Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 87 of 185
Found at i:27153032 original size:24 final size:25
Alignment explanation
Indices: 27152994--27153041 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
27152984 AAATCTTTGT
*
27152994 ACAAAAAGTTTAAAGGATAATACAA
1 ACAAAAAGTTCAAAGGATAATACAA
27153019 ACAAAAAG-TCAAAGGATAATACA
1 ACAAAAAGTTCAAAGGATAATACA
27153042 TTTACAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.17
Consensus pattern (25 bp):
ACAAAAAGTTCAAAGGATAATACAA
Found at i:27153088 original size:16 final size:16
Alignment explanation
Indices: 27153067--27153097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27153057 CAATCAATTC
*
27153067 TTAGATATTATTTTTG
1 TTAGATATAATTTTTG
27153083 TTAGATATAATTTTT
1 TTAGATATAATTTTT
27153098 TTCTCGGTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (16 bp):
TTAGATATAATTTTTG
Found at i:27159809 original size:59 final size:59
Alignment explanation
Indices: 27159717--27159836 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
27159707 CGAGTTTGGT
27159717 TACACTAACAGCTACCAAGTGTGCTTGAAAATGGCATCGTATGAAGCTCTTTATGGGCG
1 TACACTAACAGCTACCAAGTGTGCTTGAAAATGGCATCGTATGAAGCTCTTTATGGGCG
27159776 TACACTAACAGCTACCAAGTGTGCTTGAAAATGGCATCGTATGAAGCTCTTTATGGGCG
1 TACACTAACAGCTACCAAGTGTGCTTGAAAATGGCATCGTATGAAGCTCTTTATGGGCG
27159835 TA
1 TA
27159837 AATGTAGGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (59 bp):
TACACTAACAGCTACCAAGTGTGCTTGAAAATGGCATCGTATGAAGCTCTTTATGGGCG
Found at i:27166219 original size:30 final size:30
Alignment explanation
Indices: 27166185--27166243 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
27166175 AATTGCCGAA
27166185 AAATTTGAATCCAATTTCAAATGATTCGAG
1 AAATTTGAATCCAATTTCAAATGATTCGAG
*
27166215 AAATTTGAATCCAATTTCAAATTATTCGA
1 AAATTTGAATCCAATTTCAAATGATTCGA
27166244 AAAGCAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
AAATTTGAATCCAATTTCAAATGATTCGAG
Found at i:27167082 original size:19 final size:19
Alignment explanation
Indices: 27167058--27167094 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27167048 GAATGAAGAA
* *
27167058 AAGGAAAACATGGAAAAAG
1 AAGGAAAAAAGGGAAAAAG
27167077 AAGGAAAAAAGGGAAAAA
1 AAGGAAAAAAGGGAAAAA
27167095 ATGGAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.27, T:0.03
Consensus pattern (19 bp):
AAGGAAAAAAGGGAAAAAG
Found at i:27168554 original size:9 final size:9
Alignment explanation
Indices: 27168536--27168566 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27168526 TTCGAATTAA
*
27168536 AATAACTCG
1 AATAATTCG
27168545 AATAATTCG
1 AATAATTCG
27168554 AATAATTCG
1 AATAATTCG
27168563 AATA
1 AATA
27168567 TCAAACTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (9 bp):
AATAATTCG
Found at i:27171181 original size:9 final size:9
Alignment explanation
Indices: 27171169--27171195 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
27171159 AATGGGCCGT
27171169 ATGGGCTAG
1 ATGGGCTAG
27171178 ATGGGCTAG
1 ATGGGCTAG
27171187 ATGGGCTAG
1 ATGGGCTAG
27171196 TAGGCCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (9 bp):
ATGGGCTAG
Found at i:27171454 original size:27 final size:27
Alignment explanation
Indices: 27171409--27171481 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
27171399 AGAGGTCAAT
* * *
27171409 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACTGAGTTAACCCCACAGGGTA
*
27171436 AAATGACTGAGTTAACCCCATAGGGTA
1 AAATGACTGAGTTAACCCCACAGGGTA
27171463 AAATGA-TCGAGTT-ACCCCA
1 AAATGACT-GAGTTAACCCCA
27171482 TCCAAATACC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTGAGTTAACCCCACAGGGTA
Found at i:27171937 original size:28 final size:27
Alignment explanation
Indices: 27171896--27171961 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
27171886 ATTGCACTGT
* *
27171896 ATTGATACTATATTGGGCTAAGGCCCAC
1 ATTG-TACTGTATTAGGCTAAGGCCCAC
*
27171924 ATTGTTACTGTATTAGGCTAGGGCCCAC
1 ATTG-TACTGTATTAGGCTAAGGCCCAC
*
27171952 ACTGTACTGT
1 ATTGTACTGT
27171962 TACTGAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (27 bp):
ATTGTACTGTATTAGGCTAAGGCCCAC
Found at i:27190796 original size:148 final size:150
Alignment explanation
Indices: 27190627--27190985 Score: 582
Period size: 148 Copynumber: 2.4 Consensus size: 150
27190617 GTTTTTTTAT
*
27190627 AAAAACGCCGCTAAAAAATTATTTCATTTGGAATAAAACAACACTATTTTGCTATGCTAAAAGGG
1 AAAAACGCCGC-AAAAAATTATTTCATTTGGAATAAAACGACACTATTTTGCTATGCTAAAAGGG
27190692 CACTA-TTTTTTAAAGTAAAATTA-TTTTTTGTGGCATTTTTTTATAAAAACACCGCTATTGCTT
65 CACTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCA-TTTTTTATAAAAACACCGCTATTGCTT
*
27190755 ACCTTTTGCAGCGTTTATCA-G
129 ACCTTTTGCAGCGTTTATCATA
* * * *
27190776 AAAAACGCAGCAAAAAATTATTTCATTTGGAATAAAACGACATTATTTTGCTAT-ATAAAATGGC
1 AAAAACGCCGCAAAAAATTATTTCATTTGGAATAAAACGACACTATTTTGCTATGCTAAAAGGGC
*
27190840 GCTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTATAAAAACACCGCTATTGCTTAC
66 ACTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTATAAAAACACCGCTATTGCTTAC
* *
27190905 CTTTTGCGGCGTTTTTCATA
131 CTTTTGCAGCGTTTATCATA
*
27190925 AAAAACGCCGCAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAA
1 AAAAACGCCGCAAAAAATTATTTCATTTGGAATAAAACGACACTATTTTGCTATGCTAAAA
27190986 ATCTTTTATT
Statistics
Matches: 193, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
147 11 0.06
148 104 0.54
149 73 0.38
150 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (150 bp):
AAAAACGCCGCAAAAAATTATTTCATTTGGAATAAAACGACACTATTTTGCTATGCTAAAAGGGC
ACTATTTTTTTAAAGTAAAATTATTTTTTTGTGGCATTTTTTATAAAAACACCGCTATTGCTTAC
CTTTTGCAGCGTTTATCATA
Found at i:27192115 original size:14 final size:15
Alignment explanation
Indices: 27192098--27192130 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27192088 CTTAAATCAG
*
27192098 AATCCTTAA-TCCAT
1 AATCCCTAATTCCAT
27192112 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
27192127 AATC
1 AATC
27192131 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:27192217 original size:21 final size:20
Alignment explanation
Indices: 27192183--27192224 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
27192173 TAAATTAACC
*
27192183 ATATATATACCCTAAACTAT
1 ATATATAAACCCTAAACTAT
27192203 ATATATTAAACCCTAAACTAT
1 ATATA-TAAACCCTAAACTAT
27192224 A
1 A
27192225 ATGATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATATAAACCCTAAACTAT
Found at i:27192594 original size:41 final size:41
Alignment explanation
Indices: 27192537--27192760 Score: 240
Period size: 41 Copynumber: 5.5 Consensus size: 41
27192527 AAATGTTTTT
* **
27192537 GCGGCGCTTTTTGGAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
**
27192578 GCGGCGCTTCTTGGAAAACGCCGCTAAAG-CCC-AGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
27192617 GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* * ****
27192658 GCGGCACTT-TTCCAAAAATGCCGCTAAA-AATAGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
27192698 GCGCCACTTCTTCAAAAATGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
**
27192739 GCGAAGCTTCTTCAAAAACGCC
1 GCGGCGCTTCTTCAAAAACGCC
27192761 AAGAAAGCCC
Statistics
Matches: 160, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.21
40 40 0.25
41 87 0.54
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:27192681 original size:80 final size:81
Alignment explanation
Indices: 27192537--27192760 Score: 256
Period size: 81 Copynumber: 2.8 Consensus size: 81
27192527 AAATGTTTTT
* ** * * **
27192537 GCGGCGCTTTTTGGAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTCTTGGAAAACGCCGC
1 GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCACTTCTTCAAAAACGCCGC
* *
27192602 T-AAAGCCCAGCATTA
66 TAAAAACACAGCATTA
*
27192617 GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCACTT-TTCCAAAAATGCCG
1 GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCACTTCTT-CAAAAACGCCG
* *
27192681 CTAAAAATAGAGCATTA
65 CTAAAAACACAGCATTA
* * * * *
27192698 GCGCCACTTCTTCAAAAATGCCGCTAAAGCCCAGAGCATTAGC-GAAGCTTCTTCAAAAACGCC
1 GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCA-CTTCTTCAAAAACGCC
27192761 AAGAAAGCCC
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
79 2 0.02
80 57 0.47
81 61 0.50
82 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (81 bp):
GCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCCGAGCATTAGCGGCACTTCTTCAAAAACGCCGC
TAAAAACACAGCATTA
Found at i:27192768 original size:41 final size:41
Alignment explanation
Indices: 27192689--27192770 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
27192679 CGCTAAAAAT
* * ***
27192689 AGAGCATTAGCGCCACTTCTTCAAAAATGCCGCTAAAGCCC
1 AGAGCATTAGCGCAACTTCTTCAAAAACGCCAAGAAAGCCC
27192730 AGAGCATTAGCG-AAGCTTCTTCAAAAACGCCAAGAAAGCCC
1 AGAGCATTAGCGCAA-CTTCTTCAAAAACGCCAAGAAAGCCC
27192771 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.17
Consensus pattern (41 bp):
AGAGCATTAGCGCAACTTCTTCAAAAACGCCAAGAAAGCCC
Found at i:27221905 original size:49 final size:51
Alignment explanation
Indices: 27221830--27221927 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 51
27221820 ACATGTGAAA
* *
27221830 ATGTGATTATGTGATTTCTGTGTAAGACCATAGCTGGGCTATGGCATCGGT
1 ATGTGATTATGTGATTTATGTGTAAGACCATAGCTGGACTATGGCATCGGT
*
27221881 ATGTGA-TATGTGA-TTATGTGTAAGACCATAGTTGGACTATGGCATCG
1 ATGTGATTATGTGATTTATGTGTAAGACCATAGCTGGACTATGGCATCG
27221928 AGAAAACAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 31 0.70
50 7 0.16
51 6 0.14
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (51 bp):
ATGTGATTATGTGATTTATGTGTAAGACCATAGCTGGACTATGGCATCGGT
Found at i:27224227 original size:13 final size:14
Alignment explanation
Indices: 27224209--27224239 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27224199 TATAAAATCA
