Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 78 of 93
Found at i:29810663 original size:31 final size:31
Alignment explanation
Indices: 29810623--29810787 Score: 134
Period size: 31 Copynumber: 5.4 Consensus size: 31
29810613 CTCCAACAAG
* * **
29810623 TCAGCGTGTCACGCAATAAATCTGCAATGAC
1 TCAGCGTGTCAAGCCATAAATCTGCAACCAC
* * *
29810654 TCAGTGTGTCATGCCATAAATCTGCTACCAC
1 TCAGCGTGTCAAGCCATAAATCTGCAACCAC
* *
29810685 TCAGCGTGTCAAGCCATAAATCTGCTATCAC
1 TCAGCGTGTCAAGCCATAAATCTGCAACCAC
* * * * ***
29810716 TTAGAGTGTC-AGTCATAAATCAGCTTGCAC
1 TCAGCGTGTCAAGCCATAAATCTGCAACCAC
* * ** *
29810746 TCAGAGTGTGACCCCATAAATCTGCTACCAC
1 TCAGCGTGTCAAGCCATAAATCTGCAACCAC
29810777 TCAGCGTGTCA
1 TCAGCGTGTCA
29810788 CCACAAGGTG
Statistics
Matches: 108, Mismatches: 25, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
30 24 0.22
31 84 0.78
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (31 bp):
TCAGCGTGTCAAGCCATAAATCTGCAACCAC
Found at i:29810694 original size:62 final size:61
Alignment explanation
Indices: 29810623--29810787 Score: 177
Period size: 61 Copynumber: 2.7 Consensus size: 61
29810613 CTCCAACAAG
* * * *
29810623 TCAGCGTGTCACGCAATAAATCTGCAATGACTCAGTGTGTCATGCCATAAATCTGCTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCAATCACTCAGAGTGTCA-GCCATAAATCAGCTACCAC
* * * * **
29810685 TCAGCGTGTCAAGCCATAAATCTGCTATCACTTAGAGTGTCAGTCATAAATCAGCTTGCAC
1 TCAGCGTGTCACGCCATAAATCTGCAATCACTCAGAGTGTCAGCCATAAATCAGCTACCAC
* * * * * *
29810746 TCAGAGTGTGACCCCATAAATCTGCTACCACTCAGCGTGTCA
1 TCAGCGTGTCACGCCATAAATCTGCAATCACTCAGAGTGTCA
29810788 CCACAAGGTG
Statistics
Matches: 86, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
61 50 0.58
62 36 0.42
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (61 bp):
TCAGCGTGTCACGCCATAAATCTGCAATCACTCAGAGTGTCAGCCATAAATCAGCTACCAC
Found at i:29811028 original size:104 final size:106
Alignment explanation
Indices: 29810761--29811016 Score: 349
Period size: 104 Copynumber: 2.4 Consensus size: 106
29810751 GTGTGACCCC
*
29810761 ATAAATCTGCTACCACTCAGCGTGTCACCACAAGGTGTCATCGACACATGACAATTA-GGGCAGC
1 ATAAATCTGCTTCCACTCAGCGTGTCACCACAAGGTGTCATCGACACATGACAATTACGGGCA-C
* * **
29810825 GCGTGTTACCCCACAATATTGGACAAGTCAGCGTGTCACGTG
65 GCGTGTCACCCCACAATATTGGACAAGTCAACGTGTCACACG
* * *
29810867 ATCAATCTGCTTCCACTCAGCGTGTCACCACAAGGTGTCATCAACACATGACAATTACGGTGTA-
1 ATAAATCTGCTTCCACTCAGCGTGTCACCACAAGGTGTCATCGACACATGACAATTACGG-GCAC
*
29810931 GCGTGTCA-CCC-TAATATTGGACAAGTCAACGTGTCACACG
65 GCGTGTCACCCCACAATATTGGACAAGTCAACGTGTCACACG
* * * *
29810971 ATAAATCTACTTCCACTTAGTGTGTCACCACAAGATGTCATCGACA
1 ATAAATCTGCTTCCACTCAGCGTGTCACCACAAGGTGTCATCGACA
29811017 TCTACCAATT
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
104 65 0.49
105 3 0.02
106 61 0.46
107 2 0.02
108 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (106 bp):
ATAAATCTGCTTCCACTCAGCGTGTCACCACAAGGTGTCATCGACACATGACAATTACGGGCACG
CGTGTCACCCCACAATATTGGACAAGTCAACGTGTCACACG
Found at i:29814899 original size:23 final size:23
Alignment explanation
Indices: 29814840--29814899 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
29814830 GTTGTTATAT
*
29814840 GCCATGTTTAAAATATGTTACAC
1 GCCATGTTTAAAAAATGTTACAC
** * *
29814863 GTAATTTTTGAAAAATGTTACAC
1 GCCATGTTTAAAAAATGTTACAC
*
29814886 GCCATGTTCAAAAA
1 GCCATGTTTAAAAA
29814900 TATCACACGC
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (23 bp):
GCCATGTTTAAAAAATGTTACAC
Found at i:29814974 original size:21 final size:21
Alignment explanation
Indices: 29814939--29815099 Score: 92
Period size: 21 Copynumber: 7.2 Consensus size: 21
29814929 CTATATGCAT
*
29814939 TGTTCAAAAATTGTTACACGTCT
1 TGTTCAAAAA-TGTTACACG-CA
29814962 TG-TCAAAAATGTTACACGCA
1 TGTTCAAAAATGTTACACGCA
* * *
29814982 AGTTCAAAAATAATTACACGCCC
1 TGTTCAAAAAT-GTTACACG-CA
* *
29815005 TGTTCAAAAATGTTACATGTA
1 TGTTCAAAAATGTTACACGCA
* * *
29815026 AGTTAAAAAATG-TAGCACGTTA
1 TGTTCAAAAATGTTA-CACG-CA
* *
29815048 TGTTCACAATATGTTACATGCCA
1 TGTTCA-AAAATGTTACACG-CA
*
29815071 TGTTAAATAAAAATGTTACACGCCA
1 TGTT---CAAAAATGTTACACG-CA
29815096 TGTT
1 TGTT
29815100 AAATAAAAAT
Statistics
Matches: 107, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
20 4 0.04
21 30 0.28
22 26 0.24
23 26 0.24
24 2 0.02
25 18 0.17
26 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (21 bp):
TGTTCAAAAATGTTACACGCA
Found at i:29815029 original size:44 final size:43
Alignment explanation
Indices: 29814940--29815036 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
29814930 TATATGCATT
** * *
29814940 GTTCAAAAATTGTTACACGTCTTGTCAAAAATGTTACACGCAA
1 GTTCAAAAATAATTACACGCCCTGTCAAAAATGTTACACGCAA
* *
29814983 GTTCAAAAATAATTACACGCCCTGTTCAAAAATGTTACATGTAA
1 GTTCAAAAATAATTACACGCCCTG-TCAAAAATGTTACACGCAA
*
29815027 GTTAAAAAAT
1 GTTCAAAAAT
29815037 GTAGCACGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 20 0.43
44 26 0.57
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (43 bp):
GTTCAAAAATAATTACACGCCCTGTCAAAAATGTTACACGCAA
Found at i:29815087 original size:25 final size:25
Alignment explanation
Indices: 29815058--29815121 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
29815048 TGTTCACAAT
*
29815058 ATGTTACATGCCATGTTAAATAAAA
1 ATGTTACACGCCATGTTAAATAAAA
29815083 ATGTTACACGCCATGTTAAATAAAA
1 ATGTTACACGCCATGTTAAATAAAA
*
29815108 A--TTACACGTCATGT
1 ATGTTACACGCCATGT
29815122 GCTAATACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 12 0.32
25 25 0.68
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (25 bp):
ATGTTACACGCCATGTTAAATAAAA
Found at i:29822242 original size:27 final size:24
Alignment explanation
Indices: 29822203--29822256 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
29822193 TAAGGTGGAG
*
29822203 ATTTATTAGGATAGTCTTGAATTGTA
1 ATTTATTAAGATAGT-TT-AATTGTA
*
29822229 ATTTGATTAAGATAGTTTAATTTTA
1 ATTT-ATTAAGATAGTTTAATTGTA
29822254 ATT
1 ATT
29822257 AAATTAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
26 6 0.24
27 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (24 bp):
ATTTATTAAGATAGTTTAATTGTA
Found at i:29822262 original size:25 final size:27
Alignment explanation
Indices: 29822207--29822262 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
29822197 GTGGAGATTT
* **
29822207 ATTAGGATAGTCTTGAATTGTAATTTG
1 ATTAAGATAGTCTTGAATTGTAATTAA
*
29822234 ATTAAGATAGT-TT-AATTTTAATTAA
1 ATTAAGATAGTCTTGAATTGTAATTAA
29822259 ATTA
1 ATTA
29822263 GTATACCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 13 0.52
26 2 0.08
27 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (27 bp):
ATTAAGATAGTCTTGAATTGTAATTAA
Found at i:29845832 original size:20 final size:20
Alignment explanation
Indices: 29845803--29845855 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
29845793 TACGCCAGGT
*
29845803 TATCAAATTTAATTTTATAG
1 TATCAAATTTAATATTATAG
* *
29845823 TATCATATTTAATATTATAT
1 TATCAAATTTAATATTATAG
*
29845843 TATTAAATTTAAT
1 TATCAAATTTAAT
29845856 GATATGTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
TATCAAATTTAATATTATAG
Found at i:29858769 original size:3 final size:3
Alignment explanation
Indices: 29858761--29858808 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
29858751 CTGATTCGGG
* * *
29858761 TTC TTC TTC GTC GTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
29858809 ATCATCATCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.02, C:0.33, G:0.04, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:29864011 original size:21 final size:20
Alignment explanation
Indices: 29863967--29864022 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
29863957 AAAAAATTAT
* *
29863967 AAAATTCATCAAAAAAAGTC
1 AAAATTCATCGAAAAAAGCC
*
29863987 AAAATTCATCGAAAAAGGCC
1 AAAATTCATCGAAAAAAGCC
*
29864007 AAAAATCTATCGAAAA
1 AAAATTC-ATCGAAAA
29864023 TGAGTTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.57, C:0.16, G:0.09, T:0.18
Consensus pattern (20 bp):
AAAATTCATCGAAAAAAGCC
Found at i:29864993 original size:82 final size:82
Alignment explanation
Indices: 29864838--29865003 Score: 201
Period size: 82 Copynumber: 2.0 Consensus size: 82
29864828 GTTGAAAATG
* *
29864838 GACACATAAGCCCATGACAAGTGATACCAAAGCATGCATACTCAAATCTTAATTAATGTGGAACC
1 GACACATAAGCCCATGACAAGTGATACCAAAGCATGCATACTCAAATATTAATTAATGTAGAACC
**
29864903 TTATTGAGAGATATAAA
66 CCATTGAGAGATATAAA
* * * * * *
29864920 GACACATGAA-CCCGTGACAAGTGGTAGCAAAGCATGCATACTCCAATATTAATTGATTTAGAAC
1 GACACAT-AAGCCCATGACAAGTGATACCAAAGCATGCATACTCAAATATTAATTAATGTAGAA-
*
29864984 CCCCA-TGAGAGATATCAA
64 CCCCATTGAGAGATATAAA
29865002 GA
1 GA
29865004 TCGAGATAGA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
82 66 0.93
83 5 0.07
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (82 bp):
GACACATAAGCCCATGACAAGTGATACCAAAGCATGCATACTCAAATATTAATTAATGTAGAACC
CCATTGAGAGATATAAA
Found at i:29865191 original size:199 final size:197
Alignment explanation
Indices: 29864870--29865512 Score: 650
Period size: 199 Copynumber: 3.2 Consensus size: 197
29864860 GATACCAAAG
* * * * * * * * * *
29864870 CATGCATACTCAAATCTTAATTAATGT-GGAACCTTATTGAGAGATATAAAGACACATGAACCCG
1 CATGCATACTCAAATCTCAACTGATGTAGG-ACCATA-TGAAAGATATCATGACATATGAGCCCA
* * * * * *
29864934 TGACAAGTGGTAGCAAAGCATGCATACTCCAATATTAATTGATTTAGAACCCCCATGAGAGATAT
64 TGACAAGTGGTATCAAAGCATGCATACTCAAATCTTAATTGATGTGGAA-CACCATGAGAGATAT
* * **
29864999 CAAGATCGAGATAGATTCTAAAAGATGTGTTTTTTTGGTTAGAAACAGACACATGAGCTCATGAC
128 TAAGATCGAGGTAGATTCTAAAAGACATGTTTTTTTGGTTAGAAACAGACACATGAGC-CATGAC
29865064 AAGTGA
192 AAGTGA
*
29865070 CATGCATACTCAAATCTCAACTGATGTAGGATCCA-ATGAAAGATATCGTGACATATGAGCCCAT
1 CATGCATACTCAAATCTCAACTGATGTAGGA-CCATATGAAAGATATCATGACATATGAGCCCAT
* * *
29865134 TACAATTGGTATCAAAGCATGCATATTCAAATCTTAATTGATGTGGAATCACCATGAGAGATATT
65 GACAAGTGGTATCAAAGCATGCATACTCAAATCTTAATTGATGTGGAA-CACCATGAGAGATATT
* * * * * *
29865199 AAGATCGAGGTAGATTTTGAAAGACCTATCTTTTTT-GTTGGAAAC-GA-ACATGTGAGCCTGTG
129 AAGATCGAGGTAGATTCTAAAAGACATGT-TTTTTTGGTTAGAAACAGACACA--TGAGCC-ATG
*
29865261 ACAAGTAA
190 ACAAGTGA
* * * * * * *
29865269 CATGCATGCTCAAATCTTAACTGATGTGGGACCATATGAGAGATATTATGACATATGAGCTCGTG
1 CATGCATACTCAAATCTCAACTGATGTAGGACCATATGAAAGATATCATGACATATGAGCCCATG
*
29865334 ACAAGTGGTATCAAAGCATGCATACTCAAATCTTAATTGATGTGGAACTCCATGAGAGATATTAA
66 ACAAGTGGTATCAAAGCATGCATACTCAAATCTTAATTGATGTGGAACACCATGAGAGATATTAA
* * * * * * * *
29865399 AATAGAGGTAGACTCTAAAAGACATGTCTTTTTGCTTGAAAAACAGACACGTAAGCCCATGACAA
131 GATCGAGGTAGATTCTAAAAGACATGTTTTTTTGGTT-AGAAACAGACACATGAG-CCATGACAA
29865464 GTGA
194 GTGA
* * * * * *
29865468 CATACATACTTAAATC-CTAATTGATGTGGGACCTTATGAGAGATA
1 CATGCATACTCAAATCTC-AACTGATGTAGGACCATATGAAAGATA
29865513 GTCGGATTGA
Statistics
Matches: 366, Mismatches: 64, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
197 8 0.02
198 45 0.12
199 271 0.74
200 36 0.10
