Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 21 of 208
Found at i:6096313 original size:21 final size:20
Alignment explanation
Indices: 6096267--6096325 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
6096257 AATTTTTTTT
6096267 AAAAAAAATTACAAAAAGAA
1 AAAAAAAATTACAAAAAGAA
* **
6096287 ATAAAAAAATTTCAATAATTAA
1 A-AAAAAAATTACAA-AAAGAA
* *
6096309 AAAAATAATAACAAAAA
1 AAAAAAAATTACAAAAA
6096326 CTAAATTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.10
21 22 0.73
22 5 0.17
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAAATTACAAAAAGAA
Found at i:6097770 original size:27 final size:25
Alignment explanation
Indices: 6097733--6097790 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
6097723 TTTTTAGTGC
6097733 ATTTCTATTTTAATTATCTAGATTTAAT
1 ATTT-TATTTTAATTA-CTA-ATTTAAT
*
6097761 TTTTTATTTTAATTACTAATTTAAT
1 ATTTTATTTTAATTACTAATTTAAT
6097786 ATTTT
1 ATTTT
6097791 GGTCATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.39
26 3 0.11
27 11 0.39
28 3 0.11
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTTTATTTTAATTACTAATTTAAT
Found at i:6103308 original size:51 final size:51
Alignment explanation
Indices: 6103211--6103308 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
6103201 ACGATATATG
** * ** **
6103211 GCGTAAGACCATAGATGAAAGATGTTATGGTAGTTTGATATGAGGTACGTA
1 GCGTAAGACCATAGATGAAAGATGCCATGGCAGCATGATACAAGGTACGTA
*
6103262 GCGTAAGACCATGGATGAAAGATGCCATGGCAGCATGATACAAGGTA
1 GCGTAAGACCATAGATGAAAGATGCCATGGCAGCATGATACAAGGTA
6103309 AATGTATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (51 bp):
GCGTAAGACCATAGATGAAAGATGCCATGGCAGCATGATACAAGGTACGTA
Found at i:6103519 original size:33 final size:33
Alignment explanation
Indices: 6103482--6103546 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
6103472 GGGATAGTAA
* *
6103482 ACACATAACATAGATAGTCTGCCAGGACAATAT
1 ACACATAACATAGATAATCTACCAGGACAATAT
*
6103515 ACACATAACATATATAATCTACCAGGACAATA
1 ACACATAACATAGATAATCTACCAGGACAATA
6103547 AACATGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (33 bp):
ACACATAACATAGATAATCTACCAGGACAATAT
Found at i:6105796 original size:13 final size:13
Alignment explanation
Indices: 6105780--6105926 Score: 64
Period size: 13 Copynumber: 10.8 Consensus size: 13
6105770 AAATATTTTG
6105780 TATAAACATTTCA
1 TATAAACATTTCA
* *
6105793 TATAATCGTTTCA
1 TATAAACATTTCA
*
6105806 TAT-ATCTATTTCCATA
1 TATAAAC-ATTT-C--A
*
6105822 TATAAACGTTTCA
1 TATAAACATTTCA
* * *
6105835 TATTATCGTTTCA
1 TATAAACATTTCA
*
6105848 TAT-ATCTATTTCCATA
1 TATAAAC-ATTT-C--A
*
6105864 TATAAACAATTCA
1 TATAAACATTTCA
*
6105877 TATAACCATTTCA
1 TATAAACATTTCA
*
6105890 TCTAAACATTTCA
1 TATAAACATTTCA
* * *
6105903 TTTTACCATTTCA
1 TATAAACATTTCA
* *
6105916 TTTACACATTT
1 TATAAACATTT
6105927 AACACATAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
12 6 0.06
13 76 0.73
14 2 0.02
15 2 0.02
16 14 0.13
17 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (13 bp):
TATAAACATTTCA
Found at i:6105846 original size:29 final size:28
Alignment explanation
Indices: 6105792--6105852 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
6105782 TAAACATTTC
*
6105792 ATATAATCGTTTCATATATCTATTTCCAT
1 ATATAAACGTTTCATATATCTATTT-CAT
*
6105821 ATATAAACGTTTCATATTATC-GTTTCAT
1 ATATAAACGTTTCATA-TATCTATTTCAT
6105849 ATAT
1 ATAT
6105853 CTATTTCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.24
29 18 0.62
30 4 0.14
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.48
Consensus pattern (28 bp):
ATATAAACGTTTCATATATCTATTTCAT
Found at i:6105901 original size:42 final size:42
Alignment explanation
Indices: 6105780--6105890 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 42
6105770 AAATATTTTG
6105780 TATAAACATTTCATATAATCGTTTCATATATCTATTTCCATA
1 TATAAACATTTCATATAATCGTTTCATATATCTATTTCCATA
* *
6105822 TATAAACGTTTCATATTATCGTTTCATATATCTATTTCCATA
1 TATAAACATTTCATATAATCGTTTCATATATCTATTTCCATA
* * *
6105864 TATAAACAATTCATATAACCATTTCAT
1 TATAAACATTTCATATAATCGTTTCAT
6105891 CTAAACATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (42 bp):
TATAAACATTTCATATAATCGTTTCATATATCTATTTCCATA
Found at i:6105910 original size:26 final size:26
Alignment explanation
Indices: 6105866--6105926 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
6105856 TTTCCATATA
*
6105866 TAAACAATTCATATAACCATTTCATC
1 TAAACATTTCATATAACCATTTCATC
* * *
6105892 TAAACATTTCATTTTACCATTTCATT
1 TAAACATTTCATATAACCATTTCATC
*
6105918 TACACATTT
1 TAAACATTT
6105927 AACACATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAACATTTCATATAACCATTTCATC
Found at i:6116019 original size:28 final size:28
Alignment explanation
Indices: 6115986--6116041 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6115976 ACAAAATTGA
* *
6115986 ATAGTT-GAGTGATTATTTTATAATTTTC
1 ATAGTTAG-GTGACTATTTTATAACTTTC
*
6116014 ATAGTTAGGTGACTATTTTGTAACTTTC
1 ATAGTTAGGTGACTATTTTATAACTTTC
6116042 CATAATTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (28 bp):
ATAGTTAGGTGACTATTTTATAACTTTC
Found at i:6125331 original size:31 final size:31
Alignment explanation
Indices: 6125296--6125362 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
6125286 TGTACTCATA
6125296 TCTGCTTGATTATTTGTGTTTAACATAATTC
1 TCTGCTTGATTATTTGTGTTTAACATAATTC
6125327 TCTGCTTGATTATTTGTGTTTAACATAATTC
1 TCTGCTTGATTATTTGTGTTTAACATAATTC
6125358 TCTGC
1 TCTGC
6125363 CATCTACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (31 bp):
TCTGCTTGATTATTTGTGTTTAACATAATTC
Found at i:6133179 original size:48 final size:48
Alignment explanation
Indices: 6133108--6133203 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
6133098 ATAGAGCCAT
6133108 GGTGAAAATACTCAAACAGTTCCCTTCTAAGACTAGGATTGTTGCCTA
1 GGTGAAAATACTCAAACAGTTCCCTTCTAAGACTAGGATTGTTGCCTA
6133156 GGTGAAAATACTCAAACAGTTCCCTTCTAAGACTAGGATTGTTGCCTA
1 GGTGAAAATACTCAAACAGTTCCCTTCTAAGACTAGGATTGTTGCCTA
6133204 CCACTGCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (48 bp):
GGTGAAAATACTCAAACAGTTCCCTTCTAAGACTAGGATTGTTGCCTA
Found at i:6136509 original size:17 final size:16
Alignment explanation
Indices: 6136462--6136509 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
6136452 GGCCTAGAAT
*
6136462 ATTTGGATAGATTATTG
1 ATTT-GATAGATTATTA
*
6136479 ATTTGATAAAATTAGTTA
1 ATTTGAT-AGATTA-TTA
6136497 ATTTGATAGATTA
1 ATTTGATAGATTA
6136510 ACTAATTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 14 0.54
18 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
ATTTGATAGATTATTA
Found at i:6141442 original size:19 final size:21
Alignment explanation
Indices: 6141414--6141456 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
6141404 AATATTTAAA
6141414 TATAAAATA-TATAAT-TTTT
1 TATAAAATATTATAATATTTT
* *
6141433 TATAATATATTATTATATTTT
1 TATAAAATATTATAATATTTT
6141454 TAT
1 TAT
6141457 CATTTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATAAAATATTATAATATTTT
Found at i:6142273 original size:15 final size:15
Alignment explanation
Indices: 6142249--6142278 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6142239 ATGTTAGAGC
6142249 ATATAAATTTGAAAA
1 ATATAAATTTGAAAA
*
6142264 ATATAGATTTGAAAA
1 ATATAAATTTGAAAA
6142279 CTTTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
ATATAAATTTGAAAA
Found at i:6146266 original size:9 final size:10
Alignment explanation
Indices: 6146241--6146266 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6146231 AGTTTGACTT
6146241 TCTTTTTAGG
1 TCTTTTTAGG
6146251 TCTTTTTAGG
1 TCTTTTTAGG
6146261 TCTTTT
1 TCTTTT
6146267 CAATGTACAT
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:0.08, C:0.12, G:0.15, T:0.65
Consensus pattern (10 bp):
TCTTTTTAGG
Found at i:6146389 original size:12 final size:12
Alignment explanation
Indices: 6146374--6146431 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
6146364 ACCTTCTTCA
6146374 TTTTGTTC-T-T
1 TTTTGTTCTTGT
* *
6146384 TTTT-TTATTCT
1 TTTTGTTCTTGT
6146395 TTTTGTTCTTGT
1 TTTTGTTCTTGT
*
6146407 TCTTGTTCTTGT
1 TTTTGTTCTTGT
*
6146419 TCTTGTTCTTGT
1 TTTTGTTCTTGT
6146431 T
1 T
6146432 CGTATCTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
11 5 0.12
12 29 0.71
ACGTcount: A:0.02, C:0.12, G:0.12, T:0.74
Consensus pattern (12 bp):
TTTTGTTCTTGT
Found at i:6146408 original size:6 final size:6
Alignment explanation
Indices: 6146397--6146432 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
6146387 TTTATTCTTT
6146397 TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC
1 TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC
6146433 GTATCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (6 bp):
TTGTTC
Found at i:6148126 original size:17 final size:18
Alignment explanation
Indices: 6148092--6148134 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
6148082 GTTCTTTTAA
* *
6148092 CTTTTTCTTTTCCATTCT
1 CTTTTGCTTCTCCATTCT
6148110 CTTTTGCTTCTCC-TTCT
1 CTTTTGCTTCTCCATTCT
*
6148127 ATTTTGCT
1 CTTTTGCT
6148135 CTCTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.63
Consensus pattern (18 bp):
CTTTTGCTTCTCCATTCT
Found at i:6148149 original size:18 final size:17
Alignment explanation
Indices: 6148106--6148148 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
