Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 93 of 352
Found at i:29474929 original size:37 final size:37
Alignment explanation
Indices: 29474887--29474962 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
29474877 GAAATAAAAG
*
29474887 TGAATAAAAATGTAGGATGATCTATTCGAATGATGCT
1 TGAATAAAAATGTAGGATGATATATTCGAATGATGCT
29474924 TGAATAAAAATGTAGGATGATATATTCGAATGATGCT
1 TGAATAAAAATGTAGGATGATATATTCGAATGATGCT
29474961 TG
1 TG
29474963 TACCTAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (37 bp):
TGAATAAAAATGTAGGATGATATATTCGAATGATGCT
Found at i:29475083 original size:45 final size:45
Alignment explanation
Indices: 29475019--29475193 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 45
29475009 TATCGTACAG
* * * *
29475019 TACTATTCAGGCTTTTGAGCCTAGCAAGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
29475064 TACTATTCGGGCCTTTGAGCCTAACAGGCTATAATGCTGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
29475109 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
29475154 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCAGTGA
1 T-ACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
29475194 ATGAATTCGA
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
42 10 0.08
43 18 0.15
44 5 0.04
45 84 0.71
46 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:29494233 original size:24 final size:26
Alignment explanation
Indices: 29494185--29494242 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
29494175 ACGTCGGAAA
29494185 TTTAAAAATTTTAAGATGTAATCC-TC
1 TTTAAAAATTTT-AGATGTAATCCTTC
*
29494211 TTTAAAATATTTT-GAT-TAATCCTTT
1 TTTAAAA-ATTTTAGATGTAATCCTTC
29494236 TTTAAAA
1 TTTAAAA
29494243 GAAAAATTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.21
25 11 0.38
26 7 0.24
27 5 0.17
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (26 bp):
TTTAAAAATTTTAGATGTAATCCTTC
Found at i:29494239 original size:25 final size:25
Alignment explanation
Indices: 29494185--29494242 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
29494175 ACGTCGGAAA
29494185 TTTAAAAATTTTAAGATGTAATCCTC
1 TTTAAAAATTTT-AGATGTAATCCTC
*
29494211 TTTAAAATATTTT-GAT-TAATCCTT
1 TTTAAAA-ATTTTAGATGTAATCCTC
*
29494235 TTTTAAAA
1 TTTAAAAA
29494243 GAAAAATTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 1 0.03
24 13 0.45
25 3 0.10
26 7 0.24
27 5 0.17
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (25 bp):
TTTAAAAATTTTAGATGTAATCCTC
Found at i:29495501 original size:18 final size:16
Alignment explanation
Indices: 29495356--29495501 Score: 61
Period size: 17 Copynumber: 8.9 Consensus size: 16
29495346 TAAAATAATG
29495356 TATATAAATAATTAATAAA
1 TATAT-AATAA-TAAT-AA
*
29495375 TATATAATACA-AGTAA
1 TATATAATA-ATAATAA
*
29495391 -AAATAATAATAATAA
1 TATATAATAATAATAA
*
29495406 TATA-AA-AATGATAA
1 TATATAATAATAATAA
* *
29495420 TGTAAAATAATAATAA
1 TATATAATAATAATAA
** *
29495436 TA-ATTTGTGAAAAATAA
1 TATA-TAAT-AATAATAA
* * *
29495453 AACATAACAAATAATAA
1 TATATAA-TAATAATAA
29495470 TATATAATAA-AATAA
1 TATATAATAATAATAA
*
29495485 TTTTATAATATATAATA
1 -TATATAATA-ATAATA
29495502 TAAAAATAAG
Statistics
Matches: 94, Mismatches: 21, Indels: 25
0.67 0.15 0.18
Matches are distributed among these distances:
14 11 0.12
15 21 0.22
16 23 0.24
17 24 0.26
18 9 0.10
19 6 0.06
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (16 bp):
TATATAATAATAATAA
Found at i:29497621 original size:205 final size:205
Alignment explanation
Indices: 29497261--29497770 Score: 774
Period size: 205 Copynumber: 2.5 Consensus size: 205
29497251 AATCTGGTAT
* * * *
29497261 CTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAACAC
1 CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
* * ** * * *
29497326 GCGAAAGCCAAATCAGCTGTGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGTTAAATCGTGTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* *
29497391 GGATCTGCTTCAGTATAACCATCTGAAG-GTGAGATCTGCTATGTATCTGCTCC-CCATTGAAGT
131 GGATCTACTTCAGTATAACCATCTGAAGTGTGA-ATCTGCTATGTATCTGC-CCTCCATCGAAGT
29497454 GGAGATGCCAGA
194 GGAGATGCCAGA
* *
29497466 CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCGACGTAAGCAC
1 CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
29497531 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * *
29497596 GGATCTACTTCAGTATAGA-CATCTGAAGTTTGAATCTGCTATGTGTCTGCCCTCCGTCGAAGTG
131 GGATCTACTTCAGTATA-ACCATCTGAAGTGTGAATCTGCTATGTATCTGCCCTCCATCGAAGTG
29497660 GAGATGCCAGA
195 GAGATGCCAGA
* *
29497671 CTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
* *
29497736 GTGAAAGCCAAATCAACTATGTCTTTGATTTGCTC
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTC
29497771 TCCGCTAATA
Statistics
Matches: 278, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
204 2 0.01
205 272 0.98
206 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (205 bp):
CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTACTTCAGTATAACCATCTGAAGTGTGAATCTGCTATGTATCTGCCCTCCATCGAAGTGG
AGATGCCAGA
Found at i:29497915 original size:44 final size:45
Alignment explanation
Indices: 29497847--29498052 Score: 167
Period size: 44 Copynumber: 4.6 Consensus size: 45
29497837 GCTGAAATCG
* * * *
29497847 TCGATCTGCTTCGCTGTAAGCACA-GGAGTGTCAGATCTGTTAT-TT
1 TCGATCTG-TTCCCTATAAACACAGGGA-TGTCAGATCTGCTATCTT
* *
29497892 TCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATC-T
1 TCGATCTGTTCCCTATAAACACAGGGATGTCAGATCTGCTATCTT
* * **
29497936 TC-AACTTGTTCCCTATAAACACAGGGATG-C-CATGCTGAAATCTT
1 TCGATC-TGTTCCCTATAAACACAGGGATGTCAGAT-CTGCTATCTT
* * * * * *
29497980 T-GATCTACTTCGCTGTAAGCACAAGAATGTCAGATCTGCTATCTT
1 TCGATCT-GTTCCCTATAAACACAGGGATGTCAGATCTGCTATCTT
29498025 T-GATCTGTTCCCTATAAACACAGGGATG
1 TCGATCTGTTCCCTATAAACACAGGGATG
29498053 CCAAATCTTG
Statistics
Matches: 126, Mismatches: 26, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
42 2 0.02
43 10 0.08
44 86 0.68
45 26 0.21
46 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
TCGATCTGTTCCCTATAAACACAGGGATGTCAGATCTGCTATCTT
Found at i:29498030 original size:132 final size:132
Alignment explanation
Indices: 29497780--29498060 Score: 458
Period size: 132 Copynumber: 2.1 Consensus size: 132
29497770 CTCCGCTAAT
*
29497780 ACAGAGATGCCAAATCTAGTATCTTCAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAAT
1 ACAGGGATGCCAAATCTAGTATCTTCAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAAT
* * * *
29497845 CGTCGATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGTTATTTTCGATCTGTTCCCTATAA
66 CGTCGATCTACTTCGCTGTAAGCACAAGAATGTCAGATCTGCTATTTTCGATCTGTTCCCTATAA
29497910 AC
131 AC
*
29497912 ACAGGGATGCCAAATCT-GCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAA
1 ACAGGGATGCCAAATCTAG-TATCTTCAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAA
* *
29497976 TCTTTGATCTACTTCGCTGTAAGCACAAGAATGTCAGATCTGCTATCTTT-GATCTGTTCCCTAT
65 TCGTCGATCTACTTCGCTGTAAGCACAAGAATGTCAGATCTGCTAT-TTTCGATCTGTTCCCTAT
29498040 AAAC
129 AAAC
29498044 ACAGGGATGCCAAATCT
1 ACAGGGATGCCAAATCT
29498061 TGTTTCTTTG
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
131 1 0.01
132 135 0.97
133 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
ACAGGGATGCCAAATCTAGTATCTTCAACTTGTTCCCTATAAACACAGGGATACCATGCTGAAAT
CGTCGATCTACTTCGCTGTAAGCACAAGAATGTCAGATCTGCTATTTTCGATCTGTTCCCTATAA
AC
Found at i:29502196 original size:37 final size:36
Alignment explanation
Indices: 29502147--29502224 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 36
29502137 TCCTGATATG
29502147 ACCAGGAAGATATCCTTGAACTCTCGAAGTAACTCA
1 ACCAGGAAGATATCCTTGAACTCTCGAAGTAACTCA
29502183 ACCAGCGAAGATATCCTTGAACTCTCGAAGTAACTCA
1 ACCAG-GAAGATATCCTTGAACTCTCGAAGTAACTCA
29502220 ACCAG
1 ACCAG
29502225 ACCACGCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 5 0.12
37 36 0.88
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.21
Consensus pattern (36 bp):
ACCAGGAAGATATCCTTGAACTCTCGAAGTAACTCA
Found at i:29506143 original size:15 final size:16
Alignment explanation
Indices: 29506110--29506142 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
29506100 TGATGCGATG
29506110 AAATGCTATGAAATGA
1 AAATGCTATGAAATGA
29506126 AAATGC-ATG-AATGA
1 AAATGCTATGAAATGA
29506140 AAA
1 AAA
29506143 AGAATATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (16 bp):
AAATGCTATGAAATGA
