Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 20
Found at i:2631714 original size:5 final size:6
Alignment explanation
Indices: 2631674--2631713 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
2631664 AATATTTAAC
2631674 TTAATT TATAAATAT TTAATT TTAATT TTAATT TTAATT T
1 TTAATT T-T-AAT-T TTAATT TTAATT TTAATT TTAATT T
2631714 AAAAATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 21 0.68
7 4 0.13
8 4 0.13
9 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTAATT
Found at i:2632384 original size:3 final size:3
Alignment explanation
Indices: 2632378--2632430 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
2632368 ATTGCTAATA
* * * * *
2632378 ATT ATT ATC ATT A-T ATT ATT GTT ATT ATT ACT ATT ATT ACT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2632425 ATT ATT
1 ATT ATT
2632431 TTTTCATCTA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2634000 original size:2 final size:2
Alignment explanation
Indices: 2633986--2634023 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2633976 CTATTTGTTG
*
2633986 TA TA TA TC T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2634024 TTATTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2636114 original size:21 final size:20
Alignment explanation
Indices: 2636076--2636115 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2636066 GATCAACATT
*
2636076 TTTGCATCTGCACTTGCATC
1 TTTGCATCTGCACCTGCATC
*
2636096 TTTGCATTTTGCACCTGCAT
1 TTTGCA-TCTGCACCTGCAT
2636116 TCCATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTGCATCTGCACCTGCATC
Found at i:2637929 original size:4 final size:4
Alignment explanation
Indices: 2637928--2638258 Score: 365
Period size: 4 Copynumber: 82.8 Consensus size: 4
2637918 AATATGTATG
* * * *
2637928 TATA TATA TATA TATA TATA TGTG TATG TATA TATA TACA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
2637976 TATA TATA CATA TATA TACA TATA TGTA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
** * *
2638024 TATA TATA TATA TATA TATA TGCA TATA TATA TACA TATA TACA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * *
2638072 TATA CACA TGTA TATG TATA TATA TGTC TATA TATA TACA TATA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * **
2638120 TATA TATA TGTA TATA TATA TATG TATA TATA TATA TGCA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
2638168 TACA TATA TATC TATA TATA TACA TACA TATA TATA TACA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
2638216 TACA TATA TATA TATA TATA TGTA TATA TGTA GACA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
2638259 TTATCAAACC
Statistics
Matches: 265, Mismatches: 62, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 265 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:2637941 original size:10 final size:10
Alignment explanation
Indices: 2637928--2638258 Score: 365
Period size: 10 Copynumber: 33.1 Consensus size: 10
2637918 AATATGTATG
2637928 TATATATATA
1 TATATATATA
2637938 TATATATATA
1 TATATATATA
* * *
2637948 TGTGTATGTA
1 TATATATATA
*
2637958 TATATATACA
1 TATATATATA
2637968 TATATATATA
1 TATATATATA
*
2637978 TATATACATA
1 TATATATATA
*
2637988 TATATACATA
1 TATATATATA
*
2637998 TATGTATATA
1 TATATATATA
2638008 TATATATATA
1 TATATATATA
2638018 TATATATATA
1 TATATATATA
2638028 TATATATATA
1 TATATATATA
**
2638038 TATATATGCA
1 TATATATATA
2638048 TATATATATA
1 TATATATATA
* *
2638058 CATATATACA
1 TATATATATA
*
2638068 TATATATACA
1 TATATATATA
* * *
2638078 CATGTATATG
1 TATATATATA
*
2638088 TATATATATG
1 TATATATATA
*
2638098 TCTATATATA
1 TATATATATA
* *
2638108 TACATATATG
1 TATATATATA
2638118 TATATATATA
1 TATATATATA
*
2638128 TGTATATATA
1 TATATATATA
*
2638138 TATATGTATA
1 TATATATATA
*
2638148 TATATATATG
1 TATATATATA
*
2638158 CATATATATA
1 TATATATATA
*
2638168 TACATATATA
1 TATATATATA
*
2638178 TCTATATATA
1 TATATATATA
* *
2638188 TACATACATA
1 TATATATATA
*
2638198 TATATATACA
1 TATATATATA
2638208 TATATATATA
1 TATATATATA
*
2638218 CATATATATA
1 TATATATATA
*
2638228 TATATATATG
1 TATATATATA
*
2638238 TATATATGTA
1 TATATATATA
* *
2638248 GACATATATA
1 TATATATATA
2638258 T
1 T
2638259 TTATCAAACC
Statistics
Matches: 262, Mismatches: 59, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 262 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:2637959 original size:18 final size:18
Alignment explanation
Indices: 2637928--2638258 Score: 365
Period size: 18 Copynumber: 18.4 Consensus size: 18
2637918 AATATGTATG
2637928 TATATATATATATATATA
1 TATATATATATATATATA
* * *
2637946 TATGTGTATGTATATATA
1 TATATATATATATATATA
*
2637964 TACATATATATATATATA
1 TATATATATATATATATA
* *
2637982 TACATATATATACATATA
1 TATATATATATATATATA
*
2638000 TGTATATATATATATATA
1 TATATATATATATATATA
2638018 TATATATATATATATATA
1 TATATATATATATATATA
**
2638036 TATATATATGCATATATA
1 TATATATATATATATATA
* *
2638054 TATACATATATACATATA
1 TATATATATATATATATA
* * * *
2638072 TATACACATGTATATGTA
1 TATATATATATATATATA
* *
2638090 TATATATGTCTATATATA
1 TATATATATATATATATA
* *
2638108 TACATATATGTATATATA
1 TATATATATATATATATA
* *
2638126 TATGTATATATATATATG
1 TATATATATATATATATA
**
2638144 TATATATATATATGCATA
1 TATATATATATATATATA
* *
2638162 TATATATACATATATATC
1 TATATATATATATATATA
* *
2638180 TATATATATACATACATA
1 TATATATATATATATATA
*
2638198 TATATATACATATATATA
1 TATATATATATATATATA
*
2638216 TACATATATATATATATA
1 TATATATATATATATATA
* * * *
2638234 TATGTATATATGTAGACA
1 TATATATATATATATATA
2638252 TATATAT
1 TATATAT
2638259 TTATCAAACC
Statistics
Matches: 256, Mismatches: 57, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 256 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATATATATATATATA
Found at i:2639017 original size:58 final size:58
Alignment explanation
Indices: 2638942--2639055 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 58
2638932 AAAATATCAC
* *
2638942 CCTAACATAAATTAATTACGTATTAGGCAGCCTTTTAAAAATATTTACAAAACTAGAA
1 CCTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAACTAGAA
2639000 CCTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAACTAG
1 CCTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAACTAG
2639056 CACTCGGGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.31
Consensus pattern (58 bp):
CCTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAACTAGAA
Found at i:2644689 original size:2 final size:2
Alignment explanation
Indices: 2644610--2644675 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
2644600 TTCAAGTGAA
*
2644610 AT AT GT 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
2644652 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
2644676 GTAAACGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2645458 original size:58 final size:58
Alignment explanation
Indices: 2645358--2645490 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 58
2645348 ACAGTCAACT
* * * *
2645358 TTTACAAAAATAGCACCCTAACAGATATTAATTATGGATTAGGCAGCCTTTTAAAAATA
1 TTTACAAAAATAGCA-CCTAACAAAAATTAATTACGGATTAGGCACCCTTTTAAAAATA
*
2645417 TTTACAAAAATAGCACCTAATAAAAATTAATTACGTG-TTAGGCACCCTTTTAAAAATA
1 TTTACAAAAATAGCACCTAACAAAAATTAATTACG-GATTAGGCACCCTTTTAAAAATA
*
2645475 TTTACAAAACTAGCAC
1 TTTACAAAAATAGCAC
2645491 TCGGGTCGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
58 51 0.76
59 16 0.24
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (58 bp):
TTTACAAAAATAGCACCTAACAAAAATTAATTACGGATTAGGCACCCTTTTAAAAATA
Found at i:2645490 original size:29 final size:29
Alignment explanation
Indices: 2645404--2645490 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
2645394 GATTAGGCAG
2645404 CCTTTTAAAAATATTTACAAAAATAGCA-
1 CCTTTTAAAAATATTTACAAAAATAGCAC
** * ****
2645432 CCTAATAAAAATTAATTAC-GTGTTAGGCAC
1 CCTTTTAAAAA-TATTTACAAAAATA-GCAC
*
2645462 CCTTTTAAAAATATTTACAAAACTAGCAC
1 CCTTTTAAAAATATTTACAAAAATAGCAC
2645491 TCGGGTCGGG
Statistics
Matches: 41, Mismatches: 14, Indels: 7
0.66 0.23 0.11
Matches are distributed among these distances:
28 11 0.27
29 19 0.46
30 11 0.27
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (29 bp):
CCTTTTAAAAATATTTACAAAAATAGCAC
Found at i:2645532 original size:17 final size:18
Alignment explanation
Indices: 2645494--2645538 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2645484 CTAGCACTCG
*
2645494 GGTCGGGTC-GGTTAACA
1 GGTCGGGTCGGGTCAACA
*
2645511 AGTCGGGTCGGGTCAAC-
1 GGTCGGGTCGGGTCAACA
2645528 GGTCGGGTCGG
1 GGTCGGGTCGG
2645539 ACCGGTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAACA
Found at i:2649158 original size:36 final size:37
Alignment explanation
Indices: 2649116--2649192 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
2649106 TTTTCCTTAA
2649116 AAAC-AAATTTTGTCTCGCTTGAGACAGTTTATCTTG
1 AAACAAAATTTTGTCTCGCTTGAGACAGTTTATCTTG
* *
2649152 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAAATTTTGTCTCGCTTGAGACAGTTTATCTTG
2649189 AAAC
1 AAAC
2649193 GGAAACCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.11
37 34 0.89
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (37 bp):
AAACAAAATTTTGTCTCGCTTGAGACAGTTTATCTTG
Found at i:2649720 original size:140 final size:139
Alignment explanation
Indices: 2649260--2649819 Score: 667
Period size: 140 Copynumber: 4.0 Consensus size: 139
2649250 TATTGAAACA
* * *
2649260 AATTATCCCTAAATATGGCCAGA-AGTCCTCATCACGTAGGAATAGTGTCATCCACCGACCAGAT
1 AATTATCCCTAAAGATGGCTAGACA-TCCTCATCACGTAGGAACAGTGTCATCCACCGACCAGAT
* * * * * * * * *
2649324 CTCCTTATCAAGTAGGAGCATCGTCAACCTTGGATAACCATACTTTCTCATCACATAGGAAACTT
65 CTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGT
* *
2649389 GTTATCT-CT
130 GTTGTCTCCC
* * * *
2649398 AATTATCCCTAAAGATGGCTAGACTTCCTCATCACGTAAGAAGAATGTCATCCACCGACCAGATC
1 AATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAGATC
* * **
2649463 TCCTCATCACGTAAGAGCAGCGTCAACCTTAGATAATC-GACTTCCTCATCACGTAGGAACTATG
66 TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGTG
2649527 TTGTCTCCC
131 TTGTCTCCC
* * * * * *
2649536 AAATTATCCCTAAAGATGGCCAGACGTCCTCATCACGTATGAACAGTTTCATCCATCGACCAAAT
1 -AATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAGAT
* * *
2649601 CTCCTCATCACGTAGGAGTAGCGTCAACATTAGATAACCAGACTTCCTCATCACGTATGAACCGT
65 CTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGT
2649666 GTTGTCTCCC
130 GTTGTCTCCC
* * * * * * *
2649676 ACATTATCACTAAAGATGACTATACATCCTCATCATGTAGGAACATTATCATCCACCGACCAGAG
1 A-ATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAGAT
* * * * **
2649741 CTCATCATCACGTAGGAGCAGCGTCACCCTTAGATAACCAGATTTCTTCATCGTGTAGGAACCGT
65 CTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGT
*
2649806 GTTGTCTCCA
130 GTTGTCTCCC
2649816 AATT
1 AATT
2649820 TACTTTAAAA
Statistics
Matches: 360, Mismatches: 57, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
137 25 0.07
138 91 0.25
139 95 0.26
140 149 0.41
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (139 bp):
AATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAGATC
TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAACCGTG
TTGTCTCCC
Found at i:2650092 original size:3 final size:3
Alignment explanation
Indices: 2650086--2650135 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
2650076 ATTGCTAATA
* * * *
2650086 ATT ATT ATC ATT A-T ATT ATT GTT ATT ATT ACT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2650133 ATT
1 ATT
2650136 TTTTCATCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2656168 original size:41 final size:42
Alignment explanation
Indices: 2656038--2656168 Score: 183
Period size: 42 Copynumber: 3.1 Consensus size: 42
2656028 AAACATCAAG
*
2656038 AAAGTACGAGTATTTAGCGGCATTTTTGCTTAAAACGCCACT
1 AAAGTACGAGTATTTAGCGGCATTTGTGCTTAAAACGCCACT
* * * *
2656080 AAAGTACTAGTTTTTAGTGGCATTTGTGCTTAAAACACCACT
1 AAAGTACGAGTATTTAGCGGCATTTGTGCTTAAAACGCCACT
* * *
2656122 AAAGTACGAGTATTTAGCGGTATTTGTAC-AAAAACGCCACT
1 AAAGTACGAGTATTTAGCGGCATTTGTGCTTAAAACGCCACT
2656163 AAAGTA
1 AAAGTA
2656169 GCGTGATACT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 16 0.21
42 61 0.79
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (42 bp):
AAAGTACGAGTATTTAGCGGCATTTGTGCTTAAAACGCCACT
Found at i:2675384 original size:2 final size:2
Alignment explanation
Indices: 2675377--2675406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2675367 AAGCTGTCAA
2675377 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
2675407 CCCATTTACA
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:2677225 original size:156 final size:156
Alignment explanation
Indices: 2676937--2677283 Score: 565
Period size: 156 Copynumber: 2.2 Consensus size: 156
2676927 CTCGATCTTG
* * *
2676937 ATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGATGGCCCGGAGGACTTATCATCTTACTCGAAA
1 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGGCCCGGAAGACTTATCATCTTACTCGAAA
* * *
2677002 GGATGACAGATGACTCGAAGGATTTAATTATCATGCTCGGAAGGCTTACTGATGGCTTGCTTTAC
66 GGATGACAGATGACTCGAAGGATTTAATCATCATGCTCAGAAGGCTTACTGATGGCTTGCTTCAC
2677067 TACTCTTCCA-TGAAGGCTTAAGATTA
131 TACTCTT-CAGTGAAGGCTTAAGATTA
*
2677093 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGGCCCGGAATACTTATCATCTTACTC-AGA
1 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGGCCCGGAAGACTTATCATCTTACTCGA-A
*
2677157 AGGCTGACAGATGAC-CTGAAGGATTTAATCATCATGCTCAGAAGGCTTACTGATGGCTTGCTTC
65 AGGATGACAGATGACTC-GAAGGATTTAATCATCATGCTCAGAAGGCTTACTGATGGCTTGCTTC
2677221 ACTACTCTTCAGTGAAGGCTTAAGATTA
129 ACTACTCTTCAGTGAAGGCTTAAGATTA
*
2677249 ATTTGCTTCACTACTCTTCCATAAAGGCTTAAGAT
1 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGAT
2677284 TGACTTGCCC
Statistics
Matches: 179, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
155 4 0.02
156 175 0.98
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (156 bp):
ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGATGGCCCGGAAGACTTATCATCTTACTCGAAA
GGATGACAGATGACTCGAAGGATTTAATCATCATGCTCAGAAGGCTTACTGATGGCTTGCTTCAC
TACTCTTCAGTGAAGGCTTAAGATTA
Found at i:2677255 original size:37 final size:37
Alignment explanation
Indices: 2677214--2677284 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
2677204 TACTGATGGC
*
2677214 TTGCTTCACTACTCTT-CAGTGAAGGCTTAAGATTAAT
1 TTGCTTCACTACTCTTCCA-TAAAGGCTTAAGATTAAT
2677251 TTGCTTCACTACTCTTCCATAAAGGCTTAAGATT
1 TTGCTTCACTACTCTTCCATAAAGGCTTAAGATT
2677285 GACTTGCCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCATAAAGGCTTAAGATTAAT
Found at i:2678208 original size:21 final size:20
Alignment explanation
Indices: 2678182--2678281 Score: 112
Period size: 21 Copynumber: 4.8 Consensus size: 20
2678172 AGGGTGTCAA
2678182 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCC-TGC
2678203 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
2678224 AGTGCATCCATGCA-CCTGCCAC
1 AGTGCATCCATGCACCCTG---C
* * *
2678246 TAGTGCATCGATGCACCATGT
1 -AGTGCATCCATGCACCCTGC
2678267 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2678282 TCCATTTTGA
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 31 0.45
22 4 0.06
23 13 0.19
24 3 0.04
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:2678326 original size:20 final size:20
Alignment explanation
Indices: 2678301--2678344 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2678291 AATGTAATTA
2678301 GTGCATCGATACATCCTACT
1 GTGCATCGATACATCCTACT
* *
2678321 GTGCATCGATGCATCCTGCT
1 GTGCATCGATACATCCTACT
2678341 GTGC
1 GTGC
2678345 GTCCATGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATACATCCTACT
Found at i:2678352 original size:20 final size:20
Alignment explanation
Indices: 2678301--2678353 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2678291 AATGTAATTA
* *
2678301 GTGCATCGATACATCCTACT
1 GTGCATCCATGCATCCTACT
* *
2678321 GTGCATCGATGCATCCTGCT
1 GTGCATCCATGCATCCTACT
*
2678341 GTGCGTCCATGCA
1 GTGCATCCATGCA
2678354 CCAAGGCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGCATCCATGCATCCTACT
Found at i:2681717 original size:23 final size:23
Alignment explanation
Indices: 2681687--2681767 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
2681677 GCACCCCTGC
2681687 AGTGCATCCATGCACTTGCCACT
1 AGTGCATCCATGCACTTGCCACT
* *
2681710 AGTGCATCGATGCA----CCATGT
1 AGTGCATCCATGCACTTGCCA-CT
2681730 AGTGCATCCATGCACTTGCCACT
1 AGTGCATCCATGCACTTGCCACT
*
2681753 AGTGCATCGATGCAC
1 AGTGCATCCATGCAC
2681768 CATGTAGTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.06
20 14 0.29
23 28 0.58
24 3 0.06
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (23 bp):
AGTGCATCCATGCACTTGCCACT
Found at i:2681734 original size:20 final size:20
Alignment explanation
Indices: 2681666--2681787 Score: 95
Period size: 20 Copynumber: 5.8 Consensus size: 20
2681656 AGGGTGTCAA
* *
2681666 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGT
*
2681687 AGTGCATCCATGCACTTGCCA-CT
1 AGTGCATCCATGCA----CCATGT
*
2681710 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
*
2681730 AGTGCATCCATGCACTTGCCA-CT
1 AGTGCATCCATGCA----CCATGT
*
2681753 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
2681773 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2681788 TCCATTTCGA
Statistics
Matches: 81, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
19 6 0.07
20 29 0.36
21 14 0.17
23 27 0.33
24 5 0.06
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:2681744 original size:43 final size:43
Alignment explanation
Indices: 2681666--2681788 Score: 210
Period size: 43 Copynumber: 2.8 Consensus size: 43
2681656 AGGGTGTCAA
* * *
2681666 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTTGCCACT
1 AGTGCATCGATGCA-CCATGTAGTGCATCCATGCACTTGCCACT
2681710 AGTGCATCGATGCACCATGTAGTGCATCCATGCACTTGCCACT
1 AGTGCATCGATGCACCATGTAGTGCATCCATGCACTTGCCACT
2681753 AGTGCATCGATGCACCATGTAGTGCATCCATGCACT
1 AGTGCATCGATGCACCATGTAGTGCATCCATGCACT
2681789 CCATTTCGAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 63 0.83
44 13 0.17
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (43 bp):
AGTGCATCGATGCACCATGTAGTGCATCCATGCACTTGCCACT
Found at i:2681832 original size:20 final size:20
Alignment explanation
Indices: 2681807--2681859 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2681797 AATGCAACTA
2681807 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
*
2681827 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGAT
*
2681847 GTGCATCCATGCA
1 GTGCATCGATGCA
2681860 CCAAGGCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:2684959 original size:37 final size:37
Alignment explanation
Indices: 2684908--2685056 Score: 253
Period size: 37 Copynumber: 4.0 Consensus size: 37
2684898 AGACTCGATC
*
2684908 TTGATTTGTTTCACTACTCTTTCGTGAAGGCTTAAGA
1 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
** *
2684945 TTGATTTGCCTCACTACTCTTCCGTGAAGGCTTAATA
1 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
*
2684982 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAATA
1 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
2685019 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
1 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
2685056 T
1 T
2685057 GGCCCGGAGG
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (37 bp):
TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:2685285 original size:119 final size:119
Alignment explanation
Indices: 2685028--2685285 Score: 381
Period size: 119 Copynumber: 2.2 Consensus size: 119
2685018 ATTGATTTGT
* * * *
2685028 TTCACTACTCTTCCGTGAAGGCTTAAGATGGCCCGGAGGACTTATCATCTTACTCATAAGGTTGA
1 TTCACTACTCTTCCGTGAAGGATTAAAATGGCCCGGAGGACTTATCATATTACTCAGAAGGTTGA
* * *
2685093 GAGATGACCCGAAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCTTGG
66 CAAATGACCCGAAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCTTGC
* * * *
2685147 TTCACTACTCTTCCATGAAGGATTAAAATGGCCCGGAGGACTTTTCATATTGCTCGGAAGGTTGA
1 TTCACTACTCTTCCGTGAAGGATTAAAATGGCCCGGAGGACTTATCATATTACTCAGAAGGTTGA
* * *
2685212 CAAATGACCTGAAGGATTTAATCATCATTCTCGGAAGGCTTATTGATGGCTTGC
66 CAAATGACCCGAAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCTTGC
*
2685266 TTCACTACTCTTCTGTGAAG
1 TTCACTACTCTTCCGTGAAG
2685286 ACTTAAGATT
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 123 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (119 bp):
