Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 128 of 349
Found at i:40834143 original size:17 final size:17
Alignment explanation
Indices: 40834060--40834164 Score: 81
Period size: 17 Copynumber: 5.9 Consensus size: 17
40834050 TTTGTACTGC
40834060 ATTATAATTATTATTATCAT
1 ATTAT-ATTATTATTA-C-T
*
40834080 ATTATATTTAGTATTACT
1 ATTATA-TTATTATTACT
40834098 -TTAATATTA-TATTAACT
1 ATT-ATATTATTATT-ACT
40834115 ATTATATTTTATTATTACT
1 ATTATA--TTATTATTACT
* *
40834134 ATTACATTATTAGTAC-
1 ATTATATTATTATTACT
*
40834150 ATTATTTTATTATTA
1 ATTATATTATTATTA
40834165 TTTTTATTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
16 16 0.22
17 20 0.28
18 6 0.08
19 13 0.18
20 17 0.24
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATATTATTATTACT
Found at i:40834186 original size:15 final size:14
Alignment explanation
Indices: 40834176--40834208 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40834166 TTTTATTGTA
40834176 AATATTATTATTCT
1 AATATTATTATTCT
*
40834190 AATATTA-TATTAT
1 AATATTATTATTCT
40834203 AATATT
1 AATATT
40834209 TTTCATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTATTATTCT
Found at i:40834273 original size:12 final size:13
Alignment explanation
Indices: 40834245--40834277 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
40834235 TTATTTATTC
*
40834245 TTATATATGTCAT
1 TTATTTATGTCAT
40834258 TTATTTATGT-AT
1 TTATTTATGTCAT
40834270 TTATTTAT
1 TTATTTAT
40834278 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (13 bp):
TTATTTATGTCAT
Found at i:40842987 original size:19 final size:19
Alignment explanation
Indices: 40842963--40843000 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40842953 GAAATGAATA
*
40842963 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
40842982 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
40843001 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:40843289 original size:12 final size:12
Alignment explanation
Indices: 40843269--40843298 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40843259 ATAGCTAAAT
*
40843269 TATATATATATA
1 TATACATATATA
40843281 TATACATATATA
1 TATACATATATA
40843293 TATACA
1 TATACA
40843299 CACATAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
TATACATATATA
Found at i:40843925 original size:19 final size:20
Alignment explanation
Indices: 40843892--40843931 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
40843882 ATGTATATAT
40843892 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
40843911 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
40843931 A
1 A
40843932 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:40844532 original size:44 final size:44
Alignment explanation
Indices: 40844477--40845006 Score: 735
Period size: 44 Copynumber: 12.3 Consensus size: 44
40844467 CGTCTAATAT
* *
40844477 AGAGACGCCAAAT-TCGTTATCTTCGATATGCTCTCCGTCGCTAC
1 AGAGACGCCAAATCT-GTTATCTTCGATCTGCTCTCCGCCGCTAC
* * * *
40844521 AGAGATGCCAAATCTGTTATCTTTGATCTGCTCTCCACC-TTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* *
40844564 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCACTGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * *
40844608 AGAGATGCCAAATC----ATCTTCGATCTGCTCTTCGCTGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * *
40844648 AGAGACGCCAAATCTATTATATTCGATCTGCTCTTCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * *
40844692 AGAGATGCCAAATC----ATCTTCAATCTGCTCTCCGTCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
40844732 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
*
40844776 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* * * *
40844820 AGAGACGCCAAATATGTTATCTTTGATCTGGTCTCCGCCACTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
* *
40844864 AGAGACGCCAAGTCTGTTATCTTCGATCTGCTCTCCGCCGCTAT
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
40844908 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
*
40844952 AGAGACG---AATCTGTTATCTTCGATCTGCTCTCTGCCGCTAC
1 AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
40844993 AGAGACGCCAAATC
1 AGAGACGCCAAATC
40845007 ATCTTGGATT
Statistics
Matches: 434, Mismatches: 39, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
40 72 0.17
41 40 0.09
43 39 0.09
44 282 0.65
45 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.29
Consensus pattern (44 bp):
AGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTAC
Found at i:40845311 original size:61 final size:65
Alignment explanation
Indices: 40845195--40845314 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 65
40845185 TGTATCCATG
40845195 TTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
1 TTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
* *
40845260 TTTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGTTCCTAACTAAATG
1 TTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATG
40845315 AATGGTTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 29 0.55
62 1 0.02
63 1 0.02
64 1 0.02
65 21 0.40
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (65 bp):
TTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
Found at i:40857174 original size:19 final size:19
Alignment explanation
Indices: 40857150--40857187 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40857140 GAAATGAATA
*
40857150 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
40857169 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
40857188 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:40858053 original size:5 final size:5
Alignment explanation
Indices: 40858034--40858084 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
40858024 GTATATATAT
* *
40858034 ATAAA AT-AA AGAAA ATAAA ATAAA ATAAA ATAAC A-AAA ATGAAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT--AAA ATAAA
40858084 A
1 A
40858085 AATGAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.16
5 27 0.71
7 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:40858351 original size:18 final size:16
Alignment explanation
Indices: 40858328--40858367 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
40858318 AGAGATTAGG
40858328 TTTTTTTCTTTTTCTTCA
1 TTTTTTTCTTTTT-TT-A
40858346 TTTTTTTCTTTTTTTA
1 TTTTTTTCTTTTTTTA
40858362 TTTTTT
1 TTTTTT
40858368 ATTTTAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
17 2 0.09
18 13 0.59
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTA
Found at i:40860339 original size:45 final size:46
Alignment explanation
Indices: 40860251--40860345 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 46
40860241 GCAGTAGCAG
* *
40860251 ATGTGGACACATATGCGGCATTTTACTCAACAAAAACAACAACAAA
1 ATGTGGACACAAATGCGACATTTTACTCAACAAAAACAACAACAAA
* * *
40860297 ATGTGTACACAAATGCGACA-TTTACTCAACAAAAATAGCAACAAA
1 ATGTGGACACAAATGCGACATTTTACTCAACAAAAACAACAACAAA
40860342 ATGT
1 ATGT
40860346 TTATTACAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 27 0.61
46 17 0.39
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (46 bp):
ATGTGGACACAAATGCGACATTTTACTCAACAAAAACAACAACAAA
Found at i:40868421 original size:26 final size:26
Alignment explanation
Indices: 40868368--40868476 Score: 148
Period size: 26 Copynumber: 4.2 Consensus size: 26
40868358 TGATACAAAT
*
40868368 TGATAATAGGTTAGGT-AATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTCCA
40868393 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
40868419 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
40868445 TGACAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40868471 TGATAA
1 TGATAA
40868477 GAATTTCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
25 16 0.21
26 60 0.79
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40870124 original size:27 final size:27
Alignment explanation
Indices: 40870083--40870194 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
40870073 GAGGAAGCGT
*
40870083 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
40870110 TCTGGTGGCTCTGCCACATATATCTG-
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
40870136 TTTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
40870164 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
40870190 TCTGG
1 TCTGG
40870195 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 27 0.37
27 32 0.44
28 14 0.19
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:40870187 original size:53 final size:53
Alignment explanation
Indices: 40870085--40870190 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
40870075 GGAAGCGTTC
*
40870085 TGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 TGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
40870138 TGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 TGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
40870191 CTGGCAGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 29 0.62
54 18 0.38
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (53 bp):
TGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:40875295 original size:25 final size:25
Alignment explanation
Indices: 40875267--40875318 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40875257 TAAAAATTAA
40875267 CCCTTTTAATAAATATTTGGGAGTT
1 CCCTTTTAATAAATATTTGGGAGTT
40875292 CCCTTTTAATAAATATTTGGGAGTT
1 CCCTTTTAATAAATATTTGGGAGTT
40875317 CC
1 CC
40875319 AATCTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (25 bp):
CCCTTTTAATAAATATTTGGGAGTT
Found at i:40875811 original size:25 final size:25
Alignment explanation
Indices: 40875783--40875834 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40875773 TAAAAATTAA
40875783 CCCTTTTAATAAATATTTGGGAGTT
1 CCCTTTTAATAAATATTTGGGAGTT
40875808 CCCTTTTAATAAATATTTGGGAGTT
1 CCCTTTTAATAAATATTTGGGAGTT
40875833 CC
1 CC
40875835 AATCTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (25 bp):
CCCTTTTAATAAATATTTGGGAGTT
Found at i:40875927 original size:516 final size:518
Alignment explanation
Indices: 40874919--40875949 Score: 1852
Period size: 516 Copynumber: 2.0 Consensus size: 518
40874909 TCTCAGTAGG
40874919 AGTTTTAATAGTTTAATAGATATTACTTCAAAATTAAATTCTATTTCCTATAGAATCTATATTTT
1 AGTTTTAATAGTTTAATAGATATTACTTCAAAATTAAATTCTATTTCCTATAGAATCTATATTTT
*
40874984 CTAGTTCCACACTAGCTATTTTATTATGCTTTTCTAAATAAGAATTGTATTTTTGTATACAAATC
66 CTAGTTCCACACCAGCTATTTTATTATGCTTTTCTAAATAAGAATTGTATTTTTGTATACAAATC
40875049 TCATCCAATGATGGTGGTAATTTATGAAAATATTAGTTTTTCCAAAAATTTATATTTTCATTTTT
131 TCATCCAATGATGGTGGTAATTTATGAAAATATTAGTTTTTCCAAAAATTTATATTTTCATTTTT
*
40875114 TAGTTTTTGATATTTATGAAGAAATATTTTAGAAAATTCTTCTAGGTATCTTATATCACATAATT
196 TAGTTTTTGATATTTATGAAGAAATATTTTAGAAAATTCTTCTAGGTATCTTATATAACATAATT
*
40875179 TTATTTTTGACAATACATAACTAGACAAACAATCCTGATCTTTTTTATCAATATATCCGCAAAAT
261 TTATTTTTGACAATACATAACTAGACAAACAATCCTGATCTTTTTTATCAATATATCCACAAAAT
*
40875244 TCTGTTTTTAGAATAAAAATTAACCCTTTTAATAAATATTTGGGAGTTCCCTTTTAATAAATATT