27224209 CCAAAATTTAAT-T
1 CCAAAATTTAATGT
27224222 CCAAAATTTAATGT
1 CCAAAATTTAATGT
27224236 CCAA
1 CCAA
27224240 TGTCCATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (14 bp):
CCAAAATTTAATGT
Found at i:27237896 original size:15 final size:17
Alignment explanation
Indices: 27237876--27237908 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27237866 ACACACGACC
27237876 GTGTCAC-C-TGGCTGT
1 GTGTCACACATGGCTGT
27237891 GTGTCACACATGGCTGT
1 GTGTCACACATGGCTGT
27237908 G
1 G
27237909 ACACACGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.30
Consensus pattern (17 bp):
GTGTCACACATGGCTGT
Found at i:27245270 original size:21 final size:22
Alignment explanation
Indices: 27245238--27245284 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
27245228 ACTATTTTTG
*
27245238 AGAAGAAAGTTGATGCTGCAGA
1 AGAAGAAAGTTGATGCTGAAGA
*
27245260 AGAAG-AAGTTGTTGCTGAAGA
1 AGAAGAAAGTTGATGCTGAAGA
27245281 AGAA
1 AGAA
27245285 AGAGTTGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.43, C:0.06, G:0.32, T:0.19
Consensus pattern (22 bp):
AGAAGAAAGTTGATGCTGAAGA
Found at i:27245290 original size:21 final size:20
Alignment explanation
Indices: 27245238--27245291 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
27245228 ACTATTTTTG
*
27245238 AGAAGAA-AGTTGATGCTGC
1 AGAAGAAGAGTTGATGCTGA
*
27245257 AGAAGAAGAAGTTGTTGCTGA
1 AGAAGAAG-AGTTGATGCTGA
27245278 AGAAGAAAGAGTTG
1 AGAAG-AAGAGTTG
27245292 CTAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.23
21 20 0.67
22 3 0.10
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (20 bp):
AGAAGAAGAGTTGATGCTGA
Found at i:27276624 original size:50 final size:50
Alignment explanation
Indices: 27276500--27276895 Score: 422
Period size: 50 Copynumber: 7.8 Consensus size: 50
27276490 GTATATAACA
* * * ** * * * *
27276500 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * ** *
27276549 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * *
27276599 TGCCCATGCCATGTCCCAAACATGGTCTTACGA-GGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTAGG
27276649 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-AGG
* *
27276699 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* ** * *
27276749 TGCCAACGTTATCTCCCAGACATGGTCTTACAT-GGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * *
27276798 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATAATCTTAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-A-GG
* *
27276854 TGCCAATGACATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27276896 TTACCCAAAT
Statistics
Matches: 294, Mismatches: 41, Indels: 17
0.84 0.12 0.05
Matches are distributed among these distances:
49 82 0.28
50 168 0.57
51 1 0.00
53 3 0.01
54 1 0.00
56 39 0.13
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:27276818 original size:149 final size:149
Alignment explanation
Indices: 27276500--27276890 Score: 460
Period size: 149 Copynumber: 2.6 Consensus size: 149
27276490 GTATATAACA
* * ** * * * * *
27276500 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTACTGCCAATGCCATATCC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGTGCCAATGCCATGTCC
* * ** * * *
27276565 CAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCCAAACATGGTCTTAC
66 CAGACATGGTCTTACATGGGACATCTCATATAGGTGCCAACGCCATCTCCCAAACATGGTCTTAC
*
27276630 GAGGGACCTCTCATCTTGG
131 GAGGGACCTCTCATCTCGG
*
27276649 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAATGCCATGTC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-AGTGCCAATGCCATGTC
* * ** *
27276714 CCAGACATGGTCTTACATGGGACATCTCATCTCGGTGCCAACGTTATCTCCCAGACATGGTCTTA
65 CCAGACATGGTCTTACATGGGACATCTCATATAGGTGCCAACGCCATCTCCCAAACATGGTCTTA
*
27276779 C-ATGGACCTCTCATCTCGG
130 CGAGGGACCTCTCATCTCGG
* * *
27276798 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATAATCTTAATGATGCCAATGA
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-A-G-TGCCAATGC
27276863 CATGTCCCAGACATGGTCTTACATGGGA
59 CATGTCCCAGACATGGTCTTACATGGGA
27276891 TCTCTTTACC
Statistics
Matches: 207, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
149 96 0.46
150 69 0.33
152 3 0.01
153 2 0.01
154 1 0.00
155 36 0.17
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (149 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGTGCCAATGCCATGTCC
CAGACATGGTCTTACATGGGACATCTCATATAGGTGCCAACGCCATCTCCCAAACATGGTCTTAC
GAGGGACCTCTCATCTCGG
Found at i:27292881 original size:45 final size:45
Alignment explanation
Indices: 27292811--27292943 Score: 144
Period size: 45 Copynumber: 3.0 Consensus size: 45
27292801 GCTATACATC
* * * * *
27292811 AAAGATGAGTAAGACCGTAGTTGAAAGATGCTATGGCATCATGGT
1 AAAGATAAGTAAGACCATAGCTGAAAGATGATATGGCATCATGAT
* *
27292856 AAAGATAAGTAAGACCATAGCTGAAAGATGTTATAGCATCATGAT
1 AAAGATAAGTAAGACCATAGCTGAAAGATGATATGGCATCATGAT
* * *
27292901 AGAA-ATGAA-TAAGACCATAGCTAAAAGACGATATGGAATCATG
1 A-AAGAT-AAGTAAGACCATAGCTGAAAGATGATATGGCATCATG
27292944 CGAAAGCACA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
45 71 0.95
46 4 0.05
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (45 bp):
AAAGATAAGTAAGACCATAGCTGAAAGATGATATGGCATCATGAT
Found at i:27293273 original size:39 final size:39
Alignment explanation
Indices: 27293230--27293347 Score: 94
Period size: 39 Copynumber: 3.2 Consensus size: 39
27293220 CATATAAAGA
27293230 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
1 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
* * *
27293269 AATGAG-TGACTG-G----AGTG-AT-TAGTC-ATATA-AAGA
1 AATGAGTTG-GTGTGACCAAG-GAATATAGACTAT-TAGAA-T
27293302 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
1 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
*
27293341 AAGGAGT
1 AATGAGT
27293348 GACGTCAAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 28
0.62 0.08 0.30
Matches are distributed among these distances:
32 4 0.07
33 14 0.24
34 7 0.12
35 1 0.02
37 1 0.02
38 7 0.12
39 20 0.34
40 4 0.07
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (39 bp):
AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
Found at i:27293317 original size:72 final size:72
Alignment explanation
Indices: 27293200--27293350 Score: 293
Period size: 72 Copynumber: 2.1 Consensus size: 72
27293190 TGGAGTTCAC
27293200 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
1 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
*
27293265 GAATAAT
66 GAATAAG
27293272 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
1 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
27293337 GAATAAG
66 GAATAAG
27293344 GAGTGAC
1 GAGTGAC
27293351 GTCAAGGTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.26
Consensus pattern (72 bp):
GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
GAATAAG
Found at i:27294362 original size:42 final size:42
Alignment explanation
Indices: 27294289--27294372 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
27294279 GTGTCCCAAC
* * * * *
27294289 CCGTGTCTTTTCCCATGTAACTTATTGACTTGAGACACACGG
1 CCGTGTCTCTGCCCATGTAACTCACTAACTTGAGACACACGG
* *
27294331 CCGTGTCTCTGCCCATGTAACTCACTAACTTGGGTCACACGG
1 CCGTGTCTCTGCCCATGTAACTCACTAACTTGAGACACACGG
27294373 GTGCGTCGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (42 bp):
CCGTGTCTCTGCCCATGTAACTCACTAACTTGAGACACACGG
Found at i:27298511 original size:40 final size:40
Alignment explanation
Indices: 27298467--27298688 Score: 242
Period size: 40 Copynumber: 5.6 Consensus size: 40
27298457 GCTCCTCGTT
* *
27298467 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
27298507 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
27298547 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* *
27298586 CGAATGCCTTC-GGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTATCTCGCA
* * * *
27298626 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ATC-TCGCA
27298667 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
27298689 AGACATCATT
Statistics
Matches: 160, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.21
40 111 0.69
41 14 0.09
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:27298569 original size:79 final size:78
Alignment explanation
Indices: 27298467--27298684 Score: 235
Period size: 79 Copynumber: 2.7 Consensus size: 78
27298457 GCTCCTCGTT
* *
27298467 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGTACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
27298532 ATTTAGTAACTCGCA
64 ATTTAGTAACTCGCA
* * **
27298547 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACGAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACCCG
*
27298610 GATTTAGTATCTCGCA
63 GATTTAGTAACTCGCA
* * * * *
27298626 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTA
27298685 GCCCAGACAT
Statistics
Matches: 116, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
78 6 0.05
79 62 0.53
80 36 0.31
81 11 0.09
82 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGGAT
TTAGTAACTCGCA
Found at i:27306362 original size:79 final size:78
Alignment explanation
Indices: 27306260--27306484 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 78
27306250 GCTCCTCGTT
* *
27306260 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
27306325 ATTTAGTAACTCGCA
64 ATTTAGTAACTCGCA
* *
27306340 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
27306403 GATTTAGTATCTCGCA
63 GATTTAGTAACTCGCA
* * * * *
27306419 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
27306483 GA
63 GA
27306485 CATCATTCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
78 6 0.05
79 64 0.51
80 42 0.34
81 12 0.10
82 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