201 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (197 bp):
CATGCATACTCAAATCTCAACTGATGTAGGACCATATGAAAGATATCATGACATATGAGCCCATG
ACAAGTGGTATCAAAGCATGCATACTCAAATCTTAATTGATGTGGAACACCATGAGAGATATTAA
GATCGAGGTAGATTCTAAAAGACATGTTTTTTTGGTTAGAAACAGACACATGAGCCATGACAAGT
GA
Found at i:29867094 original size:2 final size:2
Alignment explanation
Indices: 29867087--29867202 Score: 80
Period size: 2 Copynumber: 58.5 Consensus size: 2
29867077 ATTTTGACCC
*
29867087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
29867128 AT AN CT A- AGT TT AT -T AGT AA AT -T A- AT TT GACC AT AT AT AT
1 AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT -A-T AT AT AT AT
* *
29867168 AT AT AT AT AT AT AT AT AT AT GT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29867203 ATTCAAAAGA
Statistics
Matches: 87, Mismatches: 18, Indels: 18
0.71 0.15 0.15
Matches are distributed among these distances:
1 5 0.06
2 79 0.91
3 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29874610 original size:27 final size:27
Alignment explanation
Indices: 29874571--29874734 Score: 143
Period size: 27 Copynumber: 6.1 Consensus size: 27
29874561 AATAACATAT
**
29874571 ACAATGCTA-TATTTTGATGAAGGTAAA
1 ACAATG-TATTATTTTGATGAAAATAAA
* * *
29874598 ACAACGTATTATTTTGATGAAAGTAAT
1 ACAATGTATTATTTTGATGAAAATAAA
* **
29874625 ACAATGTACTATTTCAATGAAAATAAA
1 ACAATGTATTATTTTGATGAAAATAAA
* * * *
29874652 ACAATGTAGTATTTTTATGGAGATAAA
1 ACAATGTATTATTTTGATGAAAATAAA
* * *
29874679 ATAAGGTATTATTTTGATGGAAATAATA
1 ACAATGTATTATTTTGATGAAAATAA-A
* *
29874707 A-AGTGTATTATTTTGATGGAAATAAA
1 ACAATGTATTATTTTGATGAAAATAAA
29874733 AC
1 AC
29874735 TTAAACCTTT
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.04
27 107 0.95
28 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (27 bp):
ACAATGTATTATTTTGATGAAAATAAA
Found at i:29874679 original size:81 final size:81
Alignment explanation
Indices: 29874571--29874734 Score: 199
Period size: 81 Copynumber: 2.0 Consensus size: 81
29874561 AATAACATAT
*
29874571 ACAATGCTATATTTTGATGAAGGTAAAACAACGTATTATTTTGAT-GAAAGTAATACAA-TGTAC
1 ACAATGCTATATTTTGATGAAGATAAAACAACGTATTATTTTGATGGAAA-TAATA-AAGTGTAC
29874634 TATTTCAATGAAAATAAA
64 TATTTCAATGAAAATAAA
* * * * *
29874652 ACAATG-TAGTATTTTTATGGAGATAAAATAAGGTATTATTTTGATGGAAATAATAAAGTGTATT
1 ACAATGCTA-TATTTTGATGAAGATAAAACAACGTATTATTTTGATGGAAATAATAAAGTGTACT
** *
29874716 ATTTTGATGGAAATAAA
65 ATTTCAATGAAAATAAA
29874733 AC
1 AC
29874735 TTAAACCTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 4 0.06
81 63 0.89
82 4 0.06
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (81 bp):
ACAATGCTATATTTTGATGAAGATAAAACAACGTATTATTTTGATGGAAATAATAAAGTGTACTA
TTTCAATGAAAATAAA
Found at i:29876996 original size:26 final size:26
Alignment explanation
Indices: 29876949--29877033 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
29876939 GTTTTGGGGG
*
29876949 AAGAAAGTAA-AAAA-AATA-AAAAGG
1 AAGAAAGTAAGAAAAGAA-ACAAAAGC
*
29876973 AAGAAACTAAGAAAAGAAACAAAAGC
1 AAGAAAGTAAGAAAAGAAACAAAAGC
29876999 AAG-AAGTAATCG-AAAGAAACAAAAGC
1 AAGAAAGTAA--GAAAAGAAACAAAAGC
29877025 AAG-AAGTAA
1 AAGAAAGTAA
29877034 TCAAAAGTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 9 0.17
25 10 0.19
26 33 0.62
27 1 0.02
ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07
Consensus pattern (26 bp):
AAGAAAGTAAGAAAAGAAACAAAAGC
Found at i:29877034 original size:26 final size:26
Alignment explanation
Indices: 29876984--29877040 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
29876974 AGAAACTAAG
29876984 AAAAGAAACAAAAGCAAGAAGTAATC
1 AAAAGAAACAAAAGCAAGAAGTAATC
*
29877010 GAAAGAAACAAAAGCAAGAAGTAATC
1 AAAAGAAACAAAAGCAAGAAGTAATC
29877036 AAAAG
1 AAAAG
29877041 TAAGGGCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.65, C:0.11, G:0.18, T:0.07
Consensus pattern (26 bp):
AAAAGAAACAAAAGCAAGAAGTAATC
Found at i:29889306 original size:17 final size:17
Alignment explanation
Indices: 29889284--29889329 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
29889274 GCGTGCCTAG
29889284 AAAGAAAGAAAAG-AGAA
1 AAAGAAAGAAAAGAAG-A
29889301 AAAGAAA-AAGAAGAAGA
1 AAAGAAAGAA-AAGAAGA
*
29889318 AAAGTAAGAAAA
1 AAAGAAAGAAAA
29889330 ATAGAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.08
17 19 0.76
18 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAAGAAAGAAAAGAAGA
Found at i:29889317 original size:12 final size:13
Alignment explanation
Indices: 29889288--29889321 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
29889278 GCCTAGAAAG
29889288 AAAGAAAAGAGAA
1 AAAGAAAAGAGAA
29889301 AAAGAAAA-AGAA
1 AAAGAAAAGAGAA
*
29889313 GAAGAAAAG
1 AAAGAAAAG
29889322 TAAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAGAA
Found at i:29891346 original size:31 final size:30
Alignment explanation
Indices: 29891308--29891810 Score: 242
Period size: 31 Copynumber: 16.4 Consensus size: 30
29891298 CATGAGAGGA
29891308 TTTAAGCCCAATTTAGCTGGCATCCAAGATG
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
* *
29891339 TTTAAGCCCAATTATATTGGCA-CGAAAGATG
1 TTTAAGCCCAATT-TACTGGCATC-CAAGATG
*
29891370 ATTAAGCCCAATTTACCTGGCATCCAAGATG
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
* * * *
29891401 TATAAGTCC-AGTTACATTGGCA-CAAAAGA-G
1 TTTAAGCCCAATTTAC--TGGCATC-CAAGATG
* * * *
29891431 TTTAAGCCCAATTTAGTTGGCGTTCAAGATA
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
* * * *
29891462 TTTAAGCCCAGTTATATTGGCAT-AAAGACG
1 TTTAAGCCCAATT-TACTGGCATCCAAGATG
* *
29891492 ATTAAGCCTAATTTAGCTGGCATCCAAGATG
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
* * * *
29891523 TATAAGTCC-AGTTACATTGGCA-CAAAGGA-G
1 TTTAAGCCCAATTTAC--TGGCATCCAA-GATG
*
29891553 TTTAAGCCCAATTTAGCTAGCATCCAAGATG
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
* * * *
29891584 TTTAAGCCCAGTTATATTGGCAT-AAAGACG
1 TTTAAGCCCAATT-TACTGGCATCCAAGATG
* *
29891614 ATTAAGCCCAATTTAGCTAGCATCCAAGATG
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
*** * *
29891645 TTTAAG-TTTAGTTACATTGGCA-CAAAAAGA-G
1 TTTAAGCCCAATTTAC--TGGCATC--CAAGATG
** * * *
29891676 TTTAAGCTTAGTTATATTGGCAT-CGAGATG
1 TTTAAGCCCAATT-TACTGGCATCCAAGATG
* * * *
29891706 TTTATGCCCAATTGAACTGGTATCTAAGATG
1 TTTAAGCCCAATT-TACTGGCATCCAAGATG
* * * * *
29891737 TTTAAGCCCAATTATATTAGTA-CAAAGATA
1 TTTAAGCCCAATT-TACTGGCATCCAAGATG
* * *
29891767 TTTAAGCTCAATTTAGCTGGCATCCAAAACG
1 TTTAAGCCCAATTTA-CTGGCATCCAAGATG
29891798 TTTAAGCCCAATT
1 TTTAAGCCCAATT
29891811 ATCTTGGCAT
Statistics
Matches: 347, Mismatches: 90, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
29 12 0.03
30 128 0.37
31 190 0.55
32 15 0.04
33 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (30 bp):
TTTAAGCCCAATTTACTGGCATCCAAGATG
Found at i:29891473 original size:61 final size:62
Alignment explanation
Indices: 29891308--29891682 Score: 463
Period size: 61 Copynumber: 6.1 Consensus size: 62
29891298 CATGAGAGGA
* * * *
29891308 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAATTATATTGGCACGAAAGATG
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAAGACG
* * * *
29891370 ATTAAGCCCAATTTACCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAAGA-G
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAAGACG
* * * * * *
29891431 TTTAAGCCCAATTTAGTTGGCGTTCAAGATATTTAAGCCCAGTTATATTGGCA-TAAAGACG
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAAGACG
* * * * *
29891492 ATTAAGCCTAATTTAGCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAGGA-G
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAAGACG
* * *
29891553 TTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGCCCAGTTATATTGGCA-TAAAGACG
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAAGACG
* * ***
29891614 ATTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTTTAGTTACATTGGCACAAAAAGA-G
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCAC-AAAAGACG
29891676 TTTAAGC
1 TTTAAGC
29891683 TTAGTTATAT
Statistics
Matches: 265, Mismatches: 43, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
60 9 0.03
61 187 0.71
62 64 0.24
63 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (62 bp):
TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAAGACG
Found at i:29891530 original size:122 final size:122
Alignment explanation
Indices: 29891308--29891682 Score: 597
Period size: 122 Copynumber: 3.1 Consensus size: 122
29891298 CATGAGAGGA
* * *
29891308 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAATTATATTGGCACGAAAGATGATT
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCA-TAAAGACGATT
*
29891373 AAGCCCAATTTACCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAAGAG
65 AAGCCCAATTTAGCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAAGAG
* * * *
29891431 TTTAAGCCCAATTTAGTTGGCGTTCAAGATATTTAAGCCCAGTTATATTGGCATAAAGACGATTA
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCATAAAGACGATTA
* *
29891496 AGCCTAATTTAGCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAGGAG
66 AGCCCAATTTAGCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAAGAG
*
29891553 TTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGCCCAGTTATATTGGCATAAAGACGATTA
1 TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCATAAAGACGATTA
* * **
29891618 AGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTTTAGTTACATTGGCACAAAAAGAG
66 AGCCCAATTTAGCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCAC-AAAAGAG
29891676 TTTAAGC
1 TTTAAGC
29891683 TTAGTTATAT
Statistics
Matches: 230, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
122 169 0.73
123 61 0.27
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (122 bp):
TTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCATAAAGACGATTA
AGCCCAATTTAGCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAAGAG
Found at i:29891752 original size:61 final size:61
Alignment explanation
Indices: 29891687--29891833 Score: 136
Period size: 61 Copynumber: 2.4 Consensus size: 61
29891677 TTAAGCTTAG
* * * * * *
29891687 TTATATTGGCATCGAGATGTTTATGCCCAATTGAACTGGTATCTAAGATGTTTAAGCCCAA
1 TTATATTGGCATCGAGATATTTAAGCCCAATTGAACTGGCATCCAAAACGTTTAAGCCCAA
* * * * * *
29891748 TTATATTAGTA-CAAAGATATTTAAGCTCAATTTAGCTGGCATCCAAAACGTTTAAGCCCAA
1 TTATATTGGCATC-GAGATATTTAAGCCCAATTGAACTGGCATCCAAAACGTTTAAGCCCAA
* *
29891809 TTATCTTGGCAT-GAGAGAATTTAAG
1 TTATATTGGCATCGAGA-TATTTAAG
29891834 TTACGTAGCC
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
60 4 0.06
61 62 0.94
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (61 bp):
TTATATTGGCATCGAGATATTTAAGCCCAATTGAACTGGCATCCAAAACGTTTAAGCCCAA
Found at i:29891922 original size:21 final size:21
Alignment explanation
Indices: 29891871--29891925 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
29891861 CCAACCTTTT
29891871 ATTCT-AAAACCTTCAGGTAC
1 ATTCTCAAAACCTTCAGGTAC
* *
29891891 ATTTTTCAAAACCTTCGGGTAC
1 A-TTCTCAAAACCTTCAGGTAC
29891913 ATTCTCAAAACCT
