Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 163 of 290
Found at i:55782886 original size:27 final size:27
Alignment explanation
Indices: 55782753--55782887 Score: 146
Period size: 27 Copynumber: 5.0 Consensus size: 27
55782743 TTTTACCCCC
* * *
55782753 ATTTTA-CCTCAACTTACAGAATTACC
1 ATTTTACCCTCGATTTACAGAATTACT
* * *
55782779 GTTTTACCCTCGATTTACAGAAGTACC
1 ATTTTACCCTCGATTTACAGAATTACT
* * * *
55782806 GTTTTATCCTTGATTTATAGAATTACT
1 ATTTTACCCTCGATTTACAGAATTACT
* *
55782833 GTTTTACCCTTGATTTACAGAATTACT
1 ATTTTACCCTCGATTTACAGAATTACT
*
55782860 ATTTTACCCTCGATTTACAAAATTACT
1 ATTTTACCCTCGATTTACAGAATTACT
55782887 A
1 A
55782888 GAATACCCTA
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 5 0.05
27 89 0.95
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTCGATTTACAGAATTACT
Found at i:55782886 original size:54 final size:53
Alignment explanation
Indices: 55782751--55782886 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 53
55782741 CATTTTACCC
* * *
55782751 CCATTTTACCTCAACTTACAGAATTACCGTTTTACCCTCGATTTACAGAAGTA
1 CCATTTTACCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAAGTA
* * * * *
55782804 CCGTTTTATCCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTA
1 CCATTTTA-CCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAAGTA
* *
55782858 CTATTTTACCCTCGATTTACAAAATTACT
1 CCATTTTA-CCTCGATTTACAGAATTACT
55782887 AGAATACCCT
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
53 7 0.10
54 61 0.90
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (53 bp):
CCATTTTACCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAAGTA
Found at i:55782894 original size:27 final size:27
Alignment explanation
Indices: 55782864--55783167 Score: 183
Period size: 27 Copynumber: 11.2 Consensus size: 27
55782854 ATTACTATTT
** *
55782864 TACCCTCGATTTACAAAATTACTAGAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* *
55782891 TACCCTAG-TCTGTAAAATTACTAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* *
55782917 TACCCTTGGTTTGTAAAATTAC-AGAAA
1 TACCCTCGATTTGTAAAATTACTA-AAA
* *
55782944 TACCCTCAATTTGTAAAATTACAAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* *
55782971 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTGTAAAATTACTAAAA
* * **
55782998 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTGTAAAATTACTAAAA
*
55783025 TACCCTC-ATTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTGTAAAATTACTAAAA
** *
55783052 TACCC-CTGATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTGTAAAATTACTA-AAA
* *
55783079 TACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTCGA-TTTGT-AAAATTACTA-AAA
* * * **
55783108 TACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* * * * *
55783135 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
*
55783162 CACCCT
1 TACCCT
55783168 TGTAGGATGA
Statistics
Matches: 224, Mismatches: 37, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
26 28 0.12
27 167 0.75
28 11 0.05
29 18 0.08
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTGTAAAATTACTAAAA
Found at i:55782975 original size:54 final size:53
Alignment explanation
Indices: 55782878--55783149 Score: 217
Period size: 54 Copynumber: 5.0 Consensus size: 53
55782868 CTCGATTTAC
* * *
55782878 AAAATTACTAG-AATACCCTAGTCTGTAAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTAC-AGAAATACCCTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
** * *
55782931 AAAATTACAGAAATACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTTTGT
1 AAAATTACAGAAATACCCT-GGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
* ** ***
55782985 AAAATTACCA-AAATACCACTGGTTTGTGAAATTACCGAAATACCCTCATTTTGT
1 AAAATTA-CAGAAATACC-CTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
* ** * * * *
55783039 AAAATTACCA-AAATACCCCTGATTTACAAAGTTACAGAAATACCCTTGACTTTCT
1 AAAATTA-CAGAAATA-CCCTGGTTTGTAAAATTACAAAAATACCCTTG-GTTTGT
* * ** *
55783094 AAAAATTATAGAAATACCATTGGTTTACAAAATTACTAAAATACCCTTGGTTTGT
1 -AAAATTACAGAAATACC-CTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
55783149 A
1 A
55783150 GATTTACCAA
Statistics
Matches: 179, Mismatches: 31, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
52 2 0.01
53 16 0.09
54 107 0.60
55 17 0.09
56 37 0.21
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (53 bp):
AAAATTACAGAAATACCCTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
Found at i:55783008 original size:81 final size:81
Alignment explanation
Indices: 55782864--55783058 Score: 268
Period size: 81 Copynumber: 2.4 Consensus size: 81
55782854 ATTACTATTT
* ** * * *
55782864 TACCCTCGATTTACAAAATTACTAGAATA-CCCTAGTCTGTAAAATTACTAAAATACCCTTGGTT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTGGTT
55782928 TGTAAAATTACAGAAA
66 TGTAAAATTACAGAAA
*
55782944 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTCTGTAAAATTACCAAAATACC-CTTGGT
* *
55783008 TTGTGAAATTACCGAAA
65 TTGTAAAATTACAGAAA
* *
55783025 TACCCTCATTTTGTAAAATTACCAAAATACCCCT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCT
55783059 GATTTACAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 24 0.24
81 77 0.75
82 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (81 bp):
TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTGGTT
TGTAAAATTACAGAAA
Found at i:55783080 original size:81 final size:81
Alignment explanation
Indices: 55782864--55783111 Score: 265
Period size: 81 Copynumber: 3.0 Consensus size: 81
55782854 ATTACTATTT
* ** * * *
55782864 TACCCTCGATTTACAAAATTACTAGAATA-CCCTAG-TCTGTAAAATTACTAAAATACCCTTGGT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGAT-TGTAAAATTACCAAAATACCCTTGGT
55782927 TTGTAAAATTACAGAAA
65 TTGTAAAATTACAGAAA
*
55782944 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGATTGTAAAATTACCAAAATACC-CTTGGT
* *
55783008 TTGTGAAATTACCGAAA
65 TTGTAAAATTACAGAAA
* *
55783025 TACCCTCATTTTGTAAAATTACCAAAATACCCCT-GATT-TACAAAGTTA-CAGAAATACCCTTG
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGATTGTA-AAA-TTACCA-AAATACCCTTG
* * *
55783087 ACTTTCTAAAAATTATAGAAA
63 -GTTTGT-AAAATTACAGAAA
55783108 TACC
1 TACC
55783112 ATTGGTTTAC
Statistics
Matches: 143, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
79 2 0.01
80 33 0.23
81 88 0.62
82 6 0.04
83 14 0.10
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGATTGTAAAATTACCAAAATACCCTTGGTT
TGTAAAATTACAGAAA
Found at i:55783264 original size:27 final size:27
Alignment explanation
Indices: 55783187--55783264 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
55783177 AAATGACTAA
* * *
55783187 AATACCCCTAT-TAGGTAAAAAGATCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
55783214 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
55783241 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
55783265 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:55784664 original size:25 final size:24
Alignment explanation
Indices: 55784585--55784778 Score: 252
Period size: 25 Copynumber: 8.0 Consensus size: 24
55784575 AGGAAGTGCA
*
55784585 AAAGGGCTTATGCCCTAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
*
55784608 AAAGGGCTTATGCCCCAATTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
55784631 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
55784656 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
*
55784681 GAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
*
55784706 AAAGGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTATAT
*
55784730 AAAGGGCTTTTGCCCCAGTTACTA-
1 AAAGGGCTTATGCCCCAGTTA-TAT
*
55784754 AAAGAGGC-TAGGCCTCCAGTTATAT
1 AAAG-GGCTTATGCC-CCAGTTATAT
55784779 GATAAAGCAG
Statistics
Matches: 156, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
23 42 0.27
24 31 0.20
25 83 0.53
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATAT
Found at i:55787316 original size:42 final size:42
Alignment explanation
Indices: 55787205--55787359 Score: 202
Period size: 42 Copynumber: 3.7 Consensus size: 42
55787195 TACTAAACCA
* * * *
55787205 ATGCCATATCCCATATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
* * *
55787247 ATGCCAATAGCCTAGCTATGGTCTTACACGAAATCTCATATTG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATTG
* * *
55787290 ATGCCATATCCTAGATATGGTCTTACACGAAGTCTCATACTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
*
55787332 ATGTCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
55787360 ATAAACTTAG
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 64 0.65
43 35 0.35
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
Found at i:55787649 original size:39 final size:39
Alignment explanation
Indices: 55787599--55787677 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
55787589 TCCCCAAATC
55787599 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
1 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
*
55787638 TAGGTCCGAACCTTGTTTCTCTTGATCTATAATAGCAAA
1 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
55787677 T
1 T
55787678 TAAACTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (39 bp):
TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
Found at i:55797877 original size:43 final size:42
Alignment explanation
Indices: 55797770--55797883 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 42
55797760 ACATTAGGTT
* *
55797770 ATCGATATGTGATTACATGTAAAACCATGTCTGGGACATTGGC
1 ATCGATATGTG-TTACATGTAAGACCATGTCTGGGACAGTGGC
* * *
55797813 ATCGTTAATCGAT-TT-CGTGTAAGACCCTGTCTGGGACAGTGGC
1 ATCGAT-AT-G-TGTTACATGTAAGACCATGTCTGGGACAGTGGC
55797856 ATCGATATGTGTTAACATGTAAGACCAT
1 ATCGATATGTGTT-ACATGTAAGACCAT
55797884 ATCTAGGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
40 1 0.02
41 3 0.05
42 2 0.04
43 45 0.79
44 4 0.07
45 1 0.02
46 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATCGATATGTGTTACATGTAAGACCATGTCTGGGACAGTGGC
Found at i:55813256 original size:20 final size:20
Alignment explanation
Indices: 55813222--55813259 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55813212 TCAACATCCC
55813222 ATATTTAAACTATCACATGA
1 ATATTTAAACTATCACATGA
55813242 ATATTATAAAC-ATCACAT
1 ATATT-TAAACTATCACAT
55813260 TTCTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (20 bp):
ATATTTAAACTATCACATGA
Found at i:55813882 original size:40 final size:41
Alignment explanation
Indices: 55813835--55813931 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
55813825 TATCTTGGTA
* *
55813835 TCGCACACTTAGTGCC-TCATATAGTCGAAGCTA-TTTCAAC
1 TCGCACACTTAGTGCCAT-ATATAGCCAAAGCTATTTTCAAC
* * *
55813875 TCGCACACTTAGTGCCATTTGTAGCCAAAGCTATTTTGAAC
