Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 119 of 279
Found at i:37760942 original size:17 final size:17
Alignment explanation
Indices: 37760920--37760957 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
37760910 TCGTTTTTAA
37760920 TCAGCAAAAATAACTAT
1 TCAGCAAAAATAACTAT
37760937 TCAGCAAAAATAACTAT
1 TCAGCAAAAATAACTAT
37760954 TCAG
1 TCAG
37760958 ACTACTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (17 bp):
TCAGCAAAAATAACTAT
Found at i:37767288 original size:38 final size:38
Alignment explanation
Indices: 37767216--37767290 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
37767206 TTTTAAGCAA
* * *
37767216 TTTTTTTATTCTTTTAACTTTCCTCTTTTTTTTTCCTT
1 TTTTTTTATTCTCTTAACTTTCCTCTTCTGTTTTCCTT
37767254 TTTTTTTATTCTCTTATACTTCTCC-C-TCTGTTTTCCT
1 TTTTTTTATTCTCTTA-ACTT-TCCTCTTCTGTTTTCCT
37767291 CTTTCTCCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 24 0.75
39 5 0.16
40 3 0.09
ACGTcount: A:0.08, C:0.23, G:0.01, T:0.68
Consensus pattern (38 bp):
TTTTTTTATTCTCTTAACTTTCCTCTTCTGTTTTCCTT
Found at i:37769931 original size:21 final size:21
Alignment explanation
Indices: 37769906--37770019 Score: 124
Period size: 21 Copynumber: 5.4 Consensus size: 21
37769896 ATATTTTACT
* * *
37769906 TTCTGTTCAACTCTTATGAGT
1 TTCTATTCAGCTCTTATGAGC
* * *
37769927 TTCTGTTTAGCTCTTACGAGC
1 TTCTATTCAGCTCTTATGAGC
37769948 TTCTATTCAGCTCTT-TCGAGC
1 TTCTATTCAGCTCTTAT-GAGC
*
37769969 TTCTATTCAGCT-TTTTCGAGC
1 TTCTATTCAGCTCTTAT-GAGC
37769990 TTCTATTCAGCTCTTATGAGC
1 TTCTATTCAGCTCTTATGAGC
*
37770011 TTCTGTTCA
1 TTCTATTCA
37770020 TCTTTCGAGC
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
20 2 0.02
21 76 0.94
22 3 0.04
ACGTcount: A:0.16, C:0.24, G:0.15, T:0.46
Consensus pattern (21 bp):
TTCTATTCAGCTCTTATGAGC
Found at i:37769990 original size:42 final size:40
Alignment explanation
Indices: 37769906--37770033 Score: 132
Period size: 42 Copynumber: 3.1 Consensus size: 40
37769896 ATATTTTACT
* * * * * *
37769906 TTCTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGC
1 TTCTATTCAGCTCTTATGAGCTTCTATTCA--TCTTTCGAGC
*
37769948 TTCTATTCAGCTCTT-TCGAGCTTCTATTCAGCTTTTTCGAGC
1 TTCTATTCAGCTCTTAT-GAGCTTCTATTCA--TCTTTCGAGC
*
37769990 TTCTATTCAGCTCTTATGAGCTTCTGTTCATCTTTCGAGC
1 TTCTATTCAGCTCTTATGAGCTTCTATTCATCTTTCGAGC
37770030 TTCT
1 TTCT
37770034 TTTGGCACAC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
40 13 0.17
41 1 0.01
42 60 0.80
43 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (40 bp):
TTCTATTCAGCTCTTATGAGCTTCTATTCATCTTTCGAGC
Found at i:37776635 original size:10 final size:10
Alignment explanation
Indices: 37776622--37776698 Score: 61
Period size: 10 Copynumber: 8.0 Consensus size: 10
37776612 GTTTTATTAA
*
37776622 TTTATATTTT
1 TTTATAATTT
*
37776632 TTTATAATCT
1 TTTATAATTT
* *
37776642 ATTAAAATTT
1 TTTATAATTT
37776652 TTTAT-A-TT
1 TTTATAATTT
*
37776660 TTTATAA-TA
1 TTTATAATTT
* *
37776669 ATTATAAGTT
1 TTTATAATTT
*
37776679 TTTATGATTT
1 TTTATAATTT
37776689 TTTATAATTT
1 TTTATAATTT
37776699 AAGTAGGTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
8 7 0.14
9 9 0.18
10 35 0.69
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTATAATTT
Found at i:37776680 original size:28 final size:29
Alignment explanation
Indices: 37776630--37776702 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
37776620 AATTTATATT
* *
37776630 TTTTTATAATCTATTA-AAATTTTTTAT-A
1 TTTTTATAAT-AATTATAAGTTTTTTATGA
37776658 TTTTTATAATAATTATAAG-TTTTTATGA
1 TTTTTATAATAATTATAAGTTTTTTATGA
37776686 TTTTT-T-ATAATT-TAAGT
1 TTTTTATAATAATTATAAGT
37776703 AGGTTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 4 0.10
26 6 0.15
27 12 0.30
28 18 0.45
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (29 bp):
TTTTTATAATAATTATAAGTTTTTTATGA
Found at i:37779167 original size:8 final size:8
Alignment explanation
Indices: 37779154--37779178 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
37779144 TACTTATGCC
37779154 CCCCCCCT
1 CCCCCCCT
37779162 CCCCCCCT
1 CCCCCCCT
37779170 CCCCCCCT
1 CCCCCCCT
37779178 C
1 C
37779179 TTTTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.88, G:0.00, T:0.12
Consensus pattern (8 bp):
CCCCCCCT
Found at i:37794587 original size:52 final size:48
Alignment explanation
Indices: 37794502--37794770 Score: 320
Period size: 46 Copynumber: 5.6 Consensus size: 48
37794492 TTTGAGTACT
* ** *
37794502 TCTGATCAAGTG--ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
37794548 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTATACTTA
37794600 TCTGATCAAGTG--ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
37794646 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* ** *
37794698 TCTGATCAAGAGAC--AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
37794744 TCTGATCAA--GAGATAAAGTGATAAGTG
1 TCTGATCAAGTGACATAAAGTGATAAGTG
37794771 GCTGCACTTA
Statistics
Matches: 198, Mismatches: 11, Indels: 28
0.84 0.05 0.12
Matches are distributed among these distances:
44 2 0.01
46 106 0.54
48 1 0.01
49 3 0.02
50 2 0.01
52 84 0.42
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (48 bp):
TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:37794622 original size:98 final size:98
Alignment explanation
Indices: 37794502--37794753 Score: 432
Period size: 98 Copynumber: 2.6 Consensus size: 98
37794492 TTTGAGTACT
*
37794502 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
37794567 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
** *
37794600 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
37794665 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
37794698 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
37794754 AGATAAAGTG
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 143 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (98 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:37794782 original size:37 final size:37
Alignment explanation
Indices: 37794734--37794879 Score: 224
Period size: 37 Copynumber: 4.0 Consensus size: 37
37794724 GATAGCTTTA
* *
37794734 GCTACACTTATCTGATCAAGAGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
37794771 GCTGCACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
37794808 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
37794845 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
37794880 ATCATACGTA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 86 0.85
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:37800105 original size:23 final size:21
Alignment explanation
Indices: 37800066--37800111 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
37800056 TTTATATGGT
*
37800066 ATTATATTATTATAAAATTAA
1 ATTATATAATTATAAAATTAA
37800087 ATTATATAATATATCAAAATTAA
1 ATTATATAAT-TAT-AAAATTAA
37800110 AT
1 AT
37800112 AGAAACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 3 0.14
23 10 0.45
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTATATAATTATAAAATTAA
Found at i:37804391 original size:3 final size:3
Alignment explanation
Indices: 37804383--37804417 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
37804373 TGATAACATA
37804383 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37804418 ATCTAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:37804606 original size:12 final size:12
Alignment explanation
Indices: 37804591--37804624 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37804581 ATTAAATAAA
37804591 TAAATAAAACAT
1 TAAATAAAACAT
* *
37804603 TAAACAATACAT
1 TAAATAAAACAT
37804615 TAAATAAAAC
1 TAAATAAAAC
37804625 CGTCTTTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAAACAT
Found at i:37809994 original size:22 final size:21
Alignment explanation
Indices: 37809950--37810010 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
37809940 TTTTCCGTTG
* *
37809950 AAATTAATAATATTATTACAAA
1 AAATTAAAAATATT-TTAAAAA
37809972 AAATGTAAAAATATTTTAAAAA
1 AAAT-TAAAAATATTTTAAAAA
* *
37809994 AAGTTTTAAAATATTTT
1 AA-ATTAAAAATATTTT
37810011 TATAAAATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (21 bp):
AAATTAAAAATATTTTAAAAA
Found at i:37810011 original size:23 final size:22
Alignment explanation
Indices: 37809953--37810017 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
37809943 TCCGTTGAAA
*
37809953 TTAATAATATTATTACAAAAAATG
1 TTAA-AATATTTTTA-AAAAAATG
* *
37809977 TAAAAATA-TTTTAAAAAAAGTT
1 TTAAAATATTTTTAAAAAAA-TG
*
37809999 TTAAAATATTTTTATAAAA
1 TTAAAATATTTTTAAAAAA
37810018 TTCTAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.18
22 12 0.35
23 13 0.38
24 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (22 bp):
TTAAAATATTTTTAAAAAAATG
Found at i:37810026 original size:21 final size:22
Alignment explanation
Indices: 37809979--37810028 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
37809969 AAAAAATGTA
*
37809979 AAAATATTTTAAAAAAAGTTTT
1 AAAATATTTTAAAAAAAGTTCT
* *
37810001 AAAATATTTTTATAAAA-TTCT
1 AAAATATTTTAAAAAAAGTTCT
37810022 AAAATAT
1 AAAATAT
37810029 AAAATTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATATTTTAAAAAAAGTTCT
Found at i:37810031 original size:15 final size:15
Alignment explanation
Indices: 37810011--37810041 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37810001 AAAATATTTT
37810011 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
37810026 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
37810041 T
1 T
