Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 129 of 310
Found at i:41629607 original size:46 final size:47
Alignment explanation
Indices: 41629501--41629622 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
41629491 TGTCTTCGAC
** * *
41629501 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
41629551 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
41629597 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
41629623 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:41629992 original size:30 final size:30
Alignment explanation
Indices: 41629958--41630018 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41629948 TCCTTTACTC
*
41629958 AAACTTTT-CAAAAATTACATTTTTGCCCCT
1 AAACTTTTGC-AAAATTACACTTTTGCCCCT
* *
41629988 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACACTTTTGCCCCT
41630018 A
1 A
41630019 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACACTTTTGCCCCT
Found at i:41630912 original size:39 final size:39
Alignment explanation
Indices: 41630869--41630969 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
41630859 AACATGTTTT
*
41630869 TGAGTATAGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
41630908 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
41630947 TGAGTATTGTGTTATATGCTTGA
1 TGAGTATTGTGATATATGCTTGA
41630970 TTATATATGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:41632101 original size:18 final size:18
Alignment explanation
Indices: 41632074--41632109 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41632064 CGACTATGTG
*
41632074 ACCCTGTTTTCAAATTTT
1 ACCCTATTTTCAAATTTT
*
41632092 ACCCTATTTTCATATTTT
1 ACCCTATTTTCAAATTTT
41632110 GATTCAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (18 bp):
ACCCTATTTTCAAATTTT
Found at i:41634448 original size:43 final size:44
Alignment explanation
Indices: 41634393--41634508 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 44
41634383 ATATCGTACA
* * *
41634393 ATGCCAAC-GTCCCAGACCTGGTCTTATATGTAA-T-CATATATCG
1 ATGCCAACTGTCCCAGACATGGTCTTACACG-AATTACATATA-CG
*
41634436 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAATTACATATACG
1 ATGCCAACTGTCCCAGACATGGTCTTACACGAATTACATATACG
*
41634479 ATGCCGA-TGTCCCAGACATGGTCTTACACG
1 ATGCCAACTGTCCCAGACATGGTCTTACACG
41634509 CTATCACTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 4 0.06
43 53 0.83
44 7 0.11
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACATGGTCTTACACGAATTACATATACG
Found at i:41637272 original size:55 final size:56
Alignment explanation
Indices: 41637207--41637321 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
41637197 AGCATGGCTG
* *
41637207 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
41637263 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
41637318 CCAG
1 CCAG
41637322 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:41637284 original size:27 final size:27
Alignment explanation
Indices: 41637232--41637321 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
41637222 GTGACAGAGT
41637232 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
41637261 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
41637288 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
41637316 CACCAG
1 CACCAG
41637322 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:41637474 original size:28 final size:28
Alignment explanation
Indices: 41637427--41637519 Score: 134
Period size: 28 Copynumber: 3.3 Consensus size: 28
41637417 AAATTAACCC
*
41637427 TAGGGGTATAGA-GGTCATTTTGCATACA
1 TAGGGGTATA-ATGGTAATTTTGCATACA
* *
41637455 TAAGGGTATAATGGTAATTTGGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
41637483 GAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
41637511 TAGGGGTAT
1 TAGGGGTAT
41637520 TCTAGTACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 1 0.02
28 56 0.98
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:41657540 original size:35 final size:35
Alignment explanation
Indices: 41657461--41657540 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
41657451 ATTGGAACTA
* * * *
41657461 AGACCATGTATGCAGAGTCAGATGGCTGTGTCGAC
1 AGACCGTGTATGCAGAGTCACACGACTGTGTCGAC
*
41657496 AGACTGTGTATGCAGAGTCACACGACTGTGTCGAC
1 AGACCGTGTATGCAGAGTCACACGACTGTGTCGAC
*
41657531 AGGCCGTGTA
1 AGACCGTGTA
41657541 ACTAACTCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (35 bp):
AGACCGTGTATGCAGAGTCACACGACTGTGTCGAC
Found at i:41659212 original size:30 final size:30
Alignment explanation
Indices: 41659178--41659238 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
41659168 CAATGTTAGC
41659178 TTAATTTTATTTAAGCTAGGATGATTGCTT
1 TTAATTTTATTTAAGCTAGGATGATTGCTT
41659208 TTAATTTTATTTAAGCTAGGATGATTGCTT
1 TTAATTTTATTTAAGCTAGGATGATTGCTT
41659238 T
1 T
41659239 GATTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (30 bp):
TTAATTTTATTTAAGCTAGGATGATTGCTT
Found at i:41674629 original size:28 final size:28
Alignment explanation
Indices: 41674598--41674652 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
41674588 CAAATTATCG
* *
41674598 AGGATCACAGTTAGTGTGTGAGACATCC
1 AGGATCACACTTAGTGTGTGACACATCC
*
41674626 AGGATGACACTTAGTGTGTGACACATC
1 AGGATCACACTTAGTGTGTGACACATC
41674653 TGTGAAGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (28 bp):
AGGATCACACTTAGTGTGTGACACATCC
Found at i:41677277 original size:23 final size:23
Alignment explanation
Indices: 41677232--41677277 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41677222 GCCCTTGTCT
**
41677232 AGTTTAATTTTAAGGTATGTTTG
1 AGTTTAATTTTAAGAAATGTTTG
* *
41677255 AGTTTAATTTTTAGAAATTTTTG
1 AGTTTAATTTTAAGAAATGTTTG
41677278 CACATTTCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.54
Consensus pattern (23 bp):
AGTTTAATTTTAAGAAATGTTTG
Found at i:41677965 original size:29 final size:29
Alignment explanation
Indices: 41677923--41678004 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
41677913 TATATATGTG
*
41677923 AATTATTGAGCACTAAGTGTGCGAAGTAA
1 AATTATCGAGCACTAAGTGTGCGAAGTAA
*
41677952 AATTATCGAGCACTAAGTGTGAGAAGTAA
1 AATTATCGAGCACTAAGTGTGCGAAGTAA
*
41677981 AACTATCGAGCACTAAGTGTGCGA
1 AATTATCGAGCACTAAGTGTGCGA
41678005 TCTCATTGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (29 bp):
AATTATCGAGCACTAAGTGTGCGAAGTAA
Found at i:41679229 original size:9 final size:9
Alignment explanation
Indices: 41679215--41679243 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41679205 CATACAAGAT
41679215 AAAAAATAA
1 AAAAAATAA
41679224 AAAAAAT-A
1 AAAAAATAA
41679232 AAAAAATAA
1 AAAAAATAA
41679241 AAA
1 AAA
41679244 TTGACTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:41681561 original size:18 final size:18
Alignment explanation
Indices: 41681523--41681557 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
41681513 ATCTTGTCTA
41681523 CCCGTGTGGGCCCACATG
1 CCCGTGTGGGCCCACATG
41681541 CCCGTGT-GGCCCACATG
1 CCCGTGTGGGCCCACATG
41681558 GCCCAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.11, C:0.40, G:0.31, T:0.17
Consensus pattern (18 bp):
CCCGTGTGGGCCCACATG
Found at i:41688306 original size:27 final size:26
Alignment explanation
Indices: 41688269--41688383 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
41688259 AGCATGGCTG
* *
41688269 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
41688295 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
41688323 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
41688350 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
41688377 CCAGAAC
1 CCAGAAC
41688384 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:41688328 original size:54 final size:54
Alignment explanation
Indices: 41688269--41688383 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
41688259 AGCATGGCTG
*
41688269 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
41688323 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
41688377 CCAGAAC
1 CCAGAAC
41688384 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:41688788 original size:8 final size:8
Alignment explanation
Indices: 41688772--41688801 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
41688762 CTCAAAATAC
41688772 CGGCTTTT
1 CGGCTTTT
*
41688780 CGGCATTT
1 CGGCTTTT
41688788 CGGCTTTT
1 CGGCTTTT
41688796 CGGCTT
1 CGGCTT
41688802 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:41690011 original size:26 final size:26
Alignment explanation
Indices: 41689980--41690087 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
41689970 TGAAATGCCC
*
41689980 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
41690006 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
41690032 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
41690058 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41690084 ATCA
1 ATCA
41690088 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41696108 original size:27 final size:27
Alignment explanation
Indices: 41696071--41696163 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
41696061 AGCATGGTTG
* * *
41696071 CCAGA-ACAGATAACATGACAGAGTCA
1 CCAGATACAGATAACGTGGCAGAGCCA
41696097 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAA-CGTGGCAGAGCCA
* *
41696125 CCAG-GACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ACGTGGCAGAGCCA
41696152 CCAGAT-CAGATA
1 CCAGATACAGATA
41696164 TTTGTGGCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
26 5 0.09
27 37 0.65
28 15 0.26
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (27 bp):
CCAGATACAGATAACGTGGCAGAGCCA
Found at i:41696135 original size:54 final size:54
Alignment explanation
Indices: 41696071--41696185 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
41696061 AGCATGGTTG
* *
41696071 CCAGAACAGATA-ACATGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGGACAGATATACATGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