1 TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTTCAAC
55813916 -CGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
55813932 AACATAGTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 43 0.86
41 7 0.14
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTTCAAC
Found at i:55814171 original size:18 final size:18
Alignment explanation
Indices: 55814148--55814185 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55814138 TTCAAAATTA
55814148 ACCCTTTTAATCACCAAC
1 ACCCTTTTAATCACCAAC
55814166 ACCCTTTTAATCACCAAC
1 ACCCTTTTAATCACCAAC
55814184 AC
1 AC
55814186 ATTCAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.26
Consensus pattern (18 bp):
ACCCTTTTAATCACCAAC
Found at i:55827236 original size:30 final size:31
Alignment explanation
Indices: 55827160--55827242 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
55827150 TAAGTCTCGA
55827160 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
55827190 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
55827221 CATATCA-TTGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
55827243 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 19 0.37
31 32 0.63
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:55827489 original size:25 final size:25
Alignment explanation
Indices: 55827461--55827530 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
55827451 CTCTTTTAAT
* *
55827461 AACTGGGACAAATCCCTTTTTGATA
1 AACTGGGACAAAGCCCTTTTCGATA
* *
55827486 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGACAAAGCCCTTTTCGATA
* *
55827511 AACTGGGGCATAGCCCTTTT
1 AACTGGGACAAAGCCCTTTT
55827531 AGTACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
AACTGGGACAAAGCCCTTTTCGATA
Found at i:55828547 original size:81 final size:81
Alignment explanation
Indices: 55828447--55828642 Score: 218
Period size: 81 Copynumber: 2.4 Consensus size: 81
55828437 GGGTGTTTTG
* *** **
55828447 TCTACAAACTAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTGTAAA-T
1 TCTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTT-TGATAATTTTACAAACT
*
55828510 CAGGGGTATTTTGGTAAT
65 -AAGGGTATTTTGGTAAT
* * * *
55828528 TTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAACTA
1 TCTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTTTGATAATTTTACAAACTA
55828593 AGGGTATTTTGGTAAT
66 AGGGTATTTTGGTAAT
** *
55828609 TCTAC-CCTATAGGGGTATTTCAGTAATTTCACAA
1 TCTACAAAT-TAAGGGTATTTCAGTAATTTCACAA
55828643 TCGAGGGTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
80 2 0.02
81 93 0.97
82 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (81 bp):
TCTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTTTGATAATTTTACAAACTA
AGGGTATTTTGGTAAT
Found at i:55828602 original size:27 final size:27
Alignment explanation
Indices: 55828449--55828609 Score: 148
Period size: 27 Copynumber: 6.0 Consensus size: 27
55828439 GTGTTTTGTC
**
55828449 TACAAACTAAGGGTATTTCAGTAATTT
1 TACAAACTAAGGGTATTTTGGTAATTT
** * * *
55828476 TGTAAACCAATGGTATTTCT-ATAATTT
1 TACAAACTAAGGGTATTT-TGGTAATTT
** *
55828503 TGTAAA-TCAGGGGTATTTTGGTAATTT
1 TACAAACT-AAGGGTATTTTGGTAATTT
* *
55828530 TACAAATTAAGGGTATTTCGGTAATTT
1 TACAAACTAAGGGTATTTTGGTAATTT
* *
55828557 CACAAAC-CAGTGGTATTTTGGTAATTT
1 TACAAACTAAG-GGTATTTTGGTAATTT
55828584 TACAAACTAAGGGTATTTTGGTAATT
1 TACAAACTAAGGGTATTTTGGTAATT
55828610 CTACCCTATA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.03
27 102 0.94
28 3 0.03
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
TACAAACTAAGGGTATTTTGGTAATTT
Found at i:55828649 original size:27 final size:26
Alignment explanation
Indices: 55828510--55828642 Score: 97
Period size: 27 Copynumber: 5.0 Consensus size: 26
55828500 TTTTGTAAAT
* *
55828510 CAGGGGTATTTTGGTAATTTTACAAA
1 CAGGGGTATTTCGGTAATTTCACAAA
* *
55828536 TTAAGGGTATTTCGGTAATTTCACAAA
1 -CAGGGGTATTTCGGTAATTTCACAAA
* * *
55828563 CCAGTGGTATTTTGGTAATTTTACAAA
1 -CAGGGGTATTTCGGTAATTTCACAAA
* * **
55828590 CTAAGGGTATTTTGGTAA-TTCTACCCTA
1 C-AGGGGTATTTCGGTAATTTC-A-CAAA
* *
55828618 TAGGGGTATTTCAGTAATTTCACAA
1 CAGGGGTATTTCGGTAATTTCACAA
55828643 TCGAGGGTAA
Statistics
Matches: 81, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
26 4 0.05
27 72 0.89
28 5 0.06
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (26 bp):
CAGGGGTATTTCGGTAATTTCACAAA
Found at i:55828671 original size:27 final size:27
Alignment explanation
Indices: 55828641--55828705 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
55828631 GTAATTTCAC
* * *
55828641 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTATA
* *
55828668 AATCGATGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
*
55828695 AATCTAGGGTA
1 AATCGAGGGTA
55828706 CATTGGTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:55830931 original size:31 final size:31
Alignment explanation
Indices: 55830882--55830949 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
55830872 TCAGTCTCGA
*
55830882 CATAT-ACTCGGCCGAAGCCTTTTCATAAAT
1 CATATCACTCGGCCAAAGCCTTTTCATAAAT
* *
55830912 TATATCACTGGGCCAAAGCCTTTTCATAAAT
1 CATATCACTCGGCCAAAGCCTTTTCATAAAT
55830943 CATATCA
1 CATATCA
55830950 TTAGTCGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (31 bp):
CATATCACTCGGCCAAAGCCTTTTCATAAAT
Found at i:55830963 original size:30 final size:31
Alignment explanation
Indices: 55830892--55830964 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
55830882 CATATACTCG
* *
55830892 GCCGAAGCCTTTTCATAAATTATATCACTGG
1 GCCGAAGCCTTTTCATAAATCATATCACTGA
* *
55830923 GCCAAAGCCTTTTCATAAATCATATCA-TTA
1 GCCGAAGCCTTTTCATAAATCATATCACTGA
*
55830953 GTCGAAGCCTTT
1 GCCGAAGCCTTT
55830965 ACTGTAAGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (31 bp):
GCCGAAGCCTTTTCATAAATCATATCACTGA
Found at i:55831203 original size:25 final size:24
Alignment explanation
Indices: 55831175--55831253 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
55831165 AGGCCTAGCT
55831175 TTTTTTAATAACTGGGGCAAAGCCC
1 TTTTTT-ATAACTGGGGCAAAGCCC
*
55831200 TTTTTGATAAACTGGGGCAAAGCCC
1 TTTTTTAT-AACTGGGGCAAAGCCC
* *
55831225 TTTTCGGTA-AACTGGGGCATAGCCC
1 TTTT--TTATAACTGGGGCAAAGCCC
55831250 TTTT
1 TTTT
55831254 AGCATTTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.04
25 44 0.94
27 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (24 bp):
TTTTTTATAACTGGGGCAAAGCCC
Found at i:55832092 original size:27 final size:27
Alignment explanation
Indices: 55832062--55832126 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
55832052 GGGCATATTC
*
55832062 GTCATTTTATCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
55832089 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
55832116 GTCTTTTTACC
1 GTCATTTTACC
55832127 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:55832210 original size:27 final size:27
Alignment explanation
Indices: 55832180--55832265 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
55832170 GTAAATCTAC
55832180 AAACCAAAGGTATTTCAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTTGT
*
55832207 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAAGGTATTTC-AGTAATTTTGT
* * *
55832233 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAAGGTATTTCAGTAATTTTGT
55832263 AAA
1 AAA
55832266 TTATGGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
26 1 0.02
27 22 0.45
28 7 0.14
29 18 0.37
30 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCAGTAATTTTGT
Found at i:55832283 original size:27 final size:26
Alignment explanation
Indices: 55832242--55832366 Score: 117
Period size: 27 Copynumber: 4.7 Consensus size: 26
55832232 TAGAAAGTCA
**
55832242 AGGGTATTTCT-GTAATTTTGTAAATT
1 AGGGTATTT-TGGTAATTTTACAAATT
*
55832268 ATGGGTATTTTGGTAATTTTACATATT
1 A-GGGTATTTTGGTAATTTTACAAATT
* * * **
55832295 AAGGGTAGTTCGGTAATTTCACAAACC
1 -AGGGTATTTTGGTAATTTTACAAATT
*
55832322 AGTGGTATTTTGGTAATTTTACAAAAT
1 AG-GGTATTTTGGTAATTTTACAAATT
55832349 AGGGGTATTTTGGTAATT
1 A-GGGTATTTTGGTAATT
55832367 CTACCCTATA
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
26 4 0.05
27 74 0.93
28 2 0.03
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAATT
Found at i:55832356 original size:81 final size:81
Alignment explanation
Indices: 55832244--55832399 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
55832234 GAAAGTCAAG
** * * * *
55832244 GGTATTTCTGTAATTTTGTAAATTATGGGTATTTTGGTAATTTTA-CATATTAAGGGTAGTTCGG
1 GGTATTTCTGTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCATA-TAAGGGTAGTTCAG
55832308 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
* * *
55832325 GGTATTT-TGGTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCCTATAGGGGTATTTCAG
1 GGTATTTCT-GTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCATATAAGGGTAGTTCAG
55832389 TAATTTCACAA
65 TAATTTCACAA
55832400 TCGATGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 1 0.02
81 60 0.94
82 3 0.05
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.42
Consensus pattern (81 bp):
GGTATTTCTGTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCATATAAGGGTAGTTCAGT
AATTTCACAAACCAGT
Found at i:55832377 original size:27 final size:27
Alignment explanation
Indices: 55832270--55832385 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 27
55832260 TGTAAATTAT
* * * *
55832270 GGGTATTTTGGTAATTTTACATATTAA
1 GGGTATTTTGGTAATTCTACAAAATAG
* * **
55832297 GGGTAGTTCGGTAATT-TCACAAACCAG
1 GGGTATTTTGGTAATTCT-ACAAAATAG
* *
55832324 TGGTATTTTGGTAATTTTACAAAATAG
1 GGGTATTTTGGTAATTCTACAAAATAG
***
55832351 GGGTATTTTGGTAATTCTACCCTATAG
1 GGGTATTTTGGTAATTCTACAAAATAG
55832378 GGGTATTT
1 GGGTATTT
55832386 CAGTAATTTC
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.01
27 69 0.97
28 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTACAAAATAG
Found at i:55832435 original size:27 final size:27
Alignment explanation
Indices: 55832398--55832462 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
55832388 GTAATTTCAC
* ** * *
55832398 AATCGATGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTATA
*
55832425 AATCGAGGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
55832452 AATCGAGGGTA
1 AATCGAGGGTA
55832463 CTTTGGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:55837146 original size:51 final size:51
Alignment explanation
Indices: 55837061--55837163 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
55837051 CGGGCATGTC
*
55837061 CCTGCCGAGCCCAAGTTTAGTCCAACTCAAAAAAGGCCAATTTTGAGGGTT
1 CCTGCCGAGCCCAAGTTTAATCCAACTCAAAAAAGGCCAATTTTGAGGGTT
* * *
55837112 CCTGCTGAGCCCAAGTTTAATCCAATTCAGAAAAGGCCAATTTTGAGGGTT
1 CCTGCCGAGCCCAAGTTTAATCCAACTCAAAAAAGGCCAATTTTGAGGGTT
55837163 C