37810042 GGTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TATAAAATTCTAAAA
Found at i:37810226 original size:20 final size:18
Alignment explanation
Indices: 37810173--37810227 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
37810163 ATTAGTATAC
37810173 ATAAAAAATAA-ATAATT
1 ATAAAAAATAATATAATT
*
37810190 ATAAAAACATAAGTATATTT
1 ATAAAAA-ATAA-TATAATT
37810210 ATTAAAAATATAATATAA
1 A-TAAAAA-ATAATATAA
37810228 ACATTACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 7 0.23
18 4 0.13
20 10 0.32
21 10 0.32
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAAAAATAATATAATT
Found at i:37813253 original size:22 final size:22
Alignment explanation
Indices: 37813225--37813300 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
37813215 ATGTGTATAT
37813225 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
37813247 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
37813271 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
37813294 ATGTGAT
1 ATGTGAT
37813301 GAACGTGAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 15 0.37
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:37813254 original size:47 final size:47
Alignment explanation
Indices: 37813200--37813385 Score: 273
Period size: 47 Copynumber: 4.0 Consensus size: 47
37813190 TTAGGATTTT
** *
37813200 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
37813247 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
37813294 ATGTGATGAACGTGAGCATGCATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
37813341 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
37813386 TAGTGTGAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 124 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:37813654 original size:37 final size:37
Alignment explanation
Indices: 37813548--37813656 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
37813538 GGAAATATAT
* * *
37813548 TCCGGGTGAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
37813585 TCCGGATAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
37813622 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
37813657 CGTCTGAGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:37815866 original size:46 final size:45
Alignment explanation
Indices: 37815816--37816204 Score: 528
Period size: 46 Copynumber: 8.4 Consensus size: 45
37815806 CATAGTGTCT
* * * * *
37815816 TTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATC
1 TTCAACCACGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATC
* ** *** *
37815861 ATTCAACCATGGTCTTATTCATTTCCCCGTCACGTTGCCATGGTATC
1 -TTCAACCACGGTCTTACACATTT-CATATCAGGTTGCCATGGTATC
* * * *
37815908 TTTCAACCATGGTCTTAAACATTTCATGTCACGTTGCCATGGTATC
1 -TTCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
*
37815954 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 -TTCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
37816000 TTTCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 -TTCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
37816046 TTCCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 TT-CAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
37816092 TTCCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 TT-CAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
37816138 TTCCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 TT-CAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
37816184 TTCCAACCACGGTCTTACACA
1 TT-CAACCACGGTCTTACACA
37816205 ATTTTCTATC
Statistics
Matches: 327, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
45 5 0.02
46 283 0.87
47 39 0.12
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (45 bp):
TTCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
Found at i:37816099 original size:138 final size:138
Alignment explanation
Indices: 37815803--37816204 Score: 581
Period size: 138 Copynumber: 2.9 Consensus size: 138
37815793 TTCAACATGA
* * * * * * *
37815803 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCATTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
* ** *** * * * *
37815867 CCATGGTCTTATTCATTTCCCCGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTAAACATTT
65 CCACGGTCTTACACATTT-CATATCAGGTTGCCATGGTATCTTCCAACCACGGTCTTACACATTT
*
37815932 CATGTCACGT
129 CATATCACGT
37815942 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
37816007 CACGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCACGGTCTTACACATTTCA
66 CACGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCACGGTCTTACACATTTCA
*
37816072 TATCAGGT
131 TATCACGT
* * *
37816080 TGCCATGGTATCTTCCAACCACGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
37816145 CACGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCACGGTCTTACACA
66 CACGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCACGGTCTTACACA
37816205 ATTTTCTATC
Statistics
Matches: 240, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
138 173 0.72
139 67 0.28
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
CACGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCACGGTCTTACACATTTCA
TATCACGT
Found at i:37818372 original size:11 final size:11
Alignment explanation
Indices: 37818356--37818407 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
37818346 TATACTAAAT
37818356 AAATAATAATA
1 AAATAATAATA
*
37818367 AAATAAT-ATT
1 AAATAATAATA
* *
37818377 AAATATCTCATA
1 AAATA-ATAATA
*
37818389 AAATATTAATA
1 AAATAATAATA
37818400 AAATAATA
1 AAATAATA
37818408 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:37822441 original size:84 final size:84
Alignment explanation
Indices: 37822284--37822443 Score: 259
Period size: 85 Copynumber: 1.9 Consensus size: 84
37822274 GGGCAAGCAA
*
37822284 ACTCTTTTTGAAAGTTCGAAGCAGACAAATTTAGCTAAAAGAAAGAAAGAACAAAAGCAAAATTG
1 ACTCTTTTTGAAAGTTCGAAGCAGACAAATTTAACTAAAAGAAAGAAAGAACAAAAGCAAAATTG
37822349 ATAAAAAAAAAAGTATAAC
66 ATAAAAAAAAAAGTATAAC
* *
37822368 ACTCTTTTTGAAAGTTGGAAGCAGACTAAATTTAACTTAAAA-AAAGAAAGAACAAAGGCAAAAT
1 ACTCTTTTTGAAAGTTCGAAGCAGAC-AAATTTAAC-TAAAAGAAAGAAAGAACAAAAGCAAAAT
*
37822432 TGCTAAAAAAAA
64 TGATAAAAAAAA
37822444 TGTAAGTATT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
84 25 0.36
85 40 0.57
86 5 0.07
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (84 bp):
ACTCTTTTTGAAAGTTCGAAGCAGACAAATTTAACTAAAAGAAAGAAAGAACAAAAGCAAAATTG
ATAAAAAAAAAAGTATAAC
Found at i:37827409 original size:14 final size:15
Alignment explanation
Indices: 37827358--37827417 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
37827348 GGTGGTTCTA
*
37827358 TGGGAA-GGTACTCG
1 TGGGAAGGGTACTTG
37827372 TGGGAA-GGTA-TTG
1 TGGGAAGGGTACTTG
*
37827385 T-GGATGGGTACTT-
1 TGGGAAGGGTACTTG
37827398 TGGGAAGGGTACTTG
1 TGGGAAGGGTACTTG
37827413 TGGGA
1 TGGGA
37827418 GGGAATACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.08
13 8 0.21
14 23 0.59
15 5 0.13
ACGTcount: A:0.20, C:0.07, G:0.45, T:0.28
Consensus pattern (15 bp):
TGGGAAGGGTACTTG
Found at i:37827827 original size:36 final size:35
Alignment explanation
Indices: 37827764--37827840 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 35
37827754 ATATATGAGG
*
37827764 GGCTTACAAGAGGTCTTGCTCCTACACATGGGAGAA
1 GGCTTACAAGAGGTCTTGCTCCCACACA-GGGAGAA
* * *
37827800 GGCTTACAGGGGGTCCTT-CTCCCACACAGGGAGAG
1 GGCTTACAAGAGGT-CTTGCTCCCACACAGGGAGAA
37827835 GGCTTA
1 GGCTTA
37827841 TAGAAAGTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 12 0.33
36 21 0.58
37 3 0.08
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (35 bp):
GGCTTACAAGAGGTCTTGCTCCCACACAGGGAGAA
Found at i:37827839 original size:35 final size:36
Alignment explanation
Indices: 37827714--37827840 Score: 97
Period size: 33 Copynumber: 3.7 Consensus size: 36
37827704 AAATGTCCTA
* * *
37827714 CTCCCACACAT-GGAG-GAGGTTTACAAGAGGTCCTA
1 CTCCCACACATGGGAGAG-GGCTTACAAGAGGTCTTG
* * *
37827749 CTCCTATATAT--GAG-GGGCTTACAAGAGGTCTTG
1 CTCCCACACATGGGAGAGGGCTTACAAGAGGTCTTG
* * * *
37827782 CTCCTACACATGGGAGAAGGCTTACAGGGGGTCCTT-
1 CTCCCACACATGGGAGAGGGCTTACAAGAGGT-CTTG
37827818 CTCCCACACA-GGGAGAGGGCTTA
1 CTCCCACACATGGGAGAGGGCTTA
37827841 TAGAAAGTCC
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 24 0.32
34 4 0.05
35 23 0.31
36 21 0.28
37 3 0.04
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.22
Consensus pattern (36 bp):
CTCCCACACATGGGAGAGGGCTTACAAGAGGTCTTG
Found at i:37840327 original size:2 final size:2
Alignment explanation
Indices: 37840320--37840366 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
37840310 GAAGTGAAAA
37840320 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37840362 AG AG A
1 AG AG A
37840367 ATCATTATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37840673 original size:61 final size:61
Alignment explanation
Indices: 37840603--37840725 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
37840593 ATCTACCTAA
*
37840603 TAATCAAATTCATAACAAAAATAACTTTTTTCAACAATTTTTAAATATCAACTCTGTTATT
1 TAATCAAATTCATAACAAAAATAACTTTTTTCAACAATTTTTAAATATCAAATCTGTTATT
37840664 TAATCAAATTCATAACAAAAATAACTTTTTTCAACAATTTTTAAATATCAAATCTGTTATT
1 TAATCAAATTCATAACAAAAATAACTTTTTTCAACAATTTTTAAATATCAAATCTGTTATT
37840725 T
1 T
37840726 GCTTCAAATC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (61 bp):
TAATCAAATTCATAACAAAAATAACTTTTTTCAACAATTTTTAAATATCAAATCTGTTATT
Found at i:37840903 original size:16 final size:16
Alignment explanation
Indices: 37840845--37840904 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