Found at i:29506185 original size:14 final size:14
Alignment explanation
Indices: 29506162--29506191 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29506152 ATTCTGGTTC
29506162 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
29506176 AACTTTATTTAGAA
1 AACTTCATTTAGAA
29506190 AA
1 AA
29506192 AGAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:29510006 original size:15 final size:15
Alignment explanation
Indices: 29509979--29510016 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
29509969 GTTTAAAATG
*
29509979 AAAT-AATACATAAT
1 AAATAAATAAATAAT
29509993 AAATAAATAAATAAT
1 AAATAAATAAATAAT
*
29510008 AATTAAATA
1 AAATAAATA
29510017 TATGTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAATAAATAAT
Found at i:29510169 original size:25 final size:27
Alignment explanation
Indices: 29510140--29510197 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
29510130 CCTATAATAA
29510140 ATAATAAATAATATA-G-AATAA-AAAT
1 ATAATAAAT-ATATAGGAAATAAGAAAT
*
29510165 ATAATAAATGTATAGGAAATAAGAAAT
1 ATAATAAATATATAGGAAATAAGAAAT
29510192 ATAATA
1 ATAATA
29510198 GCATAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 10 0.34
26 5 0.17
27 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (27 bp):
ATAATAAATATATAGGAAATAAGAAAT
Found at i:29513028 original size:19 final size:19
Alignment explanation
Indices: 29513004--29513043 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
29512994 AAGCCTAAGA
29513004 GAAAGCCACGATTTCCTGG
1 GAAAGCCACGATTTCCTGG
29513023 GAAAGCCACGATTTCCTGG
1 GAAAGCCACGATTTCCTGG
29513042 GA
1 GA
29513044 TACCTTCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (19 bp):
GAAAGCCACGATTTCCTGG
Found at i:29515619 original size:14 final size:14
Alignment explanation
Indices: 29515600--29515627 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29515590 CTTGAAGTTA
29515600 AAAGCAACTTTAAC
1 AAAGCAACTTTAAC
29515614 AAAGCAACTTTAAC
1 AAAGCAACTTTAAC
29515628 TATTGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAGCAACTTTAAC
Found at i:29517411 original size:11 final size:12
Alignment explanation
Indices: 29517395--29517426 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
29517385 CCTCAAATTT
29517395 AAAGAAAAAAA-
1 AAAGAAAAAAAG
29517406 AAAGAAAAAAAG
1 AAAGAAAAAAAG
29517418 AAA-AAAAAA
1 AAAGAAAAAA
29517427 GTAGTATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:29517908 original size:18 final size:18
Alignment explanation
Indices: 29517881--29517917 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29517871 AGAAGAGGAA
* *
29517881 GAGAGGGAAGGGGAAGAG
1 GAGAGAGAAGGCGAAGAG
29517899 GAGAGAGAAGGCGAAGAG
1 GAGAGAGAAGGCGAAGAG
29517917 G
1 G
29517918 GTGGGGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.57, T:0.00
Consensus pattern (18 bp):
GAGAGAGAAGGCGAAGAG
Found at i:29518836 original size:43 final size:43
Alignment explanation
Indices: 29518775--29518856 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
29518765 ATAGTTCGGA
*
29518775 AAAATTAAGGGAAAATGTTGATTTAAAGTAAAAATTAAGGGGC
1 AAAATTAAGGGAAAATGTTGATTTAAAATAAAAATTAAGGGGC
*
29518818 AAAATTAGGGGAAAATGTTGATTTAAAATAAAAATTAAG
1 AAAATTAAGGGAAAATGTTGATTTAAAATAAAAATTAAG
29518857 AAATTGAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.51, C:0.01, G:0.21, T:0.27
Consensus pattern (43 bp):
AAAATTAAGGGAAAATGTTGATTTAAAATAAAAATTAAGGGGC
Found at i:29521694 original size:27 final size:27
Alignment explanation
Indices: 29521664--29521841 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29521654 ATATTGAGTC
* * * *
29521664 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29521691 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29521718 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29521746 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29521773 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29521800 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29521827 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29521842 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:29521803 original size:82 final size:81
Alignment explanation
Indices: 29521685--29521840 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29521675 TGCTATATAA
* *
29521685 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29521750 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29521767 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29521831 CACTTAGTGC
65 CACTTAGTGC
29521841 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:29529747 original size:27 final size:27
Alignment explanation
Indices: 29529717--29529894 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29529707 ATATTGAGTC
* * * *
29529717 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29529744 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29529771 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29529799 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29529826 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29529853 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29529880 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29529895 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:29529856 original size:82 final size:81
Alignment explanation
Indices: 29529738--29529893 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29529728 TGCTATATAA
* *
29529738 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29529803 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29529820 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29529884 CACTTAGTGC
65 CACTTAGTGC
29529894 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:29536399 original size:47 final size:47
Alignment explanation
Indices: 29536330--29536551 Score: 187
Period size: 47 Copynumber: 4.6 Consensus size: 47
29536320 TATGGCAACA
* *
29536330 TGTGATATGTGATTTCCGTATAAGACCATACCTAGGATATGACATCTG
1 TGTGATATGTG-CTTCCGTATAAGACCATACCTGGGATATGACATCTG
* * * * *
29536378 TGTGATATGTGCTCCCATATAAGACCATAGCTGGGCTATGGCATCGGTGTG
1 TGTGATATGTGCTTCCGTATAAGACCATACCTGGGATATGACATC----TG
* *
29536429 ATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGACATCAG
1 -TGTGA-TATGTGCTTCCGTATAAGACCATACCTGGGATATGACATCTG
* * * * * *
29536478 TGAT-ATATGTGCTTCTGTGTAAGACAATATCTGGGATATGGCATCAG
1 TG-TGATATGTGCTTCCGTATAAGACCATACCTGGGATATGACATCTG
* * * *
29536525 AGAGATATGTG-ATCCGTGTAAGACCAT
1 TGTGATATGTGCTTCCGTATAAGACCAT
29536552 GTCTGGGCTA
Statistics
Matches: 144, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
46 13 0.09
47 73 0.51
48 14 0.10
49 2 0.01
51 2 0.01
52 5 0.03
53 35 0.24
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (47 bp):
TGTGATATGTGCTTCCGTATAAGACCATACCTGGGATATGACATCTG
Found at i:29536451 original size:100 final size:100
Alignment explanation
Indices: 29536329--29536522 Score: 257
Period size: 100 Copynumber: 1.9 Consensus size: 100
29536319 CTATGGCAAC
* *
29536329 ATGTGATATGTGATTTCCGTATAAGACCATACCTAGGATATGACATCTGTG-TGATATGTGCTCC
1 ATGTGATATGTGACTTCCGTATAAGACCATACCTAGGATATGACATCAGTGAT-ATATGTGCTCC
* *
29536393 CATATAAGACCATAGCTGGGCTATGGCATCGGTGTG
65 CATATAAGACAATAGCTGGGATATGGCATCGGTGTG
* * *
29536429 ATGTGATTATGTG-CTTCCGTATAAGACCATATCTGGGATATGACATCAGTGATATATGTGCTTC
1 ATGTGA-TATGTGACTTCCGTATAAGACCATACCTAGGATATGACATCAGTGATATATGTGCTCC
** * *
29536493 TGTGTAAGACAATATCTGGGATATGGCATC
65 CATATAAGACAATAGCTGGGATATGGCATC
29536523 AGAGAGATAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
100 74 0.91
101 7 0.09
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (100 bp):
ATGTGATATGTGACTTCCGTATAAGACCATACCTAGGATATGACATCAGTGATATATGTGCTCCC
ATATAAGACAATAGCTGGGATATGGCATCGGTGTG
Found at i:29536557 original size:46 final size:47
Alignment explanation
Indices: 29536436--29536565 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
29536426 GTGATGTGAT
* * * * *
29536436 TATGTGCTTCCGTATAAGACCATATCTGGGATATGACATCAGTGATA
1 TATGTGCATCCGTGTAAGACCATATCTGGGATATGGCATCAGAGAGA
* * *
29536483 TATGTGCTTCTGTGTAAGACAATATCTGGGATATGGCATCAGAGAGA
1 TATGTGCATCCGTGTAAGACCATATCTGGGATATGGCATCAGAGAGA
* *
29536530 TATGTG-ATCCGTGTAAGACCATGTCTGGGCTATGGC
1 TATGTGCATCCGTGTAAGACCATATCTGGGATATGGC
29536566 TTCGGTGTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 25 0.35