TTAGTAACTCGCA
Found at i:27306444 original size:119 final size:120
Alignment explanation
Indices: 27306260--27306484 Score: 291
Period size: 119 Copynumber: 1.9 Consensus size: 120
27306250 GCTCCTCGTT
27306260 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
27306325 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * **
27306379 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAAC
* *
27306440 CCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
62 CCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
27306485 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
118 8 0.09
119 63 0.68
120 21 0.23
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:27306484 original size:40 final size:39
Alignment explanation
Indices: 27306260--27306484 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 39
27306250 GCTCCTCGTT
* *
27306260 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
* * *
27306300 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
27306340 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAT-TCGCA
* *
27306379 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAT-TCGCA
* * *
27306419 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-A-TTCGCA
27306460 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27306485 CATCATTCAA
Statistics
Matches: 163, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
38 3 0.02
39 30 0.18
40 117 0.72
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTATTCGCA
Found at i:27309764 original size:9 final size:9
Alignment explanation
Indices: 27309750--27309800 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
27309740 GAAATCATAA
27309750 AAAAATTAT
1 AAAAATTAT
27309759 AAAAATTAT
1 AAAAATTAT
**
27309768 AAATTTTCAT
1 AAAAATT-AT
*
27309778 AAAAATCAT
1 AAAAATTAT
27309787 AAAAAATTAT
1 -AAAAATTAT
27309797 AAAA
1 AAAA
27309801 TGCATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27309768 original size:29 final size:29
Alignment explanation
Indices: 27309732--27309811 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
27309722 TTAACTTTGT
*
27309732 AAAA-TATAGAAATCATAAAAAAATTAT-A
1 AAAATTATA-AAATCATAAAAAAATCATAA
*
27309760 AAAATTATAAATTTTCAT--AAAAATCATAA
1 AAAATTATAAA--ATCATAAAAAAATCATAA
27309789 AAAATTATAAAATGCATAAAAAA
1 AAAATTATAAAAT-CATAAAAAA
27309812 TTACCTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
27 1 0.02
28 17 0.40
29 16 0.38
30 8 0.19
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAATTATAAAATCATAAAAAAATCATAA
Found at i:27309798 original size:19 final size:19
Alignment explanation
Indices: 27309732--27309814 Score: 82
Period size: 19 Copynumber: 4.4 Consensus size: 19
27309722 TTAACTTTGT
*
27309732 AAAA-TATAGAAATCATAAA
1 AAAATTATAAAAATCAT-AA
*
27309751 AAAATTATAAAAATTAT-A
1 AAAATTATAAAAATCATAA
**
27309769 AATTTTCATAAAAATCATAA
1 AAAATT-ATAAAAATCATAA
27309789 AAAATTAT-AAAATGCATAA
1 AAAATTATAAAAAT-CATAA
27309808 AAAATTA
1 AAAATTA
27309815 CCTTTAACCA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 10 0.19
19 28 0.53
20 15 0.28
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTATAAAAATCATAA
Found at i:27309806 original size:28 final size:28
Alignment explanation
Indices: 27309750--27309810 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
27309740 GAAATCATAA
* * *
27309750 AAAAATTATAAAAATTATAAATTTTCAT
1 AAAAATCATAAAAATTATAAATATGCAT
27309778 AAAAATCATAAAAAATTATAAA-ATGCAT
1 AAAAATCAT-AAAAATTATAAATATGCAT
27309806 AAAAA
1 AAAAA
27309811 ATTACCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAATCATAAAAATTATAAATATGCAT
Found at i:27309812 original size:29 final size:27
Alignment explanation
Indices: 27309732--27309812 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 27
27309722 TTAACTTTGT
*
27309732 AAAA-TATAGAAATCATAAAAAAATTATA
1 AAAATTATA-AAATCAT-AAAAAATCATA
*
27309760 AAAATTATAAATTTTCAT-AAAAATCATAA
1 AAAATTATAAA--ATCATAAAAAATCAT-A
27309789 AAAATTATAAAATGCATAAAAAAT
1 AAAATTATAAAAT-CATAAAAAAT
27309813 TACCTTTAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
27 1 0.02
28 17 0.39
29 22 0.50
30 4 0.09
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAATTATAAAATCATAAAAAATCATA
Found at i:27309935 original size:15 final size:16
Alignment explanation
Indices: 27309917--27309947 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27309907 ACATGTGACA
27309917 AAAAAT-AATAAAAGT
1 AAAAATCAATAAAAGT
27309932 AAAAATCAATAAAAGT
1 AAAAATCAATAAAAGT
27309948 TATAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAATCAATAAAAGT
Found at i:27310134 original size:10 final size:9
Alignment explanation
Indices: 27309981--27310136 Score: 52
Period size: 9 Copynumber: 16.2 Consensus size: 9
27309971 TTCTGGTACA
27309981 ATAATTTTT
1 ATAATTTTT
27309990 ATAATTTTTT
1 ATAA-TTTTT
* *
27310000 TTACGAATTTT
1 ATA--ATTTTT
*
27310011 ATATTTCTTT
1 ATAATT-TTT
27310021 AT-ATTTTT
1 ATAATTTTT
27310029 ATAA-TTTT
1 ATAATTTTT
*
27310037 ATTACGA-CTTT
1 A-TA--ATTTTT
27310048 ATAATATTTT
1 ATAAT-TTTT
27310058 ATAATATTTTT
1 AT-A-ATTTTT
* *
27310069 CTTATTTTTT
1 -ATAATTTTT
*
27310079 CTAATTTTT
1 ATAATTTTT
27310088 A-ATATTTTT
1 ATA-ATTTTT
27310097 AT-ATTTTCT
1 ATAATTTT-T
* *
27310106 ATTAAAATTTA
1 A-T-AATTTTT
27310117 ATAATTTTT
1 ATAATTTTT
*
27310126 ATAACTTTT
1 ATAATTTTT
27310135 AT
1 AT
27310137 TGATTTATAA
Statistics
Matches: 110, Mismatches: 18, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
8 17 0.15
9 41 0.37
10 26 0.24
11 18 0.16
12 8 0.07
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:27310429 original size:88 final size:89
Alignment explanation
Indices: 27310257--27310429 Score: 206
Period size: 88 Copynumber: 2.0 Consensus size: 89
27310247 TCAAAGGAAC
* * *
27310257 TTTTTGATGCATTTTGACAGTTCAAATACTCAATTGAGTGCAAAAAAAAAATAGGGGCTTAATTG
1 TTTTTGATGCATTTTAAAAGTTCAAATACTCAATTGAGTGCAAAAAAAAAATAAGGGCTTAATTG
* ** **
27310322 CTTTTTTTTTAAAGTTTGAGGGTA
66 CTTTTTCTGAAAAAATTGAGGGTA
* * * * *
27310346 TTTTTTATGCATTTTAAAAGTTTAAGTAC-CTAATTGAGTG-AACAAGAAAATAAGGGCTTAATT
1 TTTTTGATGCATTTTAAAAGTTCAAATACTC-AATTGAGTGCAAAAAAAAAATAAGGGCTTAATT
27310409 GCTTTTTCTGAAAAAATTGAG
65 GCTTTTTCTGAAAAAATTGAG
27310430 AGCTTTTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
88 37 0.53
89 33 0.47
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (89 bp):
TTTTTGATGCATTTTAAAAGTTCAAATACTCAATTGAGTGCAAAAAAAAAATAAGGGCTTAATTG
CTTTTTCTGAAAAAATTGAGGGTA
Found at i:27312630 original size:10 final size:9
Alignment explanation
Indices: 27312607--27312652 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
27312597 AACTATAACT
*
27312607 TCATTTTAA
1 TCATTTTTA
27312616 TCATTTTTA
1 TCATTTTTA
*
27312625 TACATTTTAA
1 T-CATTTTTA
27312635 TCATTTTTA
1 TCATTTTTA
27312644 TACATTTTT
1 T-CATTTTT
27312653 TTAATATGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (9 bp):
TCATTTTTA
Found at i:27312632 original size:19 final size:19
Alignment explanation
Indices: 27312608--27312651 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
27312598 ACTATAACTT
27312608 CATTTTAATCATTTTTATA
1 CATTTTAATCATTTTTATA
27312627 CATTTTAATCATTTTTATA
1 CATTTTAATCATTTTTATA
27312646 CATTTT
1 CATTTT
27312652 TTTAATATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
CATTTTAATCATTTTTATA
Found at i:27315727 original size:24 final size:24
Alignment explanation
Indices: 27315700--27315756 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
27315690 AAACCTAATT
* *
27315700 CTAATCAATGTCAAATAAATTATG
1 CTAATAAATGTCAAATAAATTATA
* *
27315724 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATAAATTATA
27315748 CTAATAAAT
1 CTAATAAAT
27315757 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATAAATTATA
Found at i:27315762 original size:24 final size:24
Alignment explanation
Indices: 27315712--27315763 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
27315702 AATCAATGTC
* **
27315712 AAATAAATTATGCTAATAAATGTT
1 AAATAAATTATACTAATAAATACT
*
27315736 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
27315760 AAAT
1 AAAT
27315764 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:27315893 original size:29 final size:29
Alignment explanation
Indices: 27315856--27315912 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
27315846 CACTTTTACT
* *
27315856 CGAATTCTCAAGGAACAAGTTCTTCACCA
1 CGAACTCTCAAGGAACAAGTTCTCCACCA
*
27315885 CGAACTCTCAATGAACAAGTTCTCCACC
1 CGAACTCTCAAGGAACAAGTTCTCCACC
27315913 TCTTCAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.23
Consensus pattern (29 bp):
CGAACTCTCAAGGAACAAGTTCTCCACCA
Found at i:27319091 original size:24 final size:24
Alignment explanation
Indices: 27319064--27319120 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
27319054 AAACCTAATT
* *
27319064 CTAATCAATGTCAAATAAATTATG
1 CTAATAAATGTCAAATAAATTATA
* *
27319088 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATAAATTATA
27319112 CTAATAAAT
1 CTAATAAAT
27319121 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATAAATTATA
Found at i:27319126 original size:24 final size:24
Alignment explanation
Indices: 27319076--27319127 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
27319066 AATCAATGTC
* **
27319076 AAATAAATTATGCTAATAAATGTT
1 AAATAAATTATACTAATAAATACT
*
27319100 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
27319124 AAAT
1 AAAT
27319128 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:27329397 original size:21 final size:21
Alignment explanation
Indices: 27329371--27329430 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
27329361 ATTTATTTAT
27329371 TTTTTATAGACAATTTGTTAA
1 TTTTTATAGACAATTTGTTAA
*