326 TCTATTTTTAGAATAAAAATTAACCCTTTTAATAAATATTTGGGAGTTCCCTTTTAATAAATATT
* * * *
40875309 TGGGAGTTCCAATCTGGTTGATTAACTGCCATTTTTGTTCTCTTCCTTTTTCTGATTCTTCCTAT
391 TGGGAGTTCCAATCTGGTTGATTAACTCCCATTTTTGCTCTCTTCCTTTTTCTGATTCTCCCCAT
*
40875374 CTTCTTAGGAATTGTAGAACATCTCCTTGAAATGTTCCAAC-AAAATAGTTTACAATTTTAAT
456 CTTCTTAGGAATTGTAGAACATCTCCTTGAAATGTTCCAACAAAAAAAGTTTACAATTTTAAT
40875436 AGTTTTAATAGTTTAATAGATATTACTTCAAAATT-AATTCTATTTCCTATAGAATCTATATTTT
1 AGTTTTAATAGTTTAATAGATATTACTTCAAAATTAAATTCTATTTCCTATAGAATCTATATTTT
* * *
40875500 CTAGTTCTACACCAGCTATTTTATTATGCTTTTCTAAATAAGAATTGTATTTTTTTATATAAATC
66 CTAGTTCCACACCAGCTATTTTATTATGCTTTTCTAAATAAGAATTGTATTTTTGTATACAAATC
* * *
40875565 TCATCCCATGGTGGTGGTAATTTATGAAAATATTGGTTTTTCCAAAAATTTATATTTTCATTTTT
131 TCATCCAATGATGGTGGTAATTTATGAAAATATTAGTTTTTCCAAAAATTTATATTTTCATTTTT
*
40875630 TAGTTTTTGATATTTATGAAGAAATTTTTTAGAAAATTCTTCTAGGTATCTTATATAACATAATT
196 TAGTTTTTGATATTTATGAAGAAATATTTTAGAAAATTCTTCTAGGTATCTTATATAACATAATT
*
40875695 TTATTTTTGACAATACATAACTAGACAAACAATCCTGATCTTTTTTATCAGTATATCCACAAAAT
261 TTATTTTTGACAATACATAACTAGACAAACAATCCTGATCTTTTTTATCAATATATCCACAAAAT
40875760 TCTATTTTTAGAATAAAAATTAACCCTTTTAATAAATATTTGGGAGTTCCCTTTTAATAAATATT
326 TCTATTTTTAGAATAAAAATTAACCCTTTTAATAAATATTTGGGAGTTCCCTTTTAATAAATATT
*
40875825 TGGGAGTTCCAATCTGGTTGATTAACTACCCA-TTTTGCTCTTTTCCTTTTTCTGATTCTCCCCA
391 TGGGAGTTCCAATCTGGTTGATTAACT-CCCATTTTTGCTCTCTTCCTTTTTCTGATTCTCCCCA
* *
40875889 TCTTTTTAGGAATTTTAGAACATCTCCTTGAAATGTTCCAACAAAAAAAGTTTACAATTTT
455 TCTTCTTAGGAATTGTAGAACATCTCCTTGAAATGTTCCAACAAAAAAAGTTTACAATTTT
40875950 TTCTTTTGAC
Statistics
Matches: 492, Mismatches: 20, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
516 437 0.89
517 55 0.11
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (518 bp):
AGTTTTAATAGTTTAATAGATATTACTTCAAAATTAAATTCTATTTCCTATAGAATCTATATTTT
CTAGTTCCACACCAGCTATTTTATTATGCTTTTCTAAATAAGAATTGTATTTTTGTATACAAATC
TCATCCAATGATGGTGGTAATTTATGAAAATATTAGTTTTTCCAAAAATTTATATTTTCATTTTT
TAGTTTTTGATATTTATGAAGAAATATTTTAGAAAATTCTTCTAGGTATCTTATATAACATAATT
TTATTTTTGACAATACATAACTAGACAAACAATCCTGATCTTTTTTATCAATATATCCACAAAAT
TCTATTTTTAGAATAAAAATTAACCCTTTTAATAAATATTTGGGAGTTCCCTTTTAATAAATATT
TGGGAGTTCCAATCTGGTTGATTAACTCCCATTTTTGCTCTCTTCCTTTTTCTGATTCTCCCCAT
CTTCTTAGGAATTGTAGAACATCTCCTTGAAATGTTCCAACAAAAAAAGTTTACAATTTTAAT
Found at i:40880854 original size:18 final size:18
Alignment explanation
Indices: 40880833--40880867 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40880823 TCCTTCTCAA
40880833 CTTCCTCGTCATCACTTC
1 CTTCCTCGTCATCACTTC
* *
40880851 CTTCCTCTTCTTCACTT
1 CTTCCTCGTCATCACTT
40880868 TCTTGCTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.43, G:0.03, T:0.46
Consensus pattern (18 bp):
CTTCCTCGTCATCACTTC
Found at i:40886507 original size:28 final size:29
Alignment explanation
Indices: 40886474--40886545 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
40886464 TATAGTAAGT
* *
40886474 CCGCACACTTAGTGTTATATAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTCGAAC
* *
40886502 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTCGAAC
40886531 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
40886546 CAATTTCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 19 0.50
29 19 0.50
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTCGAAC
Found at i:40894323 original size:29 final size:28
Alignment explanation
Indices: 40894257--40894357 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 28
40894247 TATAGTAAGT
* * *
40894257 CCGCACACTTAGTGTTATATAATCGAAC
1 CCGCACACTTAGTGCTATACAATTGAAC
*
40894285 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAA-TTGAAC
40894314 CCGCACACTTAGTGCTATACAAATTGAAC
1 CCGCACACTTAGTGCTATAC-AATTGAAC
* *
40894343 CCACACATTTAGTGC
1 CCGCACACTTAGTGC
40894358 CAATTTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
28 19 0.30
29 43 0.67
30 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATTGAAC
Found at i:40897824 original size:583 final size:584
Alignment explanation
Indices: 40896713--40897860 Score: 1850
Period size: 583 Copynumber: 2.0 Consensus size: 584
40896703 TCTGGCTCTG
* *
40896713 TCACAACAATGAAGGCAATATGCTCCTTTTGAGTGCTTTGCTCATAATGTTGCAATATTGGCACT
1 TCACAACAATGAAGGCAATATGCTCCTTTTGAGTGCTTTGCTCATAACGTTGCAACATTGGCACT
* * * *
40896778 CTGTGTTGCCAAATTACAGCCAGTCTTGTATTCCTATGCCTCTGAATGCTATCTTGCACACTCAC
66 CTGTGTTGCAAAATTACAGCCAGTCTCGTATTCCTATGCCTCTGAATGATATCCTGCACACTCAC
* * * *
40896843 TGAATATGTTACCCTTCCTTTAAGTCTATTTTGGCCCCTGAGGTCATATAAATGGTTTAAATTGC
131 TGAATATGTTACCCTTCCTTTAAGCCTATTTTGGCCCCTAAGGTCATATAAATGGTTCAAATTAC
* * * *
40896908 AATTTTTTTTATTATTGATTTCCTAAAGATGAAAGCTAAGTGAAAACATATTTAAATAGATTTAA
196 AATTTTTTTTATTATTAATTACCTAAAGATGAAAACTAAGTGAAAACATAATTAAATAGATTTAA
* *
40896973 TATAAGCTCTTTAAGTATAGAAAATAATTTAATATGCTACAATGAATTGTGACAGATCAATGCTC
261 TATAAGCTCTTTAAGTACAAAAAATAATTTAATATGCTACAATGAATTGTGACAGATCAATGCTC
* *
40897038 ACAATCCTATGGCATGCCAATAATATCCAGTGGTTCCAAGAGATCACAATGCCAACATATCACTT
326 ACAATCCTATAGCATGCCAATAATATCCAGCGGTTCCAAGAGATCACAATGCCAACATATCACTT
* *
40897103 GTATACACATTTACCTACTATTTTATGCACACTTTCACTTATCATATTCATATGTTCATAACAAT
391 ATATACACATTTACCTACTATTTTATGCACACATTCACTTATCATATTCATATGTTCATAACAAT
*
40897168 TTCATATTCACTTATAATGCACTTTTCAAGTGCTCACAAAATTTCTTAAAAGGCCATATTCACTT
456 TTCATATTAACTTATAATGCACTTTTCAAGTGCTCACAAAATTTCTTAAAAGGCCATATTCACTT
* * *
40897233 TAAGTCACTATGGTGTGCATAAAACTAGTAGTCCACTTAACATTCTCGATACCCTTTGACTGTT
521 TAAGTCACTATAGTGTACATAAAACCAGTAGTCCACTTAACATTCTCGATACCCTTTGACTGTT
* *
40897297 TCACAACACTGAAGGCAATATGCTCCTTTTGAGTGCTTTGCTCATAACGTTGCAACATTGGTACT
1 TCACAACAATGAAGGCAATATGCTCCTTTTGAGTGCTTTGCTCATAACGTTGCAACATTGGCACT
* * *
40897362 CTGTGTTGCAAAATTGCAGCTAGTCTCGTATTCCTACT-CCTCTGAATGATGTCCTGCACACTCA
66 CTGTGTTGCAAAATTACAGCCAGTCTCGTATTCCTA-TGCCTCTGAATGATATCCTGCACACTCA
* * *
40897426 TTGAATA-GTTACCCTTCCTTTAGGCCTATTTTGGCCCTTAAGGTCATATAAATGGTTCAAATTA
130 CTGAATATGTTACCCTTCCTTTAAGCCTATTTTGGCCCCTAAGGTCATATAAATGGTTCAAATTA
* * *
40897490 TAATTTTTTTTATTATTAATTACCTAAAGATGAAAACTAAGTGAAAACATAATTAAATTGCTTTA
195 CAATTTTTTTTATTATTAATTACCTAAAGATGAAAACTAAGTGAAAACATAATTAAATAGATTTA
* * *
40897555 ATATGAGCTCTTTAAGTACAAAAAATAGTTTAATATGCTACAATGAATTGTGATAGATCAATGCT
260 ATATAAGCTCTTTAAGTACAAAAAATAATTTAATATGCTACAATGAATTGTGACAGATCAATGCT
* *
40897620 CACAATCCTATAGCATGCCAATGATATCCAGCGGTTCCAAGAGATCACAATGCCAACATGTCACT
325 CACAATCCTATAGCATGCCAATAATATCCAGCGGTTCCAAGAGATCACAATGCCAACATATCACT
*
40897685 TATATACACATTTACCTACTATTTTATGCACACATTCACTTATCATATTCATATGTTCATAACAG
390 TATATACACATTTACCTACTATTTTATGCACACATTCACTTATCATATTCATATGTTCATAACAA
* * *
40897750 TTTCGTATTAACTTATAATGTACTTTTCAAGTGCTCACATAATTTCTTAAAAGGCCATATTCACT
455 TTTCATATTAACTTATAATGCACTTTTCAAGTGCTCACAAAATTTCTTAAAAGGCCATATTCACT
* * *
40897815 TTCAGTCACTATAGTGTACGTAAGACCAGTAGTCCACTTAACATTC
520 TTAAGTCACTATAGTGTACATAAAACCAGTAGTCCACTTAACATTC
40897861 ACTGTCACAT
Statistics
Matches: 516, Mismatches: 47, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
583 393 0.76
584 122 0.24
585 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (584 bp):
TCACAACAATGAAGGCAATATGCTCCTTTTGAGTGCTTTGCTCATAACGTTGCAACATTGGCACT
CTGTGTTGCAAAATTACAGCCAGTCTCGTATTCCTATGCCTCTGAATGATATCCTGCACACTCAC
TGAATATGTTACCCTTCCTTTAAGCCTATTTTGGCCCCTAAGGTCATATAAATGGTTCAAATTAC
AATTTTTTTTATTATTAATTACCTAAAGATGAAAACTAAGTGAAAACATAATTAAATAGATTTAA
TATAAGCTCTTTAAGTACAAAAAATAATTTAATATGCTACAATGAATTGTGACAGATCAATGCTC
ACAATCCTATAGCATGCCAATAATATCCAGCGGTTCCAAGAGATCACAATGCCAACATATCACTT
ATATACACATTTACCTACTATTTTATGCACACATTCACTTATCATATTCATATGTTCATAACAAT
TTCATATTAACTTATAATGCACTTTTCAAGTGCTCACAAAATTTCTTAAAAGGCCATATTCACTT
TAAGTCACTATAGTGTACATAAAACCAGTAGTCCACTTAACATTCTCGATACCCTTTGACTGTT
Found at i:40901636 original size:13 final size:13
Alignment explanation
Indices: 40901618--40901642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40901608 AACAAACTTT
40901618 CCCTTCCCTCTTA
1 CCCTTCCCTCTTA
40901631 CCCTTCCCTCTT
1 CCCTTCCCTCTT
40901643 CCTTGCCACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.56, G:0.00, T:0.40
Consensus pattern (13 bp):
CCCTTCCCTCTTA
Found at i:40909715 original size:23 final size:22
Alignment explanation
Indices: 40909664--40909715 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
40909654 CCTCGTCTTT
*
40909664 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
40909686 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
40909709 TTCTTTT
1 TTCTTTT
40909716 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:40909724 original size:12 final size:12
Alignment explanation
Indices: 40909673--40909727 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
40909663 TTTCTTTTGT
40909673 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
40909686 -TCATTTTC-TC
1 TTCTTTTTCAAC
40909696 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
40909709 TTCTTTTTCAAT
1 TTCTTTTTCAAC
40909721 TTCTTTT
1 TTCTTTT
40909728 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:40909734 original size:17 final size:18
Alignment explanation
Indices: 40909709--40909746 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40909699 TTTCTTCAAC
* *
40909709 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
40909726 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
40909744 TTC
1 TTC
40909747 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:40912962 original size:33 final size:33
Alignment explanation
Indices: 40912920--40913170 Score: 158
Period size: 33 Copynumber: 7.7 Consensus size: 33
40912910 CTCGAGGTGC
*
40912920 ACATTCCCTTTTCAAGTGGTACACACAAAGAGT
1 ACATTTCCTTTTCAAGTGGTACACACAAAGAGT
** * * * * *
40912953 ACATACCCTTTTCAATTTGTACACTCAAAGTGC
1 ACATTTCCTTTTCAAGTGGTACACACAAAGAGT
* ** * * * *
40912986 ATATAACCTTTTCAAAT-GTAGACATATAA-TGT
1 ACATTTCCTTTTCAAGTGGTACACACA-AAGAGT
* *
40913018 ACCTTTCCTTTTCAAGTGGTATACACAAAGTA-T
1 ACATTTCCTTTTCAAGTGGTACACACAAAG-AGT
* *
40913051 ACATTTCCTTTTCATA-TGGTATACTCAAAGTA-T
1 ACATTTCCTTTTCA-AGTGGTACACACAAAG-AGT
* *
40913084 ACATTTCCTTTTCATA-TGATATACACAAAGTA-T
1 ACATTTCCTTTTCA-AGTGGTACACACAAAG-AGT
* *
40913117 ACCTTTCCTTTTCAAGT-GTACACACAAAGTGT
1 ACATTTCCTTTTCAAGTGGTACACACAAAGAGT
** *
40913149 ACATAACCTTTTCAAGTTGTAC
1 ACATTTCCTTTTCAAGTGGTAC
40913171 CATTTGGGTA
Statistics
Matches: 178, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
32 48 0.27
33 129 0.72
34 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (33 bp):
ACATTTCCTTTTCAAGTGGTACACACAAAGAGT
Found at i:40913033 original size:98 final size:99
Alignment explanation
Indices: 40912926--40913170 Score: 275
Period size: 98 Copynumber: 2.5 Consensus size: 99
40912916 GTGCACATTC
* * *
40912926 CCTTTTCAAGTGGTACACACAAAGAGTACATACCCTTTTCAATTTGTACACTCAAAGTGCATATA
1 CCTTTTCAAGTGGTACACACAAAGAGTACATAACCTTTTCAATTTGTACACTCAAAGTACACATA
* *
