Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 26
Found at i:2265934 original size:36 final size:34
Alignment explanation
Indices: 2265885--2265987 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 34
2265875 TGTCTTTATC
*
2265885 TTTA-TTTTTTATTTTCTTTATATTTATATTTTTA
1 TTTACTTTTTTATTTTCTTTAT-TTTTTATTTTTA
* *
2265919 TTTACTTTTTATATTTTCTCTATTTTTT-TATTTTC
1 TTTACTTTTT-TATTTTCTTTATTTTTTAT-TTTTA
*
2265954 TTTATCTTGTTTTATTTACTTTATTTTTTATTTT
1 TTTA-CTT-TTTTATTTTCTTTATTTTTTATTTT
2265988 ATTCTCTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
34 5 0.09
35 17 0.29
36 32 0.55
37 4 0.07
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.76
Consensus pattern (34 bp):
TTTACTTTTTTATTTTCTTTATTTTTTATTTTTA
Found at i:2265980 original size:45 final size:46
Alignment explanation
Indices: 2265930--2266025 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 46
2265920 TTACTTTTTA
2265930 TATTTTCTCTATTTT-TT-TATTT-TCTTTATCTTG-TTTTATTTACTT
1 TATTTTCT-TATTTTATTCTATTTATC-TTAT-TTGTTTTTATTTACTT
* *
2265975 TATTTT-TTATTTTATTCTCTTTATCTTATTTGTTTTTCTTTACTT
1 TATTTTCTTATTTTATTCTATTTATCTTATTTGTTTTTATTTACTT
2266020 T-TTTTC
1 TATTTTC
2266026 CTAACACTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
43 6 0.14
44 10 0.23
45 26 0.59
46 2 0.05
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.74
Consensus pattern (46 bp):
TATTTTCTTATTTTATTCTATTTATCTTATTTGTTTTTATTTACTT
Found at i:2265997 original size:40 final size:41
Alignment explanation
Indices: 2265944--2266023 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
2265934 TTCTCTATTT
* *
2265944 TTTTATTTTCTTTATCTTGTTT-TATTTACTTTA-TTTTTTA
1 TTTTATTCTCTTTATCTTATTTGT-TTTACTTTACTTTTTTA
*
2265984 TTTTATTCTCTTTATCTTATTTGTTTTTCTTTACTTTTTT
1 TTTTATTCTCTTTATCTTATTTGTTTTACTTTACTTTTTT
2266024 TCCTAACACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (41 bp):
TTTTATTCTCTTTATCTTATTTGTTTTACTTTACTTTTTTA
Found at i:2268935 original size:29 final size:31
Alignment explanation
Indices: 2268854--2268931 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
2268844 TTAAAATTGT
2268854 TAAATTTAAATT-TTAAATAATATTTTATAAA
1 TAAATTTAAATTATTAAATAATATTTTAT-AA
* * *
2268885 AAAATTTAAATAATCAAATAAT-TTTTAT-A
1 TAAATTTAAATTATTAAATAATATTTTATAA
2268914 TAAA-TTAAATTATTAAAT
1 TAAATTTAAATTATTAAAT
2268932 TAATGTTGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 12 0.30
29 4 0.10
31 16 0.40
32 8 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
TAAATTTAAATTATTAAATAATATTTTATAA
Found at i:2269403 original size:150 final size:150
Alignment explanation
Indices: 2269126--2269458 Score: 443
Period size: 150 Copynumber: 2.2 Consensus size: 150
2269116 CTTAATCGGC
* * * * * * * *
2269126 TAAAATAAAATAGGTATTACATATTATATTAAACTACCTACTGGTTTGTTTGAAGTTTACTAATA
1 TAAAATAAAATAAGCACTACCTATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
* * * *
2269191 ATGTAAACAGTAAAATAAAATAGGCAATATCTATTACTTTAAAATATCTACCGGTTTATTTAAAT
66 ATGTAAACAGTAAAATAAAATAGGCAATATCTATTACGTTAAAATAGCTACCAGTTTATTTAAAG
*
2269256 GTTACTAATAATGTAAAC-A
131 GTTAATAATAATGTAAACGA
* * *
2269275 GTAAAATAAAATATGCACTACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAAT
1 -TAAAATAAAATAAGCACTACCTATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAAT
* * * * *
2269340 AATGTAAACGGTAAAATAAAATAGGCGATATCTATTACGTTAAACTAGCTATCAGTTTGTTTAAA
65 AATGTAAACAGTAAAATAAAATAGGCAATATCTATTACGTTAAAATAGCTACCAGTTTATTTAAA
*
2269405 GGTTAATAATATTGTAAACGA
130 GGTTAATAATAATGTAAACGA
*
2269426 TAAAATAAAATAAGCGCTACCTATTATGTTAAA
1 TAAAATAAAATAAGCACTACCTATTATGTTAAA
2269459 TAAGTGCTAC
Statistics
Matches: 158, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
150 157 0.99
151 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (150 bp):
TAAAATAAAATAAGCACTACCTATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACAGTAAAATAAAATAGGCAATATCTATTACGTTAAAATAGCTACCAGTTTATTTAAAG
GTTAATAATAATGTAAACGA
Found at i:2269450 original size:75 final size:75
Alignment explanation
Indices: 2269126--2269458 Score: 398
Period size: 75 Copynumber: 4.4 Consensus size: 75
2269116 CTTAATCGGC
* * * ** * * * *
2269126 TAAAATAAAATAGGTATTACATATTATATTAAACTACCTACTGGTTTGTTTGAAGTTTACTAATA
1 TAAAATAAAATAGGCAATACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAATA
2269191 ATGTAAACAG
66 ATGTAAACAG
* * * * *
2269201 TAAAATAAAATAGGCAATATCTATTACTTTAAAATATCTACCGGTTTATTTAAATGTTACTAATA
1 TAAAATAAAATAGGCAATACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAATA
2269266 ATGTAAACAG
66 ATGTAAACAG
* *
2269276 TAAAATAAAATATGCACTACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCAATACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAATA
*
2269341 ATGTAAACGG
66 ATGTAAACAG
* * * * * *
2269351 TAAAATAAAATAGGCGATATCTATTACGTTAAACTAGCTATCAGTTTGTTTAAAGGTTAATAATA
1 TAAAATAAAATAGGCAATACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAATA
*
2269416 TTGTAAAC-G
66 ATGTAAACAG
* ** *
2269425 ATAAAATAAAATAAGCGCTACCTATTATGTTAAA
1 -TAAAATAAAATAGGCAATACCTATTACGTTAAA
2269459 TAAGTGCTAC
Statistics
Matches: 223, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
74 1 0.00
75 222 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (75 bp):
TAAAATAAAATAGGCAATACCTATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACAG
Found at i:2269460 original size:23 final size:23
Alignment explanation
Indices: 2269433--2269481 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2269423 CGATAAAATA
*
2269433 AAATAAGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTACGTT
*
2269456 AAATAAGTGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
2269479 AAA
1 AAA
2269482 CTTGCTACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:2269648 original size:17 final size:17
Alignment explanation
Indices: 2269613--2269648 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2269603 CTCTAAAGAT
*
2269613 TAATAATAATATATTCA
1 TAATAATAATATATACA
*
2269630 TAATAATAATGTATACA
1 TAATAATAATATATACA
2269647 TA
1 TA
2269649 CTATCCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
TAATAATAATATATACA
Found at i:2270056 original size:107 final size:107
Alignment explanation
Indices: 2269838--2270126 Score: 318
Period size: 106 Copynumber: 2.7 Consensus size: 107
2269828 TTTGGACACA
* * * * * * ** * *
2269838 ACCTAGTATGTTAATATTTATTTATAACAAAATAAGAAATTAATTTATTTTGTTGTCGTTGGATT
1 ACCTAATATGTTGATA-ATATTAATAAAAAAATAAGTAATTAACATATTTTGTTATCGTCGGATT
*
2269903 TC-AGAGG-CTCCATTGGCTTAAACTTTAGTAACATTTTAGGCAT
65 TCTA-AGGCCT-CATTCGCTTAAACTTTAGTAACATTTTAGGCAT
* *
2269946 ACCTGATATGTTGATAATATTAATAAAAAAATAAGTAATTAACATATTTTTTTATCGTCGGATTT
1 ACCTAATATGTTGATAATATTAATAAAAAAATAAGTAATTAACATATTTTGTTATCGTCGGATTT
** *
2270011 CTAAGGCCTCA-TCGCTTAAACTTT-GATAATGTTTTAGGCGCT
66 CTAAGGCCTCATTCGCTTAAACTTTAG-TAACATTTTAGGC-AT
* * * *
2270053 ACCTAATATGTTGATAATATTGAT-AAAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTT
1 ACCTAATATGTTGATAATATTAATAAAAAAATAAGTAATTAACATATTTTGTTATCGTCGGATTT
2270117 CTAAGGCCTC
66 CTAAGGCCTC
2270127 CTCAGCTTTA
Statistics
Matches: 155, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
105 1 0.01
106 69 0.45
107 69 0.45
108 16 0.10
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (107 bp):
ACCTAATATGTTGATAATATTAATAAAAAAATAAGTAATTAACATATTTTGTTATCGTCGGATTT
CTAAGGCCTCATTCGCTTAAACTTTAGTAACATTTTAGGCAT
Found at i:2270371 original size:219 final size:220
Alignment explanation
Indices: 2269979--2270430 Score: 588
Period size: 219 Copynumber: 2.0 Consensus size: 220
2269969 TAAAAAAATA
* **
2269979 AGTAATTAACATATTTTTTTATCGTCGGATTTCTAAGGCCTCATCGCTTAAACTTTGATAATGTT
1 AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATCGCTTAAACTTTGATAACATT
* *
2270044 TTAGGCGCTACCTAATATGTTGATAATATTGATAAAAATTAAGTAATTAACCTATTTTGTTATCG
66 TTAGGCGATACCTAATATGTTG--AATA-T-ATAAAAATCAAGTAATTAACCTATTTTGTTATCG
* * * * * *
2270109 TCAGATTTCTAAGGCCTCCTCAGCTTTAAAAATGTGCTACCTATTACATTAAATAAGCTCTACTT
127 TCAGATTTCTAAGACCTCATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATAAGCACTACAT
* *
2270174 GTTATGTTATTATGGTTGATAATGTTTAT-
192 GTTATGTTATTATGATTGATAATATTT-TC
** *
2270203 AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGTTTCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATC-GCTTAAACTTTGATAACAT
* * **
2270268 TTTAGGTGATACCTAATATGTTG-ATA-ATACAAATCAAGTAATTAATTTATTTTGTTATCGTCA
65 TTTAGGCGATACCTAATATGTTGAATATATAAAAATCAAGTAATTAACCTATTTTGTTATCGTCA
* * * * *
2270331 GATTTCTAAGA-CTCTATCAGTTTTAAACAGGCGTTACCTATTACGTTACATAAGCACTACATGT
130 GATTTCTAAGACCTC-ATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATAAGCACTACATGT
2270395 TATGTTATTATGATTGATAATATTTTC
194 TATGTTATTATGATTGATAATATTTTC
2270422 AGTAATTAA
1 AGTAATTAA
2270431 TAGGTTATGT
Statistics
Matches: 200, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
218 4 0.02
219 114 0.57
222 3 0.01
224 42 0.21
225 37 0.19
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (220 bp):
AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCCTCATCGCTTAAACTTTGATAACATT
TTAGGCGATACCTAATATGTTGAATATATAAAAATCAAGTAATTAACCTATTTTGTTATCGTCAG
ATTTCTAAGACCTCATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATAAGCACTACATGTTA
TGTTATTATGATTGATAATATTTTC
Found at i:2271135 original size:5 final size:5
Alignment explanation
Indices: 2271120--2271216 Score: 58
Period size: 5 Copynumber: 19.2 Consensus size: 5
2271110 ACGCATTCAT
** *
2271120 ATAATA ATAAA ATAAA ATAAA AT-AA ATGGA A-AAA ATAAA CA-AAA GTTAAA
1 ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA -ATAAA -ATAAA
* * * *
2271170 AAAGAA ATAGAA A-ATA ATAAA ATAAA ATAAA ATACA ATACA ATAAA A
1 ATA-AA ATA-AA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
2271217 AAATAAGGTT
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
4 8 0.11
5 49 0.67
6 16 0.22
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:2271203 original size:18 final size:18
Alignment explanation