47 47 0.65
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (47 bp):
TATGTGCATCCGTGTAAGACCATATCTGGGATATGGCATCAGAGAGA
Found at i:29541978 original size:12 final size:12
Alignment explanation
Indices: 29541945--29541978 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29541935 AACCTCTCTT
29541945 AATTCACTCCTC
1 AATTCACTCCTC
* *
29541957 AAATCTCTCCTC
1 AATTCACTCCTC
29541969 AATTCACTCC
1 AATTCACTCC
29541979 AACCGATCCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.41, G:0.00, T:0.32
Consensus pattern (12 bp):
AATTCACTCCTC
Found at i:29545755 original size:37 final size:37
Alignment explanation
Indices: 29545705--29545817 Score: 199
Period size: 37 Copynumber: 3.1 Consensus size: 37
29545695 CTTTAGCTCA
* *
29545705 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
29545742 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
29545779 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
29545816 GA
1 GA
29545818 ATATATTTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:29546089 original size:48 final size:49
Alignment explanation
Indices: 29545963--29546101 Score: 201
Period size: 52 Copynumber: 2.8 Consensus size: 49
29545953 GCACATCGCC
*
29545963 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A-A
* *
29546015 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
29546063 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
29546102 TGCATGTTCA
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
48 36 0.45
49 1 0.01
51 1 0.01
52 42 0.52
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (49 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA
Found at i:29546150 original size:47 final size:47
Alignment explanation
Indices: 29546071--29546264 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
29546061 CATACATATT
* * * *
29546071 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
29546118 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
29546165 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
29546212 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
29546259 TCACAT
1 TCACAT
29546265 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:29546191 original size:22 final size:22
Alignment explanation
Indices: 29546164--29546235 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
29546154 GCTCACATTC
29546164 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
29546186 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
29546210 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
29546233 ATC
1 ATC
29546236 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:29546192 original size:94 final size:93
Alignment explanation
Indices: 29546024--29546264 Score: 297
Period size: 94 Copynumber: 2.5 Consensus size: 93
29546014 ATATATATTT
* * *
29546024 CACATTGACCATTCGGCTTTA-CCACATATGCATATCTCATACATAT-TTCACATTAGCCATTCG
1 CACATTGGCCATTCGGCCTTATCCACATATGCATA-CTC--ACAT-TCATCACATTAGCCATTCG
* *
29546087 GCTTTACCACATATATGCATGTTCATATTCAC
62 GCCTTACCACATATATGCATGTTCACATTCAC
* *
29546119 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCC
1 CACATTGGCCATTCGGCCTTATC-CACATATGCATACTCACATTCATCACATTAGCCATTCGGCC
* *
29546184 TTATCACATATATGCATGTTCACATTCAT
65 TTACCACATATATGCATGTTCACATTCAC
* * * *
29546213 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATC-CACATATGCATACTCACATTCATCACAT
29546265 AAAATCCTAA
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
93 1 0.01
94 93 0.73
95 19 0.15
96 4 0.03
97 11 0.09
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (93 bp):
CACATTGGCCATTCGGCCTTATCCACATATGCATACTCACATTCATCACATTAGCCATTCGGCCT
TACCACATATATGCATGTTCACATTCAC
Found at i:29551161 original size:46 final size:45
Alignment explanation
Indices: 29551069--29551232 Score: 147
Period size: 46 Copynumber: 3.6 Consensus size: 45
29551059 GACGAGGGCT
* * * * *
29551069 AGTGTAAGACATGTCTGGGACATGCATC-AGCCACAATATGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGA-CCTCGAGATG-TAGCC
*
29551115 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGTTAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGATG-TAGCC
* * ** * *
29551161 AAT-TTAGACATGTCTAGGACATGGGTCG-GCTACGAGATGT-GCT
1 AGTGTAAGACATGTCTAGGACATGCATCGACCT-CGAGATGTAGCC
*
29551204 AGTGTAAGACATGTTTAGGACATGCATCG
1 AGTGTAAGACATGTCTAGGACATGCATCG
29551233 GCACAGTTAC
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
43 4 0.04
44 24 0.24
45 28 0.29
46 41 0.42
47 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGATGTAGCC
Found at i:29560439 original size:47 final size:49
Alignment explanation
Indices: 29560258--29560456 Score: 174
Period size: 47 Copynumber: 4.0 Consensus size: 49
29560248 GCAACATGTG
* *
29560258 ATATGTGATTTCCATATAAGACCATATCTAGGATATGGCATC-G-GTG-T
1 ATATGTG-CTTCCGTATAAGACCATATCTAGGATATGGCATCAGAGTGAT
* * * * * * * *
29560305 GATATGTGCTCCCATATAAGACCATAGCTGGGCTGTGGCATCGGTGTGAT
1 -ATATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAGAGTGAT
* * *
29560355 GGGATTATGTGCTTCCGTATAAGATCATTTCTGGGATATGGCATCA-A-TGAT
1 ---A-TATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAGAGTGAT
* *
29560406 ATATGTGCTTCTGTGTAAGACCATATCTAGGATATGGCATCAGAGTGAT
1 ATATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAGAGTGAT
29560455 AT
1 AT
29560457 GTGATCCGTG
Statistics
Matches: 123, Mismatches: 20, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
47 64 0.52
48 10 0.08
49 9 0.07
50 1 0.01
51 4 0.03
52 2 0.02
53 33 0.27
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (49 bp):
ATATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAGAGTGAT
Found at i:29560445 original size:100 final size:100
Alignment explanation
Indices: 29560267--29560446 Score: 218
Period size: 100 Copynumber: 1.8 Consensus size: 100
29560257 GATATGTGAT
**
29560267 TTCCATATAAGACCATATCTAGGATATGGCATCGGTGTGATATGTGCTCCCATATAAGACCATAG
1 TTCCATATAAGACCATATCTAGGATATGGCATCAATGTGATATGTGCTCCCATATAAGACCATAG
* * *
29560332 CTGGGCTGTGGCATCGGTGTGATGGGATTATGTGC
66 CTAGGATATGGCATCGGTGTGATGGGATTATGTGC
* * * * * ** *
29560367 TTCCGTATAAGATCATTTCTGGGATATGGCATCAATGAT-ATATGTGCTTCTGTGTAAGACCATA
1 TTCCATATAAGACCATATCTAGGATATGGCATCAATG-TGATATGTGCTCCCATATAAGACCATA
*
29560431 TCTAGGATATGGCATC
65 GCTAGGATATGGCATC
29560447 AGAGTGATAT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
100 64 0.98
101 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (100 bp):
TTCCATATAAGACCATATCTAGGATATGGCATCAATGTGATATGTGCTCCCATATAAGACCATAG
CTAGGATATGGCATCGGTGTGATGGGATTATGTGC
Found at i:29563785 original size:33 final size:33
Alignment explanation
Indices: 29563743--29563919 Score: 257
Period size: 33 Copynumber: 5.4 Consensus size: 33
29563733 GCCAATTCAT
*
29563743 CCATTACACCAATGCTTATAAGAGCTAATCCAA
1 CCATCACACCAATGCTTATAAGAGCTAATCCAA
29563776 CCATCACACCAATGCTTATAAGAGCTAATCCAA
1 CCATCACACCAATGCTTATAAGAGCTAATCCAA
* *
29563809 CCATCACACCAATGCTCATAAGAGCTAATCGAA
1 CCATCACACCAATGCTTATAAGAGCTAATCCAA
* *
29563842 CCATCACACTAATG-TTCATAAGAGCTAAACCAA
1 CCATCACACCAATGCTT-ATAAGAGCTAATCCAA
* *
29563875 CCATCACACCAATGCTCATAAGAACTAATCCAA
1 CCATCACACCAATGCTTATAAGAGCTAATCCAA
* *
29563908 CTAGCACACCAA
1 CCATCACACCAA
29563920 ATAGAGAGTA
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
32 1 0.01
33 127 0.98
34 1 0.01
ACGTcount: A:0.41, C:0.31, G:0.09, T:0.20
Consensus pattern (33 bp):
CCATCACACCAATGCTTATAAGAGCTAATCCAA
Found at i:29565908 original size:26 final size:24
Alignment explanation
Indices: 29565826--29565918 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
29565816 GAGCTTATAG
*
29565826 ACAGTAAGGTC-TATTGAGCTG-AA
1 ACAGTAAGCTCTTA-TGAGCTGAAA
** *
29565849 ATGGTAAGCTCTGATGAGCTGAAA
1 ACAGTAAGCTCTTATGAGCTGAAA
29565873 ACAGTAAGCTCTTATGAGCTGATATA
1 ACAGTAAGCTCTTATGAGCTGA-A-A
* * *
29565899 TCAGTAAGCTCATACGAGCT
1 ACAGTAAGCTCTTATGAGCT
29565919 ATTGTGAGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 15 0.27
24 22 0.39
25 1 0.02
26 18 0.32
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (24 bp):
ACAGTAAGCTCTTATGAGCTGAAA
Found at i:29573306 original size:29 final size:29
Alignment explanation
Indices: 29573264--29573321 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
29573254 TCCGTCCATT
