Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:2229660 original size:20 final size:21
Alignment explanation
Indices: 2229637--2229679 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2229627 ACTAATCGTT
*
2229637 ACATAT-GATGTTTATCATGA
1 ACATATAGATATTTATCATGA
2229657 ACATATACGATATTTATCATGA
1 ACATATA-GATATTTATCATGA
2229679 A
1 A
2229680 TGATATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (21 bp):
ACATATAGATATTTATCATGA
Found at i:2236009 original size:24 final size:24
Alignment explanation
Indices: 2235950--2236058 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
2235940 GAATATTTTA
* *
2235950 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
** *
2235974 TCTGATACCTGATCTGAATTTTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2235998 TCTGATTTCTGA-C-GTAGATTATGT
1 TCTGATTTCTGATCTG-A-ATTCTGT
* * * *
2236022 TCTAATATCTAATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2236046 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2236059 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
22 1 0.02
23 2 0.03
24 59 0.92
25 1 0.02
26 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2240191 original size:19 final size:19
Alignment explanation
Indices: 2240167--2240232 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
2240157 TATTTTGTTT
2240167 TTTCAAAATCAACTTTTGC
1 TTTCAAAATCAACTTTTGC
2240186 TTTCAAAATCAACTTTTGC
1 TTTCAAAATCAACTTTTGC
2240205 TTTCAAAATCAACTTTTGC
1 TTTCAAAATCAACTTTTGC
2240224 TTTCAAAAT
1 TTTCAAAAT
2240233 GAAATCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (19 bp):
TTTCAAAATCAACTTTTGC
Found at i:2242138 original size:14 final size:14
Alignment explanation
Indices: 2242119--2242146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2242109 GGGCCTGACG
2242119 GTATTGGTACTATA
1 GTATTGGTACTATA
2242133 GTATTGGTACTATA
1 GTATTGGTACTATA
2242147 AGAATAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
GTATTGGTACTATA
Found at i:2245008 original size:67 final size:67
Alignment explanation
Indices: 2244929--2245076 Score: 206
Period size: 67 Copynumber: 2.2 Consensus size: 67
2244919 ATTCTTGTTG
* * * **
2244929 GTCCTAGATTGGTCCTTTAAATGCACTAAGTTATAATAATGTATCCCTGCATGTAGACAAAATTC
1 GTCCTAGATTGGTCCATTAAATGCACCAAGTTAAAATAATACATCCCTGCATGTAGACAAAATTC
2244994 CC
66 CC
* ** *
2244996 GTCCTAGATTGGTTCATTAAATGCACCAAGTTAAAATAATACATCCCTGTGTGTGGACAAAATTC
1 GTCCTAGATTGGTCCATTAAATGCACCAAGTTAAAATAATACATCCCTGCATGTAGACAAAATTC
2245061 CC
66 CC
2245063 GTCCTAGATATGGT
1 GTCCTAGAT-TGGT
2245077 GGACTATTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 67 0.94
68 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (67 bp):
GTCCTAGATTGGTCCATTAAATGCACCAAGTTAAAATAATACATCCCTGCATGTAGACAAAATTC
CC
Found at i:2247164 original size:22 final size:23
Alignment explanation
Indices: 2247150--2247206 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2247140 ATATAATATC
2247150 ATATATTA-TATAATATAATGAA
1 ATATATTATTATAATATAATGAA
*
2247172 ATATATTATTATAACACTAA--AA
1 ATATATTATTATAATA-TAATGAA
*
2247194 ATATAATATTATA
1 ATATATTATTATA
2247207 TTATTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 22 0.71
23 6 0.19
24 3 0.10
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATATTATTATAATATAATGAA
Found at i:2247214 original size:22 final size:22
Alignment explanation
Indices: 2247152--2247253 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
2247142 ATAATATCAT
*
2247152 ATATTATATAATATAATGAAATATA
1 ATATTATATTAT-TAA--AAATATA
* ** *
2247177 TTATTATAACACTAAAAATATA
1 ATATTATATTATTAAAAATATA
*
2247199 ATATTATATTATTAAAAATATTC
1 ATATTATATTATTAAAAATA-TA
* *
2247222 ATAAATATATT-TTAATAAT-TA
1 AT-ATTATATTATTAAAAATATA
*
2247243 ATATTTTATTA
1 ATATTATATTA
2247254 AAATGATACT
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
20 6 0.10
21 3 0.05
22 23 0.38
23 10 0.17
24 10 0.17
25 8 0.13
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (22 bp):
ATATTATATTATTAAAAATATA
Found at i:2247219 original size:54 final size:51
Alignment explanation
Indices: 2247123--2247236 Score: 126
Period size: 54 Copynumber: 2.2 Consensus size: 51
2247113 AATTTTTTAG
* *
2247123 ATATTATTAAAATAAGAATATAATATCATATATTATATAATA-TAATGAAAT
1 ATATTATTAAAATAAAAATATAATATCATATATTATAAAATATTAAT-AAAT
* *
2247174 ATATTATTATAACACTAAAAATATAATATTATATTATTA-AAAATATTCATAAAT
1 ATATTATTA-AA-A-TAAAAATATAATATCATA-TATTATAAAATATTAATAAAT
2247228 ATATT-TTAA
1 ATATTATTAA
2247237 TAATTAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
51 9 0.17
52 3 0.06
53 4 0.07
54 30 0.56
55 8 0.15
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (51 bp):
ATATTATTAAAATAAAAATATAATATCATATATTATAAAATATTAATAAAT
Found at i:2252681 original size:15 final size:15
Alignment explanation
Indices: 2252650--2252684 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2252640 ACCCCAAAAA
**
2252650 ATATAATTTTATGTC
1 ATATAATTTTACATC
2252665 ATATAATTTTACATC
1 ATATAATTTTACATC
2252680 ATATA
1 ATATA
2252685 TTATTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATAATTTTACATC
Found at i:2257474 original size:17 final size:17
Alignment explanation
Indices: 2257452--2257486 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2257442 AAGTTAATTA
2257452 TAGATGTCACTCATTGT
1 TAGATGTCACTCATTGT
2257469 TAGATGTCACTCATTGT
1 TAGATGTCACTCATTGT
2257486 T
1 T
2257487 TTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (17 bp):
TAGATGTCACTCATTGT
Found at i:2258028 original size:2 final size:2
Alignment explanation
Indices: 2258021--2258052 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2258011 TTATTATAAT
2258021 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
2258053 CAAAATTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2258553 original size:42 final size:42
Alignment explanation
Indices: 2258507--2258613 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
2258497 GTCATGTACT
* ** *
2258507 TTAGTGGCGTTTTTATAATAAATGCTGCAATAGTTTTATCCC
1 TTAGTGGCATTTTTATAATAAACACCGCAATAGTTTTATCCC
* * *
2258549 TTAGTGGCATTTTTGTAATAAACACCGTAATAGTTTTGTCCC
1 TTAGTGGCATTTTTATAATAAACACCGCAATAGTTTTATCCC
2258591 TTAGTGGCATTTTTA-ATATAAAC
1 TTAGTGGCATTTTTATA-ATAAAC
2258614 GACGCCATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 55 0.98
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (42 bp):
TTAGTGGCATTTTTATAATAAACACCGCAATAGTTTTATCCC
Found at i:2259259 original size:36 final size:36
Alignment explanation
Indices: 2259212--2259297 Score: 172
Period size: 36 Copynumber: 2.4 Consensus size: 36
2259202 TAATCTTAAT
2259212 TGATTGACTGATTCGCTTTCATAATAATAAAAACAC
1 TGATTGACTGATTCGCTTTCATAATAATAAAAACAC
2259248 TGATTGACTGATTCGCTTTCATAATAATAAAAACAC
1 TGATTGACTGATTCGCTTTCATAATAATAAAAACAC
2259284 TGATTGACTGATTC
1 TGATTGACTGATTC
2259298 CAATATCGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (36 bp):
TGATTGACTGATTCGCTTTCATAATAATAAAAACAC
Found at i:2259482 original size:15 final size:15
Alignment explanation
Indices: 2259462--2259495 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2259452 CTGCGGCAAT
2259462 TGTTCATGGATGCAC
1 TGTTCATGGATGCAC
2259477 TGTTCATGGATGCAC
1 TGTTCATGGATGCAC
2259492 TGTT
1 TGTT
2259496 TCAATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (15 bp):
TGTTCATGGATGCAC
Found at i:2260770 original size:16 final size:16
Alignment explanation
Indices: 2260739--2260772 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2260729 CTTGCTCCCA
2260739 TAAAATTTTATAAATT
1 TAAAATTTTATAAATT
2260755 TAAAAGTTTTAT-AATT
1 TAAAA-TTTTATAAATT
2260771 TA
1 TA
2260773 GGAGTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TAAAATTTTATAAATT
Found at i:2266335 original size:21 final size:22
Alignment explanation
Indices: 2266311--2266351 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2266301 ATGAAGCGAG
*
2266311 GGAAGTAGAGAGAGA-AGCAAC
1 GGAAGCAGAGAGAGAGAGCAAC
*
2266332 GGAAGCAGTGAGAGAGAGCA
1 GGAAGCAGAGAGAGAGAGCA
2266352 TCATATCGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.10, G:0.41, T:0.05
Consensus pattern (22 bp):
GGAAGCAGAGAGAGAGAGCAAC
Found at i:2266862 original size:85 final size:86
Alignment explanation
Indices: 2266764--2266983 Score: 300
Period size: 85 Copynumber: 2.6 Consensus size: 86
2266754 ATTTGTGGCG
*
2266764 TTTGTATCCAAAAAACGCCGCTATATACCT-GACCTTTTGCGGCGTTTGTTAAAAACACCGCTAT
1 TTTGTATCCAAAAAACGCCGCTATATATCTAGACCTTTTGCGGCGTTTGTTAAAAACACCGCTAT
2266828 AGATATAGACCGTTTACGACA
66 AGATATAGACCGTTTACGACA
* * * *
2266849 TTTTTATCCAAAAAA-GCCTCTATATATCTAAACCTTTTGCGGCGTTTGTTAAAAACGCCGCTAT
1 TTTGTATCCAAAAAACGCCGCTATATATCTAGACCTTTTGCGGCGTTTGTTAAAAACACCGCTAT
** * * *
2266913 AGATATAGACTTTTTGCGGCG
66 AGATATAGACCGTTTACGACA
* * * *
2266934 TTTGTATTCAAGAAACGCCGCTATATATCTAGACCTTTTGCAGCTTTTGT
1 TTTGTATCCAAAAAACGCCGCTATATATCTAGACCTTTTGCGGCGTTTGT
2266984 ATTCAAAAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
84 12 0.10
85 74 0.64
86 30 0.26
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (86 bp):
TTTGTATCCAAAAAACGCCGCTATATATCTAGACCTTTTGCGGCGTTTGTTAAAAACACCGCTAT
AGATATAGACCGTTTACGACA
Found at i:2266952 original size:45 final size:44
Alignment explanation
Indices: 2266755--2267028 Score: 265
Period size: 45 Copynumber: 6.3 Consensus size: 44
2266745 TTTTAGATAA
* * *
2266755 TTTGTGGCGTTTGTATCCAAAAAACGCCGCTATATACCT-GACCT
1 TTTGCGGCGTTTGTATTC-AAAAACGCCGCTATATATCTAGACCT
* * * *
2266799 TTTGCGGCGTTTG--TT-AAAAACACCGCTATAGATATAGACCG
1 TTTGCGGCGTTTGTATTCAAAAACGCCGCTATATATCTAGACCT
* * * * * * * *
2266840 TTTACGACATTTTTATCCAAAAAAGCCTCTATATATCTAAACCT
1 TTTGCGGCGTTTGTATTCAAAAACGCCGCTATATATCTAGACCT
* * *
2266884 TTTGCGGCGTTTG--TT-AAAAACGCCGCTATAGATATAGACTT
1 TTTGCGGCGTTTGTATTCAAAAACGCCGCTATATATCTAGACCT
2266925 TTTGCGGCGTTTGTATTCAAGAAACGCCGCTATATATCTAGACCT
1 TTTGCGGCGTTTGTATTCAA-AAACGCCGCTATATATCTAGACCT
* * * *
2266970 TTTGCAGCTTTTGTATTCAAAAAATGCCACTATATATCTAGACCT
1 TTTGCGGCGTTTGTATTC-AAAAACGCCGCTATATATCTAGACCT
*
2267015 TTTACGGCGTTTGT
1 TTTGCGGCGTTTGT
2267029 CCCGCAACCG
Statistics
Matches: 181, Mismatches: 40, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
40 16 0.09
41 46 0.25
42 2 0.01
43 3 0.02
44 42 0.23
45 70 0.39
46 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (44 bp):
TTTGCGGCGTTTGTATTCAAAAACGCCGCTATATATCTAGACCT
Found at i:2267056 original size:130 final size:124
Alignment explanation
Indices: 2266774--2267065 Score: 286
Period size: 130 Copynumber: 2.3 Consensus size: 124
2266764 TTTGTATCCA
*
2266774 AAAAACGCCGCTATATA-CCTGACCTTTTGCGGCGTTTGTTAAAAACACCGCTATAGATATAGAC