Indices: 2271122--2271203 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 18
2271112 GCATTCATAT
2271122 AATAATAAAATAAAATAA
1 AATAATAAAATAAAATAA
* *
2271140 AATAAATGGAAAAAATAAACAA
1 AAT-AAT--AAAATA-AAATAA
* *
2271162 AAGTTAA-AAAAGAAATAGAA
1 AA--TAATAAAATAAA-ATAA
2271182 AATAATAAAATAAAATAA
1 AATAATAAAATAAAATAA
2271200 AATA
1 AATA
2271204 CAATACAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
18 13 0.26
19 12 0.24
20 10 0.20
21 5 0.10
22 7 0.14
23 2 0.04
24 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAATAAAATAAAATAA
Found at i:2273382 original size:33 final size:35
Alignment explanation
Indices: 2273309--2273390 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 35
2273299 GGTCTTTGCT
* *
2273309 TTTCATGAGAAACATTTTCAAAGGTTTTTTCTTGTG
1 TTTCAAGAGAAACATTCTCAAAGG-TTTTTCTTGTG
2273345 TTTCAAGAGAAACGA-TCTCAAAGG-TTTT-TTGTG
1 TTTCAAGAGAAAC-ATTCTCAAAGGTTTTTCTTGTG
2273378 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
2273391 TGTCTCCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 18 0.42
34 4 0.09
36 20 0.47
37 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (35 bp):
TTTCAAGAGAAACATTCTCAAAGGTTTTTCTTGTG
Found at i:2273594 original size:37 final size:37
Alignment explanation
Indices: 2273542--2273651 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
2273532 ATTCACAGAT
* *
2273542 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGAAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* *
2273579 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
*
2273616 TTTGTTTCAAGGGAAACTGTCTCAAGCGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
2273652 CTTGGAAACT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
Found at i:2273602 original size:102 final size:103
Alignment explanation
Indices: 2273376--2273632 Score: 308
Period size: 103 Copynumber: 2.5 Consensus size: 103
2273366 AGGTTTTTTG
* * *
2273376 TGTTTCAAGAGAAACTGTCTCCATGGAGGCAAATTTTTTTTCAAGAGAAACATATTCAAAGATTG
1 TGTTTCAAGAGAAACTGTCTCAATGGAGACAAATTTTATTTCAAGAGAAACATATTCAAAGATTG
* * *
2273441 GTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
66 GTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATT
* * * *
2273479 AGTTCCAAAAGAAACTGTCTCAATGGAGACGAAA-TTTATTTCAAG-GAAAACATATTCACAGAT
1 TGTTTCAAGAGAAACTGTCTCAATGGAGAC-AAATTTTATTTCAAGAG-AAACATATTCAAAGAT
*
2273542 T-TTGTTTCAA-AGGAAACTGTCTCAAGAGAGAAAAAAATT
64 TGGTGTTTCAAGA-GAAACTGTCTCAAGAGAGAAAAAAATT
* * *
2273581 TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAATATTTTGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAACTGTCTCAATG-GAGACAA-ATTTTATTTCAAGAGAAAC
2273633 TGTCTCAAGC
Statistics
Matches: 131, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
101 4 0.03
102 58 0.44
103 65 0.50
104 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (103 bp):
TGTTTCAAGAGAAACTGTCTCAATGGAGACAAATTTTATTTCAAGAGAAACATATTCAAAGATTG
GTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATT
Found at i:2274456 original size:32 final size:31
Alignment explanation
Indices: 2274420--2274517 Score: 124
Period size: 32 Copynumber: 3.1 Consensus size: 31
2274410 CCAAAGATGC
* *
2274420 CCCAATATTCGATGTTGAATCTTAAAAAATGG
1 CCCAACATTTGATGTTGAATCTTAAAAAAT-G
* *
2274452 CCCAACATTTGATGTTAAATCTCAAAAAATG
1 CCCAACATTTGATGTTGAATCTTAAAAAATG
* *
2274483 CCTCAACATTTGATGTTGAATCTTCAAAGATG
1 CC-CAACATTTGATGTTGAATCTTAAAAAATG
2274515 CCC
1 CCC
2274518 TCATTGTTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 4 0.07
32 53 0.93
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (31 bp):
CCCAACATTTGATGTTGAATCTTAAAAAATG
Found at i:2275625 original size:27 final size:27
Alignment explanation
Indices: 2275581--2275634 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2275571 TTTTTCTTCA
**
2275581 ATTTTCCTTTGTTTTTTTAT-TTTTTT
1 ATTTTCCTTTGCCTTTTTATCTTTTTT
*
2275607 ATTTTCTCTTTGCCTTTTTCTCTTTTTT
1 ATTTTC-CTTTGCCTTTTTATCTTTTTT
2275635 TCTGACTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.26
27 11 0.48
28 6 0.26
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.76
Consensus pattern (27 bp):
ATTTTCCTTTGCCTTTTTATCTTTTTT
Found at i:2278709 original size:2 final size:2
Alignment explanation
Indices: 2278704--2278749 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2278694 AATAAGAAAC
2278704 AT AT AT AT AT AT AT AT A- 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
2278745 AT AT A
1 AT AT A
2278750 CACACACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2278835 original size:20 final size:20
Alignment explanation
Indices: 2278812--2278854 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2278802 GTTAAAAAAG
*
2278812 AAATAGAAAATAATAAAATA
1 AAATACAAAATAATAAAATA
* *
2278832 AAATACAATATAATATAATA
1 AAATACAAAATAATAAAATA
2278852 AAA
1 AAA
2278855 AAATAAGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATACAAAATAATAAAATA
Found at i:2279479 original size:97 final size:97
Alignment explanation
Indices: 2279313--2279507 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
2279303 CAACTTCTCC
2279313 ATCAGTACATCTTAAGGTCTTAAGGTGAAAAGGACTTGGGCATTGGAAGAAATGATGGAGGCAAC
1 ATCAGTACATCTTAAGGTCTTAAGGTGAAAAGGACTTGGGCATTGGAAGAAATGATGGAGGCAAC
2279378 ACATTCCTAACTCCACGTGATATCCCATCAAG
66 ACATTCCTAACTCCACGTGATATCCCATCAAG
2279410 ATCAGTACATCTTAAGGTCTTAAGGTGAAAAGGACTTGGGCATTGGAAGAAATGATGGAGGCAAC
1 ATCAGTACATCTTAAGGTCTTAAGGTGAAAAGGACTTGGGCATTGGAAGAAATGATGGAGGCAAC
2279475 ACATTCCTAACTCCACGTGATATCCCATCAAG
66 ACATTCCTAACTCCACGTGATATCCCATCAAG
2279507 A
1 A
2279508 ACCACTACGT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (97 bp):
ATCAGTACATCTTAAGGTCTTAAGGTGAAAAGGACTTGGGCATTGGAAGAAATGATGGAGGCAAC
ACATTCCTAACTCCACGTGATATCCCATCAAG
Found at i:2291302 original size:15 final size:16
Alignment explanation
Indices: 2291267--2291306 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2291257 ATGCTACTAT
2291267 ATAAAAATGTGAATATA
1 ATAAAAATGT-AATATA
*
2291284 ATAAAAATGT-ATTTA
1 ATAAAAATGTAATATA
2291299 ATAAAAAT
1 ATAAAAAT
2291307 AAACTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
17 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAAAAATGTAATATA
Found at i:2299259 original size:2 final size:2
Alignment explanation
Indices: 2299252--2299294 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
2299242 ATACCTTAAC
*
2299252 AT AT AT AT AT AT AT ACT -T A- AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
2299293 AT
1 AT
2299295 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2299272 original size:21 final size:22
Alignment explanation
Indices: 2299240--2299287 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
2299230 TTTATGTTAA
2299240 ATATACCTTAACATATATATAT
1 ATATACCTTAACATATATATAT
2299262 ATATA-CTTAACATATATATAT
1 ATATACCTTAACATATATATAT
2299283 ATATA
1 ATATA
2299288 TATATATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATACCTTAACATATATATAT
Found at i:2299299 original size:2 final size:2
Alignment explanation
Indices: 2299294--2299319 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2299284 TATATATATA
2299294 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2299320 GGGGGGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2299687 original size:21 final size:20
Alignment explanation
Indices: 2299649--2299688 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2299639 CAACTCATCT
*
2299649 CCTTCCCCATGCGTTTCAGC
1 CCTTCCCCATGCGCTTCAGC
*
2299669 CCTTTCCCATGCAGCTTCAG
1 CCTTCCCCATGC-GCTTCAG
2299689 ATTCCCATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.12, C:0.42, G:0.15, T:0.30
Consensus pattern (20 bp):
CCTTCCCCATGCGCTTCAGC
Found at i:2299839 original size:16 final size:16
Alignment explanation
Indices: 2299818--2299858 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2299808 AAAAGATTGA
2299818 AGGAGGGAGCAATCAC
1 AGGAGGGAGCAATCAC
*
2299834 AGGAGGGAGCTATCAC
1 AGGAGGGAGCAATCAC
2299850 --GAGGGAGCA
1 AGGAGGGAGCA
2299859 TTCGGGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.17, G:0.41, T:0.07
Consensus pattern (16 bp):
AGGAGGGAGCAATCAC
Found at i:2300370 original size:19 final size:19
Alignment explanation
Indices: 2300346--2300388 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2300336 AACAATAACT
*
2300346 TTAATAGTATTTATTA-TAA
1 TTAATAATA-TTATTAGTAA
*
2300365 TTAATAATATTCTTAGTAA
1 TTAATAATATTATTAGTAA
2300384 TTAAT
1 TTAAT
2300389 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
TTAATAATATTATTAGTAA
Found at i:2300665 original size:19 final size:20
Alignment explanation
Indices: 2300638--2300675 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2300628 AAAGAAAATA
*
2300638 TGAGTTACA-ATTAATGGTT
1 TGAGGTACATATTAATGGTT
*
2300657 TGAGGTACATATTTATGGT
1 TGAGGTACATATTAATGGT
2300676 ATGTCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (20 bp):
TGAGGTACATATTAATGGTT
Found at i:2302831 original size:181 final size:182
Alignment explanation
Indices: 2302484--2302847 Score: 721
Period size: 181 Copynumber: 2.0 Consensus size: 182
2302474 AGTACCAAAA
2302484 TGTCATATCCCAATAGCGAGTGTGGTGAAAGAGACATACTTTAGGTTGACTAAAGTTTGGTTTGA
1 TGTCATATCCCAATAGCGAGTGTGGTGAAAGAGACATACTTTAGGTTGACTAAAGTTTGGTTTGA
2302549 TAAAGGGAAAGAGATTGAGTGTCTGATAAATATAGGTAAAATTTAAGCTCAGATAGTGGTGGAAG
66 TAAAGGGAAAGAGATTGAGTGTCTGATAAATATAGGTAAAATTTAAGCTCAGATAGTGGTGGAAG
2302614 TAATGGAAGAAAATGAGCAATTGAAAACCTCAATGTTTGTTCATGACTTCTG
131 TAATGGAAGAAAATGAGCAATTGAAAACCTCAATGTTTGTTCATGACTTCTG
2302666 TGTCATATCCCAATAGCGAGTGTGGTGAAAGAGACATACTTTAGGTTGACTAAAGTTTGGTTTGA
1 TGTCATATCCCAATAGCGAGTGTGGTGAAAGAGACATACTTTAGGTTGACTAAAGTTTGGTTTGA
2302731 TAAAGGGAAAGAGATTGA-TGTCTGATAAATATAGGTAAAATTTAAGCTCAGATAGTGGTGGAAG
66 TAAAGGGAAAGAGATTGAGTGTCTGATAAATATAGGTAAAATTTAAGCTCAGATAGTGGTGGAAG
2302795 TAATGGAAGAAAATGAGCAATTGAAAACCTCAATGTTTGTTCATGACTTCTG
131 TAATGGAAGAAAATGAGCAATTGAAAACCTCAATGTTTGTTCATGACTTCTG
2302847 T