1 C
55837164 TTAGGCCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (51 bp):
CCTGCCGAGCCCAAGTTTAATCCAACTCAAAAAAGGCCAATTTTGAGGGTT
Found at i:55852138 original size:33 final size:32
Alignment explanation
Indices: 55852065--55852142 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
55852055 CAGTATTTAT
* * * *
55852065 ATGTAAGACCATAGCTGGGCTATATCATTCTA
1 ATGTAAGACCATAACTGGGCTATAGCATACGA
* *
55852097 ATGATAAGACCATAACTGGGTTATGGCACTACGA
1 ATG-TAAGACCATAACTGGGCTATAGCA-TACGA
55852131 ATGTAAGACCAT
1 ATGTAAGACCAT
55852143 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 29 0.76
34 6 0.16
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATAGCATACGA
Found at i:55855848 original size:62 final size:62
Alignment explanation
Indices: 55855751--55855870 Score: 222
Period size: 62 Copynumber: 1.9 Consensus size: 62
55855741 TAGCGCCTGC
*
55855751 TCCCGCACACGGGACAGCGCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATCTGT
1 TCCCGCACAAGGGACAGCGCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATCTGT
*
55855813 TCCCGCACAAGGGACAGTGCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGAT
1 TCCCGCACAAGGGACAGCGCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGAT
55855871 GAAGCTAGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (62 bp):
TCCCGCACAAGGGACAGCGCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATCTGT
Found at i:55869707 original size:39 final size:40
Alignment explanation
Indices: 55869612--55869912 Score: 408
Period size: 39 Copynumber: 7.7 Consensus size: 40
55869602 TCGAATGATG
*
55869612 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
55869650 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
55869691 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
55869730 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
55869769 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
55869808 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
55869847 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
55869886 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
55869913 AACGAGGAGC
Statistics
Matches: 242, Mismatches: 11, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
39 171 0.71
40 59 0.24
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:55877125 original size:79 final size:81
Alignment explanation
Indices: 55876988--55877171 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
55876978 TGAATGATGT
* *
55876988 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
*
55877052 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * * **
55877068 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCAAT
*
55877130 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
55877147 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
55877172 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.61
80 31 0.35
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATAA
Found at i:55877178 original size:40 final size:40
Alignment explanation
Indices: 55876987--55877171 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
55876977 TTGAATGATG
* * * *
55876987 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
55877027 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55877067 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
55877106 TCCGGGTTAAGTCCTGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55877147 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55877172 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55877194 original size:79 final size:79
Alignment explanation
Indices: 55877034--55877204 Score: 181
Period size: 79 Copynumber: 2.2 Consensus size: 79
55877024 ATATCCGGAC
* ** **
55877034 TAAGATCCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGT
1 TAAGATCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGT
*
55877099 TACTAAATCCGGGT
66 TACTAAATCCGAGT
* *
55877113 TAAG-TCCTGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACG
1 TAAGATCC-GAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACG
*
55877176 AG-TAGCTATATCC-AGT
63 AGTTA-CTAAATCCGAGT
55877192 TAA-ATTCCGAAGG
1 TAAGA-TCCGAAGG
55877205 TACGTGATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
78 5 0.06
79 44 0.57
80 28 0.36
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (79 bp):
TAAGATCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGT
TACTAAATCCGAGT
Found at i:55881490 original size:44 final size:45
Alignment explanation
Indices: 55881434--55881525 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 45
55881424 ATGTATGAGG
55881434 CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGA-A
1 CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGATA
* *
55881478 CATCCGAGCTCGTTGAGTTGGTCGGAGTTCATTATGGATGCGATA
1 CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGATA
55881523 CAT
1 CAT
55881526 GTACTTGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 41 0.91
45 4 0.09
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGATA
Found at i:55887164 original size:18 final size:18
Alignment explanation
Indices: 55887138--55887174 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55887128 ACTTGATAAG
*
55887138 TTAGTTGAATAGTATATT
1 TTAGCTGAATAGTATATT
*
55887156 TTAGCTGAATTGTATATT
1 TTAGCTGAATAGTATATT
55887174 T
1 T
55887175 CTGAGTTTGT
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:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (18 bp):
TTAGCTGAATAGTATATT
Found at i:55889456 original size:44 final size:43
Alignment explanation
Indices: 55889356--55889470 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 43
55889346 AAAATCTGAA
* *
55889356 CTCGTTGAGTTGGTCC-AGGTTCGTGATATGTATGAGGCATCCAAG
1 CTCGTTGAGTTGGTCCGA-GTTCAT--TATGGATGAGGCATCCAAG
* * * *
55889401 CTCGTTAAGTTGGTCCGAGTTCATTATGGATGCGAGCATTCGAG
1 CTCGTTGAGTTGGTCCGAGTTCATTATGGATGAG-GCATCCAAG
55889445 CTCGTTGAGTTGGTCCGAGTTCATTA
1 CTCGTTGAGTTGGTCCGAGTTCATTA
55889471 CGAATGTGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
43 8 0.13
44 32 0.52
45 20 0.33
46 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (43 bp):
CTCGTTGAGTTGGTCCGAGTTCATTATGGATGAGGCATCCAAG
Found at i:55892202 original size:31 final size:31
Alignment explanation
Indices: 55892164--55892228 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
55892154 ACTTTCATTG
55892164 CTTACAATTTTCGATTGAATTGGTATTTTTT
1 CTTACAATTTTCGATTGAATTGGTATTTTTT
55892195 CTTACAATTTTCGATTGAATTGGTATTTTTT
1 CTTACAATTTTCGATTGAATTGGTATTTTTT
55892226 CTT
1 CTT
55892229 TCTTTCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.55
Consensus pattern (31 bp):
CTTACAATTTTCGATTGAATTGGTATTTTTT
Found at i:55892409 original size:29 final size:29
Alignment explanation
Indices: 55892367--55892426 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
55892357 AGGTTCTCGG
*
55892367 TTACCTCTTGGATTGCGGTTTATATTTTC
1 TTACCTCTTGGATTGCGATTTATATTTTC
*
55892396 TTACCTCTTGGATTGCGATTTATCTTTTC
1 TTACCTCTTGGATTGCGATTTATATTTTC
55892425 TT
1 TT
55892427 GATCGATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.53
Consensus pattern (29 bp):
TTACCTCTTGGATTGCGATTTATATTTTC
Found at i:55894246 original size:20 final size:20
Alignment explanation
Indices: 55894218--55894258 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55894208 GTACACAACT
55894218 TAACAATTTAGTATGGGTCA
1 TAACAATTTAGTATGGGTCA
*
55894238 TAACGATTTAGTATGGGTCA
1 TAACAATTTAGTATGGGTCA
55894258 T
1 T
55894259 GTTTTGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (20 bp):
TAACAATTTAGTATGGGTCA
Found at i:55901122 original size:15 final size:15
Alignment explanation
Indices: 55901104--55901132 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55901094 AATATCTTCA
55901104 TCATAATTGAAGTCT
1 TCATAATTGAAGTCT
55901119 TCATAATTGAAGTC
1 TCATAATTGAAGTC
55901133 ATACATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
TCATAATTGAAGTCT
Found at i:55903248 original size:26 final size:26
Alignment explanation
Indices: 55903219--55903311 Score: 123
Period size: 26 Copynumber: 3.5 Consensus size: 26
55903209 AATGTTCTAG
*
55903219 AAATTTTGCTAAGGGCAAAATTATCA
1 AAATTTTACTAAGGGCAAAATTATCA
55903245 AAATTTTACTAAGGGCAAAATTATCA
1 AAATTTTACTAAGGGCAAAATTATCA
* * * *
55903271 AAATTTTACTAAGAGTAAAATTGTAAA
1 AAATTTTACTAAGGGCAAAATTAT-CA
*
55903298 AAAATTTACTAAGG
1 AAATTTTACTAAGG
55903312 TAAAATTGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
26 46 0.78
27 13 0.22
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (26 bp):
AAATTTTACTAAGGGCAAAATTATCA
Found at i:55905550 original size:30 final size:29
Alignment explanation
Indices: 55905495--55905551 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
55905485 ATGTATATTT
* *
55905495 TTTTATTAAATTGAATGTTATTATATGAA
1 TTTTATTAAAATGAATGATATTATATGAA
55905524 TTTTATTGAAAATGAATCGATA-TATATG
1 TTTTATT-AAAATGAAT-GATATTATATG
55905552 TTATCATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 14 0.58
31 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTTATTAAAATGAATGATATTATATGAA
Found at i:55908925 original size:27 final size:27
Alignment explanation
Indices: 55908892--55909315 Score: 264
Period size: 27 Copynumber: 15.7 Consensus size: 27
55908882 CCTCAAATTG
*
55908892 TAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ***
55908919 TAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * * ****
55908946 CAGAATTATCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ** *** *
55908973 TAGAATTATTATTTTACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *****
55909000 CAAAATTACTGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
55909027 TAAAATTACTAAAATACCCTTGGTTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* **
55909054 CAAAATTACCAAAATACCCTCGA-CCA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
55909080 GTAAAATTACCAAAATACCCTAG-TCTG
1 -TAAAATTACCAAAATACCCTCGATTTA
* * *
55909107 TAAAATTGCTAAAATACCC-CTAGTTTA
1 TAAAATTACCAAAATACCCTCGA-TTTA
* * *
55909134 TAAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCGATTTA
* *
55909161 TAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAATACCCTCGA-TTTA
* * * *
55909188 TAAAATTACCAAAATACCATTGGTTTG
1 TAAAATTACCAAAATACCCTCGATTTA
* * * *
55909215 TGAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCGATTTA
*
55909242 TAAAATTACCAAAATACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
55909269 CAAAATTA-CAGAAATACCCTTGATTTG
1 TAAAATTACCA-AAATACCCTCGATTTA
* * *
55909296 TAGATTTACCAAAACACCCT
1 TAAAATTACCAAAATACCCT
55909316 TGTAGGATGA