6148096 TTCTTTTCCA
*
6148106 TTCTCTTTTGCTTCTCC
1 TTCTATTTTGCTTCTCC
*
6148123 TTCTATTTTGCTCTCTTC
1 TTCTATTTTGCT-TCTCC
6148141 TTC-ATTTT
1 TTCTATTTT
6148149 TTAACGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.63
Consensus pattern (17 bp):
TTCTATTTTGCTTCTCC
Found at i:6148763 original size:20 final size:20
Alignment explanation
Indices: 6148738--6148781 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6148728 AAAAGCAGTT
*
6148738 CACCGGGAAAGCCCATTGAC
1 CACCGGGAAAACCCATTGAC
* *
6148758 CACCGGGAAAACCCTTTGAT
1 CACCGGGAAAACCCATTGAC
6148778 CACC
1 CACC
6148782 ATTTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (20 bp):
CACCGGGAAAACCCATTGAC
Found at i:6163531 original size:18 final size:17
Alignment explanation
Indices: 6163493--6163533 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6163483 CAAAAAAATT
6163493 ATTTTAACAAAAATTAA
1 ATTTTAACAAAAATTAA
* *
6163510 ATTTTAACATAATTTAA
1 ATTTTAACAAAAATTAA
*
6163527 AATTTAA
1 ATTTTAA
6163534 AATAAATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTTAACAAAAATTAA
Found at i:6165640 original size:2 final size:2
Alignment explanation
Indices: 6165633--6165662 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6165623 TATGATGTCT
*
6165633 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6165663 GAATACAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6166467 original size:17 final size:17
Alignment explanation
Indices: 6166430--6166477 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
6166420 TGCTAGCCTT
6166430 TCAATGTTGTTC-CAACA
1 TCAA-GTTGTTCTCAACA
6166447 --AAGTTGTTCTCAACA
1 TCAAGTTGTTCTCAACA
*
6166462 TCAAGTTGTTTTCAAC
1 TCAAGTTGTTCTCAAC
6166478 GGGATTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
17 13 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (17 bp):
TCAAGTTGTTCTCAACA
Found at i:6177888 original size:2 final size:2
Alignment explanation
Indices: 6177881--6177905 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6177871 AAAACAGCTT
6177881 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6177906 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6182299 original size:17 final size:17
Alignment explanation
Indices: 6182279--6182337 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
6182269 TTAGCATGAT
*
6182279 TAAACAATTCAATAATA
1 TAAATAATTCAATAATA
* *
6182296 TAAATAATACAA-AATT
1 TAAATAATTCAATAATA
6182312 TGAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
6182332 TAAATA
1 TAAATA
6182338 GTAGACATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 15 0.45
19 10 0.30
20 4 0.12
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:6182336 original size:19 final size:18
Alignment explanation
Indices: 6182284--6182336 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
6182274 ATGATTAAAC
6182284 AATTCAATAATATAAA-T
1 AATTCAATAATATAAATT
* *
6182301 AATACAA-AATTTGAAATTT
1 AATTCAATAATAT-AAA-TT
6182320 AATTCAATAATATAAAT
1 AATTCAATAATATAAAT
6182337 AGTAGACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 1 0.04
19 10 0.36
20 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (18 bp):
AATTCAATAATATAAATT
Found at i:6182472 original size:18 final size:19
Alignment explanation
Indices: 6182425--6182473 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
6182415 GTTTTGGGGG
*
6182425 TTTGGGAGGAAGTAAAATTT
1 TTTGGG-GGAAGTAAAATGT
6182445 TTTAGGGGGAAGTAAAA-GT
1 TTT-GGGGGAAGTAAAATGT
6182464 TTTGGGGGAA
1 TTTGGGGGAA
6182474 AATAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 13 0.48
21 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.31
Consensus pattern (19 bp):
TTTGGGGGAAGTAAAATGT
Found at i:6182497 original size:75 final size:71
Alignment explanation
Indices: 6182374--6182533 Score: 205
Period size: 75 Copynumber: 2.2 Consensus size: 71
6182364 TTGGGGTTGG
* * *
6182374 GGGGGAAGTAAAAGTTTTTGGAAGAAAATAGAAGGAAAAACGTTTTGGGGGTTTGGGAGGAAGTA
1 GGGGGAAGTAAAAGTTTTTGGAAGAAAATAAAAAGAAAAACATTTT-GGGGTTTGGG-GGAAGTA
6182439 AAATTTTTT
64 AAA-TTTTT
** *
6182448 AGGGGGAAGTAAAAG-TTTTGGGGGAAAATAAAAAAGAAAAATATTTTGGGGTTTGGGGGAAGTA
1 -GGGGGAAGTAAAAGTTTTTGGAAGAAAAT-AAAAAGAAAAACATTTTGGGGTTTGGGGGAAGTA
6182512 AAATTTTT
64 AAATTTTT
*
6182520 GGGGAAAGTAAAAG
1 GGGGGAAGTAAAAG
6182534 GGTTTTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
71 13 0.17
72 5 0.06
73 10 0.13
74 22 0.29
75 27 0.35
ACGTcount: A:0.39, C:0.01, G:0.34, T:0.26
Consensus pattern (71 bp):
GGGGGAAGTAAAAGTTTTTGGAAGAAAATAAAAAGAAAAACATTTTGGGGTTTGGGGGAAGTAAA
ATTTTT
Found at i:6185044 original size:25 final size:24
Alignment explanation
Indices: 6185016--6185094 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 24
6185006 TGCTTTCACA
6185016 AGCTATGAATCGGTAAGCTCATACG
1 AGCTA-GAATCGGTAAGCTCATACG
6185041 AGCTGAGAATCGGTAAGCTC-TCACG
1 AGCT-AGAATCGGTAAGCTCAT-ACG
*
6185066 AGCTACAAATCGGTAAGCTCATACG
1 AGCTA-GAATCGGTAAGCTCATACG
6185091 AGCT
1 AGCT
6185095 GTGGTGTGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
24 2 0.04
25 45 0.92
26 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (24 bp):
AGCTAGAATCGGTAAGCTCATACG
Found at i:6190896 original size:22 final size:22
Alignment explanation
Indices: 6190868--6190912 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6190858 GGTATGAAAA
6190868 GATAGTTGATTGAAGGATTGAT
1 GATAGTTGATTGAAGGATTGAT
6190890 GATAGTTGATTGAAGGATTGAT
1 GATAGTTGATTGAAGGATTGAT
6190912 G
1 G
6190913 TTGTTGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (22 bp):
GATAGTTGATTGAAGGATTGAT
Found at i:6196948 original size:41 final size:41
Alignment explanation
Indices: 6196898--6196979 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
6196888 ATATGAAGAG
6196898 ATTTATGTCTTTTGGATATTGGATGTGAGATGTGATGAAGC
1 ATTTATGTCTTTTGGATATTGGATGTGAGATGTGATGAAGC
6196939 ATTTATGTCTTTTGGATATTGGATGTGAGATGTGATGAAGC
1 ATTTATGTCTTTTGGATATTGGATGTGAGATGTGATGAAGC
6196980 TGATCATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.41
Consensus pattern (41 bp):
ATTTATGTCTTTTGGATATTGGATGTGAGATGTGATGAAGC
Found at i:6199368 original size:21 final size:21
Alignment explanation
Indices: 6199313--6199368 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
6199303 ATATTAAATT
*
6199313 TTACAACACCAAAATAGCATA
1 TTACAACAACAAAATAGCATA
** * *
6199334 TTTTAAAAAGAAAATAGCATA
1 TTACAACAACAAAATAGCATA
*
6199355 TTACAACATCAAAA
1 TTACAACAACAAAA
6199369 AAGTTTTACC
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.23
Consensus pattern (21 bp):
TTACAACAACAAAATAGCATA
Found at i:6203818 original size:23 final size:22
Alignment explanation
Indices: 6203775--6203818 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
6203765 TTCTAAGTCG
6203775 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
6203798 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
6203819 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:6203927 original size:45 final size:45
Alignment explanation
Indices: 6203863--6203951 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
6203853 AACAGATACT
* *
6203863 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
6203908 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAGTGATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
6203952 TCGTAGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:6216417 original size:41 final size:41
Alignment explanation
Indices: 6216348--6216433 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
6216338 TCAGCATTAA
* *
6216348 ATTTTTTTAATCTTTTTGTTCTCGAAGAATTGAGAAAGTTC
1 ATTTTTTTAATCTTTTTGTTCCCAAAGAATTGAGAAAGTTC
*
6216389 ATTTTTTTAAT-TTTGTTTTTCCCAAAGAATTGAGAAAGTTC
1 ATTTTTTTAATCTTT-TTGTTCCCAAAGAATTGAGAAAGTTC
6216430 ATTT
1 ATTT
6216434 GTTTCTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 3 0.07
41 38 0.93
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (41 bp):
ATTTTTTTAATCTTTTTGTTCCCAAAGAATTGAGAAAGTTC
Found at i:6219079 original size:31 final size:31
Alignment explanation
Indices: 6219044--6219145 Score: 156
Period size: 31 Copynumber: 3.4 Consensus size: 31
6219034 ACTACAAAAA
6219044 TAGTCACTTTTATTTGTATCAAATTACATTT
1 TAGTCACTTTTATTTGTATCAAATTACATTT
* *
6219075 TAGTCACTTTTGTTTG-A--AATGTTACATTT
1 TAGTCACTTTTATTTGTATCAA-ATTACATTT
6219104 TAGTCACTTTTATTTGTATCAAATTACATTT
1 TAGTCACTTTTATTTGTATCAAATTACATTT
6219135 TAGTCACTTTT
1 TAGTCACTTTT
6219146 GTTTAAATGT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.03
29 23 0.37
30 2 0.03
31 34 0.54
32 2 0.03
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (31 bp):
TAGTCACTTTTATTTGTATCAAATTACATTT
Found at i:6219106 original size:29 final size:29
Alignment explanation
Indices: 6219067--6219171 Score: 151
Period size: 29 Copynumber: 3.6 Consensus size: 29
6219057 TTGTATCAAA
6219067 TTACATTTTAGTCACTTTTGTTTGAAATG
1 TTACATTTTAGTCACTTTTGTTTGAAATG
* *
6219096 TTACATTTTAGTCACTTTTATTTGTATCAA-A
1 TTACATTTTAGTCACTTTTGTTTG-A--AATG
6219127 TTACATTTTAGTCACTTTTGTTT-AAATG
1 TTACATTTTAGTCACTTTTGTTTGAAATG
6219155 TTACATTTTAGTCACTT
1 TTACATTTTAGTCACTT
6219172 ACATTATTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.03