37840835 CCTTTTTAAA
37840845 ATTTTTAAAAT-ACAAT
1 ATTTTTAAAATGA-AAT
*
37840861 TTTTTTAAAATGAAAAAT
1 ATTTTTAAAATG--AAAT
***
37840879 ATAACTAAAATGAAAT
1 ATTTTTAAAATGAAAT
37840895 ATTTTTAAAA
1 ATTTTTAAAA
37840905 CCAAATGTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
16 21 0.64
18 11 0.33
19 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
ATTTTTAAAATGAAAT
Found at i:37843353 original size:13 final size:14
Alignment explanation
Indices: 37843335--37843364 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
37843325 TTCCCCTTTT
37843335 AAAATAAA-ATAAA
1 AAAATAAATATAAA
37843348 AAAATAAATATAAA
1 AAAATAAATATAAA
37843362 AAA
1 AAA
37843365 CACTCAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAATATAAA
Found at i:37844931 original size:23 final size:24
Alignment explanation
Indices: 37844904--37844954 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
37844894 ATTTAACAAC
**
37844904 ATATACATGAAATAATA-AAAGAA
1 ATATACAACAAATAATATAAAGAA
* *
37844927 ATATATAACAAATAATATAAAGAT
1 ATATACAACAAATAATATAAAGAA
37844951 ATAT
1 ATAT
37844955 GTAATAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (24 bp):
ATATACAACAAATAATATAAAGAA
Found at i:37844954 original size:24 final size:24
Alignment explanation
Indices: 37844913--37844978 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
37844903 CATATACATG
*
37844913 AAATAATA-AAAGAAATATATAAC
1 AAATAATATAAAGATATATATAAC
* *
37844936 AAATAATATAAAGATATATGTAAT
1 AAATAATATAAAGATATATATAAC
* *
37844960 AAATAACATAAAAATATAT
1 AAATAATATAAAGATATAT
37844979 GAATAGTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 8 0.22
24 29 0.78
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (24 bp):
AAATAATATAAAGATATATATAAC
Found at i:37845272 original size:25 final size:28
Alignment explanation
Indices: 37845235--37845293 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
37845225 TTATAAGAAA
37845235 ATATAACTAATAATATTGAAAA-A-ATAT
1 ATATAAC-AATAATATTGAAAACACATAT
*
37845262 ATATAAC-ATAATATTTAAAACACATAT
1 ATATAACAATAATATTGAAAACACATAT
37845289 ATATA
1 ATATA
37845294 TATGATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.41
26 1 0.03
27 16 0.55
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (28 bp):
ATATAACAATAATATTGAAAACACATAT
Found at i:37845307 original size:26 final size:24
Alignment explanation
Indices: 37845226--37845322 Score: 78
Period size: 25 Copynumber: 4.0 Consensus size: 24
37845216 CATGGAAGAT
37845226 TATAAGAAAATATA-ACTA-ATAATA
1 TATAA-AAAATATATA-TATATAATA
*
37845250 T-TGAAAAAATATATATAACATAATA
1 TAT-AAAAAATATATAT-ATATAATA
* *
37845275 TTTAAAACACATATATATATATGATA
1 TATAAAA-A-ATATATATATATAATA
37845301 TAT-AAAAAT-TATATATATAATA
1 TATAAAAAATATATATATATAATA
37845323 CACTATATGA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
22 12 0.19
23 12 0.19
24 6 0.10
25 14 0.23
26 10 0.16
27 8 0.13
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (24 bp):
TATAAAAAATATATATATATAATA
Found at i:37845470 original size:19 final size:21
Alignment explanation
Indices: 37845433--37845472 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
37845423 ATAAATAACA
37845433 GAAAATGAAAACAAGTAAATT
1 GAAAATGAAAACAAGTAAATT
37845454 GAAAAT-AAAAC-AGTAAATT
1 GAAAATGAAAACAAGTAAATT
37845473 AACAAAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (21 bp):
GAAAATGAAAACAAGTAAATT
Found at i:37846098 original size:13 final size:14
Alignment explanation
Indices: 37846082--37846111 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
37846072 AAATAGGTTT
37846082 AAAAAT-GAAATAA
1 AAAAATAGAAATAA
37846095 AAAAATAGAAATAA
1 AAAAATAGAAATAA
37846109 AAA
1 AAA
37846112 TCACCTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAATAGAAATAA
Found at i:37846532 original size:13 final size:13
Alignment explanation
Indices: 37846514--37846542 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
37846504 GTTGTAAATG
37846514 GGTTATTTGGGGT
1 GGTTATTTGGGGT
37846527 GGTTATTTGGGGT
1 GGTTATTTGGGGT
37846540 GGT
1 GGT
37846543 GAGCTGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.48, T:0.45
Consensus pattern (13 bp):
GGTTATTTGGGGT
Found at i:37846608 original size:25 final size:25
Alignment explanation
Indices: 37846552--37846608 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
37846542 TGAGCTGATG
* *
37846552 GGTTTAGTGGTATATGGGTCTGGTG
1 GGTTTAGTGGTATATGGGTCTAGTA
37846577 GGTTTAGTGGTATATGGGT-TAGTA
1 GGTTTAGTGGTATATGGGTCTAGTA
37846601 GGTATTAG
1 GGT-TTAG
37846609 GTCTGATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.18, C:0.02, G:0.40, T:0.40
Consensus pattern (25 bp):
GGTTTAGTGGTATATGGGTCTAGTA
Found at i:37846960 original size:44 final size:44
Alignment explanation
Indices: 37846819--37846960 Score: 101
Period size: 44 Copynumber: 3.2 Consensus size: 44
37846809 GACATATGCC
** *
37846819 TTGTAGCTTCAATCTACTCCGATGTAACTTTAAGGATATGAGAT
1 TTGTAGCTTCAATCTACTCTAATGTAACTTCAAGGATATGAGAT
* ** * * * * *
37846863 TTGTGGCTTTGATCTGCT-TCCATGCAGCTTCATAAAGATA--AGAT
1 TTGTAGCTTCAATCTACTCT-AATGTAACTTC--AAGGATATGAGAT
** *
37846907 TTACAGCTTCAATCTTCTCTAATGTAACTTCAAGGATATGAGAT
1 TTGTAGCTTCAATCTACTCTAATGTAACTTCAAGGATATGAGAT
*
37846951 TTGTGGCTTC
1 TTGTAGCTTC
37846961 GATCCACTTC
Statistics
Matches: 69, Mismatches: 23, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
42 6 0.09
44 56 0.81
45 1 0.01
46 6 0.09
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (44 bp):
TTGTAGCTTCAATCTACTCTAATGTAACTTCAAGGATATGAGAT
Found at i:37847079 original size:44 final size:44
Alignment explanation
Indices: 37846977--37847121 Score: 200
Period size: 44 Copynumber: 3.3 Consensus size: 44
37846967 CTTCACTTGT
* * * * * *
37846977 AACTTCAGAAAGATAAGATTTGATATCCTTGATCAGCTCCACTGC
1 AACTTCAGAGAGACAAGATTTG-TAACTTTGACCTGCTCCACTGC
* *
37847022 AACTTCAGGGAGACAAGATTTGTAACTTTGACCTGCTCTACTGC
1 AACTTCAGAGAGACAAGATTTGTAACTTTGACCTGCTCCACTGC
*
37847066 AACTTCAGAGAGACAAGATTTGCAACTTTGACCTGCTCCACTGC
1 AACTTCAGAGAGACAAGATTTGTAACTTTGACCTGCTCCACTGC
37847110 AACTTCAGAGAG
1 AACTTCAGAGAG
37847122 GCCAAATCTA
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 70 0.79
45 19 0.21
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
AACTTCAGAGAGACAAGATTTGTAACTTTGACCTGCTCCACTGC
Found at i:37847325 original size:14 final size:14
Alignment explanation
Indices: 37847306--37847339 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
37847296 AGTTTTTTTT
*
37847306 TTGAAAAATATAAA
1 TTGAAAAACATAAA
37847320 TTGAAAAACATAAA
1 TTGAAAAACATAAA
37847334 TT-AAAA
1 TTGAAAA
37847340 GGTTCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (14 bp):
TTGAAAAACATAAA
Found at i:37847392 original size:14 final size:14
Alignment explanation
Indices: 37847373--37847407 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
37847363 TGAGTTGATT
37847373 TTTGAAAAACATAA
1 TTTGAAAAACATAA
37847387 TTTG-AAAACATAA
1 TTTGAAAAACATAA
37847400 TTTGAAAA
1 TTTGAAAA
37847408 TACCTCGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (14 bp):
TTTGAAAAACATAA
Found at i:37847481 original size:15 final size:15
Alignment explanation
Indices: 37847461--37847490 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37847451 TGAGTTGATT
37847461 TTTGAAAAACAGAAA
1 TTTGAAAAACAGAAA
37847476 TTTGAAAAACAGAAA
1 TTTGAAAAACAGAAA
37847491 CTGAAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
TTTGAAAAACAGAAA
Found at i:37847495 original size:14 final size:15
Alignment explanation
Indices: 37847463--37847497 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
37847453 AGTTGATTTT
*
37847463 TGAAAAACAGAAATT
1 TGAAAAACAGAAATC
37847478 TGAAAAACAGAAA-C
1 TGAAAAACAGAAATC
37847492 TGAAAA
1 TGAAAA
37847498 TACCTCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (15 bp):
TGAAAAACAGAAATC
Found at i:37847537 original size:89 final size:88
Alignment explanation
Indices: 37847343--37847667 Score: 383
Period size: 89 Copynumber: 3.7 Consensus size: 88
37847333 ATTAAAAGGT
* * * * *
37847343 TCAACTCACCTCTCGCAATCTGAGTTGATTTTTGAAAAACATAATTTG-AAAACATAATTTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAACAGAAATTGAAA
*
37847407 ATACCTCGGCATGTGACCTGAGGC
66 ATACCTCAGCATGTGACC-GAGGC
*
37847431 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTGAAAAACAGAAACTGAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TTGAAAAACAGAAATTGAA
*
37847496 AATACCTCAGCATGTGAGCC-AAGC
65 AATACCTCAGCATGTGA-CCGAGGC
* * * * *
37847520 CCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAAGCAGAAATTGAGAAACAGAAATTCA
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAAAAACAGAAATTGA
* *
37847585 AATTACCTCAGC--GTGTCCTGAGGC
64 AAATACCTCAGCATGTGACC-GAGGC
* * **
37847609 TTAACTCACCTCTCGCAATATGAGTTGATTTTGGAAAAGTAGAAATT-AAAAACA-AAATT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAACAGAAATT
37847668 TGAGCAACAG
Statistics
Matches: 207, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
85 5 0.02
86 6 0.03
87 19 0.09
88 45 0.22
89 60 0.29
90 54 0.26
91 18 0.09
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (88 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAACAGAAATTGAAA
ATACCTCAGCATGTGACCGAGGC
Found at i:37847832 original size:192 final size:192
Alignment explanation
Indices: 37847465--37847853 Score: 491
Period size: 192 Copynumber: 2.0 Consensus size: 192
37847455 TTGATTTTTG
37847465 AAAAACAGAAATTTGAAAAACAGAAACTGAAAATACCTCAGCATGTGAGCCAAGCCCAACTCACC