27329392 TTTTTATAAACAA--T-TT--
1 TTTTTATAGACAATTTGTTAA
27329408 TTTTTATAGA-AATTTGTTAA
1 TTTTTATAGACAATTTGTTAA
27329428 TTT
1 TTT
27329431 ATTCATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
15 2 0.06
16 9 0.28
17 1 0.03
18 4 0.12
19 1 0.03
20 3 0.09
21 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTTATAGACAATTTGTTAA
Found at i:27332326 original size:42 final size:41
Alignment explanation
Indices: 27332267--27332354 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 41
27332257 AAAAGCAACT
*
27332267 TTTTGACCTTGCCCTTGATGCAATGGAGATGATAGGGATGA
1 TTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
27332308 GTTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
1 -TTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
27332350 TTTTG
1 TTTTG
27332355 GTTTAGCTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (41 bp):
TTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
Found at i:27333615 original size:25 final size:25
Alignment explanation
Indices: 27333583--27333632 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
27333573 TCGTTTTTAG
*
27333583 TTTGATGCCGAATTTGTTTGACTAA
1 TTTGATGCCGAATTTGTTGGACTAA
*
27333608 TTTGATGCTGAATTTGTTGGACTAA
1 TTTGATGCCGAATTTGTTGGACTAA
27333633 GCACTTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (25 bp):
TTTGATGCCGAATTTGTTGGACTAA
Found at i:27333851 original size:25 final size:25
Alignment explanation
Indices: 27333818--27333867 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27333808 TCACTAAGAG
27333818 ATAGAATAAAAATTATGAAAAGTAA
1 ATAGAATAAAAATTATGAAAAGTAA
27333843 ATAGAATAAAAATTATGAAAAGTAA
1 ATAGAATAAAAATTATGAAAAGTAA
27333868 GTAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (25 bp):
ATAGAATAAAAATTATGAAAAGTAA
Found at i:27333875 original size:25 final size:25
Alignment explanation
Indices: 27333822--27333880 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
27333812 TAAGAGATAG
*
27333822 AATAAAAATTATGAAAAGTAAATAG
1 AATAAAAATTATGAAAAGTAAATAA
*
27333847 AATAAAAATTATGAAAAGTAAGTAA
1 AATAAAAATTATGAAAAGTAAATAA
*
27333872 AATATAAAT
1 AATAAAAAT
27333881 AAAAGTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.25
Consensus pattern (25 bp):
AATAAAAATTATGAAAAGTAAATAA
Found at i:27335501 original size:30 final size:30
Alignment explanation
Indices: 27335465--27335562 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
27335455 AAAGTAAATC
27335465 AAAATTCAACTCAGTGCCAAAATTAAACTA
1 AAAATTCAACTCAGTGCCAAAATTAAACTA
* * * *
27335495 AAAATTCATTA-TCCA--ACCACACAGTAAA-TC
1 AAAATTCA--ACT-CAGTGCCA-AAATTAAACTA
27335525 AAAATTCAACTCAGTGCCAAAATTAAACTA
1 AAAATTCAACTCAGTGCCAAAATTAAACTA
27335555 AAAATTCA
1 AAAATTCA
27335563 TTATCCAACC
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
28 3 0.06
29 7 0.13
30 32 0.62
31 7 0.13
32 3 0.06
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.23
Consensus pattern (30 bp):
AAAATTCAACTCAGTGCCAAAATTAAACTA
Found at i:27335524 original size:60 final size:60
Alignment explanation
Indices: 27335452--27335579 Score: 247
Period size: 60 Copynumber: 2.1 Consensus size: 60
27335442 TTATTTAATT
*
27335452 CACAAAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
1 CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
27335512 CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
1 CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
27335572 CACACAGT
1 CACACAGT
27335580 TTCAATGAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.23
Consensus pattern (60 bp):
CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
Found at i:27349381 original size:37 final size:37
Alignment explanation
Indices: 27349331--27349404 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
27349321 CACCGAATTG
27349331 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
1 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
27349368 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
1 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
27349405 AAACTCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (37 bp):
GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
Found at i:27358947 original size:79 final size:77
Alignment explanation
Indices: 27358845--27359068 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 77
27358835 GCTCCTCGTT
*
27358845 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
27358910 ATTTAATAACTCGCA
64 ATTT-ATAACTCGCA
* *
27358925 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAACCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG-
* *
27358989 ATTTGTATCTCGCA
64 ATTTATAACTCGCA
* * * * * * *
27359003 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCA-AAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCG
27359067 GA
63 GA
27359069 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
78 32 0.26
79 64 0.52
80 28 0.23
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA
Found at i:27358962 original size:39 final size:40
Alignment explanation
Indices: 27358845--27359068 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
27358835 GCTCCTCGTT
* *
27358845 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
27358885 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
27358925 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
27358964 CAAATGCCTTCGGG-CTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
27359003 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
*
27359044 -AAAAGCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27359069 CAGCATTCAA
Statistics
Matches: 162, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 69 0.43
40 79 0.49
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:27368418 original size:61 final size:60
Alignment explanation
Indices: 27368281--27368540 Score: 182
Period size: 61 Copynumber: 4.3 Consensus size: 60
27368271 TAAACAGAGG
* * * * * *
27368281 TTGCCACAAAGGCTTTTCTCTAT-AA-ATTTTTTCCACAAAGGTTATCCTTTATATTCGATGC
1 TTGCCACAAAGGC-TTTCT-TGTCAAGATTTTTACCACAAAGGCTATCCTTTACATTAG-TAC
*** * * *
27368342 TCATCACAAAAGCTTTCTTGTCTAGATTTTTTCCACAAAGGCTATCCTTTACAATTAGTAC
1 TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTAC-ATTAGTAC
* * * * * * * * * *
27368403 TTGCCATAAAGGCTTTCATGTCCAGAGTTGTGCCACAAAGACCATCCTTTATATCCAGTAC
1 TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTACAT-TAGTAC
* * * * * **
27368464 TCGCCACAAAGGCTTTCTCGTCAAAATTTTTACCACAAAGGTTGTATTTTACATTCAGTAC
1 TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTACATT-AGTAC
*
27368525 TTGCCACAAGGGCTTT
1 TTGCCACAAAGGCTTT
27368541 GCTTCTCCTG
Statistics
Matches: 151, Mismatches: 43, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
59 2 0.01
60 8 0.05
61 137 0.91
62 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (60 bp):
TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTACATTAGTAC
Found at i:27375371 original size:26 final size:26
Alignment explanation
Indices: 27375320--27375371 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
27375310 ATATAATTTC
*
27375320 CAAATCATGTATCTATATATCGTGTA
1 CAAATCATGTATCTATATATCATGTA
* *
27375346 CAAATCAT-TTTCATATATCTCATGTA
1 CAAATCATGTATC-TATATATCATGTA
27375372 AATACCTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (26 bp):
CAAATCATGTATCTATATATCATGTA
Found at i:27387080 original size:38 final size:39
Alignment explanation
Indices: 27387019--27387093 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
27387009 ATCCAACCCA
*
27387019 ACCCGATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCGATTACCCAACCCAATAAAAATAAAACTAAAGTCT
*
27387058 ACCCGATTA-CCGACCCAATAAAAATAAAACTAAAGT
1 ACCCGATTACCCAACCCAATAAAAATAAAACTAAAGT
27387094 TTAACTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (39 bp):
ACCCGATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:27387276 original size:37 final size:37
Alignment explanation
Indices: 27387226--27387300 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
27387216 TGTTAATTTC
*
27387226 AAGAATTATGTAAT-TTTTATAATTATGTAGTGATTCA
1 AAGAATTAAGTAATATTTT-TAATTATGTAGTGATTCA
*
27387263 AAGACTTAAGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTAAGTAATATTTTTAATTATGTAGTGATTCA
27387300 A
1 A
27387301 TTCGGATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 31 0.89
38 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (37 bp):
AAGAATTAAGTAATATTTTTAATTATGTAGTGATTCA
Found at i:27387313 original size:9 final size:9
Alignment explanation
Indices: 27387299--27387347 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
27387289 GTAGTGATTC
*
27387299 AATTCGGAT
1 AATTCGGGT
27387308 AATTCGGGT
1 AATTCGGGT
27387317 AATTCGGGT
1 AATTCGGGT
*
27387326 AATTCGGTT
1 AATTCGGGT
*
27387335 AATTCGGCT
1 AATTCGGGT
27387344 AATT
1 AATT
27387348 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (9 bp):
AATTCGGGT
Found at i:27387530 original size:12 final size:12
Alignment explanation
Indices: 27387513--27387543 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27387503 TTCAGGTCAA
*
27387513 TTAACCGGTTGG
1 TTAACCGGTCGG
27387525 TTAACCGGTCGG
1 TTAACCGGTCGG
27387537 TTAACCG
1 TTAACCG
27387544 AATGCACACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (12 bp):
TTAACCGGTCGG
Found at i:27391123 original size:93 final size:92
Alignment explanation
Indices: 27391015--27391195 Score: 317
Period size: 93 Copynumber: 2.0 Consensus size: 92
27391005 ATATAGGGTC
* * *
27391015 CCCCTATAGAACAACACTTCTTTAATCACATCAAATAGCACATGTAGAGGGTAGTCCATAACTCA
1 CCCCTATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTCA
*
27391080 AAATATGTAGATGGTAGTCCATAGATT