** * * * * *
41696125 CCAGGACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATATCCA
1 CCAGGACAGATATACATGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
41696179 CCAGGAC
1 CCAGGAC
41696186 GCTTCCTCCA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 35 0.69
55 16 0.31
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGGACAGATATACATGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:41696164 original size:27 final size:27
Alignment explanation
Indices: 41696089--41696182 Score: 111
Period size: 27 Copynumber: 3.4 Consensus size: 27
41696079 GATAACATGA
*
41696089 CAGAGTCACCAGATACAGATA-ATCGTGG
1 CAGAGCCACCAGAT-CAGATATAT-GTGG
41696117 CAGAGCCACCAGGA-CAGATATATGTGG
1 CAGAGCCACCA-GATCAGATATATGTGG
*
41696144 CAGAGCCACCAGATCAGATATTTGTGG
1 CAGAGCCACCAGATCAGATATATGTGG
* *
41696171 CATATCCACCAG
1 CAGAGCCACCAG
41696183 GACGCTTCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.03
27 43 0.73
28 12 0.20
29 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGAGCCACCAGATCAGATATATGTGG
Found at i:41702840 original size:15 final size:15
Alignment explanation
Indices: 41702789--41702840 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
41702779 CACACACAAA
* *
41702789 TGTTCTAAATATAAGT
1 TGTTCTAAACAT-GGT
* *
41702805 TGTTCAAAACAATGAT
1 TGTTCTAAAC-ATGGT
41702821 TGTTCTAAACATGGT
1 TGTTCTAAACATGGT
41702836 TGTTC
1 TGTTC
41702841 CAAAAATTCC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 9 0.31
16 18 0.62
17 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (15 bp):
TGTTCTAAACATGGT
Found at i:41705002 original size:20 final size:20
Alignment explanation
Indices: 41704977--41705028 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
41704967 GAGGCAATGC
*
41704977 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGAG
*
41704997 ACACGCCTGTGTGCTTTGAG
1 ACACGCCCGTGTGCTTTGAG
41705017 ACACGCCCGTGT
1 ACACGCCCGTGT
41705029 CCCCTACTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.31, G:0.31, T:0.25
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTGAG
Found at i:41705122 original size:13 final size:13
Alignment explanation
Indices: 41705104--41705128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41705094 CCAAGCACAC
41705104 GCCCGTGTCCTTG
1 GCCCGTGTCCTTG
41705117 GCCCGTGTCCTT
1 GCCCGTGTCCTT
41705129 CACACGGCCT
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:0.00, C:0.40, G:0.28, T:0.32
Consensus pattern (13 bp):
GCCCGTGTCCTTG
Found at i:41706740 original size:20 final size:20
Alignment explanation
Indices: 41706715--41706766 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
41706705 GAGGCAATGC
*
41706715 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGAG
*
41706735 ACACGCCTGTGTGCTTTGAG
1 ACACGCCCGTGTGCTTTGAG
41706755 ACACGCCCGTGT
1 ACACGCCCGTGT
41706767 CCCCTACTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.31, G:0.31, T:0.25
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTGAG
Found at i:41706860 original size:13 final size:13
Alignment explanation
Indices: 41706842--41706866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41706832 CCAAGCACAC
41706842 GCCCGTGTCCTTG
1 GCCCGTGTCCTTG
41706855 GCCCGTGTCCTT
1 GCCCGTGTCCTT
41706867 CACACGGCCT
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:0.00, C:0.40, G:0.28, T:0.32
Consensus pattern (13 bp):
GCCCGTGTCCTTG
Found at i:41712910 original size:11 final size:10
Alignment explanation
Indices: 41712884--41712917 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41712874 GGAGAGCACC
*
41712884 AAGAGTCAAA
1 AAGAGCCAAA
41712894 AAGAGCCAAA
1 AAGAGCCAAA
41712904 AACGAGCCAAA
1 AA-GAGCCAAA
41712915 AAG
1 AAG
41712918 GGACAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.59, C:0.18, G:0.21, T:0.03
Consensus pattern (10 bp):
AAGAGCCAAA
Found at i:41715256 original size:23 final size:23
Alignment explanation
Indices: 41715217--41715260 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
41715207 CTGATGGATA
*
41715217 GTAAGCTCTATTTAGTTGAAACG
1 GTAAGCTCTATTGAGTTGAAACG
41715240 GTAAGCTCTGA-TGAGTTGAAA
1 GTAAGCTCT-ATTGAGTTGAAA
41715261 ATAGTAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (23 bp):
GTAAGCTCTATTGAGTTGAAACG
Found at i:41725350 original size:28 final size:28
Alignment explanation
Indices: 41725318--41725373 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
41725308 ATGGTTGACA
41725318 AAATTTTAGTTTTACGTAAACAAATGTT
1 AAATTTTAGTTTTACGTAAACAAATGTT
41725346 AAATTTTAGTTTTACGTAAACAAATGTT
1 AAATTTTAGTTTTACGTAAACAAATGTT
41725374 TTTGATAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (28 bp):
AAATTTTAGTTTTACGTAAACAAATGTT
Found at i:41728820 original size:46 final size:46
Alignment explanation
Indices: 41728753--41728919 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
41728743 ATGTAACCCG
41728753 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCA
* * *
41728799 TCCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCA
* * * * * * *
41728849 T-C-TCA-CGAACTCGGACTCAACTCTACAAACTCAGACATTCGCA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCA
*
41728892 TCCATAAGTGAACTCGGACTCAACTCAA
1 TCCATAAGCGAACTCGGACTCAACTCAA
41728920 TAAGCTCAGA
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 53 0.55
47 23 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (46 bp):
TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCA
Found at i:41728869 original size:93 final size:93
Alignment explanation
Indices: 41728761--41728933 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
41728751 CGTCCATAAG
* * * * *
41728761 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAACTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
41728826 ATGAGCTCGGATGCCTAGTTACATCTCA
66 ATAAGCTCAGATGCCTAGTTACATCTCA
*
41728854 CGAACTCGGACTCAACTCTACAAACTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAACTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41728919 ATAAGCTCAGATGCC
66 ATAAGCTCAGATGCC
41728934 CAAATATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAACTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ATAAGCTCAGATGCCTAGTTACATCTCA
Found at i:41736049 original size:46 final size:46
Alignment explanation
Indices: 41735982--41736151 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 46
41735972 TAACCCGTCT
* * *
41735982 ATAAGTGGACTCAGACTCAACTCAATGAGCTCGGGCGTTCGCATTC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATTC
* *
41736028 ATAAGTGAACTCGGACTCAACTCAACGAACTCGGATGCCTAGTT-ACA-TC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCATTC
* * * * * * *
41736077 -TCA-CGAACTCGGACTCAACTCAATGAGCTTGGACATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATTC
41736121 ATAAGTGAACTCGGACTCAACTCAACGAGCT
1 ATAAGTGAACTCGGACTCAACTCAACGAGCT
41736152 TCGATGCCCA
Statistics
Matches: 98, Mismatches: 17, Indels: 18
0.74 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 54 0.55
47 25 0.26
48 3 0.03
49 3 0.03
50 2 0.02
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATTC
Found at i:41738512 original size:40 final size:40
Alignment explanation
Indices: 41738356--41738502 Score: 249
Period size: 40 Copynumber: 3.7 Consensus size: 40
41738346 ATATATTATA
* *
41738356 TATATTCGGGTCAAATCCCGTAGGCTTCATGCTGGTAATG
1 TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATG
*
41738396 TATATCCGAGTCAAATCCCGCAGGCTTCATGCTGGTAATG
1 TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATG
*
41738436 TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
1 TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATG
*
41738476 TATATCCGGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTCAAATCCCGCAGGCTT
41738503 AGTATTGGTA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (40 bp):
TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATG
Found at i:41738512 original size:80 final size:78
Alignment explanation
Indices: 41738356--41738523 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 78
41738346 ATATATTATA
* *
41738356 TATATTCGGGTCAAATCCCGTAGGCTTCATGCTGGTAATGTATATCCGAGTCAAATCCCGCAGGC
1 TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATGTATATCCGAGTCAAATCCCGCAGGC
*
41738421 TTCATGCTGGTAAT
66 TTCATACTGGT-AT
* * *
41738435 GTATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATGTATATCCGGGTTAAATCCCGCAGG
1 -TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATGTATATCCGAGTCAAATCCCGCAGG
*
41738500 CTT-AGTATTGGTAT
65 CTTCA-TACTGGTAT
41738514 TATATCCGGG
1 TATATCCGGG
41738524 CTTAAAGTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 10 0.12
79 3 0.04
80 67 0.84
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (78 bp):
TATATCCGGGTCAAATCCCGCAGGCTTCATGCTGGTAATGTATATCCGAGTCAAATCCCGCAGGC
TTCATACTGGTAT
Found at i:41744255 original size:46 final size:46
Alignment explanation
Indices: 41744202--41744323 Score: 158
Period size: 45 Copynumber: 2.7 Consensus size: 46
41744192 GTAACTTCAA
* * * * * *
41744202 CCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGTGTTTTTA-T
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-CTATCTTCAGT
41744248 CCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGT
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGT
*
41744294 -CTGCTCCACTGCAACTTTAGGGAGATAAGA
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGA
41744324 CTACAATTGC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
45 34 0.50
46 34 0.50
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (46 bp):
CCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGT
Found at i:41744316 original size:45 final size:46
Alignment explanation
Indices: 41744196--41744323 Score: 161
Period size: 46 Copynumber: 2.8 Consensus size: 46
41744186 GAATTGGTAA
* * * * *
41744196 CTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGTGT
1 CTTCATCCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCTAT
* *
41744242 TTTTATCCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-CTAT
1 CTTCATCCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCTAT
*
41744287 CTTCAGT-CTGCTCCACTGCAACTTTAGGGAGATAAGA
1 CTTCA-TCCTGCTCCACTGCAACTTCAGGGAGATAAGA
41744324 CTACAATTGC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
45 34 0.48
46 37 0.52
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (46 bp):
CTTCATCCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTCTAT
Found at i:41744568 original size:177 final size:175
Alignment explanation
Indices: 41744249--41744790 Score: 586
Period size: 177 Copynumber: 3.1 Consensus size: 175
41744239 TGTTTTTATC
* ** * * * *
41744249 CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACTTTAG
1 CTGCTCCACTACTGCTT-AGGGAGATAAGATCTGCAATCTTCAGTCTGCTTC-CTGCAACCTCAG
* * * *
41744314 GGAGATAAGACTACAATTGCCAACTTTCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTGGCTAA
64 GGAGATAAGACTACAATT-TCAACCTGCTCTCTTGCTACCTCTGAGAGATAAGGCTAGTGGCTAA
* *
41744379 AATCTTCTCCATTACCGATACATAGAGATAAGATTCGCCGTCTTTGAT
128 AATCTGCTCCATTGCCGATACATAGAGATAAGATTCGCCGTCTTTGAT
* * * * *
41744427 TTGCTCCACTATTGCTTAGGGAGATAAGACCTGCCATCTTCAGTCTGCTTCCTTGCTACCTCAGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAGTCTGCTTCC-TGCAACCTCAGG
* * *
41744492 AAGATAAGACTACAATCTTTAACCTGCTCTCTTGCTACCTCTGAGAAATAAGGCTAGTGGCTAAA
65 GAGATAAGACTACAAT-TTCAACCTGCTCTCTTGCTACCTCTGAGAGATAAGGCTAGTGGCTAAA
* * *
41744557 ATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGAT
129 ATCTGCTCCATTGCCGATACATAGAGATAAGATTCGCCGTCTTTGAT
* * * * *
41744604 CCGCTCCGCTACTGCTTAAGGAGATAAGATCTTCAATCTTCAGTCTGCTCTACTGCAACCTCAGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAGTCTGCT-TCCTGCAACCTCAGG
*** *** * * * *
41744669 GAGATAAGACTTGTATATTGGGCCTGCTCTAC-TGC-AACTTTAGAGAGATAAGGCTTGTGGCTT
65 GAGATAAGACTACAAT-TTCAACCTGCTCT-CTTGCTACCTCT-GAGAGATAAGGCTAGTGGCTA
* ** *
41744732 AAATCTGCTCCATTGCCAATACA-AGGAGATAAGATTTTCCGTCTTTGGT
127 AAATCTGCTCCATTGCCGATACATA-GAGATAAGATTCGCCGTCTTTGAT
41744781 CTGCTCCACT
1 CTGCTCCACT
41744791 GCAACTTTAG
Statistics
Matches: 303, Mismatches: 55, Indels: 13
0.82 0.15 0.04
Matches are distributed among these distances:
176 5 0.02
177 282 0.93
178 16 0.05
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (175 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAGTCTGCTTCCTGCAACCTCAGGG
AGATAAGACTACAATTTCAACCTGCTCTCTTGCTACCTCTGAGAGATAAGGCTAGTGGCTAAAAT
CTGCTCCATTGCCGATACATAGAGATAAGATTCGCCGTCTTTGAT
Found at i:41744740 original size:44 final size:44
Alignment explanation
Indices: 41744692--41744894 Score: 114
Period size: 44 Copynumber: 4.7 Consensus size: 44
41744682 TATATTGGGC
*
41744692 CTGCTCTACTGCAACTTTAGAGAGATAAGGCTTGTGGCTTAAAT
1 CTGCTCCACTGCAACTTTAGAGAGATAAGGCTTGTGGCTTAAAT
* ** * * * ***
41744736 CTGCTCCATTGCCAA-TACA-AGGAGATAA-GATTTTCCGTCTTTGGT
1 CTGCTCCACTG-CAACTTTAGA-GAGATAAGGCTTGT--GGCTTAAAT
* * * * ** * *
41744781 CTGCTCCACTGCAACTTTAGGGAAATAAGACCTGTCACTTCAAC
1 CTGCTCCACTGCAACTTTAGAGAGATAAGGCTTGTGGCTTAAAT
* * *
41744825 CTGCTCCAGTGCAACTTTAGGGAGATAAGGC-T-T-GC-TATTAT
1 CTGCTCCACTGCAACTTTAGAGAGATAAGGCTTGTGGCTTA-AAT
*
41744866 CTGCTCTACTGCAACTTTAGAGAGATAAG
1 CTGCTCCACTGCAACTTTAGAGAGATAAG
41744895 ATTTGTTTAT
Statistics
Matches: 116, Mismatches: 35, Indels: 19
0.68 0.21 0.11
Matches are distributed among these distances:
40 1 0.01
41 28 0.24
42 1 0.01
43 6 0.05
44 52 0.45
45 26 0.22
46 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTTAGAGAGATAAGGCTTGTGGCTTAAAT
Found at i:41744849 original size:177 final size:176
Alignment explanation
Indices: 41744249--41744894 Score: 578
Period size: 177 Copynumber: 3.7 Consensus size: 176
41744239 TGTTTTTATC
* * * * *
41744249 CTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-CTATCTTCAGTCTGCTCCACTGCAACTTTA
1 CTGCTCCACTACAACTT-AGGGAGATAAGACCTGTCAATCTTCAGTCTGCTCCACTGCAACCTCA
** * * * * *
41744313 GGGAGATAAGACTACA-ATTGCCAACTTTCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTGGCT
65 GGGAGATAAGACTTGATATTG---ACCTGCTCTCTTGCAACTTTAGAGAGATAAGGCTAGTGGCT
* *
41744377 AAAATCTTCTCCATTACCGATACATA-GAGATAAGATTCGCCGTCTTTGAT
127 AAAATCTGCTCCATTGCCGATACA-AGGAGATAAGATTCGCCGTCTTTGAT
* *** * * *
41744427 TTGCTCCACTATTGCTTAGGGAGATAAGACCTG-CCATCTTCAGTCTGCTTCC-TTGCTACCTCA
1 CTGCTCCACTACAACTTAGGGAGATAAGACCTGTCAATCTTCAGTCTGC-TCCACTGCAACCTCA
* ** * * * * *
41744490 GGAAGATAAGACTACAATCTTTAACCTGCTCTCTTGCTACCTCT-GAGAAATAAGGCTAGTGGCT
65 GGGAGATAAGACT-TGAT-ATTGACCTGCTCTCTTGC-AACTTTAGAGAGATAAGGCTAGTGGCT
* * *
41744554 AAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGAT
127 AAAATCTGCTCCATTGCCGATACAAGGAGATAAGATTCGCCGTCTTTGAT
* * ** * * *
41744604 CCGCTCCGCTACTGCTTAAGGAGATAAGATCT-TCAATCTTCAGTCTGCTCTACTGCAACCTCAG
1 CTGCTCCACTACAACTTAGGGAGATAAGACCTGTCAATCTTCAGTCTGCTCCACTGCAACCTCAG
* * *
41744668 GGAGATAAGACTTGTATATTGGGCCTGCTCTAC-TGCAACTTTAGAGAGATAAGGCTTGTGGCTT
66 GGAGATAAGACTTG-ATATT-GACCTGCTCT-CTTGCAACTTTAGAGAGATAAGGCTAGTGGCTA
* ** *
41744732 AAATCTGCTCCATTGCCAATACAAGGAGATAAGATTTTCCGTCTTTGGT
128 AAATCTGCTCCATTGCCGATACAAGGAGATAAGATTCGCCGTCTTTGAT
* * ** * * *
41744781 CTGCTCCACTGCAACTTTAGGGAAATAAGACCTGTC-A-CTTCAACCTGCTCCAGTGCAACTTTA
1 CTGCTCCACTACAAC-TTAGGGAGATAAGACCTGTCAATCTTCAGTCTGCTCCACTGCAACCTCA
* * *
41744844 GGGAGATAAGGCTTGCTATT-ATCTGCTCTAC-TGCAACTTTAGAGAGATAAG
65 GGGAGATAAGACTTGATATTGACCTGCTCT-CTTGCAACTTTAGAGAGATAAG
41744895 ATTTGTTTAT
Statistics
Matches: 379, Mismatches: 75, Indels: 32
0.78 0.15 0.07
Matches are distributed among these distances:
174 29 0.08
176 12 0.03
177 301 0.79
178 33 0.09
179 2 0.01
180 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (176 bp):
CTGCTCCACTACAACTTAGGGAGATAAGACCTGTCAATCTTCAGTCTGCTCCACTGCAACCTCAG
GGAGATAAGACTTGATATTGACCTGCTCTCTTGCAACTTTAGAGAGATAAGGCTAGTGGCTAAAA
TCTGCTCCATTGCCGATACAAGGAGATAAGATTCGCCGTCTTTGAT
Found at i:41744882 original size:41 final size:43
Alignment explanation
Indices: 41744780--41745035 Score: 133
Period size: 44 Copynumber: 5.7 Consensus size: 43
41744770 CCGTCTTTGG
*
41744780 TCTGCTCCACTGCAACTTTAGGGAAATAAGACCTGTCACTTCAA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGACCTGTCACTT-AA
* * * *
41744824 CCTGCTCCAGTGCAACTTTAGGGAGATAAGGCTTG-CTA-TT-A
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGACCTGTC-ACTTAA
* * ** *
41744865 TCTGCTCTACTGCAACTTTAGAGAGATAAGATTTGTTTATTTATAGCTTCAA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGACCTG------T-CA-CTT-AA
** * * * * * *
41744917 TCTATTCCACTACAACTTCAGGGAAATAAGA-TTCTCTATCTTCAG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGACCTGTC-A-CTT-AA
* *
41744962 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGACACTTCAA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGACCTGTCACTT-AA
* * * *
41745006 CCTACTCCACTACAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAG
41745036 GTTTGTAATC
Statistics
Matches: 163, Mismatches: 34, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
41 30 0.18
43 3 0.02
44 63 0.39
45 35 0.21
46 2 0.01
48 1 0.01
50 2 0.01
51 2 0.01
52 25 0.15
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTTAGGGAGATAAGACCTGTCACTTAA
Found at i:41745020 original size:89 final size:89
Alignment explanation
Indices: 41744911--41745079 Score: 225
Period size: 89 Copynumber: 1.9 Consensus size: 89
41744901 TTATTTATAG
* * *
41744911 CTTCAATCTATTCCACTACAACTTCAGGGAAATAAGATTCTCT-ATCTTC-AGTCTGCTCCACTG
1 CTTCAACCTACTCCACTACAACTTCAGGGAAATAAGATT-TCTAATCTTCGA-TCTACTCCACTG
*
41744974 CAACTTCAGGGAGATAAGACCTGACA
64 CAACTTCAAGGAGATAAGACCTGACA
* * * * *
41745000 CTTCAACCTACTCCACTACAACTTCAGGGAGATAAGGTTTGTAATCTTCGATCTATTTCACTGCA
1 CTTCAACCTACTCCACTACAACTTCAGGGAAATAAGATTTCTAATCTTCGATCTACTCCACTGCA
41745065 ACTTCAAGGAGATAA
66 ACTTCAAGGAGATAA
41745080 AATCTGACTT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 2 0.03
89 66 0.96
90 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (89 bp):
CTTCAACCTACTCCACTACAACTTCAGGGAAATAAGATTTCTAATCTTCGATCTACTCCACTGCA
ACTTCAAGGAGATAAGACCTGACA
Found at i:41745022 original size:44 final size:44
Alignment explanation
Indices: 41744911--41745084 Score: 154
Period size: 45 Copynumber: 3.9 Consensus size: 44
41744901 TTATTTATAG
* * *
41744911 CTTCAATCTATTCCACTACAACTTCAGGGAAATAAGATTCTCTAT
1 CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGA-TCTCTAA
* * *
41744956 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-C-CTGACA
1 CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATCTCT-A-A
* * * *
41745000 CTTCAACCTACTCCACTACAACTTCAGGGAGATAAGGTTTGTAA
1 CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATCTCTAA
* * * * * *
41745044 TCTTCGATCTATTTCACTGCAACTTCAAGGAGATAAAATCT
1 -CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATCT
41745085 GACTTCATCG
Statistics
Matches: 102, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 33 0.32
45 64 0.63
46 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (44 bp):
CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATCTCTAA
Found at i:41746257 original size:3 final size:3
Alignment explanation
Indices: 41746249--41746293 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
41746239 TCGGCCTCTC
41746249 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
41746294 TTTTAAGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:41752067 original size:8 final size:8
Alignment explanation
Indices: 41752049--41752081 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
41752039 TGAAAATCTA
41752049 ATGCAAATG
1 ATGC-AATG
41752058 ATGCAATG
1 ATGCAATG
41752066 ATGCAATG
1 ATGCAATG
41752074 ATGCAATG
1 ATGCAATG
41752082 CAATACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (8 bp):
ATGCAATG
Found at i:41754522 original size:21 final size:19