1 AAAAACAGAAATTTGAAAAACAGAAACTGAAAATACCTCAGCATGTGAGCCAAGCCCAACTCACC
* * *
37847530 TCTCGCAATATAAGTTGATTTTTTTGAAAAGCAGAAATTGAGAAACAGAAATTCAAATTACCTCA
66 TCTCGCAATATAAGTTGATTTTTTTGAAAAGCAGAAATTAAAAAACAGAAATTCAAAATACCTCA
* * * *
37847595 GCGTGTCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTGGAAAAGTAGAAATT
131 GCGTGCCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAAATAGAAATT
** ** ** * * *
37847656 AAAAACA-AAATTTGAGCAACAGAATTTGAAAATACCTTGGTATGTG-GCCCAAGGCTCAACTTA
1 AAAAACAGAAATTTGAAAAACAGAAACTGAAAATACCTCAGCATGTGAG-CCAA-GCCCAACTCA
* * * *
37847719 CCTCTCGCAATATGAGTTGATTTTTTTGAAAA-CATG-CATTAAAAAAAACAGGAATTGAAAATA
64 CCTCTCGCAATATAAGTTGATTTTTTTGAAAAGCA-GAAATT--AAAAAACAGAAATTCAAAATA
* *
37847782 CCTCAGCTTGCCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAA
126 CCTCAGCGTGCCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAAATAGAAA
37847847 TT
191 TT
*
37847849 GAAAA
1 AAAAA
37847854 TACCTCAACG
Statistics
Matches: 169, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
189 1 0.01
190 41 0.24
191 47 0.28
192 59 0.35
193 21 0.12
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (192 bp):
AAAAACAGAAATTTGAAAAACAGAAACTGAAAATACCTCAGCATGTGAGCCAAGCCCAACTCACC
TCTCGCAATATAAGTTGATTTTTTTGAAAAGCAGAAATTAAAAAACAGAAATTCAAAATACCTCA
GCGTGCCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAAATAGAAATT
Found at i:37847883 original size:74 final size:74
Alignment explanation
Indices: 37847762--37847925 Score: 215
Period size: 74 Copynumber: 2.2 Consensus size: 74
37847752 ATGCATTAAA
* * * * * * *
37847762 AAAAACAGGAATTGAAAATACCTCAGCTTGCCCTGAAGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAATAGAAATTGAAAATACCTCAACGTACCCTGAAGCCCAACTCACCTCTCG-AACATGAGTT
37847827 GA-TTTTTTG
65 GATTTTTTTG
*
37847836 AAAAATAGAAATTGAAAATACCTCAACGTA-CCTCGAGGCCCAACTCACCTCTCGAACATGAGTT
1 AAAAATAGAAATTGAAAATACCTCAACGTACCCT-GAAGCCCAACTCACCTCTCGAACATGAGTT
37847900 GATTTTTTTG
65 GATTTTTTTG
*
37847910 AAAAATATAAATTGAA
1 AAAAATAGAAATTGAA
37847926 CAGAAATTGA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
73 14 0.18
74 65 0.82
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (74 bp):
AAAAATAGAAATTGAAAATACCTCAACGTACCCTGAAGCCCAACTCACCTCTCGAACATGAGTTG
ATTTTTTTG
Found at i:37847992 original size:85 final size:84
Alignment explanation
Indices: 37847842--37847997 Score: 210
Period size: 85 Copynumber: 1.8 Consensus size: 84
37847832 TTTGAAAAAT
* *
37847842 AGAAATTGAAAATACCTCAACGTACCTCGAGGCCCAACTCACCTCTCGAACATGAGTTGATTTTT
1 AGAAATTGAAAATACCTCAACGTACCTCGAGGCCCAACTCACCTATCGAACATGAGTCGATTTTT
37847907 TTGAAAAATATAAATTGAAC
66 TT-AAAAATATAAATTGAAC
* * *
37847927 AGAAATTGAAAATACCTCAGCGCGT-CCT-GAGGCTCAACTCACCTATCGTAATATGAGTCGA-T
1 AGAAATTGAAAATACCTCA--ACGTACCTCGAGGCCCAACTCACCTATCG-AACATGAGTCGATT
37847989 TTTTTAAAA
63 TTTTTAAAA
37847998 CAGAAATGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
84 4 0.06
85 43 0.68
86 13 0.21
87 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (84 bp):
AGAAATTGAAAATACCTCAACGTACCTCGAGGCCCAACTCACCTATCGAACATGAGTCGATTTTT
TTAAAAATATAAATTGAAC
Found at i:37850671 original size:20 final size:20
Alignment explanation
Indices: 37850643--37850683 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
37850633 CTTCCATGAC
* *
37850643 TTCTCTTTTGGTGATTCGCA
1 TTCTCTTTTCGTGATGCGCA
*
37850663 TTCTTTTTTCGTGATGCGCA
1 TTCTCTTTTCGTGATGCGCA
37850683 T
1 T
37850684 CAAGTCTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.51
Consensus pattern (20 bp):
TTCTCTTTTCGTGATGCGCA
Found at i:37860348 original size:25 final size:24
Alignment explanation
Indices: 37860320--37860374 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
37860310 ACATGAAATA
37860320 ATAAAAGAAATATATAACAAATAAC
1 ATAAAAG-AATATATAACAAATAAC
* * **
37860345 ATAAAAGTATATGTATGAAATAAC
1 ATAAAAGAATATATAACAAATAAC
37860369 ATAAAA
1 ATAAAA
37860375 ATATATGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (24 bp):
ATAAAAGAATATATAACAAATAAC
Found at i:37860767 original size:13 final size:14
Alignment explanation
Indices: 37860749--37860778 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
37860739 TAATAGGTTT
37860749 AAAAAT-GAAATAA
1 AAAAATAGAAATAA
37860762 AAAAATAGAAATAA
1 AAAAATAGAAATAA
37860776 AAA
1 AAA
37860779 TCACCTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAATAGAAATAA
Found at i:37861199 original size:13 final size:13
Alignment explanation
Indices: 37861181--37861209 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
37861171 GTTGTAAATG
37861181 GGTTATTTGGGGT
1 GGTTATTTGGGGT
37861194 GGTTATTTGGGGT
1 GGTTATTTGGGGT
37861207 GGT
1 GGT
37861210 GAACTGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.48, T:0.45
Consensus pattern (13 bp):
GGTTATTTGGGGT
Found at i:37861275 original size:25 final size:25
Alignment explanation
Indices: 37861219--37861275 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
37861209 TGAACTGATG
* *
37861219 GGTTTAGTGGTATATGGGCCTGGTG
1 GGTTTAGTGGTATATGGGCCTAGTA
*
37861244 GGTTTAGTGGTATATGGG-TTAGTA
1 GGTTTAGTGGTATATGGGCCTAGTA
37861268 GGTATTAG
1 GGT-TTAG
37861276 GTCTGATGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.18, C:0.04, G:0.40, T:0.39
Consensus pattern (25 bp):
GGTTTAGTGGTATATGGGCCTAGTA
Found at i:37864515 original size:15 final size:15
Alignment explanation
Indices: 37864495--37864530 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
37864485 GAAAAAAATA
*
37864495 AAAATATTGAATAAT
1 AAAATATTAAATAAT
37864510 AAAATATTAAATAAT
1 AAAATATTAAATAAT
*
37864525 TAAATA
1 AAAATA
37864531 AAATAACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATATTAAATAAT
Found at i:37866785 original size:36 final size:36
Alignment explanation
Indices: 37866738--37866812 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
37866728 TGTTATATTA
*
37866738 TGAACTATGTTAACTTGGTGAATTATATTATTATGG
1 TGAACTATGTTAACTTGGTGAATTATATTAATATGG
* * * *
37866774 TGAACTGTGTTAATTTGGTGATTTGTATTAATATGG
1 TGAACTATGTTAACTTGGTGAATTATATTAATATGG
37866810 TGA
1 TGA
37866813 GATGTATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.45
Consensus pattern (36 bp):
TGAACTATGTTAACTTGGTGAATTATATTAATATGG
Found at i:37866792 original size:18 final size:18
Alignment explanation
Indices: 37866747--37866826 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
37866737 ATGAACTATG
* * *
37866747 TTAACTTGGTGAATTATA
1 TTAATTTGGTGAACTGTA
*
37866765 TT-ATTATGGTGAACTGTG
1 TTAATT-TGGTGAACTGTA
**
37866783 TTAATTTGGTGATTTGTA
1 TTAATTTGGTGAACTGTA
*
37866801 TTAATATGGTGAGA-TGTA
1 TTAATTTGGTGA-ACTGTA
37866819 TTAATTTG
1 TTAATTTG
37866827 TCAAACTGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
17 2 0.04
18 44 0.90
19 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (18 bp):
TTAATTTGGTGAACTGTA
Found at i:37866823 original size:36 final size:36
Alignment explanation
Indices: 37866738--37866826 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
37866728 TGTTATATTA
* * * *
37866738 TGAACTATGTTAACTTGGTGAATTATATTATTATGG
1 TGAACTGTATTAATTTGGTGAATTATATTAATATGG
* * *
37866774 TGAACTGTGTTAATTTGGTGATTTGTATTAATATGG
1 TGAACTGTATTAATTTGGTGAATTATATTAATATGG
37866810 TGAGA-TGTATTAATTTG
1 TGA-ACTGTATTAATTTG
37866827 TCAAACTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 45 0.98
37 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.46
Consensus pattern (36 bp):
TGAACTGTATTAATTTGGTGAATTATATTAATATGG
Found at i:37873640 original size:6 final size:7
Alignment explanation
Indices: 37873620--37873651 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
37873610 TAATGTACAT
37873620 AATAAAA
1 AATAAAA
37873627 AATAAAA
1 AATAAAA
37873634 AATAAAA
1 AATAAAA
37873641 AATAAAA
1 AATAAAA
37873648 AATA
1 AATA
37873652 TATATTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:37874071 original size:42 final size:42
Alignment explanation
Indices: 37873960--37874079 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 42
37873950 ATATTAAGGG
* * * * *
37873960 ATAATTAATACTAATAATAATA-ATAGTAAAATACTAATAATA
1 ATAA-TAATAATAATAATAGTAGAAAATAAAATAATAATAATA
*
37874002 ATAATGATAATAATAATAGTAGAAAATAAAATAATAATAATA
1 ATAATAATAATAATAATAGTAGAAAATAAAATAATAATAATA
* * * *
37874044 ATAATAATAATATTAATAGTGGTAAATATAATAATA
1 ATAATAATAATAATAATAGTAGAAAATAAAATAATA
37874080 GAATACGAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 14 0.21
42 52 0.79
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (42 bp):
ATAATAATAATAATAATAGTAGAAAATAAAATAATAATAATA
Found at i:37874079 original size:3 final size:3
Alignment explanation
Indices: 37873960--37874061 Score: 109
Period size: 3 Copynumber: 34.0 Consensus size: 3
37873950 ATATTAAGGG
* * *
37873960 ATA ATTA ATA CTA ATA ATA ATA ATA GTA A-A ATA CTA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
37874005 ATG ATA ATA ATA ATA GTA GAAA ATA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
37874050 ATA ATA TTA ATA
1 ATA ATA ATA ATA
37874062 GTGGTAAATA
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
2 4 0.05
3 73 0.90
4 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:37881569 original size:3 final size:3
Alignment explanation
Indices: 37881555--37881610 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
37881545 CCTAACCCCT
* *
37881555 TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
37881602 TTAC TTC TT
1 TT-C TTC TT
37881611 TCCACAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:37883547 original size:22 final size:18