28 17 0.25
29 24 0.35
30 1 0.01
31 22 0.32
32 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (29 bp):
TTACATTTTAGTCACTTTTGTTTGAAATG
Found at i:6219115 original size:60 final size:59
Alignment explanation
Indices: 6219044--6219171 Score: 247
Period size: 60 Copynumber: 2.2 Consensus size: 59
6219034 ACTACAAAAA
6219044 TAGTCACTTTTATTTGTATCAAATTACATTTTAGTCACTTTTGTTTGAAATGTTACATTT
1 TAGTCACTTTTATTTGTATCAAATTACATTTTAGTCACTTTTGTTT-AAATGTTACATTT
6219104 TAGTCACTTTTATTTGTATCAAATTACATTTTAGTCACTTTTGTTTAAATGTTACATTT
1 TAGTCACTTTTATTTGTATCAAATTACATTTTAGTCACTTTTGTTTAAATGTTACATTT
6219163 TAGTCACTT
1 TAGTCACTT
6219172 ACATTATTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
59 22 0.32
60 46 0.68
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (59 bp):
TAGTCACTTTTATTTGTATCAAATTACATTTTAGTCACTTTTGTTTAAATGTTACATTT
Found at i:6220662 original size:72 final size:72
Alignment explanation
Indices: 6220523--6220654 Score: 205
Period size: 72 Copynumber: 1.9 Consensus size: 72
6220513 TTATAAAATA
*
6220523 AAACGTAGTTTTCTTGCTACCCTTTGCCTCTTTAAATTTCCTTTTATTTTTGCCCAAACTTTAAA
1 AAACGTAGTTTTCTTGCTACCCTTTGCCTCTTTAAATTTCCTTTTAATTTTGCCCAAACTTTAAA
6220588 AAATGAT
66 AAATGAT
* * * *
6220595 AAACGTAGTTTTCTTGCTACCCTTTTCTTCTTT-AATTTTC-TTTAATTTTGCCCTAACTTT
1 AAACGTAGTTTTCTTGCTACCCTTTGCCTCTTTAAATTTCCTTTTAATTTTGCCCAAACTTT
6220655 TCTAAAAACA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 18 0.33
71 6 0.11
72 31 0.56
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.48
Consensus pattern (72 bp):
AAACGTAGTTTTCTTGCTACCCTTTGCCTCTTTAAATTTCCTTTTAATTTTGCCCAAACTTTAAA
AAATGAT
Found at i:6226149 original size:2 final size:2
Alignment explanation
Indices: 6226098--6226137 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6226088 TGTTGTCTAG
6226098 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6226138 AAAGCATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6227484 original size:33 final size:34
Alignment explanation
Indices: 6227424--6227496 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
6227414 AAACTATCAT
*
6227424 ATAATAATAGTATGATAAATAAAAATGATATA-G
1 ATAATAATAGTATGATAAATAAAAATGATAAATG
* * *
6227457 ATAATAATATTATGA-ATAATGATAATGATAAATG
1 ATAATAATAGTATGATA-AATAAAAATGATAAATG
6227491 ATAATA
1 ATAATA
6227497 CATTGAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 26 0.76
34 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (34 bp):
ATAATAATAGTATGATAAATAAAAATGATAAATG
Found at i:6229387 original size:44 final size:44
Alignment explanation
Indices: 6229340--6229899 Score: 182
Period size: 44 Copynumber: 12.6 Consensus size: 44
6229330 GATCTACTCT
* * *
6229340 ACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCT
1 ACTGTAACTTCAGGGAGATAAGATCATTTATTTTAATCCGCTCC
* * ** * * *
6229384 ACTG-AAATCTCAGGGGGATCGGAT-AGTGT-CTTTAATCTGCTCC
1 ACTGTAACT-TCAGGGAGATAAGATCA-TTTATTTTAATCCGCTCC
* * **
6229427 GCTGTAA-TCTCAGGGAGATAAGATCCTAAATTTTAATCCGCTCC
1 ACTGTAACT-TCAGGGAGATAAGATCATTTATTTTAATCCGCTCC
* * * **
6229471 ACTGTAACTTCAGGGAGATAGGATTATCGGCTTCAATTTGATGTGATCTACTCTC
1 ACTGTAACTTCAGGGAGATAAGATCAT----TT--A-TT--T-TAATCCGCTC-C
** * *
6229526 -CTGTAACCCCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCATTTATTTTAATCCGCTCC
* * * * *
6229569 ACTATAATTTTAGGGAGATAAGATCCTTTATTTTAATCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCATTTATTTTAATCCGCTCC
* * * * * * *
6229613 ACTGTAATTTCAGGGAGATAGGATTACTGT-CTTCAATCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCA-TTTATTTTAATCCGCTCC
* ** * *
6229657 GCTGTAATCTT-AGGGAGATAAGATC-TGAATTTT-TTCGGTCTACTAC
1 ACTGTAA-CTTCAGGGAGATAAGATCATTTATTTTAATCCG-CT-C--C
* * * *** *** *
6229703 ACTGTAACCTCAGGGAGATAAGACCA--GA-TGCGATTTACTCT
1 ACTGTAACTTCAGGGAGATAAGATCATTTATTTTAATCCGCTCC
* * *
6229744 ACTGTAACCTCAGAGAGATAAGATC-TTAAATTTTAATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCATT-TATTTTAATCCGCTCC
* * * ** **
6229788 ACTGTAACTTCAGGGAGATAGGAT-AGTGT-CTTGGATCTACTCC
1 ACTGTAACTTCAGGGAGATAAGATCA-TTTATTTTAATCCGCTCC
* *** * *
6229831 GCTGTAA-TCTCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCC
1 ACTGTAACT-TCAGGGAGATAAGATCAT-TTATTTTAATCCGCTCC
*
6229875 ACTGTAACCTCAGGGAGATAAGATC
1 ACTGTAACTTCAGGGAGATAAGATC
6229900 TGAAATTCTT
Statistics
Matches: 376, Mismatches: 101, Indels: 78
0.68 0.18 0.14
Matches are distributed among these distances:
41 23 0.06
42 7 0.02
43 68 0.18
44 210 0.56
45 11 0.03
46 20 0.05
47 2 0.01
48 1 0.00
50 3 0.01
51 2 0.01
53 1 0.00
54 27 0.07
55 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
ACTGTAACTTCAGGGAGATAAGATCATTTATTTTAATCCGCTCC
Found at i:6229829 original size:87 final size:86
Alignment explanation
Indices: 6229580--6229894 Score: 289
Period size: 87 Copynumber: 3.6 Consensus size: 86
6229570 CTATAATTTT
* ** * *
6229580 AGGGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATTTCAGGGAGATAGGATTACTGTCT
1 AGGGAGATAAGAT-CTTAATTTTAATCTGCTCCACTGTAACCTCAGGGAGATAGGACTAGTGTCT
* * *
6229645 TCAATCTGCTCCGCTGTAATCTT
65 T-GATCTACTCCGCTGTAATCTC
* * * * *
6229668 AGGGAGATAAGATCTGAATTTT-TTCGGTCTACTACACTGTAACCTCAGGGAGATAAGACCAGAT
1 AGGGAGATAAGATCTTAATTTTAATCTG-CT-C--CACTGTAACCTCAGGGAGATAGGACTAG-T
* ** *
6229732 G-C--GATTTACTCTACTGTAACCTC
61 GTCTTGATCTACTCCGCTGTAATCTC
* * *
6229755 AGAGAGATAAGATCTTAAATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCT
1 AGGGAGATAAGATCTT-AATTTTAATCTGCTCCACTGTAACCTCAGGGAGATAGGACTAGTGTCT
6229819 TGGATCTACTCCGCTGTAATCTC
65 T-GATCTACTCCGCTGTAATCTC
*** *
6229842 AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATA
1 AGGGAGATAAGATCT-TAATTTTAATCTGCTCCACTGTAACCTCAGGGAGATA
6229895 AGATCTGAAA
Statistics
Matches: 180, Mismatches: 35, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
83 2 0.01
84 3 0.02
85 22 0.12
86 3 0.02
87 99 0.55
88 23 0.13
89 3 0.02
90 23 0.13
91 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (86 bp):
AGGGAGATAAGATCTTAATTTTAATCTGCTCCACTGTAACCTCAGGGAGATAGGACTAGTGTCTT
GATCTACTCCGCTGTAATCTC
Found at i:6229900 original size:44 final size:44
Alignment explanation
Indices: 6229526--6229900 Score: 201
Period size: 44 Copynumber: 8.6 Consensus size: 44
6229516 ATCTACTCTC
* * * * * *
6229526 CTGTAACCCCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGT-CTTCAATCTGCTCCA
* ** * * * *
6229570 CTATAATTTTAGGGAGATAAGATC-CTTTATTTTAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGT-CTTCAATCTGCTCCA
** * *
6229614 CTGTAATTTCAGGGAGATAGGAT-TACTGTCTTCAATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCT-CTGTCTTCAATCTGCTCCA
* * * * * ** * *
6229658 CTGTAATCTTAGGGAGATAAGATCTGAATTTTTTCGGTCTACTACA
1 CTGTAACCTCAGGGAGATAAGATCT--CTGTCTTCAATCTGCTCCA
* * * * * * *
6229704 CTGTAACCTCAGGGAGATAAGA-C-CAG-ATGCGATTTACTCTA
1 CTGTAACCTCAGGGAGATAAGATCTCTGTCTTCAATCTGCTCCA
* * * *
6229745 CTGTAACCTCAGAGAGATAAGATCT-TAAAT-TTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCT--GTCTTCAATCTGCTCCA
* * ** ** * *
6229789 CTGTAACTTCAGGGAGATAGGAT-AGTGTCTTGGATCTACTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCTGTCTTCAATCTGCTCCA
* *
6229832 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGTCTTCAATCTGCTCCA
6229876 CTGTAACCTCAGGGAGATAAGATCT
1 CTGTAACCTCAGGGAGATAAGATCT
6229901 GAAATTCTTC
Statistics
Matches: 252, Mismatches: 67, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
41 30 0.12
42 2 0.01
43 29 0.12
44 154 0.61
45 5 0.02
46 32 0.13
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCTCTGTCTTCAATCTGCTCCA
Found at i:6243662 original size:13 final size:13
Alignment explanation
Indices: 6243644--6243668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6243634 NNNNNNNNNN
6243644 AATAAATTCATAA
1 AATAAATTCATAA
6243657 AATAAATTCATA
1 AATAAATTCATA
6243669 GTTGCTGGAA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATTCATAA
Found at i:6243915 original size:30 final size:30
Alignment explanation
Indices: 6243881--6243938 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6243871 CCTCGACTCT
*
6243881 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
6243911 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
6243939 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:6246355 original size:33 final size:34
Alignment explanation
Indices: 6246295--6246367 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
6246285 AAACTATCAT
*
6246295 ATAATAATAGTATGATAAATAAAAATGATATA-G
1 ATAATAATAGTATGATAAATAAAAATGATAAATG
* * *
6246328 ATAATAATATTATGA-ATAATGATAATGATAAATG
1 ATAATAATAGTATGATA-AATAAAAATGATAAATG
6246362 ATAATA
1 ATAATA
6246368 CATTGAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 26 0.76
34 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (34 bp):
ATAATAATAGTATGATAAATAAAAATGATAAATG
Found at i:6255354 original size:38 final size:39
Alignment explanation
Indices: 6255298--6255376 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 39
6255288 CATTTAATTA
* * *
6255298 ATTTTTTAAATTTAAAAAATCAAAAAAATTATAAAAAAT
1 ATTTTTAAAAATTAAAAAATCAAAAAAATCATAAAAAAT
** *
6255337 ATTTTTAAAAATT-AAAAATCATTAAAATCATTAAAAAT
1 ATTTTTAAAAATTAAAAAATCAAAAAAATCATAAAAAAT