40912991 ACCTTTTCAAATG-TAGACATATAA-TGTACCTTT
66 ACCTTTTCAAATGATAGACACA-AAGTATACCTTT
* ** * * *
40913024 CCTTTTCAAGTGGTATACACAAAGTA-TACATTTCCTTTTC-ATATGGTATACTCAAAGTATACA
1 CCTTTTCAAGTGGTACACACAAAG-AGTACATAACCTTTTCAAT-TTGTACACTCAAAGTACACA
** * *
40913087 TTTCCTTTTCATATGATATACACAAAGTATACCTTT
64 TAACCTTTTCAAATGATAGACACAAAGTATACCTTT
* *
40913123 CCTTTTCAAGT-GTACACACAAAGTGTACATAACCTTTTCAAGTTGTAC
1 CCTTTTCAAGTGGTACACACAAAGAGTACATAACCTTTTCAATTTGTAC
40913171 CATTTGGGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
97 2 0.02
98 91 0.76
99 27 0.22
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (99 bp):
CCTTTTCAAGTGGTACACACAAAGAGTACATAACCTTTTCAATTTGTACACTCAAAGTACACATA
ACCTTTTCAAATGATAGACACAAAGTATACCTTT
Found at i:40928985 original size:33 final size:33
Alignment explanation
Indices: 40928936--40929052 Score: 119
Period size: 33 Copynumber: 3.5 Consensus size: 33
40928926 ATGGACTTTT
* * *
40928936 CCTTTTCTAGTTGTACACTCGAGGTGCACATTC
1 CCTTTTCAAGTTGTACACTCGAAGTGCACATAC
* * * *
40928969 CCTTTTCAAGTGGTACACACGAAGTGTATATAC
1 CCTTTTCAAGTTGTACACTCGAAGTGCACATAC
* * *
40929002 CCTTTTTCAATTTGTACACTCAAAGTGCACATAA
1 CC-TTTTCAAGTTGTACACTCGAAGTGCACATAC
*
40929036 CCTTTTCAA-ATGTACAC
1 CCTTTTCAAGTTGTACAC
40929053 ATATAGTGTA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
32 7 0.10
33 35 0.51
34 26 0.38
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (33 bp):
CCTTTTCAAGTTGTACACTCGAAGTGCACATAC
Found at i:40929040 original size:34 final size:34
Alignment explanation
Indices: 40928938--40929041 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 34
40928928 GGACTTTTCC
* * * *
40928938 TTTTCTAGTTGTACACTCGAGGTGCACAT-TCCC
1 TTTTCAAGTTGTACACTCGAAGTGCACATAACCT
* * * * *
40928971 TTTTCAAGTGGTACACACGAAGTGTATATACCCT
1 TTTTCAAGTTGTACACTCGAAGTGCACATAACCT
* *
40929005 TTTTCAATTTGTACACTCAAAGTGCACATAACCT
1 TTTTCAAGTTGTACACTCGAAGTGCACATAACCT
40929039 TTT
1 TTT
40929042 CAAATGTACA
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
33 23 0.42
34 32 0.58
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (34 bp):
TTTTCAAGTTGTACACTCGAAGTGCACATAACCT
Found at i:40929072 original size:32 final size:33
Alignment explanation
Indices: 40929036--40929195 Score: 173
Period size: 32 Copynumber: 4.9 Consensus size: 33
40929026 GTGCACATAA
* * * * *
40929036 CCTTTTCAAAT-GTACACATATAGTGTACCTTT
1 CCTTTTCAAATGGTATACACAAAGTATACATTT
*
40929068 CCTTTTCAAGTGGTATACACAAAGTATACATTT
1 CCTTTTCAAATGGTATACACAAAGTATACATTT
*
40929101 TCTTTTC-AATGGTATACACAAAGTATACATTT
1 CCTTTTCAAATGGTATACACAAAGTATACATTT
* * *
40929133 CCATTTCATATGGTATACACAAAGTATACCTTT
1 CCTTTTCAAATGGTATACACAAAGTATACATTT
* * * *
40929166 CCTTATCAAGT-GTACACACAAAGTGTACAT
1 CCTTTTCAAATGGTATACACAAAGTATACAT
40929196 AACTTTTTTC
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
32 55 0.51
33 52 0.49
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (33 bp):
CCTTTTCAAATGGTATACACAAAGTATACATTT
Found at i:40929107 original size:65 final size:65
Alignment explanation
Indices: 40929036--40929195 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
40929026 GTGCACATAA
* * * *
40929036 CCTTTTCAAATGTACACATATAGTGTACCTTTCCTTTTCA-AGTGGTATACACAAAGTATACATT
1 CCTTTTCAAATGTACACACAAAGTGTACATTTCCATTTCATA-TGGTATACACAAAGTATACATT
40929100 T
65 T
* * * *
40929101 TCTTTTC-AATGGTATACACAAAGTATACATTTCCATTTCATATGGTATACACAAAGTATACCTT
1 CCTTTTCAAAT-GTACACACAAAGTGTACATTTCCATTTCATATGGTATACACAAAGTATACATT
40929165 T
65 T
* *
40929166 CCTTATCAAGTGTACACACAAAGTGTACAT
1 CCTTTTCAAATGTACACACAAAGTGTACAT
40929196 AACTTTTTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
64 3 0.04
65 73 0.92
66 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (65 bp):
CCTTTTCAAATGTACACACAAAGTGTACATTTCCATTTCATATGGTATACACAAAGTATACATTT
Found at i:40929108 original size:33 final size:32
Alignment explanation
Indices: 40929065--40929195 Score: 174
Period size: 32 Copynumber: 4.0 Consensus size: 32
40929055 ATAGTGTACC
40929065 TTTCCTTTTCAAGTGGTATACACAAAGTATACA
1 TTTCCTTTTCAA-TGGTATACACAAAGTATACA
*
40929098 TTTTCTTTTCAATGGTATACACAAAGTATACA
1 TTTCCTTTTCAATGGTATACACAAAGTATACA
* *
40929130 TTTCCATTTCATATGGTATACACAAAGTATACC
1 TTTCCTTTTCA-ATGGTATACACAAAGTATACA
* * *
40929163 TTTCCTTATCAA-GTGTACACACAAAGTGTACA
1 TTTCCTTTTCAATG-GTATACACAAAGTATACA
40929195 T
1 T
40929196 AACTTTTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
31 1 0.01
32 46 0.53
33 40 0.46
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (32 bp):
TTTCCTTTTCAATGGTATACACAAAGTATACA
Found at i:40929209 original size:33 final size:33
Alignment explanation
Indices: 40928969--40929214 Score: 176
Period size: 33 Copynumber: 7.5 Consensus size: 33
40928959 GTGCACATTC
* * *
40928969 CCTTTTCAAGTGGTACACACGAAGTGTATATAC
1 CCTTTTCAAGTGGTACACACAAAGTGTACATAT
* * * * *
40929002 CCTTTTTCAATTTGTACACTCAAAGTGCACATAA
1 CC-TTTTCAAGTGGTACACACAAAGTGTACATAT
* * * * *
40929036 CCTTTTCAAAT-GTACACATATAGTGTACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTGTACATAT
* * *
40929068 CCTTTTCAAGTGGTATACACAAAGTATACATTT
1 CCTTTTCAAGTGGTACACACAAAGTGTACATAT
* * * *
40929101 TCTTTTCAA-TGGTATACACAAAGTATACATTT
1 CCTTTTCAAGTGGTACACACAAAGTGTACATAT
* * * * *
40929133 CCATTTCATA-TGGTATACACAAAGTATACCTTT
1 CCTTTTCA-AGTGGTACACACAAAGTGTACATAT
* *
40929166 CCTTATCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTACACACAAAGTGTACATAT
* *
40929198 CTTTTTTCAAGTTGTAC
1 C-CTTTTCAAGTGGTAC
40929215 CATTTGGGTA
Statistics
Matches: 173, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
32 71 0.41
33 72 0.42
34 30 0.17
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTGTACATAT
Found at i:40929483 original size:37 final size:37
Alignment explanation
Indices: 40929414--40929498 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
40929404 CATGTAAATC
*
40929414 ACAAATCAAGATTGACTTATTACATGTACATACCAATT
1 ACAAATC-ATATTGACTTATTACATGTACATACCAATT
* * *
40929452 ACAAATCATATTGGCTTATTACATGTGCATACCATTT
1 ACAAATCATATTGACTTATTACATGTACATACCAATT
40929489 ACAAATCATA
1 ACAAATCATA
40929499 ATGCACAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 36 0.84
38 7 0.16
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (37 bp):
ACAAATCATATTGACTTATTACATGTACATACCAATT
Found at i:40948316 original size:39 final size:39
Alignment explanation
Indices: 40948259--40948338 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
40948249 TCCAAAGAAA
40948259 GCAGTATATACTAATACATGATAACTACTTACACCATTG
1 GCAGTATATACTAATACATGATAACTACTTACACCATTG
*
40948298 GCAGTATATACTACTACATGATAACTACTTACACCATTG
1 GCAGTATATACTAATACATGATAACTACTTACACCATTG
40948337 GC
1 GC
40948339 TTATACATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (39 bp):
GCAGTATATACTAATACATGATAACTACTTACACCATTG
Found at i:40951509 original size:17 final size:18
Alignment explanation
Indices: 40951476--40951509 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40951466 TATAATGCAC
40951476 ATAAAAATAAGGTAATAT
1 ATAAAAATAAGGTAATAT
40951494 ATAAAAATAAGG-AATA
1 ATAAAAATAAGGTAATA
40951510 ATAGTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
ATAAAAATAAGGTAATAT
Found at i:40960011 original size:3 final size:3
Alignment explanation
Indices: 40960003--40960031 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40959993 AAAAGAAATG
40960003 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40960032 AAGATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40966892 original size:24 final size:24
Alignment explanation
Indices: 40966865--40966931 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
40966855 CTATCCGGAG
40966865 CTTCCTGATATGGTTCTTTGTGAA
1 CTTCCTGATATGGTTCTTTGTGAA
* *
40966889 CTTCCTGACAAGGTTCTTTGTGAA
1 CTTCCTGATATGGTTCTTTGTGAA
* *
40966913 CTTCCCGATTATGGCTCTT
1 CTTCCTGA-TATGGTTCTT
40966932 ATAAGCTTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 29 0.81
25 7 0.19
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (24 bp):
CTTCCTGATATGGTTCTTTGTGAA
Found at i:40972908 original size:12 final size:12
Alignment explanation
Indices: 40972891--40972918 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40972881 AATAATCCAC
40972891 CAGGTTAGAATG
1 CAGGTTAGAATG
40972903 CAGGTTAGAATG
1 CAGGTTAGAATG
40972915 CAGG
1 CAGG
40972919 CACAACATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (12 bp):
CAGGTTAGAATG
Found at i:40973720 original size:34 final size:35
Alignment explanation
Indices: 40973671--40973737 Score: 111
Period size: 34 Copynumber: 1.9 Consensus size: 35
40973661 AGATTCACAA
40973671 TCGGGCCTAAGCCCATGTT-AGATACAGATACAGAT
1 TCGGGCCTAAGCCCAT-TTCAGATACAGATACAGAT
40973706 TCGGG-CTAAGCCCATTTCAGATACAGATACAG
1 TCGGGCCTAAGCCCATTTCAGATACAGATACAG
40973738 TCACATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 2 0.06
34 24 0.77
35 5 0.16
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (35 bp):
TCGGGCCTAAGCCCATTTCAGATACAGATACAGAT
Found at i:40994091 original size:130 final size:131
Alignment explanation
Indices: 40993748--40994308 Score: 527
Period size: 131 Copynumber: 4.3 Consensus size: 131
40993738 ATATAACAAT
* * * * * * * * * *
40993748 AAAATAAATTGTTACTAAATATTATATTATTAGGAACGACTTTAAAATGTTGTTACATAATTTAA
1 AAAATAAGTTGTTGCTAAATGTTAAAATATTAGCAACAACCTTAAAATATCGTTACATAATTTAA
* * * * ** *
40993813 TTGTATACTTATTCATTGCAACAACACGATTTTTCATTACAAATTCTTAATAAAATGCGTAACGA
66 TTTTATGCTTATTCATTGCAACAACACGATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGA
40993878 TC
131 -C
* * *
40993880 -AAATAAATTGTTGCTAAATGTTAAAATATTAGTAACAACCTTAAAATGTCGTTACATAATTTAA
1 AAAATAAGTTGTTGCTAAATGTTAAAATATTAGCAACAACCTTAAAATATCGTTACATAATTTAA
* *
40993944 TTTTATGCTTATTCATTGCAACAATATGATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGA
66 TTTTATGCTTATTCATTGCAACAACACGATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGA
40994009 C
131 C
* * * **
40994010 AAAATAAGTTGTTG-TAAATGTTACAATATTAGCAACAGCTTTAAAATATCGTTATGTAATTTAA
1 AAAATAAGTTGTTGCTAAATGTTAAAATATTAGCAACAACCTTAAAATATCGTTACATAATTTAA
** * *
40994074 TTTTATGCTTATTCATTGCAATGACACAATTTTTCATTGCAAATT-TTCAATAAAATTTGT-AAG
66 TTTTATGCTTATTCATTGCAACAACACGATTTGTCATTGCAAATTCTT-AATAAAATTTGTAAAG
*
40994137 -T
130 AC
** ** * * * *
40994138 AAAA-AACATG-T--TAAACATTAAAATATTAGCAACAACCTTAAAATATTGATACGTAATTTAT
1 AAAATAAGTTGTTGCTAAATGTTAAAATATTAGCAACAACCTTAAAATATCGTTACATAATTTAA
* * * ** * * *
40994199 TTTTCTGCTTATTAATAGCAATGACATGATTTGAT-ATTGTGAAATAC-TAATAAAATTTGTAAC
66 TTTTATGCTTATTCATTGCAACAACACGATTTG-TCATTG-CAAATTCTTAATAAAATTTGTAA-
40994262 A-AC
128 AGAC
** *
40994265 AAAATAAGTCATTGTTAAATGTT-AAATATTAGCAACAACCTTAA
1 AAAATAAGTTGTTGCTAAATGTTAAAATATTAGCAACAACCTTAA
40994309 GATGTTGTTG
Statistics
Matches: 359, Mismatches: 58, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
125 84 0.23
126 8 0.02
127 9 0.03
128 6 0.02
129 6 0.02
130 116 0.32
131 130 0.36