1 ATTCTCAAAACCT
29891926 CTGAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 14 0.47
22 15 0.50
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (21 bp):
ATTCTCAAAACCTTCAGGTAC
Found at i:29892018 original size:22 final size:21
Alignment explanation
Indices: 29891993--29892036 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29891983 AATAACATTT
29891993 TCTTCTAAAACCTCCGGGTACA
1 TCTT-TAAAACCTCCGGGTACA
* *
29892015 TCTTTTAAACCTTCGGGTACA
1 TCTTTAAAACCTCCGGGTACA
29892036 T
1 T
29892037 TCCCAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (21 bp):
TCTTTAAAACCTCCGGGTACA
Found at i:29892078 original size:122 final size:122
Alignment explanation
Indices: 29891831--29892178 Score: 509
Period size: 122 Copynumber: 2.8 Consensus size: 122
29891821 GAGAGAATTT
* * * * *
29891831 AAGTTACGTAGCCTCATTTTGAGATGAGGACCAACCTTTTATTCTAAAACCTTCAGGTACAT-TT
1 AAGTTACGTAGCCTCATTTTGAGATGAGGAACAACATTTTCTTCTAAAACCTCCGGGTACATCTT
* ** *
29891895 TTCAAAACCTTCGGGTACATTCTCAAAACCTCTGAATAATTTGTTTCAAGATTTCTTCA
66 TT--AAACCTTCGGGTACATTCTCAAAACCTTTGGGTAATTTGTTTCAAGACTTCTTCA
*
29891954 AAGTTACGTAGCCTCATTTTGAGATGAGGAATAACATTTTCTTCTAAAACCTCCGGGTACATCTT
1 AAGTTACGTAGCCTCATTTTGAGATGAGGAACAACATTTTCTTCTAAAACCTCCGGGTACATCTT
* * *
29892019 TTAAACCTTCGGGTACATTCCCAAAACTTTTGGGTAATTTTTTTCAAGACTTCTTCA
66 TTAAACCTTCGGGTACATTCTCAAAACCTTTGGGTAATTTGTTTCAAGACTTCTTCA
* * *
29892076 AAGTTACGTAGCCTCATTTTGAGATGAGGAACAACAGTTTCTTCTAAAACCTCTGAGTACATCTT
1 AAGTTACGTAGCCTCATTTTGAGATGAGGAACAACATTTTCTTCTAAAACCTCCGGGTACATCTT
* *
29892141 TTAAACCTTCAGGTACATTCTCAAAACCTTCGGGTAAT
66 TTAAACCTTCGGGTACATTCTCAAAACCTTTGGGTAAT
29892179 CAATTCCAAG
Statistics
Matches: 203, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
122 143 0.70
123 56 0.28
124 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (122 bp):
AAGTTACGTAGCCTCATTTTGAGATGAGGAACAACATTTTCTTCTAAAACCTCCGGGTACATCTT
TTAAACCTTCGGGTACATTCTCAAAACCTTTGGGTAATTTGTTTCAAGACTTCTTCA
Found at i:29893293 original size:21 final size:20
Alignment explanation
Indices: 29893269--29893326 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
29893259 CTGCGTGCTC
29893269 AGAAAGAGAGAAAAGAGAAAA
1 AGAAAGAGAGAAAA-AGAAAA
* *
29893290 AGAAAAAGAAGAAAAAGAAGA
1 AGAAAGAG-AGAAAAAGAAAA
*
29893311 AGAAAAGAAAGAAAAA
1 AG-AAAGAGAGAAAAA
29893327 TAGAGAGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AGAAAGAGAGAAAAAGAAAA
Found at i:29893302 original size:15 final size:15
Alignment explanation
Indices: 29893269--29893326 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
29893259 CTGCGTGCTC
*
29893269 AGAAAGAGAGAAAAG-
1 AGAAAAAGA-AAAAGA
29893284 AGAAAAAGAAAAAGA
1 AGAAAAAGAAAAAGA
*
29893299 AGAAAAAGAAGAAGA
1 AGAAAAAGAAAAAGA
29893314 A-AAGAAAGAAAAA
1 AGAA-AAAGAAAAA
29893327 TAGAGAGAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 7 0.18
15 31 0.82
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAAGA
Found at i:29896671 original size:2 final size:2
Alignment explanation
Indices: 29896618--29896652 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29896608 TTACACACAC
*
29896618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29896653 CACCTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29896753 original size:106 final size:105
Alignment explanation
Indices: 29896618--29896828 Score: 413
Period size: 106 Copynumber: 2.0 Consensus size: 105
29896608 TTACACACAC
29896618 ATATATATATATATATATATATATATATGTATATACACCTAATAAATTATATATTGGTATGAGCA
1 ATATATATATATATATATATATATATATGTATATACACCTAATAAATTATATATTGGTATGAGCA
29896683 ATATTGGACTCCCGCACTGGGGGATCCGGTGGATGACGAT
66 ATATTGGACTCCCGCACTGGGGGATCCGGTGGATGACGAT
29896723 NATATATATATATATATATATATATATATGTATATACACCTAATAAATTATATATTGGTATGAGC
1 -ATATATATATATATATATATATATATATGTATATACACCTAATAAATTATATATTGGTATGAGC
29896788 AATATTGGACTCCCGCACTGGGGGATCCGGTGGATGACGAT
65 AATATTGGACTCCCGCACTGGGGGATCCGGTGGATGACGAT
29896829 GCATCAACTA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (105 bp):
ATATATATATATATATATATATATATATGTATATACACCTAATAAATTATATATTGGTATGAGCA
ATATTGGACTCCCGCACTGGGGGATCCGGTGGATGACGAT
Found at i:29896777 original size:2 final size:2
Alignment explanation
Indices: 29896724--29896758 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29896714 GATGACGATN
*
29896724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29896759 CACCTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29900298 original size:17 final size:17
Alignment explanation
Indices: 29900276--29900313 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29900266 TTAAAATTAT
29900276 TAATA-TTATAATTATAA
1 TAATATTTA-AATTATAA
29900293 TAATATTTAAATTATAA
1 TAATATTTAAATTATAA
29900310 -AATA
1 TAATA
29900314 AGATATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 13 0.65
18 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATTTAAATTATAA
Found at i:29933458 original size:2 final size:2
Alignment explanation
Indices: 29933453--29933479 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29933443 TGTGTGTGTG
29933453 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29933480 GTTAGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29934642 original size:46 final size:46
Alignment explanation
Indices: 29934575--29934669 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
29934565 TCATGTTTCA
* * * *
29934575 TTTTCCTATTGGTTTATATTGTTAATTTTTTGTCAA-GGATTTTCTC
1 TTTTCCTATTGGTTTAGATTGTTAAATTTTTATCAACAG-TTTTCTC
29934621 TTTTCCTATTGGTTTAGATTGTTAAATTTTTATCAACAGTTTTCTC
1 TTTTCCTATTGGTTTAGATTGTTAAATTTTTATCAACAGTTTTCTC
29934667 TTT
1 TTT
29934670 ATAACTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (46 bp):
TTTTCCTATTGGTTTAGATTGTTAAATTTTTATCAACAGTTTTCTC
Found at i:29939012 original size:40 final size:40
Alignment explanation
Indices: 29938940--29939018 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
29938930 TTATGAAAGA
* * *
29938940 CACCAATCGTGGCGAGGTTGAAAACCCCACTAAGGTGAAT
1 CACCAATCGTGGCAAGATTAAAAACCCCACTAAGGTGAAT
* * *
29938980 CACCAATCTTGGCAAGATTAAAAATCCGACTAAGGTGAA
1 CACCAATCGTGGCAAGATTAAAAACCCCACTAAGGTGAA
29939019 AAATAACCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (40 bp):
CACCAATCGTGGCAAGATTAAAAACCCCACTAAGGTGAAT
Found at i:29947515 original size:92 final size:92
Alignment explanation
Indices: 29947358--29947528 Score: 315
Period size: 92 Copynumber: 1.9 Consensus size: 92
29947348 AATGGAATTA
*
29947358 TTGATAATTACTCAGCTATATAAGTTTAGCATTTGAGTATGCACATGACAAGGTTATGTGGCACA
1 TTGATAATTACTCAACTATATAAGTTTAGCATTTGAGTATGCACATGACAAGGTTATGTGGCACA
29947423 GTCCACACTAACCTGCAAAGCATTGAT
66 GTCCACACTAACCTGCAAAGCATTGAT
* *
29947450 TTGATAATTACTCAACTATATAAGTTTGGCATTTGAGTATGCACATGAGAAGGTTATGTGGCACA
1 TTGATAATTACTCAACTATATAAGTTTAGCATTTGAGTATGCACATGACAAGGTTATGTGGCACA
29947515 GTCCACACTAACCT
66 GTCCACACTAACCT
29947529 ACTTTAGTTG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 76 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (92 bp):
TTGATAATTACTCAACTATATAAGTTTAGCATTTGAGTATGCACATGACAAGGTTATGTGGCACA
GTCCACACTAACCTGCAAAGCATTGAT
Found at i:29947592 original size:47 final size:47
Alignment explanation
Indices: 29947535--29947729 Score: 122
Period size: 47 Copynumber: 4.0 Consensus size: 47
29947525 ACCTACTTTA
*
29947535 GTTGTAAGTACACAACCAATGTGGGATTCATGGTCCACTATCCTTCG
1 GTTGCAAGTACACAACCAATGTGGGATTCATGGTCCACTATCCTTCG
* * *** * * * ** *
29947582 GTTGCAAGTACACAGCCTATGTCCAATTCATTTAAGTACACAATGTATGTGG
1 GTTGCAAGTACACAACCAATGTGGGATTCA--T-GGTCCACTAT-CCT-TCG
* * **
29947634 GATT-CATTTAAGTACACAATCGATACGGGATTCATGGTCCACTATCCTTCG
1 G-TTGC----AAGTACACAACCAATGTGGGATTCATGGTCCACTATCCTTCG
* * *
29947685 GTTGTAAGTACACAACCAATGTGGGATTCATGGTCCGCTGTCCTT
1 GTTGCAAGTACACAACCAATGTGGGATTCATGGTCCACTATCCTT
29947730 TGGTCCACTG
Statistics
Matches: 104, Mismatches: 33, Indels: 22
0.65 0.21 0.14
Matches are distributed among these distances:
47 58 0.56
49 1 0.01
50 9 0.09
51 4 0.04
52 5 0.05
53 9 0.09
54 1 0.01
56 17 0.16
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (47 bp):
GTTGCAAGTACACAACCAATGTGGGATTCATGGTCCACTATCCTTCG
Found at i:29947619 original size:28 final size:28
Alignment explanation
Indices: 29947587--29947652 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
29947577 CTTCGGTTGC
*
29947587 AAGTACACAGCCTATGTCCAATTCATTT
1 AAGTACACAACCTATGTCCAATTCATTT
** ***
29947615 AAGTACACAATGTATGTGGGATTCATTT
1 AAGTACACAACCTATGTCCAATTCATTT
29947643 AAGTACACAA
1 AAGTACACAA
29947653 TCGATACGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (28 bp):
AAGTACACAACCTATGTCCAATTCATTT
Found at i:29947663 original size:28 final size:28
Alignment explanation
Indices: 29947607--29947668 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
29947597 CCTATGTCCA
**
29947607 ATTCATTTAAGTACACAATGTATGTGGG
1 ATTCATTTAAGTACACAATGTATACGGG
29947635 ATTCATTTAAGTACACAATCG-ATACGGG
1 ATTCATTTAAGTACACAAT-GTATACGGG
29947663 ATTCAT
1 ATTCAT
29947669 GGTCCACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (28 bp):
ATTCATTTAAGTACACAATGTATACGGG
Found at i:29947735 original size:15 final size:15
Alignment explanation
Indices: 29947715--29947744 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29947705 GTGGGATTCA
*
29947715 TGGTCCGCTGTCCTT
1 TGGTCCACTGTCCTT
29947730 TGGTCCACTGTCCTT
1 TGGTCCACTGTCCTT
29947745 CAATTGTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.33, G:0.23, T:0.40
Consensus pattern (15 bp):
TGGTCCACTGTCCTT
Found at i:29953192 original size:18 final size:18
Alignment explanation
Indices: 29953169--29953205 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29953159 CTTAACCCAC
*
29953169 TAACCCACCAGAAGTGGA
1 TAACCCACCAAAAGTGGA
*
29953187 TAACCCATCAAAAGTGGA
1 TAACCCACCAAAAGTGGA
29953205 T
1 T
29953206 GAATACCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (18 bp):
TAACCCACCAAAAGTGGA
Found at i:29956303 original size:4 final size:4
Alignment explanation
Indices: 29956294--29956367 Score: 57
Period size: 4 Copynumber: 18.2 Consensus size: 4
29956284 TGTAGACACC
29956294 TAAA TAAA TAAA -AAA TTAAA TTAAA TAAAA TAAA TAAA TAAA -ATAA
1 TAAA TAAA TAAA TAAA -TAAA -TAAA T-AAA TAAA TAAA TAAA TA-AA
* *
29956340 T-AA TAAT TAAA AAAA TTAAA T-AA TAAA T
1 TAAA TAAA TAAA TAAA -TAAA TAAA TAAA T
29956368 TTAAAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
3 10 0.17
4 33 0.57
5 15 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:29956363 original size:23 final size:22
Alignment explanation
Indices: 29956303--29956376 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
29956293 CTAAATAAAT
29956303 AAAAAATTAAATTAAATAAAA-TA
1 AAAAAATTAAA-T-AATAAAATTA
* *
29956326 AATAAATAAAATAATAATAATTA
1 AAAAAATTAAATAATAA-AATTA
*
29956349 AAAAAATTAAATAATAAATTTA
1 AAAAAATTAAATAATAAAATTA
29956371 AAAAAA
1 AAAAAA