29573264 TTAGGAAAAACCCCTTTTGTTTTAAGGAA
1 TTAGGAAAAACCCCTTTTGTTTTAAGGAA
*
29573293 TTAGGAAAAACCCCTTTTGTTTTAGGGAA
1 TTAGGAAAAACCCCTTTTGTTTTAAGGAA
29573322 AACCGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (29 bp):
TTAGGAAAAACCCCTTTTGTTTTAAGGAA
Found at i:29575779 original size:23 final size:24
Alignment explanation
Indices: 29575739--29575832 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
29575729 AGCTCCTCCT
* *
29575739 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
29575764 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
29575787 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
29575811 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
29575833 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:29575802 original size:24 final size:24
Alignment explanation
Indices: 29575725--29575842 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
29575715 AGCTATGATT
* *
29575725 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
29575751 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
29575774 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
29575798 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
29575824 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
29575843 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:29579121 original size:51 final size:51
Alignment explanation
Indices: 29579061--29579170 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
29579051 TCATTCATGC
*
29579061 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
29579112 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
29579163 CATACTTA
1 CAT-CTTA
29579171 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:29581165 original size:23 final size:24
Alignment explanation
Indices: 29581125--29581218 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
29581115 AGCTCCTCCT
* *
29581125 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
29581150 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
29581173 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
29581197 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
29581219 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:29581188 original size:24 final size:24
Alignment explanation
Indices: 29581111--29581228 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
29581101 AGCTATGATT
* *
29581111 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
29581137 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
29581160 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
29581184 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
29581210 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
29581229 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:29584508 original size:51 final size:51
Alignment explanation
Indices: 29584448--29584557 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
29584438 TCATTCATGC
*
29584448 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
29584499 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
29584550 CATACTTA
1 CAT-CTTA
29584558 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:29586552 original size:23 final size:24
Alignment explanation
Indices: 29586512--29586605 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
29586502 AGCTCCTCCT
* *
29586512 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
29586537 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
29586560 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
29586584 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
29586606 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:29586575 original size:24 final size:24
Alignment explanation
Indices: 29586498--29586615 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
29586488 AGCTATGATT
* *
29586498 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
29586524 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
29586547 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
29586571 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
29586597 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
29586616 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:29589894 original size:51 final size:51
Alignment explanation
Indices: 29589834--29589943 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
29589824 TCATTCATGC
*
29589834 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
29589885 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
29589936 CATACTTA
1 CAT-CTTA
29589944 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:29591938 original size:23 final size:24
Alignment explanation
Indices: 29591898--29591991 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
29591888 AGCTCCTCCT
* *
29591898 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
29591923 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
29591946 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
29591970 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
29591992 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:29591961 original size:24 final size:24
Alignment explanation
Indices: 29591884--29592001 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
29591874 AGCTATGATT
* *
29591884 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
29591910 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
29591933 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
29591957 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
29591983 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
29592002 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:29595280 original size:51 final size:51
Alignment explanation
Indices: 29595220--29595329 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
29595210 TCATTCATGC
*
29595220 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
29595271 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
29595322 CATACTTA
1 CAT-CTTA
29595330 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:29597324 original size:23 final size:24
Alignment explanation
Indices: 29597284--29597377 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
29597274 AGCTCCTCCT
* *
29597284 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
29597309 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
29597332 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
29597356 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
29597378 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:29597347 original size:24 final size:24
Alignment explanation
Indices: 29597270--29597387 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
29597260 AGCTATGATT
* *
29597270 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
29597296 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
29597319 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
29597343 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
29597369 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
29597388 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:29600665 original size:51 final size:51
Alignment explanation
Indices: 29600605--29600714 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
29600595 TCATTCATGC
*
29600605 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
29600656 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
29600707 CATACTTA
1 CAT-CTTA
29600715 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:29602708 original size:23 final size:24
Alignment explanation
Indices: 29602668--29602761 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
29602658 AGCTCCTCCT
* *
29602668 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
29602693 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
29602716 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
29602740 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
29602762 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:29602731 original size:24 final size:24
Alignment explanation
Indices: 29602654--29602771 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
29602644 AGCTATGATT
* *
29602654 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