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (131 bp):
AAAATAAGTTGTTGCTAAATGTTAAAATATTAGCAACAACCTTAAAATATCGTTACATAATTTAA
TTTTATGCTTATTCATTGCAACAACACGATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGA
C
Found at i:40994224 original size:125 final size:130
Alignment explanation
Indices: 40993775--40994308 Score: 448
Period size: 130 Copynumber: 4.1 Consensus size: 130
40993765 AATATTATAT
* * * * * * * * **
40993775 TATTAGGAACGACTTTAAAATGTTGTTACATAATTTAATTGTATACTTATTCATTGCAACAACAC
1 TATTAGCAACAACCTTAAAATATCGTTACGTAATTTAATTTTATGCTTATTCATTGCAATGACAC
* * * ** * **
40993840 GATTTTTCATTACAAATTCTTAATAAAATGCGTAACGATC-AAATAA-ATTGTTGCTAAATGTTA
66 AATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGA-CAAAATAACA-TGTTG-TAAACATTA
40993903 AAA
128 AAA
* * * ** * *
40993906 TATTAGTAACAACCTTAAAATGTCGTTACATAATTTAATTTTATGCTTATTCATTGCAACAATAT
1 TATTAGCAACAACCTTAAAATATCGTTACGTAATTTAATTTTATGCTTATTCATTGCAATGACAC
* ** ** *
40993971 GATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGACAAAATAAGTTGTTGTAAATGTTACAA
66 AATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGACAAAATAACATGTTGTAAACATTAAAA
* * *
40994036 TATTAGCAACAGCTTTAAAATATCGTTATGTAATTTAATTTTATGCTTATTCATTGCAATGACAC
1 TATTAGCAACAACCTTAAAATATCGTTACGTAATTTAATTTTATGCTTATTCATTGCAATGACAC
* *
40994101 AATTTTTCATTGCAAATT-TTCAATAAAATTTGT-AAG-TAAAA-AACATG-T-TAAACATTAAA
66 AATTTGTCATTGCAAATTCTT-AATAAAATTTGTAAAGACAAAATAACATGTTGTAAACATTAAA
40994160 A
130 A
* * * * * * *
40994161 TATTAGCAACAACCTTAAAATATTGATACGTAATTTATTTTTCTGCTTATTAATAGCAATGACAT
1 TATTAGCAACAACCTTAAAATATCGTTACGTAATTTAATTTTATGCTTATTCATTGCAATGACAC
* * * *
40994226 GATTTGAT-ATTGTGAAATAC-TAATAAAATTTGTAACA-ACAAAATAAGTCA--TTGTTAA-AT
66 AATTTG-TCATTG-CAAATTCTTAATAAAATTTGTAA-AGACAAAATAA--CATGTTGTAAACAT
*
40994285 GTTAAA
126 -TAAAA
40994291 TATTAGCAACAACCTTAA
1 TATTAGCAACAACCTTAA
40994309 GATGTTGTTG
Statistics
Matches: 338, Mismatches: 50, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
125 84 0.25
126 8 0.02
127 9 0.03
128 6 0.02
129 8 0.02
130 122 0.36
131 101 0.30
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.38
Consensus pattern (130 bp):
TATTAGCAACAACCTTAAAATATCGTTACGTAATTTAATTTTATGCTTATTCATTGCAATGACAC
AATTTGTCATTGCAAATTCTTAATAAAATTTGTAAAGACAAAATAACATGTTGTAAACATTAAAA
Found at i:40994252 original size:255 final size:260
Alignment explanation
Indices: 40993787--40994301 Score: 611
Period size: 255 Copynumber: 2.0 Consensus size: 260
40993777 TTAGGAACGA
* * *
40993787 CTTTAAAATGTTGTTACATAATTTAATTGTATACTTATTCATTGCAACAACACGATTTTTCATTA
1 CTTTAAAATATCGTTACATAATTTAATTGTATACTTATTCATTGCAACAACACAATTTTTCATTA
* ** *
40993852 CAAATTCTTAATAAAATGCGTAACGATCAAATAAATTGTTGCTAAATGTTAAAATATTAGTAACA
66 CAAATTCTTAATAAAATGCGTAACGATCAAATAAAATGTT-CTAAACATTAAAATATTAGCAACA
* * * * *
40993917 ACCTTAAAATGTCGTTACATAATTTAATTTTATGCTTATTCATTGCAACAATATGATTTGTCATT
130 ACCTTAAAATATCGATACATAATTTAATTTTATGCTTATTAATAGCAACAACATGATTTGTCATT
* **
40993982 GCAAATTCTTAATAAAATTTGTAA-AGACAAAATAAGTTGTTG-TAAATGTTACAATATTAGCAA
195 GCAAATACTTAATAAAATTTGTAACA-ACAAAATAAGTCATTGTTAAATGTTA-AATATTAGCAA
40994045 CAG
258 CAG
** * * ** *
40994048 CTTTAAAATATCGTTATGTAATTTAATTTTATGCTTATTCATTGCAATGACACAATTTTTCATTG
1 CTTTAAAATATCGTTACATAATTTAATTGTATACTTATTCATTGCAACAACACAATTTTTCATTA
**
40994113 CAAATT-TTCAATAAAATTTGTAA-G-T-AAA-AAACATG-T-TAAACATTAAAATATTAGCAAC
66 CAAATTCTT-AATAAAATGCGTAACGATCAAATAAA-ATGTTCTAAACATTAAAATATTAGCAAC
* * * * **
40994171 AACCTTAAAATATTGATACGTAATTTATTTTTCTGCTTATTAATAGCAATGACATGATTTGAT-A
129 AACCTTAAAATATCGATACATAATTTAATTTTATGCTTATTAATAGCAACAACATGATTTG-TCA
*
40994235 TTGTGAAATAC-TAATAAAATTTGTAACAACAAAATAAGTCATTGTTAAATGTTAAATATTAGCA
193 TTG-CAAATACTTAATAAAATTTGTAACAACAAAATAAGTCATTGTTAAATGTTAAATATTAGCA
40994299 ACA
257 ACA
40994302 ACCTTAAGAT
Statistics
Matches: 217, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
255 115 0.53
256 16 0.07
257 4 0.02
258 5 0.02
259 1 0.00
260 3 0.01
261 73 0.34
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.38
Consensus pattern (260 bp):
CTTTAAAATATCGTTACATAATTTAATTGTATACTTATTCATTGCAACAACACAATTTTTCATTA
CAAATTCTTAATAAAATGCGTAACGATCAAATAAAATGTTCTAAACATTAAAATATTAGCAACAA
CCTTAAAATATCGATACATAATTTAATTTTATGCTTATTAATAGCAACAACATGATTTGTCATTG
CAAATACTTAATAAAATTTGTAACAACAAAATAAGTCATTGTTAAATGTTAAATATTAGCAACAG
Found at i:40995831 original size:45 final size:45
Alignment explanation
Indices: 40995781--40995866 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
40995771 ACAACCCAAC
*
40995781 CAGAGCAGAGCAGAACA-ACACAAAACAAAGCAGAGCAGAACAGAG
1 CAGAGCAAAGCAGAACATA-ACAAAACAAAGCAGAGCAGAACAGAG
* *
40995826 CAGAGCAAAGTAGAACATAACAAAACAAAGTAGAGCAGAAC
1 CAGAGCAAAGCAGAACATAACAAAACAAAGCAGAGCAGAAC
40995867 TGAACAGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 36 0.97
46 1 0.03
ACGTcount: A:0.55, C:0.20, G:0.22, T:0.03
Consensus pattern (45 bp):
CAGAGCAAAGCAGAACATAACAAAACAAAGCAGAGCAGAACAGAG
Found at i:40995865 original size:25 final size:24
Alignment explanation
Indices: 40995787--40995866 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 24
40995777 CAACCAGAGC
*
40995787 AGAGCAGAACAACACAAAACAAAGC
1 AGAGCAGAACAA-ACAAAACAAAGT
* * *
40995812 AGAGCAGAACAGAGCAGAGCAAAGT
1 AGAGCAGAACA-AACAAAACAAAGT
40995837 -----AGAACATAACAAAACAAAGT
1 AGAGCAGAACA-AACAAAACAAAGT
40995857 AGAGCAGAAC
1 AGAGCAGAAC
40995867 TGAACAGAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 16 0.39
25 24 0.59
26 1 0.02
ACGTcount: A:0.56, C:0.19, G:0.21, T:0.04
Consensus pattern (24 bp):
AGAGCAGAACAAACAAAACAAAGT
Found at i:40997414 original size:131 final size:131
Alignment explanation
Indices: 40997060--40997525 Score: 541
Period size: 131 Copynumber: 3.6 Consensus size: 131
40997050 ATACGACTTA
* * **
40997060 AATTCGTAATAAAATTTGTAAAGACAAAATAAGTTGTTG-TAAATGTTAAAATATTAACAACAAC
1 AATTCTTAATAAAATTTGTAAAGACAAAATAAGTTATTGTTAAACATTAAAATATTAACAACAAC
* * * * * * *
40997124 CTTAAAATATTGTTATGAAATTTAATTTTATGCTTATTCATTGCAATGACACAATTTTTCATTGC
66 CTTAAAATATTGTTACGTAATTTAATTTTCTGCTTATTAATTGCAATGACACGATTTATCATTGT
*
40997189 A
131 G
* * * *
40997190 AATTCTTAATAAAATTTGTAACGA-AAAA-AA-TATGTTGTTAAACATTAAAATCTTAGCAACAA
1 AATTCTTAATAAAATTTGTAAAGACAAAATAAGT-TATTGTTAAACATTAAAATATTAACAACAA
* *
40997252 CCTTAAAATATTGATACGTAATTTAATTTTCTGCTTATTAATAGCAATGACACGATTTAT-AGTT
65 CCTTAAAATATTGTTACGTAATTTAATTTTCTGCTTATTAATTGCAATGACACGATTTATCA-TT
40997316 GTG
129 GTG
* *
40997319 AATTAC-TAATAAAATTTGTAACA-ACAAAATAAGTTATTGTTAAACGTTAAAATATTAGCAACA
1 AATT-CTTAATAAAATTTGTAA-AGACAAAATAAGTTATTGTTAAACATTAAAATATTAACAACA
* * * * * * ** * *
40997382 ACCTTAAAATGTCGTTACCTATTTTAACTTTCTACTTATTGGTTGCAATAACATGATTTATCATT
64 ACCTTAAAATATTGTTACGTAATTTAATTTTCTGCTTATTAATTGCAATGACACGATTTATCATT
40997447 GTG
129 GTG
* * *
40997450 AATTCTTAATAAAGTTTGTAAATGAAAAAATGAGTTATTGTTAAACATTAAAATATTAACAACAA
1 AATTCTTAATAAAATTTGTAAA-GACAAAATAAGTTATTGTTAAACATTAAAATATTAACAACAA
40997515 CCTTAAAATAT
65 CCTTAAAATAT
40997526 CATTTGATTT
Statistics
Matches: 286, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
127 1 0.00
128 8 0.03
129 99 0.35
130 29 0.10
131 100 0.35
132 49 0.17
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (131 bp):
AATTCTTAATAAAATTTGTAAAGACAAAATAAGTTATTGTTAAACATTAAAATATTAACAACAAC
CTTAAAATATTGTTACGTAATTTAATTTTCTGCTTATTAATTGCAATGACACGATTTATCATTGT
G
Found at i:40997937 original size:21 final size:21
Alignment explanation
Indices: 40997888--40997937 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
40997878 TAGTTAAGAA
*
40997888 AAAAGACTGATCCATTTCTAT
1 AAAAGATTGATCCATTTCTAT
** * *
40997909 AAGGGATTGATCCATTTTTCT
1 AAAAGATTGATCCATTTCTAT
40997930 AAAAGATT
1 AAAAGATT
40997938 AATCGATCTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
AAAAGATTGATCCATTTCTAT
Found at i:40999399 original size:27 final size:27
Alignment explanation
Indices: 40999359--40999414 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
40999349 TTGTTTTGTT
*
40999359 AAGGTAAGTTTGTATTCCTTGAACTCG
1 AAGGTAAGTGTGTATTCCTTGAACTCG
40999386 AAGGTAAGTGTGTATTCCTTGAACTCG
1 AAGGTAAGTGTGTATTCCTTGAACTCG
40999413 AA
1 AA
40999415 CTTTATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (27 bp):
AAGGTAAGTGTGTATTCCTTGAACTCG
Found at i:41011380 original size:40 final size:39
Alignment explanation
Indices: 41011353--41011535 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 39
41011343 TACTTATTCG
*
41011353 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACA
41011393 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACA
41011433 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACA
* * *
41011473 AATGCCTTTGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACA
41011513 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
41011536 TTATCATCCA
Statistics
Matches: 135, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
39 2 0.01
40 132 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTACTCGCACA
Found at i:41013554 original size:22 final size:22
Alignment explanation
Indices: 41013529--41013572 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41013519 AATTATTAAA
41013529 ATAATGAAA-TTTAATTAATTTT
1 ATAAT-AAATTTTAATTAATTTT
*
41013551 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
41013573 GATCATTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:41027493 original size:93 final size:93
Alignment explanation
Indices: 41027334--41027504 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
41027324 GCCCATAAGT
* * *
41027334 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41027399 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
41027427 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41027492 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41027505 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41027501 original size:46 final size:46
Alignment explanation
Indices: 41027326--41027501 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
41027316 TGTAACCCGC
* * * *
41027326 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * *
41027372 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
41027422 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
41027465 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41027502 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:41029911 original size:15 final size:15
Alignment explanation
Indices: 41029882--41029931 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
41029872 CAAAGATAAC
*
41029882 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
41029896 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
41029911 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
41029926 AAGAAA
1 AAGAAA
41029932 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:41029940 original size:15 final size:15
Alignment explanation