66 AAATATGTAGAGGGTAGTCCATAGATT
27391107 CCCCTGATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTC
1 CCCCT-ATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTC
27391172 AAAATATGTAGAGGGTAGTCCATA
65 AAAATATGTAGAGGGTAGTCCATA
27391196 ACGCAAAATA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
92 5 0.06
93 79 0.94
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (92 bp):
CCCCTATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTCA
AAATATGTAGAGGGTAGTCCATAGATT
Found at i:27391193 original size:28 final size:28
Alignment explanation
Indices: 27391149--27391222 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
27391139 CAAAGAGCAC
* *
27391149 ATGTAGAGGGTACTCCATAACTCAAAAT
1 ATGTAGAGGGTAGTCCATAACGCAAAAT
27391177 ATGTAGAGGGTAGTCCATAACGCAAAAT
1 ATGTAGAGGGTAGTCCATAACGCAAAAT
27391205 ATGTAGAGGGTAGTCCAT
1 ATGTAGAGGGTAGTCCAT
27391223 GACTTTGCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (28 bp):
ATGTAGAGGGTAGTCCATAACGCAAAAT
Found at i:27393986 original size:41 final size:41
Alignment explanation
Indices: 27393931--27394037 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
27393921 TGAATTTAAG
* *
27393931 GGGTTGCTAAGTGTATATTCCTCGAATCACTGATCAAAAAA
1 GGGTTGCTAAGTGTAGATTCCTCGAAACACTGATCAAAAAA
* * *
27393972 GGGTTGCTAAGTGTAGATTCCCCGAAACTCTGATCAAAAAG
1 GGGTTGCTAAGTGTAGATTCCTCGAAACACTGATCAAAAAA
*
27394013 GGGTTGCTAAGTGCAGATTCCTCGA
1 GGGTTGCTAAGTGTAGATTCCTCGA
27394038 GAGGTTGCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (41 bp):
GGGTTGCTAAGTGTAGATTCCTCGAAACACTGATCAAAAAA
Found at i:27394101 original size:42 final size:42
Alignment explanation
Indices: 27394040--27394179 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 42
27394030 TTCCTCGAGA
* * *
27394040 GGTTGCTAAGTGTTAATTCCCCGAATTATTGATTTTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGATTTTAAAGGT
* * *
27394082 GGTTGCTAAGTGCTGATTCCACC-ATATCCTTGATTGTGAAA-GA
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATCATTGATT-TTAAAGGT
* * * ** * *
27394125 GGTTGTTATGTGCTGATTCCCCGTATCACAGAATAT-AAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGATTTTAAAGGT
27394166 GGTTGCTAAGTGCT
1 GGTTGCTAAGTGCT
27394180 AATTTCACGG
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
40 2 0.03
41 13 0.17
42 27 0.36
43 29 0.39
44 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGATTTTAAAGGT
Found at i:27398156 original size:20 final size:21
Alignment explanation
Indices: 27398106--27398156 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
27398096 TAGAGATTTG
27398106 GTATCGATAC-CTTTGCTCAA
1 GTATCGATACTCTTTGCTCAA
*
27398126 GTATCGATACTC-TTGCTCGA
1 GTATCGATACTCTTTGCTCAA
27398146 GTATCGATACT
1 GTATCGATACT
27398157 TGGGGTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTTTGCTCAA
Found at i:27400472 original size:26 final size:26
Alignment explanation
Indices: 27400436--27400488 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
27400426 TATTTTCTCG
*
27400436 AAATTTAACCAGGGGCAAAATCGTCA
1 AAATTTAACCAAGGGCAAAATCGTCA
* * *
27400462 AAATTTTACCAAGGGTAAAATCTTCA
1 AAATTTAACCAAGGGCAAAATCGTCA
27400488 A
1 A
27400489 TTTCTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (26 bp):
AAATTTAACCAAGGGCAAAATCGTCA
Found at i:27408457 original size:31 final size:30
Alignment explanation
Indices: 27408421--27408489 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
27408411 TTACAAAACG
**
27408421 GTCACTAAGCTATTTGAAAG-TTTTCATTTAA
1 GTCACTAA-CTATTCAAAAGATTTT-ATTTAA
27408452 GTCACTGAACTATTCAAAAGATTTTATTTAA
1 GTCACT-AACTATTCAAAAGATTTTATTTAA
27408483 GTCACTA
1 GTCACTA
27408490 GATTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.79
32 6 0.18
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (30 bp):
GTCACTAACTATTCAAAAGATTTTATTTAA
Found at i:27423662 original size:26 final size:28
Alignment explanation
Indices: 27423623--27423681 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
27423613 AACTATAATT
27423623 AATATAATACTAATAAATA-AATTATTAA
1 AATATAATACTAATAAATATAA-TATTAA
*
27423651 AATA-AATA-TAATAATTATAATATTAA
1 AATATAATACTAATAAATATAATATTAA
27423677 AATAT
1 AATAT
27423682 TATGTCTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 18 0.64
27 6 0.21
28 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATAATACTAATAAATATAATATTAA
Found at i:27427026 original size:29 final size:29
Alignment explanation
Indices: 27426949--27427059 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
27426939 TTTTTTTATT
* * * * *
27426949 GAGATGGCCGCAAAGGCTTACTTTTAACA
1 GAGATCGCCACAAAGGCTTCCATTTAATA
* * *
27426978 GAGGTCACCACAAAAGCTTCCATTTAATA
1 GAGATCGCCACAAAGGCTTCCATTTAATA
*
27427007 GAGATCGCCACAAAGGCTTCC-TTACAATA
1 GAGATCGCCACAAAGGCTTCCATT-TAATA
* *
27427036 GAGATAGCCACAAAGGCATCCATT
1 GAGATCGCCACAAAGGCTTCCATT
27427060 CAGAGATAGC
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
28 2 0.03
29 62 0.94
30 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (29 bp):
GAGATCGCCACAAAGGCTTCCATTTAATA
Found at i:27427071 original size:26 final size:26
Alignment explanation
Indices: 27427035--27427104 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
27427025 TCCTTACAAT
27427035 AGAGATAGCCACAAAGGCATCCATTC
1 AGAGATAGCCACAAAGGCATCCATTC
27427061 AGAGATAGCCACCAAA-GCATCCATTC
1 AGAGATAGCCA-CAAAGGCATCCATTC
* * *
27427087 AAAGATTGCCAAAAAGGC
1 AGAGATAGCCACAAAGGC
27427105 TCACTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 3 0.08
26 32 0.82
27 4 0.10
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.14
Consensus pattern (26 bp):
AGAGATAGCCACAAAGGCATCCATTC
Found at i:27428630 original size:774 final size:774
Alignment explanation
Indices: 27427142--27428692 Score: 3102
Period size: 774 Copynumber: 2.0 Consensus size: 774
27427132 ACATAAGGAT
27427142 TCGCCTATACTCACCGTTGTGTGGTTTTCCCCTCATTGCTGGCACTCACCCAACCGTCCTTTACA
1 TCGCCTATACTCACCGTTGTGTGGTTTTCCCCTCATTGCTGGCACTCACCCAACCGTCCTTTACA
27427207 TATTCCATATGATGGCATGGCGTAGCCAAGGTCTTACACTATATGATCTTCAGAGTGCCACGGTC
66 TATTCCATATGATGGCATGGCGTAGCCAAGGTCTTACACTATATGATCTTCAGAGTGCCACGGTC
27427272 TTTTCTTTTTAGAGATTAATGTTTTTAGTCCCGACAAACCCCTTTAGATGACTCCGAAGACAGAC
131 TTTTCTTTTTAGAGATTAATGTTTTTAGTCCCGACAAACCCCTTTAGATGACTCCGAAGACAGAC
27427337 ACAGACTCTTCATGGAGACTCATACTTGATAGACATAGTATTTTCAGACTTCTTCATGATAGAAG
196 ACAGACTCTTCATGGAGACTCATACTTGATAGACATAGTATTTTCAGACTTCTTCATGATAGAAG
27427402 AATTCATGCTTACAAACATGTAACACATTTCCCTTAAACTTCATGCAATGACTTACTCATAACAG
261 AATTCATGCTTACAAACATGTAACACATTTCCCTTAAACTTCATGCAATGACTTACTCATAACAG
27427467 ACACTTTCACAAAAGTCTTGTTCATGCTTTCAAATGTATATGCACACATAAGGTTCCTTTCCATT
326 ACACTTTCACAAAAGTCTTGTTCATGCTTTCAAATGTATATGCACACATAAGGTTCCTTTCCATT
27427532 TCATAGTCTAGAGTTATGTTTTTCTAGTTCTAGTTTCATACTTTAGTCAACTAGTACAGACATAT
391 TCATAGTCTAGAGTTATGTTTTTCTAGTTCTAGTTTCATACTTTAGTCAACTAGTACAGACATAT
27427597 CTAGACTACAAAACACATGTAAGAGATAGTCTAAAGACTCACCTTATAACCTTAAAGACAACTTA
456 CTAGACTACAAAACACATGTAAGAGATAGTCTAAAGACTCACCTTATAACCTTAAAGACAACTTA
27427662 AACTTCAGATCCAACCCCTTTCTTATAGAATCAACAACTTTAGCTCCAAATCATTTACTCAACCA
521 AACTTCAGATCCAACCCCTTTCTTATAGAATCAACAACTTTAGCTCCAAATCATTTACTCAACCA
27427727 GATTTTAGGGCCTCATTGCCTTGCCAAACATAGACACTTTTTAGAGTTCATTCGAGTAACCTTTC
586 GATTTTAGGGCCTCATTGCCTTGCCAAACATAGACACTTTTTAGAGTTCATTCGAGTAACCTTTC
27427792 ACCTTTACTTTAACTCAGACATATCACTAAGCCTTACTTCTTCACGTATACTTACAAATCTACAC
651 ACCTTTACTTTAACTCAGACATATCACTAAGCCTTACTTCTTCACGTATACTTACAAATCTACAC
27427857 TTCCTTAGCAGACACGGTCATCAAACCTACCTTGTTGAGAGGGAAATCACTAATAGAAA
716 TTCCTTAGCAGACACGGTCATCAAACCTACCTTGTTGAGAGGGAAATCACTAATAGAAA
27427916 TCGCCTATACTCACCGTTGTGTGGTTTTCCCCTCATTGCTGGCACTCACCCAACCGTCCTTTACA
1 TCGCCTATACTCACCGTTGTGTGGTTTTCCCCTCATTGCTGGCACTCACCCAACCGTCCTTTACA
27427981 TATTCCATATGATGGCATGGCGTAGCCAAGGTCTTACACTATATGATCTTCAGAGTGCCACGGTC
66 TATTCCATATGATGGCATGGCGTAGCCAAGGTCTTACACTATATGATCTTCAGAGTGCCACGGTC
27428046 TTTTCTTTTTAGAGATTAATGTTTTTAGTCCCGACAAACCCCTTTAGATGACTCCGAAGACAGAC
131 TTTTCTTTTTAGAGATTAATGTTTTTAGTCCCGACAAACCCCTTTAGATGACTCCGAAGACAGAC
27428111 ACAGACTCTTCATGGAGACTCATACTTGATAGACATAGTATTTTCAGACTTCTTCATGATAGAAG
196 ACAGACTCTTCATGGAGACTCATACTTGATAGACATAGTATTTTCAGACTTCTTCATGATAGAAG
27428176 AATTCATGCTTACAAACATGTAACACATTTCCCTTAAACTTCATGCAATGACTTACTCATAACAG
261 AATTCATGCTTACAAACATGTAACACATTTCCCTTAAACTTCATGCAATGACTTACTCATAACAG
27428241 ACACTTTCACAAAAGTCTTGTTCATGCTTTCAAATGTATATGCACACATAAGGTTCCTTTCCATT
326 ACACTTTCACAAAAGTCTTGTTCATGCTTTCAAATGTATATGCACACATAAGGTTCCTTTCCATT
27428306 TCATAGTCTAGAGTTATGTTTTTCTAGTTCTAGTTTCATACTTTAGTCAACTAGTACAGACATAT
391 TCATAGTCTAGAGTTATGTTTTTCTAGTTCTAGTTTCATACTTTAGTCAACTAGTACAGACATAT
27428371 CTAGACTACAAAACACATGTAAGAGATAGTCTAAAGACTCACCTTATAACCTTAAAGACAACTTA
456 CTAGACTACAAAACACATGTAAGAGATAGTCTAAAGACTCACCTTATAACCTTAAAGACAACTTA
27428436 AACTTCAGATCCAACCCCTTTCTTATAGAATCAACAACTTTAGCTCCAAATCATTTACTCAACCA
521 AACTTCAGATCCAACCCCTTTCTTATAGAATCAACAACTTTAGCTCCAAATCATTTACTCAACCA
27428501 GATTTTAGGGCCTCATTGCCTTGCCAAACATAGACACTTTTTAGAGTTCATTCGAGTAACCTTTC
586 GATTTTAGGGCCTCATTGCCTTGCCAAACATAGACACTTTTTAGAGTTCATTCGAGTAACCTTTC
27428566 ACCTTTACTTTAACTCAGACATATCACTAAGCCTTACTTCTTCACGTATACTTACAAATCTACAC
651 ACCTTTACTTTAACTCAGACATATCACTAAGCCTTACTTCTTCACGTATACTTACAAATCTACAC
27428631 TTCCTTAGCAGACACGGTCATCAAACCTACCTTGTTGAGAGGGAAATCACTAATAGAAA
716 TTCCTTAGCAGACACGGTCATCAAACCTACCTTGTTGAGAGGGAAATCACTAATAGAAA
27428690 TCG
1 TCG
27428693 GGGTTTCAAA
Statistics
Matches: 777, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
774 777 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (774 bp):
TCGCCTATACTCACCGTTGTGTGGTTTTCCCCTCATTGCTGGCACTCACCCAACCGTCCTTTACA