Statistics
Matches: 321, Mismatches: 67, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
26 22 0.07
27 295 0.92
28 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATTTA
Found at i:55909223 original size:81 final size:81
Alignment explanation
Indices: 55909027--55909260 Score: 335
Period size: 81 Copynumber: 2.9 Consensus size: 81
55909017 CCTCGATTTA
* * * ***
55909027 TAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGACCAGTAAAATTACCA
1 TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
55909092 AAATA-CCCTAGTCTG
66 AAATACCCCTAGTCTG
* * *
55909107 TAAAATTGCTAAAATACCCCTAGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
1 TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
*
55909172 AAATACCCCTAGTTTG
66 AAATACCCCTAGTCTG
* * * *
55909188 TAAAATTACCAAAATACCATTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
1 TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
55909253 AAATACCC
66 AAATACCC
55909261 TTGATTTACA
Statistics
Matches: 136, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 61 0.45
81 75 0.55
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (81 bp):
TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
AAATACCCCTAGTCTG
Found at i:55909274 original size:81 final size:81
Alignment explanation
Indices: 55909014--55909290 Score: 326
Period size: 81 Copynumber: 3.4 Consensus size: 81
55909004 ATTACTGTTT
* * * * * **
55909014 TACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGACC
1 TACCCTTGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATT
*
55909079 AGTAAAATTACCAAAA
66 TGTAAAATTACCAAAA
* * * * * * *
55909095 TACCCTAG-TCTGTAAAATTGCTAAAATACCCCTAGTTTATAAAATTACCGAAATACCCTCAATT
1 TACCCTTGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATT
55909159 TGTAAAATTACCAAAA
66 TGTAAAATTACCAAAA
* * * * *
55909175 TACCCCT-AGTTTGTAAAATTACCAAAATACCATTGGTTTGTGAAATTACCGAAATACCCTCAAT
1 TACCCTTGA-TTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAAT
55909239 TTGTAAAATTACCAAAA
65 TTGTAAAATTACCAAAA
*
55909256 TACCCTTGATTTACAAAATTA-CAGAAATACCCTTG
1 TACCCTTGATTTATAAAATTACCA-AAATACCCTTG
55909291 ATTTGTAGAT
Statistics
Matches: 166, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 68 0.41
81 97 0.58
82 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (81 bp):
TACCCTTGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATT
TGTAAAATTACCAAAA
Found at i:55909316 original size:27 final size:27
Alignment explanation
Indices: 55909014--55909317 Score: 274
Period size: 27 Copynumber: 11.3 Consensus size: 27
55909004 ATTACTGTTT
* * *
55909014 TACCCTCGATTTATAAAATTACTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* **
55909041 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* ***
55909068 TACCCTCGACCAGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * * *
55909095 TACCCTAG-TCTGTAAAATTGCTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * *
55909121 TACCCCT-AGTTTATAAAATTACCGAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
**
55909148 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
55909175 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
* * * *
55909202 TACCATTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
**
55909229 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
**
55909256 TACCCTTGATTTACAAAATTA-CAGAAA
1 TACCCTTGATTTGTAAAATTACCA-AAA
* *
55909283 TACCCTTGATTTGTAGATTTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
55909310 CACCCTTG
1 TACCCTTG
55909318 TAGGATGAAA
Statistics
Matches: 221, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
26 22 0.10
27 196 0.89
28 3 0.01
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
TACCCTTGATTTGTAAAATTACCAAAA
Found at i:55910285 original size:25 final size:26
Alignment explanation
Indices: 55910214--55910310 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
55910204 GAGGAAGTGC
* *
55910214 AAAAGGCCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
55910240 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
55910266 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
55910291 AAAATGGCTT-TACCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
55910311 ATTAAAGAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 31 0.49
26 32 0.51
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:55910291 original size:51 final size:51
Alignment explanation
Indices: 55910214--55910310 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
55910204 GAGGAAGTGC
* *
55910214 AAAAGGCCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGCCTTATGCCCCAGTTTACCGAAAAGGGCTT-TACCCCAGTTTATTG
* *
55910266 AAAAGGGCTT-TGCCCCAGTTTACCGAAAATGGCTTTACCCCAGTT
1 AAAAGGCCTTATGCCCCAGTTTACCGAAAAGGGCTTTACCCCAGTT
55910311 ATTAAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 9 0.22
51 23 0.56
52 9 0.22
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (51 bp):
AAAAGGCCTTATGCCCCAGTTTACCGAAAAGGGCTTTACCCCAGTTTATTG
Found at i:55910514 original size:42 final size:42
Alignment explanation
Indices: 55910455--55910546 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
55910445 TAGTCTCCCC
* * *** *
55910455 AAATGGGCTTGCTTACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
55910497 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
55910539 AAATGGGC
1 AAATGGGC
55910547 CTAAGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
Found at i:55910605 original size:31 final size:31
Alignment explanation
Indices: 55910570--55910646 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
55910560 CGTTTACAGT
55910570 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* * *
55910601 AAAGGCTTCGACCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
*
55910632 AAAGGCTTCAGCCCA
1 AAAGGCTTCGGCCCA
55910647 GTAACCGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:55920429 original size:13 final size:13
Alignment explanation
Indices: 55920411--55920435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55920401 ATTTTACCTC
55920411 TTTTTCTTCTTCA
1 TTTTTCTTCTTCA
55920424 TTTTTCTTCTTC
1 TTTTTCTTCTTC
55920436 CCCTTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTCTTCTTCA
Found at i:55933152 original size:20 final size:21
Alignment explanation
Indices: 55933118--55933158 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
55933108 CCAGGGGAAG
55933118 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
55933139 GAAAGAAA-AAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
55933159 TCAAAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:55933164 original size:21 final size:21
Alignment explanation
Indices: 55933119--55933165 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
55933109 CAGGGGAAGG
*
55933119 AAAGAAAGAAAAAGAGAAAAG
1 AAAGAAAGAAAAAGAGAAAAC
*
55933140 AAAGAAA-AAAAAGGGAAAATC
1 AAAGAAAGAAAAAGAGAAAA-C
55933161 AAAGA
1 AAAGA
55933166 TGTGAAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAGAAAAC
Found at i:55935099 original size:46 final size:46
Alignment explanation
Indices: 55935032--55935397 Score: 543
Period size: 46 Copynumber: 8.0 Consensus size: 46
55935022 TATGTGCTCT
* * *
55935032 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
55935078 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935124 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935170 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935216 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935262 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935308 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935354 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCA
55935398 ACATGACAGA
Statistics
Matches: 284, Mismatches: 36, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 284 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
Found at i:55935405 original size:46 final size:46
Alignment explanation
Indices: 55935032--55935443 Score: 538
Period size: 46 Copynumber: 9.0 Consensus size: 46
55935022 TATGTGCTCT
* * *
55935032 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* *
55935078 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935124 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* **
55935170 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935216 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* **
55935262 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
55935308 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* ** *
55935354 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * ** * *
55935400 ATGACA-GAAAATGAGTAAGACCATAATTGAAAGACACTATGGCA
1 CTGACATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
55935444 TCATGTCAAA
Statistics
Matches: 322, Mismatches: 43, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 321 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
Found at i:55935443 original size:92 final size:92
Alignment explanation
Indices: 55935032--55935397 Score: 671
Period size: 92 Copynumber: 4.0 Consensus size: 92
55935022 TATGTGCTCT
* * * * *
55935032 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAT-ACTATGGCAACCTGATATGAAATGTATAA
1 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAAC-ATGGCAGCGTGACATGAAATGAATAA
55935096 GACCATGGTTGAAAGATACCATGGCAGC
65 GACCATGGTTGAAAGATACCATGGCAGC
55935124 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
1 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
55935189 ACCATGGTTGAAAGATACCATGGCAGC
66 ACCATGGTTGAAAGATACCATGGCAGC
55935216 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
1 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
55935281 ACCATGGTTGAAAGATACCATGGCAGC
66 ACCATGGTTGAAAGATACCATGGCAGC
55935308 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
1 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
55935373 ACCATGGTTGAAAGATACCATGGCA
66 ACCATGGTTGAAAGATACCATGGCA
55935398 ACATGACAGA
Statistics
Matches: 268, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 266 0.99
93 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (92 bp):
CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGCGTGACATGAAATGAATAAG
ACCATGGTTGAAAGATACCATGGCAGC
Found at i:55944094 original size:28 final size:29
Alignment explanation
Indices: 55944057--55944181 Score: 144
Period size: 29 Copynumber: 4.3 Consensus size: 29
55944047 AAGTCTACAT
* *
55944057 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
55944085 TCATTCATATGGCCCTTTAGGCCTAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