Indices: 41029893--41029940 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
41029883 AGAAAACCGA
41029893 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
41029907 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
41029923 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
41029938 ATA
1 ATA
41029941 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:41033002 original size:93 final size:95
Alignment explanation
Indices: 41032831--41033003 Score: 271
Period size: 95 Copynumber: 1.8 Consensus size: 95
41032821 GCCCATAAGT
* *
41032831 GAACTCGGACTCAACTCAACGAGCTTGGGAGTTCGCATCCATGAATGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTTCGGAATTCGCATCCATGAATGTGAACTCGGACTCAACTC
41032896 AACGAGTTCGGATGCCTAGTTACATCTCAC
66 AACGAGTTCGGATGCCTAGTTACATCTCAC
*
41032926 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCAT-AA-GTGAACTCGGACTCAACT
1 GAACTCGGACTCAACTCAACGAGCTTCGGA-ATTCGCATCCATGAATGTGAACTCGGACTCAACT
* *
41032988 GAACGAGTTTGGATGC
65 CAACGAGTTCGGATGC
41033004 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
93 32 0.44
94 7 0.10
95 33 0.46
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (95 bp):
GAACTCGGACTCAACTCAACGAGCTTCGGAATTCGCATCCATGAATGTGAACTCGGACTCAACTC
AACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41039547 original size:18 final size:16
Alignment explanation
Indices: 41039506--41039550 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
41039496 GGCCAAGTTA
41039506 GGTGTGTGGGCCACAC
1 GGTGTGTGGGCCACAC
*
41039522 GGTCGTGTAGGTCCACAC
1 GGT-GTGT-GGGCCACAC
41039540 GGGTGTGTGGG
1 -GGTGTGTGGG
41039551 TTTTTGGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 3 0.12
17 6 0.25
18 12 0.50
19 3 0.12
ACGTcount: A:0.11, C:0.20, G:0.47, T:0.22
Consensus pattern (16 bp):
GGTGTGTGGGCCACAC
Found at i:41042543 original size:21 final size:21
Alignment explanation
Indices: 41042504--41042543 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41042494 TATTAGCCCT
*
41042504 AATAAGATCTATAAAGTTTAA
1 AATAAGATATATAAAGTTTAA
* *
41042525 AATAAGATATGTAAGGTTT
1 AATAAGATATATAAAGTTT
41042544 TAATAATTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
AATAAGATATATAAAGTTTAA
Found at i:41046616 original size:32 final size:32
Alignment explanation
Indices: 41046580--41046645 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
41046570 AAACAAAGAT
*
41046580 AGCCACAATAGGCAAAATATCTTAAGAAAGGG
1 AGCCACAATAAGCAAAATATCTTAAGAAAGGG
*
41046612 AGCCACAATAAGCAAAATATCTTAAGAAATGG
1 AGCCACAATAAGCAAAATATCTTAAGAAAGGG
41046644 AG
1 AG
41046646 GAAGGGAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (32 bp):
AGCCACAATAAGCAAAATATCTTAAGAAAGGG
Found at i:41048042 original size:34 final size:34
Alignment explanation
Indices: 41047999--41048063 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
41047989 ATTGGTCCTT
41047999 ATGTGGACCCGGACTAAATCAGAGAAACATGCTC
1 ATGTGGACCCGGACTAAATCAGAGAAACATGCTC
41048033 ATGTGGACCCGGACTAAATCAGAGAAACATG
1 ATGTGGACCCGGACTAAATCAGAGAAACATG
41048064 TGTCTGGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.17
Consensus pattern (34 bp):
ATGTGGACCCGGACTAAATCAGAGAAACATGCTC
Found at i:41048943 original size:5 final size:5
Alignment explanation
Indices: 41048933--41048969 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
41048923 GAAAAGTAAT
*
41048933 AATAA AATAA AATAA AATAA GATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
41048970 AGTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:41050114 original size:22 final size:21
Alignment explanation
Indices: 41050082--41050146 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 21
41050072 TTCAAATGAT
41050082 GTGTTACTCAGGCTTAGTGCC
1 GTGTTACTCAGGCTTAGTGCC
* *
41050103 AGTGTTATTCAGGCTTAGAGCC
1 -GTGTTACTCAGGCTTAGTGCC
41050125 GATGTTACTCAGGCTTAGTGCC
1 G-TGTTACTCAGGCTTAGTGCC
41050147 TAACAGGCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 1 0.03
22 37 0.97
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (21 bp):
GTGTTACTCAGGCTTAGTGCC
Found at i:41050169 original size:38 final size:38
Alignment explanation
Indices: 41050112--41050194 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
41050102 CAGTGTTATT
* *
41050112 CAGGCTTAGAGCCGATGTTACTCAGGCTTAGTGCCTAA
1 CAGGCTTAGAGCCGATGTTAATCAAGCTTAGTGCCTAA
* *
41050150 CAGGCTTA-ATGCCGGTGTTAATCAAGCTTAGTGCCTAG
1 CAGGCTTAGA-GCCGATGTTAATCAAGCTTAGTGCCTAA
41050188 CAGGCTT
1 CAGGCTT
41050195 TGAGTCAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.03
38 39 0.98
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (38 bp):
CAGGCTTAGAGCCGATGTTAATCAAGCTTAGTGCCTAA
Found at i:41050184 original size:22 final size:22
Alignment explanation
Indices: 41050082--41050184 Score: 92
Period size: 22 Copynumber: 5.0 Consensus size: 22
41050072 TTCAAATGAT
* *
41050082 GTGTTACTCAGGCTTAGTGCCA
1 GTGTTAATCAGGCTTAGTGCCG
* *
41050104 GTGTTATTCAGGCTTAGAGCCG
1 GTGTTAATCAGGCTTAGTGCCG
* *
41050126 ATGTTACTCAGGCTTAGTGCC-
1 GTGTTAATCAGGCTTAGTGCCG
*
41050147 ----TAA-CAGGCTTAATGCCG
1 GTGTTAATCAGGCTTAGTGCCG
*
41050164 GTGTTAATCAAGCTTAGTGCC
1 GTGTTAATCAGGCTTAGTGCC
41050185 TAGCAGGCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
16 12 0.18
17 2 0.03
21 3 0.05
22 48 0.74
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (22 bp):
GTGTTAATCAGGCTTAGTGCCG
Found at i:41053304 original size:10 final size:10
Alignment explanation
Indices: 41053291--41053316 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41053281 TAAAATTTTT
41053291 GTATATTTGG
1 GTATATTTGG
41053301 GTATATTTGG
1 GTATATTTGG
41053311 GTATAT
1 GTATAT
41053317 CTGAAAGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (10 bp):
GTATATTTGG
Found at i:41067030 original size:125 final size:124
Alignment explanation
Indices: 41066892--41067140 Score: 462
Period size: 125 Copynumber: 2.0 Consensus size: 124
41066882 TTCATTTACA
*
41066892 GGTTCGGCTATGGTATAATGGAATTAAACGTATATGATTGCTTATTAGATTATTTAATATATTTT
1 GGTTCGGCTATGGTATAATGGAATTAAACGTATATGATTGCTTATTAGATTATTTAATATATTTG
*
41066957 TATCCGTAAGCTTGGTTACTATGAAATTGTTGTATGAGCTAGGTCAAGAATGATAATATG
66 TATCCGTAAGCTTGGTTACT-TGAAATTGCTGTATGAGCTAGGTCAAGAATGATAATATG
41067017 GGTTCGGCTATGGTATAATGGAATTAAACGTATATGATTGCTTATTAGATTATTTAATATATTTG
1 GGTTCGGCTATGGTATAATGGAATTAAACGTATATGATTGCTTATTAGATTATTTAATATATTTG
*
41067082 TATGCGTAAGCTTGGTTACTTGAAATTGCTGTATGAGCTAGGTCAAGAATGATAATATG
66 TATCCGTAAGCTTGGTTACTTGAAATTGCTGTATGAGCTAGGTCAAGAATGATAATATG
41067141 TGATTAAAAG
Statistics
Matches: 121, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
124 38 0.31
125 83 0.69
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (124 bp):
GGTTCGGCTATGGTATAATGGAATTAAACGTATATGATTGCTTATTAGATTATTTAATATATTTG
TATCCGTAAGCTTGGTTACTTGAAATTGCTGTATGAGCTAGGTCAAGAATGATAATATG
Found at i:41067504 original size:29 final size:30
Alignment explanation
Indices: 41067472--41067533 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
41067462 GAATTATGGC
*
41067472 TTATTAAATTAT-AAGAATGTGTACATGAT
1 TTATTAAACTATCAAGAATGTGTACATGAT
***
41067501 TTA-TCGGCTATCAAGAATGTGTACATGAT
1 TTATTAAACTATCAAGAATGTGTACATGAT
41067530 TTAT
1 TTAT
41067534 CGGCGATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (30 bp):
TTATTAAACTATCAAGAATGTGTACATGAT
Found at i:41069608 original size:94 final size:94
Alignment explanation
Indices: 41069505--41069677 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 94
41069495 GTTATGTGAG
* ** *
41069505 AGCCAGTGTAAGACCATGTCTGAGACATGGTATCAGCATTGAGACGAGGCCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATAAAGACGAGGACTAGTGTAAGACATG
41069570 TCTAGGACAAGCATCAGCCACATTATGAT
66 TCTAGGACAAGCATCAGCCACATTATGAT
* * * * *
41069599 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAAAGATGAGTACTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATAAAGACGAGGACTAGTGTAAGACATG
* *
41069664 TCTGGGACATGCAT
66 TCTAGGACAAGCAT
41069678 TCACCTCAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 68 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATAAAGACGAGGACTAGTGTAAGACATG
TCTAGGACAAGCATCAGCCACATTATGAT
Found at i:41069664 original size:47 final size:47
Alignment explanation
Indices: 41069555--41069871 Score: 188
Period size: 47 Copynumber: 6.7 Consensus size: 47
41069545 GAGACGAGGC
* * * **
41069555 CTAGTGTAAGACATGTCTAGGACAAGCATCAGCC-ACATTATGA-TAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTA-AAGATGAGTAG
* *
41069601 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAAAGATGAGTA-
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTAAAGATGAGTAG
* *
41069649 CTAGTGTAAGACATGTCTGGGACATGCATTC-ACCTCAATGATG-GTAG
1 CTAGTGTAAGACATGTCTGGGACATGCA-TCGGCCT-AAAGATGAGTAG
* * * ** * ** * **
41069696 CCACTGTAAAATGTGTTTGGGACATGCATC-GAATAAA-CTTCGT-G
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTAAAGATGAGTAG
* * * *
41069740 CTAGTGTAAGACATGTCTGGGACATGCATCAGCACTTATACACGAG-AG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGC-C-TAAAGATGAGTAG
* *
41069788 CTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCT--TGATGAAGATAG
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTAAAGATG-AG-TAG
* *
41069837 CCAGTGTAAGTCCATGTCTGGGACATGGCATCGGC
1 CTAGTGTAAG-ACATGTCTGGGACAT-GCATCGGC
41069872 AACTTAACCC
Statistics
Matches: 208, Mismatches: 44, Indels: 35
0.72 0.15 0.12
Matches are distributed among these distances:
44 26 0.12
45 5 0.02
46 23 0.11
47 61 0.29
48 36 0.17
49 50 0.24
50 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (47 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTAAAGATGAGTAG
Found at i:41069717 original size:94 final size:92
Alignment explanation
Indices: 41069555--41069768 Score: 227
Period size: 94 Copynumber: 2.3 Consensus size: 92
41069545 GAGACGAGGC
* * * * * *
41069555 CTAGTGTAAGACATGTCTAGGACAAGCA-TCAGCCACATTATGATAGCCAGTGTAAGACCATGTC
1 CTAGTGTAAGACATGTCTGGGACATGCATTCACCCACATGATGATAGCCACTGTAAGAACATGTC
**
41069619 TGGGACATGGCATCGGCGTAAAGATGAGTA
66 TGGGACAT-GCATC-GAATAAA-ATGAGTA
* **
41069649 CTAGTGTAAGACATGTCTGGGACATGCATTCACCTCA-ATGATGGTAGCCACTGTAA-AATGTGT
1 CTAGTGTAAGACATGTCTGGGACATGCATTCACC-CACATGATGATAGCCACTGTAAGAACATGT
* * ** *
41069712 TTGGGACATGCATCGAATAAACTTCGTG
65 CTGGGACATGCATCGAATAAAATGAGTA
41069740 CTAGTGTAAGACATGTCTGGGACATGCAT
1 CTAGTGTAAGACATGTCTGGGACATGCAT
41069769 CAGCACTTAT
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
91 32 0.31
92 5 0.05
93 5 0.05
94 38 0.37
95 20 0.20
96 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (92 bp):
CTAGTGTAAGACATGTCTGGGACATGCATTCACCCACATGATGATAGCCACTGTAAGAACATGTC
TGGGACATGCATCGAATAAAATGAGTA
Found at i:41069813 original size:49 final size:49
Alignment explanation
Indices: 41069739--41069877 Score: 169
Period size: 49 Copynumber: 2.8 Consensus size: 49
41069729 TAAACTTCGT
*
41069739 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCACTTAT-ACACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTATGA-A-GAGA
