAATTTGTCATATGTCGATGAACAACCGTTTCGGC
1 ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
* * *
2136033 ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAATAACTGTTTAGGC
1 ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
*
2136087 ACTAAATGTGCAA
1 ACTAAGTGTGCAA
2136100 CCCACAAAAT
Statistics
Matches: 158, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 158 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (54 bp):
ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
Found at i:2136111 original size:54 final size:54
Alignment explanation
Indices: 2135871--2136127 Score: 325
Period size: 54 Copynumber: 4.8 Consensus size: 54
2135861 CCAAATAGGA
* * * * **
2135871 ACTAAGTGTGCAATTCATGAAATTCATCATATGTTGATGAAAAACCGTTTTGAT
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
2135925 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
* ** *
2135979 ACTAAGTGTGCAATTCATGGAATTTGTCATATGTCGATGAACAACCGTTTCGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
* * * *
2136033 ACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAATAACTGTTTAGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
* ** ** * *
2136087 ACTAAATGTGCAACCCACAAAATTCATAATATGTTTATGAA
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAA
2136128 TGATCGTATA
Statistics
Matches: 179, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 179 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (54 bp):
ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGC
Found at i:2136889 original size:14 final size:14
Alignment explanation
Indices: 2136870--2136897 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2136860 TTTTTGAATT
2136870 TTTTTCAAATTTTG
1 TTTTTCAAATTTTG
2136884 TTTTTCAAATTTTG
1 TTTTTCAAATTTTG
2136898 AAAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTTCAAATTTTG
Found at i:2144273 original size:15 final size:15
Alignment explanation
Indices: 2144253--2144288 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2144243 GGGAGTCATT
**
2144253 TGAGCCGAGCCGAGC
1 TGAGCCGAGAAGAGC
2144268 TGAGCCGAGAAGAGC
1 TGAGCCGAGAAGAGC
2144283 TGAGCC
1 TGAGCC
2144289 TAACCGCCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.39, T:0.08
Consensus pattern (15 bp):
TGAGCCGAGAAGAGC
Found at i:2144330 original size:17 final size:17
Alignment explanation
Indices: 2144308--2144354 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
2144298 GGATCGAGCT
2144308 GTTGACTGTTGACAACC
1 GTTGACTGTTGACAACC
2144325 GTTGACTGTTGACAACC
1 GTTGACTGTTGACAACC
2144342 GTTGACTGTTGAC
1 GTTGACTGTTGAC
2144355 GGTTGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (17 bp):
GTTGACTGTTGACAACC
Found at i:2145844 original size:43 final size:42
Alignment explanation
Indices: 2145783--2145865 Score: 157
Period size: 43 Copynumber: 2.0 Consensus size: 42
2145773 GGTGTTACAT
2145783 GTATCATCCAAAAGTATTAATGTTGGGGCACTTTTGAAGGCCC
1 GTATCATCCAAAAGTATTAATGTTGGGGCA-TTTTGAAGGCCC
2145826 GTATCATCCAAAAGTATTAATGTTGGGGCATTTTGAAGGC
1 GTATCATCCAAAAGTATTAATGTTGGGGCATTTTGAAGGC
2145866 TCATATTAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 10 0.25
43 30 0.75
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
GTATCATCCAAAAGTATTAATGTTGGGGCATTTTGAAGGCCC
Found at i:2145891 original size:43 final size:42
Alignment explanation
Indices: 2145784--2145917 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 42
2145774 GTGTTACATG
* * *
2145784 TATCATCCAAAAGTATTAATGTTGGGGCACTTTTGAAGGCCCG
1 TATCATCCAAAAATATAAATGTTGGGGCA-TTTTGAAGGCCCA
* * *
2145827 TATCATCCAAAAGTATTAATGTTGGGGCATTTTGAAGGCTCA
1 TATCATCCAAAAATATAAATGTTGGGGCATTTTGAAGGCCCA
* * * *
2145869 TATTA-GCAAGAAATAATAAATGTTGGGACATTTTTAAGGCCCA
1 TATCATCCAA-AAAT-ATAAATGTTGGGGCATTTTGAAGGCCCA
2145912 TATCAT
1 TATCAT
2145918 ACGGGAATAC
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 3 0.04
42 18 0.23
43 57 0.73
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (42 bp):
TATCATCCAAAAATATAAATGTTGGGGCATTTTGAAGGCCCA
Found at i:2147130 original size:38 final size:38
Alignment explanation
Indices: 2147087--2147688 Score: 688
Period size: 38 Copynumber: 15.7 Consensus size: 38
2147077 CAAATTTCAA
*
2147087 TGTTATTCTTAACTTCCTCGTGAAGATG-AGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTT
* *
2147125 TGTTATTATTGACTTCCTCATGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * **
2147163 TGTTATTCTTTACTCCCTCACGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * * *
2147201 TGTTATTCTTGACTTCCTCATAAAGAAAAGTTAATATT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
2147239 TGTTATTTCTTGACTCCCTTGTGAAGAGAAGTCAATCTT
1 TGTTA-TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
*
2147278 TGTTATTCCTGA-TTCCCTCGTGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTT-CCTCGTGAAGAGAAGTCAATCTT
*
2147316 TGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
2147354 TGTTATTCTTGACTTTCTCGTTAATAGAAGTCAAGCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
2147392 TGCTATTTCTTGTA-TTCCTCGTTAAGAGAAATCAATCTT
1 TGTTA-TTCTTG-ACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
2147431 TGTTATTTCTTGATTTTCTCGTGAAGAAAAGTCAATCTT
1 TGTTA-TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
2147470 TGTTATTCCTGACTCCCTCGCGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* ** *
2147508 TGTTATTTCTTAACTTTGTCGTGAAGAGAAGTTAATCTT
1 TGTTA-TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * * *
2147547 TGTTATTCCTGACTCCCTCGCGAAGAGAATTCATTCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
2147585 TTTTATTCTTGACTTCCACATGAAGAGAAATCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * **
2147623 TGTTATTCTTGACTCCCTCGTGAGGAGGAGTCAGCCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
*
2147661 TGTTATTCTTGACTTTCTCGTGAAGAGA
1 TGTTATTCTTGACTTCCTCGTGAAGAGA
2147689 TATAACACCC
Statistics
Matches: 472, Mismatches: 84, Indels: 16
0.83 0.15 0.03
Matches are distributed among these distances:
37 2 0.00
38 341 0.72
39 128 0.27
40 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (38 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
Found at i:2147335 original size:153 final size:152
Alignment explanation
Indices: 2147087--2147688 Score: 724
Period size: 153 Copynumber: 3.9 Consensus size: 152
2147077 CAAATTTCAA
* * *
2147087 TGTTATTCTTAACTTCCTCGTGAAGATG-AGTCAATCTTTGTTATTATTGACTTCCTCATGAAGA
1 TGTTATTCTTGACTCCCTCGTGAAGA-GAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGA
*
2147151 GAAGTCAATCTTTGTTATTCTTTACTCCCTCACGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
65 GAAGTCAATCTTTGTTATTCTTGACTCCCTCACGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* * * *
2147216 CCTCATAAAGAAAAGTTAATATT
130 TCTCGTAAAGAGAAGTTAATCTT
* * *
2147239 TGTTATTTCTTGACTCCCTTGTGAAGAGAAGTCAATCTTTGTTATTCCTGA-TTCCCTCGTGAAG
1 TGTTA-TTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT-CCTCATGAAG
* *
2147303 AGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACT
64 AGAAGTCAATCTTTGTTATTCTTGACTCCCTCACGAAGAGAAGTCAATCTTTGTTATTCTTGACT
* * * *
2147368 TTCTCGTTAATAGAAGTCAAGCTT
129 TTCTCGTAAAGAGAAGTTAATCTT
* * * * * * *
2147392 TGCTATTTCTTGTA-TTCCTCGTTAAGAGAAATCAATCTTTGTTATTTCTTGATTTTCTCGTGAA
1 TGTTA-TTCTTG-ACTCCCTCGTGAAGAGAAGTCAATCTTTGTTA-TTCTTGACTTCCTCATGAA
* * * *
2147456 GAAAAGTCAATCTTTGTTATTCCTGACTCCCTCGCGAAGAGAAGTCAATCTTTGTTATTTCTTAA
63 GAGAAGTCAATCTTTGTTATTCTTGACTCCCTCACGAAGAGAAGTCAATCTTTGTTA-TTCTTGA
* *
2147521 CTTTGTCGTGAAGAGAAGTTAATCTT
127 CTTTCTCGTAAAGAGAAGTTAATCTT
* * * * * *
2147547 TGTTATTCCTGACTCCCTCGCGAAGAGAATTCATTCTTTTTTATTCTTGACTTCCACATGAAGAG
1 TGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAG
* ** * * **
2147612 AAATCAATCTTTGTTATTCTTGACTCCCTCGTGAGGAGGAGTCAGCCTTTGTTATTCTTGACTTT
66 AAGTCAATCTTTGTTATTCTTGACTCCCTCACGAAGAGAAGTCAATCTTTGTTATTCTTGACTTT
*
2147677 CTCGTGAAGAGA
131 CTCGTAAAGAGA
2147689 TATAACACCC
Statistics
Matches: 385, Mismatches: 57, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
152 29 0.08
153 227 0.59
154 96 0.25
155 33 0.09
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (152 bp):
TGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAG
AAGTCAATCTTTGTTATTCTTGACTCCCTCACGAAGAGAAGTCAATCTTTGTTATTCTTGACTTT
CTCGTAAAGAGAAGTTAATCTT
Found at i:2156286 original size:21 final size:21
Alignment explanation
Indices: 2156238--2156297 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
2156228 GAGGGATTAT
*
2156238 ATGAGGTCCTTCAGGACATAC
1 ATGAGGTCCTTCGGGACATAC
** *
2156259 ACAAGGTCCTTCGGGACATAG
1 ATGAGGTCCTTCGGGACATAC
*
2156280 ATGAGGTCTTTCGGGACA
1 ATGAGGTCCTTCGGGACA
2156298 AATTTCATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (21 bp):
ATGAGGTCCTTCGGGACATAC
Found at i:2157426 original size:3 final size:3
Alignment explanation
Indices: 2157418--2157452 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
2157408 TTTTAATTTA
2157418 TAT TAT TAT TA- TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
2157453 CTTAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2157429 original size:11 final size:11
Alignment explanation
Indices: 2157415--2157452 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
2157405 GGGTTTTAAT
2157415 TTATATTATTA
1 TTATATTATTA
2157426 TTATATTATTA
1 TTATATTATTA
2157437 TTATTATTATTTA
1 TTA-TATTA-TTA
2157450 TTA
1 TTA
2157453 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 5 0.20
13 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTATTA
Found at i:2157440 original size:17 final size:16
Alignment explanation
Indices: 2157413--2157452 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
2157403 TCGGGTTTTA
2157413 ATTTA-TATTATTATT
1 ATTTATTATTATTATT
2157428 ATATTATTATTATTATT
1 AT-TTATTATTATTATT
2157445 ATTTATTA
1 ATTTATTA
2157453 CTTAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 9 0.39
17 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATTATTATT
Found at i:2161214 original size:64 final size:65
Alignment explanation
Indices: 2161146--2161309 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 65
2161136 AAATAGACTG
* *
2161146 GTGCATCGATGCATGAATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCA-GA
1 GTGCATCGATGCATGAATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
* ** * * ** * *
2161210 GTGCATCGATGCATGGAGAGTTCATTGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTG
1 GTGCATCGATGCATGAATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTAAATCA-TG
2161275 A
65 A
*
2161276 -TGCATCGATGCATGGTATTGATGCATCGGTGCAT
1 GTGCATCGATGCAT-GAATTG-TGCATCGGTGCAT
2161310 GCCTTTGAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
64 51 0.64
65 13 0.16
66 5 0.06
67 11 0.14
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATGAATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
Found at i:2161295 original size:21 final size:21
Alignment explanation
Indices: 2161271--2161310 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2161261 CAATTTATTC
2161271 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2161292 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2161311 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2163916 original size:21 final size:21
Alignment explanation
Indices: 2163863--2163917 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2163853 CATTCAAGGC
*
2163863 ATGCATCGGTGCATCATGCAG
1 ATGCATCGATGCATCATGCAG
*
2163884 ATGCAACGATGCATCATG-AGG
1 ATGCATCGATGCATCATGCA-G
*
2163905 ATGCATCTATGCA
1 ATGCATCGATGCA
2163918 CATTCAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (21 bp):
ATGCATCGATGCATCATGCAG
Found at i:2169786 original size:18 final size:17
Alignment explanation
Indices: 2169732--2169780 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2169722 TTGGACTCCT
* *
2169732 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2169750 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2169768 AGTGCATTCGATG
1 AGTGCA-TCGATG
2169781 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2169801 original size:64 final size:60
Alignment explanation
Indices: 2169732--2169911 Score: 166
Period size: 64 Copynumber: 2.8 Consensus size: 60
2169722 TTGGACTCCT
*
2169732 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * * *
2169793 CCTGGTGCATCGATGCATGGATTGTGCATTGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATC
2169858 AG
59 AG
*
2169860 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGTAATGCATTCGATGTTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCATG-AATGCATTCGATGTTT
2169912 CAATTTATTC
Statistics
Matches: 96, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 83 0.86
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (60 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:2169882 original size:19 final size:19
Alignment explanation
Indices: 2169858--2169894 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2169848 TAATTAAATC
2169858 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2169877 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
2169895 TAATGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2169989 original size:21 final size:21
Alignment explanation
Indices: 2169922--2169982 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
2169912 CAATTTATTC
2169922 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
2169943 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2169964 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2169983 CCTTTGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2170446 original size:28 final size:26
Alignment explanation
Indices: 2170389--2170460 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 26
2170379 ATATAAAGAC
*
2170389 TCTTAATATTTA-ATTAAGTGGTTGT
1 TCTTAATATTTATTTTAAGTGGTTGT
*
2170414 T-TTAATATTTATTTTCAAGTGTTTTGT
1 TCTTAATATTTATTTT-AAGTG-GTTGT
2170441 TCTTAATATTTTATTTTAAG
1 TCTTAATA-TTTATTTTAAG
2170461 ATAAAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 10 0.25
25 3 0.08
26 5 0.12
27 5 0.12
28 9 0.22
29 8 0.20
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.58
Consensus pattern (26 bp):
TCTTAATATTTATTTTAAGTGGTTGT
Found at i:2171263 original size:55 final size:55
Alignment explanation
Indices: 2171203--2171373 Score: 281
Period size: 55 Copynumber: 3.1 Consensus size: 55
2171193 AAGATAAATT
*
2171203 GATAAAATTATTTTGTTCTT-TGGATGACTTTACTCTTAATATTTTTTACGATTTA
1 GATAAAATTATTTTATT-TTCTGGATGACTTTACTCTTAATATTTTTTACGATTTA
*
2171258 GATAAAATTATTTTATTTTCTGGATGACTTTACTCTTAATATTTTTAACGATTTA
1 GATAAAATTATTTTATTTTCTGGATGACTTTACTCTTAATATTTTTTACGATTTA
* *
2171313 GATAAAATTATTTTATTTTCTGTATGACTTTATTCTTAATATTTTTTACGATTTA
1 GATAAAATTATTTTATTTTCTGGATGACTTTACTCTTAATATTTTTTACGATTTA
*
2171368 GGTAAA
1 GATAAA
2171374 GTCATCTCGT
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 2 0.02
55 107 0.98
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (55 bp):
GATAAAATTATTTTATTTTCTGGATGACTTTACTCTTAATATTTTTTACGATTTA
Found at i:2171658 original size:18 final size:16
Alignment explanation
Indices: 2171622--2171653 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2171612 TTTTTAATAG
2171622 AAAATATATAAAAATT
1 AAAATATATAAAAATT
*
2171638 AAAATATATGAAAATT
1 AAAATATATAAAAATT
2171654 TTAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATATATAAAAATT
Found at i:2172433 original size:19 final size:19
Alignment explanation
Indices: 2172409--2172471 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
2172399 GTTTGGTTGG
2172409 GGGAATGTGAGATTCCCAT
1 GGGAATGTGAGATTCCCAT
2172428 GGGAATGTGAGATTCCCAT
1 GGGAATGTGAGATTCCCAT
*
2172447 GGGAATGTGAGATTCCGAT
1 GGGAATGTGAGATTCCCAT
2172466 GGGAAT
1 GGGAAT
2172472 AAAATCCACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.27, C:0.13, G:0.35, T:0.25
Consensus pattern (19 bp):
GGGAATGTGAGATTCCCAT
Found at i:2173423 original size:2 final size:2
Alignment explanation
Indices: 2173410--2173440 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2173400 GTGAGGCATA
*
2173410 AT AT AA 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 A
2173441 ACAATGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2173714 original size:18 final size:18
Alignment explanation
Indices: 2173691--2173763 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