29956377 AAGAAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.11
22 13 0.30
23 26 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAATTAAATAATAAAATTA
Found at i:29956486 original size:13 final size:13
Alignment explanation
Indices: 29956468--29956496 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29956458 AGAAAAAGAA
29956468 AAACAAAACAAAG
1 AAACAAAACAAAG
29956481 AAACAAAACAAAG
1 AAACAAAACAAAG
29956494 AAA
1 AAA
29956497 AACAAGGAGA
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:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (13 bp):
AAACAAAACAAAG
Found at i:29971013 original size:31 final size:32
Alignment explanation
Indices: 29970967--29971033 Score: 118
Period size: 31 Copynumber: 2.1 Consensus size: 32
29970957 AAAATATTTT
29970967 CAAATTTTTGAAAAAAAATCTATGAATTTTGA
1 CAAATTTTTGAAAAAAAATCTATGAATTTTGA
*
29970999 CAAANTTTTG-AAAAAAATCTATGAATTTTGA
1 CAAATTTTTGAAAAAAAATCTATGAATTTTGA
29971030 CAAA
1 CAAA
29971034 CATAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 25 0.74
32 9 0.26
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.34
Consensus pattern (32 bp):
CAAATTTTTGAAAAAAAATCTATGAATTTTGA
Found at i:29976464 original size:27 final size:27
Alignment explanation
Indices: 29976351--29976490 Score: 106
Period size: 27 Copynumber: 5.0 Consensus size: 27
29976341 TAGAAGTGAT
**
29976351 TAGATACTTTTACCCATCAAAGTTAGA
1 TAGATACTTTTACCCATCAAAAATAGA
*
29976378 TAGATACATTTACCCA-CTAAAAAT-GA
1 TAGATACTTTTACCCATC-AAAAATAGA
*
29976404 -ATGAATACTTTTACCCACCAAAAATAGACGGA
1 TA-G-ATACTTTTACCCATCAAAAAT--A--GA
* *
29976436 TAGATACCTTGACCCATCAAAAATAGA
1 TAGATACTTTTACCCATCAAAAATAGA
* * * *
29976463 TAAATACTTTTATCCATTAGAAATAGA
1 TAGATACTTTTACCCATCAAAAATAGA
29976490 T
1 T
29976491 GAGTAGTGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
25 1 0.01
26 4 0.04
27 61 0.68
28 1 0.01
29 1 0.01
31 18 0.20
32 3 0.03
33 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (27 bp):
TAGATACTTTTACCCATCAAAAATAGA
Found at i:29977206 original size:26 final size:26
Alignment explanation
Indices: 29977177--29977233 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
29977167 CCGTTGGAAA
*
29977177 AAAAATTCAGAAAGAAAATTTC-ATTG
1 AAAAATTC-CAAAGAAAATTTCTATTG
* * *
29977203 AAAATTTCCAATGAAATTTTCTATTG
1 AAAAATTCCAAAGAAAATTTCTATTG
29977229 AAAAA
1 AAAAA
29977234 ACATTTCCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (26 bp):
AAAAATTCCAAAGAAAATTTCTATTG
Found at i:29977230 original size:13 final size:12
Alignment explanation
Indices: 29977190--29977232 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
29977180 AATTCAGAAA
29977190 GAAAATTTCATT
1 GAAAATTTCATT
*
29977202 GAAAATTTCCAAT
1 GAAAATTT-CATT
*
29977215 GAAATTTTCTATT
1 GAAAATTTC-ATT
29977228 GAAAA
1 GAAAA
29977233 AACATTTCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (12 bp):
GAAAATTTCATT
Found at i:29981080 original size:2 final size:2
Alignment explanation
Indices: 29981034--29981062 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29981024 TTAATATCTC
29981034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29981063 AACTTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29981411 original size:129 final size:130
Alignment explanation
Indices: 29981264--29981505 Score: 335
Period size: 130 Copynumber: 1.9 Consensus size: 130
29981254 TTCTAAACTA
* * *
29981264 TTATTAGTTTTTGTTTAATATATT-TTTTGATTTTATCATCTATTTTTATAAAATT-AAAAATTT
1 TTATTAGTTTTTGATTAATATATTATTCT-ATCTTATCATCTATTTTTATAAAATTAAAAAATTT
* *
29981327 ATTATGTAATTTTTATAAACATTTTAATTTTATAACATTAATGAATTTGGAGCAATTAATTTATT
65 ATTATGTAATTTTTATAAACATTTTAATGTTATAAAATTAATGAATTTGGAGCAATTAATTTATT
29981392 T
130 T
* * *
29981393 TTATTATTTTTTGATTAATTTATTATTCTATCTTATCATGTATTTTTATAAAATTAAAAAATTTA
1 TTATTAGTTTTTGATTAATATATTATTCTATCTTATCATCTATTTTTATAAAATTAAAAAATTTA
* ** * **
29981458 TTTTGTTCTTTTTATCAATTTTTTAATGTTATAAAATTAATGAATTTG
66 TTATGTAATTTTTATAAACATTTTAATGTTATAAAATTAATGAATTTG
29981506 AAATTATTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
129 45 0.46
130 52 0.54
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (130 bp):
TTATTAGTTTTTGATTAATATATTATTCTATCTTATCATCTATTTTTATAAAATTAAAAAATTTA
TTATGTAATTTTTATAAACATTTTAATGTTATAAAATTAATGAATTTGGAGCAATTAATTTATTT
Found at i:29983076 original size:25 final size:25
Alignment explanation
Indices: 29983047--29983099 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
29983037 GACTAATAAT
*
29983047 ATTAATCTTCATATAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
29983072 ATTAATCTTCATACAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
29983097 ATT
1 ATT
29983100 CGTTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (25 bp):
ATTAATCTTCATACAATAAATAAAC
Found at i:29992277 original size:19 final size:19
Alignment explanation
Indices: 29992253--29992290 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29992243 ACTTCTTAAC
29992253 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
29992272 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
29992291 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:29995101 original size:35 final size:35
Alignment explanation
Indices: 29994995--29995104 Score: 139
Period size: 35 Copynumber: 3.1 Consensus size: 35
29994985 GACTTGATTA
* * *
29994995 AAATTGTTTAATTAAGTTACTGAGTTTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
* * *
29995030 AAATTGTTTAATTAAGTCATTGGACCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
* * *
29995065 AAATTGTTTAATTAAGTTGTTGGGCTTAGTTGATT
1 AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
29995100 AAATT
1 AAATT
29995105 AAACAATTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.46
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
Found at i:29997950 original size:22 final size:22
Alignment explanation
Indices: 29997922--29997979 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
29997912 TTAAAATTGT
* *
29997922 TTAATTAAGTTGTTGGGTTTAA
1 TTAATTAAATTGTTGGGCTTAA
**
29997944 TTAATTAAATCATTGGGCTTAA
1 TTAATTAAATTGTTGGGCTTAA
29997966 TTAATTAAATTGTT
1 TTAATTAAATTGTT
29997980 TAATTAAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (22 bp):
TTAATTAAATTGTTGGGCTTAA
Found at i:29997994 original size:35 final size:35
Alignment explanation
Indices: 29997944--29998011 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
29997934 TTGGGTTTAA
*
29997944 TTAATTAAATCATTGGGCTTAATTAATTAAATTGT
1 TTAATTAAATCATTGGGCCTAATTAATTAAATTGT
* * *
29997979 TTAATTAAGTTATTGGGCCTAATTGATTAAATT
1 TTAATTAAATCATTGGGCCTAATTAATTAAATT
29998012 AAACAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (35 bp):
TTAATTAAATCATTGGGCCTAATTAATTAAATTGT
Found at i:29998646 original size:34 final size:34
Alignment explanation
Indices: 29998603--29998681 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
29998593 TGTTTGGTAC
29998603 AGGGAATAGCTAAGCTATTCCCTATCTATTCCCA
1 AGGGAATAGCTAAGCTATTCCCTATCTATTCCCA
*
29998637 AGGGAATAGCTAAGCTATTCCCTATCTTTTCCCA
1 AGGGAATAGCTAAGCTATTCCCTATCTATTCCCA
29998671 AGGGAATAGCT
1 AGGGAATAGCT
29998682 TACCTCCGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (34 bp):
AGGGAATAGCTAAGCTATTCCCTATCTATTCCCA
Found at i:29998892 original size:2 final size:2
Alignment explanation
Indices: 29998881--29998931 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
29998871 ACCCTAGACC
29998881 TA TA TA -A TA TA TA TA TA -A TA TA TA TA -A TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
29998919 AA TA AA TA TA TA T
1 TA TA TA TA TA TA T
29998932 TTTTTTCTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:29998912 original size:12 final size:12
Alignment explanation
Indices: 29998884--29998930 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
29998874 CTAGACCTAT
29998884 ATAATATATAT-
1 ATAATATATATA
29998895 ATAATATATATA
1 ATAATATATATA
29998907 ATAATATATATAA
1 ATAATATATAT-A
29998920 ATAA-ATATATA
1 ATAATATATATA
29998931 TTTTTTTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 12 0.35
12 17 0.50
13 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATATA
Found at i:30003832 original size:12 final size:12
Alignment explanation
Indices: 30003815--30003848 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
30003805 GGAAACTCTG
30003815 GCATTAAGTTAC
1 GCATTAAGTTAC
30003827 GCATTAAGTTAC
1 GCATTAAGTTAC
*
30003839 GCATCAAGTT
1 GCATTAAGTT
30003849 CTTTGATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (12 bp):
GCATTAAGTTAC
Found at i:30010913 original size:7 final size:7
Alignment explanation
Indices: 30010901--30010939 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
30010891 GTCAACCTGT
30010901 TCAAGAA
1 TCAAGAA
30010908 TCAAGAA
1 TCAAGAA
30010915 TCAAGAA
1 TCAAGAA
30010922 TCAAGAA
1 TCAAGAA
*
30010929 TCAAGAT
1 TCAAGAA
30010936 TCAA
1 TCAA
30010940 ACCCACTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (7 bp):
TCAAGAA
Found at i:30011570 original size:20 final size:20
Alignment explanation
Indices: 30011545--30011592 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
30011535 GTTTCTCTAA
30011545 TCTTCTTTCTTTGCTTTTTC
1 TCTTCTTTCTTTGCTTTTTC
30011565 TCTTCTTTCTTTGCTTTTTC
1 TCTTCTTTCTTTGCTTTTTC
30011585 TCTTCTTT
1 TCTTCTTT
30011593 TTTCAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (20 bp):
TCTTCTTTCTTTGCTTTTTC
Found at i:30011591 original size:23 final size:22
Alignment explanation
Indices: 30011536--30011596 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 22
30011526 GGGCTCTACG
30011536 TTTCTCTAATCTTCTTTCTTTGCT
1 TTTCTCT--TCTTCTTTCTTTGCT
30011560 TTT-TC-TCTTCTTTCTTTGCTT
1 TTTCTCTTCTTCTTTCTTTGC-T
*
30011581 TTTCTCTTCTTTTTTC
1 TTTCTCTTCTTCTTTC
30011597 AGAGAACAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 14 0.42
21 4 0.12
22 2 0.06
23 10 0.30
24 3 0.09
ACGTcount: A:0.03, C:0.25, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTCTCTTCTTCTTTCTTTGCT
Found at i:30026299 original size:17 final size:17
Alignment explanation
Indices: 30026277--30026321 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
30026267 AATTAATTAT
30026277 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
*
30026294 ATTAAAAAAAATATAAAA
1 ATT-AAAAATATATAAAA
* *
30026312 GTAAAAAATA
1 ATTAAAAATA
30026322 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:30026301 original size:18 final size:17
Alignment explanation
Indices: 30026280--30026321 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
30026270 TAATTATATT
*
30026280 AAAAATATATAAAAATTA
1 AAAAATATAT-AAAAGTA
*
30026298 AAAAAAATATAAAAGTA
1 AAAAATATATAAAAGTA
30026315 AAAAATA
1 AAAAATA
30026322 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAATATATAAAAGTA
Found at i:30026956 original size:5 final size:5
Alignment explanation