1 T
2302848 AAGCACCATT
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 99 0.54
182 83 0.46
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (182 bp):
TGTCATATCCCAATAGCGAGTGTGGTGAAAGAGACATACTTTAGGTTGACTAAAGTTTGGTTTGA
TAAAGGGAAAGAGATTGAGTGTCTGATAAATATAGGTAAAATTTAAGCTCAGATAGTGGTGGAAG
TAATGGAAGAAAATGAGCAATTGAAAACCTCAATGTTTGTTCATGACTTCTG
Found at i:2311160 original size:26 final size:29
Alignment explanation
Indices: 2311131--2311186 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 29
2311121 TTCCATTTTC
2311131 ACATCT-TTTTTTTTC-TTTT-TTTTCGA
1 ACATCTCTTTTTTTTCTTTTTCTTTTCGA
2311157 ACATCTCTTTTTTTTCTTTTTCTTTTCGA
1 ACATCTCTTTTTTTTCTTTTTCTTTTCGA
2311186 A
1 A
2311187 ATGTTGCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.22
27 9 0.33
28 4 0.15
29 8 0.30
ACGTcount: A:0.12, C:0.18, G:0.04, T:0.66
Consensus pattern (29 bp):
ACATCTCTTTTTTTTCTTTTTCTTTTCGA
Found at i:2311169 original size:29 final size:30
Alignment explanation
Indices: 2311136--2311212 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
2311126 TTTTCACATC
2311136 TTTTTTTTTCTTTTTTTTCGAACAT-CT-CT
1 TTTTTTTTTCTTTTTTTTCGAA-ATGCTGCT
* *
2311165 TTTTTTTCTT-TTTCTTTTCGAAATGTTGCT
1 TTTTTTT-TTCTTTTTTTTCGAAATGCTGCT
* *
2311195 GTTTTTTTCCTTTTTTTT
1 TTTTTTTTTCTTTTTTTT
2311213 TCATGGAGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.05
29 20 0.51
30 17 0.44
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.71
Consensus pattern (30 bp):
TTTTTTTTTCTTTTTTTTCGAAATGCTGCT
Found at i:2318912 original size:7 final size:7
Alignment explanation
Indices: 2318900--2318929 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2318890 CTTTACATTA
2318900 TATTCTT
1 TATTCTT
*
2318907 TATTCTA
1 TATTCTT
2318914 TATTCTT
1 TATTCTT
2318921 TATTCTT
1 TATTCTT
2318928 TA
1 TA
2318930 CATTCCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTCTT
Found at i:2318923 original size:14 final size:14
Alignment explanation
Indices: 2318898--2318926 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2318888 ATCTTTACAT
2318898 TATATTCTTTATTC
1 TATATTCTTTATTC
2318912 TATATTCTTTATTC
1 TATATTCTTTATTC
2318926 T
1 T
2318927 TTACATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATTCTTTATTC
Found at i:2322255 original size:14 final size:13
Alignment explanation
Indices: 2322234--2322317 Score: 56
Period size: 13 Copynumber: 6.8 Consensus size: 13
2322224 TACTATGCCT
2322234 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
2322247 AAGAAAG-AAAG-A
1 AA-AAAGAAAAGAA
2322259 AAAAAG--AAGAA
1 AAAAAGAAAAGAA
*
2322270 AAATA-AAAAGAA
1 AAAAAGAAAAGAA
2322282 AAATAA-AAAA-AA
1 AAA-AAGAAAAGAA
* * *
2322294 TAAAATAAAATAA
1 AAAAAGAAAAGAA
*
2322307 AAAAGGAAAAG
1 AAAAAGAAAAG
2322318 GAAATGAGAG
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.05
11 11 0.19
12 19 0.33
13 20 0.35
14 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:2322265 original size:15 final size:14
Alignment explanation
Indices: 2322236--2322292 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2322226 CTATGCCTAA
*
2322236 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
2322250 AAAGAAAGAAAAAAG
1 AAAGAAA-AAAAAAG
2322265 -AAGAAAAATAAAAAG
1 AAAG-AAAA-AAAAAG
2322280 AAA-AATAAAAAAA
1 AAAGAA-AAAAAAA
2322293 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
15 17 0.46
16 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:2322268 original size:23 final size:22
Alignment explanation
Indices: 2322254--2322298 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2322244 GAAAAGAAAG
2322254 AAAGAAAAAAGAAGAAAAATAA
1 AAAGAAAAAAGAAGAAAAATAA
2322276 AAAGAAAAATA-AA-AAAAATAA
1 AAAGAAAAA-AGAAGAAAAATAA
2322297 AA
1 AA
2322299 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 11 0.50
23 1 0.05
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (22 bp):
AAAGAAAAAAGAAGAAAAATAA
Found at i:2322282 original size:22 final size:21
Alignment explanation
Indices: 2322254--2322310 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
2322244 GAAAAGAAAG
2322254 AAAGAAAAA-AGAAGAAAAATAA
1 AAAGAAAAATA-AA-AAAAATAA
2322276 AAAGAAAAATAAAAAAAAT-A
1 AAAGAAAAATAAAAAAAATAA
*
2322296 AAA-TAAAATAAAAAA
1 AAAGAAAAATAAAAAA
2322311 GGAAAAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 11 0.33
20 4 0.12
21 6 0.18
22 11 0.33
23 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (21 bp):
AAAGAAAAATAAAAAAAATAA
Found at i:2322303 original size:10 final size:9
Alignment explanation
Indices: 2322258--2322310 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
2322248 AGAAAGAAAG
*
2322258 AAAAAAGAAG
1 AAAAAA-AAT
2322268 AAAAATAAA-
1 AAAAA-AAAT
*
2322277 AAGAAAAAT
1 AAAAAAAAT
2322286 AAAAAAAAT
1 AAAAAAAAT
2322295 AAAATAAAAT
1 AAAA-AAAAT
2322305 AAAAAA
1 AAAAAA
2322311 GGAAAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 3 0.08
9 18 0.47
10 16 0.42
11 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:2323316 original size:91 final size:91
Alignment explanation
Indices: 2323160--2323520 Score: 514
Period size: 91 Copynumber: 4.0 Consensus size: 91
2323150 AATATAAACC
* *
2323160 AATCAACATTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATCTAACGAGGGAGAAGAAGTTCA
1 AATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* *
2323225 TAATAAGAATAACTTGTTCGACCTTG
66 TAATAAGAAGAACTTGTTCAACCTTG
* * * *
2323251 GATCAAAATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
1 AATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* *
2323316 TAATGAGAAGAACTTGTTCAACATTG
66 TAATAAGAAGAACTTGTTCAACCTTG
* * *
2323342 AATCAACATTTCCAGTGGAGAGTTCATAGTGAGAA-AAGTTTATCCAACGAGGGAGAAGAAGTTC
1 AATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAA-CTCATCCAACGAGGGAGAAGAAGTTC
*
2323406 ATAAT---AAGAACTTGTTCAACGTTG
65 ATAATAAGAAGAACTTGTTCAACCTTG
* * * *
2323430 AATCAACATTTCCAGTGGGGAGTTCATAATGATAAGAACTCATCGAACGAGGGAGAAGAAGTTTA
1 AATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
*
2323495 TAATGAGAAGAACTTGTTCAACCTTG
66 TAATAAGAAGAACTTGTTCAACCTTG
2323521 GTTCAATTTC
Statistics
Matches: 239, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
88 77 0.32
89 2 0.01
90 2 0.01
91 158 0.66
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (91 bp):
AATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
TAATAAGAAGAACTTGTTCAACCTTG
Found at i:2323500 original size:179 final size:180
Alignment explanation
Indices: 2323160--2323516 Score: 538
Period size: 179 Copynumber: 2.0 Consensus size: 180
2323150 AATATAAACC
*
2323160 AATCAACATTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATCTAACGAGGGAGAAGAAGTTCA
1 AATCAACATTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* * *
2323225 TAATAAGAATAACTTGTTCGACCTTGGATCAAAATTTTCAATGGAGAGTTCATAATGAGAAGAAC
66 TAATAAG-A-AACTTGTTCAACCTTGAATCAAAATTTCCAATGGAGAGTTCATAATGAGAAGAAC
2323290 TCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTG
129 TCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTG
** * *
2323342 AATCAACATTTCCAGTGGAGAGTTCATAGTGAGAA-AAGTTTATCCAACGAGGGAGAAGAAGTTC
1 AATCAACATTTCCAGTGGAGAGTTCATAACGAGAAGAA-CTCATCCAACGAGGGAGAAGAAGTTC
* * * * *
2323406 ATAATAAG-AACTTGTTCAACGTTGAATCAACATTTCCAGTGGGGAGTTCATAATGATAAGAACT
65 ATAATAAGAAACTTGTTCAACCTTGAATCAAAATTTCCAATGGAGAGTTCATAATGAGAAGAACT
* *
2323470 CATCGAACGAGGGAGAAGAAGTTTATAATGAGAAGAACTTGTTCAAC
130 CATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
2323517 CTTGGTTCAA
Statistics
Matches: 159, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
179 93 0.58
181 2 0.01
182 64 0.40
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (180 bp):
AATCAACATTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
TAATAAGAAACTTGTTCAACCTTGAATCAAAATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
ATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTG
Found at i:2331033 original size:17 final size:17
Alignment explanation
Indices: 2331008--2331047 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2330998 GTATGTTGTT
*
2331008 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
2331025 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
2331042 CATTTA
1 CATTTA
2331048 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:2331074 original size:17 final size:17
Alignment explanation
Indices: 2331054--2331112 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2331044 TTTAGGGAAG
2331054 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
2331071 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
2331087 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
2331104 TAGTTCATT
1 TAGTTCATT
2331113 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:2331126 original size:18 final size:18
Alignment explanation
Indices: 2331103--2331148 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2331093 ATTCATGCAT
2331103 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
* *
2331121 TTAGTTTATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
2331139 TTATTTCATT
1 TTAGTTCATT
2331149 AATCAAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2334760 original size:17 final size:17
Alignment explanation
Indices: 2334721--2334762 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2334711 AAGTATGTTG
* *
2334721 TTCATTAAAGCATGTGT
1 TTCATTTAAGCATGTAT
*
2334738 TGCATTTAAGCATGTAT
1 TTCATTTAAGCATGTAT
2334755 TTCATTTA
1 TTCATTTA
2334763 GGGAAGTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (17 bp):
TTCATTTAAGCATGTAT
Found at i:2334789 original size:17 final size:17
Alignment explanation
Indices: 2334769--2334827 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2334759 TTTAGGGAAG
2334769 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
2334786 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
2334802 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
2334819 TAGTTCATT
1 TAGTTCATT