TTCACTACTCTTCCGTGAAGGATTAAAATGGCCCGGAGGACTTATCATATTACTCAGAAGGTTGA
CAAATGACCCGAAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCTTGC
Found at i:2687229 original size:99 final size:99
Alignment explanation
Indices: 2687058--2687246 Score: 288
Period size: 99 Copynumber: 1.9 Consensus size: 99
2687048 TGTAATTTGT
* *
2687058 CTTTATCAGACTAGCTAAATCTTATGCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAAGGGAC
1 CTTTATCAGACTAGCTAAATCTTATCCATAAAGCCAGGGAGTTTAACCAATTGCTCTAAAGGGAC
* *
2687123 AGTTCAAGCTTTATTGTATATATATTACAATCAC
66 AGCTCAAGCTTTATTGTATACATATTACAATCAC
* * * * * *
2687157 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGGGGAGTTTAACCAATTGCTCTAGAGGGAT
1 CTTTATCAGACTAGCTAAATCTTATCCATAAAGCCAGGGAGTTTAACCAATTGCTCTAAAGGGAC
2687222 AGCTCAAGCTTTATTGTATACATAT
66 AGCTCAAGCTTTATTGTATACATAT
2687247 AATATTATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (99 bp):
CTTTATCAGACTAGCTAAATCTTATCCATAAAGCCAGGGAGTTTAACCAATTGCTCTAAAGGGAC
AGCTCAAGCTTTATTGTATACATATTACAATCAC
Found at i:2693299 original size:13 final size:13
Alignment explanation
Indices: 2693281--2693327 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
2693271 TGAGTCAGAA
2693281 ATTTATGACGCGC
1 ATTTATGACGCGC
* *
2693294 ATTTATGACACAC
1 ATTTATGACGCGC
2693307 ATTTATGACGCGC
1 ATTTATGACGCGC
2693320 ATTTATGA
1 ATTTATGA
2693328 TGTTCATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:2696211 original size:20 final size:20
Alignment explanation
Indices: 2696182--2696274 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
2696172 TCAGCCTTGG
* *
2696182 TGCATGGATGAACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
2696202 TGCATCGATGCACAACAGGA
1 TGCATCGATGCACAGCAGGA
* *
2696222 TGCATCGATTCACATCAGGA
1 TGCATCGATGCACAGCAGGA
* *
2696242 TGCATCGGTGCATAGCAGGA
1 TGCATCGATGCACAGCAGGA
2696262 TGCATCGATGCAC
1 TGCATCGATGCAC
2696275 TAATTGCATT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:2696599 original size:21 final size:21
Alignment explanation
Indices: 2696575--2696614 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2696565 ATTTTTAATG
2696575 AAAAAAATACCAATTGTTAAC
1 AAAAAAATACCAATTGTTAAC
** *
2696596 AAAATGATATCAATTGTTA
1 AAAAAAATACCAATTGTTA
2696615 CCAATTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAAATACCAATTGTTAAC
Found at i:2697768 original size:18 final size:19
Alignment explanation
Indices: 2697730--2697769 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2697720 TCATTTTGAT
*
2697730 TTTCAAAATCAAATTTTTC
1 TTTCAAAATCAAATTTATC
*
2697749 TTTCAAATTCAAA-TTATC
1 TTTCAAAATCAAATTTATC
2697767 TTT
1 TTT
2697770 AATTTTGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCAAATTTATC
Found at i:2699728 original size:23 final size:23
Alignment explanation
Indices: 2699702--2699786 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
2699692 TCAAAATGGA
* *
2699702 GTGCATGGATGCACTAGTGGAAG
1 GTGCATCGATGCACTAGTGGCAG
2699725 GTGCATCGATGCACTAGTGGCAG
1 GTGCATCGATGCACTAGTGGCAG
2699748 GTGCATCGATGCACTAGTGGCAG
1 GTGCATCGATGCACTAGTGGCAG
* *
2699771 GGGCATGGATGCACTA
1 GTGCATCGATGCACTA
2699787 CAGGGGTGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (23 bp):
GTGCATCGATGCACTAGTGGCAG
Found at i:2699792 original size:19 final size:21
Alignment explanation
Indices: 2699702--2699806 Score: 66
Period size: 23 Copynumber: 4.7 Consensus size: 21
2699692 TCAAAATGGA
**
2699702 GTGCATGGATGCACTAGTGGAAG
1 GTGCATGGATGCACTACAGG--G
* **
2699725 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTACAGG--G
* **
2699748 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTACAGG--G
*
2699771 GGGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTACAGGG
*
2699792 GTGTATGGATGCACT
1 GTGCATGGATGCACT
2699807 TTGACACCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
21 14 0.19
23 60 0.81
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:2700053 original size:21 final size:21
Alignment explanation
Indices: 2700029--2700068 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2700019 ATGTTTAATG
2700029 AAAAAAATACCAATTGTTAAC
1 AAAAAAATACCAATTGTTAAC
** *
2700050 AAAATGATATCAATTGTTA
1 AAAAAAATACCAATTGTTA
2700069 CCAATTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAAATACCAATTGTTAAC
Found at i:2702616 original size:20 final size:20
Alignment explanation
Indices: 2702587--2702639 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2702577 GCAGCCTTGG
*
2702587 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
2702607 TGCATCGATGCACAGTAGGA
1 TGCATCGATGCACAGCAGGA
2702627 TGCATCGATGCAC
1 TGCATCGATGCAC
2702640 TAATTGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:2702685 original size:23 final size:23
Alignment explanation
Indices: 2702659--2702720 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
2702649 TCGAAATGGA
2702659 GTGCATGGATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGGCAG
*
2702682 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGGCAG
*
2702705 GGGCATGGATGCACTA
1 GTGCATGGATGCACTA
2702721 CAGGGGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (23 bp):
GTGCATGGATGCACTAGTGGCAG
Found at i:2702726 original size:19 final size:21
Alignment explanation
Indices: 2702659--2702740 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 21
2702649 TCGAAATGGA
**
2702659 GTGCATGGATGCACTAGTGGCAG
1 GTGCATGGATGCACTACAGG--G
* **
2702682 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTACAGG--G
*
2702705 GGGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTACAGGG
*
2702726 GTGTATGGATGCACT
1 GTGCATGGATGCACT
2702741 TTGACACCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
21 14 0.27
23 38 0.73
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:2702985 original size:21 final size:21
Alignment explanation
Indices: 2702961--2703000 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2702951 ATGTTTAATG
2702961 AAAAAAATACCAATTGTTAAC
1 AAAAAAATACCAATTGTTAAC
** *
2702982 AAAATGATATCAATTGTTA
1 AAAAAAATACCAATTGTTA
2703001 CCAATTGCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAAATACCAATTGTTAAC
Found at i:2704152 original size:20 final size:17
Alignment explanation
Indices: 2704109--2704166 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
2704099 GAAAGCTCTA
* *
2704109 AATTATTTTTCAAAATTT
1 AATTTTTTTTCAAAA-TC
2704127 AATTTTGATTTTCAAAATC
1 AATTTT--TTTTCAAAATC
2704146 AACTTTTTCTTTCAAAATC
1 AA-TTTTT-TTTCAAAATC
2704165 AA
1 AA
2704167 ATTATCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.18
19 15 0.44
20 13 0.38
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTTTTTTTCAAAATC
Found at i:2706016 original size:20 final size:20
Alignment explanation
Indices: 2705991--2706037 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2705981 TTGGTGCCTG
2705991 GATGCACAGCAAGATGCATC
1 GATGCACAGCAAGATGCATC
* *
2706011 GATGCATAGCAGGATGCATC
1 GATGCACAGCAAGATGCATC
2706031 GATGCAC
1 GATGCAC
2706038 TAATTGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (20 bp):
GATGCACAGCAAGATGCATC
Found at i:2706112 original size:22 final size:23
Alignment explanation
Indices: 2706057--2706117 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
2706047 TCAAAATGGA
* *
2706057 GTGCATGGATGCACTAGTGGCAG
1 GTGCATCGATGCACTAGTGGAAG
2706080 GTGCATCGATGCACTAGTGGAAG
1 GTGCATCGATGCACTAGTGGAAG
*
2706103 G-GCATTGATGCACTA
1 GTGCATCGATGCACTA
2706118 CAGGGGTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACTAGTGGAAG
Found at i:2709511 original size:20 final size:20
Alignment explanation
Indices: 2709486--2709532 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2709476 TTGGTGCATG
2709486 GATGCACAGCAGGATACATC
1 GATGCACAGCAGGATACATC
* * *
2709506 GATGCATAGCAGGATGCATT
1 GATGCACAGCAGGATACATC
2709526 GATGCAC
1 GATGCAC
2709533 TAATTGCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (20 bp):
GATGCACAGCAGGATACATC
Found at i:2709620 original size:21 final size:21
Alignment explanation
Indices: 2709552--2709630 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 21
2709542 TTGAAATGGA
* *
2709552 GTGCATGGATGAACTACA-TG
1 GTGCATGGATGCACTACAGGG
** **
2709572 GTGCATCCATGCACTAGTGGCAG
1 GTGCATGGATGCACTACAGG--G
2709595 GTGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTACAGGG
2709616 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2709631 TTGACACCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
20 13 0.28
21 16 0.35
23 17 0.37
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:2711053 original size:19 final size:20
Alignment explanation
Indices: 2711018--2711055 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2711008 CAAAATTTCA
2711018 TTTTGATTTTAAAAATCAAC
1 TTTTGATTTTAAAAATCAAC
*
2711038 TTTTGCTTTT-AAAATCAA
1 TTTTGATTTTAAAAATCAA
2711056 ATTATCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTGATTTTAAAAATCAAC
Found at i:2713000 original size:20 final size:20
Alignment explanation
Indices: 2712971--2713039 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
2712961 GTAGCCTTGG
* *
2712971 TGCATGGATGCACAGCAGGA
1 TGCATCGATGTACAGCAGGA
2712991 TGCATCGATGTACAGCAGGA
1 TGCATCGATGTACAGCAGGA
2713011 TGCATCGATGTACAGCAGGA
1 TGCATCGATGTACAGCAGGA
2713031 TGCATCGAT
1 TGCATCGAT
2713040 TAACTAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
TGCATCGATGTACAGCAGGA
Found at i:2713088 original size:20 final size:19
Alignment explanation
Indices: 2713063--2713139 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 19
2713053 TCGAAATGGA
2713063 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACA-G
**
2713083 GTGCATCCATGCACTAGTGGCAG
1 GTGCATGGATGCACTA----CAG
*
2713106 GTGCTTGGATGCACTACTAGG
1 GTGCATGGATGCACTAC-A-G
2713127 GTGCATGGATGCA
1 GTGCATGGATGCA
2713140 GTTTGACACC
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 13 0.29
23 14 0.31
24 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (19 bp):
GTGCATGGATGCACTACAG
Found at i:2713390 original size:21 final size:21
Alignment explanation