Indices: 30026946--30026972 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
30026936 TCACAAAATA
30026946 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
30026973 AACGAACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:30027642 original size:2 final size:2
Alignment explanation
Indices: 30027637--30027662 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30027627 TGTGTACGTG
30027637 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
30027663 ATCGAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30035429 original size:17 final size:17
Alignment explanation
Indices: 30035391--30035442 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
30035381 TTTAAACTTA
* *
30035391 TTTATTTAATTTTAAAT
1 TTTATTTAATTTTTATT
*
30035408 ATTATTTAATTTTTATT
1 TTTATTTAATTTTTATT
*
30035425 TTTATTTCATTTTTATT
1 TTTATTTAATTTTTATT
30035442 T
1 T
30035443 AAAATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTAATTTTTATT
Found at i:30036168 original size:195 final size:196
Alignment explanation
Indices: 30035882--30036234 Score: 464
Period size: 195 Copynumber: 1.8 Consensus size: 196
30035872 TTTCAATAAA
* * * *
30035882 AACTTTTAACTATAATTATTTTTATACTTATTATTTTTTATTTTAAAATTAAAATTTGTAAATCG
1 AACTTATAACTATAATTATTTTTATACTTATTATTATTTATTTCAAAATTAAAATTTGTAAATCA
* *
30035947 TTAAATACTTTTAACCTAAAAATATAAATTTAACTATTTATTTTTCATTAAAATTATAATTT-TT
66 TTAAATACTTTTAACCTAAAAATATAAATATAAATATTTATTTTTCATTAAAATTAT-ATTTATT
30036011 TTAATT-AGTTCACTTGTTACGTTAACTCTTAAACATTTATGTTTTTACGTCAAGGTTTTTCAAT
130 TTAATTAAG-TCACTTGTTACGTTAACTCTTAAACATTTATGTTTTTACGTCAAGGTTTTTCAAT
30036075 GGT
194 GGT
* * * * *
30036078 AACTTATAATTATAATTGTTTTTATCCTTATTATTATTTA-TTCAAAATTAAATTTTGTATA-CT
1 AACTTATAACTATAATTATTTTTATACTTATTATTATTTATTTCAAAATTAAAATTTGTAAATC-
* * * * *
30036141 ATTAATTACTTTTAGACC-GAGAATATAAATATAAATTTTTATTTTTTATTAAAATTATATTTAT
65 ATTAAATACTTTTA-ACCTAAAAATATAAATATAAATATTTATTTTTCATTAAAATTATATTTAT
* * *
30036205 TTTATTTAAGTGATTTGTTACGTTAACTCT
129 TTTAATTAAGTCACTTGTTACGTTAACTCT
30036235 CACAAATTTA
Statistics
Matches: 134, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
194 5 0.04
195 89 0.66
196 40 0.30
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (196 bp):
AACTTATAACTATAATTATTTTTATACTTATTATTATTTATTTCAAAATTAAAATTTGTAAATCA
TTAAATACTTTTAACCTAAAAATATAAATATAAATATTTATTTTTCATTAAAATTATATTTATTT
TAATTAAGTCACTTGTTACGTTAACTCTTAAACATTTATGTTTTTACGTCAAGGTTTTTCAATGG
T
Found at i:30036361 original size:15 final size:15
Alignment explanation
Indices: 30036332--30036371 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
30036322 CAATAATAAC
*
30036332 TTTTAATTATAATTAT
1 TTTTAATT-TTATTAT
30036348 TTTTAATTTTATTAT
1 TTTTAATTTTATTAT
30036363 TTTT-ATTTT
1 TTTTAATTTT
30036372 CAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTTTATTAT
Found at i:30036388 original size:251 final size:252
Alignment explanation
Indices: 30036053--30038047 Score: 1168
Period size: 251 Copynumber: 7.8 Consensus size: 252
30036043 ACATTTATGT
* ** * *
30036053 TTTTACGTCAAGGTTTTTCAATGGTAACTTATAATTATAATTGTTTTTATCCTTATTATTATTTA
1 TTTTACGTCAAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTTATCCTTATTATTATTTA
* * * * *
30036118 --TTCAAAATTAAATTTTGTATACT-ATTAATTACTTTTAGACCGAGAATATAAATATAAATTTT
66 TTTTC-AAATTAAAATTTGTATACTCATTAAATACTTTTAGACCAAGAATATAAATTTAAATATT
* * * * * *
30036180 TATTTTTTATTAAAATTATATTTATT-TTATTTAAGTGATTTGTTACGTTAACTCTCACAAATTT
130 TATTTTTCATTAAAATTAGATTT-TTATTACTTAATTGACTTGTTACGTTAACTCTCACACATTT
* * * * * * *
30036244 ACATTAAGATTTTAAATATACTTATTCCAGTTTTATAAGTTTTTACATCAACTCTTATAA
194 ACGTTAAGATTTTAAATATGCTTGTTCCACTTTTATAA-TTTTTACATCAATTTTTACAA
* * *
30036304 TTTTACATTAAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTTAAT-TTTATTATT-TTT
1 TTTTACGTCAAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTT-ATCCTTATTATTATTT
** ** *
30036367 ATTTTCAAATTAAAATTTGTATAC-CATTAAATACTTTTAG-CTTGAGAATATAAATGCAAATGT
65 ATTTTCAAATTAAAATTTGTATACTCATTAAATACTTTTAGAC-CAAGAATATAAATTTAAATAT
* * * * * *
30036430 TCTTTTTTTCATTAAAATTAGATTTTT-TCATTTAATTGACTTGTTACATTAACTCTCACATAGT
129 T-TATTTTTCATTAAAATTAGATTTTTATTACTTAATTGACTTGTTACGTTAACTCTCACACATT
* * * * * *
30036494 TATGTTAGGATTTTAAATTTGCTTGTTCCACTTTTATAACTTTTTACGTCAACTCTTACAA
193 TACGTTAAGATTTTAAATATGCTTGTTCCACTTTTATAA-TTTTTACATCAATTTTTACAA
* * * * ** ** ** *
30036555 TTTTACGTCAA--CTCTT--ATAACTTTAC-GTCAACTCTTATAACTTTACGTCAAGGCTT-TCC
1 TTTTACGTCAAGGCTTTTCAATAA--TAACTTTTAA---TTATAA--TTATTTTTATCCTTAT-T
* * * * * * * * *** *
30036614 AATAGTAACTTTGAACTATAATTATTTTTACGCTTACT-ATTTTTTA-TTTTA-A--AATTAATA
58 ATTATTTATTTTCAAAT-TAA-AATTTGTA----TACTCATTAAATACTTTTAGACCAA-GAATA
* ** * * *
30036674 TGGTACATCATTAAATACTTTTAGTCTAAAAATATAAATTTAAATGTTTG-TTTTTCATTAAAAT
116 ---TAAAT--TTAAATA--TTTA-T-T-----T-TTCA-TTAAA-ATTAGATTTTT-ATT--ACT
* * * * *
30036738 AAAATTTTTTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACTTTAAGATTTTGAATT
161 -TAA----TTGACTT----G-----TTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATA
* * *
30036803 TTCTTGTTCCACCTTTATATATTTTTATATCAATTTTTACAA
212 TGCTTGTTCCACTTTTATA-ATTTTTACATCAATTTTTACAA
* * * * * ** *
30036845 CTTTATGGTAAAGAGTTTTTCAATAATAATTTTTAATTATAATTATTTTTATCGATATTATTCTT
1 TTTTA-CGTCAAG-GCTTTTCAATAATAACTTTTAATTATAATTATTTTTATCCTTATTATTATT
* * *
30036910 TA-TTTCAAAATTAAAATTTATATA-TCGTTAAATACTTTTA-ACCCAAAAATATAAATTTAAAT
64 TATTTTC-AAATTAAAATTTGTATACTCATTAAATACTTTTAGA-CCAAGAATATAAATTTAAAT
* * * * * * * **
30036972 ATTT-GTTTTCTTTAAAATTAGATTTTTATAACTTGATTGA-TCTCTTACTTTAACTCTTACATG
127 ATTTATTTTTCATTAAAATTAGATTTTTATTACTTAATTGACT-TGTTACGTTAACTCTCACACA
* * * * * * * *
30037035 CTAACATTAAAATTTTAAATATGTTTGTTCTACTTTTATAATTTATTACGTCAATTTTTACAG
191 TTTACGTTAAGATTTTAAATATGCTTGTTCCACTTTTATAATTT-TTACATCAATTTTTACAA
** * * ** *
30037098 CCTTACATCAAAGCTTTTCAATGGTAATTTTTAACTT-TAATTATTTTTATCCTTATTATTATTT
1 TTTTACGTCAAGGCTTTTCAATAATAACTTTTAA-TTATAATTATTTTTATCCTTATTATTATTT
* * * * *
30037162 AGTTTT-AAATTAAAATTTATA-AATCGTTAAATACTTTTA-ACCCAATAATATAACTTTAAATA
65 A-TTTTCAAATTAAAATTTGTATACTCATTAAATACTTTTAGA-CCAAGAATATAAATTTAAATA
* * * * * *
30037224 TTTATTTTTCATTAAAATTATATTTTTATGACTTAATTGACCTATTACATTAACTTTCACACATT
128 TTTATTTTTCATTAAAATTAGATTTTTATTACTTAATTGACTTGTTACGTTAACTCTCACACATT
* *
30037289 TACGTTAAAATTTTAAATATGCTTATTCCACTTTTATGAATTTTTACATCAA---TT-C--
193 TACGTTAAGATTTTAAATATGCTTGTTCCACTTTTAT-AATTTTTACATCAATTTTTACAA
* ** *
30037344 ---T---TCAAGACTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTA
1 TTTTACGTCAAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTTATCCTTATTATTATTTA
* *
30037403 TTTTTAAATTAAAATTTGT-TAAC-CATTAAATACTTTTA-ACTCATGAATATAAATTTAAATAT
66 TTTTCAAATTAAAATTTGTAT-ACTCATTAAATACTTTTAGAC-CAAGAATATAAATTTAAATAT
* * * * *
30037465 TTATTTTTCATTAAAATTAGATTTTTGTAACTTAATCGACTTGTTACATTAACTCTTACACATTT
129 TTATTTTTCATTAAAATTAGATTTTTATTACTTAATTGACTTGTTACGTTAACTCTCACACATTT
* ** * * * *
30037530 AGGTTAAGATTTTAAATATGCTTGTTTTACCTTTATGAGTTTTTACGTCAATTTTTTCAA
194 ACGTTAAGATTTTAAATATGCTTGTTCCACTTTTAT-AATTTTTACATCAATTTTTACAA
* * * * * *
30037590 TTTTACGTCTAA-ACTTTGCAATAACATCTTTTAATAATTATTATTTTTATCCTTATTATTATTT
1 TTTTACGTC-AAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTTATCCTTATTATTATTT
* ** * *
30037654 AGTTTT-AAATT-AAATTTGTA-AATTGTTAAATATTTTTAGTCCCAA-AATATAAATTTAAATA
65 A-TTTTCAAATTAAAATTTGTATACTCATTAAATACTTTTAG-ACCAAGAATATAAATTTAAATA
* * * * *
30037715 TTTATTTTTTTATTAAAATTAGATTTTTATGACTTAATTAACTTGTTATGTTAACACTCACACAT
128 TTTA-TTTTTCATTAAAATTAGATTTTTATTACTTAATTGACTTGTTACGTTAACTCTCACACAT
* * * * * * * *
30037780 TTAGGTTAAGATTTTAAATATGTTTGCTCGACTTTTATGAGTTTTTAAATCGATTTTTACAG
192 TTACGTTAAGATTTTAAATATGCTTGTTCCACTTTTAT-AATTTTTACATCAATTTTTACAA
* * *** ** * *
30037842 CTTTACGTCAAGGCTTGT-AATTGCAACTTTTAACAATAATTATTTTTGTCTTTATTATTATTTA
1 TTTTACGTCAAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTTATCCTTATTATTATTTA
* * * * *
30037906 TTTTAAAATTAAAATTTGTA-AATCATTAAATATTTTTAGTCTAAGAATATAAATTTAAATATTT
66 TTTTCAAATTAAAATTTGTATACTCATTAAATACTTTTAGACCAAGAATATAAATTTAAATATTT
* * * * * * *
30037970 -TTTCTACA--AAAATTATATATTTTTTTACTTAATTGACATATTAGGTTAACTCTCACATATTT
131 ATTT-TTCATTAAAATTAGAT-TTTTATTACTTAATTGACTTGTTACGTTAACTCTCACACATTT
* *
30038032 ACATTAGGA-TTTAAAT
194 ACGTTAAGATTTTAAAT
30038048 TTTTTTTTTA
Statistics
Matches: 1363, Mismatches: 266, Indels: 232
0.73 0.14 0.12
Matches are distributed among these distances:
239 6 0.00
240 198 0.15
241 1 0.00
243 3 0.00
244 1 0.00
247 4 0.00
248 4 0.00
249 26 0.02
250 55 0.04
251 387 0.28
252 336 0.25
253 87 0.06
254 8 0.01
255 3 0.00
256 7 0.01
257 4 0.00
259 5 0.00
260 12 0.01
261 1 0.00
262 8 0.01
263 1 0.00
264 3 0.00
265 1 0.00
266 1 0.00
267 2 0.00
269 5 0.00
270 11 0.01
271 3 0.00
272 11 0.01
273 3 0.00
274 1 0.00
276 2 0.00
277 3 0.00
280 3 0.00
281 6 0.00
282 7 0.01
283 1 0.00
284 10 0.01
285 7 0.01
287 4 0.00
288 8 0.01
289 6 0.00
290 84 0.06
291 6 0.00
292 6 0.00
294 5 0.00
295 3 0.00
296 4 0.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (252 bp):
TTTTACGTCAAGGCTTTTCAATAATAACTTTTAATTATAATTATTTTTATCCTTATTATTATTTA
TTTTCAAATTAAAATTTGTATACTCATTAAATACTTTTAGACCAAGAATATAAATTTAAATATTT
ATTTTTCATTAAAATTAGATTTTTATTACTTAATTGACTTGTTACGTTAACTCTCACACATTTAC
GTTAAGATTTTAAATATGCTTGTTCCACTTTTATAATTTTTACATCAATTTTTACAA
Found at i:30036560 original size:20 final size:20
Alignment explanation
Indices: 30036536--30036605 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
30036526 TTTATAACTT
* *
30036536 TTTACGTCAACTCTTACAAT
1 TTTACGTCAACTCTTATAAC
30036556 TTTACGTCAACTCTTATAAC
1 TTTACGTCAACTCTTATAAC
30036576 TTTACGTCAACTCTTATAAC
1 TTTACGTCAACTCTTATAAC
30036596 TTTACGTCAA
1 TTTACGTCAA
30036606 GGCTTTCCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (20 bp):
TTTACGTCAACTCTTATAAC
Found at i:30036585 original size:40 final size:41
Alignment explanation
Indices: 30036527--30036605 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 41
30036517 TGTTCCACTT
*
30036527 TTATAACTTTTTACGTCAACTCTTACAATTTTACGTCAACTC
1 TTATAAC-TTTTACGTCAACTCTTACAACTTTACGTCAACTC
*
30036569 TTATAAC-TTTACGTCAACTCTTATAACTTTACGTCAA
1 TTATAACTTTTACGTCAACTCTTACAACTTTACGTCAA
30036606 GGCTTTCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 28 0.80
42 7 0.20
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (41 bp):
TTATAACTTTTACGTCAACTCTTACAACTTTACGTCAACTC
Found at i:30037514 original size:240 final size:241
Alignment explanation
Indices: 30037111--30037969 Score: 885
Period size: 252 Copynumber: 3.5 Consensus size: 241
30037101 TACATCAAAG
* * *
30037111 CTTTTCAATGGTAATTTTTAACTTTAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAA
1 CTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAA
* * *
30037176 ATTTATAAATCGTTAAATACTTTTAACCCAAT-AATATAACTTTAAATATTTATTTTTCATTAAA