Alignment explanation
Indices: 37883503--37883552 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
37883493 CCTTTTCTAT
37883503 TATATGTACATATATACA
1 TATATGTACATATATACA
*
37883521 CATATGTACATAAGTATATCA
1 TATATGTACAT-A-TATA-CA
37883542 GTATATGTACA
1 -TATATGTACA
37883553 ACATATAGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
19 1 0.04
20 4 0.15
21 2 0.08
22 9 0.35
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (18 bp):
TATATGTACATATATACA
Found at i:37889983 original size:131 final size:129
Alignment explanation
Indices: 37889843--37890198 Score: 370
Period size: 131 Copynumber: 2.7 Consensus size: 129
37889833 TGTTCGATCG
* * * * * *
37889843 TTTTGAGCAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCTCGAATTGTCAAACGCCA
1 TTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCGCGAATTG-CAAACACCA
* * * * * * *
37889908 AATATTGCCTTTGTTTTAAATAATTTTTAGAAGATATGAATGAAATTTTGAAGGGATACTCGATT
65 AATATCGCCTTCGTTTTAAAGAA-TTTTAAAAGACACGAATGAAATTTCGAAGGGATACTCGATT
37889973 A
129 A
* * * *
37889974 TTTTGAGCAAACGTGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCTAAATATC
1 TTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATT-CGCGAATTGC-AAACACC
* * * * * * * *
37890039 GAATCTCGTCTTCGTTTTGAAGAATTTTAAAAGACGCGAGTGAAATTTCGAAGTGATATTCGATT
64 AAATATCGCCTTCGTTTTAAAGAATTTTAAAAGACACGAATGAAATTTCGAAGGGATACTCGATT
37890104 A
129 A
* *
37890105 TTTTGAGCAAACGCGAAATTACAACCCAACACGTTAGGGCACGATTTCGCGAATTGCCAAACATC
1 TTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGA-TTCGCGAATTG-CAAACACC
* * * *
37890170 GAATCTCGTCTTCGTTTTGAAGAACTTTT
64 AAATATCGCCTTCGTTTTAAAGAA-TTTT
37890199 GGATGAATAC
Statistics
Matches: 192, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
131 156 0.81
132 36 0.19
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (129 bp):
TTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCGCGAATTGCAAACACCAA
ATATCGCCTTCGTTTTAAAGAATTTTAAAAGACACGAATGAAATTTCGAAGGGATACTCGATTA
Found at i:37893600 original size:13 final size:13
Alignment explanation
Indices: 37893582--37893606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37893572 TAACCTACAA
37893582 AATTAAATAACAT
1 AATTAAATAACAT
37893595 AATTAAATAACA
1 AATTAAATAACA
37893607 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:37893864 original size:10 final size:10
Alignment explanation
Indices: 37893831--37893879 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
37893821 AAAAAGGAAT
*
37893831 GAGCTGAAAC
1 GAGCTCAAAC
37893841 GAGCT-AAATTC
1 GAGCTCAAA--C
37893852 GAGCTCAAAC
1 GAGCTCAAAC
*
37893862 GAGCTAAAAC
1 GAGCTCAAAC
37893872 GAGCTCAA
1 GAGCTCAA
37893880 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:37893886 original size:20 final size:21
Alignment explanation
Indices: 37893831--37893879 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
37893821 AAAAAGGAAT
* *
37893831 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
37893852 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
37893872 GAGCTCAA
1 GAGCTCAA
37893880 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:37895998 original size:30 final size:29
Alignment explanation
Indices: 37895943--37896006 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
37895933 TTTTTCAATT
* *
37895943 TCTTTTTCACTCTCAAATTTCTTTTCGTTC
1 TCTTTTTCAATCTCAAATCTCTTTTC-TTC
*
37895973 TCTTTTTCAATCTC-AATCTCATTTTCTTT
1 TCTTTTTCAATCTCAAATCTC-TTTTCTTC
37896002 TCTTT
1 TCTTT
37896007 GTTTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (29 bp):
TCTTTTTCAATCTCAAATCTCTTTTCTTC
Found at i:37896021 original size:19 final size:20
Alignment explanation
Indices: 37895997--37896037 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
37895987 AATCTCATTT
37895997 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
37896016 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
37896036 TC
1 TC
37896038 GATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:37898488 original size:21 final size:20
Alignment explanation
Indices: 37898450--37898498 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
37898440 AAAAAGGAAT
* * *
37898450 GAGCTGAAACAAGGTAAATTC
1 GAGCTCAAACAAGCTAAA-AC
*
37898471 GAGCTCAAACGAGCTAAAAC
1 GAGCTCAAACAAGCTAAAAC
37898491 GAGCTCAA
1 GAGCTCAA
37898499 GTAAGCTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (20 bp):
GAGCTCAAACAAGCTAAAAC
Found at i:37899600 original size:133 final size:132
Alignment explanation
Indices: 37899419--37900196 Score: 1012
Period size: 133 Copynumber: 5.9 Consensus size: 132
37899409 TCTACAATCG
* *
37899419 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGG--ACGAT-AGTCTAAATCTGCTTCACTGTAA
1 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTA-G-TGACT-TAAATCTGCTTCACTGCAA
* * ** * ** * *
37899481 CATCAGGAAGCCTAGATTCACCGTCTTTGATCTGTTCCACTGCAA-TCTCAAAGAAACAAAATCT
63 CTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACT-TCAGGGAAACGAGATCT
37899545 ATATTT
127 ATATTT
* * * *
37899551 CTCAGCCTACTCCTCTACAACTTTAGGGAGCTAGGTTAGTGGCTTAAATCTGCCTCATTGCAACT
1 -TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACT
* ** *
37899616 TCAGGAAGCCTAGAGCCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGATATCTATA
65 TCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTATA
37899681 TTT
130 TTT
* * * * * *
37899684 CTTAGCTTACTCCACTACAACTTTAGAGAGCTAGGTTAGTGGCTTAAATCTACCTCACTGCAACT
1 -TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACT
* ** * *
37899749 TCAGGAAGTCTAGATTCGCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAAACGAGACCTAAA
65 TCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCT-AT
37899814 ATTT
129 ATTT
37899818 T-AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
1 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
* * * * *
37899882 CCGGGAGT-TAAAATTCGTCGTCTTTGATCTGTTCCACTGTAACTTCAGGGAAACGAGATCTATA
66 CAGGAAGTCT-AGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTATA
37899946 TTT
130 TTT
* *
37899949 T-AGCCTACTCTACTACAACTTTAGGGAGCTAGGTTAGTGACATAAATCTGCTTCACTGCAACTT
1 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
* * * *
37900013 CAGGAAGTCAAGATTCGTCGTTTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAA
66 CAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTATAT
37900078 TT
131 TT
* * *
37900080 TCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATTTGCTTCACTGTAACTT
1 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
* * *
37900145 CAGGAAGTCAAGATTCGTCGTCTTCGATCTGCTCTACTGCAACTTCAGGGAA
66 CAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAA
37900197 GCAGGATCTG
Statistics
Matches: 572, Mismatches: 65, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
131 126 0.22
132 215 0.38
133 222 0.39
134 8 0.01
135 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
CAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTATAT
TT
Found at i:37899878 original size:132 final size:132
Alignment explanation
Indices: 37899403--37900196 Score: 999
Period size: 132 Copynumber: 6.0 Consensus size: 132
37899393 TCCACTGGAG
* * * *
37899403 ACGAGATCTACAATCGTCAGCCTACTCCACTACAACTTTAGGGAGCTAGG--ACGAT-AGTCTAA
1 ACGAGATCTAAAAT-TTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTA-G-TGACT-TAA
* * * ** *
37899465 ATCTGCTTCACTGTAACATCAGGAAGCCTAGATTCACCGTCTTTGATCTGTTCCACTGCAA-TCT
62 ATCTGCTTCACTGCAACTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACT-T
**
37899529 CAAAGAA
126 CAGGGAA
* * * * *
37899536 ACAAAATCT-ATATTTCTCAGCCTACTCCTCTACAACTTTAGGGAGCTAGGTTAGTGGCTTAAAT
1 ACGAGATCTAAAATTT-T-AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAAT
* * * **
37899600 CTGCCTCATTGCAACTTCAGGAAGCCTAGAGCCGTCGTCTTTGATCTGCTCCACTGCAACTTCAG
64 CTGCTTCACTGCAACTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAG
37899665 GGAA
129 GGAA
* * * * * *
37899669 ACGATATCTATATTTCTTAGCTTACTCCACTACAACTTTAGAGAGCTAGGTTAGTGGCTTAAATC
1 ACGAGATCTAAAATT-TTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATC
* * * **
37899734 TACCTCACTGCAACTTCAGGAAGTCTAGATTCGCCGTCTTCAATCTGCTCCACTGCAACTTCAGG
65 TGCTTCACTGCAACTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGG
37899799 GAA
130 GAA
*
37899802 ACGAGACCTAAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
1 ACGAGATCTAAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
* * * * *
37899867 GCTTCACTGCAACTTCCGGGAGT-TAAAATTCGTCGTCTTTGATCTGTTCCACTGTAACTTCAGG
66 GCTTCACTGCAACTTCAGGAAGTCT-AGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGG
37899931 GAA
130 GAA
* * *
37899934 ACGAGATCT-ATATTTTAGCCTACTCTACTACAACTTTAGGGAGCTAGGTTAGTGACATAAATCT
1 ACGAGATCTAAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
* *
37899998 GCTTCACTGCAACTTCAGGAAGTCAAGATTCGTCGTTTTTGATCTGCTCCACTGCAACTTCAGGG
66 GCTTCACTGCAACTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGG
37900063 AA
131 AA
* * *
37900065 ACGAGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATTT
1 ACGAGATCTAAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
* * * *
37900130 GCTTCACTGTAACTTCAGGAAGTCAAGATTCGTCGTCTTCGATCTGCTCTACTGCAACTTCAGGG
66 GCTTCACTGCAACTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGG
37900195 AA
131 AA
37900197 GCAGGATCTG
Statistics
Matches: 576, Mismatches: 74, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
131 122 0.21
132 224 0.39
133 222 0.39
134 6 0.01
135 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
ACGAGATCTAAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
GCTTCACTGCAACTTCAGGAAGTCTAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGG
AA
Found at i:37900090 original size:263 final size:264
Alignment explanation
Indices: 37899421--37900196 Score: 1042
Period size: 263 Copynumber: 2.9 Consensus size: 264
37899411 TACAATCGTC
* * *
37899421 AGCCTACTCCACTACAACTTTAGGGAGCTAGG--ACGATAGTCTAAATCTGCTTCACTGTAACAT
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTA-G-T-GACTAAATCTGCTTCACTGCAACTT
* * * ** * * *
37899484 CAGGAAGCCTAGATTCACCGTCTTTGATCTGTTCCACTGCAA-TCTCAAAGAAACAAAATCTATA
63 CAGGAAGTCTAGATTCGCCGTCTTTGATCTGCTCCACTGCAACT-TCAGGGAAACGAGATCTAAA
* * * * *
37899548 TTTCTCAGCCTACTCCTCTACAACTTTAGGGAGCTAGGTTAGTGGCTTAAATCTGCCTCATTGCA
127 ATT-TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCA
* ** *
37899613 ACTTCAGGAAGCCT-AGAGCCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGATATC
191 ACTTCAGGAAG-TTAAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATC
37899677 TATATTTCTT
255 TATATTTCTT
* * * * *
37899687 AGCTTACTCCACTACAACTTTAGAGAGCTAGGTTAGTGGCTTAAATCTACCTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGAC-TAAATCTGCTTCACTGCAACTTCA
** *
37899752 GGAAGTCTAGATTCGCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAAACGAGACCTAAAATT
65 GGAAGTCTAGATTCGCCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATT
*
37899817 TTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
130 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
* * * * *
37899882 CCGGGAGTTAAAATTCGTCGTCTTTGATCTGTTCCACTGTAACTTCAGGGAAACGAGATCTATA-
195 CAGGAAGTTAAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTATAT
37899946 TT-TT
260 TTCTT
*
37899950 AGCCTACTCTACTACAACTTTAGGGAGCTAGGTTAGTGACATAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGAC-TAAATCTGCTTCACTGCAACTTCA
* * *
37900015 GGAAGTCAAGATTCGTCGTTTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATT
65 GGAAGTCTAGATTCGCCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATT
* * *
37900080 TCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATTTGCTTCACTGTAACTT
130 TCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTT
* * *
37900145 CAGGAAGTCAAGATTCGTCGTCTTCGATCTGCTCTACTGCAACTTCAGGGAA
195 CAGGAAGTTAAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAA
37900197 GCAGGATCTG
Statistics
Matches: 447, Mismatches: 58, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
263 224 0.50
264 3 0.01
265 115 0.26
266 102 0.23
267 2 0.00
268 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (264 bp):
AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTAAATCTGCTTCACTGCAACTTCAG
GAAGTCTAGATTCGCCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTT
CAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTC
AGGAAGTTAAGATTCGTCGTCTTTGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTATATT
TCTT
Found at i:37912198 original size:131 final size:132
Alignment explanation
Indices: 37912047--37912329 Score: 406
Period size: 131 Copynumber: 2.2 Consensus size: 132
37912037 CAAATATTGC
* * * * * * *
37912047 CTTCGTTTTAAATAATTTTTAGAAGATATGAATGAAATTTTGAAGGGATACTCGATTATTTTGAG
1 CTTCGTTTTGAAGAACTTTTAAAAGACACGAATGAAATTTCGAAGGGATACTCGATTATTTTGAG
* * *
37912112 CAAACACGAAATTGCAACCTAACACGTTAGGGCACGATTCCGCGAATTGCTAAATATCGAATCTC
66 CAAACACGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCGAATCTC
37912177 GT
131 GT
* * * * *
37912179 CTTCGTTTTGAAGAA-TTTTAAAAGACGCGAGTGAAATTTCGAAGTGATATTCTATTATTTTGAG
1 CTTCGTTTTGAAGAACTTTTAAAAGACACGAATGAAATTTCGAAGGGATACTCGATTATTTTGAG
* *
37912243 CAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGTGAATTGCCAAACATCGAATCTC
66 CAAACACGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCGAATCTC
37912308 GT
131 GT
37912310 CTTCGTTTTGAAGAACTTTT
1 CTTCGTTTTGAAGAACTTTT
37912330 GGATGAATAC
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
131 117 0.87
132 17 0.13
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (132 bp):
CTTCGTTTTGAAGAACTTTTAAAAGACACGAATGAAATTTCGAAGGGATACTCGATTATTTTGAG
CAAACACGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCGAATCTC
GT
Found at i:37916606 original size:19 final size:20
Alignment explanation
Indices: 37916582--37916626 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
37916572 CATTATAAAA
37916582 AATTTAAAATTCATTT-GTT
1 AATTTAAAATTCATTTCGTT
* * *
37916601 AATTTAATATTTATTTCTTT
1 AATTTAAAATTCATTTCGTT
37916621 AATTTA
1 AATTTA
37916627 TCATAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTTAAAATTCATTTCGTT
Found at i:37921255 original size:21 final size:21
Alignment explanation
Indices: 37921229--37921269 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
37921219 ATCTGCTCAA
* *
37921229 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
37921250 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
37921270 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:37936602 original size:16 final size:16
Alignment explanation
Indices: 37936581--37936611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37936571 TCAAAAATTA
*
37936581 TAAAAATATTCAAAAC
1 TAAAAAAATTCAAAAC
37936597 TAAAAAAATTCAAAA
1 TAAAAAAATTCAAAA
37936612 TTCAAAATTC
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:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAAAATTCAAAAC
Found at i:37936603 original size:18 final size:19
Alignment explanation
Indices: 37936568--37936605 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
37936558 TAATACAAAT
* *
37936568 TATTCAAAAATTATAAAAA
1 TATTCAAAAACTAAAAAAA
37936587 TATTC-AAAACTAAAAAAA
1 TATTCAAAAACTAAAAAAA
37936605 T
1 T
37936606 TCAAAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
TATTCAAAAACTAAAAAAA
Found at i:37936611 original size:7 final size:7
Alignment explanation
Indices: 37936601--37936637 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
37936591 CAAAACTAAA
37936601 AAAATTC
1 AAAATTC
37936608 AAAATTC
1 AAAATTC
37936615 AAAATTC
1 AAAATTC
37936622 AAAATTC
1 AAAATTC
37936629 AAAATTC
1 AAAATTC
37936636 AA
1 AA
37936638 TAAAAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:37936618 original size:16 final size:16
Alignment explanation
Indices: 37936582--37936632 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 16
37936572 CAAAAATTAT
* *
37936582 AAAAATATTCAAAACTA
1 AAAAA-ATTCAAAATTC
37936599 AAAAAATTCAAAATTC
1 AAAAAATTCAAAATTC
37936615 --AAAATTCAAAATTC
1 AAAAAATTCAAAATTC
37936629 AAAA
1 AAAA
37936633 TTCAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 14 0.47
16 11 0.37
17 5 0.17
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATTCAAAATTC
Found at i:37940488 original size:28 final size:27
Alignment explanation
Indices: 37940450--37940508 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
37940440 GATTTTTGGC
* * *
37940450 TTTTGATTTTAGCGTTTGGGCTTCTTAA
1 TTTTGAGTTTAGCGTTTGAGATTC-TAA
*
37940478 TTTTGAGTTTAGTGTTTGAGATTCTAA
1 TTTTGAGTTTAGCGTTTGAGATTCTAA
37940505 TTTT
1 TTTT
37940509 ATAATTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56
Consensus pattern (27 bp):
TTTTGAGTTTAGCGTTTGAGATTCTAA
Found at i:37941152 original size:35 final size:35
Alignment explanation
Indices: 37941109--37941178 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
37941099 GCCAAAACAT
37941109 CATTTATAGTAAAAATCAAGGGATTATTGATTAAA
1 CATTTATAGTAAAAATCAAGGGATTATTGATTAAA
37941144 CATTTATAGTAAAAATCAAGGGATTATTGATTAAA
1 CATTTATAGTAAAAATCAAGGGATTATTGATTAAA
37941179 GTTGGCAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (35 bp):
CATTTATAGTAAAAATCAAGGGATTATTGATTAAA
Found at i:37941739 original size:17 final size:17
Alignment explanation
Indices: 37941717--37941750 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37941707 ATCCACTAAT
*
37941717 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
37941734 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
37941751 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:37946369 original size:17 final size:17
Alignment explanation
Indices: 37946347--37946380 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37946337 ATCCACTAAT
*
37946347 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
37946364 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
37946381 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:37947944 original size:17 final size:17
Alignment explanation
Indices: 37947922--37947955 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
37947912 AAAGAAATTT
37947922 GGGATTGGTGCGTTCTA
1 GGGATTGGTGCGTTCTA
37947939 GGGATTGGTGCGTTCTA
1 GGGATTGGTGCGTTCTA
37947956 TCTTTTCAAG
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:0.12, C:0.12, G:0.41, T:0.35
Consensus pattern (17 bp):
GGGATTGGTGCGTTCTA
Found at i:37952573 original size:18 final size:18
Alignment explanation
Indices: 37952550--37952586 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
37952540 AAAGAACTTC
37952550 ATCTATGGGCTTAAGTAG
1 ATCTATGGGCTTAAGTAG
37952568 ATCTATGGGCTTAAGTAG
1 ATCTATGGGCTTAAGTAG
37952586 A
1 A
37952587 CTTCTCGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
ATCTATGGGCTTAAGTAG
Found at i:37955719 original size:17 final size:17
Alignment explanation
Indices: 37955697--37955730 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
37955687 AAAGAAATTT
37955697 GGGATTGGTGCGTTCTA
1 GGGATTGGTGCGTTCTA
37955714 GGGATTGGTGCGTTCTA
1 GGGATTGGTGCGTTCTA
37955731 TCTTTTCAAG