Indices: 2713366--2713405 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2713356 ATGTTTAATG
2713366 AAAAAAATACCAATTGTTAAC
1 AAAAAAATACCAATTGTTAAC
** *
2713387 AAAATGATATCAATTGTTA
1 AAAAAAATACCAATTGTTA
2713406 CCAATTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAAATACCAATTGTTAAC
Found at i:2715564 original size:20 final size:20
Alignment explanation
Indices: 2715535--2715607 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2715525 GCAGCCTTGG
*
2715535 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGTAGGA
* *
2715555 TGCATCGATGTACAGCAGGA
1 TGCATCGATGCACAGTAGGA
*
2715575 TGCATCGATGCATA-TCAGGA
1 TGCATCGATGCACAGT-AGGA
2715595 TGCATCGATGCAC
1 TGCATCGATGCAC
2715608 TAATTGCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAGTAGGA
Found at i:2715681 original size:23 final size:21
Alignment explanation
Indices: 2715627--2715705 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 21
2715617 TCGAAATGGA
*
2715627 GTGCATAGATGCACTACAT--G
1 GTGCATGGATGCACTAC-TGGG
** *
2715647 GTGCATCCATGCACTAGTGGTAG
1 GTGCATGGATGCACTACTGG--G
2715670 GTGCATGGATGCACTACTGGG
1 GTGCATGGATGCACTACTGGG
*
2715691 GTGCAAGGATGCACT
1 GTGCATGGATGCACT
2715706 TTGACACCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 14 0.29
21 15 0.31
23 18 0.38
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTACTGGG
Found at i:2718903 original size:20 final size:20
Alignment explanation
Indices: 2718874--2718946 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
2718864 GCAGCCTTGG
* *
2718874 TGCATGGATGCACAGCAAGA
1 TGCATCGATGCACAGCAGGA
*
2718894 TGCATCGATGTACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
2718914 TGCATCGATGCATAGCAGGA
1 TGCATCGATGCACAGCAGGA
2718934 TGCATCGATGCAC
1 TGCATCGATGCAC
2718947 TAATTGCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:2719248 original size:21 final size:21
Alignment explanation
Indices: 2719224--2719263 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2719214 ATGTTTAATG
2719224 AAAAAAATATCAATTGTTAAC
1 AAAAAAATATCAATTGTTAAC
**
2719245 AAAATGATATCAATTGTTA
1 AAAAAAATATCAATTGTTA
2719264 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAAAAATATCAATTGTTAAC
Found at i:2722367 original size:20 final size:20
Alignment explanation
Indices: 2722342--2722434 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
2722332 GCAGCCTTGG
2722342 TGCATGGATGCACAGCAGGA
1 TGCATGGATGCACAGCAGGA
2722362 TGCATGGATGCACAGCAGGA
1 TGCATGGATGCACAGCAGGA
2722382 TGCATGGATGCACAGCAGGA
1 TGCATGGATGCACAGCAGGA
* *
2722402 TGCATCGATGCATAGCAGGA
1 TGCATGGATGCACAGCAGGA
* *
2722422 TACATCGATGCAC
1 TGCATGGATGCAC
2722435 TAATTGCATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.30, C:0.22, G:0.31, T:0.17
Consensus pattern (20 bp):
TGCATGGATGCACAGCAGGA
Found at i:2722508 original size:23 final size:20
Alignment explanation
Indices: 2722454--2722531 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
2722444 TCGAAATGGA
*
2722454 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACAAG
**
2722474 GTGCATCCATGCACTACTGGAAG
1 GTGCATGGATGCACTAC---AAG
*
2722497 GTGCATGGATGCACTACAGG
1 GTGCATGGATGCACTACAAG
2722517 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2722532 TTGACACCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 32 0.65
23 17 0.35
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTACAAG
Found at i:2725907 original size:20 final size:20
Alignment explanation
Indices: 2725878--2725930 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2725868 GCAGCCTTGG
* *
2725878 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAAGA
2725898 TGCATCGATGCACAGCAAGA
1 TGCATCGATGCACAGCAAGA
2725918 TGCATCGATGCAC
1 TGCATCGATGCAC
2725931 TAATTGTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAAGA
Found at i:2726002 original size:23 final size:20
Alignment explanation
Indices: 2725949--2726023 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
2725939 GTTTAATGGA
2725949 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
2725969 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
* *
2725992 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACA-TG
2726013 GTGCATGGATG
1 GTGCATGGATG
2726024 TATTTTGACA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 12 0.26
23 15 0.33
24 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:2728817 original size:6 final size:6
Alignment explanation
Indices: 2728806--2728840 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2728796 AACTCTCTCA
2728806 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCC
2728841 TAAGTTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTCCC
Found at i:2731253 original size:23 final size:23
Alignment explanation
Indices: 2731227--2731305 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 23
2731217 TATCAGTTTA
2731227 AAAAATATATTATAATTAATGAT
1 AAAAATATATTATAATTAATGAT
*
2731250 AAAAATATAAACTTTTATCATTTTAA--AT
1 AAAAATAT--A---TTAT-A-ATTAATGAT
2731278 AAAAATATATTATAATTAATGAT
1 AAAAATATATTATAATTAATGAT
2731301 AAAAA
1 AAAAA
2731306 AAATTACAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
21 4 0.09
22 1 0.02
23 19 0.42
25 1 0.02
26 1 0.02
28 14 0.31
29 1 0.02
30 4 0.09
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
AAAAATATATTATAATTAATGAT
Found at i:2731319 original size:23 final size:23
Alignment explanation
Indices: 2731276--2731319 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2731266 ATCATTTTAA
* *
2731276 ATAAAAATATATTATAATTAATG
1 ATAAAAATAAATTACAATTAATG
2731299 ATAAAAA-AAATTACAAGTTAA
1 ATAAAAATAAATTACAA-TTAA
2731320 GGGAAGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
ATAAAAATAAATTACAATTAATG
Found at i:2732000 original size:14 final size:14
Alignment explanation
Indices: 2731965--2732002 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2731955 ATAATTTGTC
*
2731965 CGTTTATATTCGTT
1 CGTTTATGTTCGTT
2731979 CGTTTATGTTCGTT
1 CGTTTATGTTCGTT
*
2731993 TGTTTATGTT
1 CGTTTATGTT
2732003 TTCCAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.61
Consensus pattern (14 bp):
CGTTTATGTTCGTT
Found at i:2735380 original size:31 final size:32
Alignment explanation
Indices: 2735318--2735386 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
2735308 TTTGTAATCT
*
2735318 TAAAATGTCGAATGTAATATATAAGTATAATAA
1 TAAAATGTCGAATGTAATACAT-AGTATAATAA
2735351 TAAAATGTTC-AATGTAATACAT-GTATAATAA
1 TAAAATG-TCGAATGTAATACATAGTATAATAA
2735382 TAAAA
1 TAAAA
2735387 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (32 bp):
TAAAATGTCGAATGTAATACATAGTATAATAA
Found at i:2735470 original size:24 final size:23
Alignment explanation
Indices: 2735417--2735482 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
2735407 AAATAAAAAA
2735417 ATAATTTAA-TATATATATATAT
1 ATAATTTAATTATATATATATAT
*
2735439 ATAGATTTAATTATATATATATTTT
1 ATA-ATTTAATTATATATATA-TAT
*
2735464 TTAATTTAATCT-TATATAT
1 ATAATTTAAT-TATATATAT
2735483 TTCAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.08
23 6 0.16
24 24 0.63
25 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATAATTTAATTATATATATATAT
Found at i:2736253 original size:30 final size:31
Alignment explanation
Indices: 2736212--2736589 Score: 198
Period size: 30 Copynumber: 12.9 Consensus size: 31
2736202 TAAAATAAAG
* *
2736212 ATAAAAAATATTTTTATAA-TTAAGATAAAA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* ** *
2736242 ATATAATATA-TTTCCTAAGTTAAAATAAGA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* *
2736272 ATAAAATATATATTTT-TAAATTAA-A-ATG-
1 ATAAAATATAT-TTTTATAAGTTAAGATAAGA
* * *
2736300 A-AATATATA-ATTT-GAAGTTAAGATAAGA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* * **
2736328 AT-AAATA-ATATTTAATAATTTAAGGCAAGA
1 ATAAAATATAT-TTTTATAAGTTAAGATAAGA
* * * *
2736358 ATATAATATA-TTTAATAATTTAA-ATTATGA
1 ATAAAATATATTTTTATAAGTTAAGA-TAAGA
* * * * *
2736388 ATATAATATA-TGTAAAAAGTTAAG---ACA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* * *
2736415 A-AAAATATAATTTTAAAAGTTAAGATAATA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* *
2736445 ATAAAATATATTTTT-TAAGTTAAGGTAGGA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* *
2736475 ATAAAATATA-TTTTATAAGCTAAGATAATA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* *
2736505 TTAAAATATATTTTT-TAA-CTAAGATAAGA
1 ATAAAATATATTTTTATAAGTTAAGATAAGA
* * *
2736534 ATAAAGTATA-TTTAATAAGATAAGGA-AA-A
1 ATAAAATATATTTTTATAAGTTAA-GATAAGA
2736563 ATAAATATATATTTTTAT-A-TTAAGATA
1 ATAAA-ATATATTTTTATAAGTTAAGATA
2736590 TGATTTTAAG
Statistics
Matches: 268, Mismatches: 53, Indels: 55
0.71 0.14 0.15
Matches are distributed among these distances:
25 9 0.03
26 8 0.03
27 24 0.09
28 11 0.04
29 45 0.17
30 133 0.50
31 34 0.13
32 4 0.01
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (31 bp):
ATAAAATATATTTTTATAAGTTAAGATAAGA
Found at i:2736276 original size:60 final size:60
Alignment explanation
Indices: 2736212--2736589 Score: 247
Period size: 60 Copynumber: 6.5 Consensus size: 60
2736202 TAAAATAAAG
* ** *
2736212 ATAAAAAATATTTTTATAATTAAGATAAAAATATAATATATTTCCTAAGTTAAAATAAGA
1 ATAAAATATATTTTTATAATTAAGATAAAAATATAATATATTTAATAAGTTAAGATAAGA
* * *
2736272 ATAAAATATATATTTT-TAAATTAAAAT-GAAATAT-ATA-ATTT--GAAGTTAAGATAAGA
1 ATAAAATATAT-TTTTAT-AATTAAGATAAAAATATAATATATTTAATAAGTTAAGATAAGA
* ** * * *
2736328 AT-AAATA-ATATTTAATAATTTAAGGCAAGAATATAATATATTTAATAATTTAA-ATTATGA
1 ATAAAATATAT-TTTTATAA-TTAAGATAAAAATATAATATATTTAATAAGTTAAGA-TAAGA
* * * * * *
2736388 ATATAATATA-TGTAAAAAGTTAAGACAAAAA-AT-ATA-ATTTTAA-AAGTTAAGATAATA
1 ATAAAATATATTTTTATAA-TTAAGATAAAAATATAATATA-TTTAATAAGTTAAGATAAGA
* ** * * * *
2736445 ATAAAATATATTTTT-TAAGTTAAGGTAGGAATAAAATATATTTTATAAGCTAAGATAATA
1 ATAAAATATATTTTTATAA-TTAAGATAAAAATATAATATATTTAATAAGTTAAGATAAGA
* * * *
2736505 TTAAAATATATTTTT-TAACTAAGATAAGAATA-AAGTATATTTAATAAGATAAGGA-AA-A
1 ATAAAATATATTTTTATAATTAAGATAAAAATATAA-TATATTTAATAAGTTAA-GATAAGA
2736563 ATAAATATATATTTTTAT-ATTAAGATA
1 ATAAA-ATATATTTTTATAATTAAGATA
2736590 TGATTTTAAG
Statistics