1 AAAAAC-CCGCTATATATTC-GACCTTTTGCGGCGTTTGTTAAAAACACCGCTATAGATATAGAC
* * *
2266838 CGTTTACGACATTTTTATCCAAAAAAGCCTCTATATATCTAAACCTTTTGCGGCGTTTGTT
64 CGTTTACGACATTTTTATCCAAAAAAGCCACTATATATCTAAACCTTTTACGGCGTTTGTC
* * * * * *
2266899 AAAAACGCCGCTATAGATATAGACTTTTTGCGGCGTTTGTATTCAAGAAACGCCGCTATATATCT
1 AAAAAC-CCGCTATATAT-TCGACCTTTTGCGGCGTTTG--TT-AA-AAACACCGCTATAGATAT
* * * *
2266964 AGACCTTTTGC-AGC-TTTTGTATTCAAAAAATGCCACTATATATCTAGACCTTTTACGGCGTTT
60 AGACCGTTTACGA-CATTTT-TATCCAAAAAA-GCCACTATATATCTAAACCTTTTACGGCGTTT
2267027 GTCC
122 GT-C
*** *
2267031 CGCAA-CCGCTATATATTCGACCTTTTGCGACGTTT
1 AAAAACCCGCTATATATTCGACCTTTTGCGGCGTTT
2267066 ATTCCAAAAA
Statistics
Matches: 136, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
125 16 0.12
126 17 0.12
128 2 0.01
129 23 0.17
130 45 0.33
131 31 0.23
132 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (124 bp):
AAAAACCCGCTATATATTCGACCTTTTGCGGCGTTTGTTAAAAACACCGCTATAGATATAGACCG
TTTACGACATTTTTATCCAAAAAAGCCACTATATATCTAAACCTTTTACGGCGTTTGTC
Found at i:2267264 original size:2 final size:2
Alignment explanation
Indices: 2267257--2267281 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2267247 TGCTGTAGTG
2267257 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2267282 AAGGGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2277642 original size:21 final size:21
Alignment explanation
Indices: 2277617--2277666 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2277607 GGAGCGTGAG
2277617 GGGTATCGATACCTATCCATA
1 GGGTATCGATACCTATCCATA
2277638 GGGTATCGATACCTATCCATA
1 GGGTATCGATACCTATCCATA
2277659 GGGTATCG
1 GGGTATCG
2277667 GTACTTGCAG
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:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCTATCCATA
Found at i:2282419 original size:24 final size:22
Alignment explanation
Indices: 2282370--2282421 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
2282360 CACTTATTTT
2282370 TGTTTTCATTTTACAGAAATCA
1 TGTTTTCATTTTACAGAAATCA
2282392 -GTTTCTCATTTTACAAGCAAAT-A
1 TGTTT-TCATTTTAC-AG-AAATCA
2282415 TGTTTTC
1 TGTTTTC
2282422 TTTAACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 4 0.15
22 9 0.35
23 5 0.19
24 8 0.31
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (22 bp):
TGTTTTCATTTTACAGAAATCA
Found at i:2283260 original size:7 final size:7
Alignment explanation
Indices: 2283248--2283280 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
2283238 CCATTTCTAT
2283248 TTTACAG
1 TTTACAG
2283255 TTTACAG
1 TTTACAG
2283262 TTTACAG
1 TTTACAG
2283269 TTTACAG
1 TTTACAG
2283276 TTTAC
1 TTTAC
2283281 TATTTGTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (7 bp):
TTTACAG
Found at i:2284547 original size:155 final size:155
Alignment explanation
Indices: 2284248--2284558 Score: 581
Period size: 155 Copynumber: 2.0 Consensus size: 155
2284238 AAGTTAAGAA
2284248 AATTTTCGAGGATAAAATTATATTAAAAGGGGAGAATTAACTTTAAAGGTAGCTTTAAAAAGAAT
1 AATTTTCGAGGAT-AAATTATATTAAAAGGGGAGAATTAACTTTAAAGGTAGCTTTAAAAAGAAT
2284313 GGAGTCTTATCTTAGAAAGCGACCAAGCCTATGATAGGAGGAAGAGCTCCCCAACCGCTCCTCCG
65 GGAGTCTTATCTTAGAAAGCGACCAAGCCTATGATAGGAGGAAGAGCTCCCCAACCGCTCCTCCG
2284378 ATGAATGGACTCAATATTTTTGGACT
130 ATGAATGGACTCAATATTTTTGGACT
2284404 AATTTT-GAGGAT-AATTATATTAAAAGGGGAGAATTAACTTTAAAGGTAGCTTTAAAAAGAATG
1 AATTTTCGAGGATAAATTATATTAAAAGGGGAGAATTAACTTTAAAGGTAGCTTTAAAAAGAATG
2284467 GAGTCTTATCTTAGAAAGCGACACCAAGCCTATGATAGGAGGAAGAGCTCCCCAACCGCTCCTCC
66 GAGTCTTATCTTAGAAAGCG--ACCAAGCCTATGATAGGAGGAAGAGCTCCCCAACCGCTCCTCC
2284532 GATGAATGGACTCAATATTTTTGGACT
129 GATGAATGGACTCAATATTTTTGGACT
2284559 TAATATTTTT
Statistics
Matches: 153, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
153 71 0.46
155 76 0.50
156 6 0.04
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (155 bp):
AATTTTCGAGGATAAATTATATTAAAAGGGGAGAATTAACTTTAAAGGTAGCTTTAAAAAGAATG
GAGTCTTATCTTAGAAAGCGACCAAGCCTATGATAGGAGGAAGAGCTCCCCAACCGCTCCTCCGA
TGAATGGACTCAATATTTTTGGACT
Found at i:2284574 original size:15 final size:15
Alignment explanation
Indices: 2284538--2284577 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
2284528 CTCCGATGAA
*
2284538 TGGACTCAATATTTT
1 TGGACTTAATATTTT
2284553 TGGACTTAATATTTT
1 TGGACTTAATATTTT
2284568 TGGACTTAAT
1 TGGACTTAAT
2284578 TGAATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (15 bp):
TGGACTTAATATTTT
Found at i:2289309 original size:3 final size:3
Alignment explanation
Indices: 2289282--2289327 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
2289272 TAACAAAATG
*
2289282 TAA TAA -AA -AA TAA TTAA TTAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
2289327 T
1 T
2289328 CGACTCGGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 29 0.74
4 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2289844 original size:91 final size:92
Alignment explanation
Indices: 2289688--2289862 Score: 291
Period size: 91 Copynumber: 1.9 Consensus size: 92
2289678 GTGATAGGTC
*
2289688 GAACAAGCTCTTCTCATTATGAACTTCCTCTCCTTCTTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCCTCTCCTTCGTTCAGATGAGTTCTTCTCATTATGAACT
2289753 CTCCATTGAAAATGTTGATGTGAAGTT
66 CTCCATTGAAAATGTTGATGTGAAGTT
* *
2289780 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCGTT-AGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCCTC-TCCTTCGTTCAGATGAGTTCTTCTCATTATGAAC
*
2289843 TCTCCATTGGAAATGTTGAT
65 TCTCCATTGAAAATGTTGAT
2289863 CCATCTCTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
91 43 0.55
92 32 0.41
93 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTCCTCTCCTTCGTTCAGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTTGATGTGAAGTT
Found at i:2290100 original size:332 final size:331
Alignment explanation
Indices: 2289447--2290103 Score: 1027
Period size: 332 Copynumber: 2.0 Consensus size: 331
2289437 CGTCGTTGGA
* *
2289447 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCTTTATGAACT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTAGATGAGTTCTTCTCATTATGAACT
* *
2289512 CTTCACTGAAAATGTTGAGTCACTTATTTCTGTGGTGGACTTGAAAGGAACAAGTTCTTCTCATT
66 CTCCACTGAAAATGTTGAGTCACTTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATT
* *
2289577 ATGAACTTTCTCCTTTAAGATGAGTTCTTCTCATTATAAACTCTTTTGGAAATGTCAATCCCTCT
131 ATGAACTTTCTCCTTTAAGATGAGTTCTTCTCATTATAAACTCTTCTGAAAATGTCAATCCCTCT
* *
2289642 AACGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTA
196 AACGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTA
*
2289707 TGAACTTCCTCTCCTTCTTTCAGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGAT
261 TGAACTTCCTCTCCTTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGAT
2289772 GTGAAG
326 GTGAAG
2289778 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-TCCTCGTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCT-CTCG-TAGATGAGTTCTTCTCATTATGAA
* * *
2289842 CTCTCCATTGGAAATGTTGA-TC-CATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCT
64 CTCTCCACTGAAAATGTTGAGTCAC-T-TATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCT
* * *
2289905 TATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCC
127 CATTATGAACTTTCTCCTTTAAGATGAGTTCTTCTCATTATAAACTCTTCTGAAAATGTCAATCC
*
2289970 CTC-AAGCGAGGTATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCT
192 CTCTAA-CGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCT
* ** * * *
2290034 CATTATGAATTTTTTCTTCC-TCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAAT
256 CATTATGAACTTCCTC-TCCTTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAAT
2290098 GTTGAT
320 GTTGAT
2290104 CTGTTTATCT
Statistics
Matches: 298, Mismatches: 22, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
330 2 0.01
331 42 0.14
332 251 0.84
333 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (331 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTAGATGAGTTCTTCTCATTATGAACT
CTCCACTGAAAATGTTGAGTCACTTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATT
ATGAACTTTCTCCTTTAAGATGAGTTCTTCTCATTATAAACTCTTCTGAAAATGTCAATCCCTCT
AACGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTA
TGAACTTCCTCTCCTTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGAT
GTGAAG
Found at i:2290481 original size:15 final size:15
Alignment explanation
Indices: 2290441--2290482 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
2290431 TCAAATGAAA
*
2290441 ACTGTCTCAAACGAG
1 ACTGTCTCAAGCGAG
*
2290456 ACTGTCTCAAGGGAG
1 ACTGTCTCAAGCGAG
2290471 ACTGTCTCAAGC
1 ACTGTCTCAAGC
2290483 AAGAAGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (15 bp):
ACTGTCTCAAGCGAG
Found at i:2290564 original size:13 final size:15
Alignment explanation
Indices: 2290528--2290585 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
2290518 GGAGACAACT
2290528 TTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAA
* *
2290543 TTGTCTCAA-A-AAC
1 TTGTTTCAAGAGAAA
2290556 TTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAA
* * *
2290571 CTGTCTCAAGGGAAA
1 TTGTTTCAAGAGAAA
2290586 CAAAATTCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
13 10 0.29
14 2 0.06
15 22 0.65
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (15 bp):
TTGTTTCAAGAGAAA
Found at i:2290612 original size:36 final size:36
Alignment explanation
Indices: 2290567--2290642 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
2290557 TGTTTCAAGA
* *
2290567 GAAACTGTCTCAAGGGAAACAAAATTCATTTAAAGG
1 GAAAATGTCTCAAGAGAAACAAAATTCATTTAAAGG
* ** *
2290603 GAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAAATGTCTCAAGAGAAACAAAATTCATTTAAAGG
2290639 GAAA
1 GAAA
2290643 CATTTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAAATGTCTCAAGAGAAACAAAATTCATTTAAAGG
Found at i:2290708 original size:37 final size:38
Alignment explanation
Indices: 2290649--2290731 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 38
2290639 GAAACATTTT
* * *
2290649 CAAAGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGA
1 CAAAATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGA
2290687 CAAAATTT-TGTTTCAAGAGAAACTGTCTCAAGCGAGA
1 CAAAATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGA
2290724 CAAAATTT
1 CAAAATTT
2290732 GTCTGGAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 35 0.83
38 7 0.17
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (38 bp):
CAAAATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGA
Found at i:2293516 original size:9 final size:9
Alignment explanation
Indices: 2293489--2293560 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
2293479 CTTGACTCAA
*
2293489 TTTCATTTC
1 TTTCTTTTC
*
2293498 ATTTCATTTC
1 -TTTCTTTTC
2293508 TTTCTTTTC