29602680 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
29602703 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
29602727 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
29602753 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
29602772 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:29606049 original size:51 final size:51
Alignment explanation
Indices: 29605989--29606098 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
29605979 TCATTCATGC
*
29605989 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
29606040 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
29606091 CATACTTA
1 CAT-CTTA
29606099 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:29607992 original size:28 final size:28
Alignment explanation
Indices: 29607946--29607999 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
29607936 ACAATTCAAA
*
29607946 AAGTAATATACAGCCATGAAAGTTTCCT
1 AAGTAATATACAACCATGAAAGTTTCCT
*
29607974 AAGTAATATACAACTATGAAAGTTTC
1 AAGTAATATACAACCATGAAAGTTTC
29608000 TCGTCATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (28 bp):
AAGTAATATACAACCATGAAAGTTTCCT
Found at i:29608217 original size:33 final size:33
Alignment explanation
Indices: 29608175--29608297 Score: 158
Period size: 33 Copynumber: 3.7 Consensus size: 33
29608165 ATGCTCACTT
* *
29608175 GAGCCAATCCATCCATCACACCAATGCTTATAA
1 GAGCTAATCCAACCATCACACCAATGCTTATAA
* * *
29608208 GAGCTAATCCAACTATCACACCAGTGCTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTTATAA
*
29608241 GAGCTAAACCAACCATCACACCAATG-TTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTT-ATAA
* *
29608274 GAGCTAATCCAACTAGCACACCAA
1 GAGCTAATCCAACCATCACACCAA
29608298 ATAGAGATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
32 1 0.01
33 76 0.99
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.19
Consensus pattern (33 bp):
GAGCTAATCCAACCATCACACCAATGCTTATAA
Found at i:29610850 original size:18 final size:18
Alignment explanation
Indices: 29610813--29610851 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29610803 TTGGAAATCA
*
29610813 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
29610831 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
29610849 AAA
1 AAA
29610852 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:29613002 original size:17 final size:19
Alignment explanation
Indices: 29612960--29613003 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29612950 ATGAAATTTT
*
29612960 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
29612979 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
29612997 AA-TATTA
1 AATTATTA
29613004 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:29615393 original size:26 final size:26
Alignment explanation
Indices: 29615322--29615399 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
29615312 TAAAACTGAT
* * * *
29615322 AAAATTACTGAAATACCTTTATAGGTGG
1 AAAATTACTGATATACC-CT-TAGGAGC
* *
29615350 AAAATTTACAGATTTACCCTTAGGAGC
1 AAAA-TTACTGATATACCCTTAGGAGC
*
29615377 AAAATTACTGATATACCCCTAGG
1 AAAATTACTGATATACCCTTAGG
29615400 GTTAAGGTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 16 0.40
27 9 0.22
28 5 0.12
29 10 0.25
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (26 bp):
AAAATTACTGATATACCCTTAGGAGC
Found at i:29629230 original size:5 final size:5
Alignment explanation
Indices: 29629215--29629248 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
29629205 TTAGAATGTA
29629215 AAAATT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA
29629249 GGCTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:29630340 original size:30 final size:30
Alignment explanation
Indices: 29630306--29630363 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29630296 CACGGACTGG
*
29630306 CACATAGGAGTGTGTCCAACCCGTGTGATA
1 CACATAGGAGTGTGTCCAACCCATGTGATA
* * *
29630336 CACATGGGCGTGTGTCCTACCCATGTGA
1 CACATAGGAGTGTGTCCAACCCATGTGA
29630364 CTCCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (30 bp):
CACATAGGAGTGTGTCCAACCCATGTGATA
Found at i:29633112 original size:55 final size:56
Alignment explanation
Indices: 29633047--29633161 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
29633037 AGCATGGCTG
* * *
29633047 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTATGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTATGGCA-TAGCCA
* * * *
29633103 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTATGGCATAGCCA
29633158 CCAG
1 CCAG
29633162 GACGCCTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 28 0.56
56 21 0.42
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTATGGCATAGCCA
Found at i:29633114 original size:28 final size:27
Alignment explanation
Indices: 29633072--29633161 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
29633062 GTGACAGAGT
*
29633072 CACCAGATACAGATATTTTATGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
** *
29633101 CACCAGAACAGATATACGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
29633128 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
29633156 CACCAG
1 CACCAG
29633162 GACGCCTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:29633314 original size:28 final size:28
Alignment explanation
Indices: 29633268--29633358 Score: 155
Period size: 28 Copynumber: 3.2 Consensus size: 28
29633258 AATTAACCCT
* *
29633268 GGGGATATAAAGGTCATTTTGCATACATA
1 GGGG-TATAATGGTAATTTTGCATACATA
29633297 GGGGTATAATGGTAATTTTGCATACATA
1 GGGGTATAATGGTAATTTTGCATACATA
29633325 GGGGTATAATGGTAATTTTGCATACATA
1 GGGGTATAATGGTAATTTTGCATACATA
29633353 GGGGTA
1 GGGGTA
29633359 CTCTAGTACA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
28 56 0.93
29 4 0.07
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.33
Consensus pattern (28 bp):
GGGGTATAATGGTAATTTTGCATACATA
Found at i:29639317 original size:27 final size:28
Alignment explanation
Indices: 29639279--29639334 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
29639269 CGGAGACTGG
29639279 GTCTTATGATCGGGCTGC-GGGGATGAT
1 GTCTTATGATCGGGCTGCGGGGGATGAT
29639306 GTCTTATGATCGGGCTGCGGGGGATGAT
1 GTCTTATGATCGGGCTGCGGGGGATGAT
29639334 G
1 G
29639335 CTTTGTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.14, C:0.14, G:0.43, T:0.29
Consensus pattern (28 bp):
GTCTTATGATCGGGCTGCGGGGGATGAT
Found at i:29645466 original size:25 final size:25
Alignment explanation
Indices: 29645437--29645484 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29645427 TTATAATATG
* * *
29645437 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTGTACCCCTAGGTA
29645462 AAAATGACCATTGTACCCCTAGG
1 AAAATGACCATTGTACCCCTAGG
29645485 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTGTACCCCTAGGTA
Found at i:29645535 original size:9 final size:9
Alignment explanation
Indices: 29645523--29645599 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
29645513 TTTGATAAAC
29645523 ATGATATGT
1 ATGATATGT
*
29645532 ATGATATGGAC
1 ATGATAT-G-T
29645543 ATGATATGT
1 ATGATATGT
*
29645552 ATGATATGCAC
1 ATGATATG--T
*
29645563 ATGACATGT
1 ATGATATGT
*
29645572 ATGATATGCAC
1 ATGATATG--T
29645583 ATGATATGT
1 ATGATATGT
29645592 ATGATATG
1 ATGATATG
29645600 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 30 0.56
10 2 0.04
11 22 0.41
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:29645611 original size:20 final size:20
Alignment explanation
Indices: 29645521--29645603 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
29645511 ATTTTGATAA
*
29645521 ACATGATATGTATGATATGG
1 ACATGATATGTATGATATGC
29645541 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
29645561 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
29645581 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
29645601 ACA
1 ACA
29645604 CGAGATGTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29645729 original size:47 final size:47
Alignment explanation
Indices: 29645660--29645754 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
29645650 AAGTGCAAAT
29645660 GGGCTTATGCCCCAGTTATT-AAAAGGGCTTATGCCCCAGTTATTAAA
1 GGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCCCAGTTATTAAA
29645707 GGGCTTATGCCCCAGTTATTAAAAAAGGGCTTTGCCCCAGTTATTAAA
1 GGGCTTATGCCCCAGTTATT-AAAAAGGGCTTTGCCCCAGTTATTAAA