66 ATTTGTAAATCATTAAATACTTTTAACCCAATGAATATAAATTTAAATATTTATTTTTCATTAAA
* * * * *
30037240 ATTATATTTTTATGACTTAATTGACCTATTACATTAACTTTCACACATTTACGTTAAAATTTTAA
131 ATTAGATTTTTATGACTTAATTGACTTGTTACATTAACTTTCACACATTTAGGTTAAGATTTTAA
* *
30037305 ATATGCTTATTCCACTTTTATGAATTTTTACATCAATTCTTCA-AGA
196 ATATGCTTGTTCCACTTTTATGAGTTTTTACATCAATT-TTCATAGA
* *
30037351 CTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTATTTTTAAATTAAA
1 CTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAA
* * *
30037416 ATTTGTTAACCATTAAATACTTTTAACTC-ATGAATATAAATTTAAATATTTATTTTTCATTAAA
66 ATTTGTAAATCATTAAATACTTTTAACCCAATGAATATAAATTTAAATATTTATTTTTCATTAAA
* * *
30037480 ATTAGATTTTTGTAACTTAATCGACTTGTTACATTAACTCTT-ACACATTTAGGTTAAGATTTTA
131 ATTAGATTTTTATGACTTAATTGACTTGTTACATTAACT-TTCACACATTTAGGTTAAGATTTTA
** * *
30037544 AATATGCTTGTTTTACCTTTATGAGTTTTTACGTCAATTTTTTCAATTTTACGTCTAAA
195 AATATGCTTGTTCCACTTTTATGAGTTTTTACATCAA--TTTTC-A---TA-G-----A
* ** * *
30037603 CTTTGCAATAACATCTTTTAA-TAATTATTATTTTTATCCTTATTATTATTTAGTTTTAAATT-A
1 CTTTTCAATGGCAACTTTTAACT-ATAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAA
** * * *
30037666 AATTTGTAAATTGTTAAATATTTTTAGTCCCAA--AATATAAATTTAAATATTTATTTTTTTATT
65 AATTTGTAAATCATTAAATACTTTTA-ACCCAATGAATATAAATTTAAATATTTA-TTTTTCATT
* ** **
30037729 AAAATTAGATTTTTATGACTTAATTAACTTGTTATGTTAACACTCACACATTTAGGTTAAGATTT
128 AAAATTAGATTTTTATGACTTAATTGACTTGTTACATTAACTTTCACACATTTAGGTTAAGATTT
* * * * *
30037794 TAAATATGTTTGCTCGACTTTTATGAGTTTTTAAATCGATTTTTACAGCTTTACGTCAA
193 TAAATATGCTTGTTCCACTTTTATGAGTTTTTACATC-AATTTT-CA----TA-G---A
* * * * *
30037853 GGCTTGT-AATTGCAACTTTTAACAATAATTATTTTTGTCTTTATTATTATTTA-TTTTAAAATT
1 --CTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTAGTTTT-AAATT
* ** *
30037916 AAAATTTGTAAATCATTAAATATTTTTAGTCTAA-GAATATAAATTTAAATATTT
63 AAAATTTGTAAATCATTAAATACTTTTAACCCAATGAATATAAATTTAAATATTT
30037970 TTTCTACAAA
Statistics
Matches: 520, Mismatches: 70, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
239 2 0.00
240 201 0.39
241 5 0.01
242 3 0.01
246 1 0.00
247 1 0.00
250 7 0.01
251 95 0.18
252 203 0.39
253 2 0.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (241 bp):
CTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAA
ATTTGTAAATCATTAAATACTTTTAACCCAATGAATATAAATTTAAATATTTATTTTTCATTAAA
ATTAGATTTTTATGACTTAATTGACTTGTTACATTAACTTTCACACATTTAGGTTAAGATTTTAA
ATATGCTTGTTCCACTTTTATGAGTTTTTACATCAATTTTCATAGA
Found at i:30037658 original size:492 final size:489
Alignment explanation
Indices: 30036861--30037969 Score: 1259
Period size: 492 Copynumber: 2.2 Consensus size: 489
30036851 GGTAAAGAGT
** * * ** * *
30036861 TTTTCAATAATAATTTTTAATTATAATTATTTTTATCGATATTATTCTTTATTTCAAAATTAAAA
1 TTTTCAATGGTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTATTTTAAAATTAAAA
* * * * *
30036926 TTT-ATATATCGTTAAATACTTTTAACCCAAAAATATAAATTTAAATATTTGTTTTCTTTAAAAT
66 TTTGTTA-ATCATTAAATACTTTTAACTCAAGAATATAAATTTAAATATTTGTTTTCATTAAAAT
* * * **
30036990 TAGATTTTTATAACTTGATTGATCTCTTACTTTAACTCTTACATGCTAACATTAAAATTTTAAAT
130 TAGATTTTTATAACTTAATCGATCTCTTACATTAACTCTTACACACTAACATTAAAATTTTAAAT
* * * *
30037055 ATGTTTGTTCTACTTTTATAATTTATTACGTCAATTTTTACAGCCTTACATCAAAGCTTTTCAAT
195 ATGCTTGTTCTACCTTTATAATTTATTACGTCAATTTTTACAACCTTACATCAAAGCTTTGCAAT
*
30037120 GGTAATTTTTAACTTTAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAAATTTATAAA
260 -GAAATTTTTAACTTTAATTATTTTTATCCTTATTATTATTTAGTTTTAAATT-AAATTTATAAA
* *
30037185 TCGTTAAATACTTTTA-ACCCAATAATATAACTTTAAATATTTA-TTTTTCATTAAAATTATATT
323 TCGTTAAATACTTTTAGACCCAA-AATATAAATTTAAATATTTATTTTTTCATTAAAATTAGATT
* **
30037248 TTTATGACTTAATTGACCTATTACATTAACTTTCACACATTTACGTTAAAATTTTAAATATGCTT
387 TTTATGACTTAATTAACCTATTACATTAACACTCACACATTTACGTTAAAATTTTAAATATGCTT
* *
30037313 ATTCCACTTTTATGAATTTTTACATCAATTCTTCA-AGAC
452 ACTCCACTTTTATGAATTTTTAAATCAATT-TTCACAG-C
*
30037352 TTTTCAATGGTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTATTTTTAAATTAAAA
1 TTTTCAATGGTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTATTTTAAAATTAAAA
* * *
30037417 TTTGTTAACCATTAAATACTTTTAACTCATGAATATAAATTTAAATATTTATTTTTCATTAAAAT
66 TTTGTTAATCATTAAATACTTTTAACTCAAGAATATAAATTTAAATATTT-GTTTTCATTAAAAT
* * * * ** *
30037482 TAGATTTTTGTAACTTAATCGA-CTTGTTACATTAACTCTTACACATTTAGGTTAAGATTTTAAA
130 TAGATTTTTATAACTTAATCGATC-TCTTACATTAACTCTTACACACTAACATTAAAATTTTAAA
* * * ** *
30037546 TATGCTTGTTTTACCTTTATGAGTTT-TTACGTCAATTTTTTCAATTTTACGTCTAAA-CTTTGC
194 TATGCTTGTTCTACCTTTAT-AATTTATTACGTCAATTTTTACAACCTTACATC-AAAGCTTTGC
30037609 AAT-AACATCTTTTAA-TAATT-ATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAATTT
257 AATGAA-AT-TTTTAACT--TTAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAATTT
* * * * *
30037671 GTAAATTGTTAAATATTTTTAGTCCCAAAATATAAATTTAAATATTTATTTTTTTATTAAAATTA
318 ATAAATCGTTAAATACTTTTAGACCCAAAATATAAATTTAAATATTTATTTTTTCATTAAAATTA
* * ** * *
30037736 GATTTTTATGACTTAATTAACTTGTTATGTTAACACTCACACATTTAGGTTAAGATTTTAAATAT
383 GATTTTTATGACTTAATTAACCTATTACATTAACACTCACACATTTACGTTAAAATTTTAAATAT
* * * * * *
30037801 GTTTGCTCGACTTTTATGAGTTTTTAAATCGATTTTTACAGC
448 GCTTACTCCACTTTTATGAATTTTTAAATCAATTTTCACAGC
* * * *
30037843 TTTACGTCAAGGCTTGTAATTGCAACTTTTAACAATAATTATTTTTGTCTTTATTATTATTTATT
1 TTT---TCAA----TG-----GTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTATT
* * *
30037908 TTAAAATTAAAATTTGTAAATCATTAAATA-TTTTTAGTCTAAGAATATAAATTTAAATATTT
54 TTAAAATTAAAATTTGTTAATCATTAAATACTTTTAACTC-AAGAATATAAATTTAAATATTT
30037970 TTTCTACAAA
Statistics
Matches: 519, Mismatches: 74, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
490 1 0.00
491 151 0.29
492 257 0.50
493 9 0.02
494 4 0.01
498 2 0.00
502 7 0.01
503 88 0.17
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (489 bp):
TTTTCAATGGTAACTTTTAACTATAATTATTTTTATCCTTATTATTATTTATTTTAAAATTAAAA
TTTGTTAATCATTAAATACTTTTAACTCAAGAATATAAATTTAAATATTTGTTTTCATTAAAATT
AGATTTTTATAACTTAATCGATCTCTTACATTAACTCTTACACACTAACATTAAAATTTTAAATA
TGCTTGTTCTACCTTTATAATTTATTACGTCAATTTTTACAACCTTACATCAAAGCTTTGCAATG
AAATTTTTAACTTTAATTATTTTTATCCTTATTATTATTTAGTTTTAAATTAAATTTATAAATCG
TTAAATACTTTTAGACCCAAAATATAAATTTAAATATTTATTTTTTCATTAAAATTAGATTTTTA
TGACTTAATTAACCTATTACATTAACACTCACACATTTACGTTAAAATTTTAAATATGCTTACTC
CACTTTTATGAATTTTTAAATCAATTTTCACAGC
Found at i:30037780 original size:252 final size:248
Alignment explanation
Indices: 30037365--30038047 Score: 658
Period size: 252 Copynumber: 2.7 Consensus size: 248
30037355 TCAATGGTAA
* * *
30037365 CTTTTAACTATAATTATTTTTATCCTTATTATTATTTATTTTTAAATTAAAATTTGTTAACCATT
1 CTTTTAA-TATAATTATTTTTATCCTTATTATTATTTA-TTTTAAATTAAAATTTGTAAATCGTT
* * *
30037430 AAATACTTTTAACTCATGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTGTAA
64 AAATACTTTTAACCCA-AAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTATAA
* * * * **
30037495 CTTAATCGACTTGTTACATTAACTCTTACACATTTAGGTTAAGATTTTAAATATGCTTGTTTTAC
128 CTTAATTGACTTATTACATTAACTCTCACACATTTACGTTAAGATTTTAAATATGCTTGTTCCAC
* * * * * *
30037560 CTTTATGAGTTTTTACGTCAATTTTTTCAATTTTACGTCTAAACTTTGCAATAACAT
193 TTTTATGAATTTTTACATCAATTTTTACAACTTTACGTC-AAACTTTTCAATAACAT
* *
30037617 CTTTTAATAATTATTATTTTTATCCTTATTATTATTTAGTTTTAAATT-AAATTTGTAAATTGTT
1 CTTTTAAT-ATAATTATTTTTATCCTTATTATTATTTA-TTTTAAATTAAAATTTGTAAATCGTT
* * * *
30037681 AAATATTTTTAGTCCCAAAATATAAATTTAAATATTTATTTTTTTATTAAAATTAGATTTTTATG
64 AAATACTTTTA-ACCCAAAATATAAATTTAAATATTTA-TTTTTCATTAAAATTAGATTTTTATA
* * ** * * * * *
30037746 ACTTAATTAACTTGTTATGTTAACACTCACACATTTAGGTTAAGATTTTAAATATGTTTGCTCGA
127 ACTTAATTGACTTATTACATTAACTCTCACACATTTACGTTAAGATTTTAAATATGCTTGTTCCA
* * * * * * ** *
30037811 CTTTTATGAGTTTTTAAATCGATTTTTACAGCTTTACGTCAAGGCTTGT-AATTGCAA
192 CTTTTATGAATTTTTACATCAATTTTTACAACTTTACGTCAA-ACTTTTCAATAACAT
* * * *
30037868 CTTTTAACAATAATTATTTTTGTCTTTATTATTATTTATTTTAAAATTAAAATTTGTAAATCATT
1 CTTTTAA-TATAATTATTTTTATCCTTATTATTATTTATTTT-AAATTAAAATTTGTAAATCGTT
* ** * * * *
30037933 AAATATTTTTAGTCTAAGAATATAAATTTAAATATTT-TTTCTACA--AAAATTATATATTTTTT
64 AAATACTTTTAACCCAA-AATATAAATTTAAATATTTATTT-TTCATTAAAATTAGAT-TTTTAT
* * ** * * *
30037995 TACTTAATTGACATATTAGGTTAACTCTCACATATTTACATTAGGA-TTTAAAT
126 AACTTAATTGACTTATTACATTAACTCTCACACATTTACGTTAAGATTTTAAAT
30038048 TTTTTTTTTA
Statistics
Matches: 362, Mismatches: 59, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
249 16 0.04
250 48 0.13
251 93 0.26
252 205 0.57
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (248 bp):
CTTTTAATATAATTATTTTTATCCTTATTATTATTTATTTTAAATTAAAATTTGTAAATCGTTAA
ATACTTTTAACCCAAAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTATAACTT
AATTGACTTATTACATTAACTCTCACACATTTACGTTAAGATTTTAAATATGCTTGTTCCACTTT
TATGAATTTTTACATCAATTTTTACAACTTTACGTCAAACTTTTCAATAACAT
Found at i:30055470 original size:44 final size:43
Alignment explanation
Indices: 30055372--30055472 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 43
30055362 TGATTTTTAG
* * ** *
30055372 GCAATGCCTAAAACTAATCACGCAATGCCTATCAACGAGTCAC
1 GCAATGCCTAAAAATAATCACACAATGCCTAAAAACGAGTAAC
* ** **
30055415 GTAATATCTAAAAATCAATCACACAATGCCTAAAAATTAGTAAC
1 GCAATGCCTAAAAAT-AATCACACAATGCCTAAAAACGAGTAAC
30055459 GCAATGCCTAAAAA
1 GCAATGCCTAAAAA
30055473 CTAGTTACGT
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
43 11 0.25
44 33 0.75
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (43 bp):
GCAATGCCTAAAAATAATCACACAATGCCTAAAAACGAGTAAC
Found at i:30055477 original size:22 final size:22
Alignment explanation
Indices: 30055372--30055517 Score: 91
Period size: 22 Copynumber: 6.7 Consensus size: 22
30055362 TGATTTTTAG
*
30055372 GCAATGCCT-AAAACTAATCAC
1 GCAATGCCTAAAAACTAGTCAC
** *
30055393 GCAATGCCTATCAACGAGTCAC
1 GCAATGCCTAAAAACTAGTCAC
* ** *
30055415 GTAATATCTAAAAA-TCAATCAC
1 GCAATGCCTAAAAACT-AGTCAC
* * *
30055437 ACAATGCCTAAAAATTAGTAAC
1 GCAATGCCTAAAAACTAGTCAC
*
30055459 GCAATGCCTAAAAACTAGTTAC
1 GCAATGCCTAAAAACTAGTCAC
* ** * *
30055481 GTAATATCTAAAAGCT-GATTAC
1 GCAATGCCTAAAAACTAG-TCAC
*
30055503 GCAATGCTTAAAAAC
1 GCAATGCCTAAAAAC
30055518 AACCAAAACT
Statistics
Matches: 92, Mismatches: 29, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
21 10 0.11
22 81 0.88
23 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (22 bp):
GCAATGCCTAAAAACTAGTCAC
Found at i:30061302 original size:18 final size:18
Alignment explanation
Indices: 30061281--30061319 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30061271 GGGGTGGGGG
*
30061281 TGGCGGTGGAGGTGATGA
1 TGGCAGTGGAGGTGATGA
*
30061299 TGGCAGTGGTGGTGATGA
1 TGGCAGTGGAGGTGATGA
30061317 TGG
1 TGG
30061320 AGGCACATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.54, T:0.26
Consensus pattern (18 bp):
TGGCAGTGGAGGTGATGA
Found at i:30067606 original size:72 final size:71
Alignment explanation
Indices: 30067512--30067655 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 71
30067502 AAATTAAGCT