1 TTTCTTTTC
*
2293517 TTTTTTTCTC
1 TTTCTTT-TC
*
2293527 TTTTTTTTC
1 TTTCTTTTC
2293536 TCTT-TTTT-
1 T-TTCTTTTC
*
2293544 TTTCTTTTT
1 TTTCTTTTC
2293553 TTTCTTTT
1 TTTCTTTT
2293561 TTGATGGATG
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 29 0.52
10 20 0.36
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:2293533 original size:11 final size:11
Alignment explanation
Indices: 2293517--2293562 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
2293507 CTTTCTTTTC
2293517 TTTTTTTCTCT
1 TTTTTTTCTCT
2293528 TTTTTTTCTCT
1 TTTTTTTCTCT
2293539 TTTTTTT-TCT
1 TTTTTTTCTCT
2293549 TTTTTTTCT-T
1 TTTTTTTCTCT
2293559 TTTT
1 TTTT
2293563 GATGGATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 15 0.44
11 19 0.56
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:2293541 original size:21 final size:21
Alignment explanation
Indices: 2293515--2293562 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2293505 TTCTTTCTTT
2293515 TCTTTTTTTCTCTTTTTTTTC
1 TCTTTTTTTCTCTTTTTTTTC
*
2293536 TCTTTTTTTTTCTTTTTTTTC
1 TCTTTTTTTCTCTTTTTTTTC
2293557 T-TTTTT
1 TCTTTTT
2293563 GATGGATGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (21 bp):
TCTTTTTTTCTCTTTTTTTTC
Found at i:2293561 original size:9 final size:9
Alignment explanation
Indices: 2293504--2293562 Score: 73
Period size: 9 Copynumber: 6.1 Consensus size: 9
2293494 TTTCATTTCA
*
2293504 TTTCTTTCT
1 TTTCTTTTT
2293513 TTTCTTTTT
1 TTTCTTTTT
2293522 TTCTCTTTTTT
1 TT-TC-TTTTT
2293533 TTCTCTTTTTT
1 TT-TC-TTTTT
2293544 TTTCTTTTT
1 TTTCTTTTT
2293553 TTTCTTTTT
1 TTTCTTTTT
2293562 T
1 T
2293563 GATGGATGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
9 25 0.53
10 4 0.09
11 18 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:2295930 original size:13 final size:13
Alignment explanation
Indices: 2295912--2295941 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2295902 ATTCTCTAAA
2295912 TATCCCAAATCTT
1 TATCCCAAATCTT
2295925 TATCCCAAATCTT
1 TATCCCAAATCTT
2295938 TATC
1 TATC
2295942 AGTTCTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (13 bp):
TATCCCAAATCTT
Found at i:2297322 original size:13 final size:13
Alignment explanation
Indices: 2297290--2297325 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2297280 CTAAAAACGT
2297290 ATTTTAA-AAACA
1 ATTTTAATAAACA
2297302 ATTTTAATAAACA
1 ATTTTAATAAACA
2297315 ATTTTAATAAA
1 ATTTTAATAAA
2297326 AATCGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTTTAATAAACA
Found at i:2299818 original size:3 final size:3
Alignment explanation
Indices: 2299788--2299834 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
2299778 TAACAAAATG
2299788 TAA TAA -AA -AA TAA TTAA TTAA TTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA
2299834 T
1 T
2299835 CGACTCAGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 27 0.64
4 11 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2300129 original size:4 final size:4
Alignment explanation
Indices: 2300120--2300145 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2300110 TATTATAAAT
2300120 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
2300146 ATTATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2312394 original size:94 final size:94
Alignment explanation
Indices: 2312276--2312478 Score: 370
Period size: 94 Copynumber: 2.2 Consensus size: 94
2312266 ATTTGGTCTC
*
2312276 CACAGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACTGAAGAGTAGTGAAACAAA
1 CACAGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACAAA
*
2312341 TTCTTTTCAAGTAATACAAATTCAGCCTT
66 TTATTTTCAAGTAATACAAATTCAGCCTT
*
2312370 CACAGAAGAGTAGTGGAAGTAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACAAA
1 CACAGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACAAA
2312435 TTATTTTCAAGTAATACAAATTCAGCCTT
66 TTATTTTCAAGTAATACAAATTCAGCCTT
*
2312464 CACAAAAGAGTAGTG
1 CACAGAAGAGTAGTG
2312479 AGGTAATGCA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 105 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (94 bp):
CACAGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACAAA
TTATTTTCAAGTAATACAAATTCAGCCTT
Found at i:2312485 original size:36 final size:35
Alignment explanation
Indices: 2312445--2312514 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
2312435 TTATTTTCAA
2312445 GTAATACAAATTCAGCCTTCACAAAAGAGTAGTGAG
1 GTAATAC-AATTCAGCCTTCACAAAAGAGTAGTGAG
* * *
2312481 GTAATGCAATTTAGCCTTCACGAAAGAGTAGTGA
1 GTAATACAATTCAGCCTTCACAAAAGAGTAGTGA
2312515 AGCGTTGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (35 bp):
GTAATACAATTCAGCCTTCACAAAAGAGTAGTGAG
Found at i:2312524 original size:35 final size:34
Alignment explanation
Indices: 2312453--2312550 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 34
2312443 AAGTAATACA
2312453 AATTCAGCCTTCACAAAAGAGTAGTGAGGTAATGC
1 AATTCAGCCTTCACAAAAGAGTAGTGAGGT-ATGC
* *
2312488 AATTTAGCCTTCACGAAAGAGTAGTGAAGCGT-TGC
1 AATTCAGCCTTCACAAAAGAGTAGTG-AG-GTATGC
* * **
2312523 AAATCCAACCTTCGTAAAAGAGTAGTGA
1 -AATTCAGCCTTCACAAAAGAGTAGTGA
2312551 AGCAAGAACA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 28 0.54
36 22 0.42
37 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (34 bp):
AATTCAGCCTTCACAAAAGAGTAGTGAGGTATGC
Found at i:2314783 original size:28 final size:28
Alignment explanation
Indices: 2314747--2314806 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
2314737 TGAAAATTTA
2314747 CAGAAACCATCTAAGTATGAGAATTATG
1 CAGAAACCATCTAAGTATGAGAATTATG
2314775 CAGAAACCATCTAAGTATGAGAATTATG
1 CAGAAACCATCTAAGTATGAGAATTATG
2314803 CAGA
1 CAGA
2314807 TTTACTAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (28 bp):
CAGAAACCATCTAAGTATGAGAATTATG
Found at i:2317155 original size:3 final size:3
Alignment explanation
Indices: 2317147--2317238 Score: 80
Period size: 3 Copynumber: 29.3 Consensus size: 3
2317137 GATTAAAATC
* * *
2317147 ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA AAA ATT GTA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
2317193 A-A TATA ATA ATA AT- ATA AGTAA ATA ATA TTA TATA ATA TATA ATA
1 ATA -ATA ATA ATA ATA ATA A-T-A ATA ATA ATA -ATA ATA -ATA ATA
2317238 A
1 A
2317239 AAGATGATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
2 3 0.04
3 57 0.78
4 11 0.15
5 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2318453 original size:16 final size:16
Alignment explanation
Indices: 2318432--2318462 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2318422 TATGTTGTGA
2318432 GTTCTAGAATAGTTTT
1 GTTCTAGAATAGTTTT
2318448 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
2318463 GTTAGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
GTTCTAGAATAGTTTT
Found at i:2319216 original size:14 final size:14
Alignment explanation
Indices: 2319197--2319234 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
2319187 AAATATAAAT
2319197 CATTTTCCAGAAGA
1 CATTTTCCAGAAGA
2319211 CATTTTCCAGAAGA
1 CATTTTCCAGAAGA
*
2319225 TATTTTCCAG
1 CATTTTCCAG
2319235 TGTTTGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (14 bp):
CATTTTCCAGAAGA
Found at i:2320155 original size:31 final size:31
Alignment explanation
Indices: 2320112--2320207 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
2320102 ATAGAAATTT
*
2320112 TCAAGACACTGATGCATCTAATGCAGTTCGA
1 TCAAAACACTGATGCATCTAATGCAGTTCGA
*
2320143 TCAAAACACTGATACATCTAATGCAGTTCGA
1 TCAAAACACTGATGCATCTAATGCAGTTCGA
2320174 TCAAAACACTGATGCATCTAATGCAGTTCGA
1 TCAAAACACTGATGCATCTAATGCAGTTCGA
2320205 TCA
1 TCA
2320208 CCATATATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (31 bp):
TCAAAACACTGATGCATCTAATGCAGTTCGA
Found at i:2327456 original size:21 final size:21
Alignment explanation
Indices: 2327419--2327501 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
2327409 TTTTGGTGCA
*
2327419 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
* **
2327439 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
2327460 GAAGGGGAACCGATTCCCCCCAT
1 G-A-GGGAACCGATTCCCCCCAT
* *
2327483 -AGGGGAATCGATACCCCCC
1 GA-GGGAACCGATTCCCCCC
2327502 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.18
21 25 0.49
22 1 0.02
23 16 0.31
ACGTcount: A:0.24, C:0.34, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:2329503 original size:17 final size:17
Alignment explanation
Indices: 2329478--2329511 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2329468 TTGAATATTT
*
2329478 TGGAATGTTTGATTTTG
1 TGGAATGTTGGATTTTG
*
2329495 TGGATTGTTGGATTTTG
1 TGGAATGTTGGATTTTG
2329512 GATTTATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (17 bp):
TGGAATGTTGGATTTTG
Found at i:2330172 original size:21 final size:20
Alignment explanation
Indices: 2330125--2330164 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
2330115 GATTGCTCAG
*
2330125 AGGGAACCGATTCCCCCCCA
1 AGGGTACCGATTCCCCCCCA
2330145 AGGGGGTACCGATTCCCCCC
1 A--GGGTACCGATTCCCCCC
2330165 TGAAGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
22 16 0.94
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.12
Consensus pattern (20 bp):
AGGGTACCGATTCCCCCCCA
Found at i:2331996 original size:74 final size:74
Alignment explanation
Indices: 2331875--2332022 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
2331865 AAGTTCATTA
* * *
2331875 TATTTTCTAAAGAGAAATAAATACTGCCCATTTCATGTGGATCTTGTTCGGAAGTTTGGACATCA
1 TATTTTCTAAAGAGAAATAAATACTCCCCATTTCATGTGAATCTTGTTCGGAAGTTCGGACATCA
2331940 AGCTTCCTT
66 AGCTTCCTT
*
2331949 TATTTTCTAAAGAGAAATAAATACTCCCCATTTCCTGTGAATCTTGTTCGGAAGTTCGGACATCA
1 TATTTTCTAAAGAGAAATAAATACTCCCCATTTCATGTGAATCTTGTTCGGAAGTTCGGACATCA
2332014 AGCTTCCTT
66 AGCTTCCTT
2332023 GACAGGTGCA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (74 bp):
TATTTTCTAAAGAGAAATAAATACTCCCCATTTCATGTGAATCTTGTTCGGAAGTTCGGACATCA
AGCTTCCTT
Found at i:2333139 original size:182 final size:182
Alignment explanation
Indices: 2332754--2333227 Score: 725
Period size: 182 Copynumber: 2.6 Consensus size: 182
2332744 GATCCAAATT
* * * * **
2332754 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGAAAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
2332819 AAACTGGTAAAGCGGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
2332884 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
2332936 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
2333001 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
2333065 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
2333117 AAAAATGTATCGATCAAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
2333182 AAAACCGGTAAAATGATACCAGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