2334828 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:2334841 original size:18 final size:18
Alignment explanation
Indices: 2334818--2334863 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2334808 ATTCATGCAT
2334818 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
2334836 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
2334854 TTATTTCATT
1 TTAGTTCATT
2334864 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2338980 original size:10 final size:9
Alignment explanation
Indices: 2338959--2339044 Score: 54
Period size: 8 Copynumber: 9.3 Consensus size: 9
2338949 TAATTATTAT
2338959 TATATAAGTA
1 TATATAA-TA
2338969 TATAGTAATA
1 TATA-TAATA
2338979 TATATAA-A
1 TATATAATA
2338987 TATAT-ATA
1 TATATAATA
*
2338995 TAAAGTAATA
1 TATA-TAATA
*
2339005 TGATATAATG
1 T-ATATAATA
* *
2339015 TA-AAAATGG
1 TATATAAT-A
2339024 TAATATAATA
1 T-ATATAATA
2339034 TA-ATAATA
1 TATATAATA
2339042 TAT
1 TAT
2339045 GTGTACGTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
7 1 0.02
8 22 0.36
9 8 0.13
10 21 0.34
11 9 0.15
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.38
Consensus pattern (9 bp):
TATATAATA
Found at i:2339145 original size:5 final size:5
Alignment explanation
Indices: 2339138--2339181 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
2339128 GGGGATATAT
*
2339138 ATTAT ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTA
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTA
2339182 TAAATGATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAC
Found at i:2343029 original size:66 final size:65
Alignment explanation
Indices: 2342914--2343095 Score: 204
Period size: 66 Copynumber: 2.8 Consensus size: 65
2342904 GGGTATGATG
** * * *
2342914 GTTTCAAGAGAAACCGTTTCAAGAGAGACAAAATATGTTTCAAGGGAAAC-AATCTCAAAGGTTG
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT-TATTTCAAGGGAAACAAAT-TCAAAGATTG
*
2342978 GT
64 GA
* * * *
2342980 TTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCCAGTGAAACAAATTCAAAGATTGG
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT-ATTTCAAGGGAAACAAATTCAAAGATTGG
2343045 A
65 A
* * *
2343046 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTATTTCAAGGGAAAC
2343096 TGTCCAAGAG
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
65 1 0.01
66 90 0.94
67 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (65 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTATTTCAAGGGAAACAAATTCAAAGATTGGA
Found at i:2343131 original size:102 final size:102
Alignment explanation
Indices: 2342981--2343205 Score: 337
Period size: 102 Copynumber: 2.2 Consensus size: 102
2342971 AAGGTTGGTT
* *
2342981 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCCAGTGAAACAAATTCAAAGATTGGA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGATTGGA
2343046 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
66 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
* * ** * *
2343083 TTTCAAGGGAAACTGTC-CAAGAGATACAAAATTTTGTTTCAAGGGAAACATATTCAAAGATTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAAACAAATTCAAAGATTGG
*
2343147 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
65 AGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
2343185 TTTCAAGGGAAACATAT-TCAA
1 TTTCAAGGGAAAC-TATCTCAA
2343206 ATATTGGTGT
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
101 13 0.12
102 92 0.84
103 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (102 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGATTGGA
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
Found at i:2343187 original size:66 final size:66
Alignment explanation
Indices: 2343081--2343783 Score: 907
Period size: 66 Copynumber: 10.6 Consensus size: 66
2343071 AGACAAAATT
* * *
2343081 TGTTTCAAGGGAAACTGTC-CAAGAGATACAAAATTTTGTTTCAAGGGAAACATATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAGATTCAAAGATT
2343145 TG
65 TG
* * * *
2343147 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAATATTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
2343212 G
66 G
* * * *
2343213 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGCGAAACATATTCAAAGATTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
2343278 G
66 G
* * * * *
2343279 TGTTTCAAGGGAAACTGTCTCAACAGAGATAAAGTTTGATTCAAGGGAAAC-GATCTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATT
2343343 TG
65 TG
* * * *
2343345 TGTTTCAAGAGAAACTGTCGCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
2343410 G
66 G
* *
2343411 TGTTTCAAGAGAAACTGTCTCAAGAGATACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
2343476 G
66 G
* * *
2343477 TGTTGCAAGAGAAAATGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGA-TT
2343542 TG
65 TG
* * * * *
2343544 TGTTTCAAGGGAAGTA-T-TCTCAAGGGAGATAAAATTTGTTTCAAGAGAAACAGACTCAAAGAT
1 TGTTTCAAGAGAA--ACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGA-
2343607 TTTG
63 TTTG
* *
2343611 TGTTTCAAGAGAAACTGTCTTAA-AGGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATT
*
2343675 TA
65 TG
* * * * *
2343677 AGTTTCAAGAAAAACTGCCTCAAGAGAGATAAAATTTATTTCAAGGGAAACAGATTCAAAGA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
2343741 G
66 G
* * *
2343742 ATGTTTTAA-AGGAAACTATCTCAAGAGAGACAAAATTCGTTT
1 -TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATTTGTTT
2343784 TGATTAAAAA
Statistics
Matches: 564, Mismatches: 61, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
65 6 0.01
66 428 0.76
67 128 0.23
68 1 0.00
69 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
G
Found at i:2343206 original size:168 final size:168
Alignment explanation
Indices: 2342914--2343263 Score: 479
Period size: 168 Copynumber: 2.1 Consensus size: 168
2342904 GGGTATGATG
* *
2342914 GTTTCAAGAGAAACCGTTTCAAGAGAGACAAAATATGTTTCAAGGGAAACAATCTCAAAGGTTGG
1 GTTTCAAGAGAAACCGTTCCAAGAGAGACAAAATATGTTTCAAGGGAAACAATCTCAAAGATTGG
* * * *
2342979 TTTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCCAGTGAAACAAATTCAAAGATTG
66 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGATTG
*
2343044 GAGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
131 GAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
2343082 GTTTCAAGGGAAACTG-TCCAAGAGATACAAAATTTTGTTTCAAGGGAAACATAT-TCAAAGATT
1 GTTTCAAGAGAAACCGTTCCAAGAGAGACAAAA-TATGTTTCAAGGGAAACA-ATCTCAAAGATT
* * * ** * *
2343145 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAATAT
64 GGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGAT
* *
2343210 TGGTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
129 TGGAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
2343250 GTTTCAAGCGAAAC
1 GTTTCAAGAGAAAC
2343264 ATATTCAAAG
Statistics
Matches: 159, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
167 14 0.09
168 143 0.90
169 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (168 bp):
GTTTCAAGAGAAACCGTTCCAAGAGAGACAAAATATGTTTCAAGGGAAACAATCTCAAAGATTGG
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGATTG
GAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:2343389 original size:234 final size:229
Alignment explanation
Indices: 2342914--2343359 Score: 576
Period size: 234 Copynumber: 1.9 Consensus size: 229
2342904 GGGTATGATG
* *
2342914 GTTTCAAGAGAAACCGTTTCAAGAGAGACAAAATATGTTTCAAGGGAAACAATCTCAAAGGTTGG
1 GTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAATCTCAAAGATTGG
* * *
2342979 TTTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCCAGTGAAACAAATTCAAAGATTG
66 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGCGAAACAAATTCAAAGATTG
** *
2343044 GAGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCCAAGAGATA
131 GAGTTTCAAGAGAAACTGTCTCAACAGAGACAAAATTTGATTCAAGGGAAACTGTCCAAGAGAT-
* * * *
2343109 CAAAATTTTGTTTCAAGGGAAACATATTCAAAGATTTGT
195 ----ATTGTGTTTCAAGAGAAACATATGCAAAGAATTGT
* * * *
2343148 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATAT-TCAAATATTG
1 GTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATATGTTTCAAGGGAAACA-ATCTCAAAGATTG
* ** *
2343212 GTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGCGAAACATATTCAAAGATT
65 GTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGCGAAACAAATTCAAAGATT
* * * *
2343277 GGTGTTTCAAGGGAAACTGTCTCAACAGAGATAAAGTTTGATTCAAGGGAAAC-GATCTCAA-AG
130 GGAGTTTCAAGAGAAACTGTCTCAACAGAGACAAAATTTGATTCAAGGGAAACTG-TC-CAAGAG
2343340 AT-TTGTGTTTCAAGAGAAAC
193 ATATTGTGTTTCAAGAGAAAC
2343360 TGTCGCAAGG
Statistics
Matches: 187, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
228 16 0.09
233 1 0.01
234 165 0.88
235 5 0.03
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (229 bp):
GTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAATCTCAAAGATTGG
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGCGAAACAAATTCAAAGATTG
GAGTTTCAAGAGAAACTGTCTCAACAGAGACAAAATTTGATTCAAGGGAAACTGTCCAAGAGATA
TTGTGTTTCAAGAGAAACATATGCAAAGAATTGT
Found at i:2348551 original size:30 final size:30
Alignment explanation
Indices: 2348490--2348601 Score: 120
Period size: 30 Copynumber: 3.7 Consensus size: 30
2348480 AATTGGTATT
* * *
2348490 AATAGAAAATTAAAGGACCAAAATAGA-AAA
1 AATAGAAACTTAAGGGACTAAAATA-ACAAA
* *
2348520 AACA-ACAACTTAGGGGACTAAAATAACAAA
1 AATAGA-AACTTAAGGGACTAAAATAACAAA
* * *
2348550 AATAGAAATTTAAAGGACTAAAATTACAAA
1 AATAGAAACTTAAGGGACTAAAATAACAAA
2348580 AATAGAAACTTAAGGGACTAAA
1 AATAGAAACTTAAGGGACTAAA
2348602 CAATAAATAA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 2 0.03
30 64 0.96
31 1 0.01
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (30 bp):
AATAGAAACTTAAGGGACTAAAATAACAAA
Found at i:2351039 original size:19 final size:19
Alignment explanation
Indices: 2351007--2351051 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2350997 GTATCAATGT
*
2351007 GAAACAAAATAATTTAAGTA
1 GAAA-AAAACAATTTAAGTA
*
2351027 GAAAAAAACAATTTAAGTG
1 GAAAAAAACAATTTAAGTA
2351046 GAAAAA
1 GAAAAA
2351052 TACATATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (19 bp):
GAAAAAAACAATTTAAGTA