6255375 AT
1 AT
6255377 AAAAAACATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 23 0.68
39 11 0.32
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (39 bp):
ATTTTTAAAAATTAAAAAATCAAAAAAATCATAAAAAAT
Found at i:6255362 original size:10 final size:10
Alignment explanation
Indices: 6255347--6255386 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
6255337 ATTTTTAAAA
6255347 ATTAAAAATC
1 ATTAAAAATC
6255357 ATT-AAAATC
1 ATTAAAAATC
6255366 ATTAAAAAT-
1 ATTAAAAATC
*
6255375 A-TAAAAAAC
1 ATTAAAAATC
6255384 ATT
1 ATT
6255387 TTTTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 6 0.23
9 11 0.42
10 9 0.35
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (10 bp):
ATTAAAAATC
Found at i:6255409 original size:47 final size:47
Alignment explanation
Indices: 6255295--6255410 Score: 112
Period size: 47 Copynumber: 2.5 Consensus size: 47
6255285 CATCATTTAA
* * *
6255295 TTAAT-TTTTTAAATTTAAAAAATCAAAAAAATTATAAAAAATATTTT
1 TTAATATTATTAAATTT-TAAAATCAAAAAAATTATAAAAAACATTTT
* * * * *
6255342 TAAAAATTA-AAAATCATTAAAATCATTAAAAA-TATAAAAAACATTTT
1 TTAATATTATTAAAT-TTTAAAATCA-AAAAAATTATAAAAAACATTTT
6255389 TTAATATTATTAAATTTTAAAA
1 TTAATATTATTAAATTTTAAAA
6255411 AATAATTAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
47 41 0.77
48 12 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (47 bp):
TTAATATTATTAAATTTTAAAATCAAAAAAATTATAAAAAACATTTT
Found at i:6256912 original size:17 final size:17
Alignment explanation
Indices: 6256876--6257282 Score: 191
Period size: 18 Copynumber: 22.7 Consensus size: 17
6256866 TGAAACAATT
*
6256876 TTTTTTAAACACGAAAAA
1 TTTTTAAAACACG-AAAA
* *
6256894 TTTTTAAAACATGAGAA
1 TTTTTAAAACACGAAAA
*
6256911 -TTTTAGAGACACGAAAA
1 TTTTTA-AAACACGAAAA
* * *
6256928 TTCTTAAAAATACCAAAA
1 TT-TTTAAAACACGAAAA
*
6256946 TTTTTGAAAACACGGAAA
1 TTTTT-AAAACACGAAAA
* *
6256964 TTTTTAAAACACGGGAAT
1 TTTTTAAAACAC-GAAAA
*
6256982 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAAAA
* **
6257000 TTTTTTAAACA--AATTTT
1 TTTTTAAAACACGAA--AA
6257017 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
6257035 TTTTTAAAACACCG-GAA
1 TTTTTAAAACA-CGAAAA
**
6257052 TTTTTGAAAACACGAGGA
1 TTTTT-AAAACACGAAAA
*
6257070 TTTTTGAAACAC-AAAA
1 TTTTTAAAACACGAAAA
*
6257086 TTTTCCTTGAAAACAC-AAAT
1 -TTT--TT-AAAACACGAAAA
** * *
6257106 TTTTTTTATCACCAGAAA
1 TTTTTAAAACACGA-AAA
*
6257124 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
6257141 TTTTTGAAATATCG-AAA
1 TTTTTAAAACA-CGAAAA
* *
6257158 TTTTTGAAAACGCGGAAA
1 TTTTT-AAAACACGAAAA
*
6257176 TTTATAAAACACGGAAAAA
1 TTTTTAAAACAC-G-AAAA
*
6257195 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-T-AAAACACGAAAA
* * **
6257216 -TTTTGAAATACGGGAA
1 TTTTTAAAACACGAAAA
6257232 TTTTTGAAAACACGAGAAA
1 TTTTT-AAAACACGA-AAA
6257251 TTTTTTTGAAAACACGAAAA
1 --TTTTT-AAAACACGAAAA
6257271 TTTTTAAAACAC
1 TTTTTAAAACAC
6257283 AATTTTATTT
Statistics
Matches: 295, Mismatches: 60, Indels: 69
0.70 0.14 0.16
Matches are distributed among these distances:
15 2 0.01
16 18 0.06
17 96 0.33
18 116 0.39
19 19 0.06
20 14 0.05
21 22 0.07
22 2 0.01
23 6 0.02
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:6256983 original size:35 final size:35
Alignment explanation
Indices: 6256882--6257282 Score: 255
Period size: 35 Copynumber: 11.2 Consensus size: 35
6256872 AATTTTTTTT
* * *
6256882 AAACACGAAAAATTTTTAAAACATGAGAATTTTAG-
1 AAACACG-AAAATTTTTAAAACACGAAAATTTTTGA
* * * *
6256917 AGACACGAAAATTCTTAAAAATACCAAAATTTTTGA
1 AAACACGAAAATT-TTTAAAACACGAAAATTTTTGA
* * *
6256953 AAACACGGAAATTTTTAAAACACGGGAATTTTTTGA
1 AAACACGAAAATTTTTAAAACAC-GAAAATTTTTGA
* * **
6256989 AAACATGAAAATTTTTTAAACA--AATTTTTTTTTGA
1 AAACACGAAAATTTTTAAAACACGAA--AATTTTTGA
*
6257024 AAACACGAAAATTTTTAAAACACCG-GAATTTTTGA
1 AAACACGAAAATTTTTAAAACA-CGAAAATTTTTGA
** *
6257059 AAACACGAGGATTTTTGAAACAC-AAAATTTTCCTTGA
1 AAACACGAAAATTTTTAAAACACGAAAA-TTT--TTGA
* ** * *
6257096 AAACAC-AAATTTTTTTTATCACCAGAAA-TTTTGA
1 AAACACGAAAATTTTTAAAACACGA-AAATTTTTGA
* *
6257130 AAACACGAAAATTTTTGAAATATCG-AAATTTTTGA
1 AAACACGAAAATTTTTAAAACA-CGAAAATTTTTGA
* * *
6257165 AAACGCGGAAATTTATAAAACACGGAAAAATTTTTTCTGA
1 AAACACGAAAATTTTTAAAACAC-G-AAAA--TTTT-TGA
* * * **
6257205 AAACAAGAAAA-TTTTGAAATACGGGAATTTTTGA
1 AAACACGAAAATTTTTAAAACACGAAAATTTTTGA
6257239 AAACACGAGAAATTTTTTTGAAAACACGAAAATTTTT-A
1 AAACACGA-AAA--TTTTT-AAAACACGAAAATTTTTGA
6257277 AAACAC
1 AAACAC
6257283 AATTTTATTT
Statistics
Matches: 280, Mismatches: 58, Indels: 53
0.72 0.15 0.14
Matches are distributed among these distances:
33 1 0.00
34 33 0.12
35 127 0.45
36 52 0.19
37 16 0.06
38 15 0.05
39 25 0.09
40 11 0.04
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (35 bp):
AAACACGAAAATTTTTAAAACACGAAAATTTTTGA
Found at i:6257110 original size:71 final size:70
Alignment explanation
Indices: 6256850--6257191 Score: 230
Period size: 71 Copynumber: 4.9 Consensus size: 70
6256840 TTTTAAAAAA
* ** *
6256850 AAAACACGAAGATTTTTG-AAAC--AATTTT--TTTTAAACACGAAAAATTTTTAAAACA-TGAG
1 AAAACACGAAAATTTTTGAAAACAAAATTTTCCTTGAAAACACG--AAATTTTTAAAACACCG-G
*
6256909 AATTTTAG
63 AATTTTTG
* ** *
6256917 -AGACACGAAAATTCTTAAAAATACCAAAA-TTT--TTGAAAACACGGAAATTTTTAAAACACGG
1 AAAACACGAAAATT-TTTGAAA-A-CAAAATTTTCCTTGAAAACAC-GAAATTTTTAAAACACCG
6256978 GAATTTTTTG
62 GAA-TTTTTG
* * * **
6256988 AAAACATGAAAATTTTT-TAAACAAATTTTTTTTTGAAAACACGAAAATTTTTAAAACACCGGAA
1 AAAACACGAAAATTTTTGAAAACAAAATTTTCCTTGAAAACACG-AAATTTTTAAAACACCGGAA
6257052 TTTTTG
65 TTTTTG
** ** * *
6257058 AAAACACGAGGATTTTTGAAACACAAAATTTTCCTTGAAAACAC-AAATTTTTTTTATCACCAGA
1 AAAACACGAAAATTTTTGAAA-ACAAAATTTTCCTTGAAAACACGAAA-TTTTTAAAACACCGGA
*
6257122 AATTTTG
64 ATTTTTG
* * *
6257129 AAAACACGAAAATTTTTGAAATATCGAAA-TTT--TTGAAAACGCGGAAATTTATAAAACA-CGG
1 AAAACACGAAAATTTTTGAAA-A-CAAAATTTTCCTTGAAAACAC-GAAATTTTTAAAACACCGG
6257190 AA
63 AA
6257192 AAATTTTTTC
Statistics
Matches: 219, Mismatches: 36, Indels: 38
0.75 0.12 0.13
Matches are distributed among these distances:
66 11 0.05
67 2 0.01
68 6 0.03
69 18 0.08
70 51 0.23
71 94 0.43
72 37 0.17
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (70 bp):
AAAACACGAAAATTTTTGAAAACAAAATTTTCCTTGAAAACACGAAATTTTTAAAACACCGGAAT
TTTTG
Found at i:6257242 original size:57 final size:55
Alignment explanation
Indices: 6257154--6257280 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 55
6257144 TTGAAATATC
*
6257154 GAAATTTTTGAAAACGCGGAAATTTATAAAACACGGAAAAATTTTTTCTGAAAACAA
1 GAAAATTTTGAAAACGCGGAAATTTATAAAACAC-GAAAAATTTTTT-TGAAAACAA
* * *
6257211 GAAAATTTTGAAATACG-GG-AATTTTTGAAAACACGAGAAATTTTTTTGAAAACAC
1 GAAAATTTTGAAA-ACGCGGAAATTTAT-AAAACACGAAAAATTTTTTTGAAAACAA
*
6257266 GAAAATTTTTAAAAC
1 GAAAATTTTGAAAAC
6257281 ACAATTTTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
54 2 0.03
55 20 0.32
56 17 0.27
57 21 0.33
58 3 0.05
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (55 bp):
GAAAATTTTGAAAACGCGGAAATTTATAAAACACGAAAAATTTTTTTGAAAACAA
Found at i:6257257 original size:21 final size:20
Alignment explanation
Indices: 6257124--6257275 Score: 82
Period size: 17 Copynumber: 8.1 Consensus size: 20
6257114 TCACCAGAAA
6257124 TTTTGAAAACACGAAAA--T
1 TTTTGAAAACACGAAAATTT
*
6257142 TTTTGAAATA-TCG-AAA--T
1 TTTTGAAA-ACACGAAAATTT
* *
6257159 TTTTGAAAACGCGGAAA--T
1 TTTTGAAAACACGAAAATTT
*
6257177 TTAT-AAAACACGGAAAAATTT
1 TTTTGAAAACAC-G-AAAATTT
*
6257198 TTTCTGAAAACAAGAAAA---
1 TTT-TGAAAACACGAAAATTT
* **
6257216 TTTTG-AAATACGGGAA--T
1 TTTTGAAAACACGAAAATTT
6257233 TTTTGAAAACACGAGAAATTT
1 TTTTGAAAACACGA-AAATTT
6257254 TTTTGAAAACACGAAAATTT
1 TTTTGAAAACACGAAAATTT
6257274 TT
1 TT
6257276 AAAACACAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 26
0.73 0.10 0.18
Matches are distributed among these distances:
16 8 0.08
17 27 0.25
18 27 0.25
19 6 0.06
20 8 0.08
21 22 0.21
22 2 0.02
23 6 0.06
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (20 bp):
TTTTGAAAACACGAAAATTT
Found at i:6257420 original size:16 final size:17
Alignment explanation
Indices: 6257378--6257424 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
6257368 TTATTATTAT
6257378 TTTTGAAACACGAGAAA
1 TTTTGAAACACGAGAAA
*
6257395 TTTTGAAAACATGA-AAA
1 TTTTG-AAACACGAGAAA
6257412 TTTTGAAACACGA
1 TTTTGAAACACGA
6257425 TTAGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 13 0.48
18 7 0.26
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.28
Consensus pattern (17 bp):
TTTTGAAACACGAGAAA
Found at i:6258244 original size:9 final size:9
Alignment explanation
Indices: 6258217--6258283 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
6258207 GTCGACAGAC
6258217 TCTTTTTGTT
1 TCTTTTT-TT
6258227 T-TATTTTTT
1 TCT-TTTTTT
*
6258236 T-ATTTTTT
1 TCTTTTTTT
*
6258244 TC-CTTTTT
1 TCTTTTTTT
6258252 TCTTCTTTTT
1 TCTT-TTTTT
*
6258262 TCTTCTTTT
1 TCTTTTTTT
6258271 TCTTTTTTT
1 TCTTTTTTT
6258280 TCTT
1 TCTT
6258284 CTCCTTCGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 14 0.29
9 20 0.42
10 14 0.29
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.82
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:6258251 original size:10 final size:10
Alignment explanation
Indices: 6258246--6258285 Score: 66