2333228 CGTAAGTACG
Statistics
Matches: 264, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 82 0.31
182 182 0.69
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:2333171 original size:20 final size:19
Alignment explanation
Indices: 2333148--2333194 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2333138 CGATATAACA
2333148 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2333168 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2333188 GGTAAAA
1 GGTAAAA
2333195 TGATACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2333196 original size:17 final size:19
Alignment explanation
Indices: 2333157--2333199 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2333147 AGGTAAAAAT
2333157 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
2333177 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
2333194 ATGATA
1 ATGATA
2333200 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:2335477 original size:21 final size:21
Alignment explanation
Indices: 2335451--2335491 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2335441 AAGACAATCA
2335451 AGAGTCGAAGATAAACTTGAT
1 AGAGTCGAAGATAAACTTGAT
*
2335472 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGATAAACTTGA
2335492 GATGCATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.22
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTTGAT
Found at i:2338881 original size:182 final size:182
Alignment explanation
Indices: 2338254--2339818 Score: 2682
Period size: 182 Copynumber: 8.6 Consensus size: 182
2338244 TTTTACCTTT
* *
2338254 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * **
2338319 AATAATATAACAAGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGCAAAGCGCTGT
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
2338384 CGGTTATATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
2338436 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
2338500 AACAATATAACATGTCAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2338565 CGGTTATCTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
2338615 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
2338679 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
2338744 CCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
2338797 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
2338862 AACAATATAACAGGTAAAAATATGACAAAACTGGTCTTGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2338927 CGGTTA-GATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATG-TTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
2338979 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
2339043 AACAATATAACATGAAAAAATATGACAAAACGGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
2339108 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
2339158 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
2339222 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* *
2339287 CCGGTTATGTTGAAAGTGTCAATAATTTATTATAAGTATCGACACTTTTAGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * *
2339340 TTTAAAAGGGAAGAAGCTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
2339405 AACAATATAACAGGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
2339470 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
2339522 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
2339587 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACTGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2339652 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
2339704 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * **
2339768 TAATAATATAACATGTAAAATTATGATAAAACCGGTCTATAAATGACAAAA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
2339819 GGTGAACGCA
Statistics
Matches: 1314, Mismatches: 56, Indels: 26
0.94 0.04 0.02
Matches are distributed among these distances:
178 8 0.01
179 36 0.03
180 304 0.23
181 299 0.23
182 659 0.50
183 8 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:2339281 original size:543 final size:543
Alignment explanation
Indices: 2338254--2339818 Score: 2790
Period size: 543 Copynumber: 2.9 Consensus size: 543
2338244 TTTTACCTTT
* * *
2338254 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
* * * **
2338319 AATAATATAACAAGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGCAAAGCGCTGT
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2338384 CGGTTATATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTAGATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
2338449 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
196 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
* *
2338514 TCAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATCTTGAAA
261 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
2338579 GTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
326 GTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
2338644 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
391 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
*
2338709 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTAT
456 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCAATAATTTAT
*
2338774 TATAAGTATCGACACTTTTGGAA
521 TATAAGTATCGACACTTTTAGAA
2338797 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
* *
2338862 AACAATATAACAGGTAAAAATATGACAAAACTGGTCTTGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
2338927 CGGTTAGATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTAGATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
2338992 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
196 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
* *
2339057 AAAAAATATGACAAAACGGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
261 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
2339122 GTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
326 GTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
2339187 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
391 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
*
2339252 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCAATAATTTAT
456 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCAATAATTTAT
2339317 TATAAGTATCGACACTTTTAGAA
521 TATAAGTATCGACACTTTTAGAA
* *
2339340 TTTAAAAGGGAAGAAGCTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
*
2339405 AACAATATAACAGGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2339470 CGGTTATG-TTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
131 CGGTTA-GATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAA
* *
2339534 GAAGTTATAGCGTCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACA
195 G-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
* * *
2339599 GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACTGGTAAAGCGCTACCGGATATGTTGA
259 TGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
2339664 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGC
324 AAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGC
* * *
2339729 CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAATTATGA
387 CAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
* **
2339794 TAAAACCGGTCTATAAATGACAAAA
452 CAAAACCGGTCTCGAAATGACAAAA
2339819 GGTGAACGCA
Statistics
Matches: 981, Mismatches: 37, Indels: 5
0.96 0.04 0.00
Matches are distributed among these distances:
543 712 0.73
544 150 0.15
546 119 0.12
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (543 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTAGATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
GTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCAATAATTTAT
TATAAGTATCGACACTTTTAGAA
Found at i:2339645 original size:725 final size:724
Alignment explanation
Indices: 2338254--2339818 Score: 2701
Period size: 725 Copynumber: 2.2 Consensus size: 724
2338244 TTTTACCTTT
* *
2338254 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* **
2338319 AATAATATAACAAGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGCAAAGCGCTGT
66 AATAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGCAAAGCGCTAC
*
2338384 CGGTTATATTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTATATTGAAAGTGTCGATAATTTATTATAAGTATCGA-ACTTTTGGAATTTAAAAGAGAAG
2338449 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
195 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
*
2338514 TCAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATCTTGAAA
260 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATCTTGAAA
* * *
2338579 GTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
325 GTGTCAATAATTTATTATAAGTATCGACTTTTAGAATTAATAAGAGAAGAAGCTATAGCGCCAAT
* * *
2338644 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
390 AAAGTGTCGATACTTGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
2338709 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTAT
455 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTAT
*
2338774 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAC
520 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCAATAC
* *
2338839 TTGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACTGGTCTTGAAA
585 TTGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAA
* *
2338904 TGACAAAACAGGTAAAGCGCTACCGGTTA-GATTGAAAGTGTCGATAATTTATTATACGTATCGA
650 TGACAAAACAGGTAAAGCGCTACCGGATATG-TTGAAAGTGTCGATAATTTATTATAAGTATCGA
2338968 CACTTTTGGAA
714 CACTTTTGGAA
2338979 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * *
2339043 AACAATATAACATGAAAAAATATGACAAAACGGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AATAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGCAAAGCGCTAC
*
2339108 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG-ACTTTTGGAA-TTAATAAGAGAAG
131 CGGTTATATTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAATTTAA-AAGAGAAG
*
2339171 AAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAT
195 -AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAT
*
2339236 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
259 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATCTTGAA
*
2339301 AGTGTCAATAATTTATTATAAGTATCGACACTTTTAGAATTTAA-AAGGGAAGAAGCTATAGCGC
324 AGTGTCAATAATTTATTATAAGTATCG--ACTTTTAGAA-TTAATAAGAGAAGAAGCTATAGCGC
*
2339365 CAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCATAACAATATAACAGGTAATAATATGA
386 CAATAAAGTGTCGATACTTGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
*
2339430 CAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAAT
451 CAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAAT
*
2339495 TTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCA
516 TTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCA
*
2339560 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTC
581 ATACTTGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTC
*
2339625 GAAATGACAAAACTGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAT
646 GAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAT
2339690 CGACACTTTTGGAA
711 CGACACTTTTGGAA
2339704 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * **
2339768 TAATAATATAACATGTAAAATTATGATAAAACCGGTCTATAAATGACAAAA
65 TAATAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
2339819 GGTGAACGCA
Statistics
Matches: 794, Mismatches: 38, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
721 4 0.01
722 18 0.02
723 152 0.19
724 149 0.19
725 372 0.47
726 99 0.12
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (724 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AATAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGCAAAGCGCTAC
CGGTTATATTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAATTTAAAAGAGAAGA
GTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGT
AAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATCTTGAAAG
TGTCAATAATTTATTATAAGTATCGACTTTTAGAATTAATAAGAGAAGAAGCTATAGCGCCAATA
AAGTGTCGATACTTGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA
CCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATT
ATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCAATACT
TGATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAT
GACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACA
CTTTTGGAA
Found at i:2340057 original size:86 final size:87
Alignment explanation
Indices: 2339954--2340115 Score: 290
Period size: 86 Copynumber: 1.9 Consensus size: 87
2339944 AAATAGGTCA
2339954 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
2340019 -CGGTTAAATACCTGTTTTATT
66 CCAGTTAAATACCTGTTTTATT
* *
2340040 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
2340105 CCAGTTAAATA
66 CCAGTTAAATA
2340116 ATATAACATA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 63 0.88
87 9 0.12
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATACCTGTTTTATT
Found at i:2340087 original size:23 final size:23
Alignment explanation
Indices: 2340037--2340081 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2340027 TACCTGTTTT
* *
2340037 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
2340060 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
2340082 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:2340157 original size:16 final size:16
Alignment explanation
Indices: 2340138--2340182 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2340128 CGATCTAAAT
2340138 TTTAACCGGTCACTTA
1 TTTAACCGGTCACTTA
2340154 TTTAACCGGTCACTTA
1 TTTAACCGGTCACTTA
*
2340170 TTTAACCGTTCAC
1 TTTAACCGGTCAC
2340183 GTCGTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (16 bp):
TTTAACCGGTCACTTA
Found at i:2345744 original size:16 final size:17
Alignment explanation
Indices: 2345716--2345751 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2345706 CGTATCGCCG
2345716 ACGAAATTTTACTATTC
1 ACGAAATTTTACTATTC
2345733 ACGAAA-TTTACTATTC
1 ACGAAATTTTACTATTC
2345749 ACG
1 ACG
2345752 TTAGTAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
ACGAAATTTTACTATTC
Found at i:2352115 original size:3 final size:3
Alignment explanation
Indices: 2352102--2352163 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
2352092 ATTAATATAT
*
2352102 TAA TAAA TAA TAA TAA TAA TAA TAA TTAA TAA -ACA AAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA
2352149 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
2352164 AATTAAAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
2 1 0.02
3 46 0.85
4 7 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2352583 original size:132 final size:133
Alignment explanation
Indices: 2352366--2352686 Score: 412
Period size: 132 Copynumber: 2.4 Consensus size: 133
2352356 GTTCTGGTCG
* ** * * *
2352366 TCTAAGGGTGACA-TAGCTCCTACGTAATGAAGATATATGGTCAGGGGATGGCACTGCTCATACG
1 TCTAAGGGTGACACGA-CTCCTACG--ATGAAGAGGTCTGGTCAGGGGATGACACTGCTCATACA
*
2352430 TGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGAC
63 TGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACACGATGAGGACGAC
*
2352495 TGGTTA
128 TGATTA
* * * *
2352501 TCTAGGGGTGACACGGCTCCTAC-ATGAGGAGGTCTGGTCGGGGGATGACACTGCTCATACATGA
1 TCTAAGGGTGACACGACTCCTACGATGAAGAGGTCTGGTCAGGGGATGACACTGCTCATACATGA
* * * * *
2352565 TGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACACGATGTGGATGGCTGA
66 TGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACACGATGAGGACGACTGA
2352630 TTA
131 TTA
* *
2352633 TCTAAGGGTGACACGACTCCTACGTGATGAAGAGGTCTGGTCAAGGAATGACAC
1 TCTAAGGGTGACACGACTCCTAC--GATGAAGAGGTCTGGTCAGGGGATGACAC
2352687 GGTAACTACA
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
132 116 0.73
135 43 0.27
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (133 bp):
TCTAAGGGTGACACGACTCCTACGATGAAGAGGTCTGGTCAGGGGATGACACTGCTCATACATGA
TGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACACGATGAGGACGACTGA
TTA
Found at i:2352778 original size:40 final size:40
Alignment explanation
Indices: 2352636--2352826 Score: 127
Period size: 40 Copynumber: 4.7 Consensus size: 40
2352626 CTGATTATCT
** *
2352636 AAGGG-TGACACGACTCCTACGTGATGAAGAGGTCTGGTC
1 AAGGGATGACACGGTTCCTACGTGATGAAGAGGTCTAGTC
* ** * * * *
2352675 AAGGAATGACACGGTAACTACATGACGAGGACGACTGATTTA-TC
1 AAGGGATGACACGGTTCCTACGTGATGA--A-GA--GGTCTAGTC
* * * * * *
2352719 TATGGG-TGACACGGCTCCTACATGATGAAGTGGTTTGGTC
1 -AAGGGATGACACGGTTCCTACGTGATGAAGAGGTCTAGTC
*
2352759 AAGGGATGACACGGTTCCTACGTGATGAGGAGGTCTAGTC
1 AAGGGATGACACGGTTCCTACGTGATGAAGAGGTCTAGTC
* **
2352799 AGGGGATGACACATTTCCTACGTGATGA
1 AAGGGATGACACGGTTCCTACGTGATGA
2352827 GGATGGCTGG
Statistics
Matches: 114, Mismatches: 29, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
39 12 0.11
40 71 0.62
41 1 0.01
42 2 0.02
43 2 0.02
44 20 0.18
45 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (40 bp):
AAGGGATGACACGGTTCCTACGTGATGAAGAGGTCTAGTC
Found at i:2352789 original size:84 final size:83
Alignment explanation
Indices: 2352603--2352789 Score: 239
Period size: 84 Copynumber: 2.2 Consensus size: 83
2352593 GGTGATAACT
* * * * *
2352603 CGGTTCCTACACGATGTGGATGGCTGATTATCTAAGGGTGACACGACTCCTACGTGATGAAGAGG
1 CGGTTCCTACATGATGAGGACGACTGATTATCTAAGGGTGACACGACTCCTACATGATGAAGAGG
2352668 TCTGGTCAAGGAATGACA
66 TCTGGTCAAGGAATGACA
** * * * *
2352686 CGGTAACTACATGACGAGGACGACTGATTTATCTATGGGTGACACGGCTCCTACATGATGAAGTG
1 CGGTTCCTACATGATGAGGACGACTGA-TTATCTAAGGGTGACACGACTCCTACATGATGAAGAG
* *
2352751 GTTTGGTCAAGGGATGACA
65 GTCTGGTCAAGGAATGACA
*
2352770 CGGTTCCTACGTGATGAGGA
1 CGGTTCCTACATGATGAGGA
2352790 GGTCTAGTCA
Statistics
Matches: 86, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
83 20 0.23
84 66 0.77
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (83 bp):
CGGTTCCTACATGATGAGGACGACTGATTATCTAAGGGTGACACGACTCCTACATGATGAAGAGG
TCTGGTCAAGGAATGACA
Found at i:2353237 original size:38 final size:38
Alignment explanation
Indices: 2353184--2353272 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
2353174 TAAAGAAATG
* * *
2353184 ACTCAACGATATTTTTCATTATATTTCAAGTGAAACAG
1 ACTCAAAGATTTTTTTCATTATATTTCAAGTGAAACAA
* ** *
2353222 ACTCACAGATTTTTTTTGTTTTATTTCAAGTGAAACAA
1 ACTCAAAGATTTTTTTCATTATATTTCAAGTGAAACAA
2353260 ACTCAAAGATTTT
1 ACTCAAAGATTTT
2353273 GTGTTTCCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (38 bp):
ACTCAAAGATTTTTTTCATTATATTTCAAGTGAAACAA
Found at i:2353607 original size:32 final size:32
Alignment explanation
Indices: 2353570--2353694 Score: 110
Period size: 32 Copynumber: 3.9 Consensus size: 32
2353560 GGATGAAACC
*
2353570 TTGTTTCCAGAGAAACAAACTCAAAGATGATA
1 TTGTTTCAAGAGAAACAAACTCAAAGATGATA
* * ** *
2353602 TTGTTTTAAGAGAAA-ATATCTCAAGAGACAAAA
1 TTGTTTCAAGAGAAACA-AACTCAA-AGATGATA
* * * *
2353635 TTTGTTTCAAGGGAAAC-GACTCAAAGATGGTT
1 -TTGTTTCAAGAGAAACAAACTCAAAGATGATA
*
2353667 TTATTTCAAGAGAAACAAACTCAAAGAT
1 TTGTTTCAAGAGAAACAAACTCAAAGAT
2353695 TTTGTATTTC
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
31 15 0.21
32 32 0.46
33 10 0.14
34 13 0.19
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (32 bp):
TTGTTTCAAGAGAAACAAACTCAAAGATGATA
Found at i:2353703 original size:31 final size:30
Alignment explanation
Indices: 2353639--2353713 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
2353629 ACAAAATTTG
* *
2353639 TTTCAAGGGAAACGACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAACTCAAAGAT-GTTTTA
2353670 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATGTTT-TA
* *
2353701 TTTCTACAGAAAC
1 TTTCAAGAGAAAC
2353714 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 25 0.66
32 10 0.26
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTA
Found at i:2354180 original size:69 final size:66
Alignment explanation
Indices: 2354107--2354248 Score: 166
Period size: 66 Copynumber: 2.1 Consensus size: 66
2354097 AGAGACAAAT
* *
2354107 TTTGTTTTTAA-AGAAACA-AACTCAAAATGATTTGTTGTTTCATGAGAAAAG-GTCTTAAGGAA
1 TTTGTTTTTAAGAGAAA-AGAACTCAAAA--A-TGGTTGTTTCAT-A-AAAAGAGTCTCAAGGAA
2354169 AATAAGA
60 AATAAGA
*
2354176 TTTG-TTTTAAGAGAAAAGATCTCAAAAATGGTTGTTTCATAAAAAGCAGTCTCAAGGAAAATAA
1 TTTGTTTTTAAGAGAAAAGAACTCAAAAATGGTTGTTTCATAAAAAG-AGTCTCAAGGAAAATAA
2354240 GA
65 GA
2354242 TTTGTTT
1 TTTGTTT
2354249 CAAAAGATAC
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
64 5 0.08
65 1 0.02
66 32 0.49
67 3 0.05
68 7 0.11
69 17 0.26
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.34
Consensus pattern (66 bp):
TTTGTTTTTAAGAGAAAAGAACTCAAAAATGGTTGTTTCATAAAAAGAGTCTCAAGGAAAATAAG
A
Found at i:2356394 original size:18 final size:18
Alignment explanation
Indices: 2356371--2356411 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2356361 AGGCATTTGA
*
2356371 TCCTCTGGTTGTGCTTGT
1 TCCTCTGGTCGTGCTTGT
2356389 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGTGCTTGT
2356407 TCCTC
1 TCCTC
2356412 GTGCTGTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGGTCGTGCTTGT
Found at i:2357513 original size:13 final size:15
Alignment explanation
Indices: 2357480--2357518 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2357470 TTAATGGGCA
2357480 AAGTTTTGAAAAACT
1 AAGTTTTGAAAAACT
*
2357495 ATG-TTTGAAAAAC-
1 AAGTTTTGAAAAACT
2357508 AAGTTTTGAAA
1 AAGTTTTGAAA