29645755 AGAGGCTAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 20 0.43
48 16 0.35
49 10 0.22
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (47 bp):
GGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCCAGTTATTAAA
Found at i:29645771 original size:25 final size:24
Alignment explanation
Indices: 29645660--29645775 Score: 166
Period size: 23 Copynumber: 4.8 Consensus size: 24
29645650 AAGTGCAAAT
29645660 GGGCTTATGCCCCAGTTATTAAAA
1 GGGCTTATGCCCCAGTTATTAAAA
29645684 GGGCTTATGCCCCAGTTATT-AAA
1 GGGCTTATGCCCCAGTTATTAAAA
29645707 GGGCTTATGCCCCAGTTATTAAAAAA
1 GGGCTTATGCCCCAGTTATT--AAAA
29645733 GGGCTT-TGCCCCAGTTATTAAAA
1 GGGCTTATGCCCCAGTTATTAAAA
*
29645756 GAGGC-TAGGCCTCCAGTTAT
1 G-GGCTTATGCC-CCAGTTAT
29645776 ATGATAAAGC
Statistics
Matches: 85, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
23 29 0.34
24 26 0.31
25 21 0.25
26 9 0.11
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
GGGCTTATGCCCCAGTTATTAAAA
Found at i:29646006 original size:31 final size:31
Alignment explanation
Indices: 29645968--29646031 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29645958 CGTTTACCGT
29645968 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
29645999 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29646030 AA
1 AA
29646032 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29650205 original size:55 final size:55
Alignment explanation
Indices: 29650091--29650225 Score: 157
Period size: 55 Copynumber: 2.5 Consensus size: 55
29650081 GCCTTGGGTG
* * *
29650091 AACCTGCCAAAACAAAATC-GGCGTGCGACACGCCCGTGCCTAGAAACCGTGGCTG
1 AACCTGCCAAAACAACA-CGGGCGTGCGACACGCCCGTGCCAAGAAACCGTGGCTA
* ** * * *
29650146 AACCTGTCAAATTAACATGGGCGTGCGACACGCCTGTGCCAAGAAACTGTTGGC-A
1 AACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCAAGAAACCG-TGGCTA
29650201 AACCTGCCAAAACAACACGGGCGTG
1 AACCTGCCAAAACAACACGGGCGTG
29650226 GAAGGAGCAA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
55 61 0.94
56 4 0.06
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (55 bp):
AACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCAAGAAACCGTGGCTA
Found at i:29654925 original size:42 final size:42
Alignment explanation
Indices: 29654832--29654982 Score: 178
Period size: 42 Copynumber: 3.5 Consensus size: 42
29654822 GTTACAAATG
* * * *
29654832 TGGTCTTACATGTAATCAAATATCGATACCACTATCCCAGACA
1 TGGTCTTACACGAAATCAAATA-CGATGCCAATATCCCAGACA
* *
29654875 GGGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGACA
1 TGGTCTTACACGAAATCAAATACGATGCCAATATCCCAGACA
* *
29654917 TGGTCTTACACGTAAATCTCAAAT-CGATGCCAACATCCCAGACG
1 TGGTCTTACACG-AAA--TCAAATACGATGCCAATATCCCAGACA
*
29654961 TGGTCTTAAACGAAATCAAATA
1 TGGTCTTACACGAAATCAAATA
29654983 TAAAAAATTC
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
41 6 0.06
42 28 0.30
43 25 0.27
44 28 0.30
45 6 0.06
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATACGATGCCAATATCCCAGACA
Found at i:29654958 original size:44 final size:43
Alignment explanation
Indices: 29654865--29654977 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 43
29654855 CGATACCACT
* *
29654865 ATCCCAGACAGGGTCTTACACGAAA--TCAAATACGATGCCAAT
1 ATCCCAGACATGGTCTTACACGAAATCTCAAAT-CGATGCCAAC
*
29654907 GTCCCAGACATGGTCTTACACGTAAATCTCAAATCGATGCCAAC
1 ATCCCAGACATGGTCTTACACG-AAATCTCAAATCGATGCCAAC
* *
29654951 ATCCCAGACGTGGTCTTAAACGAAATC
1 ATCCCAGACATGGTCTTACACGAAATC
29654978 AAATATAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 20 0.32
43 8 0.13
44 28 0.45
45 6 0.10
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (43 bp):
ATCCCAGACATGGTCTTACACGAAATCTCAAATCGATGCCAAC
Found at i:29660402 original size:33 final size:33
Alignment explanation
Indices: 29660355--29660419 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
29660345 AAATCTTAGG
* *
29660355 TAACTCATTCTCTCGGAACCACATATATCAACA
1 TAACTCATTCTCTCGAAACCACAGATATCAACA
* *
29660388 TAACTCATTTTCTCGAAACCATAGATATCAAC
1 TAACTCATTCTCTCGAAACCACAGATATCAAC
29660420 GTCTTCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (33 bp):
TAACTCATTCTCTCGAAACCACAGATATCAACA
Found at i:29661255 original size:41 final size:41
Alignment explanation
Indices: 29661210--29661291 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
29661200 CGTATAAAAG
29661210 TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
1 TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
*
29661251 TTTCCAGACACTTAGAAAAATTTCTTGTAATCATAGGTCAC
1 TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
29661292 ACACCCGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (41 bp):
TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
Found at i:29662610 original size:42 final size:44
Alignment explanation
Indices: 29662545--29662629 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
29662535 ACATGTAATC
29662545 AAATATCGATGCCACTGTCCCAGAAAGGGTCTTACACA-AAATA
1 AAATATCGATGCCACTGTCCCAGAAAGGGTCTTACACATAAATA
* *
29662588 AAATA-CGATGCCGA-TGTCCCAGACATGGTCTTACACATAAAT
1 AAATATCGATGCC-ACTGTCCCAGAAAGGGTCTTACACATAAAT
29662630 CTCAAATCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 28 0.74
43 10 0.26
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (44 bp):
AAATATCGATGCCACTGTCCCAGAAAGGGTCTTACACATAAATA
Found at i:29662976 original size:15 final size:17
Alignment explanation
Indices: 29662956--29662995 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
29662946 ATCTATATAA
*
29662956 ATTCAAATCTGAC-TT-
1 ATTCAAATCTCACATTC
29662971 ATTC-AATCTCACATTC
1 ATTCAAATCTCACATTC
29662987 ATTCAAATC
1 ATTCAAATC
29662996 AATCCATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.33
15 6 0.29
16 4 0.19
17 4 0.19
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTCAAATCTCACATTC
Found at i:29664695 original size:22 final size:22
Alignment explanation
Indices: 29664669--29664713 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
29664659 ATTATGTGTA
29664669 TTAATTAATAATATAAT-TAATT
1 TTAATT-ATAATATAATCTAATT
*
29664691 TTAATTATAATCTAATCTAATT
1 TTAATTATAATATAATCTAATT
29664713 T
1 T
29664714 GGGTCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTATAATATAATCTAATT
Found at i:29665108 original size:20 final size:20
Alignment explanation
Indices: 29665070--29665109 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29665060 TTTTGGGTTA
*
29665070 TTATTCTATTTTATATTATT
1 TTATTCTATTTGATATTATT
* *
29665090 TTATTCTCTTTGATTTTATT
1 TTATTCTATTTGATATTATT
29665110 GTACTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (20 bp):
TTATTCTATTTGATATTATT
Found at i:29676684 original size:3 final size:3
Alignment explanation
Indices: 29676676--29676722 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
29676666 GGATTCCGAT
*
29676676 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
29676723 TCCCATAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29678915 original size:16 final size:16
Alignment explanation
Indices: 29678896--29678928 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29678886 TAATTCATAA
29678896 TATAAT-CAATTTTAAT
1 TATAATCCAA-TTTAAT
29678912 TATAATCCAATTTAAT
1 TATAATCCAATTTAAT
29678928 T
1 T
29678929 TGGGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAATCCAATTTAAT
Found at i:29689832 original size:49 final size:52
Alignment explanation
Indices: 29689756--29689933 Score: 224
Period size: 51 Copynumber: 3.5 Consensus size: 52
29689746 ATTAGTGCCT
29689756 CAAGTGTGGTACTATGTGAAGGCCACTTTGA-GAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAGAAGATAGCTTTGGTCA
* *
29689805 CAAGTGTGGTACTGTGTGAAGGTCACTTT-ATGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAG-AAGATAGCTTTGGTCA
* * * *
29689857 CAAGTGCGGTACTATGTGAAGGCCACTTTG-TGAATAAGGTAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAGAAGATAGCTTTGGTC-A
* *
29689908 CAAGGGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
29689934 CGGGAATCCG
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
48 1 0.01
49 31 0.28
50 2 0.02
51 41 0.37
52 37 0.33
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAGAAGATAGCTTTGGTCA
Found at i:29695424 original size:15 final size:14
Alignment explanation
Indices: 29695404--29695461 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 14
29695394 AATAATAAAT