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:0.12, C:0.12, G:0.41, T:0.35
Consensus pattern (17 bp):
GGGATTGGTGCGTTCTA
Found at i:37960348 original size:18 final size:18
Alignment explanation
Indices: 37960325--37960361 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
37960315 AAAGAACTTC
37960325 ATCTATGGGCTTAAGTAG
1 ATCTATGGGCTTAAGTAG
37960343 ATCTATGGGCTTAAGTAG
1 ATCTATGGGCTTAAGTAG
37960361 A
1 A
37960362 CTTCTCGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
ATCTATGGGCTTAAGTAG
Found at i:37968890 original size:25 final size:26
Alignment explanation
Indices: 37968842--37968924 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
37968832 CATGAAATTC
37968842 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
37968868 TTATCATGAAACA-TTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
37968893 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
37968919 TTATCA
1 TTATCA
37968925 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
25 24 0.44
26 30 0.56
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:37969277 original size:27 final size:29
Alignment explanation
Indices: 37969247--37969306 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
37969237 CCTAACAATC
* *
37969247 TAAACAAATCATAA-AATGTCCAAAAT-T
1 TAAACAAACCATAATAAAGTCCAAAATGT
*
37969274 TAAACAAACCATAATAAAGTCCTAAATGT
1 TAAACAAACCATAATAAAGTCCAAAATGT
37969303 TAAA
1 TAAA
37969307 TTTAAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 13 0.46
28 10 0.36
29 5 0.18
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (29 bp):
TAAACAAACCATAATAAAGTCCAAAATGT
Found at i:37971698 original size:26 final size:26
Alignment explanation
Indices: 37971663--37971715 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
37971653 AATAATATCA
37971663 CACGCAAAACCATTGTTGACAACTTT
1 CACGCAAAACCATTGTTGACAACTTT
*
37971689 CACGCAAAACTATTGTTGACAACTTT
1 CACGCAAAACCATTGTTGACAACTTT
37971715 C
1 C
37971716 TACTTTCCAT
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:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (26 bp):
CACGCAAAACCATTGTTGACAACTTT
Found at i:37972157 original size:16 final size:17
Alignment explanation
Indices: 37972120--37972157 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
37972110 AACGTGTTAT
*
37972120 GAAATAAATAATAAAAC
1 GAAATAAATAACAAAAC
37972137 G-AATAAATAACAAAA-
1 GAAATAAATAACAAAAC
37972152 GAAATA
1 GAAATA
37972158 GAAGAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.05
16 17 0.89
17 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (17 bp):
GAAATAAATAACAAAAC
Found at i:37973695 original size:34 final size:33
Alignment explanation
Indices: 37973641--37973709 Score: 77
Period size: 34 Copynumber: 2.0 Consensus size: 33
37973631 AGAAGTAAAC
*
37973641 TATTTTATGTTTAACGTTGATACAATTGATCTAT
1 TATTTTATGTTTAAC-TTGATACAATCGATCTAT
* *
37973675 TATTTTATGTTTGGAA-TTGATGCTATCGATCTAT
1 TATTTTATGTTT--AACTTGATACAATCGATCTAT
37973709 T
1 T
37973710 GGTGTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
34 28 0.93
36 2 0.07
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (33 bp):
TATTTTATGTTTAACTTGATACAATCGATCTAT
Found at i:37977032 original size:38 final size:38
Alignment explanation
Indices: 37976981--37977058 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
37976971 TCTTTTCAAG
37976981 TTAATTTATGACCCAATGCATATTGTTTTAAGTAATTT
1 TTAATTTATGACCCAATGCATATTGTTTTAAGTAATTT
37977019 TTAATTTATGACCCAATGCATATTGTTTTAAGTAATTT
1 TTAATTTATGACCCAATGCATATTGTTTTAAGTAATTT
37977057 TT
1 TT
37977059 TAATCATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (38 bp):
TTAATTTATGACCCAATGCATATTGTTTTAAGTAATTT
Found at i:37979758 original size:15 final size:16
Alignment explanation
Indices: 37979733--37979767 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
37979723 CAATATGTCT
*
37979733 AAAATATTTTAGATAA
1 AAAATATTTTACATAA
37979749 AAAATA-TTTACATAA
1 AAAATATTTTACATAA
37979764 AAAA
1 AAAA
37979768 GTATGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATATTTTACATAA
Found at i:37981019 original size:243 final size:243
Alignment explanation
Indices: 37980579--37981021 Score: 667
Period size: 243 Copynumber: 1.8 Consensus size: 243
37980569 TTTGTTTCAA
* *
37980579 GGGTGTTGATCTTTTAAATAAAAATTATAACCTTAGCAATATATATTAACATCTGTCATTACTCA
1 GGGTGTTGATCTTTTAAATAAAAATTATAACCTTAACAATATATATTAACATCTGGCATTACTCA
* *
37980644 ATGTCAGTATGAACCTCTATATATTATCTCCTCTCACTCAGATAAAATTAATTTTCCTCCCATTC
66 ATGCCAGTATGAACCTCTATATATTATCTCCTCTCACTCAGATAAAATTAATTTTCCTCCCACTC
* *
37980709 AAACTTATTTCTTCTCTACTCTCATTTTTTCATCTTTTTCTCTTTGTTAGATGATGTTAAAATGA
131 AAACTTATTTCTTCTCTACTCTCATTTCTTCATCTTTTTCTCTTTGTTAGATGATGCTAAAATGA
37980774 TGAAACGGTATGATCGAAAGGGTAGATTTGATAACATTATGATCGAAG
196 TGAAACGGTATGATCGAAAGGGTAGATTTGATAACATTATGATCGAAG
* * *
37980822 GGGTGTTGATCTTTTAAATAAAAGTTATAACCTTAACAATATATATTGACATTTGGCATTACTCA
1 GGGTGTTGATCTTTTAAATAAAAATTATAACCTTAACAATATATATTAACATCTGGCATTACTCA
* * * * * *
37980887 GTGCCGGTATGAACTTCTATATATTCTCTCTTCTCAGC-CA-ACTAAACTTAATTCTT-CTCCCA
66 ATGCCAGTATGAACCTCTATATATTATCTCCTCTCA-CTCAGA-TAAAATTAATT-TTCCTCCCA
* * * *
37980949 CTCAACCTTATTTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATGCTAAGA
128 CTCAAACTTATTTCTTCTCTACTCTCATTTCTTCATCTTTTTCTCTTTGTTAGATGATGCTAAAA
37981014 TGATGAAA
193 TGATGAAA
37981022 GGAAAAGAAA
Statistics
Matches: 178, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
242 1 0.01
243 174 0.98
244 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (243 bp):
GGGTGTTGATCTTTTAAATAAAAATTATAACCTTAACAATATATATTAACATCTGGCATTACTCA
ATGCCAGTATGAACCTCTATATATTATCTCCTCTCACTCAGATAAAATTAATTTTCCTCCCACTC
AAACTTATTTCTTCTCTACTCTCATTTCTTCATCTTTTTCTCTTTGTTAGATGATGCTAAAATGA
TGAAACGGTATGATCGAAAGGGTAGATTTGATAACATTATGATCGAAG
Found at i:37985037 original size:19 final size:20
Alignment explanation
Indices: 37985009--37985047 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
37984999 TTTTAACAAT
37985009 ATTCATTTTTTTTCTTAAAA
1 ATTCATTTTTTTTCTTAAAA
37985029 ATTCA-TTTTTTTCTTAAAA
1 ATTCATTTTTTTTCTTAAAA
37985048 TCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTCATTTTTTTTCTTAAAA
Found at i:37987302 original size:47 final size:47
Alignment explanation
Indices: 37987193--37987303 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
37987183 CCGGGATAAG
* * *
37987193 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
37987240 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
37987287 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
37987304 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:37990016 original size:4 final size:4
Alignment explanation
Indices: 37990007--37990035 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
37989997 CCCTTTTCTA
37990007 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
37990036 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:37992929 original size:17 final size:16
Alignment explanation
Indices: 37992909--37992967 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
37992899 ATATATAAAA
37992909 TATAATAACAAAATATT
1 TATAATAA-AAAATATT
*
37992926 TATAA-AAGAATAATAAT
1 TATAATAA-AA-AATATT
*
37992943 TAT-ATAAAAAATATA
1 TATAATAAAAAATATT
*
37992958 TAAAATAAAA
1 TATAATAAAA
37992968 GTAGGTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 15 0.44
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
TATAATAAAAAATATT
Found at i:37992949 original size:11 final size:11
Alignment explanation
Indices: 37992898--37992962 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
37992888 TTTGCTATAT
37992898 AATATATAAAA
1 AATATATAAAA
*
37992909 TATA-ATAACAA
1 AATATATAA-AA
* *
37992920 AATATTTATAA
1 AATATATAAAA
* *
37992931 AAGA-ATAATA
1 AATATATAAAA
*
37992941 ATTATATAAAA
1 AATATATAAAA
37992952 AATATATAAAA
1 AATATATAAAA
37992963 TAAAAGTAGG
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
10 9 0.23
11 28 0.72
12 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
AATATATAAAA
Found at i:37993362 original size:20 final size:18
Alignment explanation
Indices: 37993337--37993390 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
37993327 AATAATAAGG
37993337 ATAAAAATAAATATCAATAT
1 ATAAAAATAAATAT--ATAT
*
37993357 ATAAAAATATATATATAT
1 ATAAAAATAAATATATAT
*
37993375 ATATAGAATAAATATA
1 ATA-AAAATAAATATA
37993391 GGACTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.23
19 10 0.33
20 13 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAAAATAAATATATAT
Found at i:37996156 original size:30 final size:30
Alignment explanation
Indices: 37996115--37996246 Score: 158
Period size: 30 Copynumber: 4.4 Consensus size: 30
37996105 GAAAAATAAA
*
37996115 AAATTACATTTTAACCCCTAAACTTTTCTT
1 AAATTTCATTTTAACCCCTAAACTTTTCTT
* * * *
37996145 AAATTTTATTTTGACCCCTAAACTTTCCCT
1 AAATTTCATTTTAACCCCTAAACTTTTCTT
* *
37996175 AAATTTCATTTTGACCCCCAAAC-TTTCTTT
1 AAATTTCATTTTAACCCCTAAACTTTTC-TT
* * *
37996205 AAATTTCAATTTAATCCCTAAAATTTTCTT
1 AAATTTCATTTTAACCCCTAAACTTTTCTT
37996235 AAATTTCATTTT
1 AAATTTCATTTT
37996247 GACCTTAAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 3 0.04
30 78 0.92
31 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTAACCCCTAAACTTTTCTT
Found at i:37997774 original size:18 final size:17
Alignment explanation
Indices: 37997719--37997779 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
37997709 ATTTCTCGGG
**
37997719 TTTCAAAGATTCTCAGGT