2173681 ACTGAATATT
*
2173691 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
2173709 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
2173728 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
2173747 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2173764 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 2 0.04
20 15 0.32
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2173738 original size:38 final size:38
Alignment explanation
Indices: 2173690--2173766 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
2173680 CACTGAATAT
* *
2173690 TTGTCCCGAAGGATCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
* *
2173728 TTGTTCCGAAGAACCACTATGTCTCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
2173766 T
1 T
2173767 AATCCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Found at i:2179098 original size:23 final size:23
Alignment explanation
Indices: 2179070--2179117 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2179060 GGCCACTGTG
2179070 GATGATTTGTGTAGGTTTCACAT
1 GATGATTTGTGTAGGTTTCACAT
2179093 GATGATTTGTGTAGGTTTCACAT
1 GATGATTTGTGTAGGTTTCACAT
2179116 GA
1 GA
2179118 GATGCTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (23 bp):
GATGATTTGTGTAGGTTTCACAT
Found at i:2181435 original size:21 final size:21
Alignment explanation
Indices: 2181406--2181448 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 21
2181396 CAATTAAAAT
2181406 ATTTCTATAGATTT-TTATACAA
1 ATTTCTATA-ATTTATTAT-CAA
2181428 ATTT-TATAATTTATTATCAA
1 ATTTCTATAATTTATTATCAA
2181448 A
1 A
2181449 GTTCAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.40
21 8 0.40
22 4 0.20
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTCTATAATTTATTATCAA
Found at i:2188555 original size:83 final size:82
Alignment explanation
Indices: 2188291--2188648 Score: 341
Period size: 83 Copynumber: 4.3 Consensus size: 82
2188281 TAGCAACATT
* * * * *
2188291 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAAG-ATGCGTACTTTAGCGGCGTTTCTATAAAAA
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGAAT-CGTACTTTAGTGGCGTTTTTATACAAA
* * * **
2188355 CGCTGTTAAAGA-TTGTAC
64 CGCCGCTATAGACTCATAC
* * * * * * * * *
2188373 TTTAGTGGCGTTTCTGTAAAAACGCTGTTAAAGACT-GTACTTTAGTTGCGTTTTCATAAAAACG
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCGTACTTTAGTGGCGTTTTTATACAAACG
*
2188437 CCGCTAAAGACTCATAC
66 CCGCTATAGACTCATAC
* *
2188454 ATTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTGA-TTTAGTGGCGTTTGTGTTTACA
1 -TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCGT-ACTTTAGTGGCGTTT-T-TATACA
2188518 AACGCCGCTATAGACTCATAC
62 AACGCCGCTATAGACTCATAC
* ** * *
2188539 CTTAGTGG-GTTTTTATACAAACGCAACTAAAGACTTGTACTTTAGTGGCGTTTTTATACAAACG
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCGTACTTTAGTGGCGTTTTTATACAAACG
**
2188603 CCGCTATAGACTCATGT
66 CCGCTATAGACTCATAC
2188620 TTTAGTGGCGTTTGTT-TAACAAACGCCGC
1 TTTAGTGGCGTTT-TTAT-ACAAACGCCGC
2188649 AAGTTTACAA
Statistics
Matches: 225, Mismatches: 40, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
80 32 0.14
81 48 0.21
82 50 0.22
83 63 0.28
84 9 0.04
85 23 0.10
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (82 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCGTACTTTAGTGGCGTTTTTATACAAACG
CCGCTATAGACTCATAC
Found at i:2188609 original size:124 final size:124
Alignment explanation
Indices: 2188373--2188648 Score: 351
Period size: 124 Copynumber: 2.2 Consensus size: 124
2188363 AAGATTGTAC
* * * * * * * *
2188373 TTTAGTGGCGTTTCTGTAA-AAACGCTGTTAAAGACT-GTACTTTAGTTGCGTTTTCATAAAAAC
1 TTTAGTGGCGTTTGTTTAACAAACGCCGCTATAGACTCATACCTTAG-TGGGTTTTCATAAAAAC
** *
2188436 GCCGCTAAAGACTCATACATTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTGA
65 GCAACTAAAGACTCATACATTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCATGA
* * *
2188496 TTTAGTGGCGTTTGTGTTTACAAACGCCGCTATAGACTCATACCTTAGTGGGTTTTTATACAAAC
1 TTTAGTGGCGTTTGT-TTAACAAACGCCGCTATAGACTCATACCTTAGTGGGTTTTCATAAAAAC
** * *
2188561 GCAACTAAAGACTTGTAC-TTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATGT
65 GCAACTAAAGACTCATACATTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCATGA
2188620 TTTAGTGGCGTTTGTTTAACAAACGCCGC
1 TTTAGTGGCGTTTGTTTAACAAACGCCGC
2188649 AAGTTTACAA
Statistics
Matches: 131, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
123 27 0.21
124 55 0.42
125 42 0.32
126 7 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (124 bp):
TTTAGTGGCGTTTGTTTAACAAACGCCGCTATAGACTCATACCTTAGTGGGTTTTCATAAAAACG
CAACTAAAGACTCATACATTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCATGA
Found at i:2188614 original size:41 final size:41
Alignment explanation
Indices: 2188291--2188648 Score: 332
Period size: 40 Copynumber: 8.7 Consensus size: 41
2188281 TAGCAACATT
* *
2188291 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAAGA-TGCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACT-CGTAC
* * * * * *
2188333 TTTAGCGGCGTTTCTATAAAAACGCTGTTAAAGA-TTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
2188373 TTTAGTGGCGTTTCTGTAAAAACGCTGTTAAAGACT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
2188413 TTTAGTTGCGTTTTCATAAAAACGCCGCTAAAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
2188454 ATTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTGA-
1 -TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT-AC
* * *
2188496 TTTAGTGGCGTTTGTGTTTACAAACGCCGCTATAGACTCATAC
1 TTTAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTAC
* ** *
2188539 CTTAGTGG-GTTTTTATACAAACGCAACTAAAGACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * **
2188579 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATGT
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
2188620 TTTAGTGGCGTTTGTT-TAACAAACGCCGC
1 TTTAGTGGCGTTT-TTAT-ACAAACGCCGC
2188649 AAGTTTACAA
Statistics
Matches: 267, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
40 98 0.37
41 72 0.27
42 67 0.25
43 30 0.11
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:2192732 original size:43 final size:42
Alignment explanation
Indices: 2192671--2193020 Score: 405
Period size: 43 Copynumber: 8.2 Consensus size: 42
2192661 AGAAATTAGT
* * *
2192671 GGCGTTTGTATCCAAAAACGCCGCTATATATCTGATCTTTTGC
1 GGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTATTGC
2192714 GGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTATTGC
1 GGCGTTTGTTCC-AAAAACGCCGCTATAGATCTGACCTATTGC
* * * * *
2192757 GGCGTTTGTTCCAAAAATGCCTCTATAGATATCACCCTTTTGC
1 GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA-CCTATTGC
* *
2192800 GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTAC
1 GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTATTGC
* * *
2192842 AGCGTTTGTTCCAAGAAACGCTGCTATATATCTGACCTATTGC
1 GGCGTTTGTTCCAA-AAACGCCGCTATAGATCTGACCTATTGC
** * * * * * *
2192885 ACCGTTAGTTCCAAAAATGTCGCTATAGATATCAACCTTTTGC
1 GGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTATTGC
* *
2192928 GGCGTTTTTTTCC-AAAACGCCACTATAGATCTTGACCTATTGC
1 GGCG-TTTGTTCCAAAAACGCCGCTATAGATC-TGACCTATTGC
*
2192971 GGCGTTTGTTCCAAAAACGCCGCTATAGATCTTAACCTATTGC
1 GGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTATTGC
2193014 GGCGTTT
1 GGCGTTT
2193021 TTGGTTCTCA
Statistics
Matches: 260, Mismatches: 40, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
42 61 0.23
43 192 0.74
44 7 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (42 bp):
GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTATTGC
Found at i:2192911 original size:128 final size:127
Alignment explanation
Indices: 2192671--2193013 Score: 481
Period size: 128 Copynumber: 2.7 Consensus size: 127
2192661 AGAAATTAGT
* *
2192671 GGCGTTTGTATCCAAAAACGCCGCTATATATCTGATCTTTTGCGGCGTTTGTTCCAAAAAACGCC
1 GGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC-AAAAACGCC
** * * *
2192736 GCTATAGATCTGACCTATTGCGGCGTTTGTTCCAAAAATGCCTCTATAGATATCACCCTTTTGC
64 GCTATAGATCTGACCTATTGCACCGTTAGTTCCAAAAATGCCGCTATAGATATCAACCTTTTGC
* * *
2192800 GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTACAGCGTTTGTTCCAAGAAACGCTG