TATTCCATATGATGGCATGGCGTAGCCAAGGTCTTACACTATATGATCTTCAGAGTGCCACGGTC
TTTTCTTTTTAGAGATTAATGTTTTTAGTCCCGACAAACCCCTTTAGATGACTCCGAAGACAGAC
ACAGACTCTTCATGGAGACTCATACTTGATAGACATAGTATTTTCAGACTTCTTCATGATAGAAG
AATTCATGCTTACAAACATGTAACACATTTCCCTTAAACTTCATGCAATGACTTACTCATAACAG
ACACTTTCACAAAAGTCTTGTTCATGCTTTCAAATGTATATGCACACATAAGGTTCCTTTCCATT
TCATAGTCTAGAGTTATGTTTTTCTAGTTCTAGTTTCATACTTTAGTCAACTAGTACAGACATAT
CTAGACTACAAAACACATGTAAGAGATAGTCTAAAGACTCACCTTATAACCTTAAAGACAACTTA
AACTTCAGATCCAACCCCTTTCTTATAGAATCAACAACTTTAGCTCCAAATCATTTACTCAACCA
GATTTTAGGGCCTCATTGCCTTGCCAAACATAGACACTTTTTAGAGTTCATTCGAGTAACCTTTC
ACCTTTACTTTAACTCAGACATATCACTAAGCCTTACTTCTTCACGTATACTTACAAATCTACAC
TTCCTTAGCAGACACGGTCATCAAACCTACCTTGTTGAGAGGGAAATCACTAATAGAAA
Found at i:27431377 original size:29 final size:29
Alignment explanation
Indices: 27431340--27431439 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
27431330 AAGCATCTTT
* **
27431340 TTTTTACAGAGATGGTCACAAAGGCTTCC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
*
27431369 TTTTAACAGAGATCATCACCAAGGCTTCC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
* * * *
27431398 ATTTAACAAAGATCACCACAAAGGCTTTC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
* *
27431427 TTATAATAGAGAT
1 TTTTAACAGAGAT
27431440 AGCCACAATG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTTAACAGAGATCATCACAAAGGCTTCC
Found at i:27433523 original size:23 final size:23
Alignment explanation
Indices: 27433497--27433540 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27433487 TGAAATAAGT
*
27433497 CTAAGAAAATAAAAATAAAGCAA
1 CTAAAAAAATAAAAATAAAGCAA
27433520 CTAAAAAAATAAAAATAAAGC
1 CTAAAAAAATAAAAATAAAGC
27433541 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (23 bp):
CTAAAAAAATAAAAATAAAGCAA
Found at i:27433622 original size:12 final size:12
Alignment explanation
Indices: 27433607--27433639 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
27433597 AAGGTAGTAG
27433607 TAAAAATAATAC
1 TAAAAATAATAC
27433619 T-AAAA-AATAC
1 TAAAAATAATAC
27433629 TAAAAATAATA
1 TAAAAATAATA
27433640 GAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.32
11 8 0.42
12 5 0.26
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAAATAATAC
Found at i:27433648 original size:22 final size:22
Alignment explanation
Indices: 27433607--27433648 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27433597 AAGGTAGTAG
*
27433607 TAAAAATAATACTAAAAAATAC
1 TAAAAATAATACGAAAAAATAC
27433629 TAAAAATAATA-GAAATAAAT
1 TAAAAATAATACGAAA-AAAT
27433649 TAAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAATAATACGAAAAAATAC
Found at i:27433695 original size:18 final size:18
Alignment explanation
Indices: 27433672--27433775 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 18
27433662 AAATCTAAGC
27433672 ATAAGAAAAATAAAAAAA
1 ATAAGAAAAATAAAAAAA
27433690 ATAAGAAAAAATAAGAAAATA
1 ATAAG-AAAAATAA-AAAA-A
* * *
27433711 GATAAAAAATAATATAACAA
1 -ATAAGAAA-AATAAAAAAA
* *
27433731 ATAATAATAAAT-AATAAA
1 ATAAGAA-AAATAAAAAAA
*
27433749 ATAA-TAAAATAAAATAAA
1 ATAAGAAAAATAAAA-AAA
27433767 ATAAAGAAA
1 AT-AAGAAA
27433776 TGGGTAAAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.06
17 3 0.05
18 17 0.26
19 19 0.29
20 8 0.12
21 7 0.11
22 8 0.12
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (18 bp):
ATAAGAAAAATAAAAAAA
Found at i:27433743 original size:41 final size:37
Alignment explanation
Indices: 27433677--27433775 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 37
27433667 TAAGCATAAG
27433677 AAAAATAAAAAAAATAAGAAAAAATAAGAAAATAGATA
1 AAAAATAAAAAAAATAAGAAAAAATAAGAAAATA-ATA
* * *
27433715 AAAAATAATATAACAAATAATAATAAATAATAAAATAAT-
1 AAAAATAA-A-AA-AAATAAGAAAAAATAAGAAAATAATA
27433754 -AAAATAAAATAAAATAAAGAAA
1 AAAAATAAAA-AAAAT-AAGAAA
27433776 TGGGTAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
36 5 0.10
37 6 0.12
38 15 0.29
39 1 0.02
40 4 0.08
41 20 0.39
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (37 bp):
AAAAATAAAAAAAATAAGAAAAAATAAGAAAATAATA
Found at i:27433746 original size:25 final size:26
Alignment explanation
Indices: 27433683--27433770 Score: 53
Period size: 25 Copynumber: 3.5 Consensus size: 26
27433673 TAAGAAAAAT
* *
27433683 AAAA-AAAATAAGAAAA-AATAAGAA
1 AAAATAAAATAATAAAATAATAATAA
* *
27433707 AATAGATAAAA-AATAATATAACAA-ATA
1 AA-A-ATAAAATAATAAAATAATAATA-A
*
27433734 ATAAT-AAATAATAAAATAATAA-AA
1 AAAATAAAATAATAAAATAATAATAA
27433758 TAAAATAAAATAA
1 -AAAATAAAATAA
27433771 AGAAATGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
24 6 0.12
25 19 0.39
26 14 0.29
27 10 0.20
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAATAAAATAATAAAATAATAATAA
Found at i:27433771 original size:10 final size:9
Alignment explanation
Indices: 27433672--27433767 Score: 75
Period size: 10 Copynumber: 9.7 Consensus size: 9
27433662 AAATCTAAGC
*
27433672 ATAAGAAAA
1 ATAAAAAAA
27433681 ATAAAAAAA
1 ATAAAAAAA
27433690 ATAAGAAAAA
1 ATAA-AAAAA
27433700 ATAAGAAAATA
1 ATAA-AAAA-A
27433711 GATAAAAAATA
1 -ATAAAAAA-A
* *
27433722 ATATAACAA
1 ATAAAAAAA
*
27433731 ATAATAATAA
1 ATAA-AAAAA
27433741 ATAATAAAATA
1 ATAA-AAAA-A
27433752 ATAAAATAAA
1 ATAAAA-AAA
27433762 ATAAAA
1 ATAAAA
27433768 TAAAGAAATG
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
9 16 0.21
10 41 0.55
11 14 0.19
12 4 0.05
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:27434446 original size:20 final size:20
Alignment explanation
Indices: 27434421--27434496 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
27434411 CCACGCCTAT
* *
27434421 GTGAGAGCCCACATGCTCGA
1 GTGAGAGCCCACACGCCCGA
* **
27434441 GTGAGAGCCCACTCAACCGA
1 GTGAGAGCCCACACGCCCGA
*
27434461 GTGAGAGCCCACACGCCCGT
1 GTGAGAGCCCACACGCCCGA
*
27434481 GTGAGAGCCTACACGC
1 GTGAGAGCCCACACGC
27434497 TCGTGCGGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.25, C:0.34, G:0.29, T:0.12
Consensus pattern (20 bp):
GTGAGAGCCCACACGCCCGA
Found at i:27436048 original size:21 final size:21
Alignment explanation
Indices: 27436023--27436065 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27436013 CTTTAACAGC
*
27436023 TTGAGAATTTTACCAAATTGT
1 TTGAGAATTTTACAAAATTGT
27436044 TTGAGAATTTTACAAAATTGT
1 TTGAGAATTTTACAAAATTGT
27436065 T
1 T
27436066 CGTTCATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (21 bp):
TTGAGAATTTTACAAAATTGT
Found at i:27437732 original size:18 final size:18
Alignment explanation
Indices: 27437692--27437734 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27437682 AAATTAGAAT
*
27437692 TAAAAATTAAACTAGAAA
1 TAAAAATTAAACTAAAAA
*
27437710 CAAAAATTATAA-TAAAAA
1 TAAAAATTA-AACTAAAAA
27437728 TAAAAAT
1 TAAAAAT
27437735 GGCCAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAATTAAACTAAAAA
Found at i:27440144 original size:29 final size:29
Alignment explanation
Indices: 27440102--27440338 Score: 196
Period size: 29 Copynumber: 8.1 Consensus size: 29
27440092 TCGCTATAAG
*
27440102 GGCTTCCTTTTAATAGAGATAGCCACAAA
1 GGCTTCCATTTAATAGAGATAGCCACAAA
* * * *
27440131 GACATCCATTTAATTGAGATAGCCATAAA
1 GGCTTCCATTTAATAGAGATAGCCACAAA
* * * * * *
27440160 AGCATCCTTTTTTACAGAGATGGCCACAAA
1 GGCTTCC-ATTTAATAGAGATAGCCACAAA
* * * *
27440190 AGCTTCCTTTTAATAGAGATCA-TCACCAA
1 GGCTTCCATTTAATAGAGAT-AGCCACAAA
* *
27440219 GGCTTCCATTTAACAAAGA-ACGCCACAAA
1 GGCTTCCATTTAATAGAGATA-GCCACAAA
*
27440248 GGCTTCCATTTAATAGAGATCGCCACAAA
1 GGCTTCCATTTAATAGAGATAGCCACAAA
* *
27440277 GGCTTCCTTTTAACA-ATGATCA-CCACAAA
1 GGCTTCCATTTAATAGA-GAT-AGCCACAAA
*
27440306 GGCTTCC-TTATAATAGAGATATCCACAAA
1 GGCTTCCATT-TAATAGAGATAGCCACAAA
27440335 GGCT
1 GGCT
27440339 CACTTATACA
Statistics
Matches: 166, Mismatches: 32, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.01
28 4 0.02
29 138 0.83
30 23 0.14
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (29 bp):
GGCTTCCATTTAATAGAGATAGCCACAAA
Found at i:27442267 original size:42 final size:43
Alignment explanation
Indices: 27442189--27442275 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 43
27442179 TCTCTAATCA
** **
27442189 TCCTTTAATTTTGTATGGTTTAGGAAAATTTGATCTTTATCGT
1 TCCTTTAATCGTGTATGGTTTAGGAAAATTCAATCTTTATCGT
27442232 TCCTTTAATCGTGTATGG-TTAGGAAAATTCAATCTTTATCGT
1 TCCTTTAATCGTGTATGGTTTAGGAAAATTCAATCTTTATCGT
27442274 TC
1 TC
27442276 GGCAACTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (43 bp):
TCCTTTAATCGTGTATGGTTTAGGAAAATTCAATCTTTATCGT
Found at i:27446530 original size:13 final size:13
Alignment explanation
Indices: 27446512--27446538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27446502 TTTTCTGATT
27446512 AATTTGTTGGATG
1 AATTTGTTGGATG
27446525 AATTTGTTGGATG
1 AATTTGTTGGATG
27446538 A
1 A
27446539 TTTTTTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (13 bp):
AATTTGTTGGATG
Found at i:27454729 original size:20 final size:20
Alignment explanation
Indices: 27454706--27454745 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27454696 CTTATATTTA
*
27454706 ATTTAAA-ATTATTATAAAAT
1 ATTTAAATAATATT-TAAAAT
27454726 ATTTAAATAATATTTAAAAT
1 ATTTAAATAATATTTAAAAT
27454746 GCTTAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAATAATATTTAAAAT
Found at i:27458316 original size:5 final size:5
Alignment explanation
Indices: 27458296--27458332 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
27458286 AGAAACAAAT
*
27458296 TTTG- TTTGA TTCGA TTTGA TTTGA TTTGA TTTGA TTT
1 TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTT
27458333 TCTTTCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.16, C:0.03, G:0.19, T:0.62
Consensus pattern (5 bp):
TTTGA
Found at i:27459277 original size:44 final size:45
Alignment explanation
Indices: 27459162--27459497 Score: 114