1 TTTCAAA-ATTCTTGGGT
* *
37997737 TTTCAAGAATTTTTGTGT
1 TTTCAA-AATTCTTGGGT
37997755 TTTCAAAATCTCTTGGG-
1 TTTCAAAAT-TCTTGGGT
37997772 TTTCAAAA
1 TTTCAAAA
37997780 AAAAAATTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 11 0.31
18 23 0.66
19 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (17 bp):
TTTCAAAATTCTTGGGT
Found at i:37997831 original size:16 final size:17
Alignment explanation
Indices: 37997791--37997831 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
37997781 AAAAATTTCA
*
37997791 AGTTTCAAAATTTTCGT
1 AGTTTCAAAATTCTCGT
*
37997808 AATTTCAAAATTCTCGT
1 AGTTTCAAAATTCTCGT
37997825 -GTTTCAA
1 AGTTTCAA
37997832 TCGGATCATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (17 bp):
AGTTTCAAAATTCTCGT
Found at i:38009813 original size:5 final size:5
Alignment explanation
Indices: 38009803--38009840 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
38009793 ATTTGTGAAA
*
38009803 AAAAT AAAAT AAAAT AAAAT AAAGAA AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AA
38009841 CACAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:38017149 original size:45 final size:45
Alignment explanation
Indices: 38017099--38017193 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
38017089 CTTTATAGAT
* *
38017099 AAAATCTAGTTTTGTTGAAAATAATCACTAAAATAAATATAAGCC
1 AAAATCTAGTTTCGTTGAAAATAATCAATAAAATAAATATAAGCC
38017144 AAAATCTAGTTTCGTTGAAAATAATCAATAAAATAAATATAAGCC
1 AAAATCTAGTTTCGTTGAAAATAATCAATAAAATAAATATAAGCC
38017189 AAAAT
1 AAAAT
38017194 GGTGAGGCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (45 bp):
AAAATCTAGTTTCGTTGAAAATAATCAATAAAATAAATATAAGCC
Found at i:38019144 original size:18 final size:18
Alignment explanation
Indices: 38019117--38019209 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
38019107 TACGACCGTT
38019117 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38019135 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38019153 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38019171 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38019189 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
38019207 TAC
1 TAC
38019210 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:38027923 original size:22 final size:22
Alignment explanation
Indices: 38027877--38027923 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38027867 GTAATATGAT
* * *
38027877 AACGAAATGGTACCAAAATAGC
1 AACGAAATGGCACCAAAACAAC
*
38027899 AACGAAATGGCAGCAAAACAAC
1 AACGAAATGGCACCAAAACAAC
38027921 AAC
1 AAC
38027924 AAGATAGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.21, G:0.17, T:0.09
Consensus pattern (22 bp):
AACGAAATGGCACCAAAACAAC
Found at i:38029004 original size:24 final size:24
Alignment explanation
Indices: 38028977--38029092 Score: 84
Period size: 25 Copynumber: 4.9 Consensus size: 24
38028967 TTAATGTTAA
*
38028977 AAAATTATAAAATATTTAAAAAAT
1 AAAATTATAAAATATTAAAAAAAT
*
38029001 AAAAAGTTA-AGAAAT-TGAAAAAAAT
1 -AAAA-TTATA-AAATATTAAAAAAAT
38029026 --AATTATAAAATA-TAAAAAAAT
1 AAAATTATAAAATATTAAAAAAAT
* *
38029047 AAAAATATTTAAAT-TATAAAAAATAT
1 AAAATTA-TAAAATAT-TAAAAAA-AT
*
38029073 AAAATTATAAATTA-TAAAAA
1 AAAATTATAAAATATTAAAAA
38029093 CTATTAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
21 15 0.21
22 3 0.04
23 4 0.06
24 11 0.15
25 24 0.33
26 15 0.21
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (24 bp):
AAAATTATAAAATATTAAAAAAAT
Found at i:38029067 original size:17 final size:17
Alignment explanation
Indices: 38029032--38029146 Score: 67
Period size: 17 Copynumber: 6.6 Consensus size: 17
38029022 AAATAATTAT
**
38029032 AAAATATAAAAAAAT-A
1 AAAATATAAAATTATAA
*
38029048 AAAATATTTAAATTATAA
1 AAAATA-TAAAATTATAA
38029066 AAAATATAAAATTATAA
1 AAAATATAAAATTATAA
** *
38029083 ATTATA-AAAACTATTAA
1 AAAATATAAAATTA-TAA
*
38029100 AAATATATAAAAATCATAGA
1 AAA-ATAT-AAAATTATA-A
* *
38029120 ATAAATA-AAATTTCTAA
1 A-AAATATAAAATTATAA
38029137 AAAA-ATAAAA
1 AAAATATAAAA
38029147 AATATATATA
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
15 1 0.01
16 18 0.24
17 26 0.35
18 16 0.21
19 2 0.03
20 10 0.13
21 2 0.03
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.29
Consensus pattern (17 bp):
AAAATATAAAATTATAA
Found at i:38029069 original size:47 final size:45
Alignment explanation
Indices: 38028975--38029111 Score: 114
Period size: 47 Copynumber: 2.9 Consensus size: 45
38028965 ACTTAATGTT
* * *
38028975 AAAAAATTATAAAATATTTAAAAAATAAAAA-GTTAAGAAATTGAAAA
1 AAAAAATTATAAAATA-TAAAAAAATAAAAATATTTA-AAATT-AAAA
* *
38029022 AAATAATTATAAAATATAAAAAAATAAAAATATTTAAATTATAAAAA
1 AAAAAATTATAAAATATAAAAAAATAAAAATATTTAAA--ATTAAAA
* * *
38029069 ATATAAAATTATAAATTATAAAAACTATTAAAAATATATAAAA
1 A-A-AAAATTATAAAATATAAAAA--AATAAAAATATTTAAAA
38029112 ATCATAGAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
46 15 0.20
47 23 0.31
48 3 0.04
49 19 0.26
51 14 0.19
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (45 bp):
AAAAAATTATAAAATATAAAAAAATAAAAATATTTAAAATTAAAA
Found at i:38029070 original size:10 final size:9
Alignment explanation
Indices: 38028976--38029113 Score: 71
Period size: 9 Copynumber: 15.7 Consensus size: 9
38028966 CTTAATGTTA
38028976 AAAAATTAT
1 AAAAATTAT
38028985 AAAATATT-T
1 AAAA-ATTAT
38028994 AAAAA--AT
1 AAAAATTAT
38029001 AAAAAGTTA-
1 AAAAA-TTAT
* *
38029010 AGAAATTGAA
1 AAAAATT-AT
*
38029020 AAAAATAATT
1 AAAAATTA-T
38029030 ATAAAA-TAT
1 A-AAAATTAT
*
38029039 AAAAA-AAT
1 AAAAATTAT
38029047 AAAAA-TAT
1 AAAAATTAT
**
38029055 TTAAATTAT
1 AAAAATTAT
*
38029064 AAAAAATAT
1 AAAAATTAT
38029073 -AAAATTAT
1 AAAAATTAT
38029081 --AAATTAT
1 AAAAATTAT
*
38029088 AAAAACTATT
1 AAAAATTA-T
38029098 AAAAATATAT
1 AAAAAT-TAT
38029108 AAAAAT
1 AAAAAT
38029114 CATAGAATAA
Statistics
Matches: 100, Mismatches: 15, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
7 13 0.13
8 26 0.26
9 31 0.31
10 24 0.24
11 6 0.06
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:38029075 original size:9 final size:9
Alignment explanation
Indices: 38029032--38029152 Score: 67
Period size: 9 Copynumber: 13.9 Consensus size: 9
38029022 AAATAATTAT
38029032 AAAATATAA
1 AAAATATAA
38029041 AAAA-AT-A
1 AAAATATAA
**
38029048 AAAATATTT
1 AAAATATAA
*
38029057 AAATTATAA
1 AAAATATAA
38029066 AAAATAT--
1 AAAATATAA
*
38029073 AAAAT-TAT
1 AAAATATAA
*
38029081 AAATTATAA
1 AAAATATAA
* *
38029090 AAACTATTA
1 AAAATATAA
38029099 AAAATATATA
1 AAAATATA-A
38029109 AAAATCATAGA
1 AAAAT-ATA-A
*
38029120 ATAA-ATAA
1 AAAATATAA
** *
38029128 AATTTCTAA
1 AAAATATAA
38029137 AAAA-ATAA
1 AAAATATAA
38029145 AAAATATA
1 AAAATATA
38029153 TATATTGGCA
Statistics
Matches: 83, Mismatches: 20, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
6 1 0.01
7 10 0.12
8 17 0.20
9 42 0.51
10 6 0.07
11 7 0.08
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAATATAA
Found at i:38029100 original size:25 final size:24
Alignment explanation
Indices: 38029026--38029106 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 24
38029016 TGAAAAAAAT
* * *
38029026 AATTATAAAATATAAAAAAATAAA
1 AATTATAAATTATAAAAATATTAA
*
38029050 AATATTTAAATTATAAAAA-ATATAA
1 AAT-TATAAATTATAAAAATAT-TAA
38029075 AATTATAAATTATAAAAACTATTAA
1 AATTATAAATTATAAAAA-TATTAA
*
38029100 AAATATA
1 AATTATA
38029107 TAAAAATCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
24 19 0.40
25 27 0.56
26 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTATAAATTATAAAAATATTAA
Found at i:38030906 original size:21 final size:21
Alignment explanation
Indices: 38030882--38030921 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38030872 ACGCGTCTGA
**
38030882 CACCAGCTGCCACCGCCCAAG
1 CACCAGCCACCACCGCCCAAG
*
38030903 CACCTGCCACCACCGCCCA
1 CACCAGCCACCACCGCCCA
38030922 TGCCCACTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.57, G:0.15, T:0.05
Consensus pattern (21 bp):
CACCAGCCACCACCGCCCAAG
Found at i:38038741 original size:15 final size:15
Alignment explanation
Indices: 38038721--38038754 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38038711 TTTACTTTTG
* *
38038721 TTATTTTTGCTCGTA
1 TTATTTTTACTCGCA
38038736 TTATTTTTACTCGCA
1 TTATTTTTACTCGCA
38038751 TTAT
1 TTAT
38038755 CGTAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (15 bp):
TTATTTTTACTCGCA
Found at i:38042432 original size:19 final size:19
Alignment explanation
Indices: 38042383--38042433 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
38042373 GTTTATGAAA
*
38042383 TTTAATATTTTAAAATATT
1 TTTAATATATTAAAATATT
*
38042402 TTTAATTTTATATTAAAATTTT
1 TTTAA---TATATTAAAATATT
38042424 TTTAATATAT
1 TTTAATATAT
38042434 GCCATCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 10 0.37
22 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATATATTAAAATATT
Found at i:38043895 original size:49 final size:50
Alignment explanation
Indices: 38043842--38043946 Score: 133
Period size: 53 Copynumber: 2.1 Consensus size: 50
38043832 ATAATAAAGA
* *
38043842 TAAATAATATTTA-ATTAGAA-TAAAGATAATTAATATTTATCTTAATATT
1 TAAATAATATTTATATTA-AATTAAAGATAAATAATATTCATCTTAATATT
*
38043891 TAAATAATATTTATATTAAATTCGTAAAGATAAATATTATTCATCTTAATATT
1 TAAATAATATTTATATTAAA-T--TAAAGATAAATAATATTCATCTTAATATT
38043944 TAA
1 TAA
38043947 GTTTCTTATC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
49 15 0.31
50 4 0.08
53 29 0.60
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (50 bp):
TAAATAATATTTATATTAAATTAAAGATAAATAATATTCATCTTAATATT
Done.