* *
41069787 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGC-CTTGATGAAGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTT-ATGAAGAGA
* *
41069836 GCCAGTGTAAGTCCATGTCTGGGACATGGCATCGGCAACTTA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACTTA
41069878 ACCCATGTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
48 12 0.15
49 52 0.66
50 11 0.14
51 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (49 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTATGAAGAGA
Found at i:41070734 original size:55 final size:55
Alignment explanation
Indices: 41070619--41070749 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 55
41070609 CTTAAACTTT
* * * *
41070619 TAAGTCAGTATTGTCCATGGGTAGGCCACACGAGCGTGTGCCATAGTCGTGTCTA
1 TAAGTCAGTGTTGTCCATGGGTAGGCCACACAAGCGTGTGCCATAGCCGTGCCTA
* * *
41070674 TAAGTCAGTGTTGTCCATGGGTAGGCTACACAAGCGTGTGTCATGGCCGTGCCCTA
1 TAAGTCAGTGTTGTCCATGGGTAGGCCACACAAGCGTGTGCCATAGCCGTG-CCTA
*
41070730 -AAGTCAATGTTG-CACATGGG
1 TAAGTCAGTGTTGTC-CATGGG
41070750 CTAAGGGCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
54 1 0.02
55 62 0.94
56 3 0.05
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (55 bp):
TAAGTCAGTGTTGTCCATGGGTAGGCCACACAAGCGTGTGCCATAGCCGTGCCTA
Found at i:41074926 original size:21 final size:20
Alignment explanation
Indices: 41074898--41074950 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
41074888 AATAGCGGTG
* *
41074898 GCAGTGAGATTGGTTATTGTA
1 GCAGTGAGATT-GATACTGTA
*
41074919 GCGGTGAGAATTGATACTGTA
1 GCAGTGAG-ATTGATACTGTA
41074940 GCAGTGAGATT
1 GCAGTGAGATT
41074951 AGAAACAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (20 bp):
GCAGTGAGATTGATACTGTA
Found at i:41077012 original size:32 final size:32
Alignment explanation
Indices: 41076967--41077114 Score: 233
Period size: 32 Copynumber: 4.6 Consensus size: 32
41076957 TATCTTAAGG
*
41076967 TTTACATATAAAAAGGTAGATCATACATTAGT
1 TTTACATATAAAAAAGTAGATCATACATTAGT
* *
41076999 TTTGCATATAAAAAAGTAGATCATACATTAGG
1 TTTACATATAAAAAAGTAGATCATACATTAGT
*
41077031 TTCACATATAAAAAAGTAGATCATACATTAGT
1 TTTACATATAAAAAAGTAGATCATACATTAGT
* *
41077063 TTTGCATATGAAAAAGTAGATCATACATTAGT
1 TTTACATATAAAAAAGTAGATCATACATTAGT
41077095 TTTACATATAAAAAAAGTAG
1 TTTACATAT-AAAAAAGTAG
41077115 CATAGTTATA
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 95 0.91
33 9 0.09
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.32
Consensus pattern (32 bp):
TTTACATATAAAAAAGTAGATCATACATTAGT
Found at i:41077032 original size:64 final size:64
Alignment explanation
Indices: 41076964--41077114 Score: 257
Period size: 64 Copynumber: 2.3 Consensus size: 64
41076954 AAATATCTTA
*
41076964 AGGTTTACATATAAAAAGGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATCATACATT
1 AGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATCATACATT
* *
41077028 AGGTTCACATATAAAAAAGTAGATCATACATTAGTTTTGCATATGAAAAAGTAGATCATACATT
1 AGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATCATACATT
*
41077092 AGTTTTACATATAAAAAAAGTAG
1 AGGTTTACATAT-AAAAAAGTAG
41077115 CATAGTTATA
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 71 0.88
65 10 0.12
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (64 bp):
AGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATCATACATT
Found at i:41078223 original size:13 final size:13
Alignment explanation
Indices: 41078205--41078230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41078195 CAACGTCAGC
41078205 TCATCATCCCAAA
1 TCATCATCCCAAA
41078218 TCATCATCCCAAA
1 TCATCATCCCAAA
41078231 CAGCTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
TCATCATCCCAAA
Found at i:41085869 original size:55 final size:55
Alignment explanation
Indices: 41085762--41085870 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 55
41085752 TTTAAGTTAG
* * *
41085762 TATTGTCCACGGGTAGGCCACACGGGCGTGTGCCATAGCCGTGTCTATAAGTCAC
1 TATTGTCCACGAGTAGGCCACACGGGCGTATGCCATAGCCGTGCCTATAAGTCAC
*
41085817 TATTGTCCACGAGTAGGCCACACGGGCGTATGTCAT-GACCGTGCCCTA-AAGTCA
1 TATTGTCCACGAGTAGGCCACACGGGCGTATGCCATAG-CCGTG-CCTATAAGTCA
41085871 TGTTACACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 1 0.02
55 44 0.92
56 3 0.06
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.23
Consensus pattern (55 bp):
TATTGTCCACGAGTAGGCCACACGGGCGTATGCCATAGCCGTGCCTATAAGTCAC
Found at i:41089701 original size:12 final size:11
Alignment explanation
Indices: 41089664--41089701 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
41089654 CTGCAATTTA
41089664 AATTTTATTCT
1 AATTTTATTCT
*
41089675 AAATTTATTCT
1 AATTTTATTCT
41089686 AATTTTATTACT
1 AATTTTATT-CT
41089698 AATT
1 AATT
41089702 CTTCTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTTTATTCT
Found at i:41092422 original size:47 final size:45
Alignment explanation
Indices: 41092369--41092489 Score: 127
Period size: 47 Copynumber: 2.6 Consensus size: 45
41092359 TGGCCATGAT
41092369 ATGTGATAAGGCCGAATGGCCAATGTGATGA-ATGTGGAAGTGCATAC
1 ATGTGATAAGGCCGAATGGCCAATGTGAT-ATATGTGGAAGTG-A-AC
* ** * * *
41092416 ATGTGATAAGGCCGGATGGTTAATGTGATATATGTGTACGTGAAT
1 ATGTGATAAGGCCGAATGGCCAATGTGATATATGTGGAAGTGAAC
* *
41092461 ATGTGAAAAGGCCGAATGACCAATTGTGA
1 ATGTGATAAGGCCGAATGGCCAA-TGTGA
41092490 AAAGTGTGCA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
45 19 0.31
46 7 0.11
47 35 0.57
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (45 bp):
ATGTGATAAGGCCGAATGGCCAATGTGATATATGTGGAAGTGAAC
Found at i:41092623 original size:39 final size:40
Alignment explanation
Indices: 41092564--41092648 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
41092554 ATATGAATTG
* * * * *
41092564 TGCTGAGATTGTATCTGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
*
41092603 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
41092643 TGCTGG
1 TGCTGG
41092649 TGAATTAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.31
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:41109622 original size:13 final size:13
Alignment explanation
Indices: 41109604--41109638 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
41109594 CCTCACACAC
41109604 GGGCGTGTGACTT
1 GGGCGTGTGACTT
41109617 GGGCGTGTGACTT
1 GGGCGTGTGACTT
*
41109630 GGCCGTGTG
1 GGGCGTGTG
41109639 GCATAAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.17, G:0.49, T:0.29
Consensus pattern (13 bp):
GGGCGTGTGACTT
Found at i:41111163 original size:23 final size:23
Alignment explanation
Indices: 41111117--41111163 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
41111107 AATCAAACGA
* * *
41111117 CATAATTCATTGTAGGGTTTATT
1 CATAATTCATCGTAGGATTCATT
41111140 CATAATTCATCGTAGGATTCATT
1 CATAATTCATCGTAGGATTCATT
41111163 C
1 C
41111164 CCCCTAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (23 bp):
CATAATTCATCGTAGGATTCATT
Found at i:41118711 original size:28 final size:28
Alignment explanation
Indices: 41118679--41118762 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
41118669 AACACACCAG
* *
41118679 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
41118707 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
* *
41118735 TATAATCCATCCAAAATACACTAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
41118763 GCACAGAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 33 0.67
29 16 0.33
ACGTcount: A:0.46, C:0.29, G:0.04, T:0.21
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:41118734 original size:23 final size:23
Alignment explanation
Indices: 41118665--41118735 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
41118655 AAATGTCCAA
*
41118665 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
41118688 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
41118716 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
41118736 ATAATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:41118826 original size:13 final size:14
Alignment explanation
Indices: 41118803--41118832 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41118793 GGATATAAAC
41118803 ATCAGCATCTCCAA
1 ATCAGCATCTCCAA
41118817 ATCA-CATCTCCAA
1 ATCAGCATCTCCAA
41118830 ATC
1 ATC
41118833 CCTTCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAGCATCTCCAA
Found at i:41118839 original size:13 final size:13
Alignment explanation
Indices: 41118808--41118846 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
41118798 TAAACATCAG
*
41118808 CATCTCCAAATCA
1 CATCTCCAAATCC
41118821 CATCTCCAAATCC
1 CATCTCCAAATCC
* *
41118834 CTTCTCAAAATCC
1 CATCTCCAAATCC
41118847 TATGGCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (13 bp):
CATCTCCAAATCC
Found at i:41118941 original size:17 final size:17
Alignment explanation
Indices: 41118919--41118957 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
41118909 TTATTTTATT
*
41118919 TCAATTTCATTTCCATA
1 TCAATTTCAATTCCATA
*
41118936 TCAATTTCAATTCCATT
1 TCAATTTCAATTCCATA
41118953 TCAAT
1 TCAAT
41118958 ATACAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (17 bp):
TCAATTTCAATTCCATA
Found at i:41118943 original size:23 final size:24
Alignment explanation
Indices: 41118916--41118964 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
41118906 TTTTTATTTT
* *
41118916 ATTTCAATTTCATTTCCATAT-CA
1 ATTTCAATTCCATTTCAATATACA
41118939 ATTTCAATTCCATTTCAATATACA
1 ATTTCAATTCCATTTCAATATACA
41118963 AT
1 AT
41118965 CAATTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCAATTCCATTTCAATATACA
Found at i:41118984 original size:16 final size:17
Alignment explanation
Indices: 41118945--41118990 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
41118935 ATCAATTTCA
*
41118945 ATTCCATTTCAATATAC
1 ATTCCAATTCAATATAC
*
41118962 AAT-CAATTCAATATAC
1 ATTCCAATTCAATATAC
41118978 -TTCCAATCTCAAT
1 ATTCCAAT-TCAAT
41118991 CCACATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 16 0.67
17 7 0.29
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTCCAATTCAATATAC
Found at i:41120654 original size:40 final size:40
Alignment explanation
Indices: 41120564--41120824 Score: 271
Period size: 40 Copynumber: 6.5 Consensus size: 40
41120554 CTCAAGTAAT
* * * *
41120564 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
41120602 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
41120642 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41120682 CTTCGGGTCTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * **
41120722 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * *
41120762 CTTC-GGATCTTAGTCCGGTTATAGTCACCTATCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
41120803 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
41120825 CATTCGAATA
Statistics
Matches: 188, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
38 11 0.06
39 18 0.10
40 130 0.69
41 26 0.14
42 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41120695 original size:80 final size:80