1 GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAA-AAACGCCG
* *
2192865 CTATATATCTGACCTATTGCACCGTTAGTTCCAAAAATGTCGCTATAGATATCAACCTTTTGC
65 CTATAGATCTGACCTATTGCACCGTTAGTTCCAAAAATGCCGCTATAGATATCAACCTTTTGC
* * *
2192928 GGCGTTTTTTTCC-AAAACGCCACTATAGATCTTGACCTATTGCGGCGTTTGTTCCAAAAACGCC
1 GGCG-TTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
*
2192992 GCTATAGATCTTAACCTATTGC
64 GCTATAGATC-TGACCTATTGC
2193014 GGCGTTTTTG
Statistics
Matches: 190, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
127 2 0.01
128 140 0.74
129 48 0.25
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (127 bp):
GGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
TATAGATCTGACCTATTGCACCGTTAGTTCCAAAAATGCCGCTATAGATATCAACCTTTTGC
Found at i:2192957 original size:171 final size:171
Alignment explanation
Indices: 2192672--2193002 Score: 445
Period size: 171 Copynumber: 1.9 Consensus size: 171
2192662 GAAATTAGTG
* * ** *
2192672 GCGTTTGTATCCAAAAACGCCGCTATATATCTGATCTTTTGCGGCGTTTGTTCCAAAAAACGCCG
1 GCGTTTGTATCCAAAAACGCCGCTATATATCTGACCTATTGCACCGTTAGTTCCAAAAAACGCCG
* * * * *
2192737 CTATAGATCTGACCTATTGCGGCGTTTGTTCCAAAAATGCCTCTATAGAT-ATCACCCTTTTGCG
66 CTATAGATATAACCTATTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCATCA-CCTATTGCG
2192801 GCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTACA
130 GCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTACA
* * *
2192843 GCGTTTGT-TCCAAGAAACGCTGCTATATATCTGACCTATTGCACCGTTAGTTCC-AAAAATGTC
1 GCGTTTGTATCCAA-AAACGCCGCTATATATCTGACCTATTGCACCGTTAGTTCCAAAAAACGCC
* * * *
2192906 GCTATAGATATCAACCTTTTGCGGCGTTTTTTTCC-AAAACGCCACTATAGATCTTGACCTATTG
65 GCTATAGATAT-AACCTATTGCGGCG-TTTGTTCCAAAAACGCCACTATAGATCATCACCTATTG
2192970 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCT
128 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCT
2193003 TAACCTATTG
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
170 22 0.16
171 108 0.78
172 9 0.06
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (171 bp):
GCGTTTGTATCCAAAAACGCCGCTATATATCTGACCTATTGCACCGTTAGTTCCAAAAAACGCCG
CTATAGATATAACCTATTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCATCACCTATTGCGG
CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTACA
Found at i:2203968 original size:16 final size:16
Alignment explanation
Indices: 2203944--2203977 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2203934 TATCGCCGAC
*
2203944 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
2203960 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
2203976 CA
1 CA
2203978 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:2206992 original size:22 final size:22
Alignment explanation
Indices: 2206959--2207023 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
2206949 GACCACTATG
* * *
2206959 TCCCGAATGACCACAGTATATG
1 TCCCGAAGGACCACTGTATATA
* *
2206981 TTCTGAAGGACCACTGTATATA
1 TCCCGAAGGACCACTGTATATA
2207003 TCCCGAAGGACCACTGTATAT
1 TCCCGAAGGACCACTGTATAT
2207024 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (22 bp):
TCCCGAAGGACCACTGTATATA
Found at i:2207929 original size:20 final size:20
Alignment explanation
Indices: 2207904--2207958 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
2207894 TGAAATTCCC
2207904 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
2207924 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
2207944 ATGCATCGATGCACC
1 ATGCATCGATGCACC
2207959 TTCAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:2217773 original size:30 final size:30
Alignment explanation
Indices: 2217719--2217939 Score: 184
Period size: 29 Copynumber: 7.5 Consensus size: 30
2217709 ATAACAACAG
* *
2217719 ATTAAAGGGCTAAAACAG-AAAAATAGAAA
1 ATTAAAGGACTAAAATAGCAAAAATAGAAA
*
2217748 ATTAAAGGACTAAAATGGCAAAAATAGAAA
1 ATTAAAGGACTAAAATAGCAAAAATAGAAA
* * **
2217778 CA-T-AGGGACTAAAATAGTAATTATAG-AA
1 -ATTAAAGGACTAAAATAGCAAAAATAGAAA
* *
2217806 ATTTAGGGACTAAAATAGCACAAAATAGAAA
1 ATTAAAGGACTAAAATAGCA-AAAATAGAAA
* * * * **
2217837 CTT-AAGGACTAAAATAGTAATAACAGTCA
1 ATTAAAGGACTAAAATAGCAAAAATAGAAA
* * * *
2217866 CTTAAAGGA-TTAATTAGTAAAAATAGAAA
1 ATTAAAGGACTAAAATAGCAAAAATAGAAA
* *
2217895 CTTAAAAGACTAAAATAGCAAAAATAGAAA
1 ATTAAAGGACTAAAATAGCAAAAATAGAAA
*
2217925 GTTAAAGGACTAAAA
1 ATTAAAGGACTAAAA
2217940 AGTAATTACA
Statistics
Matches: 154, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.01
28 3 0.02
29 79 0.51
30 66 0.43
31 5 0.03
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.20
Consensus pattern (30 bp):
ATTAAAGGACTAAAATAGCAAAAATAGAAA
Found at i:2217804 original size:59 final size:59
Alignment explanation
Indices: 2217723--2217939 Score: 215
Period size: 59 Copynumber: 3.7 Consensus size: 59
2217713 CAACAGATTA
* * * * *
2217723 AAGGGCTAAAACAG-AAAAATAGAAAATTAAAGGACTAAAATGGCAAAAATAGAAACAT
1 AAGGACTAAAATAGTAATAATAGAAAATTAAAGGACTAAAATAGCAAAAATAGAAACTT
* * * *
2217781 AGGGACTAAAATAGTAATTATAG-AAATTTAGGGACTAAAATAGCACAAAATAGAAACTT
1 AAGGACTAAAATAGTAATAATAGAAAATTAAAGGACTAAAATAGCA-AAAATAGAAACTT
* ** * * * *
2217840 AAGGACTAAAATAGTAATAACAGTCACTTAAAGGA-TTAATTAGTAAAAATAGAAACTT
1 AAGGACTAAAATAGTAATAATAGAAAATTAAAGGACTAAAATAGCAAAAATAGAAACTT
* * * *
2217898 AAAAGACTAAAATAGCAAAAATAGAAAGTTAAAGGACTAAAA
1 -AAGGACTAAAATAGTAATAATAGAAAATTAAAGGACTAAAA
2217940 AGTAATTACA
Statistics
Matches: 126, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
58 43 0.34
59 73 0.58
60 10 0.08
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (59 bp):
AAGGACTAAAATAGTAATAATAGAAAATTAAAGGACTAAAATAGCAAAAATAGAAACTT
Found at i:2219618 original size:35 final size:34
Alignment explanation
Indices: 2219579--2219689 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
2219569 AAAACATTCC
2219579 TCAATTTCATTCTAAACCCTAAATTCAAAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTCAAAA-TAAT
* *
2219614 TCAATTTCATTCCAAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATT-CAAAATAAT
* * *
2219649 TCAATTACATTCTAAAACCC-AAATTCTAAATATT
1 TCAATTTCATTCT-AAACCCTAAATTCAAAATAAT
2219683 TCAATTT
1 TCAATTT
2219690 AAGGAGGAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 13 0.20
35 43 0.65
36 10 0.15
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCTAAATTCAAAATAAT
Found at i:2220796 original size:35 final size:34
Alignment explanation
Indices: 2220747--2220859 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
2220737 AAAAAAGACA
*
2220747 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGGG-TTTAGAAT
* *
2220782 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
* * *
2220817 AAAATTGAATTACTTTAGAATTTGTGGTTTAGAAA
1 GAAATTGAATTATTTTAGAATTTG-GGTTTAGAAT
2220852 GAAATTGA
1 GAAATTGA
2220860 GGATTGTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.94
36 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:2221000 original size:31 final size:30
Alignment explanation
Indices: 2220958--2221033 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
2220948 TCATTGGTGC
* *
2220958 GGGGACCATATTGCAAACGGATTAAATGTTG
1 GGGGACTATATTGCAAA-GGATTAAAAGTTG
* **
2220989 GGGGACTATATTAC-AAGTTTTAAAAGTTG
1 GGGGACTATATTGCAAAGGATTAAAAGTTG
2221018 GGGGACCTA-ATTGCAA
1 GGGGA-CTATATTGCAA
2221034 GCTTCAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 19 0.51
30 6 0.16
31 12 0.32
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (30 bp):
GGGGACTATATTGCAAAGGATTAAAAGTTG
Found at i:2222905 original size:20 final size:20
Alignment explanation
Indices: 2222877--2222928 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2222867 CAACTTATGT
*
2222877 AGTATCGATACTACTAACAC
1 AGTACCGATACTACTAACAC
2222897 AGTACCGATACTACTAACAC
1 AGTACCGATACTACTAACAC
2222917 AGTACCGATACT
1 AGTACCGATACT
2222929 TCTATACTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (20 bp):
AGTACCGATACTACTAACAC
Found at i:2224489 original size:26 final size:26
Alignment explanation
Indices: 2224453--2224588 Score: 200
Period size: 26 Copynumber: 5.2 Consensus size: 26
2224443 GCATGACACG
* *
2224453 GTCAACGGAAGTTTCTAGAAGGTTCA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