2357519 TTAATATGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (15 bp):
AAGTTTTGAAAAACT
Found at i:2358006 original size:23 final size:23
Alignment explanation
Indices: 2357980--2358071 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
2357970 CAGAACCCCC
* *
2357980 AGGGGGTATCGATTCCCCTACAG
1 AGGGGGAATCGATTCCCCTTCAG
* *
2358003 A-GGGGAAT-TAGTTCCCCTTCAA
1 AGGGGGAATCGA-TTCCCCTTCAG
*
2358025 AGGGGGAATCGGTTCCCCTTCAAG
1 AGGGGGAATCGATTCCCCTTC-AG
* *
2358049 GGGGGGTATCGATTCCCTCTTCA
1 AGGGGGAATCGATTCCC-CTTCA
2358072 CCAAAAATGC
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.02
22 16 0.30
23 17 0.31
24 16 0.30
25 4 0.07
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCCTTCAG
Found at i:2358007 original size:22 final size:22
Alignment explanation
Indices: 2357982--2358071 Score: 65
Period size: 22 Copynumber: 3.9 Consensus size: 22
2357972 GAACCCCCAG
* *
2357982 GGGGTATCGATTCCCCTACAGA
1 GGGGAATCGATTCCCCTTCAGA
* *
2358004 GGGGAAT-TAGTTCCCCTTCAAA
1 GGGGAATCGA-TTCCCCTTCAGA
* *
2358026 GGGGGAATCGGTTCCCCTTCAAGGG
1 -GGGGAATCGATTCCCCTTC-A-GA
*
2358051 GGGGTATCGATTCCCTCTTCA
1 GGGGAATCGATTCCC-CTTCA
2358072 CCAAAAATGC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
21 1 0.02
22 16 0.31
23 16 0.31
24 15 0.29
25 4 0.08
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.26
Consensus pattern (22 bp):
GGGGAATCGATTCCCCTTCAGA
Found at i:2358433 original size:21 final size:22
Alignment explanation
Indices: 2358393--2358433 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2358383 CTAAAGGATT
* *
2358393 TGTAAAGATATCCACTAATTGA
1 TGTAAAGATATCAACAAATTGA
2358415 TGTAAAG-TATCAACAAATT
1 TGTAAAGATATCAACAAATT
2358434 CTAGAACTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (22 bp):
TGTAAAGATATCAACAAATTGA
Found at i:2361915 original size:20 final size:20
Alignment explanation
Indices: 2361872--2361915 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2361862 GATTATTTTC
* *
2361872 ATTTTTAATTTTGAAATATC
1 ATTTTTAATTTTGAAAAATA
2361892 ATTTTTATATTTT-AAAAATA
1 ATTTTTA-ATTTTGAAAAATA
2361912 ATTT
1 ATTT
2361916 ATCATAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTTAATTTTGAAAAATA
Found at i:2363875 original size:23 final size:25
Alignment explanation
Indices: 2363834--2363880 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2363824 AAACCATTCA
2363834 GGGGGGAATCGGTACCCCT-TGGGG
1 GGGGGGAATCGGTACCCCTCTGGGG
*
2363858 GGGGGGAATCGGT-TCCCTCTGGG
1 GGGGGGAATCGGTACCCCTCTGGG
2363881 CAATCTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (25 bp):
GGGGGGAATCGGTACCCCTCTGGGG
Found at i:2364428 original size:4 final size:4
Alignment explanation
Indices: 2364419--2364782 Score: 701
Period size: 4 Copynumber: 91.0 Consensus size: 4
2364409 TTTATGTATC
* * *
2364419 ATGT ATGT ATGT ATGT ATGA ATAT ATAT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364467 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364515 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364563 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364611 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364659 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364707 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364755 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2364783 TTTCTCGATC
Statistics
Matches: 356, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 356 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2365026 original size:34 final size:31
Alignment explanation
Indices: 2364980--2365042 Score: 72
Period size: 33 Copynumber: 1.9 Consensus size: 31
2364970 GAGAGATATT
* *
2364980 TGTTAAATTCCAAGATATGCCTCCAATATTCGA
1 TGTTAAATTCCAA-AGATGCC-CCAACATTCGA
*
2365013 TGTTGAATCTCCAAAGATGCCCCAACATTC
1 TGTTAAAT-TCCAAAGATGCCCCAACATTC
2365043 AATTTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 8 0.31
33 13 0.50
34 5 0.19
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (31 bp):
TGTTAAATTCCAAAGATGCCCCAACATTCGA
Found at i:2366127 original size:17 final size:18
Alignment explanation
Indices: 2366096--2366140 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
2366086 TTCTTTACTC
*
2366096 TTTTCTTTG-TTTTTGTT
1 TTTTCTTTGCTCTTTGTT
2366113 TTTT-TTTGCTCTTTGTT
1 TTTTCTTTGCTCTTTGTT
2366130 TTTTCTTTGCT
1 TTTTCTTTGCT
2366141 ATTTTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTCTTTGCTCTTTGTT
Found at i:2366132 original size:18 final size:17
Alignment explanation
Indices: 2366096--2366153 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
2366086 TTCTTTACTC
*
2366096 TTTTCTTTG-TTTTTGT
1 TTTTCTTTGCTCTTTGT
*
2366112 TTTTTTTTGCTCTTTGTT
1 TTTTCTTTGCTCTTTG-T
*
2366130 TTTTCTTTGCT-ATT-T
1 TTTTCTTTGCTCTTTGT
2366145 TTTTCTTTG
1 TTTTCTTTG
2366154 TTTTTTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 10 0.28
16 8 0.22
17 7 0.19
18 11 0.31
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTCTTTGCTCTTTGT
Found at i:2366136 original size:11 final size:11
Alignment explanation
Indices: 2366096--2366159 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 11
2366086 TTCTTTACTC
2366096 TTTTCTTTGTT
1 TTTTCTTTGTT
2366107 TTTGT-TTT-TT
1 TTT-TCTTTGTT
2366117 TTTGCTCTTTGTT
1 TTT--TCTTTGTT
2366130 TTTTCTTTGCTATTT
1 TTTTCTTTG----TT
2366145 TTTTCTTTGTT
1 TTTTCTTTGTT
2366156 TTTT
1 TTTT
2366160 TGTTCTCTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
10 5 0.11
11 19 0.43
12 4 0.09
13 5 0.11
15 11 0.25
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (11 bp):
TTTTCTTTGTT
Found at i:2366160 original size:15 final size:15
Alignment explanation
Indices: 2366096--2366165 Score: 68
Period size: 15 Copynumber: 4.4 Consensus size: 15
2366086 TTCTTTACTC
2366096 TTTTCTTTGTTTTTGT
1 TTTTCTTTGTTTTT-T
*
2366112 TTTTTTTTGCTCTTTGTT
1 TTTTCTTTG-T-TTT-TT
* *
2366130 TTTTCTTTGCTATTT
1 TTTTCTTTGTTTTTT
2366145 TTTTCTTTGTTTTTT
1 TTTTCTTTGTTTTTT
*
2366160 TGTTCT
1 TTTTCT
2366166 CTTCGCTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 20 0.45
16 10 0.23
17 1 0.02
18 12 0.27
19 1 0.02
ACGTcount: A:0.01, C:0.10, G:0.10, T:0.79
Consensus pattern (15 bp):
TTTTCTTTGTTTTTT
Found at i:2371958 original size:3 final size:3
Alignment explanation
Indices: 2371945--2372150 Score: 104
Period size: 3 Copynumber: 66.3 Consensus size: 3
2371935 ATTAATATTT
*
2371945 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA -ACA AAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA
* *
2371992 TAA TAA TAA TAA TAA TAA TAA TAA -AA TTAA -AA TTA -AA TAGA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA-A TAA
* * * * * ** * *
2372036 GACC TAGA CAA AAA TGAG TGTC TACA GGAA T-A TAA TTAA T-A TAT TAA
1 TA-A TA-A TAA TAA T-AA T-AA TA-A -TAA TAA TAA -TAA TAA TAA TAA
*
2372083 TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA -ACA AAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA
2372130 TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
2372151 TAAAATTAAA
Statistics
Matches: 160, Mismatches: 22, Indels: 42
0.71 0.10 0.19
Matches are distributed among these distances:
2 13 0.08
3 118 0.74
4 28 0.17
5 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2372168 original size:132 final size:135
Alignment explanation
Indices: 2371933--2372193 Score: 411
Period size: 132 Copynumber: 2.0 Consensus size: 135
2371923 TACAAAAATG
* *
2371933 TAATTAATATTTTAATAAATAATAATAATAATAATAATAATTAATAAACAAAATAATAATAATAA
1 TAATTAATATATTAATAAATAATAATAATAATAATAATAATTAATAAACAAAATAACAATAATAA
* *
2371998 TAATAATAATAATAATAAAATTAAAATTAAATAGAAAAGACCTAGACAAAAATGAGTGTCTACAG
66 TAATAATAATAATAATAAAATTAAAATTAAATAGAAAAGACCAAGACAAAAACGAGTGTCTACAG
2372063 GAATA
131 GAATA
** *
2372068 TAATTAATATATTAATAAATAATAATAATAATAATAATAA-TAATAATTAATA-AACAA-AATAA
1 TAATTAATATATTAATAAATAATAATAATAATAATAATAATTAATAAACAAAATAACAATAATAA
* * *
2372130 TAATAATAATAATAATATAATTAAAATTAAATAGAAAAGATCAAGATAAAAACGAGTGTCTACA
66 TAATAATAATAATAATAAAATTAAAATTAAATAGAAAAGACCAAGACAAAAACGAGTGTCTACA
2372194 TAAATAAAGA
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
132 64 0.55
133 4 0.03
134 9 0.08
135 39 0.34
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (135 bp):
TAATTAATATATTAATAAATAATAATAATAATAATAATAATTAATAAACAAAATAACAATAATAA
TAATAATAATAATAATAAAATTAAAATTAAATAGAAAAGACCAAGACAAAAACGAGTGTCTACAG
GAATA
Found at i:2377164 original size:98 final size:99
Alignment explanation
Indices: 2376989--2377186 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 99
2376979 TTTTATAAGG
2376989 GAATATTCAAAGGAGGATGCCTACCTATCCTATGCAAATATCGAACGTAGAATTTATCAACACAT
1 GAATATTCAAAGGAGGATGCCTACCTATCCTATGCAAATATCGAACGTAGAATTTATCAACACAT
2377054 CGAGTCAAAGTTTTAAACCATCAATTTCATTCTT
66 CGAGTCAAAGTTTTAAACCATCAATTTCATTCTT
2377088 GAATA-TCAAAGGAGGATGCCTACCTATCCTATGCAAATATCGAACGTAGAATTTATCAACACAT
1 GAATATTCAAAGGAGGATGCCTACCTATCCTATGCAAATATCGAACGTAGAATTTATCAACACAT
2377152 CGAGTCAAAGTTTTAAACCATCAATTTCATTCTT
66 CGAGTCAAAGTTTTAAACCATCAATTTCATTCTT
2377186 G
1 G
2377187 TGGGGGATTA
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 94 0.95
99 5 0.05
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (99 bp):
GAATATTCAAAGGAGGATGCCTACCTATCCTATGCAAATATCGAACGTAGAATTTATCAACACAT
CGAGTCAAAGTTTTAAACCATCAATTTCATTCTT
Found at i:2383208 original size:21 final size:21
Alignment explanation
Indices: 2383164--2383210 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2383154 AACAATTCTC
* *
2383164 TTCATGAAAAGATTGAGTCAT
1 TTCATGAAAAGATTAAGCCAT
* *
2383185 TTCATGAAAATATTAAGCCCT
1 TTCATGAAAAGATTAAGCCAT
2383206 TTCAT
1 TTCAT
2383211 CCAAAGGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCATGAAAAGATTAAGCCAT
Found at i:2383296 original size:15 final size:15
Alignment explanation
Indices: 2383276--2383332 Score: 87
Period size: 15 Copynumber: 3.8 Consensus size: 15
2383266 CTTTGAATTA
* *
2383276 CTTTCAATTTACTTC
1 CTTTCAATTCATTTC
*
2383291 CTTTCAACTCATTTC
1 CTTTCAATTCATTTC
2383306 CTTTCAATTCATTTC
1 CTTTCAATTCATTTC
2383321 CTTTCAATTCAT
1 CTTTCAATTCAT
2383333 CAAACTTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (15 bp):
CTTTCAATTCATTTC
Found at i:2387844 original size:67 final size:67
Alignment explanation
Indices: 2387736--2387869 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
2387726 CAAAGAAGAG
2387736 GAGCCTGCAGTAACTGTAACTGTAACTTCCTCCAACAATACCCTCCCATAAAACATTTATAAAAA
1 GAGCCTGCAGTAACTGTAACTGTAACTTCCTCCAACAATACCCTCCCATAAAACATTTATAAAAA
2387801 AA
66 AA
2387803 GAGCCTGCAGTAACTGTAACTGTAACTTCCTCCAACAATACCCTCCCATAAAACATTTATAAAAA