Period size: 9 Copynumber: 4.2 Consensus size: 10
6258236 TATTTTTTTC
6258246 CTTTTTTCTT
1 CTTTTTTCTT
6258256 CTTTTTTCTT
1 CTTTTTTCTT
6258266 C-TTTTTCTT
1 CTTTTTTCTT
6258275 -TTTTTTCTT
1 CTTTTTTCTT
6258284 CT
1 CT
6258286 CCTTCGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:6258252 original size:19 final size:19
Alignment explanation
Indices: 6258230--6258289 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
6258220 TTTTGTTTTA
*
6258230 TTTTTTTATTTTTT-TCCT
1 TTTTTTTTTTTTTTCTCCT
* *
6258248 TTTTTCTTCTTTTTTCTTCT
1 TTTTT-TTTTTTTTTCTCCT
6258268 TTTTCTTTTTTTTCTTCTCCT
1 TTTT-TTTTTTTT-TTCTCCT
6258289 T
1 T
6258290 CGTTCAGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 13 0.38
21 8 0.24
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTTTTTTCTCCT
Found at i:6258279 original size:8 final size:8
Alignment explanation
Indices: 6258225--6258279 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
6258215 ACTCTTTTTG
*
6258225 TTTTATTT
1 TTTTCTTT
*
6258233 TTTTATTT
1 TTTTCTTT
*
6258241 TTTTCCTT
1 TTTTCTTT
6258249 TTTTCTTCTT
1 TTTTC-T-TT
6258259 TTTTCTTCT
1 TTTTCTT-T
6258268 TTTTCTTT
1 TTTTCTTT
6258276 TTTT
1 TTTT
6258280 TCTTCTCCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 25 0.61
9 9 0.22
10 7 0.17
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:6258280 original size:18 final size:18
Alignment explanation
Indices: 6258238--6258285 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
6258228 TATTTTTTTA
*
6258238 TTTTTTTCCT-TTTTTCT
1 TTTTTTTCTTCTTTTTCT
6258255 TCTTTTTTCTTCTTTTTCT
1 T-TTTTTTCTTCTTTTTCT
6258274 TTTTTTTCTTCT
1 TTTTTTTCTTCT
6258286 CCTTCGTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.04
18 19 0.68
19 8 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTCTTCTTTTTCT
Found at i:6258822 original size:30 final size:29
Alignment explanation
Indices: 6258801--6258961 Score: 205
Period size: 30 Copynumber: 5.4 Consensus size: 29
6258791 TTTGGGGCCG
* *
6258801 AAATGTAATTTTGATAAAGTTTAAGGGTCA
1 AAATGTAATTTTGA-AAATTTTAGGGGTCA
** *
6258831 AAATGTAATTTCAAGAAATTTTAAGGGTCA
1 AAATGTAATTTTGA-AAATTTTAGGGGTCA
* **
6258861 AAATGTAATTTAGAAAATTTTAGGGGTTG
1 AAATGTAATTTTGAAAATTTTAGGGGTCA
*
6258890 AAATGTAATTTTGAAAAAGTTTAGGGGTCA
1 AAATGTAATTTTG-AAAATTTTAGGGGTCA
6258920 AAATGTAATTTTAGAAAATTTTAGGGGTCA
1 AAATGTAATTTT-GAAAATTTTAGGGGTCA
6258950 AAATGTAATTTT
1 AAATGTAATTTT
6258962 TTTAAACACG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
29 24 0.21
30 90 0.78
31 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (29 bp):
AAATGTAATTTTGAAAATTTTAGGGGTCA
Found at i:6258870 original size:60 final size:58
Alignment explanation
Indices: 6258801--6258960 Score: 212
Period size: 59 Copynumber: 2.7 Consensus size: 58
6258791 TTTGGGGCCG
* * *
6258801 AAATGTAATTTTGATAAAGTTTAAGGGTCAAAATGTAATTTCAAGAAATTTTAAGGGTCA
1 AAATGTAATTTTGA-AAATTTTAGGGGTCAAAATGTAATTTCAA-AAAGTTTAAGGGTCA
* ** * *
6258861 AAATGTAATTTAGAAAATTTTAGGGGTTGAAATGTAATTTTGAAAAAGTTTAGGGGTCA
1 AAATGTAATTTTGAAAATTTTAGGGGTCAAAATGTAA-TTTCAAAAAGTTTAAGGGTCA
6258920 AAATGTAATTTTAGAAAATTTTAGGGGTCAAAATGTAATTT
1 AAATGTAATTTT-GAAAATTTTAGGGGTCAAAATGTAATTT
6258961 TTTTAAACAC
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 46 0.53
60 41 0.47
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (58 bp):
AAATGTAATTTTGAAAATTTTAGGGGTCAAAATGTAATTTCAAAAAGTTTAAGGGTCA
Found at i:6260655 original size:21 final size:21
Alignment explanation
Indices: 6260631--6260677 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
6260621 AAAATAATGG
* *
6260631 AATATATATATAATAATA-AAA
1 AATATAT-TATAACAAAATAAA
6260652 AATAT-TTATAACAAAATAAA
1 AATATATTATAACAAAATAAA
6260672 AATATA
1 AATATA
6260678 AAAATGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 5 0.23
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATATATTATAACAAAATAAA
Found at i:6260656 original size:19 final size:20
Alignment explanation
Indices: 6260634--6260677 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
6260624 ATAATGGAAT
* *
6260634 ATATATATAATAATA-AAAA
1 ATATATATAACAAAATAAAA
*
6260653 ATATTTATAACAAAATAAAA
1 ATATATATAACAAAATAAAA
6260673 ATATA
1 ATATA
6260678 AAAATGGTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATATAACAAAATAAAA
Found at i:6260774 original size:2 final size:2
Alignment explanation
Indices: 6260761--6260798 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6260751 AATGTGTATG
*
6260761 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6260799 CTATTAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6261026 original size:3 final size:3
Alignment explanation
Indices: 6261018--6261076 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
6261008 GTACATAGAA
6261018 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6261066 AAT AAT AAT AA
1 AAT AAT AAT AA
6261077 GGAGAAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6263001 original size:26 final size:26
Alignment explanation
Indices: 6262952--6263017 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
6262942 CATTCCAACC
* *
6262952 CACAGCTCATGTAAGCAGACCCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
6262978 TAC-GACTCGTGTGAGCAGACCCATTT
1 CACAG-CTCGTGTGAGCAGACCCATTT
6263004 CACAGCTCGTGTGA
1 CACAGCTCGTGTGA
6263018 ACACTATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 32 0.94
27 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGACCCATTT
Found at i:6263156 original size:16 final size:17
Alignment explanation
Indices: 6263135--6263175 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
6263125 AATGGCATGA
6263135 TATTTATACAATTGGG-
1 TATTTATACAATTGGGT
6263151 TATTTATACAATTGGGT
1 TATTTATACAATTGGGT
6263168 TATTTATA
1 TATTTATA
6263176 ACCCCAGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (17 bp):
TATTTATACAATTGGGT
Found at i:6263494 original size:18 final size:18
Alignment explanation
Indices: 6263471--6263507 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6263461 TCATCATTAT
6263471 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
6263489 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
6263507 T
1 T
6263508 CAACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:6263698 original size:17 final size:17
Alignment explanation
Indices: 6263678--6263711 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6263668 ATACATACAT
6263678 TTTTTTAAAAAAAGAAA
1 TTTTTTAAAAAAAGAAA
6263695 TTTTTTAAAAAAAGAAA
1 TTTTTTAAAAAAAGAAA
6263712 AAAAAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
TTTTTTAAAAAAAGAAA
Found at i:6265360 original size:26 final size:26
Alignment explanation
Indices: 6265304--6265365 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
6265294 CCAACCCACA
* *
6265304 ACTCATGTAAGCAGACCCATTTCACG
1 ACTCGTGTGAGCAGACCCATTTCACG
6265330 ACTCGTGTGAGCAGACCCATTTCAC-
1 ACTCGTGTGAGCAGACCCATTTCACG
6265355 AGCTCGTGTGA
1 A-CTCGTGTGA
6265366 ACACTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (26 bp):
ACTCGTGTGAGCAGACCCATTTCACG
Found at i:6266617 original size:27 final size:25
Alignment explanation
Indices: 6266586--6266646 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
6266576 TATTTATTTG
6266586 ATTAAATTATAGAATAAAAATTTAAAT
1 ATTAAATTA-AGAATAAAAA-TTAAAT
* *
6266613 ATTAAAATTAAGTATATAAATTAAAT
1 ATT-AAATTAAGAATAAAAATTAAAT
*
6266639 CTTAAATT
1 ATTAAATT
6266647 TGAACAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 8 0.27
27 11 0.37
28 6 0.20
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (25 bp):
ATTAAATTAAGAATAAAAATTAAAT
Found at i:6266643 original size:26 final size:28
Alignment explanation
Indices: 6266589--6266644 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
6266579 TTATTTGATT
6266589 AAATTATAGAATAAAAATTTAAATATTA
1 AAATTATAGAATAAAAATTTAAATATTA
* * *
6266617 AAATTA-AGTATATAAA-TTAAATCTTA
1 AAATTATAGAATAAAAATTTAAATATTA
6266643 AA
1 AA
6266645 TTTGAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 8 0.32
28 6 0.24
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (28 bp):
AAATTATAGAATAAAAATTTAAATATTA
Found at i:6269576 original size:100 final size:98
Alignment explanation
Indices: 6269373--6269602 Score: 424
Period size: 100 Copynumber: 2.3 Consensus size: 98
6269363 CTAAATGAAG
*
6269373 CATTAAATTTATAACACATTTGTTAGCAGTATCTGTCATTATATACATACATGGACTTATGTGAC
1 CATTAAATTTATAACACATTTGTTAGCAGTATCTGACATTATATACATACATGGACTTATGTGAC
*
6269438 TTATAGGACTTTAATGTTTTATTTACATACATA
66 TTATAGGACTTTAATGTTTTATATACATACATA
6269471 CATTAAATTTATAACACATTTGTTAGCAGTATCTGACATTATATACATACATGTGGACTTATGTG
1 CATTAAATTTATAACACATTTGTTAGCAGTATCTGACATTATATACATACA--TGGACTTATGTG
6269536 ACTTATAGGACTTTAATGTTTTATATACATACATA
64 ACTTATAGGACTTTAATGTTTTATATACATACATA
6269571 CATTAAATTTATAACACATTTGTTAGCAGTAT
1 CATTAAATTTATAACACATTTGTTAGCAGTAT
6269603 TTGTTAGACA
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 50 0.39
100 78 0.61
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (98 bp):
CATTAAATTTATAACACATTTGTTAGCAGTATCTGACATTATATACATACATGGACTTATGTGAC
TTATAGGACTTTAATGTTTTATATACATACATA
Found at i:6272255 original size:39 final size:39