Alignment explanation
Indices: 41120564--41120824 Score: 303
Period size: 80 Copynumber: 3.3 Consensus size: 80
41120554 CTCAAGTAAT
* * * * * *
41120564 CTTCGGGATTTAG-CCGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
41120627 CACTAGCACAGATGC
66 CACTAGCACAAATGC
* *
41120642 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
*
41120706 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * ** * * *
41120722 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCATGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
* * *
41120787 CACCTATCATAAAAGC
66 CA-CTAGCACAAATGC
41120803 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
41120825 CATTCGAATA
Statistics
Matches: 155, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
78 12 0.08
79 16 0.10
80 96 0.62
81 31 0.20
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:41127796 original size:25 final size:25
Alignment explanation
Indices: 41127767--41127814 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41127757 TTATAACATG
41127767 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCGTTTTGCCCCTAGGTA
41127792 AAAATGACCGTTTTGCCCCTAGG
1 AAAATGACCGTTTTGCCCCTAGG
41127815 GTTTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAATGACCGTTTTGCCCCTAGGTA
Found at i:41127880 original size:20 final size:20
Alignment explanation
Indices: 41127851--41127897 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
41127841 ATTTTGATAA
*
41127851 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
41127871 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
41127891 ACATGAT
1 ACATGAT
41127898 GTAATCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:41127977 original size:23 final size:23
Alignment explanation
Indices: 41127947--41128041 Score: 156
Period size: 23 Copynumber: 4.1 Consensus size: 23
41127937 AGGAAGTGAA
41127947 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41127970 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41127993 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
41128015 AAAAGGGCTTTTGCCCTAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
41128039 AAA
1 AAA
41128042 AGAGGCTAGG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
22 10 0.15
23 49 0.72
24 9 0.13
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:41132221 original size:16 final size:16
Alignment explanation
Indices: 41132202--41132234 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41132192 ATTATAGTAG
41132202 AATGACTTTATAATTA
1 AATGACTTTATAATTA
*
41132218 AATGAGTTTATAATTA
1 AATGACTTTATAATTA
41132234 A
1 A
41132235 TAGGCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (16 bp):
AATGACTTTATAATTA
Found at i:41132624 original size:17 final size:17
Alignment explanation
Indices: 41132598--41132637 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41132588 ACGAAATTAA
*
41132598 AATTTGATTGAGAAAA-T
1 AATTTAATTGA-AAAATT
41132615 AATTTAATTGAAAAATT
1 AATTTAATTGAAAAATT
41132632 AATTTA
1 AATTTA
41132638 TCTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (17 bp):
AATTTAATTGAAAAATT
Found at i:41132721 original size:13 final size:13
Alignment explanation
Indices: 41132703--41132728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41132693 ATTGAGTTAG
41132703 ATTAAATTATAAA
1 ATTAAATTATAAA
41132716 ATTAAATTATAAA
1 ATTAAATTATAAA
41132729 GTGTAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAATTATAAA
Found at i:41151043 original size:45 final size:45
Alignment explanation
Indices: 41150984--41151193 Score: 144
Period size: 45 Copynumber: 4.7 Consensus size: 45
41150974 AATCCTACAG
41150984 ATCCTG-CTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAA
1 ATCCTGACTT-CCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAA
* * * ** * *
41151029 ATCTTGACTTCCTGAAGTTGCAGTGAAGTAGATTTAAGTC-ACTA
1 ATCCTGACTTCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAA
* * * * * * **** *
41151073 A-CCT-AGCTCCCTAAAGTTGTAGTGGAGTAGGTTG-AGATTTTAG
1 ATCCTGA-CTTCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAA
* * * *
41151116 ATCCT-ACTTCCCTGAAGTTACAGTGGAGCAGATCAAAAACGACGA
1 ATCCTGACTT-CCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAA
*
41151161 ATCCTGACTTCCTGAAGTTGCAGTGAAGCAGAT
1 ATCCTGACTTCCTGAAGTTGCAGTGGAGCAGAT
41151194 TTAAGTCACT
Statistics
Matches: 121, Mismatches: 37, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
42 3 0.02
43 27 0.22
44 26 0.21
45 58 0.48
46 7 0.06
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (45 bp):
ATCCTGACTTCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAA
Found at i:41151195 original size:132 final size:130
Alignment explanation
Indices: 41150990--41151806 Score: 1080
Period size: 132 Copynumber: 6.2 Consensus size: 130
41150980 ACAGATCCTG
* *
41150990 CTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAAATCTTGACTTCCTGAAGTTGCAGTGA
1 CTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGACTTCCTGAAGTTGCAGTGA
* * *
41151055 AGTAGATTTAAGTCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAGATTTTAGATCC
66 AGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGAT-C
41151120 T
130 T
* * *
41151121 ACTTCCCTGAAGTTACAGTGGAGCAGATCAAAAACGACGAATCCTGACTTCCTGAAGTTGCAGTG
1 -CTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGACTTCCTGAAGTTGCAGTG
* * * *
41151186 AAGCAGATTTAAGTCACTAACCTTGTTCCCTAAAGTTGTAGTGGAGTAGGTTAAAATTTTAGATC
65 AAGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGATC
41151251 T
130 T
* * * * * *
41151252 CGTTTCCCTGAAGTTGCAGTGGAGTAAATCAAAGACAACGAATCTTGACTTCCTGAAGTTGCAGC
1 C--TTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGACTTCCTGAAGTTGCAGT
* * *
41151317 AAAGCAGATTTAAGTCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTCGAT
64 GAAGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGAT
41151382 CT
129 CT
* *
41151384 CGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAAT-CTGAGCTTCTTGAAGTTGCAG
1 C--TTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGA-CTTCCTGAAGTTGCAG
* *
41151448 TGAAGCAGATTTAAGCCACTAACCTAGCTCCCTAGAGTTGTAGTAGAGTAGGTTGAAATTTTAGA
63 TGAAGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGA
41151513 TCT
128 TCT
*
41151516 CGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAAT-CTGAGCTTCCTGAAGTTGCAG
1 C--TTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGA-CTTCCTGAAGTTGCAG
* * *
41151580 TGAAGTAGATTTAAGCCACCAACCCAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGA
63 TGAAGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGA
*
41151645 TTTT
128 -TCT
* * * ** * * * *
41151649 GTTTCCCTGAAGTTGCAGTGAAACAGATCGAAGACGGTGAATCTTGACTTCTTGAAATTGCAATG
1 -CTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGACTTCCTGAAGTTGCAGTG
* * * * *
41151714 AAGTAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGCGGAGTAGGTTGAAGATTGTAGAT
65 AAGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-ATTTTAGAT
41151779 CTT
129 C-T
*
41151782 GTCTCCCTGAAGTTGCAGTGGAGCA
1 CT-TCCCTGAAGTTGCAGTGGAGCA
41151807 TATTGAAGCT
Statistics
Matches: 618, Mismatches: 58, Indels: 17
0.89 0.08 0.02
Matches are distributed among these distances:
130 1 0.00
131 5 0.01
132 579 0.94
133 33 0.05
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (130 bp):
CTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACGAATCCTGACTTCCTGAAGTTGCAGTGA
AGCAGATTTAAGCCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTTTAGATCT
Found at i:41151573 original size:45 final size:44
Alignment explanation
Indices: 41151390--41151581 Score: 131
Period size: 45 Copynumber: 4.3 Consensus size: 44
41151380 ATCTCGTTTC
41151390 CCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTGAGCTT
1 CCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCT-AGCTT
* * ** ** * * *
41151435 CTTGAAGTTGCAGTGAAGCAGATTTAAG-CCACTAACCTAGCTC
1 CCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGCTT
* * * * * **** * *
41151478 CCT-AGAGTTGTAGTAGAGTAGGTTGAA-A-TTTTAGATCTCGTTT
1 CCTGA-AGTTGCAGTGGAGCAGATCGAAGACGGCGA-ATCTAGCTT
41151521 CCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTGAGCTT
1 -CCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCT-AGCTT
41151567 CCTGAAGTTGCAGTG
1 CCTGAAGTTGCAGTG
41151582 AAGTAGATTT
Statistics
Matches: 105, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
42 3 0.03
43 27 0.26
44 26 0.25
45 45 0.43
46 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (44 bp):
CCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGCTT
Found at i:41154623 original size:131 final size:131
Alignment explanation
Indices: 41154368--41154625 Score: 338
Period size: 131 Copynumber: 2.0 Consensus size: 131
41154358 AAATTCTTTA
* * * * *
41154368 AAAACGAAGGCAAGATTCGATGTTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCGA
1 AAAACGAAGACAAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * **
41154433 TTTCGCGTTTGCTCAAAATAATCGAATATCACTTCGAAATTTCACTCATGCCTTTTAAAATTCCT
66 TTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATACCTCCTAAAATTCCT
41154498 C
131 C
* *
41154499 AAAACGAAGACGAGGTTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACAAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* ** * * *
41154564 TTTTGCGTTTGCTCAAAATAATCGGGCT-TCCCTTCAAAATTCCATTCATATCTCCTAAAATT
66 TTTCGCGTTTGCTCAAAATAATC-GAATATCACTTCAAAATTCCACTCATACCTCCTAAAATT
41154626 TTTTAAACGA
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
131 106 0.98
132 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (131 bp):
AAAACGAAGACAAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATACCTCCTAAAATTCCT
C
Found at i:41158948 original size:45 final size:45
Alignment explanation
Indices: 41158848--41158974 Score: 138
Period size: 45 Copynumber: 2.9 Consensus size: 45
41158838 TTTTCTCAAA
* *
41158848 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
41158890 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * * *
41158934 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCGGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
41158975 ATCAAGTCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 39 0.53
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:41159352 original size:43 final size:43
Alignment explanation
Indices: 41159291--41159479 Score: 249
Period size: 43 Copynumber: 4.4 Consensus size: 43
41159281 ACATATCATT
* *
41159291 TCACCGGCATTACGCCTGCTAGGCACAAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACA
* *
41159334 TCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACA
* * * *
41159377 TCACTGACATTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACA
*
41159420 TCACCGGCACTAAGCCTGCTAGGCACGAAA-GCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCAC-AAAGGCCCGAATACACA
* *
41159462 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