Matches: 253, Mismatches: 42, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
54 8 0.03
55 10 0.04
56 20 0.08
57 33 0.13
58 27 0.11
59 59 0.23
60 79 0.31
61 16 0.06
62 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (60 bp):
ATAAAATATATTTTTATAATTAAGATAAAAATATAATATATTTAATAAGTTAAGATAAGA
Found at i:2736330 original size:26 final size:25
Alignment explanation
Indices: 2736267--2736336 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
2736257 TAAGTTAAAA
* *
2736267 TAAGAATAAAATATATATTTTTAAAT
1 TAAG-ATAAAATATATAATTTGAAAT
* * *
2736293 TAAAATGAAATATATAATTTGAAGT
1 TAAGATAAAATATATAATTTGAAAT
*
2736318 TAAGATAAGAATAAATAAT
1 TAAGATAA-AATATATAAT
2736337 ATTTAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 23 0.66
26 12 0.34
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
TAAGATAAAATATATAATTTGAAAT
Found at i:2736544 original size:59 final size:60
Alignment explanation
Indices: 2736416--2736578 Score: 197
Period size: 59 Copynumber: 2.7 Consensus size: 60
2736406 GTTAAGACAA
* * * * *
2736416 AAAATATAATTTTAAAAGTTAAGATAATAATAAAATATATTTTTTAAGTTAAGGTAGGAAT
1 AAAATAT-ATTTTATAAGATAAGATAATAATAAAATATATTTTTTAAGCTAAGATAAGAAT
* *
2736477 AAAATATATTTTATAAGCTAAGATAATATTAAAATATATTTTTTAA-CTAAGATAAGAAT
1 AAAATATATTTTATAAGATAAGATAATAATAAAATATATTTTTTAAGCTAAGATAAGAAT
* *
2736536 AAAGTATATTTAATAAGATAAGGA-AA-AATAAATATATATTTTT
1 AAAATATATTTTATAAGATAA-GATAATAATAAA-ATATATTTTT
2736579 ATATTAAGAT
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 5 0.06
59 40 0.44
60 38 0.42
61 7 0.08
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (60 bp):
AAAATATATTTTATAAGATAAGATAATAATAAAATATATTTTTTAAGCTAAGATAAGAAT
Found at i:2736587 original size:59 final size:60
Alignment explanation
Indices: 2736194--2736589 Score: 188
Period size: 59 Copynumber: 6.8 Consensus size: 60
2736184 TTTATTCTTA
* * * * *
2736194 TAATATGATAAAATAA-AGATAAA-AAATATTTTTATAATTAAGATAAAAATATAATATATT
1 TAATAAGATAAGATAATA-ATAAATATATATTTTTAT-ATTAAGATAAGAATAAAATATATT
** * * * * * * *
2736254 TCCTAAGTTAAAATAAGAATAAAATATATATTTTTAAATTAAAATGA-AAT-ATATA-ATT
1 TAATAAGATAAGATAATAAT-AAATATATATTTTTATATTAAGATAAGAATAAAATATATT
* * * * ** *
2736312 T--GAAGTTAAGATAAGAATAAATA-ATA-TTTAATAATTTAAGGCAAGAATATAATATATT
1 TAATAAGATAAGATAATAATAAATATATATTTTTAT-A-TTAAGATAAGAATAAAATATATT
** * * * * * *
2736370 TAATAATTTAA-AT--T-ATGAATATAATATATGTA-A-AAAGTTAAGACAAAAAATATAATTT
1 TAATAAGATAAGATAATAATAAATAT-ATATTTTTATATTAAGATAAGA-ATAAAATAT-A-TT
* * *
2736428 TAA-AAGTTAAGATAATAATAAA-ATATATTTTT-TAAGTTAAGGTAGGAATAAAATATATT
1 TAATAAGATAAGATAATAATAAATATATATTTTTAT-A-TTAAGATAAGAATAAAATATATT
* * * * *
2736487 TTATAAGCTAAGATAATATTAAA-ATATATTTTT-TAACTAAGATAAGAATAAAGTATATT
1 TAATAAGATAAGATAATAATAAATATATATTTTTAT-ATTAAGATAAGAATAAAATATATT
2736546 TAATAAGATAAGGA-AA-AATAAATATATATTTTTATATTAAGATA
1 TAATAAGATAA-GATAATAATAAATATATATTTTTATATTAAGATA
2736590 TGATTTTAAG
Statistics
Matches: 257, Mismatches: 51, Indels: 57
0.70 0.14 0.16
Matches are distributed among these distances:
53 4 0.02
54 4 0.02
55 17 0.07
56 31 0.12
57 11 0.04
58 23 0.09
59 65 0.25
60 61 0.24
61 24 0.09
62 17 0.07
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (60 bp):
TAATAAGATAAGATAATAATAAATATATATTTTTATATTAAGATAAGAATAAAATATATT
Found at i:2736596 original size:18 final size:17
Alignment explanation
Indices: 2736569--2736622 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2736559 AAAAATAAAT
2736569 ATATATTTTTATATTAAG
1 ATATA-TTTTATATTAAG
2736587 ATATGATTTTA-AGTTAAG
1 ATAT-ATTTTATA-TTAAG
* *
2736605 ATATATATAATATTAAG
1 ATATATTTTATATTAAG
2736622 A
1 A
2736623 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 11 0.35
18 19 0.61
19 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.46
Consensus pattern (17 bp):
ATATATTTTATATTAAG
Found at i:2740213 original size:64 final size:64
Alignment explanation
Indices: 2740130--2740269 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
2740120 TTCTTCTAAG
* * * * * * *
2740130 GGAATATCAGATCTAGGGATGTTAATCCATTGAATTGGGGTAGACTTGTTCCACTGTCATTCAA
1 GGAATATCAAATATAGGGATGTTAATCCATTGAATCGAGGCAGACTTATTCCACTGTCACTCAA
* * ** *
2740194 GGAATATCAAATATAGGGATGTTGATCCATTGAATCGAGGCAGTCTTATTCTGCTGTCACTCAG
1 GGAATATCAAATATAGGGATGTTAATCCATTGAATCGAGGCAGACTTATTCCACTGTCACTCAA
2740258 GGAATATCAAAT
1 GGAATATCAAAT
2740270 CTTGGAAGAG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (64 bp):
GGAATATCAAATATAGGGATGTTAATCCATTGAATCGAGGCAGACTTATTCCACTGTCACTCAA
Found at i:2741159 original size:233 final size:233
Alignment explanation
Indices: 2740608--2742282 Score: 2595
Period size: 233 Copynumber: 7.2 Consensus size: 233
2740598 AAATCATGCA
* * * * * * *
2740608 AAAACATCCTGCCCGAAGGGCTTATGGATGACCCAAAGGATTTATCATCTTGCTCGAAAAGCTTA
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
* * * * * * * *
2740673 CAGATAACCCGAAGAATTTATGCATCATGCTCAAAAGACTTACTGACGACCCAAAGGATTTGTAA
66 CAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAA
* *
2740738 ACTTTAGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT-AAAACATTTCAATTTTTAGAT
131 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAA-ATTTCAATTTTTAGAT
*
2740802 TTAATATGAGAAACCTTTCTCATATTTCGATAGACATGTG
195 TTAA-ATGAGAAACCTTTCTCATATTTCAATAGACATGTG
* * *
2740842 AAAACATCCTGCCTAAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTGATCGAAAGGCTTA
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
* * * * *
2740907 CAGATGACCCGAAGGATTTAAGCATCACGCTCAAAAGACTTACTGATGACCTGAAGAATTTATAA
66 CAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAA
* *
2740972 ATTTTGGAAATAGTTTACTAGGTAATAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGATA
131 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGATT
* * * *
2741037 TGAATGAGAAACATTTCTCATATTTCAATAGATATGTA
196 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
* *
2741075 AAAACATCCTGCCCAAAGGTCTTATAGATGGCCCGAATGACTTATCATCTCT-CTTGAAAGGCTT
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCT-TGCTCGAAAGGCTT
* * *
2741139 ACAGACGACCTGAGGGATTTAAGCATCATGCTCGAAAGACTTGCTGATGACCCGAAGGATTTATA
65 ACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATA
* *
2741204 AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTAAATTTTTAGAT
130 AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGAT
2741269 TTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
195 TTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
*
2741308 AAAACATTCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
* * *
2741373 CAGATGA-CTCGAAGGATTTAAGAATCA-GCCTTGAAAGACTTACTGATGACCCGATGGATTTAT
66 CAGATGACCT-GAAGGATTTAAGCATCATG-CTCGAAAGACTTACTGATGACCCGAAGGATTTAT
* *
2741436 AAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTTAATTTTCAGA
129 AAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGA
*
2741501 TTTAAATGAGAAACCTTTCTCATATTTCAATAGATATGTG
194 TTTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
* * *
2741541 AAATCATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATTTTTCTCGAAAGGCTTA
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
* * *
2741606 TAAATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTGCTGATGACCCGAAGGATTTATAA
66 CAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAA
* *
2741671 ATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTAAATTTTTAGATT
131 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGATT
2741736 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
196 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
*
2741774 AAAACATTCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
* * * *
2741839 CATATGA-CTCGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGAACCGATGGATTTATA
66 CAGATGACCT-GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATA
* * *
2741903 AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTTAATTTTCATAT
130 AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGAT
*
2741968 TTAAATGAGAAACCTTTCTCATATTTCAATAGATATGTG
195 TTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
* * *
2742007 AAATCATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATTTTTCTCGAAAGGCTTA
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
* * *
2742072 TAAAAGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAA
66 CAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAA
*
2742137 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATT
131 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGATT
*
2742202 TAAATGAGAAACATTTCTCATATTTCAATAGACATGTG
196 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
* * *
2742240 AAAATATCCTGCCCAAAGGTCTTATGGATGGTCCGAAGGACTT
1 AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTT
2742283 GTAAATTTTG
Statistics
Matches: 1325, Mismatches: 107, Indels: 19
0.91 0.07 0.01
Matches are distributed among these distances:
232 6 0.00
233 1140 0.86
234 175 0.13
235 4 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (233 bp):
AAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTA
CAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAA
ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGATT
TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG
Found at i:2742405 original size:150 final size:150
Alignment explanation
Indices: 2742116--2742522 Score: 661
Period size: 150 Copynumber: 2.7 Consensus size: 150
2742106 AAGACTTACT
* * *
2742116 GATGACCCGAAGGATTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * * *
2742181 AAAAATTTCAATTTTCAGATTTAAATGAGAAACATTTCTCATATTTCAATAGACATGTGAAAATA
66 AAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATATTTCAATAGACATCTAAAAACA
2742246 TCCTGCCCAAAGGTCTTATG
131 TCCTGCCCAAAGGTCTTATG
* *
2742266 GATGGTCCGAAGGACTTGTAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
*
2742331 AAAAATTTCAATTTTTAGATTTAAATGAGAAACCTTTCTCATATTTCAATAGACATCTAAAAACA
66 AAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATATTTCAATAGACATCTAAAAACA
* * *
2742396 TCTTTCCCAAATGTCTTATG
131 TCCTGCCCAAAGGTCTTATG
* *
2742416 GATGGCCCAAATGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* *