30067512 AAAGTTGTTTGGTAAATTTTTTTTTATAAGTTCTTTTTTATAAATTATAATTTTTGTTAAAATTA
1 AAAGTTGTTTGGTAAATTTTTTTTTATAAGTTCTTTTTTATAAATTATAATTTTTGTTAAAATTA
30067577 TCATAG
66 TCATAG
30067583 NAAAGTTGTTTGGTTAAA-TTTTTTTTATAAGTTCTTTTTTATAAATTATAATTTTTGTTAAAAT
1 -AAAGTTGTTTGG-TAAATTTTTTTTTATAAGTTCTTTTTTATAAATTATAATTTTTGTTAAAAT
30067647 TATCATAG
64 TATCATAG
30067655 A
1 A
30067656 TGGTATTTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
71 1 0.01
72 66 0.93
73 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (71 bp):
AAAGTTGTTTGGTAAATTTTTTTTTATAAGTTCTTTTTTATAAATTATAATTTTTGTTAAAATTA
TCATAG
Found at i:30080511 original size:38 final size:38
Alignment explanation
Indices: 30080457--30080533 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
30080447 AAGCAACTGT
*
30080457 TAAATTTACCAACGTATTTTCATAATTACATCTTGGAA
1 TAAATTTACCAACGTATTTTCATAATTACATATTGGAA
*
30080495 TAAATTTACCATCGTATTTTCATAATTACATATTGGAA
1 TAAATTTACCAACGTATTTTCATAATTACATATTGGAA
30080533 T
1 T
30080534 TGAGTGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (38 bp):
TAAATTTACCAACGTATTTTCATAATTACATATTGGAA
Found at i:30083076 original size:21 final size:24
Alignment explanation
Indices: 30083052--30083101 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
30083042 TTTTTCTATT
*
30083052 TAAAATAAA-ATTTTGA-A-AATA
1 TAAAATAAATATTTTCATATAATA
30083073 TAAAA-AAATATTTTCATATAATA
1 TAAAATAAATATTTTCATATAATA
30083096 TAAAAT
1 TAAAAT
30083102 TTATAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 1 0.04
23 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAATAAATATTTTCATATAATA
Found at i:30089958 original size:17 final size:17
Alignment explanation
Indices: 30089936--30089969 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30089926 TTTTGAGAAG
30089936 TTTTTTAAAAAGAACAA
1 TTTTTTAAAAAGAACAA
**
30089953 TTTTTTTTAAAGAACAA
1 TTTTTTAAAAAGAACAA
30089970 AATAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TTTTTTAAAAAGAACAA
Found at i:30101354 original size:2 final size:2
Alignment explanation
Indices: 30101349--30101395 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
30101339 TATTTTTTAA
* * *
30101349 AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AC CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
30101390 GT AT AT
1 AT AT AT
30101396 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30120183 original size:26 final size:26
Alignment explanation
Indices: 30120147--30120198 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
30120137 ACAAAAAGTA
30120147 AACAAAATCTACCGCATCCCTTATTC
1 AACAAAATCTACCGCATCCCTTATTC
30120173 AACAAAATCTACCGCATCCCTTATTC
1 AACAAAATCTACCGCATCCCTTATTC
30120199 CCATGAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.04, T:0.27
Consensus pattern (26 bp):
AACAAAATCTACCGCATCCCTTATTC
Found at i:30130049 original size:12 final size:12
Alignment explanation
Indices: 30130028--30130069 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
30130018 GTGCCTAAAA
*
30130028 GGAGAAAGAGAG
1 GGAGAGAGAGAG
*
30130040 AGAGAGAGAGAG
1 GGAGAGAGAGAG
*
30130052 GGAGAGGGAGAG
1 GGAGAGAGAGAG
30130064 GGAGAG
1 GGAGAG
30130070 TTTCTGCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
GGAGAGAGAGAG
Found at i:30130844 original size:18 final size:16
Alignment explanation
Indices: 30130821--30130858 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
30130811 TATATTTTCC
30130821 TTTTCTTCATTCATTTTT
1 TTTTCTTCATT--TTTTT
30130839 TTTTCTTCATTTTTTT
1 TTTTCTTCATTTTTTT
30130855 TTTT
1 TTTT
30130859 AACCTACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTCATTTTTTT
Found at i:30130857 original size:15 final size:14
Alignment explanation
Indices: 30130830--30130856 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30130820 CTTTTCTTCA
30130830 TTCATTTTTTTTTC
1 TTCATTTTTTTTTC
30130844 TTCATTTTTTTTT
1 TTCATTTTTTTTT
30130857 TTAACCTACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCATTTTTTTTTC
Found at i:30135532 original size:11 final size:11
Alignment explanation
Indices: 30135516--30135540 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30135506 TACCAATTTC
30135516 TTTTTTTTGTT
1 TTTTTTTTGTT
30135527 TTTTTTTTGTT
1 TTTTTTTTGTT
30135538 TTT
1 TTT
30135541 GTGAATGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:30139796 original size:14 final size:15
Alignment explanation
Indices: 30139772--30139816 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
30139762 AAGATTTTAC
*
30139772 AAAACTCTAAAAGAA
1 AAAAATCTAAAAGAA
30139787 AAAAAT-TAAAA-AA
1 AAAAATCTAAAAGAA
*
30139800 CAAAATCTAAAAGAA
1 AAAAATCTAAAAGAA
30139815 AA
1 AA
30139817 CTTTAGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 8 0.32
ACGTcount: A:0.73, C:0.09, G:0.04, T:0.13
Consensus pattern (15 bp):
AAAAATCTAAAAGAA
Found at i:30141603 original size:3 final size:3
Alignment explanation
Indices: 30141595--30141620 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30141585 ACATTATCTT
30141595 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
30141621 TGACAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30151936 original size:24 final size:25
Alignment explanation
Indices: 30151900--30151949 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
30151890 TTTACTAACT
30151900 AAACCAAATTTAA-ATCAT-AAACAA
1 AAACCAAATTTAATAT-ATAAAACAA
30151924 AAACC-AATATTAATATATAAAACAA
1 AAACCAAAT-TTAATATATAAAACAA
30151949 A
1 A
30151950 CCCTACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 3 0.13
24 11 0.48
25 9 0.39
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (25 bp):
AAACCAAATTTAATATATAAAACAA
Found at i:30154023 original size:68 final size:68
Alignment explanation
Indices: 30153914--30154045 Score: 212
Period size: 68 Copynumber: 1.9 Consensus size: 68
30153904 TCTTTACTTT
* **
30153914 GTCTTCCAAAGTCACACTTCGTCTTCTAGAGTTATGAGAAGAGAACTTGGACTGGACTTAAGATT
1 GTCTTCCAAAGTCACACTTCGTCTTCTAGAGTCACAAGAAGAGAACTTGGACTGGACTTAAGATT
30153979 TTA
66 TTA
*
30153982 GTCTTCCAGAGTCACACTTCGTCTT-TCAGAGTCACAAGAAGAGAACTTGGACTGGACTTAAGAT
1 GTCTTCCAAAGTCACACTTCGTCTTCT-AGAGTCACAAGAAGAGAACTTGGACTGGACTTAAGAT
30154046 AACAGAACTT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 1 0.02
68 58 0.98
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (68 bp):
GTCTTCCAAAGTCACACTTCGTCTTCTAGAGTCACAAGAAGAGAACTTGGACTGGACTTAAGATT
TTA
Found at i:30154087 original size:34 final size:34
Alignment explanation
Indices: 30154048--30154115 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
30154038 CTTAAGATAA
*
30154048 CAGAACTTGAACTGGACTTAAGATTTAGTACTTC
1 CAGAACTTGAACTAGACTTAAGATTTAGTACTTC
*
30154082 CAGAACTTGGACTAGACTTAAGATTTAGTACTTC
1 CAGAACTTGAACTAGACTTAAGATTTAGTACTTC
30154116 GTCTTCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (34 bp):
CAGAACTTGAACTAGACTTAAGATTTAGTACTTC
Found at i:30154647 original size:81 final size:80
Alignment explanation
Indices: 30154511--30154738 Score: 253
Period size: 81 Copynumber: 2.8 Consensus size: 80
30154501 AATTTGATTT
* * * * *
30154511 TTATCTCCATATTATCATAATTT-TTTAGAGATAAATTAGATGACCAATTAGTAAATTTTAATTG
1 TTATCTCTATATTATCTTAATTTATTTAGAGATAAATT-GATGAACAATAATTAAATTTTAATTG
* *
30154575 ATAAAAAATATGAATC
65 ATAAAAAATATAAATA
* * *
30154591 TTATCTCTATATTATCTTAATTTATTTAGAAATAAATTGGATGATCAACAATTAAATTTTAATTG
1 TTATCTCTATATTATCTTAATTTATTTAGAGATAAATT-GATGAACAATAATTAAATTTTAATTG
* *
30154656 GTTAAAAATATAAATA
65 ATAAAAAATATAAATA
* * * * *
30154672 TTATATCTAAATTACCTTGATTTATTTTAGAGATAAATTAAT-AACTAATAATTAAATTTTAATT
1 TTATCTCTATATTATCTTAATTTA-TTTAGAGATAAATTGATGAAC-AATAATTAAATTTTAATT
30154736 GAT
64 GAT
30154739 CCAATTTTGT
Statistics
Matches: 124, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
80 23 0.19
81 88 0.71
82 13 0.10
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (80 bp):
TTATCTCTATATTATCTTAATTTATTTAGAGATAAATTGATGAACAATAATTAAATTTTAATTGA
TAAAAAATATAAATA
Found at i:30160118 original size:33 final size:33
Alignment explanation
Indices: 30160081--30160164 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
30160071 TTTGTAACGT
30160081 TATAAT-T-AAAATAAAAACCATTAAAATAAAATA
1 TATAATATAAAAATAAAAA--ATTAAAATAAAATA
30160114 TATAATATAAAAATAAAAAATTAAAATAAAATA
1 TATAATATAAAAATAAAAAATTAAAATAAAATA
*
30160147 -A-AATATAAGAAATTAAAA
1 TATAATATAA-AAATAAAAA
30160165 TTTATATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 7 0.15
32 9 0.19
33 20 0.43
34 1 0.02
35 10 0.21
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.26
Consensus pattern (33 bp):
TATAATATAAAAATAAAAAATTAAAATAAAATA
Found at i:30160154 original size:25 final size:24
Alignment explanation
Indices: 30160115--30160165 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
30160105 AATAAAATAT
*
30160115 ATAATATAAAAATAAAAAATTAAA
1 ATAAAATAAAAATAAAAAATTAAA
*
30160139 ATAAAATAAAATATAAGAAATTAAA
1 ATAAAATAAAA-ATAAAAAATTAAA
30160164 AT
1 AT
30160166 TTATATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
ATAAAATAAAAATAAAAAATTAAA
Found at i:30160468 original size:15 final size:15
Alignment explanation
Indices: 30160445--30160499 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
30160435 ATTTTCCCTA
* *
30160445 CAATTACATTGCTTG
1 CAATCACATTACTTG
30160460 CAATCACATTACTTG
1 CAATCACATTACTTG
* *
30160475 CAATTATATTACTTG
1 CAATCACATTACTTG
*
30160490 TAATCACATT
1 CAATCACATT
30160500 GCATTGTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
CAATCACATTACTTG
Found at i:30161172 original size:43 final size:43
Alignment explanation
Indices: 30161072--30161178 Score: 103
Period size: 45 Copynumber: 2.4 Consensus size: 43
30161062 ATTTTAAAAT
* * *
30161072 TTTATAACTTATTTTTA--TTTTTTGAAATTTTATAATTTCGTTG
1 TTTATAA-TAATTTTTATTTTTTTTGAAATTATATAATTTC-TTC
* *
30161115 TTTTTAATATATTTTTATTTTTTTTGAAATTATATCATTT-TATC
1 TTTATAATA-ATTTTTATTTTTTTTGAAATTATATAATTTCT-TC
30161159 TTTATAATAATTTTTTATTT
1 TTTATAATAA-TTTTTATTT
30161179 GGTGAGATGC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 1 0.02
43 15 0.28
44 18 0.34
45 19 0.36
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (43 bp):
TTTATAATAATTTTTATTTTTTTTGAAATTATATAATTTCTTC
Found at i:30172678 original size:22 final size:21
Alignment explanation
Indices: 30172633--30172683 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
30172623 TTTATCTTTG
30172633 ATTAATTTTTATAATTATAATT
1 ATTAA-TTTTATAATTATAATT
* **
30172655 ATCTAATTTTATTATTATTTTT
1 AT-TAATTTTATAATTATAATT
30172677 ATTAATT
1 ATTAATT
30172684 AAAAAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 17 0.68
23 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTAATTTTATAATTATAATT
Found at i:30176593 original size:2 final size:2
Alignment explanation
Indices: 30176586--30176627 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
30176576 AAAGTCAAAC