Alignment explanation
Indices: 41754497--41754548 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
41754487 TTTAAAAGCA
41754497 ATAAATTATATATAAATAGAT
1 ATAAATTATATAT-AA-AGAT
* * *
41754518 TTAAAATATATATAACGAT
1 ATAAATTATATATAAAGAT
41754537 ATAAATTATATA
1 ATAAATTATATA
41754549 CAAAACAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.50
20 2 0.08
21 11 0.42
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
ATAAATTATATATAAAGAT
Found at i:41754636 original size:14 final size:15
Alignment explanation
Indices: 41754608--41754636 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41754598 AGTTTAATAT
41754608 AAATAATATATGTAA
1 AAATAATATATGTAA
41754623 AAATAATA-ATGTAA
1 AAATAATATATGTAA
41754637 TATTTGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AAATAATATATGTAA
Found at i:41755486 original size:10 final size:10
Alignment explanation
Indices: 41755456--41755495 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
41755446 CTCAAACAAT
*
41755456 AAACTCAAAG
1 AAACTTAAAG
*
41755466 AAAACTGAAAG
1 -AAACTTAAAG
41755477 AAACTTAAAG
1 AAACTTAAAG
41755487 AAACTTAAA
1 AAACTTAAA
41755496 TCAGAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (10 bp):
AAACTTAAAG
Found at i:41755859 original size:24 final size:24
Alignment explanation
Indices: 41755831--41755893 Score: 101
Period size: 24 Copynumber: 2.6 Consensus size: 24
41755821 ATTTGTTTTA
41755831 TTTGGGTATT-GGGTTATGGGTTTG
1 TTTGGGT-TTAGGGTTATGGGTTTG
41755855 TTTGGGTTTAGGGTTATGGGTTTG
1 TTTGGGTTTAGGGTTATGGGTTTG
*
41755879 TTTTGGTTTAGGGTT
1 TTTGGGTTTAGGGTT
41755894 TAGTTAGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (24 bp):
TTTGGGTTTAGGGTTATGGGTTTG
Found at i:41756869 original size:41 final size:41
Alignment explanation
Indices: 41756735--41756929 Score: 232
Period size: 41 Copynumber: 4.8 Consensus size: 41
41756725 AATAGGGTTT
**
41756735 TAGCGGCATTTTTGGTAAAACGCCGCTAAAAA-CAGAGCAA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAATCAGAGCAA
* * * *
41756775 TAGCGGCGTTTTTTTGTTAAAACACTGCTAAAAAT-AGAGCAA
1 TAGCGGCG--CTTTTGGTAAAACGCCGCTAAAAATCAGAGCAA
** * *
41756817 TAGCGATGCTTTTGGTAAAACGCCGCTAAAAGTCGGAGCAA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAATCAGAGCAA
* * *
41756858 TAGCTGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCAT
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAATCAGAGCAA
*
41756899 TAGCGGCGCTTTTGGTAAAACGCCGTTAAAA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
41756930 GTCATATAAC
Statistics
Matches: 130, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
40 27 0.21
41 69 0.53
42 34 0.26
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAATCAGAGCAA
Found at i:41757027 original size:53 final size:54
Alignment explanation
Indices: 41756942--41757057 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 54
41756932 CATATAACCC
* * * * *
41756942 CTAAAACCCTAAACCCTAAAAAATCATGAACACTGATCTATAACCCCTAAAATA
1 CTAAACCCCTAAACCCTAAAAAATCATAAACACTAAACTATAACCCCTAAAACA
* ** *
41756996 CTAAACCCCTGAACCCT-AAAAA-CACTAAACACTAAACTATAACTTCTAAAACC
1 CTAAACCCCTAAACCCTAAAAAATCA-TAAACACTAAACTATAACCCCTAAAACA
41757049 CTAAACCCC
1 CTAAACCCC
41757058 AAAAAACATC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
52 2 0.04
53 35 0.67
54 15 0.29
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.19
Consensus pattern (54 bp):
CTAAACCCCTAAACCCTAAAAAATCATAAACACTAAACTATAACCCCTAAAACA
Found at i:41757194 original size:7 final size:7
Alignment explanation
Indices: 41757184--41757231 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
41757174 CGGCTTAATA
41757184 TTTAAGG
1 TTTAAGG
41757191 TTTAAGG
1 TTTAAGG
* *
41757198 TCTATGG
1 TTTAAGG
*
41757205 TTTAGGG
1 TTTAAGG
*
41757212 TTTTATGG
1 -TTTAAGG
41757220 TTTAAGG
1 TTTAAGG
41757227 TTTAA
1 TTTAA
41757232 TGGCCATGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:41757220 original size:15 final size:15
Alignment explanation
Indices: 41757184--41757234 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
41757174 CGGCTTAATA
*
41757184 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
41757198 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
41757213 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
41757228 TTAATGG
1 TTTATGG
41757235 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:41757842 original size:8 final size:8
Alignment explanation
Indices: 41757829--41757908 Score: 135
Period size: 8 Copynumber: 10.1 Consensus size: 8
41757819 AAATAAACTC
41757829 AAAAATTA
1 AAAAATTA
41757837 AAAAATTA
1 AAAAATTA
41757845 AAAAATT-
1 AAAAATTA
41757852 AAAAATTA
1 AAAAATTA
41757860 AAAAATTA
1 AAAAATTA
41757868 AAAAATTA
1 AAAAATTA
41757876 AAAAATTA
1 AAAAATTA
41757884 AAAAATTA
1 AAAAATTA
*
41757892 AAAACTTA
1 AAAAATTA
*
41757900 AAAATTTA
1 AAAAATTA
41757908 A
1 A
41757909 TATTTAATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
7 7 0.10
8 62 0.90
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATTA
Found at i:41757915 original size:23 final size:23
Alignment explanation
Indices: 41757829--41757905 Score: 136
Period size: 23 Copynumber: 3.3 Consensus size: 23
41757819 AAATAAACTC
41757829 AAAAATTAAAAAATTAAAAAATT
1 AAAAATTAAAAAATTAAAAAATT
41757852 AAAAATTAAAAAATTAAAAAATT
1 AAAAATTAAAAAATTAAAAAATT
*
41757875 AAAAAATTAAAAAATTAAAAACTT
1 -AAAAATTAAAAAATTAAAAAATT
41757899 AAAAATT
1 AAAAATT
41757906 TAATATTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
23 30 0.58
24 22 0.42
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAATTAAAAAATTAAAAAATT
Found at i:41760831 original size:23 final size:23
Alignment explanation
Indices: 41760801--41761128 Score: 260
Period size: 23 Copynumber: 14.3 Consensus size: 23
41760791 TGGCTGCTGT
41760801 TGTTTAAATGCTGCAAATTGAAG
1 TGTTTAAATGCTGCAAATTGAAG
*
41760824 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGCTGCAAATTGAAG
* *
41760847 TGTTTAAATGTTGTAAATTGAAG
1 TGTTTAAATGCTGCAAATTGAAG
* *
41760870 TGTTTAAGTACTGCAAATTGAAG
1 TGTTTAAATGCTGCAAATTGAAG
* *
41760893 TGTTTAACTACTGCAAATTGAAG
1 TGTTTAAATGCTGCAAATTGAAG
** *
41760916 TGTTTAGTTGCTGGAAATTG-AG
1 TGTTTAAATGCTGCAAATTGAAG
* *
41760938 ATGTTT-TATCGCTG-TAATTG-AG
1 -TGTTTAAAT-GCTGCAAATTGAAG
* * **
41760960 TTGTATAAATGTTGTTAATTG-AG
1 -TGTTTAAATGCTGCAAATTGAAG
41760983 ATG-TTAAAGTGCTGCAAATTGAAG
1 -TGTTTAAA-TGCTGCAAATTGAAG
*
41761007 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGCTGCAAATTGAAG
* ** * *
41761030 TGCTTAAATATTGTAAAATGAAG
1 TGTTTAAATGCTGCAAATTGAAG
* *
41761053 TGTTT-TATGAACTACAAATTGAAG
1 TGTTTAAATG--CTGCAAATTGAAG
** *
41761077 TGTTTAGTTGCTGGAAATTG-AG
1 TGTTTAAATGCTGCAAATTGAAG
*
41761099 ATGTTT-TATCGCTGCAAATTGAAG
1 -TGTTTAAAT-GCTGCAAATTGAAG
41761123 TGTTTA
1 TGTTTA
41761129 GTTGCTGGAA
Statistics
Matches: 249, Mismatches: 42, Indels: 27
0.78 0.13 0.08
Matches are distributed among these distances:
22 26 0.10
23 198 0.80
24 23 0.09
25 2 0.01
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.39
Consensus pattern (23 bp):
TGTTTAAATGCTGCAAATTGAAG
Found at i:41761057 original size:114 final size:114
Alignment explanation
Indices: 41760804--41761079 Score: 281
Period size: 114 Copynumber: 2.4 Consensus size: 114
41760794 CTGCTGTTGT
* * * * *
41760804 TTAAATGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAA
1 TTAAATACTGGAAAATGAAGTGTTT-TATGCTGTAAATTGAAGTGTATAAATGTTGTAAATTGAA
* * *
41760869 GTGTTTAAGTACTGCAAATTGAAGTGTTTAACTACTGCAAATTGAAGTGT
65 GTGTTAAAGTACTGCAAATTGAAGTGTTTAAATACTGCAAATTGAAGTGC
** * * *
41760919 TTAGTTGCTGGAAATTG-AGATGTTTTATCGCTGT-AATTG-AGTTGTATAAATGTTGTTAATTG
1 TTAAATACTGGAAAATGAAG-TGTTTTAT-GCTGTAAATTGAAG-TGTATAAATGTTGTAAATTG
* * *
41760981 -AGATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGC
63 AAG-TGTTAAAGTACTGCAAATTGAAGTGTTTAAATACTGCAAATTGAAGTGC
* * **
41761033 TTAAATATTGTAAAATGAAGTGTTTTATGAACTACAAATTGAAGTGT
1 TTAAATACTGGAAAATGAAGTGTTTTATG--CTGTAAATTGAAGTGT
41761080 TTAGTTGCTG
Statistics
Matches: 132, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
113 5 0.04
114 89 0.67
115 28 0.21
116 8 0.06
117 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (114 bp):
TTAAATACTGGAAAATGAAGTGTTTTATGCTGTAAATTGAAGTGTATAAATGTTGTAAATTGAAG
TGTTAAAGTACTGCAAATTGAAGTGTTTAAATACTGCAAATTGAAGTGC
Found at i:41761911 original size:44 final size:43
Alignment explanation
Indices: 41761806--41761968 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 43
41761796 TTTCATGACC
* * *
41761806 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGCT
1 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCACGACT
* *
41761849 TTTAGCGGCGTTTGTGGGAAAAGTACTGCTAAAGGTCACGACTT
1 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCACGAC-T
* * * * *
41761893 TTTAGCGGCGTTTGTGGGAAAAACACCGTTACATGTCGCGACT
1 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCACGACT
*
41761936 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAA
41761969 AGCCTAAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 67 0.65
44 36 0.35
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCACGACT
Found at i:41761967 original size:87 final size:87
Alignment explanation
Indices: 41761806--41761968 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
41761796 TTTCATGACC
* * * *
41761806 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGCTTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAACACCGCTAAAGGTCACGACTTTTAGCGGCGTTTGTGGGAAAA
* *
41761871 GTACTGCTAAAGGTCACGACTT
66 GCACCGCTAAAGGTCACGACTT
* * * *
41761893 TTTAGCGGCGTTTGTGGGAAAAACACCGTTACATGTCGCGACTTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAACACCGCTAAAGGTCACGACTTTTAGCGGCGTTTGTGGGAAAA
*
41761958 GCGCCGCTAAA
66 GCACCGCTAAA
41761969 AGCCTAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (87 bp):
TTTAGCGGCGTTTGTGGGAAAAACACCGCTAAAGGTCACGACTTTTAGCGGCGTTTGTGGGAAAA