1 GAGCCTGCAGTAACTGTAACTGTAACTTCCTCCAACAATACCCTCCCATAAAACATTTATAAAAA
2387868 AA
66 AA
2387870 CATAGTAATC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (67 bp):
GAGCCTGCAGTAACTGTAACTGTAACTTCCTCCAACAATACCCTCCCATAAAACATTTATAAAAA
AA
Found at i:2391298 original size:60 final size:60
Alignment explanation
Indices: 2391225--2391344 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
2391215 TGGAAAGTAG
2391225 AGTAATACAAAACTACCATTAGATGCTGAAGAACGTGCATATAATAGATAAACATATAAT
1 AGTAATACAAAACTACCATTAGATGCTGAAGAACGTGCATATAATAGATAAACATATAAT
2391285 AGTAATACAAAACTACCATTAGATGCTGAAGAACGTGCATATAATAGATAAACATATAAT
1 AGTAATACAAAACTACCATTAGATGCTGAAGAACGTGCATATAATAGATAAACATATAAT
2391345 TTCTTACTGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (60 bp):
AGTAATACAAAACTACCATTAGATGCTGAAGAACGTGCATATAATAGATAAACATATAAT
Found at i:2391949 original size:12 final size:12
Alignment explanation
Indices: 2391934--2391980 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2391924 TATTTCAGGT
2391934 CAGATATCAGAA
1 CAGATATCAGAA
*
2391946 CAGA-ATCCAGAT
1 CAGATAT-CAGAA
* *
2391958 CAAAAATCAGAA
1 CAGATATCAGAA
2391970 CAGATATCAGA
1 CAGATATCAGA
2391981 TAAAACATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (12 bp):
CAGATATCAGAA
Found at i:2391971 original size:24 final size:23
Alignment explanation
Indices: 2391939--2391985 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2391929 CAGGTCAGAT
2391939 ATCAGAACAGA-ATCCAGATCAAAA
1 ATCAGAACAGATAT-CAGAT-AAAA
2391963 ATCAGAACAGATATCAGATAAAA
1 ATCAGAACAGATATCAGATAAAA
2391986 CATTCATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 16 0.73
25 2 0.09
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (23 bp):
ATCAGAACAGATATCAGATAAAA
Found at i:2401208 original size:761 final size:761
Alignment explanation
Indices: 2399747--2401271 Score: 2870
Period size: 761 Copynumber: 2.0 Consensus size: 761
2399737 CCTAGAAAAC
2399747 GACTCCTAAAGTGCTCTCTAAAGAAATCCCAACTCAAACGATCGATCGGAACACTGCTGACCACA
1 GACTCCTAAAGTGCTCTCTAAAGAAATCCCAACTCAAACGATCGATCGGAACACTGCTGACCACA
*
2399812 GACTCCCACCAGGTGTGGGCATTCCCATCCAACATAGAAATTGCTCCTAAATAACATCGATGCGG
66 GACTCCCACCAGGTGTGGGCATTCCCATCCAACATAGAAATTGCTCCTAAATAACATCGATGCAG
*
2399877 ATCGAAACTTAACTAATCTATGTGTCGTTCAATATCACTGAGCCAATCCTCAGCCTCAGTCGGGT
131 ATCGAAACTTAACTAATCCATGTGTCGTTCAATATCACTGAGCCAATCCTCAGCCTCAGTCGGGT
2399942 CTCCACCAGTAAGGCCACTAAACGTCTTGACTCTATTTGCAATAAGGGTCTGAGAGATAGAAACC
196 CTCCACCAGTAAGGCCACTAAACGTCTTGACTCTATTTGCAATAAGGGTCTGAGAGATAGAAACC
2400007 TTGGGTACAACACCAGCAGCTCAGACCGCTCCCTGAATTAACTGACAAAATTGTCTACCAAGATT
261 TTGGGTACAACACCAGCAGCTCAGACCGCTCCCTGAATTAACTGACAAAATTGTCTACCAAGATT
*
2400072 CTCATCTAATACAACTCTAGTATACTCAGGCTTAGTAACGGTCGCTCCTATAATCAGAGTAGTCA
326 CTCATCTAATACAACTCTAGTAGACTCAGGCTTAGTAACGGTCGCTCCTATAATCAGAGTAGTCA
2400137 AACCAATACCAAAAATAGGACGCATATCCGTCGGGGTCGGAGAAGTAAGATCATCTATCGGAGAC
391 AACCAATACCAAAAATAGGACGCATATCCGTCGGGGTCGGAGAAGTAAGATCATCTATCGGAGAC
* * *
2400202 GGTGGATCTACATGTATCTCATCTACCGGGTCTACAAATCTAGCCACTCGGCCGTGACAACGACT
456 GATGGATCTACATGTATCTCATCTACCGGGTCTACAAATCTAGCCACTCGGCCGCGACAACGACC
2400267 AAATCGATGACCAGATCTAGCACTCATCTTGGTGGATCTCAAGTTTACTACAGAAGATAAAGCAT
521 AAATCGATGACCAGATCTAGCACTCATCTTGGTGGATCTCAAGTTTACTACAGAAGATAAAGCAT
2400332 ATGGTTAGATTGGCACTTGGAGTTCTGAACACCATTAAACTCGTAAAAACTTTGTGACATGGCCT
586 ATGGTTAGATTGGCACTTGGAGTTCTGAACACCATTAAACTCGTAAAAACTTTGTGACATGGCCT
2400397 TCATGACTTGTTTTATAAAACATTTCAAAATAGTATTTTTTTGTTTGGACCCATTCACAGTCCGA
651 TCATGACTTGTTTTATAAAACATTTCAAAATAGTATTTTTTTGTTTGGACCCATTCACAGTCCGA
*
2400462 TATTTAAAAACCAAAAGCTCTTATACCAATTAAATGTAACCCCCTA
716 GATTTAAAAACCAAAAGCTCTTATACCAATTAAATGTAACCCCCTA
* * * *
2400508 GACTCCTAAAGTGCTCTCTGAATAAATCCCAACTCAAACGATCGGTTGGAACACTGCTGACCACA
1 GACTCCTAAAGTGCTCTCTAAAGAAATCCCAACTCAAACGATCGATCGGAACACTGCTGACCACA
*
2400573 GACTCCCACCAGGTGTGGGCATTCCCATCCAACATAGAAATTGCTCCTAAATAACGTCGATGCAG
66 GACTCCCACCAGGTGTGGGCATTCCCATCCAACATAGAAATTGCTCCTAAATAACATCGATGCAG
* *
2400638 ATCGAAACTTAACTGATCCATGTGTCGTTCAGTATCACTGAGCCAATCCTCAGCCTCAGTCGGGT
131 ATCGAAACTTAACTAATCCATGTGTCGTTCAATATCACTGAGCCAATCCTCAGCCTCAGTCGGGT
2400703 CTCCACCAGTAAGGCCACTAAACGTCTTGACTCTATTTGCAATAAGGGTCTGAGAGATAGAAACC
196 CTCCACCAGTAAGGCCACTAAACGTCTTGACTCTATTTGCAATAAGGGTCTGAGAGATAGAAACC
2400768 TTGGGTACAACACCAGCAGCTCAGACCGCTCCCTGAATTAACTGACAAAATTGTCTACCAAGATT
261 TTGGGTACAACACCAGCAGCTCAGACCGCTCCCTGAATTAACTGACAAAATTGTCTACCAAGATT
2400833 CTCATCTAATACAACTCTAGTAGACTCAGGCTTAGTAACGGTCGCTCCTATAATCAGAGTAGTCA
326 CTCATCTAATACAACTCTAGTAGACTCAGGCTTAGTAACGGTCGCTCCTATAATCAGAGTAGTCA
*
2400898 AACCAATACCAAAAATAGGAGGCATATCCGTCGGGGTCGGAGAAGTAAGATCATCTATCGGAGAC
391 AACCAATACCAAAAATAGGACGCATATCCGTCGGGGTCGGAGAAGTAAGATCATCTATCGGAGAC
* * *
2400963 GATGGATCTACATGTATCTCATCTACCGGGTCTGCAAATCTAGCCACTCGGCCGCGACCACGGCC
456 GATGGATCTACATGTATCTCATCTACCGGGTCTACAAATCTAGCCACTCGGCCGCGACAACGACC
*
2401028 AAATCGATGACCAGATCTAGCACTCATCTTGGTGGATCTTAAGTTTACTACAGAAGATAAAGCAT
521 AAATCGATGACCAGATCTAGCACTCATCTTGGTGGATCTCAAGTTTACTACAGAAGATAAAGCAT
2401093 ATGGTTAGATTGGCACTTGGAGTTCTGAACACCATTAAACTCGTAAAAACTTTGTGACATGGCCT
586 ATGGTTAGATTGGCACTTGGAGTTCTGAACACCATTAAACTCGTAAAAACTTTGTGACATGGCCT
*
2401158 TCATGACTTGTTTTATAAAACATTTCAAAATCGTATTTTTTTGTTTGGACCCATTCACAGTCCGA
651 TCATGACTTGTTTTATAAAACATTTCAAAATAGTATTTTTTTGTTTGGACCCATTCACAGTCCGA
2401223 GATTTAAAAACCAAAAGCTCTTATACCAATTAAATGTAACCCCCTA
716 GATTTAAAAACCAAAAGCTCTTATACCAATTAAATGTAACCCCCTA
2401269 GAC
1 GAC
2401272 CCAACCTATC
Statistics
Matches: 744, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
761 744 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (761 bp):
GACTCCTAAAGTGCTCTCTAAAGAAATCCCAACTCAAACGATCGATCGGAACACTGCTGACCACA
GACTCCCACCAGGTGTGGGCATTCCCATCCAACATAGAAATTGCTCCTAAATAACATCGATGCAG
ATCGAAACTTAACTAATCCATGTGTCGTTCAATATCACTGAGCCAATCCTCAGCCTCAGTCGGGT
CTCCACCAGTAAGGCCACTAAACGTCTTGACTCTATTTGCAATAAGGGTCTGAGAGATAGAAACC
TTGGGTACAACACCAGCAGCTCAGACCGCTCCCTGAATTAACTGACAAAATTGTCTACCAAGATT
CTCATCTAATACAACTCTAGTAGACTCAGGCTTAGTAACGGTCGCTCCTATAATCAGAGTAGTCA
AACCAATACCAAAAATAGGACGCATATCCGTCGGGGTCGGAGAAGTAAGATCATCTATCGGAGAC
GATGGATCTACATGTATCTCATCTACCGGGTCTACAAATCTAGCCACTCGGCCGCGACAACGACC
AAATCGATGACCAGATCTAGCACTCATCTTGGTGGATCTCAAGTTTACTACAGAAGATAAAGCAT
ATGGTTAGATTGGCACTTGGAGTTCTGAACACCATTAAACTCGTAAAAACTTTGTGACATGGCCT
TCATGACTTGTTTTATAAAACATTTCAAAATAGTATTTTTTTGTTTGGACCCATTCACAGTCCGA
GATTTAAAAACCAAAAGCTCTTATACCAATTAAATGTAACCCCCTA
Found at i:2402701 original size:18 final size:18
Alignment explanation
Indices: 2402677--2402727 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
2402667 TTTTGGTCAA
2402677 AGTCAACGGTCAATGGTC
1 AGTCAACGGTCAATGGTC
* * *
2402695 GGTCAACGGTAAACGGTC
1 AGTCAACGGTCAATGGTC
2402713 AGTCAACGGTCAATG
1 AGTCAACGGTCAATG
2402728 TTGAACTGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (18 bp):
AGTCAACGGTCAATGGTC
Found at i:2408612 original size:21 final size:21
Alignment explanation
Indices: 2408579--2408631 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2408569 TGCAGCTTCC
* *
2408579 ATTA-AAAGCCAATGAGCCTT
1 ATTACAAAGTCAATGAGCATT
*
2408599 GTTACAAAGTCAATGAGCATT
1 ATTACAAAGTCAATGAGCATT
*
2408620 ATTGCAAAGTCA
1 ATTACAAAGTCA
2408632 TAGCTCATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (21 bp):
ATTACAAAGTCAATGAGCATT
Found at i:2435282 original size:24 final size:22
Alignment explanation
Indices: 2435233--2435279 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2435223 AAATCCTTTT
2435233 AGAAAATAGAGAAAAAAAAATG
1 AGAAAATAGAGAAAAAAAAATG
*
2435255 AGAAAATAG-GTAGAAAAAAATG
1 AGAAAATAGAG-AAAAAAAAATG
2435277 AGA
1 AGA
2435280 GAATCTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (22 bp):
AGAAAATAGAGAAAAAAAAATG
Found at i:2443323 original size:21 final size:21
Alignment explanation
Indices: 2443297--2443372 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
2443287 GGTGTCAAAA
2443297 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCACCCCTGCAG
2443318 TGCATCCATGCACCACC-GCAG
1 TGCATCCATGCACC-CCTGCAG
*
2443339 TGCATCCATGCA-CCCTGTAG
1 TGCATCCATGCACCCCTGCAG
2443359 TGCATCCATGCACC
1 TGCATCCATGCACC
2443373 TGGCATTAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
19 2 0.04
20 16 0.31
21 31 0.61
22 2 0.04
ACGTcount: A:0.21, C:0.41, G:0.18, T:0.20
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAG
Found at i:2443386 original size:23 final size:20
Alignment explanation
Indices: 2443297--2443414 Score: 121
Period size: 20 Copynumber: 5.7 Consensus size: 20
2443287 GGTGTCAAAA
*
2443297 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCA-CCCTGTAG
* *
2443318 TGCATCCATGCACCACCGCAG
1 TGCATCCATGCACC-CTGTAG
2443339 TGCATCCATGCACCCTGTAG
1 TGCATCCATGCACCCTGTAG
2443359 TGCATCCATGCA-CCTGGCATTAG
1 TGCATCCATGCACCCT-G---TAG
* *
2443382 TGCATCGATGCACCATGTAG
1 TGCATCCATGCACCCTGTAG
*
2443402 TTCATCCATGCAC
1 TGCATCCATGCAC
2443415 TCCATTTCGA
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.04
20 33 0.39
21 31 0.37
23 15 0.18
24 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (20 bp):
TGCATCCATGCACCCTGTAG
Found at i:2444904 original size:9 final size:9
Alignment explanation
Indices: 2444878--2444907 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2444868 AAGGGAAGAG
*
2444878 AAGAAGAAG
1 AAGAAGAAT
2444887 AAGAAGAAT
1 AAGAAGAAT
2444896 AAGAAGAAT
1 AAGAAGAAT
2444905 AAG
1 AAG
2444908 GAGGTAGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (9 bp):
AAGAAGAAT
Found at i:2446592 original size:21 final size:19
Alignment explanation
Indices: 2446548--2446606 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 19
2446538 CAACAATTGG
*
2446548 TAACAATTAATATCTTTTT
1 TAACAATTGATATCTTTTT
2446567 TAACAATTGATATCCTTTTGT
1 TAACAATTGATAT-CTTTT-T
*
2446588 TAACAATTGATATATTTTT
1 TAACAATTGATATCTTTTT
2446607 CATTAAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.36
20 9 0.25
21 14 0.39
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:2446856 original size:21 final size:21
Alignment explanation
Indices: 2446830--2446906 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
2446820 GGGTGTTAAA
2446830 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCACCCCTGCAG
* * *
2446851 TGCATCCATGAACCACTACAG
1 TGCATCCATGCACCCCTGCAG
*
2446872 TGCATCCATGCACCCCTGTAG
1 TGCATCCATGCACCCCTGCAG
2446893 TGCATCCATGCACC
1 TGCATCCATGCACC
2446907 TGCCACTAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAG
Found at i:2446921 original size:23 final size:21
Alignment explanation
Indices: 2446830--2446948 Score: 93
Period size: 21 Copynumber: 5.6 Consensus size: 21