29695404 AAATAACAATAACTA
1 AAATAACAATAA-TA
29695419 AAATAACAAATTAATA
1 AAATAAC-AA-TAATA
*
29695435 AAATAATAATAAT-
1 AAATAACAATAATA
29695448 -AATAACAA-AATA
1 AAATAACAATAATA
29695460 AA
1 AA
29695462 GTAAAATGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
13 1 0.03
14 4 0.11
15 9 0.24
16 10 0.27
17 3 0.08
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAACAATAATA
Found at i:29720031 original size:25 final size:25
Alignment explanation
Indices: 29719996--29720043 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
29719986 ATCGTTCATC
29719996 TAATGACAAGATTCAAGAACAAACA
1 TAATGACAAGATTCAAGAACAAACA
* *
29720021 TAATGATAAGATTCAATAACAAA
1 TAATGACAAGATTCAAGAACAAA
29720044 ACACAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.21
Consensus pattern (25 bp):
TAATGACAAGATTCAAGAACAAACA
Found at i:29722411 original size:20 final size:19
Alignment explanation
Indices: 29722369--29722411 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29722359 ATTAAACTTT
*
29722369 AAAATTAGACCTGAGATCC
1 AAAATTAGACCTGAGACCC
*
29722388 AAAATTGGACCTGAGAACCC
1 AAAATTAGACCTGAG-ACCC
29722408 AAAA
1 AAAA
29722412 CCGAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATTAGACCTGAGACCC
Found at i:29722924 original size:58 final size:59
Alignment explanation
Indices: 29722797--29722927 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 59
29722787 TTAATATTAA
* * * *
29722797 ATTAAA-TTAATATAATATTTATCTTGTAGATAAATATTCTATTAATTTAATAGATTTAAT
1 ATTAAATTTAATCTAATATTTATCTTGTA-ATAAATATTATATTAAATTAATA-ATTAAAT
*
29722857 ATTAAATTTAATCTAATATTTATCTT-T-ATAAGTATTATATTAAATTAAT-ATTAAACT
1 ATTAAATTTAATCTAATATTTATCTTGTAATAAATATTATATTAAATTAATAATTAAA-T
*
29722914 GATTCAATTTAATC
1 -ATTAAATTTAATC
29722928 ATAGTGGAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 31 0.50
60 7 0.11
61 18 0.29
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (59 bp):
ATTAAATTTAATCTAATATTTATCTTGTAATAAATATTATATTAAATTAATAATTAAAT
Found at i:29728448 original size:25 final size:25
Alignment explanation
Indices: 29728420--29728481 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
29728410 ATGCTAATTT
29728420 GAGCTA-AAGATCGATATGCTCTCAC
1 GAGCTATAA-ATCGATATGCTCTCAC
*
29728445 GAGCTATAAATCGGTATGCTCTCAC
1 GAGCTATAAATCGATATGCTCTCAC
29728470 GAGCTATAAATC
1 GAGCTATAAATC
29728482 AGTAACCCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (25 bp):
GAGCTATAAATCGATATGCTCTCAC
Found at i:29731299 original size:22 final size:20
Alignment explanation
Indices: 29731251--29731299 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 20
29731241 ATTTCACTAC
29731251 TCAAATCCATGGCCAAAACA
1 TCAAATCCATGGCCAAAACA
*
29731271 TACCAAATCCATATGCCAAAATCA
1 T--CAAATCCAT-GGCCAAAA-CA
29731295 TCAAA
1 TCAAA
29731300 CATACATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
22 13 0.54
23 7 0.29
24 3 0.12
ACGTcount: A:0.47, C:0.29, G:0.06, T:0.18
Consensus pattern (20 bp):
TCAAATCCATGGCCAAAACA
Found at i:29733214 original size:3 final size:3
Alignment explanation
Indices: 29733206--29733251 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
29733196 TATAGTGGCT
29733206 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
29733252 TGTAACACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:29736425 original size:40 final size:40
Alignment explanation
Indices: 29736381--29736551 Score: 265
Period size: 40 Copynumber: 4.3 Consensus size: 40
29736371 GCTCCTCGTT
* *
29736381 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
29736421 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
29736461 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
29736501 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
29736540 CAAATGCCTTCG
1 CAAATGCCTTCG
29736552 ATTCTTAGTC
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
39 33 0.27
40 88 0.72
41 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29736565 original size:79 final size:80
Alignment explanation
Indices: 29736381--29736605 Score: 249
Period size: 80 Copynumber: 2.8 Consensus size: 80
29736371 GCTCCTCGTT
* * *
29736381 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGAGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
29736445 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
* * *
29736461 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
29736525 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
** ** * * * * * *
29736540 CAAATGCCTTCGATTCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGAGACTTAGCCCG
1 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCG
29736604 GA
65 GA
29736606 CATCATTCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
79 57 0.46
80 66 0.53
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:29736565 original size:119 final size:120
Alignment explanation
Indices: 29736383--29736605 Score: 281
Period size: 119 Copynumber: 1.9 Consensus size: 120
29736373 TCCTCGTTCA
* *
29736383 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGAT
* * *
29736448 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACC
* * ** **
29736503 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGATTCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGA
* * *
29736566 TATGGTCACTTAGCACAAAGCCTTCGAGACTTAGCCCGGA
65 TATAGTAACTTAGCACAAAGCCTTCGAGACTTAACCCGGA
29736606 CATCATTCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
118 1 0.01
119 66 0.76
120 20 0.23
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:29744595 original size:119 final size:120
Alignment explanation
Indices: 29744413--29744635 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
29744403 TCCTCGTTCA
* *
29744413 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGAT
* *
29744478 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
29744533 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGG
* * *
29744595 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
29744636 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:29744635 original size:40 final size:40
Alignment explanation
Indices: 29744411--29744635 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
29744401 GCTCCTCGTT
* *
29744411 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29744451 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29744491 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
29744531 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
29744570 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
29744611 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29744636 CATCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 119 0.73
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:29746852 original size:27 final size:26
Alignment explanation
Indices: 29746806--29746920 Score: 81
Period size: 27 Copynumber: 4.3 Consensus size: 26
29746796 TCCCTGTTTA
* *
29746806 AAATACTTTAGTTTACTAAAATTACCG
1 AAATACCTTAGTTT-GTAAAATTACCG
* *
29746833 AAATACGCTTAGTTTGTAAAAATACTG
1 AAATAC-CTTAGTTTGTAAAATTACCG
* * *
29746860 AAATACCCTGGATTTGTAAAATTA-CT
1 AAATACCTTAG-TTTGTAAAATTACCG
* *
29746886 AAAGTACCTTCGACTTGTAAAATTACC-
1 AAA-TACCTTAG-TTTGTAAAATTACCG
29746913 AAAGTACC
1 AAA-TACC
29746921 CCCGATTTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
26 6 0.08
27 58 0.81
28 8 0.11
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (26 bp):
AAATACCTTAGTTTGTAAAATTACCG
Found at i:29747003 original size:27 final size:27
Alignment explanation
Indices: 29746964--29747083 Score: 141
Period size: 27 Copynumber: 4.4 Consensus size: 27
29746954 TTACCTCGAC
* *
29746964 TTACAGAATTACCGTTTTACCCTCGAT
1 TTACAAAATTACCGTTTTACCCTTGAT
* * *
29746991 TTATAAAAGTACCGTTTTATCCTTGAT
1 TTACAAAATTACCGTTTTACCCTTGAT
* * *
29747018 TTATAGAATTACTGTTTTACCCTTGAT
1 TTACAAAATTACCGTTTTACCCTTGAT
* **
29747045 TTACAGAATTACTATTTTACCCTTGAT
1 TTACAAAATTACCGTTTTACCCTTGAT
29747072 TTACAAAATTAC
1 TTACAAAATTAC
29747084 TAGAATACCC
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (27 bp):
TTACAAAATTACCGTTTTACCCTTGAT
Found at i:29747035 original size:54 final size:54
Alignment explanation
Indices: 29746949--29747084 Score: 157
Period size: 54 Copynumber: 2.5 Consensus size: 54
29746939 CATTTTACCC
* * * *