2224479 GTCAGCGGAAGTTTCTAGAAGGTCCA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
**
2224505 GTCAGCAAAAGTTTCTAGAAGGTCCA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
*
2224531 GTCAGCGGAAGTTTCTAGAAGGTACA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
* * *
2224557 GTCAGCGGAAGTTTCTGGAAGATCTA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
2224583 GTCAGC
1 GTCAGC
2224589 ACGCCTTCTG
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 99 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (26 bp):
GTCAGCGGAAGTTTCTAGAAGGTCCA
Found at i:2225485 original size:17 final size:17
Alignment explanation
Indices: 2225463--2225495 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2225453 AAATTATCTT
*
2225463 TTATTTAATCTCTTTTA
1 TTATTTAATATCTTTTA
2225480 TTATTTAATATCTTTT
1 TTATTTAATATCTTTT
2225496 TACCAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTAATATCTTTTA
Found at i:2240927 original size:22 final size:23
Alignment explanation
Indices: 2240902--2240944 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2240892 ATATAAAACT
2240902 ATTATAAAATA-ATTAAATAATA
1 ATTATAAAATATATTAAATAATA
*
2240924 ATTATAAGATATATTAAATAA
1 ATTATAAAATATATTAAATAA
2240945 ATTTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTATAAAATATATTAAATAATA
Found at i:2242283 original size:18 final size:19
Alignment explanation
Indices: 2242257--2242293 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2242247 TATGACTAAG
2242257 GTTTAATTTGATT-TTTTT
1 GTTTAATTTGATTCTTTTT
*
2242275 GTTTGATTTGATTCTTTTT
1 GTTTAATTTGATTCTTTTT
2242294 TTAGTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.70
Consensus pattern (19 bp):
GTTTAATTTGATTCTTTTT
Found at i:2244611 original size:18 final size:17
Alignment explanation
Indices: 2244572--2244612 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2244562 TTCACACCCG
*
2244572 ACCCCCTCCCTATAAAT
1 ACCCCCACCCTATAAAT
2244589 ACCCCCACCCTATAAAT
1 ACCCCCACCCTATAAAT
2244606 ACCCCCA
1 ACCCCCA
2244613 TTCACAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCCCACCCTATAAAT
Found at i:2244732 original size:9 final size:9
Alignment explanation
Indices: 2244718--2244767 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
2244708 ATATTTTGTT
2244718 TTTAATTTA
1 TTTAATTTA
2244727 TTTAA-TTA
1 TTTAATTTA
*
2244735 TTTAAATTA
1 TTTAATTTA
2244744 TTTAA--TA
1 TTTAATTTA
*
2244751 TTTTATTTA
1 TTTAATTTA
*
2244760 ATTAATTT
1 TTTAATTT
2244768 TTTTTTGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
7 6 0.17
8 8 0.23
9 21 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTAATTTA
Found at i:2244755 original size:17 final size:16
Alignment explanation
Indices: 2244716--2244769 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
2244706 TAATATTTTG
*
2244716 TTTTTAATTTATTTAA
1 TTTTTAAATTATTTAA
2244732 TTATTTAAATTATTTAA
1 TT-TTTAAATTATTTAA
* *
2244749 TATTTT-ATTTAATTAA
1 T-TTTTAAATTATTTAA
2244765 TTTTT
1 TTTTT
2244770 TTTTGCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 4 0.12
16 11 0.33
17 17 0.52
18 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAAATTATTTAA
Found at i:2262753 original size:18 final size:18
Alignment explanation
Indices: 2262730--2262774 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2262720 AAAATTGTTT
*
2262730 TAAAATAAAAGATGAGGA
1 TAAAATAAAAGATAAGGA
2262748 TAAAATAAAAGATAAGGA
1 TAAAATAAAAGATAAGGA
2262766 TAAAATAAA
1 TAAAATAAA
2262775 TAAATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.18
Consensus pattern (18 bp):
TAAAATAAAAGATAAGGA
Found at i:2263911 original size:15 final size:15
Alignment explanation
Indices: 2263893--2263968 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
2263883 GTGAAATTCT
2263893 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
2263908 AATTATTTATATAAA
1 AATTATTTAAATAAA
**
2263923 AATTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
2263936 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
* *
2263950 AAATATTTATATAAA
1 AATTATTTAAATAAA
2263965 AATT
1 AATT
2263969 CATCGATAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 6 0.13
15 32 0.68
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:2263939 original size:21 final size:21
Alignment explanation
Indices: 2263915--2263982 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2263905 AAAAATTATT
2263915 TATATAAAAATTCATCGATAA
1 TATATAAAAATTCATCGATAA
** * *** *
2263936 TATATTTAAA-TAAAAAATATT
1 TATATAAAAATTCATCGATA-A
2263957 TATATAAAAATTCATCGATAA
1 TATATAAAAATTCATCGATAA
2263978 TATAT
1 TATAT
2263983 TATTTTATTA
Statistics
Matches: 31, Mismatches: 14, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
20 5 0.16
21 21 0.68
22 5 0.16
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAAAATTCATCGATAA
Found at i:2263943 original size:42 final size:42
Alignment explanation
Indices: 2263892--2263983 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
2263882 AGTGAAATTC
*
2263892 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAATATATTTAAATAAAAAATATTTATATAAAAATTCATCGA
2263933 TAATATATTTAAATAAAAAATATTTATATAAAAATTCATCGA
1 TAATATATTTAAATAAAAAATATTTATATAAAAATTCATCGA
2263975 TAATATATT
1 TAATATATT
2263984 ATTTTATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (42 bp):
TAATATATTTAAATAAAAAATATTTATATAAAAATTCATCGA
Found at i:2273163 original size:10 final size:10
Alignment explanation
Indices: 2273115--2273154 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
2273105 CAGACCCTAT
*
2273115 ACACTCACAG
1 ACACACACAG
*
2273125 GCACACACAG
1 ACACACACAG
2273135 ACACACACAG
1 ACACACACAG
2273145 ACACACACAG
1 ACACACACAG
2273155 CCACGCACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.45, C:0.40, G:0.12, T:0.03
Consensus pattern (10 bp):
ACACACACAG
Found at i:2277325 original size:20 final size:20
Alignment explanation
Indices: 2277302--2277365 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
2277292 ATTCCTTTTA
*
2277302 CATTTACATGTTGTAT-TTTG
1 CATTT-CATGTTGCATCTTTG
2277322 CATTCTCAT-TTGCATCTTTG
1 CATT-TCATGTTGCATCTTTG
2277342 CATTTGCATG-TGCATCTTTG
1 CATTT-CATGTTGCATCTTTG
2277362 CATT
1 CATT
2277366 AGTATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 6 0.15
20 32 0.82
21 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTTCATGTTGCATCTTTG
Found at i:2278698 original size:16 final size:17
Alignment explanation
Indices: 2278662--2278770 Score: 79
Period size: 16 Copynumber: 6.8 Consensus size: 17
2278652 AGATATAGCA
* * *
2278662 AAAAGAAAAAATAACAT
1 AAAAGAAAGAAGAAAAT
*
2278679 AAAA-AAAGGAGAAAAT
1 AAAAGAAAGAAGAAAAT
*
2278695 AAAAGAAAGAAGAAAAAG
1 AAAAGAAAGAAG-AAAAT
*
2278713 AAAAGAAAG-A-ATAA-
1 AAAAGAAAGAAGAAAAT
*
2278727 AAAAGAAAGAAAAAAAT
1 AAAAGAAAGAAGAAAAT
* *
2278744 -AAAGAAAAAAGAATA-
1 AAAAGAAAGAAGAAAAT
2278759 AAAAG-AAGAAGA
1 AAAAGAAAGAAGA
2278771 GAGAAAACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.12
15 10 0.14
16 31 0.42
17 11 0.15
18 13 0.18
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.06
Consensus pattern (17 bp):
AAAAGAAAGAAGAAAAT
Found at i:2278714 original size:23 final size:24
Alignment explanation
Indices: 2278679--2278756 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
2278669 AAAATAACAT
*
2278679 AAAA-AAAGGAGAAAATAAAAGAA
1 AAAAGAAAGAAGAAAATAAAAGAA
* * *
2278702 AGAAGAAA-AAGAAAAGAAAGAATAA
1 AAAAGAAAGAAGAAAA-TAA-AAGAA
*
2278727 AAAAGAAAGAAAAAAAT-AAAGAA
1 AAAAGAAAGAAGAAAATAAAAGAA
2278750 AAAAGAA
1 AAAAGAA
2278757 TAAAAAGAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
23 20 0.47
24 6 0.14
25 11 0.26
26 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAGAAAGAAGAAAATAAAAGAA
Found at i:2278731 original size:19 final size:18
Alignment explanation
Indices: 2278690--2278777 Score: 85
Period size: 18 Copynumber: 5.0 Consensus size: 18
2278680 AAAAAAGGAG
* *
2278690 AAAATAAAAGAAAGAAGA
1 AAAAGAAAAGAAAGAAAA
2278708 AAAAGAAAAGAAAGAATAA
1 AAAAGAAAAGAAAGAA-AA
2278727 AAAAG-AAAGAAA-AAAA
1 AAAAGAAAAGAAAGAAAA
* *
2278743 TAAAG-AAA-AAAGAATA
1 AAAAGAAAAGAAAGAAAA
*
2278759 AAAAGAAGAAGAGAGAAAA