2742481 AAAAATTTCAATTTTCAAATTTGAATGAGAAACCTTTCTCAT
66 AAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCAT
2742523 TTTTTCACTT
Statistics
Matches: 237, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
150 237 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (150 bp):
GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
AAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATATTTCAATAGACATCTAAAAACA
TCCTGCCCAAAGGTCTTATG
Found at i:2744293 original size:14 final size:14
Alignment explanation
Indices: 2744274--2744303 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2744264 AGTTCACAAA
*
2744274 TCATTCTAGATCAT
1 TCATTCCAGATCAT
2744288 TCATTCCAGATCAT
1 TCATTCCAGATCAT
2744302 TC
1 TC
2744304 TTTGGCATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (14 bp):
TCATTCCAGATCAT
Found at i:2750121 original size:21 final size:22
Alignment explanation
Indices: 2750092--2750133 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2750082 CTTCCAATGC
2750092 GAAGTGGTCTTCAT-GTCTTTGT
1 GAAGTGGTCTT-ATCGTCTTTGT
2750114 GAAG-GGTCTTATCGTCTTTG
1 GAAGTGGTCTTATCGTCTTTG
2750134 GTATGAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (22 bp):
GAAGTGGTCTTATCGTCTTTGT
Found at i:2752075 original size:177 final size:177
Alignment explanation
Indices: 2751779--2752132 Score: 672
Period size: 177 Copynumber: 2.0 Consensus size: 177
2751769 ATGGTGAATG
*
2751779 AAATTCCTATTACAATGGCTATTTGTTCTTGTTTTTTTTCATTCCCCGTTTTCCTTCTATTCATC
1 AAATTCCTATTACAATGGCTATTTATTCTTGTTTTTTTTCATTCCCCGTTTTCCTTCTATTCATC
2751844 AACCCATGTTCAAATGGTTTCCATGCTTTTATAGTGGAATTTGGTTACTGCATGACCTCCTCTAG
66 AACCCATGTTCAAATGGTTTCCATGCTTTTATAGTGGAATTTGGTTACTGCATGACCTCCTCTAG
2751909 TGGCAGTAAAGGATAATGGTAGAGTATGTATTTATTTTTAAGGTTTA
131 TGGCAGTAAAGGATAATGGTAGAGTATGTATTTATTTTTAAGGTTTA
*
2751956 AAATTCCTATTACAATGGCTATTTATTCTTGTTTTTTTTCATTCCCCGTTTTCCTTCTATTCGTC
1 AAATTCCTATTACAATGGCTATTTATTCTTGTTTTTTTTCATTCCCCGTTTTCCTTCTATTCATC
2752021 AACCCATGTTCAAATGGTTTCCATGCTTTTATAGTGGAATTTGGTTACTGCATGACCTCCTCTAG
66 AACCCATGTTCAAATGGTTTCCATGCTTTTATAGTGGAATTTGGTTACTGCATGACCTCCTCTAG
* *
2752086 TGGCAGTAAAGGATAATGGTGGAGTATGTATTTATTTTTTAGGTTTA
131 TGGCAGTAAAGGATAATGGTAGAGTATGTATTTATTTTTAAGGTTTA
2752133 TTGGGTATGT
Statistics
Matches: 173, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 173 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (177 bp):
AAATTCCTATTACAATGGCTATTTATTCTTGTTTTTTTTCATTCCCCGTTTTCCTTCTATTCATC
AACCCATGTTCAAATGGTTTCCATGCTTTTATAGTGGAATTTGGTTACTGCATGACCTCCTCTAG
TGGCAGTAAAGGATAATGGTAGAGTATGTATTTATTTTTAAGGTTTA
Found at i:2752723 original size:23 final size:23
Alignment explanation
Indices: 2752697--2752740 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2752687 ATGCATTAAT
2752697 AATATATTCT-TATTATAAACTAA
1 AATA-ATTCTGTATTATAAACTAA
* *
2752720 AATAATTTTGTATTATGAACT
1 AATAATTCTGTATTATAAACT
2752741 TATCAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (23 bp):
AATAATTCTGTATTATAAACTAA
Found at i:2753351 original size:9 final size:9
Alignment explanation
Indices: 2753337--2753374 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
2753327 CTTTGTATTT
2753337 TATATTTAA
1 TATATTTAA
2753346 TATATTTAA
1 TATATTTAA
*
2753355 TATATTGAA
1 TATATTTAA
2753364 TATA-TTAA
1 TATATTTAA
2753372 TAT
1 TAT
2753375 TTTTTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TATATTTAA
Found at i:2755569 original size:20 final size:21
Alignment explanation
Indices: 2755544--2755589 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2755534 TAATGTAATA
2755544 AAAAAAAG-GAAAAAAATAA-C
1 AAAAAAAGTGAAAAAAA-AATC
*
2755564 AAAAAAAGTTAAAAAAAAATC
1 AAAAAAAGTGAAAAAAAAATC
2755585 AAAAA
1 AAAAA
2755590 TCAAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (21 bp):
AAAAAAAGTGAAAAAAAAATC
Found at i:2756362 original size:2 final size:2
Alignment explanation
Indices: 2756357--2756390 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2756347 TTATATATTT
2756357 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2756391 GGTTTGGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2757242 original size:33 final size:31
Alignment explanation
Indices: 2757191--2757259 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2757181 TTTGTAATCT
*
2757191 TAAAATGTCGAATGTAATATACAAGTATAATAA
1 TAAAATGTCGAATAT-A-ATACAAGTATAATAA
*
2757224 TAAAATGTTC-AATATAATACATGTATAATAA
1 TAAAATG-TCGAATATAATACAAGTATAATAA
2757255 TAAAA
1 TAAAA
2757260 ATTATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 19 0.58
32 1 0.03
33 11 0.33
34 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.32
Consensus pattern (31 bp):
TAAAATGTCGAATATAATACAAGTATAATAA
Found at i:2757992 original size:32 final size:30
Alignment explanation
Indices: 2757954--2758041 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 30
2757944 AATTGAATAT
2757954 ATATTTTATTCTTATCTTAACTAAAGAAAAAA
1 ATATTTTATT-TTATCTTAACTAAA-AAAAAA
* * * *
2757986 ATATTTTAGTTTTTTCTAAACTTAAAAAATAT
1 ATATTTTA-TTTTATCTTAAC-TAAAAAAAAA
*
2758018 ATATTTTATTTTTACCTTAACTAA
1 ATATTTTA-TTTTATCTTAACTAA
2758042 TTTTTTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 3 0.07
32 37 0.80
33 6 0.13
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATTTTATTTTATCTTAACTAAAAAAAAA
Found at i:2758121 original size:30 final size:30
Alignment explanation
Indices: 2758085--2758451 Score: 195
Period size: 30 Copynumber: 12.6 Consensus size: 30
2758075 AAATAAAGAT
*
2758085 AAATATATTTTTATAATTAAGATAAAAATA
1 AAATATATTTTTATAATTAAGATAAGAATA
** *
2758115 AAATATA-TTTCCTAATTAAAATAAGAATA
1 AAATATATTTTTATAATTAAGATAAGAATA
* *
2758144 AATATATATATTTA-AATTAA-A-ATG-A-A
1 AA-ATATATTTTTATAATTAAGATAAGAATA
* * * *
2758170 ATATATAATTTGA-AGTTAAGATAAGAAT-
1 AAATATATTTTTATAATTAAGATAAGAATA
* *
2758198 AAATA-ATATTTAATAATTTAACG-CAAGAATA
1 AAATATAT-TTTTATAA-TTAA-GATAAGAATA
* *
2758229 TAATATA-TTTAATAATTTAA-ATTAAGAATA
1 AAATATATTTTTATAA-TTAAGA-TAAGAATA
* * * * *
2758259 TAATATA--TGTAAAATGTTAAAATAAAAAT-
1 AAATATATTTTTATAA--TTAAGATAAGAATA
* * *
2758288 AAATATATTTTTAAAAATTAAAATAATAATA
1 AAATATATTTTT-ATAATTAAGATAAGAATA
* *
2758319 AAATATATTTTTA-AGTTAAGATAGGAATA
1 AAATATATTTTTATAATTAAGATAAGAATA
* *
2758348 AAATATA-TTTTATAAACTAAGATAAGATTA
1 AAATATATTTTTAT-AATTAAGATAAGAATA
* *
2758378 AAATATATATTTT-TAACTATGATAAGAATA
1 AAATATAT-TTTTATAATTAAGATAAGAATA
*
2758408 AAATATA-TTTAATAAGTTAAGGA-AA-AAT-
1 AAATATATTTTTATAA-TTAA-GATAAGAATA
2758436 AAATATATTTTT-TAAT
1 AAATATATTTTTATAAT
2758452 ATTAATATAT
Statistics
Matches: 266, Mismatches: 43, Indels: 59
0.72 0.12 0.16
Matches are distributed among these distances:
25 13 0.05
26 3 0.01
27 5 0.02
28 29 0.11
29 60 0.23
30 122 0.46
31 25 0.09
32 9 0.03
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (30 bp):
AAATATATTTTTATAATTAAGATAAGAATA
Found at i:2758171 original size:25 final size:24
Alignment explanation
Indices: 2758130--2758180 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
2758120 TATTTCCTAA
2758130 TTAAAATAAGAATAAATATATATAT
1 TTAAAATAAGAATAAATATATA-AT
*
2758155 TTAAATTAA-AATGAAATATATAAT
1 TTAAAATAAGAAT-AAATATATAAT
2758179 TT
1 TT
2758181 GAAGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
TTAAAATAAGAATAAATATATAAT
Found at i:2758215 original size:84 final size:85
Alignment explanation
Indices: 2758101--2758339 Score: 220
Period size: 90 Copynumber: 2.8 Consensus size: 85
2758091 ATTTTTATAA
**
2758101 TTAAGATAAAAATAAA-ATATATTTCCTAATTAAAATAAGAATAAATATATATATTTAAATTAA-
1 TTAAGATAAAAATAAATATATATTTAATAATTAAAATAAGAATAAATATATATATTTAAATTAAG
* **
2758164 AATGA-AATATATAATTTGAA-G
66 AAT-ATAATATAT--GTAAAATG
* ***
2758185 TTAAGATAAGAATAAATA-ATATTTAATAATTTAACGCAAGAATATAATATATTTAATAATTTAA
1 TTAAGATAAAAATAAATATATATTTAATAA-TTAAAATAAGAATA-AATATA--T-AT-ATTTAA
2758249 ATTAAGAATATAATATATGTAAAATG
60 ATTAAGAATATAATATATGTAAAATG
* * * * * *
2758275 TTAAAATAAAAATAAATATATTTTTAAAAATTAAAATAATAATAAA-ATATATTTTTAAGTTAAG
1 TTAAGATAAAAATAAATATATATTTAATAATTAAAATAAGAATAAATATATATATTTAAATTAAG
2758339 A
66 A
2758340 TAGGAATAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 22
0.75 0.11 0.13
Matches are distributed among these distances:
84 35 0.28
85 14 0.11
86 7 0.06
88 4 0.03
89 7 0.06
90 39 0.31
91 19 0.15
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (85 bp):
TTAAGATAAAAATAAATATATATTTAATAATTAAAATAAGAATAAATATATATATTTAAATTAAG
AATATAATATATGTAAAATG
Found at i:2759155 original size:30 final size:31
Alignment explanation
Indices: 2759119--2759187 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 31
2759109 TTTTACTTTG
2759119 TATTTTTATA-TTTAATATATTAATAATTT-T
1 TATTTTTATATTTTAA-ATATTAATAATTTCT
*
2759149 TATTTTTATATTTTAAATTTTAATAATTTCT
1 TATTTTTATATTTTAAATATTAATAATTTCT
2759180 TAGTTTTT
1 TA-TTTTT
2759188 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 22 0.63
31 8 0.23
32 5 0.14
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (31 bp):
TATTTTTATATTTTAAATATTAATAATTTCT
Found at i:2759159 original size:23 final size:24
Alignment explanation
Indices: 2759120--2759164 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2759110 TTTACTTTGT
2759120 ATTTTTATATTTAATATATTAATA
1 ATTTTTATATTTAATATATTAATA
* *
2759144 ATTTTTAT-TTTTATATTTTAA
1 ATTTTTATATTTAATATATTAA
2759165 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTTTATATTTAATATATTAATA
Found at i:2761564 original size:2 final size:2
Alignment explanation
Indices: 2761557--2761632 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
2761547 AACCTATTCA
2761557 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
2761599 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
2761633 GTATGTATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2763570 original size:3 final size:3
Alignment explanation
Indices: 2763562--2763617 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
2763552 AACAAAAATG
* * *
2763562 TAA TAA TAA TAT TAA TGA T-A TAA TAA TAA TAA TATA TAA TTAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TAA
*