2446820 GGGTGTTAAA
*
2446830 TGCATCCATGCACCCCTGC-AG
1 TGCATCCATGCACCCC-ACTAG
* *
2446851 TGCATCCATGAACCACTAC-AG
1 TGCATCCATGCACC-CCACTAG
**
2446872 TGCATCCATGCACCCCTGTAG
1 TGCATCCATGCACCCCACTAG
2446893 TGCATCCATGCACCTGCCACTAG
1 TGCATCCATGCACC--CCACTAG
* * *
2446916 TTCATCGATGCA--CCATGTAG
1 TGCATCCATGCACCCCA-CTAG
2446936 TGCATCCATGCAC
1 TGCATCCATGCAC
2446949 TCCATTTTGA
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.18
21 45 0.58
22 1 0.01
23 15 0.19
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TGCATCCATGCACCCCACTAG
Found at i:2446942 original size:43 final size:42
Alignment explanation
Indices: 2446830--2446948 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
2446820 GGGTGTTAAA
* * * *
2446830 TGCATCCATGCACCCCTGCAGTGCATCCATGAACCACTACAG
1 TGCATCCATGCACCCATGTAGTGCATCCATGCACCACCACAG
* *
2446872 TGCATCCATGCACCCCTGTAGTGCATCCATGCACCTGCCACTAG
1 TGCATCCATGCACCCATGTAGTGCATCCATGCACC-ACCAC-AG
* *
2446916 TTCATCGATGCA-CCATGTAGTGCATCCATGCAC
1 TGCATCCATGCACCCATGTAGTGCATCCATGCAC
2446949 TCCATTTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 33 0.49
43 23 0.34
44 12 0.18
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TGCATCCATGCACCCATGTAGTGCATCCATGCACCACCACAG
Found at i:2455302 original size:21 final size:21
Alignment explanation
Indices: 2455276--2455315 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2455266 TTACAAAGGA
2455276 AGTACTGATACTCC-CTATAAG
1 AGTACTGATAC-CCTCTATAAG
2455297 AGTACTGATACCCTCTATA
1 AGTACTGATACCCTCTATA
2455316 TTGGGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (21 bp):
AGTACTGATACCCTCTATAAG
Found at i:2456002 original size:11 final size:11
Alignment explanation
Indices: 2455986--2456048 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 11
2455976 GTTCACAATC
2455986 GTGTTCATTTA
1 GTGTTCATTTA
2455997 GTGTTCATTCTCA
1 GTGTTCATT-T-A
2456010 TTTAGTGTTCATTTA
1 ----GTGTTCATTTA
*
2456025 GCGTTCATTTA
1 GTGTTCATTTA
*
2456036 GTGTTCGTTTA
1 GTGTTCATTTA
2456047 GT
1 GT
2456049 ATTTGTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 30 0.70
12 1 0.02
13 1 0.02
15 1 0.02
16 1 0.02
17 9 0.21
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.52
Consensus pattern (11 bp):
GTGTTCATTTA
Found at i:2456012 original size:17 final size:17
Alignment explanation
Indices: 2455990--2456022 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2455980 ACAATCGTGT
2455990 TCATTTAGTGTTCATTC
1 TCATTTAGTGTTCATTC
2456007 TCATTTAGTGTTCATT
1 TCATTTAGTGTTCATT
2456023 TAGCGTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (17 bp):
TCATTTAGTGTTCATTC
Found at i:2456035 original size:22 final size:22
Alignment explanation
Indices: 2455988--2456047 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
2455978 TCACAATCGT
2455988 GTTCATTTAGTGTTCA-TT--C
1 GTTCATTTAGTGTTCATTTAGC
2456007 --TCATTTAGTGTTCATTTAGC
1 GTTCATTTAGTGTTCATTTAGC
*
2456027 GTTCATTTAGTGTTCGTTTAG
1 GTTCATTTAGTGTTCATTTAG
2456048 TATTTGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 14 0.40
18 2 0.06
20 1 0.03
22 18 0.51
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (22 bp):
GTTCATTTAGTGTTCATTTAGC
Found at i:2463978 original size:28 final size:28
Alignment explanation
Indices: 2463938--2464027 Score: 153
Period size: 28 Copynumber: 3.2 Consensus size: 28
2463928 TTTTACGCAG
*
2463938 TCCTTCGGGACATATATGTTATATGTCT
1 TCCTTCGAGACATATATGTTATATGTCT
2463966 TCCTTCGAGACATATATGTTATATGTCT
1 TCCTTCGAGACATATATGTTATATGTCT
* *
2463994 TCCTTCGAGACATATATGTTATATATCG
1 TCCTTCGAGACATATATGTTATATGTCT
2464022 TCCTTC
1 TCCTTC
2464028 AGGACATTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (28 bp):
TCCTTCGAGACATATATGTTATATGTCT
Found at i:2467410 original size:74 final size:75
Alignment explanation
Indices: 2467322--2467473 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 75
2467312 GCATCTCAGC
* *
2467322 TTGGTTTATATAGTTTTGACTATCGAAGTT-TTCTCATACCAAT-ATTGATAGTTCTCATAAGTT
1 TTGGTTTATATAGTTTTGACTATCGAAGTTCTT-TCACACCAATAATTGATAATTCTCATAAGTT
2467385 TGATTATTTGA
65 TGATTATTTGA
*
2467396 TTGGTTTATATAGTTTTTACTATCGAAGTTCTTTCACACCAATAAAATTGATAATTCTCATAAGT
1 TTGGTTTATATAGTTTTGACTATCGAAGTTCTTTCACACCAAT--AATTGATAATTCTCATAAGT
2467461 TTGATTATTTGA
64 TTGATTATTTGA
2467473 T
1 T
2467474 GGGAGATTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
74 38 0.54
75 2 0.03
77 31 0.44
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (75 bp):
TTGGTTTATATAGTTTTGACTATCGAAGTTCTTTCACACCAATAATTGATAATTCTCATAAGTTT
GATTATTTGA
Found at i:2473112 original size:3 final size:3
Alignment explanation
Indices: 2473104--2473129 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2473094 TATAAATTGA
2473104 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2473130 AATATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2474068 original size:6 final size:6
Alignment explanation
Indices: 2474057--2474081 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2474047 GACACATATT
2474057 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2474082 GCCGAGCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2474089 original size:5 final size:5
Alignment explanation
Indices: 2474079--2474127 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
2474069 ACCACGACCA
* * * *
2474079 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
2474128 ACAGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.35, G:0.41, T:0.04
Consensus pattern (5 bp):
CGAGC
Found at i:2479812 original size:6 final size:6
Alignment explanation
Indices: 2479801--2479831 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2479791 GACACGTATT
2479801 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
2479832 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2480255 original size:3 final size:3
Alignment explanation
Indices: 2480242--2480421 Score: 116
Period size: 3 Copynumber: 57.7 Consensus size: 3
2480232 TTTTTAAATT
* * *
2480242 TTA TATA TTA TTA TTAA TTA TTA TCA TTA -CA TTTA TTA GTA TTA TTA
1 TTA T-TA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * *
2480289 TTA CTAA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA -AA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* ** * * **
2480334 TAAA TTA -TA TTA GTTA CAA TTA TTA GTTAA GGTG TTA GGA TTA TTA
1 T-TA TTA TTA TTA -TTA TTA TTA TTA -TT-A -TTA TTA TTA TTA TTA
2480380 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
2480422 TCTATTTGTT
Statistics
Matches: 139, Mismatches: 24, Indels: 28
0.73 0.13 0.15
Matches are distributed among these distances:
2 6 0.04
3 107 0.77
4 23 0.17
5 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2484747 original size:2 final size:2
Alignment explanation
Indices: 2484740--2484802 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
2484730 ATTCTTCAAT
2484740 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
2484782 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2484803 TAAACTTGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2485398 original size:55 final size:55
Alignment explanation
Indices: 2485301--2485615 Score: 454
Period size: 55 Copynumber: 5.7 Consensus size: 55
2485291 GGATACGATC
* * * * *
2485301 ATTCACAAACTCATTATGAATTACGT-AGGTTGCACACATAGTGTCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAA
* * * * *
2485355 ATTTATAAACTCATTATAAATTTTGTGGGGTTGCACACATAGTGCCATTACAAAA
1 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAA
* *
2485410 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTACCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAA
* * *
2485465 ATTCATAAACTTATTATGAATTTCGTCGGGTTGCACACATAGTGCTAATAC-ATAA
1 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGA-AA
2485520 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAA
* *
2485575 ATTCATAAACTCATTATGAATTTCGTGGGGTTACATACATA
1 ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATA
2485616 TACATTAAAG
Statistics
Matches: 231, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
54 21 0.09
55 209 0.90
56 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (55 bp):
ATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAA
Found at i:2485957 original size:22 final size:20
Alignment explanation
Indices: 2485915--2485984 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2485905 GACTAAATAT
2485915 TATCGATACCTCTCTTTTGG
1 TATCGATACCTCTCTTTTGG
*
2485935 TATCGATACTTCTCTTCTATGG
1 TATCGATACCTCTCTT-T-TGG
* * *
2485957 TACCGATACC-C-ATTTCGG
1 TATCGATACCTCTCTTTTGG
2485975 TATCGATACC
1 TATCGATACC
2485985 ATTCTAGCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.26
19 1 0.02
20 17 0.40
21 2 0.05
22 11 0.26
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (20 bp):
TATCGATACCTCTCTTTTGG
Found at i:2488703 original size:79 final size:80
Alignment explanation
Indices: 2488620--2488955 Score: 425
Period size: 79 Copynumber: 4.3 Consensus size: 80
2488610 GCATTTTATT
* * * * * *
2488620 TATGGAATCTTTTCATGTCAATAATGCACCCATAAGCATTATTCGTTTATGTCAG-TAATGCATC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCAGATAATGCACC
2488684 CATATGCATTTCAGC
66 CATATGCATTTCAGC
* * * *
2488699 TATGGCATCATTTTATGCCAATAATGCACCCATATGCATTATTATTTTA--TAATGATAATGCAC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCA-GATAATGCAC
*
2488762 CCATATGCTTTTCAGC
65 CCATATGCATTTCAGC
* * * * *
2488778 TATGGCGTCCTTTCATGCCAATAATGTACCCATATGCATTATTCTTGTA-GGCTGATAATGCACC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCAGATAATGCACC
*
2488842 CATGTGCATTTCAGC
66 CATATGCATTTCAGC
*
2488857 TATGGCATCCTTTCATGCCAA-AATGCACCCATATGCATTATTCTTTTATG-CTGATAATGCA-C
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCAGATAATGCACC
* *
2488919 CATATACATTTTAGC
66 CATATGCATTTCAGC
*
2488934 TATGGCATCATTTCATGCCAAT
1 TATGGCATCCTTTCATGCCAAT
2488956 TTAATTATGA
Statistics
Matches: 224, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
77 35 0.16
78 37 0.17
79 152 0.68
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (80 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCAGATAATGCACC
CATATGCATTTCAGC
Found at i:2489471 original size:20 final size:20
Alignment explanation
Indices: 2489446--2489501 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
2489436 CGATGTTGTC
* *
2489446 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCATAACA
*
2489466 TGGTATCGATACTACCATAATA
1 TGGTATCGATAC--CCATAACA
2489488 TGGTATCGATACCC
1 TGGTATCGATACCC
2489502 CATTCCGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (20 bp):
TGGTATCGATACCCATAACA
Done.