1 AAAAGAA-AAGAAAGAAAA
2278778 CAAATCAAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
15 3 0.05
16 16 0.28
17 3 0.05
18 24 0.41
19 12 0.21
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAGAAAGAAAA
Found at i:2278760 original size:14 final size:13
Alignment explanation
Indices: 2278695--2278753 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
2278685 AGGAGAAAAT
*
2278695 AAAAGAAAG-AAG
1 AAAAAAAAGAAAG
2278707 AAAAAGAAAAGAAAG
1 -AAAA-AAAAGAAAG
2278722 AATAAAAAAGAAAG
1 AA-AAAAAAGAAAG
*
2278736 -AAAAAAATAAAG
1 AAAAAAAAGAAAG
2278748 AAAAAA
1 AAAAAA
2278754 GAATAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 10 0.25
13 10 0.25
14 15 0.38
15 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:2278763 original size:46 final size:50
Alignment explanation
Indices: 2278661--2278768 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 50
2278651 AAGATATAGC
* * *
2278661 AAAAAGAAAAAATAACATAAAAAAAGGAGAAAATAAAAGAAAGAAGAAAA
1 AAAAAGAAAAAATAACATAAAAAAAGAAAAAAATAAAAGAAAAAAGAAAA
* *
2278711 AGAAAAGAAAGAATAA-A-AAAGAAAGAAAAAAAT-AAAGAAAAAAGAATAA
1 A-AAAAGAAAAAATAACATAAAAAAAGAAAAAAATAAAAGAAAAAAGAA-AA
2278760 AAAGAAGAA
1 AAA-AAGAA
2278769 GAGAGAAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
48 14 0.28
49 21 0.42
50 2 0.04
51 13 0.26
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.06
Consensus pattern (50 bp):
AAAAAGAAAAAATAACATAAAAAAAGAAAAAAATAAAAGAAAAAAGAAAA
Found at i:2280792 original size:53 final size:54
Alignment explanation
Indices: 2280689--2280854 Score: 208
Period size: 54 Copynumber: 3.1 Consensus size: 54
2280679 CCAAAAAATG
* * * *
2280689 TGATGTCTTCAAATGAATTTTTAAAGAAACTATGCCTAGTTTTCATGGGTTTCT
1 TGATGTCTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAGGGGTTTCT
* * * * *
2280743 TGATATCTCCAAATGAATGTTT-AAGAATCTAAGCCTATTTTTTAGGGGTTTCT
1 TGATGTCTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAGGGGTTTCT
* * * *
2280796 TAATGTTTTCAGATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 TGATGTCTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAGGGGTTTCT
2280850 TGATG
1 TGATG
2280855 ATAACTAAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 42 0.45
54 52 0.55
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (54 bp):
TGATGTCTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAGGGGTTTCT
Found at i:2281801 original size:136 final size:136
Alignment explanation
Indices: 2281552--2282239 Score: 916
Period size: 136 Copynumber: 5.1 Consensus size: 136
2281542 TAAACCAATC
**
2281552 AACATTTTAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAA-AGGGAGAAGAAGTTCATA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAGAGGGAGAAGAAGTTCATA
* * * **
2281616 ATGAGAAGAACTTGTTTGACTTATTGCTCGATTCAC-AGTATTTCGAATCAGCAATGCGACACTT
65 ATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGA-TATTTCGAATCAGCAACGCCTCACTT
2281680 GAGGGATT
129 GAGGGATT
2281688 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAA
* * * * *
2281753 TGAGAAGAACTTGTTCGACCTATTGCTCAATTCACGATATTTCAAATCAGTAACACCTCGCTTGA
66 TGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGCAACGCCTCACTTGA
2281818 GGGATT
131 GGGATT
* * * * * ** * *
2281824 AATATTTCTAATGAATAGTTCATAATGAGAAAAACTCATCCGACGGAAGGAGAAAAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAA
* * * * *
2281889 TGAGAAGAACTTGTTCAACATATTGCTCGATTCACGACATTTCGAATCATCAACACCTC-CTTTG
66 TGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGCAACGCCTCAC-TTG
2281953 AGGGATT
130 AGGGATT
** *
2281960 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTTGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAA
* * * * * * *
2282025 TAAGAAGAACTTGTTTGACCTATTGCTCGATTCACGACATTTCTAATCTGTAACGCATCACTTGA
66 TGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGCAACGCCTCACTTGA
*
2282090 GGGAGT
131 GGGATT
* **
2282096 AACATTTCCAATGGAAAGTTCATAATGAGAAGAACTCATATGAAAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAA
* * *
2282161 AGAGAAGAACTTGTTCAACCTATTGCTCGATTCACG-TCATTTCGAATCAGCAACGCCTCGCTTG
66 TGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGAT-ATTTCGAATCAGCAACGCCTCACTTG
*
2282225 AGGGATC
130 AGGGATT
2282232 AACATTTC
1 AACATTTC
2282240 TAGTATAAAG
Statistics
Matches: 483, Mismatches: 64, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
135 3 0.01
136 478 0.99
137 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (136 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGATATTTCGAATCAGCAACGCCTCACTTGA
GGGATT
Found at i:2286244 original size:20 final size:20
Alignment explanation
Indices: 2286219--2286256 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2286209 GCTGCTGAAA
2286219 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACCAGTTTTG
*
2286239 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCAGTTT
2286257 GACCGGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
AACCGGTTTGACCAGTTTTG
Found at i:2286252 original size:9 final size:9
Alignment explanation
Indices: 2286220--2286279 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
2286210 CTGCTGAAAA
2286220 ACCGGTTTG
1 ACCGGTTTG
*
2286229 ACCAGTTTTG
1 ACC-GGTTTG
2286239 AACCGGTTTG
1 -ACCGGTTTG
2286249 ACCGGTTTG
1 ACCGGTTTG
*
2286258 ACCGGTCTG
1 ACCGGTTTG
*
2286267 AACCGGGTTG
1 -ACCGGTTTG
2286277 ACC
1 ACC
2286280 CGACCCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 23 0.53
10 17 0.40
11 3 0.07
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2286271 original size:19 final size:18
Alignment explanation
Indices: 2286220--2286279 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
2286210 CTGCTGAAAA
* *
2286220 ACCGGTTTGACCAGTTTTG
1 ACCGGTCTGACC-GGTTTG
*
2286239 AACCGGTTTGACCGGTTTG
1 -ACCGGTCTGACCGGTTTG
*
2286258 ACCGGTCTGAACCGGGTTG
1 ACCGGTCTG-ACCGGTTTG
2286277 ACC
1 ACC
2286280 CGACCCGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.22
19 16 0.44
20 12 0.33
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:2286275 original size:29 final size:28
Alignment explanation
Indices: 2286220--2286279 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
2286210 CTGCTGAAAA
* *
2286220 ACCGGTTTGACCAGTTTTGAACCGGTTTG
1 ACCGGTTTGACCAGGTCTGAACCGG-TTG
2286249 ACCGGTTTGACC-GGTCTGAACCGGGTTG
1 ACCGGTTTGACCAGGTCTGAACC-GGTTG
2286277 ACC
1 ACC
2286280 CGACCCGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCAGGTCTGAACCGGTTG
Found at i:2286295 original size:17 final size:17
Alignment explanation
Indices: 2286273--2286347 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
2286263 TCTGAACCGG
*
2286273 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
2286290 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
2286307 GTTGACTCGACCCGACC
1 GTTGACCCGACCCGACC
2286324 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2286341 GTTGACC
1 GTTGACC
2286348 GTGACCGTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:2287346 original size:63 final size:64
Alignment explanation
Indices: 2287229--2287353 Score: 157
Period size: 63 Copynumber: 2.0 Consensus size: 64
2287219 CTAATGTGAC
* ** *
2287229 TCTTAGGTAGGCTCTGCGGCCCCTGAGATCATTCTCGGGTAGGCCCTACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCTGAAATCATTCTCGGGTAGGCCCTACGGCCCTAAGATGTGT
* *
2287293 TCTTAGGTAGGCCCCACGGCCCC-GAAATC-TATCTTGGGTAGGCTCT-CAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCTGAAATCAT-TCTCGGGTAGGCCCTAC-GGCCCTAAGATGT
2287354 TCCTTTAGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 2 0.04
63 31 0.58
64 20 0.38
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.26
Consensus pattern (64 bp):
TCTTAGGTAGGCCCCACGGCCCCTGAAATCATTCTCGGGTAGGCCCTACGGCCCTAAGATGTGT
Found at i:2293625 original size:17 final size:17
Alignment explanation
Indices: 2293603--2293728 Score: 225
Period size: 17 Copynumber: 7.4 Consensus size: 17
2293593 TCTGAAGCGG
*
2293603 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
2293620 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
2293637 GTTGACCCGACCTGACC
1 GTTGACCCGACCCGACC