GCACCGCTAAAGGTCACGACTT
Found at i:41764887 original size:25 final size:26
Alignment explanation
Indices: 41764835--41764903 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
41764825 TCACTCTTTC
*
41764835 GAGCT-ATGAACAGTAAGCTCCTCCT
1 GAGCTAATGAACAGTAAGCTCCTACT
* *
41764860 GAGCTAATGGACAGTAAGCT-CTATT
1 GAGCTAATGAACAGTAAGCTCCTACT
*
41764885 GAGCTAA--AACGGTAAGCTC
1 GAGCTAATGAACAGTAAGCTC
41764904 TGACGAGCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
23 9 0.24
25 15 0.41
26 13 0.35
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (26 bp):
GAGCTAATGAACAGTAAGCTCCTACT
Found at i:41764903 original size:23 final size:23
Alignment explanation
Indices: 41764843--41764948 Score: 81
Period size: 23 Copynumber: 4.4 Consensus size: 23
41764833 TCGAGCTATG
**
41764843 AACAGTAAGCTCCTCCTGAGCTAA
1 AACAGTAAGCT-CTATTGAGCTAA
*
41764867 TGGACAGTAAGCTCTATTGAGCTAA
1 --AACAGTAAGCTCTATTGAGCTAA
* *
41764892 AACGGTAAGCTCTGA-CGAGCTGAA
1 AACAGTAAGCTCT-ATTGAGCT-AA
* *
41764916 AATAGTAAGCTCT-TATGAGCTGA
1 AACAGTAAGCTCTAT-TGAGCTAA
41764939 AACAGTAAGC
1 AACAGTAAGC
41764949 CCCAACGAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
23 26 0.40
24 19 0.29
25 10 0.15
26 10 0.15
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (23 bp):
AACAGTAAGCTCTATTGAGCTAA
Found at i:41764923 original size:24 final size:24
Alignment explanation
Indices: 41764896--41764985 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
41764886 AGCTAAAACG
*
41764896 GTAAGCTCTGACGAGCTGAAAATA
1 GTAAGCTCTTACGAGCTGAAAATA
* *
41764920 GTAAGCTCTTATGAGCTG-AAACA
1 GTAAGCTCTTACGAGCTGAAAATA
* ** *
41764943 GTAAGCCCCAACGAGTTGAAAATA
1 GTAAGCTCTTACGAGCTGAAAATA
*
41764967 GTAATCTCTTACGAGCTGA
1 GTAAGCTCTTACGAGCTGA
41764986 TATATCGGTA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 17 0.33
24 34 0.67
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (24 bp):
GTAAGCTCTTACGAGCTGAAAATA
Found at i:41764926 original size:47 final size:47
Alignment explanation
Indices: 41764872--41764983 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
41764862 GCTAATGGAC
* * **
41764872 AGTAAGCTC-TATTGAGCTAAAACGGTAAGCTCTGACGAGCTGAAAAT
1 AGTAAGCTCTTA-TGAGCTAAAACAGTAAGCCCCAACGAGCTGAAAAT
* *
41764919 AGTAAGCTCTTATGAGCTGAAACAGTAAGCCCCAACGAGTTGAAAAT
1 AGTAAGCTCTTATGAGCTAAAACAGTAAGCCCCAACGAGCTGAAAAT
* *
41764966 AGTAATCTCTTACGAGCT
1 AGTAAGCTCTTATGAGCT
41764984 GATATATCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 54 0.96
48 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (47 bp):
AGTAAGCTCTTATGAGCTAAAACAGTAAGCCCCAACGAGCTGAAAAT
Found at i:41771063 original size:43 final size:44
Alignment explanation
Indices: 41770995--41771123 Score: 147
Period size: 46 Copynumber: 2.9 Consensus size: 44
41770985 CTTTTATTCA
* * *
41770995 TTCACCGGCATT-TCGCCTGCTAGGCTCG-AGGCCTGATATCAT-
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA-ATAATG
41771037 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAATG
1 TTCACCGGCATTATAGCCTGCTAGGCTCG-AAGGCCCGAATAATG
* * * *
41771082 TCTCACCGGCATAATAGCCTCCTAGGCTCAAAGGCTCGAATA
1 T-TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
41771124 TAATACCAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 12 0.16
43 15 0.20
44 4 0.05
45 19 0.25
46 25 0.33
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAATG
Found at i:41771172 original size:38 final size:38
Alignment explanation
Indices: 41771121--41771278 Score: 217
Period size: 38 Copynumber: 4.1 Consensus size: 38
41771111 AAAGGCTCGA
* * * *
41771121 ATATAATACCAGCACTAGGCCTACTGGATTTAACCCGG
1 ATATAATACCAGCACAAAGCCTGCGGGATTTAACCCGG
*
41771159 ATATAATACCAGCACAAAGCCTGTGGGATTTAACCCGG
1 ATATAATACCAGCACAAAGCCTGCGGGATTTAACCCGG
*
41771197 ATATATTACCAGCACAAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACAAAGCCTGCGGGATTTAACCCGG
* * *
41771235 TTATATTACCAGCACGAAGCCTGCGGGATTTTAAGCCCGG
1 ATATAATACCAGCACAAAGCCTGCGGGA-TTTAA-CCCGG
41771275 ATAT
1 ATAT
41771279 CATATTTCGA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 95 0.88
39 5 0.05
40 8 0.07
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (38 bp):
ATATAATACCAGCACAAAGCCTGCGGGATTTAACCCGG
Found at i:41779063 original size:27 final size:27
Alignment explanation
Indices: 41779032--41779164 Score: 185
Period size: 27 Copynumber: 4.9 Consensus size: 27
41779022 TACCAAAGGG
*
41779032 TAGAATTACTGTTTTACCCTTGATTTA
1 TAGAATTACTGTTTTACCCTCGATTTA
41779059 TAGAATTACTGTTTTACCCTCGATTTA
1 TAGAATTACTGTTTTACCCTCGATTTA
* *
41779086 CAAAATTACTGTTTTACCCTCGATTTA
1 TAGAATTACTGTTTTACCCTCGATTTA
* ** *
41779113 TAAAATTACCATTTTACCCTTGATTTA
1 TAGAATTACTGTTTTACCCTCGATTTA
* *
41779140 CAGAATTACCGTTTTACCCTCGATT
1 TAGAATTACTGTTTTACCCTCGATT
41779165 GTGAAATTAC
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 95 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
TAGAATTACTGTTTTACCCTCGATTTA
Found at i:41779186 original size:27 final size:27
Alignment explanation
Indices: 41779163--41779292 Score: 147
Period size: 27 Copynumber: 4.8 Consensus size: 27
41779153 TTACCCTCGA
*
41779163 TTGTGAAATTACTAAAATACCCCT-GT
1 TTGTGAAATTACCAAAATACCCCTAGT
**
41779189 AGGAT-AGAATTACCAAAATACCCCTAGT
1 TTG-TGA-AATTACCAAAATACCCCTAGT
* *
41779217 TTGTAAAATTACCAAAATACCCTTAGT
1 TTGTGAAATTACCAAAATACCCCTAGT
* * *
41779244 TTGTAAAATTACCAAAATACCACTGGT
1 TTGTGAAATTACCAAAATACCCCTAGT
*
41779271 TTGTGAAATTACCGAAATACCC
1 TTGTGAAATTACCAAAATACCC
41779293 TTATGTTCCG
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.02
27 82 0.93
28 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (27 bp):
TTGTGAAATTACCAAAATACCCCTAGT
Found at i:41779237 original size:54 final size:54
Alignment explanation
Indices: 41779163--41779292 Score: 163
Period size: 54 Copynumber: 2.4 Consensus size: 54
41779153 TTACCCTCGA
* * *
41779163 TTGTGAAATTACTAAAATACCCCT-GTAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCAAAATACCCCTAGTAGG-TAAAATTACCAAAATACCACTAGT
* * ** *
41779217 TTGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTGGT
1 TTGTGAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
*
41779271 TTGTGAAATTACCGAAATACCC
1 TTGTGAAATTACCAAAATACCC
41779293 TTATGTTCCG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 62 0.95
55 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (54 bp):
TTGTGAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
Found at i:41780129 original size:25 final size:25
Alignment explanation
Indices: 41780091--41780160 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41780081 AGGAAGTGCT
* *
41780091 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
41780116 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
41780141 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
41780161 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:41780173 original size:24 final size:24
Alignment explanation
Indices: 41780090--41780185 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 24
41780080 GAGGAAGTGC
*
41780090 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAGTTTA-T
* *
41780115 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
41780139 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
41780163 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
41780186 ATATGATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 43 0.72
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:41780184 original size:50 final size:50
Alignment explanation
Indices: 41780091--41780185 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
41780081 AGGAAGTGCT
**
41780091 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
* **
41780141 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
41780186 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:41780478 original size:29 final size:28
Alignment explanation
Indices: 41780444--41780498 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
41780434 AGACTGAATT
* *
41780444 AGGGCTTAGGCCCATACTGCTACTGTTTA
1 AGGGCTAAGGCCCAGACTG-TACTGTTTA
41780473 AGGGCTAAGGCCCAGACTGTACTGTT
1 AGGGCTAAGGCCCAGACTGTACTGTT
41780499 ACTAAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (28 bp):
AGGGCTAAGGCCCAGACTGTACTGTTTA
Found at i:41782664 original size:26 final size:27
Alignment explanation
Indices: 41782605--41782668 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
41782595 ATTACTAAAG
* *
41782605 TACCCTTGATTTATAGAATCACTATTT
1 TACCCTCGATTTACAGAATCACTATTT
* *
41782632 TACCCTCGATTTACA-AATTACTGTTT
1 TACCCTCGATTTACAGAATCACTATTT
41782658 TACCCTCGATT
1 TACCCTCGATT
41782669 GTGAAATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATCACTATTT
Found at i:41782687 original size:26 final size:26
Alignment explanation
Indices: 41782561--41782688 Score: 66
Period size: 26 Copynumber: 4.8 Consensus size: 26
41782551 AATACTTTAG
* * *
41782561 TTTACCAATTACAGAAATGCCCTCGA
1 TTTACAAATTACTGAAATACCCTCGA
*
41782587 CTTGTA-AAATTACT-AAAGTACCCTTGA
1 -TT-TACAAATTACTGAAA-TACCCTCGA
* * **
41782614 TTTATAGAATCACT-ATTTTACCCTCGA
1 TTTACA-AATTACTGA-AATACCCTCGA
***
41782641 TTTACAAATTACTGTTTTACCCTCGA
1 TTTACAAATTACTGAAATACCCTCGA
*
41782667 TTGT-GAAATTACTGAAATACCC
1 TT-TACAAATTACTGAAATACCC
41782689 CTATAGGGTA
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
25 2 0.03
26 39 0.49
27 36 0.46
28 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (26 bp):
TTTACAAATTACTGAAATACCCTCGA
Found at i:41782956 original size:26 final size:27
Alignment explanation
Indices: 41782897--41782960 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
41782887 ATTACTAAAG
* *
41782897 TACCCTTGATTTATAGAATCACTATTT
1 TACCCTCGATTTACAGAATCACTATTT
* *
41782924 TACCCTCGATTTACA-AATTACTGTTT
1 TACCCTCGATTTACAGAATCACTATTT
41782950 TACCCTCGATT
1 TACCCTCGATT
41782961 GTGAAATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATCACTATTT
Found at i:41782982 original size:292 final size:292
Alignment explanation
Indices: 41782458--41783041 Score: 1141
Period size: 292 Copynumber: 2.0 Consensus size: 292
41782448 CATATTTGTG
*
41782458 GCTAGATTTGGACTAAAAGGGCCACACGAGCGTGTGGGCCTATTTGGGCTGAGAAAGGGCTTTAG
1 GCTAGATTTGGACTAAAAGGGCCACACGAGCGTGTGGGCCCATTTGGGCTGAGAAAGGGCTTTAG
41782523 GGCCATTCGTATTGTTATCCCTGTTTAGAATACTTTAGTTTACCAATTACAGAAATGCCCTCGAC
66 GGCCATTCGTATTGTTATCCCTGTTTAGAATACTTTAGTTTACCAATTACAGAAATGCCCTCGAC
41782588 TTGTAAAATTACTAAAGTACCCTTGATTTATAGAATCACTATTTTACCCTCGATTTACAAATTAC
131 TTGTAAAATTACTAAAGTACCCTTGATTTATAGAATCACTATTTTACCCTCGATTTACAAATTAC
41782653 TGTTTTACCCTCGATTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATACCCCT
196 TGTTTTACCCTCGATTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATACCCCT
41782718 AGTTTGTAAAATTACCAAAATACCACTGGTTT
261 AGTTTGTAAAATTACCAAAATACCACTGGTTT
*
41782750 GCTAGATTTGGGCTAAAAGGGCCACACGAGCGTGTGGGCCCATTTGGGCTGAGAAAGGGCTTTAG
1 GCTAGATTTGGACTAAAAGGGCCACACGAGCGTGTGGGCCCATTTGGGCTGAGAAAGGGCTTTAG
41782815 GGCCATTCGTATTGTTATCCCTGTTTAGAATACTTTAGTTTACCAATTACAGAAATGCCCTCGAC
66 GGCCATTCGTATTGTTATCCCTGTTTAGAATACTTTAGTTTACCAATTACAGAAATGCCCTCGAC
41782880 TTGTAAAATTACTAAAGTACCCTTGATTTATAGAATCACTATTTTACCCTCGATTTACAAATTAC
131 TTGTAAAATTACTAAAGTACCCTTGATTTATAGAATCACTATTTTACCCTCGATTTACAAATTAC
41782945 TGTTTTACCCTCGATTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATACCCCT
196 TGTTTTACCCTCGATTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATACCCCT
*
41783010 AGTTTGTAAAATTACCAAAATATCACTGGTTT
261 AGTTTGTAAAATTACCAAAATACCACTGGTTT
41783042 CTGAAATTAC
Statistics
Matches: 289, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
292 289 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (292 bp):
GCTAGATTTGGACTAAAAGGGCCACACGAGCGTGTGGGCCCATTTGGGCTGAGAAAGGGCTTTAG
GGCCATTCGTATTGTTATCCCTGTTTAGAATACTTTAGTTTACCAATTACAGAAATGCCCTCGAC
TTGTAAAATTACTAAAGTACCCTTGATTTATAGAATCACTATTTTACCCTCGATTTACAAATTAC
TGTTTTACCCTCGATTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATACCCCT
AGTTTGTAAAATTACCAAAATACCACTGGTTT
Found at i:41783022 original size:27 final size:27
Alignment explanation
Indices: 41782992--41783115 Score: 110
Period size: 27 Copynumber: 4.6 Consensus size: 27
41782982 TATAGGGTAG
41782992 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * * *
41783019 AATTACCAAAATATCACTGGTTTCTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
41783046 AATTACCGAAATA-CCCTCAATTTGTGA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
41783073 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
41783100 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
41783116 TTGACTTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
26 5 0.06
27 69 0.88
28 4 0.05
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:41783103 original size:54 final size:55
Alignment explanation
Indices: 41782992--41783172 Score: 149
Period size: 54 Copynumber: 3.3 Consensus size: 55
41782982 TATAGGGTAG
* * * * *
41782992 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATATCACTGGTTTCTGA
1 AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTCTAA
* *
41783046 AATTACCGAAATACCCTC-AATTTGTGAAATTACCAAAATACCCCTGATTTAC-AA
1 AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTT-CTAA
* * * * * *
41783100 AATTACAGAAATACCCT-TGACTTTTTAAAAATTA-TAGAAATACCATTGGTTTAC-AA
1 AATTACCGAAATACCCTCT-AATTTGT-AAAATTACCA-AAATACCACTGATTT-CTAA
*
41783156 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
41783173 TGGTTTGTAG
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
54 59 0.56
55 8 0.08
56 38 0.36
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (55 bp):
AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTCTAA
Found at i:41783166 original size:27 final size:27
Alignment explanation
Indices: 41783072--41783178 Score: 101
Period size: 27 Copynumber: 3.9 Consensus size: 27
41783062 TCAATTTGTG
** * *
41783072 AAATTACCAAAATACCCCTGATTTACA
1 AAATTACTGAAATACCCTTGGTTTACA
* *
41783099 AAATTACAGAAATACCCTTGACTTTTTA-A
1 AAATTACTGAAATACCCTTG---GTTTACA
*
41783128 AAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACT-GAAATACCCTTGGTTTACA
41783155 AAATTACTGAAATACCCTTGGTTT
1 AAATTACTGAAATACCCTTGGTTT
41783179 GTAGATTTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.06
27 39 0.59
28 1 0.02
29 18 0.27
30 4 0.06
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACTGAAATACCCTTGGTTTACA
Found at i:41783296 original size:27 final size:26
Alignment explanation
Indices: 41783219--41783296 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
41783209 AAATGACTAA
* *
41783219 AATACCCCTAATAGGTAAAAAGACCGT
1 AATACCCCTTAT-GGTAAAATGACCGT
* *
41783246 AA-AGCCCCTATAGGGTAAAGTGACCGT
1 AATA-CCCCT-TATGGTAAAATGACCGT
41783273 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCT-TATGGTAAAATGAC
41783297 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 38 0.93
28 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (26 bp):
AATACCCCTTATGGTAAAATGACCGT
Found at i:41784144 original size:25 final size:25
Alignment explanation
Indices: 41784106--41784175 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41784096 AGGAAGTGCT
* *
41784106 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
41784131 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
41784156 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
41784176 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:41784188 original size:24 final size:24
Alignment explanation
Indices: 41784105--41784200 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 24
41784095 GAGGAAGTGC
*
41784105 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAGTTTA-T
* *
41784130 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
41784154 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
41784178 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
41784201 ATATGATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 43 0.72
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:41784199 original size:50 final size:50
Alignment explanation
Indices: 41784106--41784200 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
41784096 AGGAAGTGCT
**
41784106 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
* **
41784156 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
41784201 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:41785387 original size:15 final size:15
Alignment explanation
Indices: 41785367--41785395 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41785357 TTAGATCACT
41785367 ATGTTTTGTATTGGG
1 ATGTTTTGTATTGGG
41785382 ATGTTTTGTATTGG
1 ATGTTTTGTATTGG
41785396 CATTTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.55
Consensus pattern (15 bp):
ATGTTTTGTATTGGG
Found at i:41786102 original size:43 final size:43
Alignment explanation
Indices: 41785954--41786111 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 43
41785944 ATGTGATTTT
* * *
41785954 GTGTAAGACCACATCTGGGACGTTGGCATCGAT-TTGAGATTTAC
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATT-TGA-TTAC
* * * **
41785998 GTGTAAGACCATGTCTGGGACATCGACATCG-TATTTGATTTT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTAC
*
41786040 GTGTCAGACC-C-TACCTGGGACATTGGCATCGATATTTGATTAC
1 GTGTAAGACCACGT--CTGGGACATTGGCATCGATATTTGATTAC
* * *
41786083 ATGTAAGACCACGTTTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACATTGGCAT
41786112 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.01
42 26 0.29
43 33 0.37
44 29 0.32
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTAC
Found at i:41794289 original size:17 final size:17
Alignment explanation
Indices: 41794267--41794301 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41794257 TTGATTTAAG
*
41794267 TCATTTATTTTTCTTAT
1 TCATTTATTTTTATTAT
41794284 TCATTTATTTTTATTAT
1 TCATTTATTTTTATTAT
41794301 T
1 T
41794302 TAAATTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TCATTTATTTTTATTAT
Found at i:41794668 original size:6 final size:6
Alignment explanation
Indices: 41794657--41794681 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41794647 TTAATTTTTG
41794657 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
41794682 CAAGTCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:41802780 original size:27 final size:27
Alignment explanation
Indices: 41802750--41802927 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41802740 ATATTGAGTC
* * * *
41802750 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41802777 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41802804 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41802832 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41802859 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41802886 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41802913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41802928 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41802889 original size:82 final size:81
Alignment explanation
Indices: 41802771--41802926 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41802761 TGCTATATAA
* *
41802771 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41802836 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41802853 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41802917 CACTTAGTGC
65 CACTTAGTGC
41802927 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41805124 original size:28 final size:28
Alignment explanation
Indices: 41805082--41805196 Score: 140
Period size: 28 Copynumber: 4.1 Consensus size: 28
41805072 CATGACTATA
**
41805082 AAAGTGATTGGGCCTGACAGGCCATATG
1 AAAGTGATTGGGCCTGATGGGCCATATG
* *
41805110 AAAGTGATTGCGCCTGATGGGCTATATG
1 AAAGTGATTGGGCCTGATGGGCCATATG
* *