Alignment explanation
Indices: 6272189--6272264 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
6272179 CATTTAATTA
* * *
6272189 ATTTTTTAAATTTAAAAAATCAAAAAATTATAAAAAAAT
1 ATTTTTAAAAATTAAAAAATCAAAAAATCATAAAAAAAT
* *
6272228 ATTTTTAAAAATT-AAAAATCATTAAAATCATTAAAAA
1 ATTTTTAAAAATTAAAAAATCA-AAAAATCATAAAAAA
6272265 TATAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 8 0.26
39 23 0.74
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (39 bp):
ATTTTTAAAAATTAAAAAATCAAAAAATCATAAAAAAAT
Found at i:6272279 original size:27 final size:26
Alignment explanation
Indices: 6272232--6272307 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
6272222 AAAAATATTT
*
6272232 TTAAAAATTAAAAATCATTAAAATCA
1 TTAAAAATTAAAAATAATTAAAATCA
* *
6272258 TTAAAAATATAAAAA-AATTTAATATTA
1 TTAAAAAT-TAAAAATAA-TTAAAATCA
**
6272285 TTAAATTTTAAAAAATAATTAAA
1 TTAAAAATT-AAAAATAATTAAA
6272308 TATTGATGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 10 0.25
27 28 0.70
28 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
TTAAAAATTAAAAATAATTAAAATCA
Found at i:6276220 original size:3 final size:3
Alignment explanation
Indices: 6276214--6276249 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6276204 TATACAGTAG
6276214 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6276250 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6277923 original size:50 final size:50
Alignment explanation
Indices: 6277869--6278402 Score: 213
Period size: 50 Copynumber: 10.7 Consensus size: 50
6277859 TGCAATGTTG
* ** *
6277869 GGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCA-AGATCA
*** * * * *
6277919 GGGAAGTAAGATCCGCCGTCGTGGCTTTAATCTTTTAAATCGCAAGATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAGATCA
** *
6277969 GGGAAACCAGATCCGCCGTCGTAGCTTCAATC---TACTCCGC-TGTACTGCTA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAG-A-T-C-A
* *** * * * * *
6278019 AGGAAGTAAGATCTGCCGTTGTGGCTTCAATCCT-TTAAATCGCAATATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAAT-CTGTTAAACCGCAAGATCA
** *
6278069 GGGAAACCAGATCCGCCGTCGTAGCTTCAATC---TACTCCGC-TGTACTGCTA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAG-A-T-C-A
* *** * * * * * *
6278119 AGGAAGTAAGATCCGTCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAGATCA
* *
6278169 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCT---CCGC-TGTACTGCTA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAG-A-T-C-A
* *** * * * * * *
6278219 AGGAAGTAAGATCCGCTGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAGATCA
* * * *
6278269 GGGAAACCAGATCCGCTGTCATAGCTTCAATCTGCT---CCGC-TGTACTGCTA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAG-A-T-C-A
* ** * * * * * *
6278319 AGGAAATAAGATCCGCTGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAGATCA
* *
6278369 GGGAAACCAGATCCACCGTCGTAGCTTTAATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTG
6278403 CTCCACTGTA
Statistics
Matches: 339, Mismatches: 112, Indels: 66
0.66 0.22 0.13
Matches are distributed among these distances:
46 1 0.00
47 20 0.06
48 4 0.01
49 6 0.02
50 279 0.82
51 5 0.01
52 4 0.01
53 20 0.06
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (50 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTAAACCGCAAGATCA
Found at i:6277987 original size:100 final size:100
Alignment explanation
Indices: 6277869--6278454 Score: 940
Period size: 100 Copynumber: 5.9 Consensus size: 100
6277859 TGCAATGTTG
* * * * * * *
6277869 GGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGAAGTAAGATCC
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCT-AAGGAAGTAAGATCC
* * *
6277933 GCCGTCGTGGCTTTAATCTTTTAAATCGCAAGATCA
65 GCCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
* *
6277969 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTACTCCGCTGTACTGCTAAGGAAGTAAGATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
*
6278034 CCGTTGTGGCTTCAATCCTTTAAATCGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
*
6278069 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTACTCCGCTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
*
6278134 TCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
6278169 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
*
6278234 CTGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
* * *
6278269 GGGAAACCAGATCCGCTGTCATAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAATAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
*
6278334 CTGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
* * *
6278369 GGGAAACCAGATCCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
*
6278434 CCGTTGTGGCTTCAACCTTTT
66 CCGTTGTGGCTTCAATCTTTT
6278455 TACTTTTCAA
Statistics
Matches: 455, Mismatches: 30, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
100 454 1.00
101 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (100 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCGCTGTACTGCTAAGGAAGTAAGATCCG
CCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
Found at i:6280944 original size:3 final size:3
Alignment explanation
Indices: 6280938--6280973 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6280928 TTATTTATAT
6280938 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6280974 CTACTGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6292889 original size:50 final size:50
Alignment explanation
Indices: 6292835--6293206 Score: 238
Period size: 50 Copynumber: 7.4 Consensus size: 50
6292825 AGTAAAAAGG
*
6292835 TTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAGCAGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGTGGAGCAGA
* * ** * * * * ** **
6292885 TTGAAGCTACGACGGCGGATCTGGTTTCCCT-GATATTGC-GATTTAAAAGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAG-CAGTACAG-TGGAGCAGA
*
6292935 TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGCGGAGCAGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGTGGAGCAGA
* * ** * ** * **
6292985 TTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-A-TATTGTGATTTAAAAGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGTG---GAGCAGA
* *
6293035 TTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGTGGAGCAGA
* * ** * * * * ** *
6293085 TTGAAGCTACGACGGCGGATCTGGTTTCCCT-GATATTGC-GATTTA-AAGGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAG-CAGTACAG-TGGAGCA-GA
* * *
6293135 TTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGA
1 TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGTGGAGCAGA
* *
6293185 TTGAAGCTACGACGGCGGATCT
1 TTGAAGCCACAACGGCGGATCT
6293207 GGTTTCCCTG
Statistics
Matches: 227, Mismatches: 79, Indels: 32
0.67 0.23 0.09
Matches are distributed among these distances:
47 4 0.02
48 1 0.00
49 6 0.03
50 205 0.90
51 6 0.03
52 1 0.00
53 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (50 bp):
TTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGTGGAGCAGA
Found at i:6293237 original size:50 final size:49
Alignment explanation
Indices: 6292882--6293414 Score: 271
Period size: 50 Copynumber: 10.7 Consensus size: 49
6292872 ACAGTGGAGC
6292882 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTT-AA
* * ** * ** **
6292932 AGATTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGCGGA---GC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-A-TATTGC-GATTTAA
*
6292982 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGTGATTTAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTT-AA
* * *** * ** **
6293032 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGA---GC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-A-TATTGC-GATTTAA
6293082 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAA
* * * *** * ** **
6293131 AGGATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTACAGCGGA---GC
1 A-GATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-A-TATTGC-GATTTAA
6293182 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAA
* * ** *** * ** *
6293231 AGGATTGAAGCCACAACGGTAGATCTTACTTCCTTAGCAGTACAGCGGA-GT--
1 A-GATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-A-TATTGC-GATTTAA
* * *
6293282 AGATTGAAGCTACGATGGCGGATCTGGTTTCCCTGATCTTACGATTTAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTT-AA
* *** *** * **
6293332 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAA
* *
6293381 CAAATTGAAGCTACGACGGCGGATTTGGTTTCCC
1 -AGATTGAAGCTACGACGGCGGATCTGGTTTCCC
6293415 CAACATTGCA
Statistics
Matches: 345, Mismatches: 105, Indels: 66
0.67 0.20 0.13
Matches are distributed among these distances:
46 8 0.02
47 14 0.04
48 4 0.01
49 8 0.02
50 277 0.80
51 6 0.02
52 4 0.01
53 16 0.05
54 8 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (49 bp):
AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCGATTTAA
Found at i:6293440 original size:100 final size:100
Alignment explanation
Indices: 6292829--6293414 Score: 958
Period size: 100 Copynumber: 5.9 Consensus size: 100
6292819 TTGAAAAGTA
* *
6292829 AAAAGGTTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
6292894 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
*
6292929 AAAAGATTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