Period size: 44 Copynumber: 7.7 Consensus size: 45
27459152 AGCTTTAATT
* *
27459162 TGCTCCACTGCAACTTCAGGGAGATAAGATTTACCATCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTACCATATTCAATC
** * * * *
27459207 TGC-CTTGCTGCAACTTTA-GGAGGATAAGACTT-GCTTAATT-AGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTACCAT-ATTCAATC
* * * *
27459251 TGCTCCACTGCAACTTCAGGGAGATAA-A---ACTAGATGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTACCATATTCAATC
* * ** * *** *
27459292 TACT-CTCTGCAACTTCAAAGAGGTAAGA-TCTAAGGT-TTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT-TACCATATTCAATC
* * * *** *
27459335 --CTCTCACTGCAACTTTAGCGAGATAGGA-TTACCGGCTTTAATC
1 TGCTC-CACTGCAACTTCAGGGAGATAAGACTTACCATATTCAATC
* * * * ** *
27459378 TGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTACCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTACCATATTCAATC
* * *
27459423 TAC-CTCACTGCAACTTCA-GGAGGATAAGACTTGCC-TACTT-AGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTACCATA-TTCAATC
* *
27459467 TACTCCACTGTAACTTCAGGGAGATAAGACT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT
27459498 CGATCTGTTA
Statistics
Matches: 214, Mismatches: 55, Indels: 45
0.68 0.18 0.14
Matches are distributed among these distances:
40 20 0.09
41 8 0.04
42 3 0.01
43 31 0.14
44 80 0.37
45 72 0.34
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (45 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTACCATATTCAATC
Found at i:27459447 original size:216 final size:217
Alignment explanation
Indices: 27459011--27459493 Score: 689
Period size: 216 Copynumber: 2.2 Consensus size: 217
27459001 ATCTTGGAAA
* * * * *
27459011 GATAAGATTTGCCTTATTCGATCTGCTCCACTACAACTTCAGGGAGATAATACTAGATGCGATCT
1 GATAAGACTTGCCTAATTAG-TCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCT
* *
27459076 ACTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCCCCACTACAACTTTAGGGAG
65 ACTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAACCCGCCCCACTACAACTTTAGCGAG
** * * *
27459141 ATAGGATTGTCAGCTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTACCATCTTCAAT
130 ATAGGATTACCAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTACCACCTTCAAT
* ** *
27459206 CTGCCTTGCTGCAACTTTAGGAG
195 CTACCTCACTGCAACTTCAGGAG
*
27459229 GATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTA
1 GATAAGACTTGCCTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTA
* * * * *
27459294 CTCTCTGCAACTTCAAAGAGGTAAGATCTAAGGTTTTAATCC-TCTCACTGCAACTTTAGCGAGA
66 CTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAACCCGCCCCACTACAACTTTAGCGAGA
* * * *
27459358 TAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTACCTTCAGTC
131 TAGGATTACCAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTACCACCTTCAATC
27459423 TACCTCACTGCAACTTCAGGAG
196 TACCTCACTGCAACTTCAGGAG
* * *
27459445 GATAAGACTTGCCTACTTAGTCTACTCCACTGTAACTTCAGGGAGATAA
1 GATAAGACTTGCCTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
27459494 GACTCGATCT
Statistics
Matches: 235, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
216 137 0.58
217 82 0.35
218 16 0.07
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (217 bp):
GATAAGACTTGCCTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTA
CTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAACCCGCCCCACTACAACTTTAGCGAGA
TAGGATTACCAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTACCACCTTCAATC
TACCTCACTGCAACTTCAGGAG
Found at i:27459449 original size:45 final size:44
Alignment explanation
Indices: 27459380--27459497 Score: 145
Period size: 44 Copynumber: 2.7 Consensus size: 44
27459370 CTTTAATCTG
*
27459380 CTCCACTGCAACTTCAAGGA-GATAAGATTTG-CTACCTTCAGTCTA
1 CTCCACTGCAACTTC-AGGAGGATAAGACTTGCCTA-CTT-AGTCTA
27459425 C-CTCACTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGTCTA
1 CTC-CACTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGTCTA
*
27459469 CTCCACTGTAACTTCAGG-GAGATAAGACT
1 CTCCACTGCAACTTCAGGAG-GATAAGACT
27459498 CGATCTGTTA
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
43 1 0.02
44 35 0.53
45 27 0.41
46 3 0.05
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGTCTA
Found at i:27467748 original size:19 final size:20
Alignment explanation
Indices: 27467711--27467748 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
27467701 TATAAGAAAA
*
27467711 CTTTACTAGAAATTAAATTC
1 CTTTACTAGAAAGTAAATTC
*
27467731 CTTTAC-AGAAAGTGAATT
1 CTTTACTAGAAAGTAAATT
27467749 ACAAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
CTTTACTAGAAAGTAAATTC
Found at i:27476321 original size:21 final size:21
Alignment explanation
Indices: 27476295--27476337 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27476285 TTTAGCAACT
*
27476295 TCTTCTTCAACAACAACTTCC
1 TCTTCTGCAACAACAACTTCC
* *
27476316 TCTTCTGCAGCAGCAACTTCC
1 TCTTCTGCAACAACAACTTCC
27476337 T
1 T
27476338 TCTCAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.37, G:0.07, T:0.33
Consensus pattern (21 bp):
TCTTCTGCAACAACAACTTCC
Found at i:27480644 original size:14 final size:15
Alignment explanation
Indices: 27480625--27480655 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27480615 CTTAATTCCA
27480625 TTAG-TTTATTTAAC
1 TTAGTTTTATTTAAC
27480639 TTAGTTTTATTTAAC
1 TTAGTTTTATTTAAC
27480654 TT
1 TT
27480656 TTACAGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (15 bp):
TTAGTTTTATTTAAC
Found at i:27488993 original size:28 final size:28
Alignment explanation
Indices: 27488909--27488993 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 28
27488899 CATATGATAG
* * *
27488909 TCTTGATGGACATCCCTATTTAATACAG
1 TCTTGATGGACATCCCCATTTAAGACAA
* * * * * *
27488937 TCTTGACGGGCTTTCACA-TTAAGATAA
1 TCTTGATGGACATCCCCATTTAAGACAA
27488964 TCTTGATGGACATCCCCATTTAAGACAA
1 TCTTGATGGACATCCCCATTTAAGACAA
27488992 TC
1 TC
27488994 CTAACGAACT
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (28 bp):
TCTTGATGGACATCCCCATTTAAGACAA
Found at i:27489010 original size:55 final size:55
Alignment explanation
Indices: 27488904--27489011 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
27488894 CCACTCATAT
* * * * * * ** *
27488904 GATAGTCTTGATGGACATCCCTATTTAATACAGTCTTGACGGGCTTTCACATTAA
1 GATAATCTTGATGGACATCCCCATTTAAGACAATCCTAACGAACTTCCACATTAA
27488959 GATAATCTTGATGGACATCCCCATTTAAGACAATCCTAACGAACTTCCACATT
1 GATAATCTTGATGGACATCCCCATTTAAGACAATCCTAACGAACTTCCACATT
27489012 TACGGTAATG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (55 bp):
GATAATCTTGATGGACATCCCCATTTAAGACAATCCTAACGAACTTCCACATTAA
Found at i:27501753 original size:6 final size:6
Alignment explanation
Indices: 27501737--27501769 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
27501727 CATCTCTTTC
27501737 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
27501770 GCCACAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:27509214 original size:120 final size:120
Alignment explanation
Indices: 27508982--27509240 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
27508972 TTGAATGATG
* * *
27508982 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
27509047 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTCA-CTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGT-AGCTAAA
* * * **
27509102 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCTGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
27509165 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAA
* *
27509222 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
27509241 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 17 0.14
120 91 0.77
121 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAA
Found at i:27509221 original size:40 final size:40
Alignment explanation
Indices: 27508982--27509207 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
27508972 TTGAATGATG
* * * *
27508982 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
27509022 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
27509062 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTCACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27509102 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
27509142 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
27509183 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27509208 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 156 0.93
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27517376 original size:40 final size:40
Alignment explanation
Indices: 27517137--27517362 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
27517127 TTGAATGATG
* * * *
27517137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
27517177 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27517217 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
27517257 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27517297 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
27517338 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27517363 AACGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27526680 original size:20 final size:20
Alignment explanation
Indices: 27526655--27526703 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
27526645 GAAGCACTCA
*
27526655 ATTTACTTTCTTACCATTCC
1 ATTTACTTACTTACCATTCC
** *
27526675 ATTTACTTACTTTTCATTTC
1 ATTTACTTACTTACCATTCC
27526695 ATTTACTTA
1 ATTTACTTA
27526704 GCATAACTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTACTTACTTACCATTCC
Found at i:27532825 original size:29 final size:29
Alignment explanation
Indices: 27532789--27532853 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
27532779 AATAATTGCC
*
27532789 ACAAAGGCTTTCCTATCTAGAGTTTTACA