41805138 AATGTGATTGGGCCCGATGGGCCATATG
1 AAAGTGATTGGGCCTGATGGGCCATATG
* * *
41805166 AATGAGATTGGGCCTAAATGGGCCATATG
1 AAAGTGATTGGGCCT-GATGGGCCATATG
41805195 AA
1 AA
41805197 TGAATATAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 61 0.81
29 14 0.19
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (28 bp):
AAAGTGATTGGGCCTGATGGGCCATATG
Found at i:41807978 original size:28 final size:28
Alignment explanation
Indices: 41807947--41808018 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
41807937 GAGTGTGATT
41807947 TGGGCCTAATGGGCCACATAAATGTAAA
1 TGGGCCTAATGGGCCACATAAATGTAAA
41807975 TGGGCCTAATGGGCCACATAAATGTAAA
1 TGGGCCTAATGGGCCACATAAATGTAAA
41808003 TGGGCCTAATGGGCCA
1 TGGGCCTAATGGGCCA
41808019 TATGAAAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (28 bp):
TGGGCCTAATGGGCCACATAAATGTAAA
Found at i:41809088 original size:39 final size:38
Alignment explanation
Indices: 41809025--41809197 Score: 220
Period size: 39 Copynumber: 4.4 Consensus size: 38
41809015 GAAGCCAGCG
* * * * *
41809025 GGACTTTAGCCCGGACATATTTCCAGCACGTAGCCTGC
1 GGACTTAAGTCCGGATATAATTCCAGCACATAGCCTGC
* *
41809063 GGATCTTAAGTTCGGTTATAATTCCAGCACATAGCCTGC
1 GGA-CTTAAGTCCGGATATAATTCCAGCACATAGCCTGC
*
41809102 GGACCTTAAGTCCGGATATAATTCCAGCACATAGCTTGC
1 GGA-CTTAAGTCCGGATATAATTCCAGCACATAGCCTGC
* *
41809141 AGACTCTAAGTCCGGATATAATTCCAGCACATAGCCTGT
1 GGACT-TAAGTCCGGATATAATTCCAGCACATAGCCTGC
41809180 GGACTCTAAGTCCGGATA
1 GGACT-TAAGTCCGGATA
41809198 AACATCACTG
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 5 0.04
39 113 0.96
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (38 bp):
GGACTTAAGTCCGGATATAATTCCAGCACATAGCCTGC
Found at i:41814641 original size:28 final size:28
Alignment explanation
Indices: 41814609--41814692 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
41814599 AACTTCGATC
41814609 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
41814637 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
41814659 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
41814687 ACGTGT
1 ACGTGT
41814693 ATCAGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:41814682 original size:50 final size:49
Alignment explanation
Indices: 41814505--41814736 Score: 295
Period size: 49 Copynumber: 4.7 Consensus size: 49
41814495 TCAATTGTGA
*
41814505 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CTGGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATAATT
* * * * * *
41814554 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAA-TT
* **
41814604 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
41814654 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
* * * *
41814704 GGCCGCATGTGTAGTACTAAGTGTAGGCTACTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
41814737 TGCGTACCAG
Statistics
Matches: 158, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
49 69 0.44
50 51 0.32
51 38 0.24
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
Found at i:41821744 original size:28 final size:28
Alignment explanation
Indices: 41821704--41821815 Score: 109
Period size: 28 Copynumber: 4.0 Consensus size: 28
41821694 CATGACTGTT
*
41821704 AATGTGATTTGGGCCTAGT-GGCCATATG
1 AATGTGA-TTGGGCCTAATGGGCCATATG
* *
41821732 AATGTGATTTGGGCCTAATGGGCCACATA
1 AATGTGA-TTGGGCCTAATGGGCCATATG
* * *
41821761 AATGTGAATGTGCCTAATGGGCAATATG
1 AATGTGATTGGGCCTAATGGGCCATATG
* * * *
41821789 AAAGAGATTAGGCCTAGTGGGCCATAT
1 AATGTGATTGGGCCTAATGGGCCATAT
41821816 ATAGGTACGT
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 54 0.79
29 14 0.21
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATGGGCCATATG
Found at i:41826359 original size:28 final size:28
Alignment explanation
Indices: 41826326--41826428 Score: 116
Period size: 28 Copynumber: 3.7 Consensus size: 28
41826316 ATTGCATGAC
* *
41826326 TATGAAAGTGATTAGGCCTGACGGGCCA
1 TATGAAAGTGATTGGGCCTGATGGGCCA
* * *
41826354 TATGAAATTAATTGGGCCTAATGGGCCA
1 TATGAAAGTGATTGGGCCTGATGGGCCA
* *
41826382 TATGAATGTGATTGGGCCCGATGGGCCA
1 TATGAAAGTGATTGGGCCTGATGGGCCA
* * *
41826410 AATGAATGAGATTGGGCCT
1 TATGAAAGTGATTGGGCCT
41826429 AAAGGGGCCA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (28 bp):
TATGAAAGTGATTGGGCCTGATGGGCCA
Found at i:41826393 original size:56 final size:57
Alignment explanation
Indices: 41826326--41826446 Score: 147
Period size: 56 Copynumber: 2.1 Consensus size: 57
41826316 ATTGCATGAC
* * * * *
41826326 TATGAAAGTGATTAGGCCTGACGGGCCATATGAAATTA-ATTGGGCCT-AATGGGCCA
1 TATGAATGTGATTAGGCCCGACGGGCCAAATG-AATGAGATTGGGCCTAAAGGGGCCA
* *
41826382 TATGAATGTGATTGGGCCCGATGGGCCAAATGAATGAGATTGGGCCTAAAGGGGCCA
1 TATGAATGTGATTAGGCCCGACGGGCCAAATGAATGAGATTGGGCCTAAAGGGGCCA
*
41826439 AATGAATG
1 TATGAATG
41826447 AGTATGGATC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
55 4 0.07
56 36 0.65
57 15 0.27
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (57 bp):
TATGAATGTGATTAGGCCCGACGGGCCAAATGAATGAGATTGGGCCTAAAGGGGCCA
Found at i:41826445 original size:29 final size:28
Alignment explanation
Indices: 41826364--41826448 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
41826354 TATGAAATTA
* *
41826364 ATTGGGCCTAATGGGCCATATGAATGTG
1 ATTGGGCCTAATGGGCCAAATGAATGAG
**
41826392 ATTGGGCCCGATGGGCCAAATGAATGAG
1 ATTGGGCCTAATGGGCCAAATGAATGAG
*
41826420 ATTGGGCCTAAAGGGGCCAAATGAATGAG
1 ATTGGGCCT-AATGGGCCAAATGAATGAG
41826449 TATGGATCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.21
Consensus pattern (28 bp):
ATTGGGCCTAATGGGCCAAATGAATGAG
Found at i:41828333 original size:27 final size:27
Alignment explanation
Indices: 41828302--41828479 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41828292 TAAATTGTAC
41828302 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41828329 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41828355 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41828383 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41828411 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41828438 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41828465 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41828480 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41828416 original size:82 final size:81
Alignment explanation
Indices: 41828303--41828458 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41828293 AAATTGTACA
* *
41828303 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41828367 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41828384 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41828449 TGCGAGTTGA
65 TGCGAATTGA
41828459 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41828470 original size:82 final size:81
Alignment explanation
Indices: 41828299--41828479 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41828289 GATTAAATTG
* *
41828299 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41828364 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41828380 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41828444 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41828462 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41828480 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41843355 original size:44 final size:44
Alignment explanation
Indices: 41843288--41843403 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 44
41843278 ATTCTACGTA
* ** *
41843288 TAAGACCAGATCTATGACGTTAGCATCGACT-TCT-ATTTTGCGTG
1 TAAGACCATATCTGGGACATTAGCATCGACTATCTGATTTT--GTG
*
41843332 TAAGACCATGTCTGGGACATTAGCATCG--TATCTGATTTTGTG
1 TAAGACCATATCTGGGACATTAGCATCGACTATCTGATTTTGTG
* * *
41843374 TAAGACCCTATCTGGGACAGTGGCATCGAC
1 TAAGACCATATCTGGGACATTAGCATCGAC
41843404 GTTTGATTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
42 28 0.47
43 3 0.05
44 28 0.47
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (44 bp):
TAAGACCATATCTGGGACATTAGCATCGACTATCTGATTTTGTG
Found at i:41846390 original size:39 final size:39
Alignment explanation
Indices: 41846322--41846579 Score: 374
Period size: 39 Copynumber: 6.5 Consensus size: 39
41846312 AGAAAGCATG
* * *
41846322 CGGGACTTTAAGCCCGGATATAATACCAGCATAAA-GCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACAAATGCCTT
* * *
41846362 CGGGACTTTAGCTCGGATATAATACCAGCATAAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACAAATGCCTT
*
41846402 CGGGACTTAGCCCGGATATAACACTAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
*
41846441 CGGGACTTAGCCTGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
*
41846480 CGGGACTTAGCCCGGATATAACACCAGCGCAAATGCCTTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCC-TT
* *
41846520 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
41846559 CGGGACTTAGCCCGGATATAA
1 CGGGACTTAGCCCGGATATAA
41846580 NNNNNNNNNN
Statistics
Matches: 203, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 148 0.73
40 55 0.27
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
Found at i:41860185 original size:42 final size:44
Alignment explanation
Indices: 41860103--41860188 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 44
41860093 TAAGTTTGGA
*
41860103 ACATTGGCATCGATTTGAGATTTACGTGCAAGACCATGTCTGGG
1 ACATTGGCATCGATATGAGATTTACGTGCAAGACCATGTCTGGG
* *
41860147 ACATTGGCATC-ATAT-ATGATTT-CGTGTAAGACCCTGTCTGGG
1 ACATTGGCATCGATATGA-GATTTACGTGCAAGACCATGTCTGGG
41860189 GTAGTAGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 19 0.50
43 8 0.21
44 11 0.29
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (44 bp):
ACATTGGCATCGATATGAGATTTACGTGCAAGACCATGTCTGGG
Found at i:41868937 original size:46 final size:47
Alignment explanation
Indices: 41868836--41868962 Score: 134
Period size: 46 Copynumber: 2.7 Consensus size: 47
41868826 AATCAATAAG
* **
41868836 TACCAATACCATGGCCTATAGCCAAATCAAGGTAACTTATCCCAGGG
1 TACCTATACCATGGCCTATAGCCAAATCAAGGTAACTTATCCCAGAA