*
6292994 CGACGGCGGATCTGGTTTCCCTGATATTGTGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
6293029 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
6293094 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
* *
6293129 AAAGGATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
6293194 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
* ** *
6293229 AAAGGATTGAAGCCACAACGGTAGATCTTACTTCCTTAGCAGTACAGCGGAGTAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
* * *
6293294 CGATGGCGGATCTGGTTTCCCTGATCTTACGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
* * * * * * * *
6293329 AAAAGATTGAAGCCACGACGGCGGATCTTACTTCCCT-GACGGTGCGGTGGAACAAATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTACAGCGGAGCAGATTGAAGCT
*
6293393 ACGACGGCGGATTTGGTTTCCC
65 ACGACGGCGGATCTGGTTTCCC
6293415 CAACATTGCA
Statistics
Matches: 456, Mismatches: 29, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
99 1 0.00
100 455 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
Found at i:6296225 original size:13 final size:13
Alignment explanation
Indices: 6296207--6296283 Score: 127
Period size: 13 Copynumber: 5.9 Consensus size: 13
6296197 AGTTCTTCAT
6296207 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
6296220 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
6296233 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
*
6296246 TGATTTTGAGAAG
1 TGCTTTTGAGAAG
6296259 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
6296272 TGATTTTGAGAA
1 TGCTTTTGAGAA
6296284 ATTTAAGTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:6299455 original size:30 final size:30
Alignment explanation
Indices: 6299420--6299480 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
6299410 AAGGGCAGAA
* *
6299420 CAAAGAATCAGCAGA-AGGCAGAGATGAGGG
1 CAAAGAAGCAGCAGAGA-GCAGAGATAAGGG
6299450 CAAAGAAGCAGCAGAGAGCAGAGATAAGGG
1 CAAAGAAGCAGCAGAGAGCAGAGATAAGGG
6299480 C
1 C
6299481 GTTCGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.36, T:0.05
Consensus pattern (30 bp):
CAAAGAAGCAGCAGAGAGCAGAGATAAGGG
Found at i:6300866 original size:23 final size:23
Alignment explanation
Indices: 6300840--6300939 Score: 139
Period size: 23 Copynumber: 4.3 Consensus size: 23
6300830 ATAAGTGTCA
*
6300840 CACTGATGTGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
6300863 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
**
6300886 CACTG-TAATGTAGCCGTAGCTAC
1 CACTGAT-ATGTAGCCAAAGCTAC
*
6300909 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
6300932 CACTGATA
1 CACTGATA
6300940 AATAACACTG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
22 1 0.01
23 67 0.99
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:6304149 original size:52 final size:52
Alignment explanation
Indices: 6304078--6304177 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
6304068 ATCAAGTGAC
** * *
6304078 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTGG
* *
6304130 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
6304178 AGTGATAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTGG
Found at i:6304291 original size:36 final size:37
Alignment explanation
Indices: 6304151--6304369 Score: 356
Period size: 37 Copynumber: 6.0 Consensus size: 37
6304141 TAATAGCTTC
* *
6304151 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
6304188 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
6304225 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
6304262 GGCTACACTTATCTGATC-AGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
6304298 GGCTACACTTATCTGATC-AGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
6304334 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
6304369 G
1 G
6304370 ATCATACGTA
Statistics
Matches: 176, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
35 11 0.06
36 75 0.43
37 90 0.51
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:6305623 original size:26 final size:26
Alignment explanation
Indices: 6305594--6305653 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
6305584 CATTCCAACC
*
6305594 CACAGCTCATGTAAGCAGACCCATTT
1 CACAACTCATGTAAGCAGACCCATTT
** *
6305620 CACAACTTGTGTGAGCAGACCCATTT
1 CACAACTCATGTAAGCAGACCCATTT
6305646 CACAACTC
1 CACAACTC
6305654 GTGTGAACAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (26 bp):
CACAACTCATGTAAGCAGACCCATTT
Found at i:6305657 original size:26 final size:26
Alignment explanation
Indices: 6305607--6305659 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
6305597 AGCTCATGTA
*
6305607 AGCAGACCCATTTCACAACTTGTGTG
1 AGCAGACCCATTTCACAACTCGTGTG
6305633 AGCAGACCCATTTCACAACTCGTGTG
1 AGCAGACCCATTTCACAACTCGTGTG
6305659 A
1 A
6305660 ACACTATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (26 bp):
AGCAGACCCATTTCACAACTCGTGTG
Found at i:6310849 original size:14 final size:14
Alignment explanation
Indices: 6310821--6310870 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
6310811 TCTAAATATT
**
6310821 AATATTAAATATTA
1 AATATTAAACCTTA
*
6310835 AATGTTAAACCTTA
1 AATATTAAACCTTA
* *
6310849 AATTTTAAACCCTA
1 AATATTAAACCTTA
6310863 AATATTAA
1 AATATTAA
6310871 CCCAAAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (14 bp):
AATATTAAACCTTA
Found at i:6317081 original size:17 final size:17
Alignment explanation
Indices: 6317059--6317091 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6317049 ATATTTAATA
6317059 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
6317076 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
6317092 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:6317956 original size:22 final size:22
Alignment explanation
Indices: 6317914--6317956 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6317904 TGATGTTGTT
*
6317914 TTGCTATCATTTTGTTATTATA
1 TTGCTATCATTTTATTATTATA
*
6317936 TTGCTA-CTATTTTATTGTTAT
1 TTGCTATC-ATTTTATTATTAT
6317957 TGTTCGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60
Consensus pattern (22 bp):
TTGCTATCATTTTATTATTATA
Found at i:6319762 original size:52 final size:53
Alignment explanation
Indices: 6319671--6319779 Score: 143
Period size: 52 Copynumber: 2.1 Consensus size: 53
6319661 TTATATTCTT
**
6319671 TATATTTTTTCATGTTTTCATAATTTGTTTATTTATATATATACATACTTATA
1 TATATTTTTTCATGTTTTCATAATTTGTTTATTTATATATATACATACGCATA
* *
6319724 TATATTTTTT-ATGTTTT-ATAATTT-TTATATATTCTATATATATATACGCATA
1 TATATTTTTTCATGTTTTCATAATTTGTT-TAT-TTATATATATACATACGCATA
6319776 TATA
1 TATA
6319780 CATACTTACA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
50 2 0.04
51 10 0.20
52 28 0.56
53 10 0.20
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (53 bp):
TATATTTTTTCATGTTTTCATAATTTGTTTATTTATATATATACATACGCATA
Found at i:6321614 original size:46 final size:46
Alignment explanation
Indices: 6321507--6321805 Score: 489
Period size: 46 Copynumber: 6.6 Consensus size: 46
6321497 TACGTATGAT
* *
6321507 CACTTATCAC-TTGTCTCTT-ATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
6321550 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
6321596 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
6321642 CACTTATCACTTTATCACTTGATCAGATACGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
6321688 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
6321734 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
6321780 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
6321806 AGTACTCAAA
Statistics
Matches: 241, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
43 10 0.04
44 7 0.03
45 25 0.10
46 199 0.83
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:6331622 original size:22 final size:21
Alignment explanation
Indices: 6331583--6331624 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6331573 AGATTTCAAT
*
6331583 AAATAAAAAATATTAATATTA
1 AAATAAAAAATATAAATATTA
*
6331604 AAATAATATAATATAAATATT
1 AAATAA-AAAATATAAATATT
6331625 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAAAAATATAAATATTA
Found at i:6333103 original size:33 final size:32
Alignment explanation
Indices: 6333066--6333140 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 32
6333056 TGGTATAATT
*
6333066 ATATATATAAAATTTTAATTGTGGTTCAAATG
1 ATATATATAAAATTTTAATTGTGATTCAAATG
* *
6333098 -TATATATAAAATTTTAATTTTGATTCAATTG
1 ATATATATAAAATTTTAATTGTGATTCAAATG
6333129 CATATATATAAA
1 -ATATATATAAA
6333141 GGAATAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 28 0.74
33 10 0.26
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (32 bp):
ATATATATAAAATTTTAATTGTGATTCAAATG
Found at i:6343868 original size:3 final size:3
Alignment explanation
Indices: 6343860--6343903 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6343850 ATGAATTAAA
6343860 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6343904 ACTAATACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6343950 original size:16 final size:16
Alignment explanation
Indices: 6343929--6343959 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6343919 AAATAAAGTA
*
6343929 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
6343945 AAAGAAGAAAAGAAA
1 AAAGAAGAAAAGAAA