30176586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30176628 TACTATGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30183065 original size:21 final size:21
Alignment explanation
Indices: 30183041--30183128 Score: 98
Period size: 18 Copynumber: 4.5 Consensus size: 21
30183031 ATACGACATG
30183041 ACACGATTAATAATACGTTTA
1 ACACGATTAATAATACGTTTA
*
30183062 ACACGATTAATAATACGATTA
1 ACACGATTAATAATACGTTTA
*
30183083 ACACGA-T--TAACACGTTTA
1 ACACGATTAATAATACGTTTA
* *
30183101 GCACGATTAA-CAT--GTTTA
1 ACACGATTAATAATACGTTTA
30183119 ACACGATTAA
1 ACACGATTAA
30183129 ATAAAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
18 28 0.49
19 1 0.02
20 2 0.04
21 26 0.46
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (21 bp):
ACACGATTAATAATACGTTTA
Found at i:30183079 original size:12 final size:12
Alignment explanation
Indices: 30183043--30183083 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
30183033 ACGACATGAC
30183043 ACGATTAATAAT
1 ACGATTAATAAT
*
30183055 ACG-TT--TAAC
1 ACGATTAATAAT
30183064 ACGATTAATAAT
1 ACGATTAATAAT
30183076 ACGATTAA
1 ACGATTAA
30183084 CACGATTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 14 0.58
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (12 bp):
ACGATTAATAAT
Found at i:30183088 original size:9 final size:9
Alignment explanation
Indices: 30183076--30183128 Score: 70
Period size: 9 Copynumber: 5.9 Consensus size: 9
30183066 GATTAATAAT
30183076 ACGATTAAC
1 ACGATTAAC
30183085 ACGATTAAC
1 ACGATTAAC
* *
30183094 ACGTTTAGC
1 ACGATTAAC
30183103 ACGATTAAC
1 ACGATTAAC
* *
30183112 ATGTTTAAC
1 ACGATTAAC
30183121 ACGATTAA
1 ACGATTAA
30183129 ATAAAAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (9 bp):
ACGATTAAC
Found at i:30183420 original size:18 final size:18
Alignment explanation
Indices: 30183378--30183413 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30183368 TATGTCATGT
*
30183378 ATACATGTTTAAACACGA
1 ATACACGTTTAAACACGA
30183396 ATACACGTTTAAACACGA
1 ATACACGTTTAAACACGA
30183414 TAACACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (18 bp):
ATACACGTTTAAACACGA
Found at i:30183425 original size:18 final size:18
Alignment explanation
Indices: 30183386--30183425 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
30183376 GTATACATGT
*
30183386 TTAAACACGAATACACGT
1 TTAAACACGAATACACGA
30183404 TTAAACACG-ATAACACGA
1 TTAAACACGAAT-ACACGA
30183422 TTAA
1 TTAA
30183426 GTAAGCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (18 bp):
TTAAACACGAATACACGA
Found at i:30194878 original size:15 final size:15
Alignment explanation
Indices: 30194851--30194898 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
30194841 GTTTGGCACT
*
30194851 TTACAATGTAATGTTA
1 TTACAA-GTAATGTGA
*
30194867 TTACAGGTAATGTGA
1 TTACAAGTAATGTGA
*
30194882 TTGCAAGTAATGTGA
1 TTACAAGTAATGTGA
30194897 TT
1 TT
30194899 GTAAACAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 23 0.82
16 5 0.18
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (15 bp):
TTACAAGTAATGTGA
Found at i:30194899 original size:15 final size:15
Alignment explanation
Indices: 30194858--30194931 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
30194848 ACTTTACAAT
* * *
30194858 GTAATGTTATTACAG
1 GTAATGTGATTGCAA
30194873 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
*
30194888 GTAATGTGATTGTAA
1 GTAATGTGATTGCAA
** *
30194903 ACAATGTGATTGTAA
1 GTAATGTGATTGCAA
**
30194918 ACAATGTGATTGCA
1 GTAATGTGATTGCA
30194932 GGAAAAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:30195314 original size:33 final size:32
Alignment explanation
Indices: 30195253--30195316 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
30195243 TATTATATAA
30195253 TTTTTCATTTCTTATATTTTATTTTATTTTAT
1 TTTTTCATTTCTTATATTTTATTTTATTTTAT
*
30195285 TTTTTGATTT-TTATATTATATATTTTATTTTA
1 TTTTTCATTTCTTATATT-T-TATTTTATTTTA
30195317 ATTATAACGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 7 0.24
32 10 0.34
33 12 0.41
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (32 bp):
TTTTTCATTTCTTATATTTTATTTTATTTTAT
Found at i:30195479 original size:13 final size:13
Alignment explanation
Indices: 30195461--30195493 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
30195451 AATGTGATTG
30195461 CATTGCAATTTTA
1 CATTGCAATTTTA
30195474 CATTGCAATTTTA
1 CATTGCAATTTTA
30195487 CATTGCA
1 CATTGCA
30195494 GTAGTCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (13 bp):
CATTGCAATTTTA
Found at i:30205751 original size:60 final size:59
Alignment explanation
Indices: 30205666--30205839 Score: 208
Period size: 60 Copynumber: 2.9 Consensus size: 59
30205656 TTGTAAAAAA
* * *
30205666 GGACCTGAAGCCCCGATTCATATTAGGTGGTGTGGGCAGTTCCCATGAGTAGGTAAAGGG
1 GGACCTGAAGCCTCGATTC-TATTAGGTGGCGTGGGCAGTTCCCATGAGTAGGTAAAAGG
* * *
30205726 GGACCTGAAGCCTCGATTCGCATTAGGTGGGGTGGGCAATTCCCACT-AGTAGGTAAAAGG
1 GGACCTGAAGCCTCGATTC-TATTAGGTGGCGTGGGCAGTTCCCA-TGAGTAGGTAAAAGG
* * *
30205786 AGACTTGAAGCCTCGATT-TATATATGGTGGCGTGGGCAGTTCCCACGAGTAGGT
1 GGACCTGAAGCCTCGATTCTAT-TA-GGTGGCGTGGGCAGTTCCCATGAGTAGGT
30205840 GATGATGTCT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
60 93 0.95
61 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (59 bp):
GGACCTGAAGCCTCGATTCTATTAGGTGGCGTGGGCAGTTCCCATGAGTAGGTAAAAGG
Found at i:30207830 original size:108 final size:108
Alignment explanation
Indices: 30207675--30207884 Score: 334
Period size: 108 Copynumber: 1.9 Consensus size: 108
30207665 TATAAGAAAT
* *
30207675 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTGCAAAAGAA-TGTGTA
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTAGGTAAGAGTTAAATAATTGCAAAAGAACT-TGTA
* *
30207739 TTTGTAAATTGTGAAAGTTGTAACTAAATCAACTTATTTTTTTAA
65 TTTATAAATTGTGAAAGTTGTAA-TAAATCAACATATTTTTTTAA
*
30207784 TTTGAGTAAATTTAAATAAAAA-GTAAATTAGGTAAGAGTTAAATAATTTCAAAAGAACTTGTAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTAGGTAAGAGTTAAATAATTGCAAAAGAACTTGTAT
*
30207848 TTATAAATTGTGAAAGTTGTAATTAATCAACATATTT
66 TTATAAATTGTGAAAGTTGTAATAAATCAACATATTT
30207885 AATTATTTTA
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 13 0.14
108 58 0.62
109 23 0.24
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAAGGTAAATTAGGTAAGAGTTAAATAATTGCAAAAGAACTTGTAT
TTATAAATTGTGAAAGTTGTAATAAATCAACATATTTTTTTAA
Found at i:30216831 original size:18 final size:18
Alignment explanation
Indices: 30216810--30216844 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30216800 AATTAATTAA
30216810 TTATT-AATTATAAAGTAC
1 TTATTAAATT-TAAAGTAC
30216828 TTATTAAATTTAAAGTA
1 TTATTAAATTTAAAGTA
30216845 AAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTATTAAATTTAAAGTAC
Found at i:30217600 original size:15 final size:15
Alignment explanation
Indices: 30217575--30217609 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
30217565 AGAACACAAC
30217575 ACTTATCTTGCTCTTG
1 ACTT-TCTTGCTCTTG
30217591 ACTTTCTTGCTCTTG
1 ACTTTCTTGCTCTTG
30217606 -CTTT
1 ACTTT
30217610 TTCTCTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 11 0.58
16 4 0.21
ACGTcount: A:0.09, C:0.26, G:0.11, T:0.54
Consensus pattern (15 bp):
ACTTTCTTGCTCTTG
Found at i:30255636 original size:27 final size:27
Alignment explanation
Indices: 30255605--30255811 Score: 176
Period size: 27 Copynumber: 7.9 Consensus size: 27
30255595 TTATGACGTG
* *
30255605 TAATAATTAAATTTTTAAAATAAAATA
1 TAATAATTAAATTTTTAACATAATATA
* * * * *
30255632 AAAT-ATTTATTTTTTAACATAGTATG
1 TAATAATTAAATTTTTAACATAATATA
* * *
30255658 TTATAATTAAATTTTTAATATAATATG
1 TAATAATTAAATTTTTAACATAATATA
* *
30255685 TAATAATTATATTTTTTAATATAATATA
1 TAATAATTA-AATTTTTAACATAATATA
* *
30255713 TAATAATTAAATTTTTAACATGATAAA
1 TAATAATTAAATTTTTAACATAATATA
* *
30255740 TAA-AATTAAA-TCTT----TAATATG
1 TAATAATTAAATTTTTAACATAATATA
* *
30255761 TAATAACTAAATTTTTAATATAATATA
1 TAATAATTAAATTTTTAACATAATATA
* *
30255788 TAATAATTATATTTTTAATATAAT
1 TAATAATTAAATTTTTAACATAAT
30255812 TATTTATCGT
Statistics
Matches: 143, Mismatches: 29, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
21 7 0.05
22 6 0.04
23 3 0.02
25 3 0.02
26 25 0.17
27 74 0.52
28 25 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TAATAATTAAATTTTTAACATAATATA
Found at i:30255646 original size:55 final size:53
Alignment explanation
Indices: 30255586--30255803 Score: 141
Period size: 53 Copynumber: 4.1 Consensus size: 53
30255576 ACGTAAAATA
30255586 ATTTTTTCATTATGACGTGTAATAATTAAATTTTTAAAATAAAATAAAAT-ATT-T
1 ATTTTTTCA-TATGA--TGTAATAATTAAATTTTTAAAATAAAATAAAATAATTAT
* * * **
30255640 ATTTTTTAACATA-GTATGTTATAATTAAATTTTTAATATAATATGTAATAATTAT
1 ATTTTTT--CATATG-ATGTAATAATTAAATTTTTAAAATAAAATAAAATAATTAT
* * * *
30255695 ATTTTTTAATATAATATATAATAATTAAATTTTTAACATGATAAAT--AA-AATTA-
1 ATTTTTTCATAT--GATGTAATAATTAAATTTTTAAAAT-A-AAATAAAATAATTAT
* * * * * *
30255748 AATCTTT-A-AT-ATGTAATAACTAAATTTTTAATATAATATATAATAATTAT
1 ATTTTTTCATATGATGTAATAATTAAATTTTTAAAATAAAATAAAATAATTAT
30255798 ATTTTT
1 ATTTTT
30255804 AATATAATTA
Statistics
Matches: 131, Mismatches: 19, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
46 3 0.02
47 1 0.01
48 23 0.18
49 5 0.04
50 4 0.03
51 2 0.02
52 1 0.01
53 36 0.27
54 16 0.12
55 34 0.26
56 3 0.02
57 3 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (53 bp):
ATTTTTTCATATGATGTAATAATTAAATTTTTAAAATAAAATAAAATAATTAT
Found at i:30255695 original size:33 final size:30
Alignment explanation
Indices: 30255669--30255728 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
30255659 TATAATTAAA
*
30255669 TTTTTAATATAATATGTAATAATTAT-A-T
1 TTTTTAATATAATATATAATAATTATAATT
30255697 TTTTTAATATAATATATAATAATTA-AATT
1 TTTTTAATATAATATATAATAATTATAATT
30255726 TTT
1 TTT
30255729 AACATGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TTTTTAATATAATATATAATAATTATAATT
Found at i:30255765 original size:48 final size:49
Alignment explanation
Indices: 30255706--30255809 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 49
30255696 TTTTTTAATA
* *
30255706 TAATATATAATAATTAAATTTTTAACATGATAAATAA-AATTAAATCTT
1 TAATATATAATAACTAAATTTTTAACATAATAAATAATAATTAAATCTT
* * * * *
30255754 TAATATGTAATAACTAAATTTTTAATATAATATATAATAATTATATTTT
1 TAATATATAATAACTAAATTTTTAACATAATAAATAATAATTAAATCTT
30255803 TAATATA
1 TAATATA
30255810 ATTATTTATC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
48 32 0.68
49 15 0.32
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (49 bp):
TAATATATAATAACTAAATTTTTAACATAATAAATAATAATTAAATCTT
Found at i:30267786 original size:5 final size:5
Alignment explanation
Indices: 30267776--30267800 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30267766 CATAAACCTT
30267776 TTCTG TTCTG TTCTG TTCTG TTCTG
1 TTCTG TTCTG TTCTG TTCTG TTCTG
30267801 GTCATATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.20, T:0.60
Consensus pattern (5 bp):
TTCTG
Done.