2293654 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2293671 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2293688 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2293705 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2293722 GTTGACC
1 GTTGACC
2293729 GTGACCGTTG
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 106 1.00
ACGTcount: A:0.17, C:0.44, G:0.24, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:2293735 original size:6 final size:7
Alignment explanation
Indices: 2293718--2293747 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2293708 GACCCGACCC
2293718 GACCGTT
1 GACCGTT
2293725 GACCG-T
1 GACCGTT
2293731 GACCGTT
1 GACCGTT
2293738 GACCGTT
1 GACCGTT
2293745 GAC
1 GAC
2293748 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:2293736 original size:13 final size:13
Alignment explanation
Indices: 2293718--2293743 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2293708 GACCCGACCC
2293718 GACCGTTGACCGT
1 GACCGTTGACCGT
2293731 GACCGTTGACCGT
1 GACCGTTGACCGT
2293744 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:2294691 original size:32 final size:31
Alignment explanation
Indices: 2294617--2294693 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
2294607 CTAATGTGAC
* *
2294617 TCTTAGGTAGGCTCTGCGGCACTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCACTAAGATCAT
** * **
2294648 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCACTAAGAT-CAT
2294680 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
2294694 CAAGTCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCACTAAGATCAT
Found at i:2296073 original size:60 final size:60
Alignment explanation
Indices: 2295959--2296077 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
2295949 AATAGTCATG
* * * * *
2295959 TGATTATTTTGTAACTTTTAATAGTCGAGGGTCTCAACAAAACAACATCTTATAGTCGGA
1 TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAGTCGGA
** *
2296019 TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGTATCACCCTATAGTCGG
1 TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAGTCGG
2296078 GGATTATTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (60 bp):
TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAGTCGGA
Found at i:2300205 original size:18 final size:17
Alignment explanation
Indices: 2300170--2300208 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2300160 AAAGATATTA
*
2300170 AAATAATAAAAGCGATT
1 AAATAATAAAAGCAATT
*
2300187 AAATAAATAAAAGTAATT
1 AAAT-AATAAAAGCAATT
2300205 AAAT
1 AAAT
2300209 TAAAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (17 bp):
AAATAATAAAAGCAATT
Found at i:2302380 original size:30 final size:30
Alignment explanation
Indices: 2302181--2302389 Score: 121
Period size: 30 Copynumber: 7.1 Consensus size: 30
2302171 CTAACACGGT
*
2302181 AATAGCAAAAAATAGAAAA-TTAAAGGATTAA
1 AATAGC-AAAAATA-AAAACTTAAAGGACTAA
* * *
2302212 AATGGAAAAAATAAAAA--TATAGGGACTAA
1 AATAGCAAAAATAAAAACTTA-AAGGACTAA
* ** *
2302241 AATAGTAATTATAGAAA-TT-AAGGACTAA
1 AATAGCAAAAATAAAAACTTAAAGGACTAA
* * *
2302269 AATAGAACAAAACAGAAACTT-AAGGACTAA
1 AATAGCA-AAAATAAAAACTTAAAGGACTAA
* * * *
2302299 AATA-C-TAATTCCAGACACTTAAAGGACT-A
1 AATAGCAAAAAT--AAAAACTTAAAGGACTAA
* *
2302328 AATAGTAAAAATAAAAACTTAAAAGACTAA
1 AATAGCAAAAATAAAAACTTAAAGGACTAA
* * *
2302358 AATAGCAAAAGTAGAAAGTTAAAGGACTAA
1 AATAGCAAAAATAAAAACTTAAAGGACTAA
2302388 AA
1 AA
2302390 AGTAATTACA
Statistics
Matches: 138, Mismatches: 30, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
27 2 0.01
28 16 0.12
29 55 0.40
30 58 0.42
31 7 0.05
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.20
Consensus pattern (30 bp):
AATAGCAAAAATAAAAACTTAAAGGACTAA
Found at i:2303813 original size:3 final size:3
Alignment explanation
Indices: 2303805--2303829 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2303795 TATGTAAATG
2303805 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
2303830 TAAATTAAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2306299 original size:20 final size:21
Alignment explanation
Indices: 2306271--2306362 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 21
2306261 ATTGAGTTTG
*
2306271 GGATAGATCCATTCAC-AAAA
1 GGATCGATCCATTCACAAAAA
* *
2306291 TGATCGATCCATTGAC-AAAA
1 GGATCGATCCATTCACAAAAA
* * * *
2306311 TGATTGATCCCTTCCCAAAAA
1 GGATCGATCCATTCACAAAAA
* *
2306332 GGATCGATCCCTTCCCAAAAA
1 GGATCGATCCATTCACAAAAA
2306353 GGATCGATCC
1 GGATCGATCC
2306363 CTTTGGCATG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
20 29 0.47
21 33 0.53
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (21 bp):
GGATCGATCCATTCACAAAAA
Found at i:2306340 original size:21 final size:21
Alignment explanation
Indices: 2306307--2306365 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
2306297 ATCCATTGAC
* *
2306307 AAAATGATTGATCCCTTCCCA
1 AAAAGGATCGATCCCTTCCCA
2306328 AAAAGGATCGATCCCTTCCCA
1 AAAAGGATCGATCCCTTCCCA
2306349 AAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
2306366 TGGCATGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTCCCA
Found at i:2306351 original size:41 final size:42
Alignment explanation
Indices: 2306287--2306365 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 42
2306277 ATCCATTCAC
* * * *
2306287 AAAATGATCGATCCATTGAC-AAAATGATTGATCCCTTCCCA
1 AAAAGGATCGATCCATTCACAAAAAGGATCGATCCCTTCCCA
* *
2306328 AAAAGGATCGATCCCTTCCCAAAAAGGATCGATCCCTT
1 AAAAGGATCGATCCATTCACAAAAAGGATCGATCCCTT
2306366 TGGCATGATG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 16 0.52
42 15 0.48
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (42 bp):
AAAAGGATCGATCCATTCACAAAAAGGATCGATCCCTTCCCA
Found at i:2312716 original size:18 final size:18
Alignment explanation
Indices: 2312689--2312757 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
2312679 AACGAACTAG
*
2312689 GTATCGATACTCATAGGA
1 GTATCAATACTCATAGGA
2312707 GTATCAATACT-ATAGGTA
1 GTATCAATACTCATAGG-A
*
2312725 GTATATCACTACTCCCCATAGGA
1 G--TATCAATACT---CATAGGA
2312748 GTATCAATAC
1 GTATCAATAC
2312758 CGAGGGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
17 5 0.12
18 12 0.29
20 9 0.22
21 8 0.20
23 2 0.05
24 5 0.12
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (18 bp):
GTATCAATACTCATAGGA
Found at i:2313781 original size:66 final size:66
Alignment explanation
Indices: 2313664--2313793 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
2313654 TAGGTCCATA
* * * *
2313664 AGGAATTACCAGTCGGTGCTAAACCTCTAAAAGGAATTAATAGCAGCGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCGGTACTAAACCTATAAAAGGAATTAACAGCAACGACTGAACCTGCCAGAGA
2313729 T
66 T
* * * * * *
2313730 AGGAATTACCAGTCGGTATTGAACCTATACAAGGAATTACCAGCAATGACTGAACCTTCCAGAG
1 AGGAATTACCAGTCGGTACTAAACCTATAAAAGGAATTAACAGCAACGACTGAACCTGCCAGAG
2313794 TCTTCTTACC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (66 bp):
AGGAATTACCAGTCGGTACTAAACCTATAAAAGGAATTAACAGCAACGACTGAACCTGCCAGAGA
T
Found at i:2315581 original size:14 final size:14
Alignment explanation
Indices: 2315562--2315662 Score: 82
Period size: 14 Copynumber: 7.2 Consensus size: 14
2315552 AAGTCAATGG
*
2315562 GTTGACTCAAACGA
1 GTTGACTCAGACGA
* *
2315576 GTTGACTTAGATGA
1 GTTGACTCAGACGA
*
2315590 GTTGATTCAGACGA
1 GTTGACTCAGACGA
* * *
2315604 GTTCACTTAGATGA
1 GTTGACTCAGACGA
2315618 GTTGACT-AGAACGA
1 GTTGACTCAG-ACGA
*
2315632 GTTGACGT-AGATGA
1 GTTGAC-TCAGACGA
2315646 GTTGACT-AGAACGA
1 GTTGACTCAG-ACGA
2315660 GTT
1 GTT
2315663 AACCCGGTCG
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
13 5 0.07
14 62 0.89
15 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:2315594 original size:28 final size:28
Alignment explanation
Indices: 2315562--2315662 Score: 143
Period size: 28 Copynumber: 3.6 Consensus size: 28
2315552 AAGTCAATGG
2315562 GTTGACTCA-AACGAGTTGACTTAGATGA
1 GTTGACT-AGAACGAGTTGACTTAGATGA
* *
2315590 GTTGATTCAG-ACGAGTTCACTTAGATGA
1 GTTGACT-AGAACGAGTTGACTTAGATGA
*
2315618 GTTGACTAGAACGAGTTGACGTAGATGA
1 GTTGACTAGAACGAGTTGACTTAGATGA
2315646 GTTGACTAGAACGAGTT
1 GTTGACTAGAACGAGTT
2315663 AACCCGGTCG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.03
28 64 0.97
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (28 bp):