** * *
55944114 ACATTTGTGTGGTCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
55944143 ACATTCATACGGCCTATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
55944172 ACATTCATAT
1 ACATTCATAT
55944182 ACATGCTTTC
Statistics
Matches: 77, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
28 19 0.25
29 58 0.75
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:55944413 original size:16 final size:16
Alignment explanation
Indices: 55944392--55944427 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
55944382 GTAGCCAAAC
*
55944392 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGACA
55944408 TTTCAGCTTTTCGACA
1 TTTCAGCTTTTCGACA
55944424 TTTC
1 TTTC
55944428 GGGATTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.47
Consensus pattern (16 bp):
TTTCAGCTTTTCGACA
Found at i:55945781 original size:18 final size:17
Alignment explanation
Indices: 55945740--55945781 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
55945730 AAATTAGGCC
55945740 GTGTGGGCCACATGGGA
1 GTGTGGGCCACATGGGA
* *
55945757 GTATGGGCCCACATGGGT
1 GTGTGGG-CCACATGGGA
55945775 GTGTGGG
1 GTGTGGG
55945782 AAAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.14, C:0.17, G:0.48, T:0.21
Consensus pattern (17 bp):
GTGTGGGCCACATGGGA
Found at i:55945914 original size:5 final size:5
Alignment explanation
Indices: 55945904--55945937 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
55945894 TTAATACTTA
55945904 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
55945938 ACAAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:55946028 original size:26 final size:26
Alignment explanation
Indices: 55945986--55946037 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
55945976 AAGTTCAAAC
55945986 AAAATAGAGAAGAAAAAGAATGAAAAG
1 AAAATAGAGAAGAAAAAGAA-GAAAAG
*
55946013 AAAA-AGAGAA-AGAAAAGGAGAAAAG
1 AAAATAGAGAAGA-AAAAGAAGAAAAG
55946038 TTAGGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (26 bp):
AAAATAGAGAAGAAAAAGAAGAAAAG
Found at i:55951916 original size:1 final size:1
Alignment explanation
Indices: 55951910--55951935 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
55951900 CTGGAATGCN
55951910 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
55951936 GATTAGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55952245 original size:17 final size:16
Alignment explanation
Indices: 55952212--55952245 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55952202 ATATATAATC
*
55952212 TGAAGTTTAATTTATT
1 TGAAGTTTAAATTATT
55952228 TGAAGTTTATAATTATT
1 TGAAGTTTA-AATTATT
55952245 T
1 T
55952246 TTTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TGAAGTTTAAATTATT
Found at i:55952651 original size:16 final size:16
Alignment explanation
Indices: 55952626--55952670 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
55952616 ACCATCATTG
*
55952626 ATATACTTAATAATTA
1 ATATAATTAATAATTA
55952642 ATATAATTAATAA-T-
1 ATATAATTAATAATTA
55952656 ATATAATT-ATAATTA
1 ATATAATTAATAATTA
55952671 TAGCACAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 1 0.04
16 12 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAATTAATAATTA
Found at i:55963392 original size:10 final size:10
Alignment explanation
Indices: 55963377--55963403 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55963367 TGAGTTGAAG
55963377 TTGAGCTGAT
1 TTGAGCTGAT
55963387 TTGAGCTGAT
1 TTGAGCTGAT
55963397 TTGAGCT
1 TTGAGCT
55963404 TGAAGAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:55968124 original size:44 final size:43
Alignment explanation
Indices: 55968026--55968191 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 43
55968016 AGCGTGTACA
** ** * * ** *
55968026 ATGCCAATGTCTTAGACGTGGTCTTACATGTAATCAACTATTG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAAAATCG
* * * *
55968069 ATGCCACTGTCCTAGACAAGGTCTTACCCGTAAATCACAAATCG
1 ATGCCAATGTCCCAGACAAGGTCTTACACG-AAATCAAAAATCG
* * *
55968113 ATGCCAATGTCCCAAACGAGGTCTTACACGAAATCAAAAATTG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAAAATCG
* * *
55968156 ATGTCAACGTCCCAGACATGGTCTTACACGAAATCA
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCA
55968192 TATATCGGAA
Statistics
Matches: 99, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
43 66 0.67
44 33 0.33
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAAAATCG
Found at i:55968210 original size:87 final size:87
Alignment explanation
Indices: 55968026--55968191 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 87
55968016 AGCGTGTACA
** * * * * ** * *
55968026 ATGCCAATGTCTTAGACGTGGTCTTACATGTAATCAACTATTGATGCCACTGTCCTAGACAAGGT
1 ATGCCAATGTCCCAAACGAGGTCTTACACGAAATCAAAAATTGATGCAACTGTCCCAGACAAGGT
*
55968091 CTTACCCGTAAATCACAAATCG
66 CTTACACGTAAATCACAAATCG
*
55968113 ATGCCAATGTCCCAAACGAGGTCTTACACGAAATCAAAAATTGATGTCAAC-GTCCCAGACATGG
1 ATGCCAATGTCCCAAACGAGGTCTTACACGAAATCAAAAATTGATG-CAACTGTCCCAGACAAGG
55968177 TCTTACACG-AAATCA
65 TCTTACACGTAAATCA
55968192 TATATCGGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
86 6 0.09
87 57 0.86
88 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (87 bp):
ATGCCAATGTCCCAAACGAGGTCTTACACGAAATCAAAAATTGATGCAACTGTCCCAGACAAGGT
CTTACACGTAAATCACAAATCG
Found at i:55970777 original size:106 final size:106
Alignment explanation
Indices: 55970641--55970853 Score: 417
Period size: 106 Copynumber: 2.0 Consensus size: 106
55970631 TAATGACGAT
55970641 TGAACTCACGACATCTAATAGATTATTTGAGTTCAAAAAAAATATACTAGAATGTTAGGTCAAGC
1 TGAACTCACGACATCTAATAGATTATTTGAGTTCAAAAAAAATATACTAGAATGTTAGGTCAAGC
55970706 TTAGGGCAGGTTCAATAGCATACTCCAAGGATTAATTGGAA
66 TTAGGGCAGGTTCAATAGCATACTCCAAGGATTAATTGGAA
55970747 TGAACTCACGACATCTAATAGATTATTTGAGTTCAAAAAAAATATACTAGAATGTTAGGTCAAGC
1 TGAACTCACGACATCTAATAGATTATTTGAGTTCAAAAAAAATATACTAGAATGTTAGGTCAAGC
*
55970812 TTAGGGCAGGTTCAATATCATACTCCAAGGATTAATTGGAA
66 TTAGGGCAGGTTCAATAGCATACTCCAAGGATTAATTGGAA
55970853 T
1 T
55970854 TGGTGTTGAT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (106 bp):
TGAACTCACGACATCTAATAGATTATTTGAGTTCAAAAAAAATATACTAGAATGTTAGGTCAAGC
TTAGGGCAGGTTCAATAGCATACTCCAAGGATTAATTGGAA
Found at i:55972149 original size:62 final size:59
Alignment explanation
Indices: 55972041--55972161 Score: 179
Period size: 62 Copynumber: 2.0 Consensus size: 59
55972031 ATTATTTCAA
* * *
55972041 TATTAAATTAATATAATATTTATCAAGAAAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAACTAATAGAATATTTATCAAGAAAAATATTAAATTAAATTTAATATTAAATCT
*
55972100 TATTAAACTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAAATCT
1 TATTAAACTAATAGAATATTTA--T-CAAGAAAAATATTAAATTAAATTTAATATTAAATCT
55972162 ACTAAAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
59 20 0.36
61 1 0.02
62 34 0.62
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (59 bp):
TATTAAACTAATAGAATATTTATCAAGAAAAATATTAAATTAAATTTAATATTAAATCT
Found at i:55972612 original size:9 final size:9
Alignment explanation
Indices: 55972590--55972619 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
55972580 AAATATTATT
55972590 TTAATTTAAA
1 TTAATTT-AA
55972600 TTAATTTAA
1 TTAATTTAA
55972609 TTAATTTAA
1 TTAATTTAA
55972618 TT
1 TT
55972620 TTACTCGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTAATTTAA
Found at i:55980359 original size:11 final size:11
Alignment explanation
Indices: 55980333--55980375 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
55980323 TCTTAATTCA
*
55980333 TTTTTATAAAAT
1 TTTTTAT-AATT
55980345 TTTTTATAATT
1 TTTTTATAATT
* *
55980356 TTTTAATAGTT
1 TTTTTATAATT
55980367 TTTTTATAA
1 TTTTTATAA
55980376 ATTATCTATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:55980433 original size:30 final size:30
Alignment explanation
Indices: 55980393--55980464 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
55980383 ATCATTTCTA
55980393 AAAATCAATTAAAAAATCATAAAATAATAAT
1 AAAAT-AATTAAAAAATCATAAAATAATAAT
*** **
55980424 AAAATAATTAAATCCTCATAAAATAATTTT
1 AAAATAATTAAAAAATCATAAAATAATAAT
55980454 AAAA-AATTAAA
1 AAAATAATTAAA
55980465 TCAAATTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 7 0.19
30 24 0.67
31 5 0.14
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (30 bp):
AAAATAATTAAAAAATCATAAAATAATAAT
Found at i:55980525 original size:24 final size:23
Alignment explanation
Indices: 55980496--55980543 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
55980486 CATCAATTTT
55980496 TCATATAAACTACCACGTCAATCA
1 TCATATAAACTACCACGTC-ATCA
*
55980520 TCATATAATCTACCACGTCATCA
1 TCATATAAACTACCACGTCATCA
55980543 T
1 T
55980544 TCAATGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (23 bp):
TCATATAAACTACCACGTCATCA
Found at i:55989140 original size:13 final size:13
Alignment explanation
Indices: 55989122--55989146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55989112 CATATGGATC
55989122 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
55989135 AAAAAAGAAAAA
1 AAAAAAGAAAAA
55989147 GAAACTTGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:55996256 original size:84 final size:84
Alignment explanation
Indices: 55996135--55996302 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
55996125 TTAAAGGGAG
55996135 ATCTCCAGTCTTGATGATGAATCAAGCTCTTGAGATGGATCAATCGGCTTTCCTTGAGTAATTCC
1 ATCTCCAGTCTTGATGATGAATCAAGCTCTTGAGATGGATCAATCGGCTTTCCTTGAGTAATTCC
*
55996200 TTCTTCTTCCTCTGCGCCC
66 TTCTTCTGCCTCTGCGCCC
55996219 ATCTCCAGTCTTGATGATGAATCAAGCTCTTGAGATGGATCAATCGGCTTTCCTTGAGTAATTCC
1 ATCTCCAGTCTTGATGATGAATCAAGCTCTTGAGATGGATCAATCGGCTTTCCTTGAGTAATTCC
55996284 TTCTTCTGCCTCTGCGCCC
66 TTCTTCTGCCTCTGCGCCC
55996303 CCTTCCTAAG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (84 bp):
ATCTCCAGTCTTGATGATGAATCAAGCTCTTGAGATGGATCAATCGGCTTTCCTTGAGTAATTCC
TTCTTCTGCCTCTGCGCCC
Found at i:55997661 original size:324 final size:324
Alignment explanation
Indices: 55997072--55997720 Score: 1298
Period size: 324 Copynumber: 2.0 Consensus size: 324
55997062 ATGAGAAGTT
55997072 ATTACCATAGGCTTGCTTAAAAATCAAATCTCCACCACTATATATTGAGATGATACCTCAATCAA
1 ATTACCATAGGCTTGCTTAAAAATCAAATCTCCACCACTATATATTGAGATGATACCTCAATCAA
55997137 AAAGGTCTTTAGAGGGTTGTAACGTGGCTTTGGTTAGAGGGTATGGTCACAAGCGAAAAGAAAAG
66 AAAGGTCTTTAGAGGGTTGTAACGTGGCTTTGGTTAGAGGGTATGGTCACAAGCGAAAAGAAAAG
55997202 GTTAGAATCGAGATTGAATTGAAAAATTACCTATCTAGAAAAATGACTACTATTCAGTTGAATAC
131 GTTAGAATCGAGATTGAATTGAAAAATTACCTATCTAGAAAAATGACTACTATTCAGTTGAATAC
55997267 AAGTGAGCTTTTTCTCAGAATATGGAATTAACACTCAAGCTCAAAAAATGGCGAATTACTACTAA
196 AAGTGAGCTTTTTCTCAGAATATGGAATTAACACTCAAGCTCAAAAAATGGCGAATTACTACTAA