1 ACAAAGGCTTTCCTATCAAGAGTTTTACA
* * *
27532818 ACAAAGGCTTTCTTGTCAAGAGTTTTACC
1 ACAAAGGCTTTCCTATCAAGAGTTTTACA
27532847 ACAAAGG
1 ACAAAGG
27532854 TTGTCCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (29 bp):
ACAAAGGCTTTCCTATCAAGAGTTTTACA
Found at i:27532883 original size:61 final size:61
Alignment explanation
Indices: 27532818--27533012 Score: 223
Period size: 61 Copynumber: 3.2 Consensus size: 61
27532808 GAGTTTTACA
* *
27532818 ACAAAGGCTTTCTTGTCAAGAGTTTTACCACAAAGGTTGTCCTTTAAATTCAGTACTCACC
1 ACAAAGGCTTTCTTGTCAAGAGTTTTACCACAAAGGTTGTCCTTTAAATTCAGTACTTAAC
* * * * * * * *
27532879 ACAAAAGCTTTCCTGTCCAGAGTTTTGCCACAAAGTTTGTCCATTACACTCAGTACTTAAC
1 ACAAAGGCTTTCTTGTCAAGAGTTTTACCACAAAGGTTGTCCTTTAAATTCAGTACTTAAC
* ** * *
27532940 ACAAAGGCTTACATT-TCCAA-AGTTTTAGAACAATGGTTGTCCTTTATATTCAGTACTTAAC
1 ACAAAGGCTTTC-TTGT-CAAGAGTTTTACCACAAAGGTTGTCCTTTAAATTCAGTACTTAAC
27533001 ACAAAGGCTTTC
1 ACAAAGGCTTTC
27533013 CTTCTCCTGG
Statistics
Matches: 109, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
61 106 0.97
62 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (61 bp):
ACAAAGGCTTTCTTGTCAAGAGTTTTACCACAAAGGTTGTCCTTTAAATTCAGTACTTAAC
Found at i:27541034 original size:16 final size:15
Alignment explanation
Indices: 27541007--27541040 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
27540997 ATAACTAGTA
*
27541007 TATAATTATATTTAT
1 TATAATTATATTAAT
27541022 TATAATATATATTAAT
1 TATAAT-TATATTAAT
27541038 TAT
1 TAT
27541041 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:27541734 original size:25 final size:23
Alignment explanation
Indices: 27541706--27541764 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 23
27541696 AATTTTCTAC
*
27541706 TAAATTTTAATTTTATTTAATTATT
1 TAAATTTTAA-TTTATTGAATTA-T
27541731 TAAATTTTCAATTTATTGAATTAT
1 TAAATTTT-AATTTATTGAATTAT
27541755 TAATATTTTA
1 TAA-ATTTTA
27541765 TACTAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 5 0.16
25 24 0.77
26 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TAAATTTTAATTTATTGAATTAT
Found at i:27544338 original size:35 final size:35
Alignment explanation
Indices: 27544289--27544360 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
27544279 ATTTAACATG
* *
27544289 TCTTTATTGTGTAAGAATTTAGTCTATTTTTGCTA
1 TCTTTATTGAGTAAGAATTTAGCCTATTTTTGCTA
*
27544324 TCTTTATTGAGTAAGCATTTAGCCTATTTTTGCTA
1 TCTTTATTGAGTAAGAATTTAGCCTATTTTTGCTA
27544359 TC
1 TC
27544361 ATAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.51
Consensus pattern (35 bp):
TCTTTATTGAGTAAGAATTTAGCCTATTTTTGCTA
Found at i:27566005 original size:26 final size:26
Alignment explanation
Indices: 27565990--27566041 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
27565980 TGCTTCAGTT
27565990 GTTTATGAATATTGATAGAATTATTG
1 GTTTATGAATATTGATAGAATTATTG
27566016 GTTTATGAATATTGATAGAATTATTG
1 GTTTATGAATATTGATAGAATTATTG
27566042 AATTACTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (26 bp):
GTTTATGAATATTGATAGAATTATTG
Found at i:27575276 original size:50 final size:50
Alignment explanation
Indices: 27575165--27575389 Score: 186
Period size: 50 Copynumber: 4.4 Consensus size: 50
27575155 GTCATGTTCT
* * * * * *
27575165 AGACATGGTCTTACATGGGATTTTTCTTTTAC--TGCCAATGTCATATCCC
1 AGACATGGTCTTACATGGGAATTCTCATAT-CGGTGCCAATGCCATGTCCC
* * *
27575214 AGATATGATCTTACATGGGAATTCTCATATCGGTGCCCATGCCATGTCCC
1 AGACATGGTCTTACATGGGAATTCTCATATCGGTGCCAATGCCATGTCCC
* ** * *
27575264 AGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCC
1 AGACATGGTCTTACATGGGAATTCTCATATCGGTGCCAATGCCATGTCCC
* * * *
27575314 AGACATGGTCATACATGGGACCTT-TCATAACATCAATGATGTCAATGCCATGTCCC
1 AGACATGGTCTTACATGGGA-ATTCTCAT---ATC---GGTGCCAATGCCATGTCCC
*
27575370 AGACATTGTCTTACATGGGA
1 AGACATGGTCTTACATGGGA
27575390 TCTCTTTACC
Statistics
Matches: 141, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 24 0.17
50 78 0.55
51 2 0.01
53 2 0.01
56 34 0.24
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
AGACATGGTCTTACATGGGAATTCTCATATCGGTGCCAATGCCATGTCCC
Found at i:27575370 original size:56 final size:50
Alignment explanation
Indices: 27575197--27575394 Score: 189
Period size: 50 Copynumber: 3.8 Consensus size: 50
27575187 TTTCTTTTAC
* * * * ** * *
27575197 TGCCAATGTCATATCCCAGATATGATCTTACATGGGAATTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
* * *
27575247 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
* * *
27575297 TGCCAACGCCATGTCCCAGACATGGTCATACATGGGACCTTTCATAACATCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT--C-TC---GA
* * *
27575353 TGTCAATGCCATGTCCCAGACATTGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27575395 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 81 0.67
52 1 0.01
53 2 0.02
56 37 0.31
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
Found at i:27577622 original size:12 final size:12
Alignment explanation
Indices: 27577605--27577639 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
27577595 TTCCTTTTTC
27577605 CCTATTCCTCCG
1 CCTATTCCTCCG
27577617 CCTATTCCTCCG
1 CCTATTCCTCCG
27577629 CCTATTCCTCC
1 CCTATTCCTCC
27577640 ATTCGCCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.51, G:0.06, T:0.34
Consensus pattern (12 bp):
CCTATTCCTCCG
Found at i:27578175 original size:30 final size:30
Alignment explanation
Indices: 27578140--27578200 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
27578130 CCTTTCTTTC
27578140 ATCCATAAGTAAAAAGAGGTAAGAAAACTT
1 ATCCATAAGTAAAAAGAGGTAAGAAAACTT
* * *
27578170 ATCCATAATTAAAGAGAGGTAAGGAAACTT
1 ATCCATAAGTAAAAAGAGGTAAGAAAACTT
27578200 A
1 A
27578201 CCAATTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (30 bp):
ATCCATAAGTAAAAAGAGGTAAGAAAACTT
Found at i:27582938 original size:25 final size:25
Alignment explanation
Indices: 27582894--27582968 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
27582884 ATACATGTAT
27582894 GCTTATACGAGC-GATGAATCGGTATA
1 GCTTATACGAGCTGA-GAATCGGTA-A
*
27582920 -CTT-TCACGAGCTGTA-AATCAGTAA
1 GCTTAT-ACGAGCTG-AGAATCGGTAA
27582944 GCTTATACGAGCTGAGAATCGGTAA
1 GCTTATACGAGCTGAGAATCGGTAA
27582969 CCCTGATGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
24 3 0.07
25 35 0.85
26 2 0.05
27 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (25 bp):
GCTTATACGAGCTGAGAATCGGTAA
Found at i:27590228 original size:25 final size:25
Alignment explanation
Indices: 27590190--27590265 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
27590180 TCCTGTACAT
27590190 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACGAGCTATGAATCG
* *
27590215 GTATGCTC-TCACGAGCTGTAAATCG
1 GTATGCTCAT-ACGAGCTATGAATCG
*
27590240 GTAAGCTCATACGAGCTGA-GAATCG
1 GTATGCTCATACGAGCT-ATGAATCG
27590265 G
1 G
27590266 GAACCCTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 41 0.95
26 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCG
Found at i:27593087 original size:25 final size:26
Alignment explanation
Indices: 27593053--27593101 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
27593043 AATAATTTAA
*
27593053 AAATTGTAAAAAGATAT-TAAAAATC
1 AAATTGTAAAAAAATATATAAAAATC
*
27593078 AAATTTTAAAAAAATATATAAAAA
1 AAATTGTAAAAAAATATATAAAAA
27593102 GTTCATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
AAATTGTAAAAAAATATATAAAAATC
Found at i:27600292 original size:26 final size:26
Alignment explanation
Indices: 27600239--27600294 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
27600229 AATTTTAAAA
** * *
27600239 TATTTTTAAAATACTTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTAGTGTT
*
27600265 TATTTTTAAAATAAATTTTTGGTGTT
1 TATTTTTAAAATAAATTTTTAGTGTT
27600291 TATT
1 TATT
27600295 AAAAAATGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTTTTAAAATAAATTTTTAGTGTT
Found at i:27601000 original size:31 final size:33
Alignment explanation
Indices: 27600965--27601033 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
27600955 CCAAATACTA
*
27600965 ATATATTG-TAACGA-TAATATATAATGTCATC
1 ATATATTGATAACAAGTAATATATAATGTCATC
*
27600996 ATATATTGATGACAATGTAATATATAATGTCATC
1 ATATATTGATAACAA-GTAATATATAATGTCATC
27601030 ATAT
1 ATAT
27601034 GACTAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 8 0.24
32 4 0.12
34 21 0.64
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (33 bp):
ATATATTGATAACAAGTAATATATAATGTCATC
Found at i:27602820 original size:19 final size:19
Alignment explanation
Indices: 27602785--27602821 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27602775 CTTTACCAAT
*
27602785 AAATTTTAAAATTATACAC
1 AAATTTTAAAATAATACAC
*
27602804 AAATTTTAATATAATACA
1 AAATTTTAAAATAATACA
27602822 ATTATACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTAAAATAATACAC
Found at i:27603041 original size:14 final size:14
Alignment explanation
Indices: 27603022--27603077 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
27603012 TTAATCAAAT
27603022 TAAAATTTCATATA
1 TAAAATTTCATATA
* *
27603036 TAAAATTATACAAAAA
1 TAAAATT-T-CATATA
27603052 T-AAATTTCATATA
1 TAAAATTTCATATA
* *
27603065 TATAATTACATAT
1 TAAAATTTCATAT
27603078 TGAACCATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 5 0.15
14 17 0.52
15 6 0.18
16 5 0.15
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATTTCATATA
Found at i:27603567 original size:16 final size:16
Alignment explanation
Indices: 27603546--27603586 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
27603536 CATAATTATT
27603546 TAAAAAATATGAAAAA
1 TAAAAAATATGAAAAA
* * *
27603562 TAAAAATTCTGTAAAA
1 TAAAAAATATGAAAAA
27603578 TAAAAAATA
1 TAAAAAATA
27603587 GATTTTTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (16 bp):
TAAAAAATATGAAAAA
Done.