41159480 AGGATTTATC
Statistics
Matches: 130, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 15 0.12
42 2 0.02
43 111 0.85
44 2 0.02
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACA
Found at i:41159443 original size:86 final size:86
Alignment explanation
Indices: 41159298--41159458 Score: 286
Period size: 86 Copynumber: 1.9 Consensus size: 86
41159288 ATTTCACCGG
*
41159298 CATTACGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAA
1 CATTAAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAA
*
41159363 GGCCCGAATACACATCACTGA
66 AGCCCGAATACACATCACTGA
* *
41159384 CATTAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAAGCCTGCTAGGCACGAA
1 CATTAAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAA
41159449 AGCCCGAATA
66 AGCCCGAATA
41159459 TAATACCAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.32, C:0.33, G:0.22, T:0.13
Consensus pattern (86 bp):
CATTAAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAA
AGCCCGAATACACATCACTGA
Found at i:41163889 original size:53 final size:53
Alignment explanation
Indices: 41163821--41164085 Score: 296
Period size: 53 Copynumber: 5.0 Consensus size: 53
41163811 AGTATTGTAG
* *
41163821 GACCATATCTTGTAAGACCGTAACTGGTGGGTTATGGTATCATATGGGAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGGAAGAA
* * * * * *
41163874 GACTATATTGTGTAAGACTGTAACTAGTGGGTTATGACATCATATGGGAAAAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGGAAGAA
* * * ** *
41163927 TACCATAGCGTGTAAAACTATAACTGGTGGGTTATGACATCATATGGGAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGGAAGAA
* * * ** *
41163980 GACCATATCATATAAGACCGTAACTGATGGGTTATGGCATCATATAAGTAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGGAAGAA
* * * ** *
41164033 GACCATATTGTGTAAAATCGTAACTGGCAGGTTATGGCATCATATAGGAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGGAAGAA
41164086 CTAAAGGAAA
Statistics
Matches: 174, Mismatches: 38, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 174 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGGAAGAA
Found at i:41164277 original size:61 final size:60
Alignment explanation
Indices: 41164201--41164366 Score: 170
Period size: 61 Copynumber: 2.7 Consensus size: 60
41164191 AGAAAAAAAG
* * * *
41164201 ATGCCTTTGTGGTAAAACTCTAGACAGGAAAGCCTTTGTGGCAAGTATTGGATTTAAAGGA
1 ATGCCTTTGTGGTAAAACT-TAGAAAGGAAAGCCTTTGTGGCAAGTACTAGATGTAAAGGA
* * * * *
41164262 CTGCCTTTGTGGTAAAACATTGGATAGGAAAGCATTTGTGGCGAGTACTAGATGTAAAGGA
1 ATGCCTTTGTGGTAAAAC-TTAGAAAGGAAAGCCTTTGTGGCAAGTACTAGATGTAAAGGA
** *** *
41164323 AAACCTTTGTGGCGGAACTTTAGAAAGGTAAGCCTTTGTGGCAA
1 ATGCCTTTGTGGTAAAAC-TTAGAAAGGAAAGCCTTTGTGGCAA
41164367 CCTCTGTTTA
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
61 83 0.99
62 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (60 bp):
ATGCCTTTGTGGTAAAACTTAGAAAGGAAAGCCTTTGTGGCAAGTACTAGATGTAAAGGA
Found at i:41167676 original size:16 final size:16
Alignment explanation
Indices: 41167656--41167710 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
41167646 GTTTGGTTCA
41167656 CTGTAATTGAATA-AG
1 CTGTAATTGAATAGAG
41167671 ACTGTAATTGAATAGAG
1 -CTGTAATTGAATAGAG
*
41167688 CTGTAATGGAATAGAG
1 CTGTAATTGAATAGAG
41167704 CTGTAAT
1 CTGTAAT
41167711 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
16 35 0.95
17 2 0.05
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:41167785 original size:44 final size:46
Alignment explanation
Indices: 41167692--41167785 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
41167682 ATAGAGCTGT
*
41167692 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGCTTGAATGG
1 AATGGAATAGAACTGTAATCAGTAATTCAACTGTTTGCTTGAATGG
*** *
41167738 AATGGAATAGAACTGTAAT-AGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATCAGTAATTCAACTGTTTGCTTGAATGG
41167782 AATG
1 AATG
41167786 ATGTTGGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 22 0.51
45 3 0.07
46 18 0.42
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATCAGTAATTCAACTGTTTGCTTGAATGG
Found at i:41167917 original size:14 final size:14
Alignment explanation
Indices: 41167881--41167921 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
41167871 GTTATTAAAT
*
41167881 TTTAAT-AAAATTA
1 TTTAATAAAAATAA
*
41167894 -TTATTAAAAATAA
1 TTTAATAAAAATAA
41167907 TTTAATAAAAATAA
1 TTTAATAAAAATAA
41167921 T
1 T
41167922 AAATAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATAAAAATAA
Found at i:41167951 original size:58 final size:57
Alignment explanation
Indices: 41167877--41168035 Score: 189
Period size: 58 Copynumber: 2.8 Consensus size: 57
41167867 TATTGTTATT
* * *
41167877 AAATTTTAATAAAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATAATTATTATTAAAAATAACTTAAT-AAAATAATAAATAATTTAACA
* * * * *
41167935 ATATTTTAACATAATTATTATTAAATATAACTTAATAAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAAAATAACTTAATAAAATAATAAATAATTTAACA
* *
41167992 AAATTCTTAATATAATTATTATTATAAA-AA-TTAA-AAAATCATAA
1 AAATT-TTAATATAATTATTATTAAAAATAACTTAATAAAATAATAA
41168036 CTATTATTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 8 0.09
56 4 0.05
57 24 0.28
58 50 0.58
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAAAATAACTTAATAAAATAATAAATAATTTAACA
Found at i:41171824 original size:26 final size:26
Alignment explanation
Indices: 41171781--41171831 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
41171771 GTCTCTAAAC
* * *
41171781 TTATCCTAATTTTGCCTCAAAGGCAA
1 TTATCCAAATCTTACCTCAAAGGCAA
*
41171807 TTATCCAAATCTTACCTCAAGGGCA
1 TTATCCAAATCTTACCTCAAAGGCA
41171832 TCATAGAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (26 bp):
TTATCCAAATCTTACCTCAAAGGCAA
Found at i:41171897 original size:23 final size:23
Alignment explanation
Indices: 41171836--41171928 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
41171826 AGGGCATCAT
*
41171836 AGAATACGCCACACAA-G-TATCAC
1 AGAATACGCCACA-AAGGCT-TTAC
* * * *
41171859 AGAATAGGCTAGAAAGGCTTTAT
1 AGAATACGCCACAAAGGCTTTAC
*
41171882 AGAATATGCCACAAAGTG-TTTAC
1 AGAATACGCCACAAAG-GCTTTAC
*
41171905 AGAATACGCCACAAAAGCTTTAC
1 AGAATACGCCACAAAGGCTTTAC
41171928 A
1 A
41171929 AAATGTTATG
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
22 3 0.05
23 50 0.91
24 2 0.04
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (23 bp):
AGAATACGCCACAAAGGCTTTAC
Found at i:41171925 original size:46 final size:46
Alignment explanation
Indices: 41171834--41171926 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
41171824 CAAGGGCATC
* * * *
41171834 ATAGAATACGCCACACAAGTATCACAGAATAGGCTAGAAAGGCTTT
1 ATAGAATACGCCACACAAGTATCACAGAATACGCCACAAAAGCTTT
* * *
41171880 ATAGAATATGCCACA-AAGTGTTTACAGAATACGCCACAAAAGCTTT
1 ATAGAATACGCCACACAAGT-ATCACAGAATACGCCACAAAAGCTTT
41171926 A
1 A
41171927 CAAAATGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 4 0.10
46 35 0.90
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (46 bp):
ATAGAATACGCCACACAAGTATCACAGAATACGCCACAAAAGCTTT
Found at i:41175293 original size:35 final size:35
Alignment explanation
Indices: 41175248--41175320 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
41175238 TGGTCGAACT
41175248 AAAAACCAATGGTTTGATCACAATTCTGATTCTAA
1 AAAAACCAATGGTTTGATCACAATTCTGATTCTAA
*
41175283 AAAAATCAATGGTTTGATCACAATTCTGATTCTAA
1 AAAAACCAATGGTTTGATCACAATTCTGATTCTAA
41175318 AAA
1 AAA
41175321 CATTATTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (35 bp):
AAAAACCAATGGTTTGATCACAATTCTGATTCTAA
Found at i:41178262 original size:18 final size:19
Alignment explanation
Indices: 41178231--41178268 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
41178221 TAATATTATA
41178231 AAATAAAATAATTAT-TTT
1 AAATAAAATAATTATGTTT
* *
41178249 AAATATAATTATTATGTTT
1 AAATAAAATAATTATGTTT
41178268 A
1 A
41178269 TATGTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATAAAATAATTATGTTT
Found at i:41178399 original size:22 final size:22
Alignment explanation
Indices: 41178391--41178456 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
41178381 TATCCAGAGT
41178391 TGGATATCGCAATATCATTGTC
1 TGGATATCGCAATATCATTGTC
41178413 TGGATATCGCAATATCATTGTC
1 TGGATATCGCAATATCATTGTC
41178435 TGGATATCGCAATATCATTGTC
1 TGGATATCGCAATATCATTGTC
41178457 ATCAAGGGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGATATCGCAATATCATTGTC
Found at i:41178421 original size:44 final size:44
Alignment explanation
Indices: 41178371--41178456 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
41178361 TACTGACAAT
*
41178371 GATATCGCGATATCCAGAGT-TGGATATCGCAATATCATTGTCTG
1 GATATCGCAATAT-CAGAGTCTGGATATCGCAATATCATTGTCTG
**
41178415 GATATCGCAATATCATTGTCTGGATATCGCAATATCATTGTC
1 GATATCGCAATATCAGAGTCTGGATATCGCAATATCATTGTC
41178457 ATCAAGGGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 4 0.11
44 34 0.89
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (44 bp):
GATATCGCAATATCAGAGTCTGGATATCGCAATATCATTGTCTG
Found at i:41184834 original size:14 final size:14
Alignment explanation
Indices: 41184815--41184849 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
41184805 AATGACATTG
*
41184815 CACACGGTCGTGGA
1 CACACGGCCGTGGA
41184829 CACACGGCCGTGGA
1 CACACGGCCGTGGA
41184843 CACACGG
1 CACACGG
41184850 GTGCATCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.34, G:0.34, T:0.09
Consensus pattern (14 bp):
CACACGGCCGTGGA
Found at i:41187148 original size:40 final size:40
Alignment explanation
Indices: 41187064--41187248 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
41187054 TCGAATGATG
* *
41187064 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
41187103 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
41187144 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
41187183 TCTGGGTTAAGTCCCGAAGGTATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41187222 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41187249 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
39 34 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41187270 original size:79 final size:78
Alignment explanation
Indices: 41187065--41187283 Score: 223
Period size: 79 Copynumber: 2.8 Consensus size: 78
41187055 CGAATGATGT
* * *
41187065 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGTATT
*
41187128 TGTGCGAGTTACTAATT
62 TGTGCGAGTTACTAATA
* * *
41187145 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCA-CTAAATCTGGGTTAAGTCCCGAAGGTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-AGCTATATC-CGGTTAAGT-CCGAAGGTATTT
41187208 GTGCGAGTTACT-ATAA
63 GTGCGAGTTACTAAT-A
* ** *
41187224 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGGTA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGGTA
41187284 CGTGATTCGG
Statistics
Matches: 116, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
78 3 0.03
79 68 0.59
80 45 0.39
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGTATTTGTG
CGAGTTACTAATA
Done.