6343960 TAGAGACCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:6346910 original size:31 final size:32
Alignment explanation
Indices: 6346875--6346943 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
6346865 TCAAATCATC
* *
6346875 AAAATCAATATTAAGTGATAAAATTTAA-TT-A
1 AAAATCAAAATT-AGTGACAAAATTTAATTTGA
* *
6346906 AAAATAAAAATTAGTGACAAATTTTAATTTGA
1 AAAATCAAAATTAGTGACAAAATTTAATTTGA
6346938 AAAATC
1 AAAATC
6346944 TCATTATAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 13 0.42
31 12 0.39
32 6 0.19
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.33
Consensus pattern (32 bp):
AAAATCAAAATTAGTGACAAAATTTAATTTGA
Found at i:6348566 original size:13 final size:13
Alignment explanation
Indices: 6348550--6348595 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
6348540 GGTGGTAGGA
6348550 TTCTGTATATCTG
1 TTCTGTATATCTG
*
6348563 TTCTGTTTATCTG
1 TTCTGTATATCTG
6348576 ATTCTG-ATATCTG
1 -TTCTGTATATCTG
6348589 TATCTGT
1 T-TCTGT
6348596 TATGGACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 5 0.18
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TTCTGTATATCTG
Found at i:6352851 original size:20 final size:21
Alignment explanation
Indices: 6352826--6352866 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6352816 CTTTTTTAAA
6352826 TATATAATATA-GATTATTTT
1 TATATAATATATGATTATTTT
* *
6352846 TATATATTATATTATTATTTT
1 TATATAATATATGATTATTTT
6352867 AAACACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATATAATATATGATTATTTT
Found at i:6352852 original size:22 final size:21
Alignment explanation
Indices: 6352825--6352866 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6352815 ACTTTTTTAA
6352825 ATATATAATATAGATTATTTTT
1 ATATATAATAT-GATTATTTTT
* *
6352847 ATATATTATATTATTATTTT
1 ATATATAATATGATTATTTT
6352867 AAACACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATAATATGATTATTTTT
Found at i:6355971 original size:19 final size:18
Alignment explanation
Indices: 6355949--6355988 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
6355939 TGAATAAAAC
6355949 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
6355968 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
6355986 TTA
1 TTA
6355989 AATATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:6364382 original size:17 final size:18
Alignment explanation
Indices: 6364360--6364393 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6364350 TGAAACAAAA
6364360 TAATTATATTTA-ATATT
1 TAATTATATTTATATATT
*
6364377 TAATTATGTTTATATAT
1 TAATTATATTTATATAT
6364394 AGTTAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATTATATTTATATATT
Found at i:6364745 original size:3 final size:3
Alignment explanation
Indices: 6364737--6364793 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
6364727 AAACTTACAC
6364737 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6364785 TAT TAT TAT
1 TAT TAT TAT
6364794 GGTGAGAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6365225 original size:41 final size:39
Alignment explanation
Indices: 6365164--6365240 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 39
6365154 GGGATTTAAG
6365164 GTTTAAGGTTCGAGTTCGGGTTTTG-GGCTCAAGGTTCAA
1 GTTTAAGGTTCGAGTTCGGG-TTTGAGGCTCAAGGTTCAA
* * *
6365203 GTTTAGGGTTTGAGATTACGGGTTTGAGGTTCAAGGTT
1 GTTTAAGGTTCGAG-TT-CGGGTTTGAGGCTCAAGGTT
6365241 TGAGTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 12 0.38
40 6 0.19
41 14 0.44
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (39 bp):
GTTTAAGGTTCGAGTTCGGGTTTGAGGCTCAAGGTTCAA
Found at i:6376685 original size:14 final size:13
Alignment explanation
Indices: 6376666--6376704 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
6376656 CCTGCTTTTA
6376666 TTATTATTACTAT
1 TTATTATTACTAT
6376679 GTTATTATTATCTAT
1 -TTATTATTA-CTAT
6376694 TTATTTATTAC
1 TTA-TTATTAC
6376705 CTCTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (13 bp):
TTATTATTACTAT
Found at i:6376701 original size:15 final size:15
Alignment explanation
Indices: 6376669--6376718 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
6376659 GCTTTTATTA
6376669 TTATTA-CTATGTTA-
1 TTATTATCTAT-TTAT
6376683 TTATTATCTATTTAT
1 TTATTATCTATTTAT
* *
6376698 TTATTACCTCTTTAT
1 TTATTATCTATTTAT
6376713 TT-TTAT
1 TTATTAT
6376719 ACATACTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (15 bp):
TTATTATCTATTTAT
Found at i:6377395 original size:17 final size:18
Alignment explanation
Indices: 6377373--6377406 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6377363 TCATTTATTT
*
6377373 ATTATTACTA-TAATATG
1 ATTATTAATATTAATATG
6377390 ATTATTAATATTAATAT
1 ATTATTAATATTAATAT
6377407 TATCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTATTAATATTAATATG
Found at i:6379456 original size:21 final size:22
Alignment explanation
Indices: 6379423--6379465 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6379413 TTTTTATTTA
6379423 AAATTTAATTATAAAA-TATAT
1 AAATTTAATTATAAAATTATAT
6379444 AAATATTAA-TATAAAATTATAT
1 AAAT-TTAATTATAAAATTATAT
6379466 TTTATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTTAATTATAAAATTATAT
Found at i:6380945 original size:6 final size:6
Alignment explanation
Indices: 6380936--6380970 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
6380926 AAATAAAATT
6380936 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
6380971 GTCTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:6381016 original size:9 final size:9
Alignment explanation
Indices: 6381002--6381050 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
6380992 GTAGTGATTC
*
6381002 AATTCGGTT
1 AATTCGGGT
6381011 AATTCGGGT
1 AATTCGGGT
6381020 AATTCGGGT
1 AATTCGGGT
*
6381029 AATTCGGTT
1 AATTCGGGT
6381038 AATTCGGGT
1 AATTCGGGT
6381047 AATT
1 AATT
6381051 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:6386798 original size:14 final size:15
Alignment explanation
Indices: 6386774--6386827 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
6386764 CCCCTAAAAC
6386774 TTTTACTCCCTCACA
1 TTTTACTCCCTCACA
* *
6386789 TTTT-CTCCCTAAAA
1 TTTTACTCCCTCACA
*
6386803 CTTTTGCTCCCTCACA
1 -TTTTACTCCCTCACA
6386819 TTTT-CTCCC
1 TTTTACTCCC
6386828 CAAAACTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 13 0.39
15 12 0.36
16 8 0.24
ACGTcount: A:0.17, C:0.39, G:0.02, T:0.43
Consensus pattern (15 bp):
TTTTACTCCCTCACA
Found at i:6386801 original size:30 final size:30
Alignment explanation
Indices: 6386761--6386843 Score: 141
Period size: 30 Copynumber: 2.8 Consensus size: 30
6386751 ATCTCTTTAC
6386761 TTTC-CCCTAAAACTTTTACTCCCTCACAT
1 TTTCTCCCTAAAACTTTTACTCCCTCACAT
*
6386790 TTTCTCCCTAAAACTTTTGCTCCCTCACAT
1 TTTCTCCCTAAAACTTTTACTCCCTCACAT
*
6386820 TTTCTCCCCAAAACTTTTACTCCC
1 TTTCTCCCTAAAACTTTTACTCCC
6386844 CTCCCATCTC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 4 0.08
30 46 0.92
ACGTcount: A:0.22, C:0.39, G:0.01, T:0.39
Consensus pattern (30 bp):
TTTCTCCCTAAAACTTTTACTCCCTCACAT
Found at i:6386814 original size:16 final size:15
Alignment explanation
Indices: 6386761--6386843 Score: 73
Period size: 16 Copynumber: 5.5 Consensus size: 15
6386751 ATCTCTTTAC
6386761 TTTC-CCCTAAAACT
1 TTTCTCCCTAAAACT
* *
6386775 TTTACTCCCTCACA-T
1 TTT-CTCCCTAAAACT
6386790 TTTCTCCCTAAAACT
1 TTTCTCCCTAAAACT
* *
6386805 TTTGCTCCCTCACA-T
1 TTT-CTCCCTAAAACT
*
6386820 TTTCTCCCCAAAACT
1 TTTCTCCCTAAAACT
6386835 TTTACTCCC
1 TTT-CTCCC
6386844 CTCCCATCTC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.33
15 17 0.31
16 19 0.35
ACGTcount: A:0.22, C:0.39, G:0.01, T:0.39
Consensus pattern (15 bp):
TTTCTCCCTAAAACT
Found at i:6386844 original size:16 final size:15
Alignment explanation
Indices: 6386763--6386844 Score: 55
Period size: 15 Copynumber: 5.3 Consensus size: 15
6386753 CTCTTTACTT
6386763 TCCCCTAAAACTTTTAC
1 TCCCC-AAAACTTTT-C
*
6386780 TCCCTC-ACA-TTTTC
1 TCCC-CAAAACTTTTC
*
6386794 TCCCTAAAACTTTTGC
1 TCCCCAAAACTTTT-C
*
6386810 TCCCTC-ACA-TTTTC
1 TCCC-CAAAACTTTTC
6386824 TCCCCAAAACTTTTAC
1 TCCCCAAAACTTTT-C
6386840 TCCCC
1 TCCCC
6386845 TCCCATCTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
13 1 0.02
14 14 0.27
15 16 0.31
16 15 0.29
17 4 0.08
18 1 0.02
ACGTcount: A:0.22, C:0.40, G:0.01, T:0.37
Consensus pattern (15 bp):
TCCCCAAAACTTTTC
Found at i:6386950 original size:27 final size:28
Alignment explanation
Indices: 6386898--6386950 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
6386888 TTTTTGAATA
*
6386898 TCCCCCCCCAAATTTTACTCCATTTATT
1 TCCCCCCCAAAATTTTACTCCATTTATT
6386926 TCCCCCCCAAAATTTTACTCC-TTTA
1 TCCCCCCCAAAATTTTACTCCATTTA
6386951 GCCCCCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.38
Consensus pattern (28 bp):
TCCCCCCCAAAATTTTACTCCATTTATT
Found at i:6392619 original size:27 final size:28
Alignment explanation
Indices: 6392577--6392630 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
6392567 ATTGAATATA
*
6392577 AAGGGGATTGCTAAGTGCTGATTCCCCC
1 AAGGGGATTACTAAGTGCTGATTCCCCC
6392605 AAGGGG-TTACTAAGTGCTGATTCCCC
1 AAGGGGATTACTAAGTGCTGATTCCCC
6392631 GAATCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (28 bp):
AAGGGGATTACTAAGTGCTGATTCCCCC
Done.