55997332 TATGTATGTAAGTATTGTTGTTGTTGTTTTTTTTAAGAACAAGTCAAATACATAGAAGAACAAA
261 TATGTATGTAAGTATTGTTGTTGTTGTTTTTTTTAAGAACAAGTCAAATACATAGAAGAACAAA
55997396 ATTACCATAGGCTTGCTTAAAAATCAAATCTCCACCACTATATATTGAGATGATACCTCAATCAA
1 ATTACCATAGGCTTGCTTAAAAATCAAATCTCCACCACTATATATTGAGATGATACCTCAATCAA
55997461 AAAGGTCTTTAGAGGGTTGTAACGTGGCTTTGGTTAGAGGGTATGGTCACAAGCGAAAAGAAAAG
66 AAAGGTCTTTAGAGGGTTGTAACGTGGCTTTGGTTAGAGGGTATGGTCACAAGCGAAAAGAAAAG
55997526 GTTAGAATCGAGATTGAATTGAAAAATTACCTATCTAGAAAAATGACTACTATTCAGTTGAATAC
131 GTTAGAATCGAGATTGAATTGAAAAATTACCTATCTAGAAAAATGACTACTATTCAGTTGAATAC
55997591 AAGTGAGCTTTTTCTCAGAATATGGAATTAACACTCAAGCTCAAAAAATGGCGAATTACTACTAA
196 AAGTGAGCTTTTTCTCAGAATATGGAATTAACACTCAAGCTCAAAAAATGGCGAATTACTACTAA
55997656 TATGTATGTAAGTATTGTTGTTGTTGTTTTTTTTAAGAACAAGTCAAATACATAGAAGAACAAA
261 TATGTATGTAAGTATTGTTGTTGTTGTTTTTTTTAAGAACAAGTCAAATACATAGAAGAACAAA
55997720 A
1 A
55997721 CATAGCTAAG
Statistics
Matches: 325, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
324 325 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (324 bp):
ATTACCATAGGCTTGCTTAAAAATCAAATCTCCACCACTATATATTGAGATGATACCTCAATCAA
AAAGGTCTTTAGAGGGTTGTAACGTGGCTTTGGTTAGAGGGTATGGTCACAAGCGAAAAGAAAAG
GTTAGAATCGAGATTGAATTGAAAAATTACCTATCTAGAAAAATGACTACTATTCAGTTGAATAC
AAGTGAGCTTTTTCTCAGAATATGGAATTAACACTCAAGCTCAAAAAATGGCGAATTACTACTAA
TATGTATGTAAGTATTGTTGTTGTTGTTTTTTTTAAGAACAAGTCAAATACATAGAAGAACAAA
Found at i:56004305 original size:77 final size:77
Alignment explanation
Indices: 56004218--56004368 Score: 293
Period size: 77 Copynumber: 2.0 Consensus size: 77
56004208 TGTTTCTAAG
*
56004218 GAAACTAGACTCAAAAATGAATCTATAAATATATGGCATGACTTCTAATTATCTTTGGTTAATTT
1 GAAACTAGACTCAAAAAGGAATCTATAAATATATGGCATGACTTCTAATTATCTTTGGTTAATTT
56004283 ATAGTGAATAAT
66 ATAGTGAATAAT
56004295 GAAACTAGACTCAAAAAGGAATCTATAAATATATGGCATGACTTCTAATTATCTTTGGTTAATTT
1 GAAACTAGACTCAAAAAGGAATCTATAAATATATGGCATGACTTCTAATTATCTTTGGTTAATTT
56004360 ATAGTGAAT
66 ATAGTGAAT
56004369 TTCCAAAGTC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (77 bp):
GAAACTAGACTCAAAAAGGAATCTATAAATATATGGCATGACTTCTAATTATCTTTGGTTAATTT
ATAGTGAATAAT
Found at i:56005377 original size:40 final size:40
Alignment explanation
Indices: 56005287--56005506 Score: 241
Period size: 40 Copynumber: 5.5 Consensus size: 40
56005277 ACCCAAGTAT
* ** * *
56005287 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
56005325 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
56005365 CTTTGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
56005405 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * ** *
56005445 CTTC-GGATTTTAGTCCGGATATAGTCACTAGCGTAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
56005485 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
56005507 CATTCGAATA
Statistics
Matches: 150, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.07
39 18 0.12
40 117 0.78
41 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:56008757 original size:30 final size:29
Alignment explanation
Indices: 56008673--56008747 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 29
56008663 GGATGGAAGG
56008673 GGAGTAAAAGTTTTTGGGAGAAAGTGGGAA
1 GGAGTAAAAG-TTTTGGGAGAAAGTGGGAA
*
56008703 TGAGTAAAAAGTTTTGGGAGAAAGTGGGAA
1 GGAGT-AAAAGTTTTGGGAGAAAGTGGGAA
56008733 GGAGTAAAAGTTTTG
1 GGAGTAAAAGTTTTG
56008748 AGGGAAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
29 10 0.24
30 27 0.64
31 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.25
Consensus pattern (29 bp):
GGAGTAAAAGTTTTGGGAGAAAGTGGGAA
Found at i:56015022 original size:26 final size:26
Alignment explanation
Indices: 56014985--56015038 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
56014975 TAAGGGAACT
*
56014985 TGATGTTCTGCCTTCACTTATTGGCA
1 TGATGTTCTGCCTTCACTTACTGGCA
* * *
56015011 TGATGTTTTGCCTTTACTTGCTGGCA
1 TGATGTTCTGCCTTCACTTACTGGCA
56015037 TG
1 TG
56015039 TGAGACAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.44
Consensus pattern (26 bp):
TGATGTTCTGCCTTCACTTACTGGCA
Found at i:56030937 original size:27 final size:27
Alignment explanation
Indices: 56030906--56031083 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
56030896 TAAATTGTAC
56030906 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
56030933 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56030959 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
56030987 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
56031015 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56031042 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
56031069 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
56031084 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:56031020 original size:82 final size:81
Alignment explanation
Indices: 56030907--56031062 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
56030897 AAATTGTACA
* *
56030907 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
56030971 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
56030988 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
56031053 TGCGAGTTGA
65 TGCGAATTGA
56031063 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:56031074 original size:82 final size:81
Alignment explanation
Indices: 56030903--56031083 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
56030893 GATTAAATTG
* *
56030903 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
56030968 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
56030984 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
56031048 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
56031066 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
56031084 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:56035064 original size:145 final size:145
Alignment explanation
Indices: 56034801--56035091 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
56034791 ACGAGGTACG
56034801 GTCACTACGAGTTCTTAGTGATGCCGTTCGGGCTCACTAATGCCCCTGCGGTGTTTATGGATTTG
1 GTCACTACGAGTTCTTAGTGATGCCGTTCGGGCTCACTAATGCCCCTGCGGTGTTTATGGATTTG
56034866 ATGAATCGGATCTTCAGGCCGTATTTGGATCGGTTCGTAGTTGTGTTTATTGATGACATCTTGGT
66 ATGAATCGGATCTTCAGGCCGTATTTGGATCGGTTCGTAGTTGTGTTTATTGATGACATCTTGGT
56034931 CTATTCAAGAGATGA
131 CTATTCAAGAGATGA
56034946 GTCACTACGAGTTCTTAGTGATGCCGTTCGGGCTCACTAATGCCCCTGCGGTGTTTATGGATTTG
1 GTCACTACGAGTTCTTAGTGATGCCGTTCGGGCTCACTAATGCCCCTGCGGTGTTTATGGATTTG
56035011 ATGAATCGGATCTTCAGGCCGTATTTGGATCGGTTCGTAGTTGTGTTTATTGATGACATCTTGGT
66 ATGAATCGGATCTTCAGGCCGTATTTGGATCGGTTCGTAGTTGTGTTTATTGATGACATCTTGGT
56035076 CTATTCAAGAGATGA
131 CTATTCAAGAGATGA
56035091 G
1 G
56035092 ACCGAACATG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (145 bp):
GTCACTACGAGTTCTTAGTGATGCCGTTCGGGCTCACTAATGCCCCTGCGGTGTTTATGGATTTG
ATGAATCGGATCTTCAGGCCGTATTTGGATCGGTTCGTAGTTGTGTTTATTGATGACATCTTGGT
CTATTCAAGAGATGA
Found at i:56039500 original size:27 final size:27
Alignment explanation
Indices: 56039469--56039645 Score: 194
Period size: 27 Copynumber: 6.5 Consensus size: 27
56039459 TAAATTGTAC
56039469 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
56039496 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56039522 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
56039550 GGCACTAAGTGTGGGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
56039578 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56039605 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
56039632 AGCACTGAGTGTGC
1 AGCACTAAGTGTGC
56039646 AGGCTCAATA
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:56039583 original size:82 final size:81
Alignment explanation
Indices: 56039470--56039625 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
56039460 AAATTGTACA
* *
56039470 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
56039534 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
56039551 GCACTAAGTGTGGGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
56039616 TGCGAGTTGA
65 TGCGAATTGA
56039626 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 14 0.21
82 51 0.77
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:56039637 original size:82 final size:81
Alignment explanation
Indices: 56039466--56039645 Score: 218
Period size: 82 Copynumber: 2.2 Consensus size: 81
56039456 GATTAAATTG
* *
56039466 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
56039531 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
56039547 TGCGGCACTAAGTGTGGGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
56039611 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
56039629 TATAGCACTGAGTGTGC
1 TACAGCACTAAGTGTGC
56039646 AGGCTCAATA
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:56040013 original size:32 final size:32
Alignment explanation
Indices: 56039972--56040035 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
56039962 TCGATAGGTT
56039972 GGAGGAACTATGGTATGGTTCGGAATGGATGG
1 GGAGGAACTATGGTATGGTTCGGAATGGATGG
* *
56040004 GGAGGAACTATGGTCTGGTTCGGTATGGATGG
1 GGAGGAACTATGGTATGGTTCGGAATGGATGG
56040036 AGTAAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.08, G:0.44, T:0.27
Consensus pattern (32 bp):
GGAGGAACTATGGTATGGTTCGGAATGGATGG
Found at i:56041001 original size:79 final size:79
Alignment explanation
Indices: 56040870--56041026 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 79
56040860 GGGAAAAATT
*
56040870 ACGAAACTGATTTTCGAGTTACGAAACTCAAGATATGATTTTTAAAACGACTAGTACACAGATTG
1 ACGAAACTGATTTTCAAGTTACGAAACTCAAGATATGATTTTTAAAACGACTAGTACACAGATTG
56040935 GGCAGTGTCTGGAC
66 GGCAGTGTCTGGAC
56040949 ACGAAACTGATTTTCAAGTTACGAAACTCAAGATATGATTTTTAAAACGACTAGTACACAGATTG
1 ACGAAACTGATTTTCAAGTTACGAAACTCAAGATATGATTTTTAAAACGACTAGTACACAGATTG
56041014 GGCAGTGTCTGGA
66 GGCAGTGTCTGGA
56041027 AAATAAATTT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (79 bp):
ACGAAACTGATTTTCAAGTTACGAAACTCAAGATATGATTTTTAAAACGACTAGTACACAGATTG
GGCAGTGTCTGGAC
Found at i:56045864 original size:147 final size:149
Alignment explanation
Indices: 56045632--56045922 Score: 412
Period size: 147 Copynumber: 2.0 Consensus size: 149
56045622 AATTTTTTGA
56045632 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTAAAAAATAAAAAAAATTGTTTTTTTAGTAATTTTA
1 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTAAAAAAT-AAAAAAATTGTTTTTTTAGTAATTTTA
* *
56045697 AGGGAAAGTTTAAATTTTTAAAACAAAG-TTTAAATTTTTTCCAACTATTTC-AAAGTAAAAGCT
65 AGGGAAAGTTTAAAATTTTAAAACAAAGTTTTAAATTTTTTCCAACTATTTCGAAA-T-AAAGAT
56045760 TTAATCTTTAAGAAAAATAGTG
128 TTAATCTTTAAGAAAAATAGTG