GTTGACTAGAACGAGTTGACTTAGATGA
Found at i:2317761 original size:31 final size:31
Alignment explanation
Indices: 2317726--2317830 Score: 86
Period size: 31 Copynumber: 3.3 Consensus size: 31
2317716 CCAGTTGGTG
2317726 CTGAACCTATACAAGGAATTACCAACAATGA
1 CTGAACCTATACAAGGAATTACCAACAATGA
* * * * * *
2317757 CTGAACCTGCCAGAGATAAGAATTTCCAGTCGAT-A
1 CTGAACCT---ATACA-AGGAATTACCA-ACAATGA
*
2317792 CTGAACCTATACAAGGAATTACCAGCAATGA
1 CTGAACCTATACAAGGAATTACCAACAATGA
*
2317823 CTAAACCT
1 CTGAACCT
2317831 TCTAGAGTCT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
30 3 0.05
31 25 0.45
32 3 0.05
34 3 0.05
35 18 0.33
36 3 0.05
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (31 bp):
CTGAACCTATACAAGGAATTACCAACAATGA
Found at i:2326486 original size:22 final size:22
Alignment explanation
Indices: 2326464--2326551 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
2326454 AGAACCCCAG
*
2326464 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTACAA
* *
2326485 GGGGGAAATCGGTTCCCCTTCAAA
1 GGGGG-AATCGATTCCCCTAC-AA
* * *
2326509 TGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTACAA
*
2326531 GGGGGTATCGATTCCCTCTAC
1 GGGGGAATCGATTCCC-CTAC
2326552 CCTAAAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
21 5 0.09
22 27 0.49
23 18 0.33
24 5 0.09
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTACAA
Found at i:2326520 original size:23 final size:24
Alignment explanation
Indices: 2326486--2326530 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
2326476 TCCCCTACAG
2326486 GGGGAAATCGGTTCCCCTTCAAAT
1 GGGGAAATCGGTTCCCCTTCAAAT
2326510 GGGG-AATCGGTTCCCCTTCAA
1 GGGGAAATCGGTTCCCCTTCAA
2326531 GGGGGTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (24 bp):
GGGGAAATCGGTTCCCCTTCAAAT
Found at i:2345601 original size:32 final size:32
Alignment explanation
Indices: 2345560--2345645 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
2345550 TAAGGTAACC
*
2345560 CTTGGGTAGGCTCTGAGGCCCTGAGAATCTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAATCTTT
2345592 CTTGGGTAGGCTCTGAGGCCCCGAGAATCTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAATCTTT
* *
2345624 CTTGGATAGGCTCTCAGGCCCC
1 CTTGGGTAGGCTCTGAGGCCCC
2345646 AAGGTGCTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (32 bp):
CTTGGGTAGGCTCTGAGGCCCCGAGAATCTTT
Found at i:2347572 original size:15 final size:15
Alignment explanation
Indices: 2347549--2347633 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 15
2347539 ATTCTATTTA
2347549 CCGAGTCAACTCAGT
1 CCGAGTCAACTCAGT
* *
2347564 CCGAATCAACTCGGT
1 CCGAGTCAACTCAGT
*
2347579 CTGAGTCAACTC-GAT
1 CCGAGTCAACTCAG-T
* * * *
2347594 CTGAGTCAACCCGGC
1 CCGAGTCAACTCAGT
* *
2347609 CCAAGTCAACTCGGT
1 CCGAGTCAACTCAGT
*
2347624 CAGAGTCAAC
1 CCGAGTCAAC
2347634 CCGTATGAGT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
14 1 0.02
15 54 0.96
16 1 0.02
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (15 bp):
CCGAGTCAACTCAGT
Found at i:2347603 original size:30 final size:29
Alignment explanation
Indices: 2347551--2347657 Score: 83
Period size: 30 Copynumber: 3.7 Consensus size: 29
2347541 TCTATTTACC
* *
2347551 GAGTCAACTC-AGTCCGAATCAACTCGGTCT
1 GAGTCAACTCGA-TCTGAGTCAAC-CGGTCT
* *
2347581 GAGTCAACTCGATCTGAGTCAACCCGGCCC
1 GAGTCAACTCGATCTGAGTCAA-CCGGTCT
* * * * *
2347611 AAGTCAACTCGGTCAGAGTCAACCCGTAT
1 GAGTCAACTCGATCTGAGTCAACCGGTCT
*
2347640 GAGTTAACTCG-TCTGAGT
1 GAGTCAACTCGATCTGAGT
2347658 TGACCCGTTG
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
28 6 0.10
29 12 0.20
30 41 0.67
31 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (29 bp):
GAGTCAACTCGATCTGAGTCAACCGGTCT
Found at i:2350137 original size:31 final size:31
Alignment explanation
Indices: 2350071--2350139 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
2350061 GTTGATGTTG
* ** * *
2350071 GTAATTCCTTTTATAGGTTCAGTTATTGTTG
1 GTAATTCCTTTTATAGGTTCAGTAACCGCTA
2350102 GTAATTCCTTTTATAGGTTCAG-AACCGACTA
1 GTAATTCCTTTTATAGGTTCAGTAACCG-CTA
2350133 GTAATTC
1 GTAATTC
2350140 TTTATGAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (31 bp):
GTAATTCCTTTTATAGGTTCAGTAACCGCTA
Found at i:2351825 original size:38 final size:38
Alignment explanation
Indices: 2351782--2351858 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2351772 CGCAAAAGAT
2351782 AACTTGTAAACTTTATTGAATTTAAGTTTTTGCACTGA
1 AACTTGTAAACTTTATTGAATTTAAGTTTTTGCACTGA
2351820 AACTTGTAAACTTTATTGAATTTAAGTTTTTGCACTGA
1 AACTTGTAAACTTTATTGAATTTAAGTTTTTGCACTGA
2351858 A
1 A
2351859 TTTTATTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (38 bp):
AACTTGTAAACTTTATTGAATTTAAGTTTTTGCACTGA
Found at i:2351858 original size:19 final size:19
Alignment explanation
Indices: 2351798--2351861 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
2351788 TAAACTTTAT
2351798 TGAATTTAAGTTTTTGCAC
1 TGAATTTAAGTTTTTGCAC
** *
2351817 TGAAACTTGTAA-ACTTT--AT
1 TG-AA-TT-TAAGTTTTTGCAC
2351836 TGAATTTAAGTTTTTGCAC
1 TGAATTTAAGTTTTTGCAC
2351855 TGAATTT
1 TGAATTT
2351862 TATTGTTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
18 2 0.06
19 13 0.39
20 2 0.06
21 5 0.15
22 3 0.09
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (19 bp):
TGAATTTAAGTTTTTGCAC
Found at i:2358315 original size:25 final size:25
Alignment explanation
Indices: 2358256--2358321 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
2358246 TTTATTTTTT
*
2358256 AAAAAATAAAATCTATTTTAAAATTT
1 AAAAAATAAAAT-TATTTTAAAATTC
* *
2358282 TAAATATAAAATTA-TTTAAATATTC
1 AAAAAATAAAATTATTTTAAA-ATTC
2358307 AAAAAATAAATATTA
1 AAAAAATAAA-ATTA
2358322 ACAATATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 6 0.18
25 13 0.39
26 14 0.42
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAAAATAAAATTATTTTAAAATTC
Found at i:2360521 original size:16 final size:16
Alignment explanation
Indices: 2360500--2360547 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
2360490 TGTTTTTCGA
2360500 AAATATAATAATTTGG
1 AAATATAATAATTTGG
2360516 AAATATAATAATTTTGG
1 AAATATAATAA-TTTGG
*
2360533 AAATATATTAATTTG
1 AAATATAATAATTTG
2360548 AGTTTAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
AAATATAATAATTTGG
Found at i:2360531 original size:17 final size:17
Alignment explanation
Indices: 2360500--2360546 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
2360490 TGTTTTTCGA
2360500 AAATATAATAA-TTTGG
1 AAATATAATAATTTTGG
2360516 AAATATAATAATTTTGG
1 AAATATAATAATTTTGG
*
2360533 AAATATATTAATTT
1 AAATATAATAATTT
2360547 GAGTTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 11 0.38
17 18 0.62
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
AAATATAATAATTTTGG
Found at i:2372957 original size:19 final size:19
Alignment explanation
Indices: 2372933--2372971 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2372923 ATTAGAAATT
2372933 AAAAATAAAAGAAAAAGAA
1 AAAAATAAAAGAAAAAGAA
*
2372952 AAAAATAAAAGAAAATGAA
1 AAAAATAAAAGAAAAAGAA
2372971 A
1 A
2372972 TTTTTAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (19 bp):
AAAAATAAAAGAAAAAGAA
Found at i:2373146 original size:13 final size:14
Alignment explanation
Indices: 2373130--2373168 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2373120 ATTGTAGATG
2373130 AGTA-ATCAAGAAC
1 AGTAGATCAAGAAC
*
2373143 AGTAGATCGAGAAC
1 AGTAGATCAAGAAC
*
2373157 AGTAGATGAAGA
1 AGTAGATCAAGA
2373169 GTCAAGAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.49, C:0.10, G:0.26, T:0.15
Consensus pattern (14 bp):
AGTAGATCAAGAAC
Found at i:2373211 original size:35 final size:35
Alignment explanation
Indices: 2373123--2373211 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
2373113 AATGAGAATT
* *
2373123 GTAGATGAGTAATCAAGAACAGTAGATCGAGAACA
1 GTAGATGAGAAATCAAGAACAATAGATCGAGAACA
* **
2373158 GTAGATGA-AGAGTCAAGAACAATAGATCGCTAACA
1 GTAGATGAGA-AATCAAGAACAATAGATCGAGAACA
*
2373193 GTAGATGAGAAATAAAGAA
1 GTAGATGAGAAATCAAGAA
2373212 TAGTAAATGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
35 44 0.98
36 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (35 bp):
GTAGATGAGAAATCAAGAACAATAGATCGAGAACA
Done.