2763608 TTA TAA TAA T
1 TAA TAA TAA T
2763618 TTTTAACCCC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:2763584 original size:17 final size:16
Alignment explanation
Indices: 2763564--2763617 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
2763554 CAAAAATGTA
2763564 ATAATAATATTAATGAT
1 ATAATAATATTAAT-AT
*
2763581 ATAATAATAATAATAT
1 ATAATAATATTAATAT
*
2763597 ATAATTAATATTTATA-
1 ATAA-TAATATTAATAT
2763613 ATAAT
1 ATAAT
2763618 TTTTAACCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 1 0.03
16 10 0.30
17 22 0.67
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATAATAATATTAATAT
Found at i:2763586 original size:14 final size:14
Alignment explanation
Indices: 2763562--2763617 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
2763552 AACAAAAATG
*
2763562 TAATAATAATATTAA
1 TAAT-ATAATAATAA
*
2763577 TGATATAATAATAA
1 TAATATAATAATAA
2763591 TAATAT-ATAATTAA
1 TAATATAATAA-TAA
*
2763605 TATTTATAATAAT
1 TA-ATATAATAAT
2763618 TTTTAACCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.12
14 19 0.56
15 7 0.21
16 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:2763605 original size:20 final size:20
Alignment explanation
Indices: 2763562--2763617 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2763552 AACAAAAATG
* *
2763562 TAATAATAATATTAATGATA
1 TAATAATAATAATAATAATA
2763582 TAATAATAATAATATATAAT-
1 TAATAATAATAATA-ATAATA
* *
2763602 TAATATTTATAATAAT
1 TAATAATAATAATAAT
2763618 TTTTAACCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 25 0.81
21 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:2763999 original size:135 final size:135
Alignment explanation
Indices: 2763753--2764084 Score: 472
Period size: 135 Copynumber: 2.5 Consensus size: 135
2763743 GAACAGGTTA
* *
2763753 TTCTCATTATGAACTTCTTCTCTCT--TATGGACGAGTTCTTCTCATTATGAACTCTTCACTAAA
1 TTCTCATTATGAACTTCTTCTCTCTCGT-TGGATGAGTTCTTCTCATTATGAACTCTTCACTGAA
* * *
2763816 AATGTTGATCCCTCAAGCGAGGCATCACTGATTTGAAATGCTGTGAATCGAGTGCTAGGTCAAAC
65 AATGTTGATCCCTCAAGCGAGGCATCACTGATTCGAAATGCAGTGAATCGAGTGATAGGTCAAAC
2763881 AAGCTC
130 AAGCTC
*
2763887 TTCTCATTATGAACTTCTTCTCTCTCGTTGAATGAGTTCTTCTCATTATGAACTCTTCACTGAAA
1 TTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGAAA
* * * * *
2763952 ATGTTGATTCCTCAAGTGAGGCGTGACTGATTCGAAATGTCAG-GAATCGAGTGATAGGTCGAAC
66 ATGTTGATCCCTCAAGCGAGGCATCACTGATTCGAAATG-CAGTGAATCGAGTGATAGGTCAAAC
2764016 AAGCTC
130 AAGCTC
* * * * *
2764022 TTCTCATTATAAACCTCTTCTCCCTCTGTTGGATAAGTTCTTCTCATTATGAACTCTCCACTG
1 TTCTCATTATGAACTTCTTCTCTCTC-GTTGGATGAGTTCTTCTCATTATGAACTCTTCACTG
2764085 GAAACTCTGA
Statistics
Matches: 177, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
134 25 0.14
135 116 0.66
136 36 0.20
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (135 bp):
TTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGAAA
ATGTTGATCCCTCAAGCGAGGCATCACTGATTCGAAATGCAGTGAATCGAGTGATAGGTCAAACA
AGCTC
Found at i:2764226 original size:15 final size:16
Alignment explanation
Indices: 2764201--2764234 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2764191 CAAGTGAGGC
2764201 GTCACTGATTCGAAAT
1 GTCACTGATTCGAAAT
2764217 GTCA-TGATTCGAAAT
1 GTCACTGATTCGAAAT
2764232 GTC
1 GTC
2764235 GAACAAGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (16 bp):
GTCACTGATTCGAAAT
Found at i:2764810 original size:15 final size:15
Alignment explanation
Indices: 2764787--2764836 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2764777 AGACAAAAAT
*
2764787 TTGTTTCAAGAGAAA
1 TTGTCTCAAGAGAAA
*
2764802 TTGTCTCAA-A-AAC
1 TTGTCTCAAGAGAAA
*
2764815 TTGTTTCAAGAGAAA
1 TTGTCTCAAGAGAAA
*
2764830 CTGTCTC
1 TTGTCTC
2764837 GAGGGAGACA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 15 0.56
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (15 bp):
TTGTCTCAAGAGAAA
Found at i:2764820 original size:28 final size:28
Alignment explanation
Indices: 2764780--2764836 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2764770 TTAAGGGAGA
* *
2764780 CAAAAATTTGTTTCAAGAGAAATTGTCT
1 CAAAAACTTGTTTCAAGAGAAACTGTCT
2764808 CAAAAACTTGTTTCAAGAGAAACTGTCT
1 CAAAAACTTGTTTCAAGAGAAACTGTCT
2764836 C
1 C
2764837 GAGGGAGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (28 bp):
CAAAAACTTGTTTCAAGAGAAACTGTCT
Found at i:2764856 original size:36 final size:36
Alignment explanation
Indices: 2764810--2765090 Score: 211
Period size: 36 Copynumber: 8.1 Consensus size: 36
2764800 AATTGTCTCA
* *
2764810 AAAACTTGTTTCAAGAGAAACTGTCTCGAGGGAGAC
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
*
2764846 AAAATTTGTTTCAAGGGAAAC-GTTCTC-----A-A-
1 AAAATTTGTTTCAAGAGAAACTG-TCTCAAGGGAGAC
** *
2764875 AATTTTGTGTTTCAAGAGAAAC-GATCTTAAGGGAGAC
1 AAAATT-TGTTTCAAGAGAAACTG-TCTCAAGGGAGAC
* * *
2764912 AAAATTTGTTTCAAGGGAAAATGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
* *
2764948 AAAATTTGTTTCAAGGGAAAC-GTTTTCAA---AG--
1 AAAATTTGTTTCAAGAGAAACTG-TCTCAAGGGAGAC
* *
2764979 ---TTTATGTTTCAAGAGAAACTGTCTCAAGGGAAAC
1 AAAATT-TGTTTCAAGAGAAACTGTCTCAAGGGAGAC
*
2765013 AAAATTTTGTTTCAAAAGAAACTGTCTCAAGGGAGAC
1 AAAA-TTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
* * * * *
2765050 AAAATTTGTTTCAAGGGAAACTATCTAAAGCGAGAT
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
2765086 AAAAT
1 AAAAT
2765091 CTCCTGTTTC
Statistics
Matches: 195, Mismatches: 28, Indels: 44
0.73 0.10 0.16
Matches are distributed among these distances:
28 2 0.01
29 23 0.12
30 20 0.10
31 1 0.01
32 1 0.01
33 2 0.01
35 3 0.02
36 104 0.53
37 37 0.19
38 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
Found at i:2764875 original size:64 final size:66
Alignment explanation
Indices: 2764772--2764940 Score: 220
Period size: 66 Copynumber: 2.6 Consensus size: 66
2764762 AAACCATTTT
* *
2764772 AAGGGAGACAAAAATTTGTTTCAAGAGAAATTGTCTCAAAA-ACT-TGTTTCAAGAGAAACTG-T
1 AAGGGAGAC-AAAATTTGTTTCAAGGGAAAGTGTCTCAAAATACTGTGTTTCAAGAGAAAC-GAT
2764834 CTC
64 CTC
* **
2764837 GAGGGAGACAAAATTTGTTTCAAGGGAAACGT-TCTCAAAATTTTGTGTTTCAAGAGAAACGATC
1 AAGGGAGACAAAATTTGTTTCAAGGGAAA-GTGTCTCAAAATACTGTGTTTCAAGAGAAACGATC
*
2764901 TT
65 TC
*
2764903 AAGGGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAA
1 AAGGGAGACAAAATTTGTTTCAAGGGAAAGTGTCTCAA
2764941 GAGAGACAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
64 27 0.30
65 12 0.13
66 52 0.57
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (66 bp):
AAGGGAGACAAAATTTGTTTCAAGGGAAAGTGTCTCAAAATACTGTGTTTCAAGAGAAACGATCT
C
Found at i:2764929 original size:21 final size:21
Alignment explanation
Indices: 2764903--2764965 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
2764893 AAACGATCTT
2764903 AAGGGAGACAAAATTTGTTTC
1 AAGGGAGACAAAATTTGTTTC
*
2764924 AA-GG-G--AAAA--TGTCTC
1 AAGGGAGACAAAATTTGTTTC
*
2764939 AAGAGAGACAAAATTTGTTTC
1 AAGGGAGACAAAATTTGTTTC
2764960 AAGGGA
1 AAGGGA
2764966 AACGTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 7 0.22
16 1 0.03
17 5 0.16
19 5 0.16
20 2 0.06
21 12 0.38
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (21 bp):
AAGGGAGACAAAATTTGTTTC
Found at i:2765022 original size:102 final size:102
Alignment explanation
Indices: 2764810--2765070 Score: 391
Period size: 102 Copynumber: 2.6 Consensus size: 102
2764800 AATTGTCTCA
* *
2764810 AAAACTTGTTTCAAGAGAAACTGTCTCGAGGGAGACAAAATTTGTTTCAAGGGAAACGTTCTCAA
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACGTTCTCAA
* * * *
2764875 AATTTTGTGTTTCAAGAGAAACGATCTTAAGGGAGAC
66 AAGTTTATGTTTCAAGAGAAACGATCTCAAGGGAAAC
* * * *
2764912 AAAATTTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGTTTTC-A
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACGTTCTCAA
2764976 AAGTTTATGTTTCAAGAGAAACTG-TCTCAAGGGAAAC
66 AAGTTTATGTTTCAAGAGAAAC-GATCTCAAGGGAAAC
*
2765013 AAAATTTTGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1 AAAA-TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
2765071 TATCTAAAGC
Statistics
Matches: 143, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
101 36 0.25
102 107 0.75
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (102 bp):
AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACGTTCTCAA
AAGTTTATGTTTCAAGAGAAACGATCTCAAGGGAAAC
Found at i:2765033 original size:37 final size:37
Alignment explanation
Indices: 2764974--2765063 Score: 137
Period size: 37 Copynumber: 2.4 Consensus size: 37
2764964 GAAACGTTTT
* *
2764974 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAAA
1 CAAAATTT-TGTTTCAAAAGAAACTGTCTCAAGGGAAA
*
2765012 CAAAATTTTGTTTCAAAAGAAACTGTCTCAAGGGAGA
1 CAAAATTTTGTTTCAAAAGAAACTGTCTCAAGGGAAA
2765049 CAAAA-TTTGTTTCAA
1 CAAAATTTTGTTTCAA
2765064 GGGAAACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
36 10 0.20
37 32 0.65
38 7 0.14
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAACTGTCTCAAGGGAAA
Found at i:2765542 original size:40 final size:40
Alignment explanation
Indices: 2765054--2765519 Score: 623
Period size: 40 Copynumber: 11.7 Consensus size: 40
2765044 GGAGACAAAA
* * ** *
2765054 TTTGTTTCAAGG-GAAACTATCTAAAGCGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
** * * *
2765093 CCTGTTTCGAGGAAAACCAATCTTGAGCGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
** * * * *
2765133 AATGTTTCAAGAAAAAATAATCTTTAATGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
* * *
2765173 TCTGTTTCAAGGAAAAATAATCTTGAGTGTGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
*
2765213 TTTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
2765253 TATT-TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
1 T-TTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
* * *
2765293 TTTTTTTCAAGGAAAAACAATCTTGAATGAAATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
*
2765333 TTTGTTTCAAGGAAAAACAATCTTTAGTGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
* * *
2765373 TCTGTTTCAAGGAAAAACAATCTTTACTGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
* *
2765413 TATGTTTCAAGGAAAAATAATCTTGAGTGAGAT-AAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
* *
2765452 TATGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATCT
1 TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
2765492 TTTGTTTCAAGGAAAAACAATCTTGAGT
1 TTTGTTTCAAGGAAAAACAATCTTGAGT
2765520 CAAATGAAAT
Statistics
Matches: 379, Mismatches: 44, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
39 48 0.13
40 329 0.87
41 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (40 bp):
TTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT
Found at i:2771121 original size:90 final size:90
Alignment explanation
Indices: 2771020--2771199 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
2771010 ATATAGTCAG
2771020 TGCAGGACTTATACCTTTCTCCAATCTGTCCAAGAAATCTGCAACAGCAGCCTCAACATGGAACA
1 TGCAGGACTTATACCTTTCTCCAATCTGTCCAAGAAATCTGCAACAGCAGCCTCAACATGGAACA
2771085 AAGTCTTTGGAAATATCACTAGACC
66 AAGTCTTTGGAAATATCACTAGACC
2771110 TGCAGGACTTATACCTTTCTCCAATCTGTCCAAGAAATCTGCAACAGCAGCCTCAACATGGAACA
1 TGCAGGACTTATACCTTTCTCCAATCTGTCCAAGAAATCTGCAACAGCAGCCTCAACATGGAACA
2771175 AAGTCTTTGGAAATATCACTAGACC
66 AAGTCTTTGGAAATATCACTAGACC
2771200 ATTCATGATA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (90 bp):
TGCAGGACTTATACCTTTCTCCAATCTGTCCAAGAAATCTGCAACAGCAGCCTCAACATGGAACA
AAGTCTTTGGAAATATCACTAGACC
Found at i:2771602 original size:13 final size:13
Alignment explanation
Indices: 2771584--2771613 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2771574 ATTCTCTAAA
2771584 TATCCCAAATCTC
1 TATCCCAAATCTC
*
2771597 TATCCCAAATCTT
1 TATCCCAAATCTC
2771610 TATC
1 TATC
2771614 AGATCTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (13 bp):
TATCCCAAATCTC
Found at i:2772936 original size:16 final size:18
Alignment explanation
Indices: 2772915--2772952 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2772905 AACGTCTTTT
2772915 AAAAACA-ATTTTAAGA-
1 AAAAACATATTTTAAGAC
*
2772931 AAAAACATTTTTTAAGAC
1 AAAAACATATTTTAAGAC
2772949 AAAA
1 AAAA
2772953 GCTAGTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAACATATTTTAAGAC
Found at i:2773637 original size:2 final size:2
Alignment explanation
Indices: 2773630--2773673 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2773620 TAACCTATTC
2773630 AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT AT -T 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
2773669 AT AT A
1 AT AT A
2773674 AGTTAAACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2773659 original size:18 final size:18
Alignment explanation
Indices: 2773625--2773674 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
2773615 CAAAGTAACC
2773625 TATTCATATATAT-ATATA
1 TATT-ATATATATAATATA
2773643 TATTATATATATAATATA
1 TATTATATATATAATATA
2773661 T-TATATATATATAA
1 TAT-TATATATATAA
2773675 GTTAAACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATATATATAATATA
Found at i:2773661 original size:16 final size:17
Alignment explanation
Indices: 2773625--2773673 Score: 82
Period size: 16 Copynumber: 2.9 Consensus size: 17
2773615 CAAAGTAACC
2773625 TATTCATATATATATATA
1 TATT-ATATATATATATA
2773643 TATTATATATATA-ATA
1 TATTATATATATATATA
2773659 TATTATATATATATA
1 TATTATATATATATA
2773674 AGTTAAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.53
17 10 0.33
18 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATATATATATATA
Found at i:2774395 original size:15 final size:15
Alignment explanation
Indices: 2774375--2774426 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
2774365 TTTAAAACAA
2774375 ATCCTCTGCGCCGAT
1 ATCCTCTGCGCCGAT
2774390 ATCCTCTGCGCCGAT
1 ATCCTCTGCGCCGAT
* *
2774405 ATCCTCTGCGTCGTT
1 ATCCTCTGCGCCGAT
2774420 ATCCTCT
1 ATCCTCT
2774427 TCTTCTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.12, C:0.38, G:0.17, T:0.33
Consensus pattern (15 bp):
ATCCTCTGCGCCGAT
Found at i:2775675 original size:3 final size:3
Alignment explanation
Indices: 2775667--2775725 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
2775657 AACAAAAATG
* *
2775667 TAA TAA TAA TAT TAA TGA T-A TAA TAA TAA TAA TAA TATA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA
* *
2775713 TAT TTA TAA TAA T
1 TAA TAA TAA TAA T
2775726 TTTTAATCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:2775689 original size:17 final size:17
Alignment explanation
Indices: 2775669--2775714 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2775659 CAAAAATGTA
* *
2775669 ATAATAATATTAATGAT
1 ATAATAATAATAATAAT
2775686 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
2775703 AT-ATAATTAATA
1 ATAATAA-TAATA
2775715 TTTATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:2775692 original size:20 final size:19
Alignment explanation
Indices: 2775667--2775714 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
2775657 AACAAAAATG
*
2775667 TAATAATAATATTAATGATA
1 TAATAATAATAATAAT-ATA
2775687 TAATAATAATAATAATATA
1 TAATAATAATAATAATATA
2775706 TAATTAATA
1 TAA-TAATA
2775715 TTTATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATAATAATAATAATATA
Found at i:2775713 original size:14 final size:14
Alignment explanation
Indices: 2775670--2775714 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2775660 AAAAATGTAA
2775670 TAATAATAT-TAAT
1 TAATAATATATAAT
*
2775683 GATATAATA-ATAA-
1 TA-ATAATATATAAT
2775696 TAATAATATATAAT
1 TAATAATATATAAT
2775710 TAATA
1 TAATA
2775715 TTTATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 6 0.23
14 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TAATAATATATAAT
Found at i:2775713 original size:23 final size:23
Alignment explanation
Indices: 2775667--2775725 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
2775657 AACAAAAATG
* *
2775667 TAATAATAATATTAATGATATAA
1 TAATAATAATAATAATAATATAA
2775690 TAATAATAATAATATATAAT-TAA
1 TAATAATAATAATA-ATAATATAA
* *
2775713 TATTTATAATAAT
1 TAATAATAATAAT
2775726 TTTTAATCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAATAATAATAATAATATAA
Found at i:2777206 original size:30 final size:30
Alignment explanation
Indices: 2777170--2777231 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
2777160 TTCAAGGAGT
*
2777170 TATTAATAAAATACATTTGAGTTATTAAAA
1 TATTAATAAAATAAATTTGAGTTATTAAAA
2777200 TATTAATAAAATAAATTTGAGTTATTAAAA
1 TATTAATAAAATAAATTTGAGTTATTAAAA
2777230 TA
1 TA
2777232 AGAGCAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (30 bp):
TATTAATAAAATAAATTTGAGTTATTAAAA
Found at i:2778729 original size:30 final size:31
Alignment explanation
Indices: 2778695--2778770 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
2778685 AAGTTAAAGA
*
2778695 TAAGAATAATTAATAT-T-TAATAATTTAAGT
1 TAAGAATAA-TAATATATATAATAATTTAAAT
2778725 TAAGAAT-ATAATATATATAATAATTTAAAT
1 TAAGAATAATAATATATATAATAATTTAAAT
* *
2778755 TAATAAT-ATAGTATAT
1 TAAGAATAATAATATAT
2778771 GTAAAAAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 6 0.15
29 2 0.05
30 33 0.80
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (31 bp):
TAAGAATAATAATATATATAATAATTTAAAT
Found at i:2778775 original size:22 final size:22
Alignment explanation
Indices: 2778733--2778775 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2778723 GTTAAGAATA
*
2778733 TAATATATATAATAATTTAAAT
1 TAATATATATAATAATGTAAAT
*
2778755 TAATA-ATATAGTATATGTAAA
1 TAATATATATAATA-ATGTAAA
2778776 AAGTTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
TAATATATATAATAATGTAAAT
Found at i:2778838 original size:58 final size:56
Alignment explanation
Indices: 2778776--2778961 Score: 146
Period size: 58 Copynumber: 3.2 Consensus size: 56
2778766 TATATGTAAA
*
2778776 AAGTTAAGATAAAAATGAAATATAGTTTTAAAATTTAAGATAATAAAATATATTTTTT
1 AAGTTAAGATAAGAAT-AAATATA-TTTTAAAATTTAAGATAATAAAATATATTTTTT
** * * * **
2778834 AAGTTGTGGTAGGAATAAAATATATTTTATAAGCTAAGATAAGATTAAAATATATTTTTT
1 AAGTTAAGATAAGAAT-AAATATATTTTAAAATTTAAGAT-A-A-TAAAATATATTTTTT
* *
2778894 AA-CTAAGATAAGAATAACATATA-TTTAATATGTTAAGA-AA-AATTAATATATTTTTT
1 AAGTTAAGATAAGAATAA-ATATATTTTAAAAT-TTAAGATAATAA--AATATATTTTTT
*
2778950 AATATTAAGATA
1 AA-GTTAAGATA
2778962 TGATTTTAAG
Statistics
Matches: 100, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
54 2 0.02
56 15 0.15
57 14 0.14
58 33 0.33
59 19 0.19
60 17 0.17
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (56 bp):
AAGTTAAGATAAGAATAAATATATTTTAAAATTTAAGATAATAAAATATATTTTTT
Found at i:2778853 original size:30 final size:30
Alignment explanation
Indices: 2778817--2778919 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
2778807 AATTTAAGAT
* ** * *
2778817 AATAAAATATATTTTTTAAGTTGTGGTAGG
1 AATAAAATATATTTTTTAAGCTAAGATAAG
*
2778847 AATAAAATATATTTTATAAGCTAAGATAAG
1 AATAAAATATATTTTTTAAGCTAAGATAAG
*
2778877 ATTAAAATATATTTTTTAA-CTAAGATAAG
1 AATAAAATATATTTTTTAAGCTAAGATAAG
*
2778906 AATAACATATATTT
1 AATAAAATATATTT
2778920 AATATGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
29 22 0.35
30 41 0.65
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.40
Consensus pattern (30 bp):
AATAAAATATATTTTTTAAGCTAAGATAAG
Found at i:2778917 original size:59 final size:59
Alignment explanation
Indices: 2778819--2778951 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 59
2778809 TTTAAGATAA
* ** * * * *
2778819 TAAAATATATTTTTTAAGTTGTGGTAGGAATAAAATATATTTTATAAGCTAAGATAAGAT
1 TAAAATATATTTTTTAAGCTAAGATAAGAATAAAATATATTTAATAAGCTAAGA-AAAAT
* * *
2778879 TAAAATATATTTTTTAA-CTAAGATAAGAATAACATATATTTAATATGTTAAGAAAAAT
1 TAAAATATATTTTTTAAGCTAAGATAAGAATAAAATATATTTAATAAGCTAAGAAAAAT
2778937 T--AATATATTTTTTAA
1 TAAAATATATTTTTTAA
2778952 TATTAAGATA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
56 14 0.22
58 5 0.08
59 27 0.43
60 17 0.27
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (59 bp):
TAAAATATATTTTTTAAGCTAAGATAAGAATAAAATATATTTAATAAGCTAAGAAAAAT
Found at i:2783187 original size:21 final size:22
Alignment explanation
Indices: 2783153--2783193 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2783143 GGTTCTACGA
*
2783153 GGTCCTTTGAGACA-TATATGT
1 GGTCCTTCGAGACATTATATGT
*
2783174 GGTCCTTCGGGACATTATAT
1 GGTCCTTCGAGACATTATAT
2783194 ATGGCACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (22 bp):
GGTCCTTCGAGACATTATATGT
Done.