** * *
56045782 TTTTTTTTAAATGGAGAAAGTTTAGATTTTAAAAAAT-AAAAATTTG-TTTTTTAGTCATTTT-A
1 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTAAAAAATAAAAAAATTGTTTTTTTAGTAATTTTAA
* * *
56045844 GAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCGAAATAAAGATTT
66 G-GGAAAGTTTAAAATTTTAAAACAAAGTTTTAAATTTTTTCCAACTATTTCGAAATAAAGATTT
* *
56045909 GATTTTTAAGAAAA
130 AATCTTTAAGAAAA
56045923 TTAATAAATT
Statistics
Matches: 127, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
146 2 0.02
147 58 0.46
148 29 0.23
149 3 0.02
150 35 0.28
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (149 bp):
TTTTTTTTAAAAAGAGAAAGTTTAGATTTTAAAAAATAAAAAAATTGTTTTTTTAGTAATTTTAA
GGGAAAGTTTAAAATTTTAAAACAAAGTTTTAAATTTTTTCCAACTATTTCGAAATAAAGATTTA
ATCTTTAAGAAAAATAGTG
Found at i:56050525 original size:53 final size:53
Alignment explanation
Indices: 56050427--56050531 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 53
56050417 ACAAACTACG
* * * * * * *
56050427 ATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC
1 ATAACGCAAAGATACCACGTAAGACCATGCCAAGACATAGAAATGGTAAGTTC
* *
56050480 ATAACGCAAAGATACCACGTAAGACCTTGTCAAGACATAGAAATGGTAAGTT
1 ATAACGCAAAGATACCACGTAAGACCATGCCAAGACATAGAAATGGTAAGTT
56050532 TAAAAAGGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (53 bp):
ATAACGCAAAGATACCACGTAAGACCATGCCAAGACATAGAAATGGTAAGTTC
Found at i:56057029 original size:46 final size:46
Alignment explanation
Indices: 56056718--56057027 Score: 406
Period size: 46 Copynumber: 6.7 Consensus size: 46
56056708 TTATCTTTGA
* * * * * *
56056718 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
** * *
56056764 CATGTTATCATGGTATCTTTCAGCCATGGTCTTATTCCTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
56056810 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * * **
56056856 CACGCTGTCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* *
56056902 CATGTTGCCATGGTATCTTTCAGCCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* ** *
56056948 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
*
56056994 CATGTTTCCATGGTATCTTTCAACCATGGTCTTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
56057028 CATATTTCAT
Statistics
Matches: 229, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 4 0.02
46 225 0.98
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:56057035 original size:138 final size:138
Alignment explanation
Indices: 56056733--56057028 Score: 450
Period size: 138 Copynumber: 2.1 Consensus size: 138
56056723 TGCCATAGTG
* * * *
56056733 TCTTTCAACTATGGTCTTACTCATTTTCTATCATGTTATCATGGTATCTTTCAGCCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCATCATGTTACCATGGTATCTTTCAGCCATGGTCTTA
* ** *
56056798 TTCCTTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTG
66 TTCCTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTG
56056863 TCATGGTA
131 TCATGGTA
* * *
56056871 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAGCCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCATCATGTTACCATGGTATCTTTCAGCCATGGTCTTA
* * *
56056936 TTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG-TT
66 TTCCTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTG
56057000 TCCATGGTA
131 T-CATGGTA
56057009 TCTTTCAACCATGGTCTTAC
1 TCTTTCAACCATGGTCTTAC
56057029 ATATTTCATT
Statistics
Matches: 142, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
137 2 0.01
138 140 0.99
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACTCATTTCCCATCATGTTACCATGGTATCTTTCAGCCATGGTCTTA
TTCCTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTG
TCATGGTA
Found at i:56061034 original size:29 final size:29
Alignment explanation
Indices: 56060971--56061038 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
56060961 TAATCAACCG
56060971 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
56061000 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
56061029 CGCACACTTA
1 CGCACACTTA
56061039 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:56061151 original size:174 final size:174
Alignment explanation
Indices: 56060860--56061187 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
56060850 AACTCAAGGT
* *
56060860 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
56060925 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
56060990 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
56061034 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
56061099 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
56061164 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
56061188 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:56061179 original size:29 final size:30
Alignment explanation
Indices: 56061140--56061218 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
56061130 CTTAATAATC
56061140 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
56061170 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
56061199 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
56061219 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:56068974 original size:27 final size:27
Alignment explanation
Indices: 56068944--56069121 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
56068934 ATATTGAGTC
* * * *
56068944 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
56068971 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
56068998 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
56069026 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
56069053 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
56069080 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
56069107 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56069122 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:56069083 original size:82 final size:81
Alignment explanation
Indices: 56068965--56069120 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
56068955 TGCTATATAA
* *
56068965 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
56069030 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
56069047 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
56069111 CACTTAGTGC
65 CACTTAGTGC
56069121 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:56072015 original size:42 final size:42
Alignment explanation
Indices: 56071968--56072055 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
56071958 CCTTAGGCCT
* ** *
56071968 ATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
56072010 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
56072052 ATTT
1 ATTT
56072056 GGGGAGACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (42 bp):
ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
Found at i:56072242 original size:26 final size:26
Alignment explanation
Indices: 56072200--56072421 Score: 314
Period size: 26 Copynumber: 8.8 Consensus size: 26
56072190 CCTCTTTAAT
56072200 AACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* *
56072225 AATTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
56072251 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
56072277 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* *
56072303 AACT------TATGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
56072323 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
56072349 AACTGGGGCATAAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* *
56072375 AACTGGGGCATAAGCCTTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
56072401 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
56072422 GCACTTCCTC
Statistics
Matches: 175, Mismatches: 15, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
20 17 0.10
25 9 0.05
26 149 0.85
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGATA
Found at i:56072325 original size:72 final size:72
Alignment explanation
Indices: 56072238--56072378 Score: 255
Period size: 72 Copynumber: 2.0 Consensus size: 72
56072228 TGGGGCATAA
**
56072238 GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
1 GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCAATA
56072303 AACTTAT
66 AACTTAT
*
56072310 GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
1 GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCAATA
56072375 AACT
66 AACT
56072379 GGGGCATAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (72 bp):
GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCAATA
AACTTAT
Found at i:56072338 original size:98 final size:98
Alignment explanation
Indices: 56072212--56072404 Score: 332
Period size: 98 Copynumber: 2.0 Consensus size: 98
56072202 CTGGGGCAAA
* ** *
56072212 GCCCTTTTCGATAAATTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCGGTA
1 GCCCTTTTCGATAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
56072277 AACTGGGGCATAAGCCCTTTTCAATAAACTTAT
66 AACTGGGGCATAAGCCCTTTTCAATAAACTTAT
*
56072310 GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
1 GCCCTTTTCGATAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
*
56072375 AACTGGGGCATAAGCCTTTTTCAATAAACT
66 AACTGGGGCATAAGCCCTTTTCAATAAACT
56072405 GGGGCATAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (98 bp):
GCCCTTTTCGATAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
AACTGGGGCATAAGCCCTTTTCAATAAACTTAT
Found at i:56073355 original size:27 final size:27
Alignment explanation
Indices: 56073325--56073967 Score: 267
Period size: 27 Copynumber: 23.7 Consensus size: 27
56073315 TTTCATCCTA
* * *
56073325 CAAGGGTGTTTTGGTAAATCTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
**
56073352 CAAGGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
*
56073379 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * *
56073406 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
56073432 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTACAAAT
* * * **
56073459 CTAGGGGTGTTTTGGTAATTCTACCCTAT
1 C-AAGGGTATTTTGGTAATTTTA-CAAAT
* ** * *
56073488 -AGGGGTATTTCAGTGATTTCAC-AAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** **** **
56073513 TGAGGGTAAAACGGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*** * * **
56073540 CAAGGGTAAAATAGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *** ** * *
56073567 CGAGGGTAAAATAATAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
56073594 CGAGGGTACTTTGGTAATTTTTACAAGT
1 CAAGGGTATTTTGGTAA-TTTTACAAAT
* **
56073622 CGAGGGTATTTCAGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
56073649 CAGGGGGTATTTTAGTAATTTTACAAAC
1 CA-AGGGTATTTTGGTAATTTTACAAAT
* *
56073677 CAGGGGTATTTTAGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * ** *