Found at i:2351320 original size:28 final size:27
Alignment explanation
Indices: 2351289--2351381 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 27
2351279 TTTTTTTATC
*
2351289 TAAGTATTTGAAATATTTTTGGTCAAAA
1 TAAGTATCT-AAATATTTTTGGTCAAAA
2351317 TAAGTATCTAAACATATCTTTTTGGTCAAAA
1 TAAGTATCT-AA-ATA--TTTTTGGTCAAAA
* *
2351348 TAGGTACCTAAAGTATTTTTGGTCAAAA
1 TAAGTATCTAAA-TATTTTTGGTCAAAA
2351376 TAAGTA
1 TAAGTA
2351382 CCCTAAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 28 0.50
29 4 0.07
30 4 0.07
31 20 0.36
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (27 bp):
TAAGTATCTAAATATTTTTGGTCAAAA
Found at i:2351341 original size:31 final size:28
Alignment explanation
Indices: 2351299--2351383 Score: 116
Period size: 31 Copynumber: 2.9 Consensus size: 28
2351289 TAAGTATTTG
*
2351299 AAATATTTTTGGTCAAAATAAGTATCTA
1 AAATATTTTTGGTCAAAATAAGTACCTA
*
2351327 AACATATCTTTTTGGTCAAAATAGGTACCTA
1 AA-ATA--TTTTTGGTCAAAATAAGTACCTA
*
2351358 AAGTATTTTTGGTCAAAATAAGTACC
1 AAATATTTTTGGTCAAAATAAGTACC
2351384 CTAAGTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 22 0.44
29 3 0.06
30 2 0.04
31 23 0.46
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (28 bp):
AAATATTTTTGGTCAAAATAAGTACCTA
Found at i:2351382 original size:28 final size:28
Alignment explanation
Indices: 2351302--2351393 Score: 114
Period size: 28 Copynumber: 3.2 Consensus size: 28
2351292 GTATTTGAAA
* *
2351302 TATTTTTGGTCAAAATAAGTATCTAAACA
1 TATTTTTGGTCAAAATAAGTACCTAAA-G
*
2351331 TATCTTTTTGGTCAAAATAGGTACCTAAAG
1 TA--TTTTTGGTCAAAATAAGTACCTAAAG
2351361 TATTTTTGGTCAAAATAAGTACCCT-AAG
1 TATTTTTGGTCAAAATAAGTA-CCTAAAG
2351389 TATTT
1 TATTT
2351394 AATTTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 26 0.46
29 5 0.09
30 2 0.04
31 23 0.41
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (28 bp):
TATTTTTGGTCAAAATAAGTACCTAAAG
Found at i:2352556 original size:2 final size:2
Alignment explanation
Indices: 2352549--2352674 Score: 159
Period size: 2 Copynumber: 63.5 Consensus size: 2
2352539 TTTTCTCATG
* *
2352549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CA T- TGA CA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* * * *
2352589 TT TT TC TCA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2352632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2352674 T
1 T
2352675 GTGTGTGTAT
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
1 3 0.03
2 107 0.96
3 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2352923 original size:21 final size:21
Alignment explanation
Indices: 2352899--2352964 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
2352889 GCAAATTCGC
2352899 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
2352920 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
2352940 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
2352961 GTTG
1 GTTG
2352965 AAATCGCAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:2352971 original size:20 final size:20
Alignment explanation
Indices: 2352907--2352971 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2352897 GCGTTGCATT
2352907 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTG-AAA
* * **
2352928 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
2352948 TCGCGTTGCGATAGTTGAAA
1 TCGCGTTGCGATAGTTGAAA
2352968 TCGC
1 TCGC
2352972 AACGCGATCT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
TCGCGTTGCGATAGTTGAAA
Found at i:2353058 original size:19 final size:19
Alignment explanation
Indices: 2353034--2353078 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2353024 GAAAATCGCG
2353034 TTGCGATTTTCCAAATTCA
1 TTGCGATTTTCCAAATTCA
*
2353053 TTGCGATTTTCCAAATTCG
1 TTGCGATTTTCCAAATTCA
2353072 TTGCGAT
1 TTGCGAT
2353079 AGTCTACAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (19 bp):
TTGCGATTTTCCAAATTCA
Found at i:2353757 original size:6 final size:5
Alignment explanation
Indices: 2353709--2353753 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
2353699 TCCTCTCGTC
2353709 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
2353754 TGGTAATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 28 0.72
6 11 0.28
ACGTcount: A:0.00, C:0.20, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:2353891 original size:41 final size:41
Alignment explanation
Indices: 2353842--2354029 Score: 299
Period size: 41 Copynumber: 4.5 Consensus size: 41
2353832 TAACTATCAT
2353842 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
1 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
2353883 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
1 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
*
2353924 AACGCGAA-ATGGAAAATCGCAACGACAACTGTAGACTATCGC
1 AA--CGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
*
2353966 AACGAATTTGGAAAATCGCAATGACAACTGTAGACTATCGC
1 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
*
2354007 AACGCGAA-ATGGAAAATCGCAAC
1 AA--CGAATTTGGAAAATCGCAAC
2354030 ACGATTTTCA
Statistics
Matches: 137, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
40 4 0.03
41 77 0.56
42 48 0.35
43 8 0.06
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (41 bp):
AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGC
Found at i:2353902 original size:19 final size:19
Alignment explanation
Indices: 2353842--2353906 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
2353832 TAACTATCAT
2353842 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
* * **
2353861 AACGACAACTGTAGACTATCGC
1 AACG--AA-TTTGGAAAATCGC
2353883 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
2353902 AACGA
1 AACGA
2353907 CAACTGTAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 18 0.51
20 2 0.06
21 2 0.06
22 13 0.37
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (19 bp):
AACGAATTTGGAAAATCGC
Found at i:2353950 original size:83 final size:83
Alignment explanation
Indices: 2353850--2354029 Score: 351
Period size: 83 Copynumber: 2.2 Consensus size: 83
2353840 ATAACGAATT
2353850 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTA
2353915 GACTATCGCAACGCGAAA
66 GACTATCGCAACGCGAAA
*
2353933 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAATGACAACTGTA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTA
2353998 GACTATCGCAACGCGAAA
66 GACTATCGCAACGCGAAA
2354016 TGGAAAATCGCAAC
1 TGGAAAATCGCAAC
2354030 ACGATTTTCA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 96 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (83 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTA
GACTATCGCAACGCGAAA
Found at i:2354044 original size:41 final size:41
Alignment explanation
Indices: 2353850--2354058 Score: 266
Period size: 41 Copynumber: 5.0 Consensus size: 41
2353840 ATAACGAATT
*
2353850 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAAC-ACAACTGTAGACTATCGCAACGCGAA-A
2353891 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAAC-ACAACTGTAGACTATCGCAACGCGAAA
*
2353933 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAAC-ACAACTGTAGACTATCGCAACGCGAA-A
*
2353974 TGGAAAATCGCAATGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAA-CACAACTGTAGACTATCGCAACGCGAAA
* * *
2354016 TGGAAAATCGCAACACGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACACAACTGT-AGACTATCGCAACGCGAAA
2354057 TG
1 TG
2354059 CAACGCGAAT
Statistics
Matches: 153, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
40 4 0.03
41 92 0.60
42 49 0.32
43 8 0.05
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACACAACTGTAGACTATCGCAACGCGAAA
Found at i:2354062 original size:21 final size:21
Alignment explanation
Indices: 2353999--2354062 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
2353989 ACAACTGTAG
*
2353999 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
2354020 A-AATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATGCA
2354040 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
2354061 AC
1 AC
2354063 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:2354802 original size:31 final size:31
Alignment explanation
Indices: 2354747--2354824 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
2354737 CTTTTTGAAC
** *
2354747 TTGCAATACAGTCCCCCAATATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
* * *
2354778 TTGTAATATGGTCCCTCAACATTTAGTTCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
2354809 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
2354825 GATGTAACTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCGT
Found at i:2358852 original size:21 final size:22
Alignment explanation
Indices: 2358827--2358876 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2358817 GAATATGAAG
2358827 AGTTATAAGAGAAC-AAATATA
1 AGTTATAAGAGAACGAAATATA
* *
2358848 AGTTATATGATAACGAAATATA
1 AGTTATAAGAGAACGAAATATA
2358870 AGATTAT
1 AG-TTAT
2358877 GTGAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 9 0.36
23 4 0.16
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (22 bp):
AGTTATAAGAGAACGAAATATA
Found at i:2359635 original size:12 final size:13
Alignment explanation
Indices: 2359609--2359649 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
2359599 GATTATGGGT
2359609 ATATGTGATATGA
1 ATATGTGATATGA
2359622 ATATGTGA-ATGA
1 ATATGTGATATGA
* *
2359634 ATA-ATAATATGA
1 ATATGTGATATGA
2359646 ATAT
1 ATAT
2359650 TACTGCCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 14 0.58
13 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (13 bp):
ATATGTGATATGA
Found at i:2359960 original size:16 final size:17
Alignment explanation
Indices: 2359939--2359972 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2359929 GTGCACAATC
2359939 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
2359955 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
2359972 T
1 T
2359973 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:2360887 original size:25 final size:26
Alignment explanation