* * *
41868883 TACCTATACCATGGCC-ATAGTCAAATCAAGGTAACTCT-TCTCTGAA
1 TACCTATACCATGGCCTATAGCCAAATCAAGGTAACT-TATCCCAGAA
* * *
41868929 TACTTATACCATGGCCCGA-AGCAAAATCAAGGTA
1 TACCTATACCATGG-CCTATAGCCAAATCAAGGTA
41868963 TCACTCGCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
46 36 0.53
47 31 0.46
48 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (47 bp):
TACCTATACCATGGCCTATAGCCAAATCAAGGTAACTTATCCCAGAA
Found at i:41869206 original size:17 final size:19
Alignment explanation
Indices: 41869164--41869207 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41869154 ATGAAATTTT
*
41869164 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
41869183 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
41869201 AA-TATTA
1 AATTATTA
41869208 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:41876775 original size:29 final size:29
Alignment explanation
Indices: 41876730--41876805 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
41876720 TATATATGTG
41876730 AATTATCGAGCACTAAGTGTGCAAAGTAA
1 AATTATCGAGCACTAAGTGTGCAAAGTAA
* *
41876759 AATTATCGAGCATTAAGTGTGCGAAGTAA
1 AATTATCGAGCACTAAGTGTGCAAAGTAA
*
41876788 AACTATCGAGCACTAAGT
1 AATTATCGAGCACTAAGT
41876806 CTGCTATCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (29 bp):
AATTATCGAGCACTAAGTGTGCAAAGTAA
Found at i:41881708 original size:54 final size:55
Alignment explanation
Indices: 41881645--41881755 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
41881635 CGCTTGGATT
41881645 AAGGAGTGATAAGGGGAGAGATTTAA-GGATTGGGAGAGAGGCTAGGAGTTCGCC
1 AAGGAGTGATAAGGGGAGAGATTTAAGGGATTGGGAGAGAGGCTAGGAGTTCGCC
41881699 AAGGAGTGATAAGGGGAGAGATTTAAGGGATTGGGAGAGAGGCTAGGAGTTCGCC
1 AAGGAGTGATAAGGGGAGAGATTTAAGGGATTGGGAGAGAGGCTAGGAGTTCGCC
41881754 AA
1 AA
41881756 ATTTTGGGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 26 0.46
55 30 0.54
ACGTcount: A:0.32, C:0.07, G:0.42, T:0.18
Consensus pattern (55 bp):
AAGGAGTGATAAGGGGAGAGATTTAAGGGATTGGGAGAGAGGCTAGGAGTTCGCC
Found at i:41882647 original size:48 final size:48
Alignment explanation
Indices: 41882576--41882669 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
41882566 TTTGTAAATA
*
41882576 AGAACTATGCTAATCAATTGTAGGACATCGAAAGAGATCTCAGTAGTG
1 AGAACTATACTAATCAATTGTAGGACATCGAAAGAGATCTCAGTAGTG
* * *
41882624 AGAACTGTACTAATCAATTGTAGGACATCGAAAGGGATCTCGGTAG
1 AGAACTATACTAATCAATTGTAGGACATCGAAAGAGATCTCAGTAG
41882670 CAGTTGTCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (48 bp):
AGAACTATACTAATCAATTGTAGGACATCGAAAGAGATCTCAGTAGTG
Found at i:41894829 original size:29 final size:29
Alignment explanation
Indices: 41894784--41894863 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
41894774 TATATATGTG
41894784 AATTATCGAGCACTAAGTGTGCAAAGTAA
1 AATTATCGAGCACTAAGTGTGCAAAGTAA
* *
41894813 AATTATCGAGCATTAAGTGTGCGAAGTAA
1 AATTATCGAGCACTAAGTGTGCAAAGTAA
*
41894842 AACTATCGAGCACTAAGTGTGC
1 AATTATCGAGCACTAAGTGTGC
41894864 TATCTCATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (29 bp):
AATTATCGAGCACTAAGTGTGCAAAGTAA
Found at i:41902903 original size:41 final size:43
Alignment explanation
Indices: 41902855--41903006 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 43
41902845 AACCGCACGA
* * *
41902855 AGCCTGCTAGACTTTAAGTCTGA-ACTCA-TTCACCGGCATT-T
1 AGCCTGCTAGACTTGAAGCCCGATA-TCATTTCACCGGCATTAT
* *
41902896 CGCCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGCATTAT
1 AGCCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATTAT
* ** * *
41902939 AGCCTGCTAGGCCCGAAGCCCGATATTATCTCACCGGCATTAT
1 AGCCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATTAT
* **
41902982 AGCCTGCTAGGCCCGAAGCCCGATA
1 AGCCTGCTAGACTTGAAGCCCGATA
41903007 ATATTATTCA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
41 21 0.21
42 13 0.13
43 64 0.65
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (43 bp):
AGCCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATTAT
Found at i:41902957 original size:43 final size:43
Alignment explanation
Indices: 41902883--41903053 Score: 197
Period size: 43 Copynumber: 4.0 Consensus size: 43
41902873 TCTGAACTCA
* **
41902883 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCCGATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
*
41902925 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
*
41902968 CTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATAAT-ATT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGAT-ATCA-T
* * * *
41903012 ATTCACCAGC-TTAAAGCTTGCTAGG-CCGAGGCCCGAATATCA
1 -TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCG-ATATCA
41903054 CATTTCGATA
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
42 12 0.11
43 75 0.66
44 19 0.17
45 7 0.06
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
Found at i:41904956 original size:14 final size:15
Alignment explanation
Indices: 41904927--41904956 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41904917 CAAAATTTAG
41904927 ACATGATACTTTCAC
1 ACATGATACTTTCAC
41904942 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
41904956 A
1 A
41904957 AATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:41914227 original size:5 final size:6
Alignment explanation
Indices: 41914212--41914246 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
41914202 TTTAGCCATT
41914212 TTTTTA TTTTTA TTTTTA -TTTTA TTTTTAA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTTTT
41914247 CTTAAATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:41914227 original size:12 final size:12
Alignment explanation
Indices: 41914212--41914246 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
41914202 TTTAGCCATT
41914212 TTTTTATTTTTA
1 TTTTTATTTTTA
41914224 TTTTTA-TTTTA
1 TTTTTATTTTTA
41914235 TTTTTAATTTTT
1 TTTTT-ATTTTT
41914247 CTTAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.48
12 7 0.33
13 4 0.19
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:41914235 original size:17 final size:18
Alignment explanation
Indices: 41914213--41914246 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41914203 TTAGCCATTT
41914213 TTTTATTTTT-ATTTTTA
1 TTTTATTTTTAATTTTTA
41914230 TTTTATTTTTAATTTTT
1 TTTTATTTTTAATTTTT
41914247 CTTAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTATTTTTAATTTTTA
Found at i:41916240 original size:20 final size:20
Alignment explanation
Indices: 41916207--41916255 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
41916197 CTGACTAATT
* * *
41916207 GACACAGGCGTGTTGGATTG
1 GACACGGGCATGTTAGATTG
41916227 GACACGGGCATGTTAGATTG
1 GACACGGGCATGTTAGATTG
*
41916247 GAAACGGGC
1 GACACGGGC
41916256 GTGGGAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.20
Consensus pattern (20 bp):
GACACGGGCATGTTAGATTG
Found at i:41917955 original size:20 final size:19
Alignment explanation
Indices: 41917926--41917968 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
41917916 ATCCTGAATA
* *
41917926 ATTGACACGGGCGTGTTGG
1 ATTGACACGGACATGTTGG
41917945 ATTGCACACGGACATGTTGG
1 ATTG-ACACGGACATGTTGG
41917965 ATTG
1 ATTG
41917969 GACGCAGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.28
Consensus pattern (19 bp):
ATTGACACGGACATGTTGG
Found at i:41936372 original size:46 final size:46
Alignment explanation
Indices: 41936311--41936478 Score: 187
Period size: 46 Copynumber: 3.6 Consensus size: 46
41936301 CGAGGCCAAT
* *
41936311 GCATGTCCCAAACATGTCTTACTCTGGCACTCATAATATGGCTGAA
1 GCATGTCCCAAACATGTCTTACACTGGCACTCATAATATGGCCGAA
* * * * * * *
41936357 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTAGAT-GCCGAT
1 GCATGTCCCAAACATGTCTTACACTGGCACTCAT-AATATGGCCGAA
* *
41936403 GCCATGT-CCAACACATGATCTTACACTGGCTCTCATAATGTGGCCGAA
1 G-CATGTCCCAA-ACATG-TCTTACACTGGCACTCATAATATGGCCGAA
41936451 GCATGTCCCAAACATGTCTTACACTGGC
1 GCATGTCCCAAACATGTCTTACACTGGC
41936479 GCACAAATCT
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
46 49 0.49
47 25 0.25
48 25 0.25
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (46 bp):
GCATGTCCCAAACATGTCTTACACTGGCACTCATAATATGGCCGAA
Found at i:41940128 original size:48 final size:45
Alignment explanation
Indices: 41940065--41940470 Score: 137
Period size: 47 Copynumber: 8.8 Consensus size: 45
41940055 TGGGTTATGT
* *
41940065 GAGA-GCTAGTATAAGACCATGTCTGGGACATGGCATCGGTATTGA
1 GAGAGGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA
* * * * **
41940110 GACGAGGGCTAGTGTAAGACGTGTTTGGGACATACGTCAGCCACATT-A
1 GA-GA-GGCTAGTGTAAGACATGTCTGGGACAT--GGCATCGGCATTGA
* * * *
41940158 TGATA-GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGA
1 -GAGAGGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA
* *
41940204 GATGAGTGCTAGTGTAAGACATGTCTGGGGCAT-GCATCAGCCACATT-A
1 GA-GAG-GCTAGTGTAAGACATGTCTGGGACATGGCATC-G--GCATTGA
* *
41940252 TGATA-GCCAGTGTAAGACCATGTCTGGGAC---G-AT--GC---GA
1 -GAGAGGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA
* *
41940289 GATGAGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGA
1 GA-GAG-GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGA
* * ** * *
41940335 TGATGATAGCCAGCATAAGACGTGTCTGGGACAT-GCATCAGCACGTAT-A
1 -GA-GA-GGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCA--T-TGA
* * * * *
41940384 CACGAGATCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
1 GA-GAG-GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA
* * *
41940432 TGGAGATAGCCAGCGTAAGACCATGTCTGGGACATGGCA
1 --GAGA-GGCTAGTGTAAGA-CATGTCTGGGACATGGCA
41940471 GCAGCAACTT
Statistics
Matches: 265, Mismatches: 56, Indels: 76
0.67 0.14 0.19
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
38 12 0.05
39 12 0.05
40 1 0.00
41 2 0.01
43 2 0.01
44 2 0.01
45 11 0.04
46 33 0.12
47 83 0.31
48 39 0.15
49 56 0.21
50 8 0.03
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (45 bp):
GAGAGGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGA
Done.