56073703 CTAGGGGTGTTTTGGTAATTTTATTATT
1 C-AAGGGTATTTTGGTAATTTTACAAAT
* ** *
56073731 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
** **
56073758 CAAGGGTATTTCAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** *** * **
56073785 TGAGGGTAAAATGGTAATTCTATCTTA-
1 CAAGGGTATTTTGGTAATTTTA-CAAAT
* *
56073812 CAAGAGTATTTTAGTAATTTTACAAAAT
1 CAAGGGTATTTTGGTAATTTTAC-AAAT
* ** *
56073840 CGAGGGTATTTCAGTAATTTTGCAAAAT
1 CAAGGGTATTTTGGTAATTTTAC-AAAT
* * *
56073868 -GAGGGTATTTCGGTAATTTTACTAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * *
56073894 CGAGGATATTTGGGTAATTTTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*** * *
56073921 TGGGGGTACTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* **
56073948 CGAGGGTATTTCAGTAATTT
1 CAAGGGTATTTTGGTAATTT
56073968 GGTAAACTAA
Statistics
Matches: 475, Mismatches: 125, Indels: 32
0.75 0.20 0.05
Matches are distributed among these distances:
25 2 0.00
26 21 0.04
27 377 0.79
28 75 0.16
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:56073837 original size:190 final size:190
Alignment explanation
Indices: 56073627--56073973 Score: 434
Period size: 190 Copynumber: 1.8 Consensus size: 190
56073617 CAAGTCGAGG
* * *
56073627 GTATTTCAGTAATTTTAC-AAATCAGGGGGTATTTTAGTAATTTTACAAACCA-G-GGGTATTTT
1 GTATTTCAGTAATTTTACAAAATC-GAGGGTATTTCAGTAATTTTACAAA--ATGAGGGTATTTC
* * * * *
56073689 AGTAATTTTACAAACTAG-GGGTGTTTTGGTAATTTTAT-TATTCGAGGGTATTTTGGTAATTTT
63 AGTAATTTTACAAA-TAGAGGATATTTGGGTAATTTTATAAATT-GAGGGTACTTTGGTAATTTT
** *
56073752 GTAAACCAAGGGTATTTCAGTAATTTTGTAAATTGAGGGTAAAATGGTAATTCTATCTTACAAGA
126 ACAAACCAAGGGTATTTCAGTAATTTGGTAAATTGAGGGTAAAATGGTAATTCTATCTTACAAGA
* * *
56073817 GTATTTTAGTAATTTTACAAAATCGAGGGTATTTCAGTAATTTTGCAAAATGAGGGTATTTCGGT
1 GTATTTCAGTAATTTTACAAAATCGAGGGTATTTCAGTAATTTTACAAAATGAGGGTATTTCAGT
* * * *
56073882 AATTTTACTAATCGAGGATATTTGGGTAATTTTATAAATTGGGGGTACTTTGGTAATTTTACAAG
66 AATTTTACAAATAGAGGATATTTGGGTAATTTTATAAATTGAGGGTACTTTGGTAATTTTACAAA
* *
56073947 TCGAGGGTATTTCAGTAATTTGGTAAA
131 CCAAGGGTATTTCAGTAATTTGGTAAA
56073974 CTAAAGTATT
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
188 1 0.01
189 3 0.02
190 120 0.91
191 8 0.06
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.40
Consensus pattern (190 bp):
GTATTTCAGTAATTTTACAAAATCGAGGGTATTTCAGTAATTTTACAAAATGAGGGTATTTCAGT
AATTTTACAAATAGAGGATATTTGGGTAATTTTATAAATTGAGGGTACTTTGGTAATTTTACAAA
CCAAGGGTATTTCAGTAATTTGGTAAATTGAGGGTAAAATGGTAATTCTATCTTACAAGA
Found at i:56089838 original size:79 final size:82
Alignment explanation
Indices: 56089727--56089911 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
56089717 GCTACTCGTT
* * *
56089727 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
56089790 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
56089807 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
56089870 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
56089887 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56089912 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:56089911 original size:40 final size:40
Alignment explanation
Indices: 56089708--56089911 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
56089698 CGGAATTTAA
** *
56089708 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
56089748 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
56089788 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56089827 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56089867 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56089907 CCGGA
1 CCGGA
56089912 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:56092864 original size:29 final size:29
Alignment explanation
Indices: 56092801--56092868 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
56092791 TAATCAACCG
56092801 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
56092830 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
56092859 CGCACACTTA
1 CGCACACTTA
56092869 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:56092988 original size:174 final size:173
Alignment explanation
Indices: 56092691--56093017 Score: 591
Period size: 174 Copynumber: 1.9 Consensus size: 173
56092681 AACTCAAGGT
* *
56092691 ACTTACCTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATAG
1 ACTTACCTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAG
*
56092756 AAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGCA
66 AAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
56092821 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
56092864 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACC-TTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
56092929 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
65 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
56092994 ACTTTAAACTCGCACACTTAGTGC
130 ACTTTAAACTCACACACTTAGTGC
56093018 TGTACAATTT
Statistics
Matches: 147, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
173 7 0.05
174 140 0.95
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAG
AAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:56093009 original size:29 final size:30
Alignment explanation
Indices: 56092970--56093048 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
56092960 CTTAATAATC
56092970 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
56093000 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
56093029 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
56093049 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:56102274 original size:37 final size:37
Alignment explanation
Indices: 56102221--56102323 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
56102211 CGAATAGTCC
* *
56102221 CCACACGTAGTTATCGGGTCTTACTCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
56102258 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
56102295 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
56102324 ATACATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:56102428 original size:48 final size:48
Alignment explanation
Indices: 56102367--56102786 Score: 653
Period size: 48 Copynumber: 8.8 Consensus size: 48
56102357 TGTTACAACA
* * *
56102367 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
56102415 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
56102463 TTCACATTAGCCATTCGGCTTTACCACATATACGTATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
56102511 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
56102559 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
56102607 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
56102655 TTCACATTCGTCATTCGGCTTT-CCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
56102702 TTCACATTAGCCATTCGGCTTTACCACATACACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
56102750 TTCACATTAGCCATTCGGCTTCACCACACATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATAT
56102787 ATTTATCTTG
Statistics
Matches: 341, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 42 0.12
48 299 0.88
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.35
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:56118066 original size:30 final size:30
Alignment explanation
Indices: 56118022--56118110 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
56118012 CAAAGATAAC
56118022 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
56118051 GAGAAACCCAGAATAAATAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
56118081 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
56118111 CGATACTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 9 0.19
30 37 0.77
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:56118078 original size:15 final size:15
Alignment explanation
Indices: 56118022--56118101 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
56118012 CAAAGATAAC
*
56118022 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
56118036 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
56118051 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
56118066 AATAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
56118081 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
56118096 AAGAAA
1 AAGAAA
56118102 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 43 0.81
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:56118110 original size:15 final size:15
Alignment explanation
Indices: 56118033--56118110 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
56118023 AGAAAACCGA
56118033 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
56118048 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
*
56118062 AATAAATAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
56118077 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
56118093 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
56118108 ATA
1 ATA
56118111 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 4 0.08
15 43 0.86
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:56121267 original size:93 final size:93
Alignment explanation
Indices: 56121155--56121325 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
56121145 TGCCCATAAG
* *
56121155 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
56121220 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
56121248 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
56121313 ACGAGTTCGGATG
66 ACGAGCTCGGATG
56121326 TCCAAACATC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:56121323 original size:46 final size:46
Alignment explanation
Indices: 56121148--56121323 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
56121138 TGTAACCTGC
* * *
56121148 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
56121194 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
56121240 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
56121287 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
56121324 TGTCCAAACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:56123757 original size:30 final size:30
Alignment explanation
Indices: 56123713--56123801 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
56123703 CAAAGATAAC
56123713 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
56123742 GAGAAACCCAGAATAAATAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
56123772 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
56123802 CGATACTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 9 0.19
30 37 0.77
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Done.