Indices: 2360859--2360915 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
2360849 GTATTTTCTA
* * *
2360859 TTTATTTTTTAATA-TTTATATATTT
1 TTTATTTTTGAAAATTTTAAATATTT
*
2360884 TTTA-TATTGAAAATTTTAAATATTT
1 TTTATTTTTGAAAATTTTAAATATTT
2360909 TTTATTT
1 TTTATTT
2360916 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTATTTTTGAAAATTTTAAATATTT
Found at i:2360920 original size:25 final size:25
Alignment explanation
Indices: 2360873--2360922 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2360863 TTTTTTAATA
*
2360873 TTTATATATTTTTTATATTGAAAAT
1 TTTAAATATTTTTTATATTGAAAAT
2360898 TTTAAATATTTTTTAT-TTAGAAAAT
1 TTTAAATATTTTTTATATT-GAAAAT
2360923 AAAATAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTAAATATTTTTTATATTGAAAAT
Found at i:2361182 original size:11 final size:11
Alignment explanation
Indices: 2361166--2361206 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2361156 GTATTGTTTT
2361166 TATATAAATTA
1 TATATAAATTA
2361177 TATATATAA-TA
1 TATATA-AATTA
2361188 TATATAAATT-
1 TATATAAATTA
*
2361198 TATAAAAAT
1 TATATAAAT
2361207 GACACTACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.37
11 15 0.56
12 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATAAATTA
Found at i:2361967 original size:21 final size:21
Alignment explanation
Indices: 2361943--2361992 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2361933 TACACCACAA
2361943 TTTAAAATTTTTAACTTCACC
1 TTTAAAATTTTTAACTTCACC
2361964 TTTAAAATTTTTAACTTCACC
1 TTTAAAATTTTTAACTTCACC
2361985 TTTAAAAT
1 TTTAAAAT
2361993 GATTATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAAATTTTTAACTTCACC
Found at i:2366199 original size:18 final size:20
Alignment explanation
Indices: 2366164--2366200 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2366154 CACGGAATGT
2366164 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
2366184 AAGATTACC-G-GGGAATA
1 AAGATTACCAGTGGGAATA
2366201 GGATTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:2367799 original size:19 final size:20
Alignment explanation
Indices: 2367762--2367800 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2367752 TAATGTTTGT
**
2367762 TTTTTTATAAAATTTAAGAA
1 TTTTTTATAAAATAAAAGAA
2367782 TTTTTT-TAAAATAAAAGAA
1 TTTTTTATAAAATAAAAGAA
2367801 ATAAAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTTTATAAAATAAAAGAA
Found at i:2371450 original size:18 final size:18
Alignment explanation
Indices: 2371426--2371560 Score: 114
Period size: 18 Copynumber: 7.6 Consensus size: 18
2371416 ATATGCATAC
2371426 TAGTTCATTTAAGCATGT
1 TAGTTCATTTAAGCATGT
* * *
2371444 TAATTCATATAAGCATGG
1 TAGTTCATTTAAGCATGT
**
2371462 TAGTTCATTTAAATAT-T
1 TAGTTCATTTAAGCATGT
**
2371479 CTAGTTCATTTAAATATGT
1 -TAGTTCATTTAAGCATGT
* ***
2371498 TAGTTCATTTAAGTAACC
1 TAGTTCATTTAAGCATGT
* **
2371516 TAGTTCACTTAAATATGT
1 TAGTTCATTTAAGCATGT
2371534 TAGTTCATTTAAG--TGT
1 TAGTTCATTTAAGCATGT
2371550 TAGTTCATTTA
1 TAGTTCATTTA
2371561 GCTTGCATGG
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
16 14 0.15
18 81 0.84
19 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (18 bp):
TAGTTCATTTAAGCATGT
Found at i:2371488 original size:54 final size:55
Alignment explanation
Indices: 2371425--2371546 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 55
2371415 AATATGCATA
*** *
2371425 CTAGTTCATTTAAGCATGTTAATTCATATAAGCATGGTAGTTCATTTAAATAT-T
1 CTAGTTCATTTAAGCATGTTAATTCATATAAGCAACCTAGTTCACTTAAATATGT
** * * *
2371479 CTAGTTCATTTAAATATGTTAGTTCATTTAAGTAACCTAGTTCACTTAAATATGT
1 CTAGTTCATTTAAGCATGTTAATTCATATAAGCAACCTAGTTCACTTAAATATGT
2371534 -TAGTTCATTTAAG
1 CTAGTTCATTTAAG
2371547 TGTTAGTTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 56 0.98
55 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (55 bp):
CTAGTTCATTTAAGCATGTTAATTCATATAAGCAACCTAGTTCACTTAAATATGT
Found at i:2371546 original size:36 final size:36
Alignment explanation
Indices: 2371462--2371547 Score: 136
Period size: 36 Copynumber: 2.4 Consensus size: 36
2371452 ATAAGCATGG
* ** *
2371462 TAGTTCATTTAAATATTCTAGTTCATTTAAATATGT
1 TAGTTCATTTAAGTAACCTAGTTCACTTAAATATGT
2371498 TAGTTCATTTAAGTAACCTAGTTCACTTAAATATGT
1 TAGTTCATTTAAGTAACCTAGTTCACTTAAATATGT
2371534 TAGTTCATTTAAGT
1 TAGTTCATTTAAGT
2371548 GTTAGTTCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (36 bp):
TAGTTCATTTAAGTAACCTAGTTCACTTAAATATGT
Found at i:2373672 original size:15 final size:15
Alignment explanation
Indices: 2373654--2373683 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2373644 AATTAAAAAT
2373654 AATAGTAAGAAAACA
1 AATAGTAAGAAAACA
2373669 AATAGTAAGAAAACA
1 AATAGTAAGAAAACA
2373684 GTAAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAGTAAGAAAACA
Found at i:2375798 original size:136 final size:136
Alignment explanation
Indices: 2375412--2375798 Score: 594
Period size: 136 Copynumber: 2.8 Consensus size: 136
2375402 TGAGTCATCA
*
2375412 CTGATTCGAAGTGTTGTGAATCTAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 CTGATTCGAAGTGTTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * *
2375477 CCCTCTGTCGGATGAGTTCTTCTTATTATGAACTCTCCATTGGAAATGTCAATCCCTCGAGCGAG
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAACGAG
2375542 GAATTG
131 GAATTG
* * * *
2375548 CTGATTCAAAGTGATGTGAATCGAGCAATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT
1 CTGATTCGAAGTGTTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * * * *
2375613 CCCTATGTCAGATAAATTCTTCTCATTATGAACTCTTCATTGGAAATGTTAATCCGTCAAACGAG
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAACGAG
**
2375678 GTGTTG
131 GAATTG
* *
2375684 CTGATTCGAAGTGTTGTGAATCTAGCAATAGGTCAAACAAGTTCTTATCATTATGAACTTCTTCT
1 CTGATTCGAAGTGTTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
*
2375749 CCCTCTGTCGGATGAGCTCTTCTCATTATGAACTCTCCATTGGAAATGTT
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTT
2375799 GATCGGTTCA
Statistics
Matches: 222, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 222 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (136 bp):
CTGATTCGAAGTGTTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAACGAG
GAATTG
Found at i:2376750 original size:10 final size:9
Alignment explanation
Indices: 2376721--2376746 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2376711 GCGGTTCTTT
2376721 TTATTTTTC
1 TTATTTTTC
2376730 TTATTTTTC
1 TTATTTTTC
2376739 TTATTTTT
1 TTATTTTT
2376747 TCTTTCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TTATTTTTC
Found at i:2393238 original size:25 final size:25
Alignment explanation
Indices: 2393183--2393243 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
2393173 TTAAATTAAT
2393183 AATAAAAAAACAAATAATAAAAAAC
1 AATAAAAAAACAAATAATAAAAAAC
*
2393208 AGTAAAAAAACATAA-AATAAAAATA-
1 AATAAAAAAACA-AATAATAAAAA-AC
2393233 AATAAATAAAA
1 AATAAA-AAAA
2393244 TACAAGGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (25 bp):
AATAAAAAAACAAATAATAAAAAAC
Found at i:2394772 original size:16 final size:16
Alignment explanation
Indices: 2394751--2394793 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2394741 TGGGGTTTTA
2394751 TTTGGGTTTAGGTTGG
1 TTTGGGTTTAGGTTGG
*
2394767 TTTGGGTTTTA-TTTGG
1 TTTGGG-TTTAGGTTGG
*
2394783 TTTGGGCTTAG
1 TTTGGGTTTAG
2394794 TAAAAGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 16 0.70
17 4 0.17
ACGTcount: A:0.07, C:0.02, G:0.37, T:0.53
Consensus pattern (16 bp):
TTTGGGTTTAGGTTGG
Found at i:2396958 original size:15 final size:15
Alignment explanation
Indices: 2396926--2396968 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2396916 TTTGTTTTTA
* *
2396926 TTTTATTTTTTATTT
1 TTTTATTTTATATAT
*
2396941 TTTTATTTTATCTAT
1 TTTTATTTTATATAT
*
2396956 TTTAATTTTATAT
1 TTTTATTTTATAT
2396969 TACATAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTATATAT
Found at i:2399560 original size:54 final size:54
Alignment explanation
Indices: 2399502--2399906 Score: 152
Period size: 54 Copynumber: 7.5 Consensus size: 54
2399492 TGGTGTCTAT
* * **
2399502 ACGGTCATTCATAAACATATTATGAATGATGTGGGTTGCACACCTAGTGTAGAA
1 ACGGTCATTCATAAACATATGATGAATGATATGAATTGCACACCTAGTGTAGAA
** * * ** * *
2399556 ACGGTTGTTCATCAACGTATGATGAATTCTATGAATTGCACACTTAGTGTCGAA
1 ACGGTCATTCATAAACATATGATGAATGATATGAATTGCACACCTAGTGTAGAA
** * * * * * **
2399610 ACGGTTGTTCATCAACGTATGATGAAT-TTCGTGAATTGCACACTTAGTGCCGAA
1 ACGGTCATTCATAAACATATGATGAATGAT-ATGAATTGCACACCTAGTGTAGAA
** * * * * * ***
2399664 ACGGTTGTTCTTCAACATATGATGAAT-TTCGTGAATTGCACACTTAGTACCGAA
1 ACGGTCATTCATAAACATATGATGAATGAT-ATGAATTGCACACCTAGTGTAGAA
** ** * **** **
2399718 ATAGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTG-ACGAA
1 ACGGTCATTCATAAACATATGATGAATGATATGAATTGCACACCTAGTGTA-GAA
** * * ** * * * ***
2399772 ACGGTTGTTCATCAACATATGACGAATTCTGTGAATTACACACTTAGTACCGAA
1 ACGGTCATTCATAAACATATGATGAATGATATGAATTGCACACCTAGTGTAGAA
** * **** * *
2399826 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGT-TCCGAA
1 ACGGTCATTCATAAACATATGATGAATGATATGAATTGCACACCTAGTGT-AGAA
* **
2399880 ACAGTTGTTCATAAACATATGATGAAT
1 ACGGTCATTCATAAACATATGATGAAT
2399907 TCCGTGAATT
Statistics
Matches: 306, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.00
54 305 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
ACGGTCATTCATAAACATATGATGAATGATATGAATTGCACACCTAGTGTAGAA
Found at i:2399907 original size:54 final size:54
Alignment explanation
Indices: 2399553--2399923 Score: 546
Period size: 54 Copynumber: 6.9 Consensus size: 54
2399543 ACCTAGTGTA
* **
2399553 GAAACGGTTGTTCATCAACGTATGATGAATTCTATGAATTGCACACTTAGTGT-C
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGT-TCC
* * *
2399607 GAAACGGTTGTTCATCAACGTATGATGAATTTCGTGAATTGCACACTTAGTGCC
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
* * *
2399661 GAAACGGTTGTTCTTCAACATATGATGAATTTCGTGAATTGCACACTTAGTACC
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
** * **
2399715 GAAATAGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGAC
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
* * * *
2399769 GAAACGGTTGTTCATCAACATATGACGAATTCTGTGAATTACACACTTAGTACC
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
2399823 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
* *
2399877 GAAACAGTTGTTCATAAACATATGATGAATTCCGTGAATTGCACACT
1 GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACT
2399924 AAGTGCCTAT
Statistics
Matches: 288, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
54 288 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (54 bp):
GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTTCC
Found at i:2400298 original size:19 final size:21
Alignment explanation
Indices: 2400253--2400303 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
2400243 TGGCTCCATA
2400253 GTATCGATACTACTATACTATG
1 GTATCGATACTACTATA-TATG
* *
2400275 TTATCGATACT-CTAT-TGTG
1 GTATCGATACTACTATATATG
*
2400294 GTATCAATAC
1 GTATCGATAC
2400304 AATTTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 11 0.44
21 4 0.16
22 10 0.40
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (21 bp):
GTATCGATACTACTATATATG
Found at i:2405391 original size:49 final size:45
Alignment explanation
Indices: 2405294--2405414 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 45
2405284 GTAACCATGC
*
2405294 AAATAAGCTTATGAACTTATGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
* * * **
2405339 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAA
*
2405388 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
2405415 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
45 24 0.38
46 1 0.02
48 1 0.02
49 38 0.59
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:2407164 original size:6 final size:6
Alignment explanation
Indices: 2407153--2407189 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
2407143 AAGACCTATG
* *
2407153 GGTCAT GGTCAT GGTCAT GGTCAC GGTCAC GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
2407190 ATACAAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (6 bp):
GGTCAT
Found at i:2416876 original size:54 final size:54
Alignment explanation
Indices: 2416836--2417279 Score: 624
Period size: 54 Copynumber: 8.2 Consensus size: 54
2416826 TGTGGGCTGT
* * * * *
2416836 ACACCTAGTGCTGAAACGATTGTTCATCAACGTATGATGAATT-TCATGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCT-GTGAATTGC
* * ** *
2416890 ACACTTAGTGCCGAAACGCTTGTCCATCAATGTATGATGAATTTTGTGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGC
* * * *
2416944 ACACTTAGTGCCGAAATGGTTGTCCATCAACGTATGATGAATTCCGTGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGC
* *
2416998 ACACTTAGTGCCGAAATGGTTGTTCATCAACATATGATGAATTCCGTGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGC
*
2417052 ACACTTAGTGCTGAAACGGTTGTTCATCAACATATGATGAATTCCT-TGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-CTGTGAATTGC
2417106 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCT-TGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-CTGTGAATTGC
* * * * *
2417160 ACACTTAGTGCCGAAAAGATTGTTCATCAACATATGATGAATTCCGTAAATTTC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGC
* *
2417214 ACACTTAGTGCCGAAACGATTGTTCATCAACATATGATGAATTCCGTGAATTGC
1 ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGC
2417268 ACACTTAGTGCC
1 ACACTTAGTGCC
2417280 TATTTGGTAA
Statistics
Matches: 362, Mismatches: 25, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.00
54 359 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (54 bp):
ACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGC
Found at i:2424269 original size:72 final size:72
Alignment explanation
Indices: 2424183--2424326 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
2424173 CGATGATTCA
2424183 ATATAACGAAGCTCTCGAGTCAGTTAGAATTAAATAATAATAAATATGAAAATTAATTAGGATTT
1 ATATAACGAAGCTCTCGAGTCAGTTAGAATTAAATAATAATAAATATGAAAATTAATTAGGATTT
2424248 AATTATG
66 AATTATG
*
2424255 ATATAACGAAGCTCTCGTGTCAGTTAGAATTAAATAATAATAAATATGAAAATTAATTAGGATTT
1 ATATAACGAAGCTCTCGAGTCAGTTAGAATTAAATAATAATAAATATGAAAATTAATTAGGATTT
2424320 AATTATG
66 AATTATG
2424327 TCAATTTCTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (72 bp):
ATATAACGAAGCTCTCGAGTCAGTTAGAATTAAATAATAATAAATATGAAAATTAATTAGGATTT
AATTATG
Found at i:2424764 original size:13 final size:13
Alignment explanation
Indices: 2424746--2424772 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2424736 ATCGGTGAAA
2424746 AAATAGTATTTAT
1 AAATAGTATTTAT
2424759 AAATAGTATTTAT
1 AAATAGTATTTAT
2424772 A
1 A
2424773 TACTATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AAATAGTATTTAT
Found at i:2425200 original size:13 final size:13
Alignment explanation
Indices: 2425182--2425208 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2425172 TATCGGTGAA
2425182 AAATAGTATTTAT
1 AAATAGTATTTAT
2425195 AAATAGTATTTAT
1 AAATAGTATTTAT
2425208 A
1 A
2425209 TAGTATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AAATAGTATTTAT
Found at i:2425693 original size:2 final size:2
Alignment explanation
Indices: 2425682--2425723 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2425672 GAGTGTGTAC
*
2425682 AT AT AC 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
2425724 TTGACATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2426116 original size:22 final size:22
Alignment explanation
Indices: 2426091--2426133 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2426081 CTCATACGCT
2426091 CGTGAATG-CTGTAGCAAAACCA
1 CGTGAA-GACTGTAGCAAAACCA
2426113 CGTGAAGACTGTAGCAAAACC
1 CGTGAAGACTGTAGCAAAACC
2426134 CTTCAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (22 bp):
CGTGAAGACTGTAGCAAAACCA
Found at i:2426363 original size:20 final size:20
Alignment explanation
Indices: 2426338--2426399 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
2426328 AGAAGGGGAG
*
2426338 AAGAAAGACGATAAAAGAAT
1 AAGAAAGAAGATAAAAGAAT
* *
2426358 AAGAAAGAAGAGAAAAGAAA
1 AAGAAAGAAGATAAAAGAAT
*
2426378 AAGAAAGAAGATAAGAGAAT
1 AAGAAAGAAGATAAAAGAAT
2426398 AA
1 AA
2426400 AGTTAAAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.69, C:0.02, G:0.23, T:0.06
Consensus pattern (20 bp):
AAGAAAGAAGATAAAAGAAT
Found at i:2426737 original size:17 final size:18
Alignment explanation
Indices: 2426712--2426750 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2426702 GTAGATTATT
*
2426712 TTTAGATTAAAT-TAATG
1 TTTAGATTAAATATAATC
*
2426729 TTTATATTAAATATAATC
1 TTTAGATTAAATATAATC
2426747 TTTA
1 TTTA
2426751 AATTGAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTAGATTAAATATAATC
Found at i:2431823 original size:20 final size:20
Alignment explanation
Indices: 2431790--2431833 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2431780 ATTCATTTAT
* *
2431790 AGAAATAAAGGAAAGGAAGA
1 AGAAAGAAAGGAAAGGAAAA
*
2431810 AGAAAGAAATGAAAGGAAAA
1 AGAAAGAAAGGAAAGGAAAA
2431830 AGAA
1 AGAA
2431834 TAAATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (20 bp):
AGAAAGAAAGGAAAGGAAAA
Found at i:2433845 original size:21 final size:21
Alignment explanation
Indices: 2433819--2433860 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2433809 TTCCAACAGA
*
2433819 GATATGAGAGTAAAGTGGTGG
1 GATATGAGAGCAAAGTGGTGG
*
2433840 GATATGAGAGCATAGTGGTGG
1 GATATGAGAGCAAAGTGGTGG
2433861 ACATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.43, T:0.24
Consensus pattern (21 bp):
GATATGAGAGCAAAGTGGTGG
Found at i:2434749 original size:11 final size:11
Alignment explanation
Indices: 2434728--2434758 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2434718 CCTTTGTAAT
2434728 TAAATATTAAAA
1 TAAA-ATTAAAA
2434740 TAAAATTAAAA
1 TAAAATTAAAA
2434751 TAAAATTA
1 TAAAATTA
2434759 TTTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAATTAAAA
Found at i:2438198 original size:33 final size:33
Alignment explanation
Indices: 2438161--2438224 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2438151 TTTCGTAACA
* * * *
2438161 GGGTATAGGCTGAATGTAGGGTATGGTTTAAAG
1 GGGTATAGACTGAATGCACGATATGGTTTAAAG
*
2438194 GGGTATAGACTGCATGCACGATATGGTTTAA
1 GGGTATAGACTGAATGCACGATATGGTTTAA
2438225 GGCTGCTACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (33 bp):
GGGTATAGACTGAATGCACGATATGGTTTAAAG
Found at i:2446396 original size:18 final size:18
Alignment explanation
Indices: 2446375--2446409 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2446365 TCTTTTTGAA
*
2446375 TTCTTTTTTTCTTTTCTT
1 TTCTTTTCTTCTTTTCTT
2446393 TTCTTTTCTTCTTTTCT
1 TTCTTTTCTTCTTTTCT
2446410 GATTTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTTTTCTTCTTTTCTT
Found at i:2449109 original size:10 final size:10
Alignment explanation
Indices: 2449094--2449119 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2449084 AAAAGTAAGA
2449094 GATTTTGGTT
1 GATTTTGGTT
2449104 GATTTTGGTT
1 GATTTTGGTT
2449114 GATTTT
1 GATTTT
2449120 CAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.27, T:0.62
Consensus pattern (10 bp):
GATTTTGGTT
Found at i:2449970 original size:23 final size:23
Alignment explanation
Indices: 2449913--2450015 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 23
2449903 TCGAGGGTTT
* * *
2449913 TATGTGGTCCTTCGGGAC-AA-T
1 TATGTGGTCATTCGGTACAAACC
2449934 TATGTGG-CACTTCGGTACAAACC
1 TATGTGGTCA-TTCGGTACAAACC
* * *
2449957 TATATGGTCATTCGGGAC-AA-T
1 TATGTGGTCATTCGGTACAAACC
*
2449978 TATGTGG-CACTTCGGTGCAAACC
1 TATGTGGTCA-TTCGGTACAAACC
2450001 TATGTGGTCATTCGG
1 TATGTGGTCATTCGG
2450016 GATAATTATA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.05
21 26 0.41
22 6 0.09
23 25 0.39
24 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
TATGTGGTCATTCGGTACAAACC
Found at i:2450038 original size:44 final size:44
Alignment explanation
Indices: 2449913--2450038 Score: 207
Period size: 44 Copynumber: 2.9 Consensus size: 44
2449903 TCGAGGGTTT
* *
2449913 TATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTACAAACC
1 TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAACC
*
2449957 TATATGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAACC
* *
2450001 TATGTGGTCATTCGGGATAATTATATGGCACTTCGGTG
1 TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTG
2450039 TAAATTACGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (44 bp):
TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAACC
Found at i:2451922 original size:14 final size:14
Alignment explanation
Indices: 2451899--2451928 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2451889 TTATGTAGGC
*
2451899 TATGTTTATGATTA
1 TATGTATATGATTA
2451913 TATGTATATGATTA
1 TATGTATATGATTA
2451927 TA
1 TA
2451929 GAAATGTGAC
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:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (14 bp):
TATGTATATGATTA
Found at i:2466876 original size:21 final size:21
Alignment explanation
Indices: 2466852--2466908 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2466842 TACGATGAAC
2466852 AGTATCGATATTGATTGAAGT
1 AGTATCGATATTGATTGAAGT
2466873 AGTATCGATATTGATTGAAGT
1 AGTATCGATATTGATTGAAGT
2466894 AGTATCGATATTGAT
1 AGTATCGATATTGAT
2466909 GTATAGGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (21 bp):
AGTATCGATATTGATTGAAGT
Found at i:2467644 original size:53 final size:53
Alignment explanation
Indices: 2467579--2468058 Score: 649
Period size: 53 Copynumber: 9.1 Consensus size: 53
2467569 TCGCTATTTA
* * *
2467579 TGCATCCATGGTATTCATAATTAGCTTGTGTATTACTATTTCGGCACTATGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * ** *
2467632 TGCATCCTTGGTATTCATAATTAGTTTGTGAATTACTATTT-TTCACTATATG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* *
2467684 TGCATCCATGGTATTCATAATTAATTTGTGAATTACCATTTCGGCACTATATG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * *
2467737 TGCATCCGTGGTATTCATAATTAGTTTGTTAATTACCATTTCGGTACTATGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * * *
2467790 TGCATCCATGGTATTCGTAATGAGTTTGTGAATTAACATTTCGACACTATGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * *
2467843 TGCATCCATTGTATTCATAATTAGTTTGTGAATTACCATTTCGACACTAAGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * * *
2467896 TGCAT-CTTGGTATTCATAATGAGTTTGTAAATTACCATTTTGGCACTATGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * * *
2467948 TGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCAGTAATATGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
* * * * *
2468001 TGCATCCATAGTATTCATAATGAGTTTGTTAATTATCATTTCGACACTATGTG
1 TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
2468054 TGCAT
1 TGCAT
2468059 TCACATTTGA
Statistics
Matches: 377, Mismatches: 48, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
52 91 0.24
53 286 0.76
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (53 bp):
TGCATCCATGGTATTCATAATTAGTTTGTGAATTACCATTTCGGCACTATGTG
Found at i:2467907 original size:158 final size:159
Alignment explanation
Indices: 2467579--2468058 Score: 659
Period size: 158 Copynumber: 3.0 Consensus size: 159
2467569 TCGCTATTTA
* * * *
2467579 TGCATCCATGGTATTCATAATTAGCTTGTGT-ATTACTATTTCGGCACTATGTGTGCATCCTTGG
1 TGCATCCGTGGTATTCATAATTAGTTTGT-TAATTACCATTTCGGCACTATGTGTGCATCCATGG
* ** * *
2467643 TATTCATAATTAGTTTGTGAATT-ACTATTT-TTCACTATATGTGCATCCATGGTATTCATAATT
65 TATTCATAATGAGTTTGTGAATTAAC-ATTTCGACACTATGTGTGCATCCATAGTATTCATAATT
* *
2467706 AATTTGTGAATTACCATTTCGGCACTATA-TG
129 AGTTTGTGAATTACCATTTCGACACTA-AGTG
*
2467737 TGCATCCGTGGTATTCATAATTAGTTTGTTAATTACCATTTCGGTACTATGTGTGCATCCATGGT
1 TGCATCCGTGGTATTCATAATTAGTTTGTTAATTACCATTTCGGCACTATGTGTGCATCCATGGT
* *
2467802 ATTCGTAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCATCCATTGTATTCATAATTAG
66 ATTCATAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCATCCATAGTATTCATAATTAG
2467867 TTTGTGAATTACCATTTCGACACTAAGTG
131 TTTGTGAATTACCATTTCGACACTAAGTG
* * * *
2467896 TGCAT-CTTGGTATTCATAATGAGTTTGTAAATTACCATTTTGGCACTATGTGTGCATCCATGGT
1 TGCATCCGTGGTATTCATAATTAGTTTGTTAATTACCATTTCGGCACTATGTGTGCATCCATGGT
* *
2467960 ATTCATAATGAGTTTGTGAATTACCATTTCAGTA-A-TATGTGTGCATCCATAGTATTCATAATG
66 ATTCATAATGAGTTTGTGAATTAACATTTC-G-ACACTATGTGTGCATCCATAGTATTCATAATT
* * *
2468023 AGTTTGTTAATTATCATTTCGACACTATGTG
129 AGTTTGTGAATTACCATTTCGACACTAAGTG
2468054 TGCAT
1 TGCAT
2468059 TCACATTTGA
Statistics
Matches: 291, Mismatches: 25, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
157 1 0.00
158 224 0.77
159 65 0.22
160 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (159 bp):
TGCATCCGTGGTATTCATAATTAGTTTGTTAATTACCATTTCGGCACTATGTGTGCATCCATGGT
ATTCATAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCATCCATAGTATTCATAATTAG
TTTGTGAATTACCATTTCGACACTAAGTG
Found at i:2467943 original size:211 final size:211
Alignment explanation
Indices: 2467579--2468058 Score: 698
Period size: 211 Copynumber: 2.3 Consensus size: 211
2467569 TCGCTATTTA
* * * *
2467579 TGCATCCATGGTATTCATAATTAGCTTGTGTATT-ACTATTTCGGCACTATGTGTGCATCCTTGG
1 TGCATCCATGGTATTCATAATGAGTTTGTGAATTAAC-ATTTCGACACTATGTGTGCATCCTTGG
* ** *
2467643 TATTCATAATTAGTTTGTGAATTACTATTTTTCACTATATGTGCATCCATGGTATTCATAATTAA
65 TATTCATAATTAGTTTGTGAATTACCATTTGACACTATATGTGCATCCATGGTATTCATAATGAA
* * * *
2467708 TTTGTGAATTACCATTTCGGCACTATATGTGCATCCGTGGTATTCATAATTAGTTTGTTAATTAC
130 TTTGTAAATTACCATTTCGGCACTATATGTGCATCCATGGTATTCATAATGAGTTTGTGAATTAC
* *
2467773 CATTTCGGTACTATGTG
195 CATTTCAGTAATATGTG
*
2467790 TGCATCCATGGTATTCGTAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCATCCATT-G
1 TGCATCCATGGTATTCATAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCATCC-TTGG
*
2467854 TATTCATAATTAGTTTGTGAATTACCATTTCGACACTA-AGTGTGCAT-CTTGGTATTCATAATG
65 TATTCATAATTAGTTTGTGAATTACCATTT-GACACTATA-TGTGCATCCATGGTATTCATAATG
* * *
2467917 AGTTTGTAAATTACCATTTTGGCACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATT
128 AATTTGTAAATTACCATTTCGGCACTATATGTGCATCCATGGTATTCATAATGAGTTTGTGAATT
2467982 ACCATTTCAGTAATATGTG
193 ACCATTTCAGTAATATGTG
* * *
2468001 TGCATCCATAGTATTCATAATGAGTTTGTTAATTATCATTTCGACACTATGTGTGCAT
1 TGCATCCATGGTATTCATAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCAT
2468059 TCACATTTGA
Statistics
Matches: 242, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
211 226 0.93
212 16 0.07
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (211 bp):
TGCATCCATGGTATTCATAATGAGTTTGTGAATTAACATTTCGACACTATGTGTGCATCCTTGGT
ATTCATAATTAGTTTGTGAATTACCATTTGACACTATATGTGCATCCATGGTATTCATAATGAAT
TTGTAAATTACCATTTCGGCACTATATGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACC
ATTTCAGTAATATGTG
Found at i:2470324 original size:3 final size:3
Alignment explanation
Indices: 2470300--2470368 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
2470290 ACTTTTAAAA
* * *
2470300 ATT ATT A-T ATT TTT ATT CTT ATT A-T ATT A-T ATT ATT ATT CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2470345 A-T ATT ATT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT
2470369 TATTTTTGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 8 0.15
3 44 0.80
4 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2470328 original size:22 final size:22
Alignment explanation
Indices: 2470302--2470372 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
2470292 TTTTAAAAAT
2470302 TATTATATTTTTATTCTTATTA
1 TATTATATTTTTATTCTTATTA
*
2470324 TATTATATTATTATTCTTATTA
1 TATTATATTTTTATTCTTATTA
*
2470346 TATTATTATTATTTATTATTATT-
1 TATTA-TATT-TTTATTCTTATTA
2470369 TATT
1 TATT
2470373 TTTGACAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.59
23 8 0.18
24 10 0.23
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTATATTTTTATTCTTATTA
Found at i:2470335 original size:30 final size:30
Alignment explanation
Indices: 2470300--2470375 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 30
2470290 ACTTTTAAAA
*
2470300 ATTATTATATTTTTATTCTTATTATATTA-T
1 ATTATTATATTTTTATTATTATTAT-TTATT
*
2470330 ATTATTATTCTTATTATATTATTATTATTTATT
1 ATTATTA-TATT-TT-TATTATTATTATTTATT
2470363 ATTATT-TATTTTT
1 ATTATTATATTTTT
2470376 GACAACTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 1 0.03
30 9 0.23
31 6 0.15
32 5 0.13
33 18 0.46
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (30 bp):
ATTATTATATTTTTATTATTATTATTTATT
Found at i:2470372 original size:17 final size:19
Alignment explanation
Indices: 2470300--2470364 Score: 77
Period size: 17 Copynumber: 3.7 Consensus size: 19
2470290 ACTTTTAAAA
2470300 ATTATTATATT-T-TTATT
1 ATTATTATATTATATTATT
*
2470317 CTTATTATATTATATTATT
1 ATTATTATATTATATTATT
*
2470336 ATT-CT-TATTATATTATT
1 ATTATTATATTATATTATT
2470353 ATTATT-TATTAT
1 ATTATTATATTAT
2470365 TATTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 25 0.61
18 9 0.22
19 7 0.17
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTATATTATATTATT
Found at i:2471084 original size:2 final size:2
Alignment explanation
Indices: 2471079--2471120 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
2471069 TTCTTTTGAA
* * *
2471079 CT CT CT CT CC CT -T CT CT CT CT TT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2471120 C
1 C
2471121 ATGCAAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:2471105 original size:10 final size:10
Alignment explanation
Indices: 2471080--2471119 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
2471070 TCTTTTGAAC
*
2471080 TCTCTCTCCCT
1 TCTCTCT-CTT
2471091 TCTCTCTCTT
1 TCTCTCTCTT
2471101 TCTCTCTCTT
1 TCTCTCTCTT
2471111 TCTCTCTCT
1 TCTCTCTCT
2471120 CATGCAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (10 bp):
TCTCTCTCTT
Found at i:2471592 original size:2 final size:2
Alignment explanation
Indices: 2471587--2471641 Score: 85
Period size: 2 Copynumber: 27.5 Consensus size: 2
2471577 AAACATTTTT
2471587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2471629 GTA T- TA AA TA TA T
1 -TA TA TA TA TA TA T
2471642 TTTTGTGGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Done.