29746949 CCATTTTA-CCTCGACTTACAGAATTACCGTTTTACCCTCGATTTATAAAAGTA
1 CCATTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAAGTA
* * * * * *
29747002 CCGTTTTATCCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTA
1 CCATTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAAGTA
* *
29747056 CTATTTTACCCTTGATTTACAAAATTACT
1 CCATTTTACCCTTGATTTACAGAATTACT
29747085 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:0.21, G:0.09, T:0.42
Consensus pattern (54 bp):
CCATTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAAGTA
Found at i:29747084 original size:27 final size:27
Alignment explanation
Indices: 29746951--29747085 Score: 137
Period size: 27 Copynumber: 5.0 Consensus size: 27
29746941 TTTTACCCCC
* * *
29746951 ATTTTA-CCTCGACTTACAGAATTACC
1 ATTTTACCCTTGATTTACAGAATTACT
* * * * * *
29746977 GTTTTACCCTCGATTTATAAAAGTACC
1 ATTTTACCCTTGATTTACAGAATTACT
* * *
29747004 GTTTTATCCTTGATTTATAGAATTACT
1 ATTTTACCCTTGATTTACAGAATTACT
*
29747031 GTTTTACCCTTGATTTACAGAATTACT
1 ATTTTACCCTTGATTTACAGAATTACT
*
29747058 ATTTTACCCTTGATTTACAAAATTACT
1 ATTTTACCCTTGATTTACAGAATTACT
29747085 A
1 A
29747086 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:0.19, G:0.09, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTGATTTACAGAATTACT
Found at i:29747092 original size:27 final size:27
Alignment explanation
Indices: 29747035--29747347 Score: 165
Period size: 27 Copynumber: 11.6 Consensus size: 27
29747025 ATTACTGTTT
** * ***
29747035 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTTGATTTGTAAAATTACTAGAA
**
29747062 TACCCTTGATTTACAAAATTACTAGAA
1 TACCCTTGATTTGTAAAATTACTAGAA
* * *
29747089 TACCCTAG-TCTGTAAAATTACTAAAA
1 TACCCTTGATTTGTAAAATTACTAGAA
*
29747115 TACCCTTGGTTTGTAAAATTAC-AGAAA
1 TACCCTTGATTTGTAAAATTACTAG-AA
** * *
29747142 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACTAGAA
* * *
29747169 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACTAGAA
* * *
29747196 TACCAC-TGGTTTGTGAAATTAC-CGAAA
1 TACC-CTTGATTTGTAAAATTACTAG-AA
** * *
29747223 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACTAGAA
* ** *
29747250 TACCCCTGATTTACAAAGTTAC-AGAAA
1 TACCCTTGATTTGTAAAATTACTAG-AA
*
29747277 TACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTGT-AAAATTACTAG-AA
* * **
29747306 TACCATTGGTTTACAAAATTACT-GAAA
1 TACCCTTGATTTGTAAAATTACTAG-AA
*
29747333 TACCCTTGGTTTGTA
1 TACCCTTGATTTGTA
29747348 GATTTACCAA
Statistics
Matches: 226, Mismatches: 46, Indels: 28
0.75 0.15 0.09
Matches are distributed among these distances:
26 25 0.11
27 174 0.77
28 9 0.04
29 18 0.08
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTGTAAAATTACTAGAA
Found at i:29747181 original size:54 final size:53
Alignment explanation
Indices: 29747076--29747254 Score: 209
Period size: 54 Copynumber: 3.3 Consensus size: 53
29747066 CTTGATTTAC
* * * * * *
29747076 AAAATTACTAGAATACCCTAGTCTGTAAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGT
*
29747129 AAAATTA-CAGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCA-AAATACCCT-AGTTTGTAAAATTACCAAAATACCCCTAGTTTGT
* * * *
29747183 AAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACC-CTAGTTTGTAAAATTACCAAAATACCCCT-AGTTTGT
29747237 AAAATTACCAAAATACCC
1 AAAATTACCAAAATACCC
29747255 CTGATTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
52 1 0.01
53 20 0.18
54 84 0.77
55 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (53 bp):
AAAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGT
Found at i:29747206 original size:81 final size:81
Alignment explanation
Indices: 29747076--29747256 Score: 285
Period size: 81 Copynumber: 2.2 Consensus size: 81
29747066 CTTGATTTAC
* * *
29747076 AAAATTACTAGAATA-CCCTAGTCTGTAAAATTACTAAAATACCCTTGGTTTGTAAAATTACAGA
1 AAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACAGA
29747140 AATACCCTCAATTTGT
66 AATACCCTCAATTTGT
* * *
29747156 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCG
1 AAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACC-CTTGGTTTGTAAAATTACAG
29747220 AAATACCCTCAATTTGT
65 AAATACCCTCAATTTGT
29747237 AAAATTACCAAAATACCCCT
1 AAAATTACCAAAATACCCCT
29747257 GATTTACAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
80 13 0.14
81 79 0.85
82 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACAGA
AATACCCTCAATTTGT
Found at i:29747278 original size:81 final size:81
Alignment explanation
Indices: 29747076--29747309 Score: 282
Period size: 81 Copynumber: 2.9 Consensus size: 81
29747066 CTTGATTTAC
* * *
29747076 AAAATTACTAGAATA-CCCTAG-TCTGTAAAATTACTAAAATACCCTTGGTTTGTAAAATTACAG
1 AAAATTACCAAAATACCCCTAGAT-TGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACAG
29747139 AAATACCCTCAATTTGT
65 AAATACCCTCAATTTGT
* * *
29747156 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCG
1 AAAATTACCAAAATACCCCTAGATTGTAAAATTACCAAAATACC-CTTGGTTTGTAAAATTACAG
29747220 AAATACCCTCAATTTGT
65 AAATACCCTCAATTTGT
* *
29747237 AAAATTACCAAAATACCCCT-GATT-TACAAAGTTA-CAGAAATACCCTTGACTTTCTAAAAATT
1 AAAATTACCAAAATACCCCTAGATTGTA-AAA-TTACCA-AAATACCCTTG-GTTTGT-AAAATT
*
29747299 ATAGAAATACC
61 ACAGAAATACC
29747310 ATTGGTTTAC
Statistics
Matches: 134, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
79 2 0.01
80 22 0.16
81 90 0.67
82 6 0.04
83 14 0.10
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCTAGATTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACAGA
AATACCCTCAATTTGT
Found at i:29747462 original size:27 final size:27
Alignment explanation
Indices: 29747385--29747462 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
29747375 AAATGACTAA
* *
29747385 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
29747412 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
29747439 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
29747463 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:29748720 original size:9 final size:9
Alignment explanation
Indices: 29748708--29748764 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
29748698 TTTGATAAAC
29748708 ATGATATGT
1 ATGATATGT
*
29748717 ATGATATGCAC
1 ATGATATG--T
*
29748728 ATGACATGT
1 ATGATATGT
*
29748737 ATGATATGCAC
1 ATGATATG--T
29748748 ATGATATGT
1 ATGATATGT
29748757 ATGATATG
1 ATGATATG
29748765 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:29748731 original size:20 final size:20
Alignment explanation
Indices: 29748706--29748776 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
29748696 ATTTTGATAA
29748706 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
29748726 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
29748746 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
29748766 ACATGAGATGT
1 ACATGATATGT
29748777 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29748753 original size:11 final size:11
Alignment explanation
Indices: 29748717--29748771 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
29748707 CATGATATGT
29748717 ATGATATGCAC
1 ATGATATGCAC
* *
29748728 ATGACATG--T
1 ATGATATGCAC
29748737 ATGATATGCAC
1 ATGATATGCAC
*
29748748 ATGATATG--T
1 ATGATATGCAC
29748757 ATGATATGCAC
1 ATGATATGCAC
29748768 ATGA
1 ATGA
29748772 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:29748902 original size:25 final size:24
Alignment explanation
Indices: 29748823--29749016 Score: 243
Period size: 25 Copynumber: 8.0 Consensus size: 24
29748813 AGGAAGTGCA
*
29748823 AAAGGGCTTATGCCCTAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
*
29748846 AAAGGGCTTATGCCCCAATTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
29748869 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
29748894 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
* *
29748919 GAAGGGCTTATGCTCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
*
29748944 AAAGGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTATAT
*
29748968 AAAGGGCTTTTGCCCCAGTTACTA-
1 AAAGGGCTTATGCCCCAGTTA-TAT
*
29748992 AAAGAGGC-TAGGCCTCCAGTTATAT
1 AAAG-GGCTTATGCC-CCAGTTATAT
29749017 GATAAAGCAG
Statistics
Matches: 154, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
23 42 0.27
24 31 0.20
25 81 0.53
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATAT
Found at i:29749237 original size:7 final size:7
Alignment explanation
Indices: 29749225--29749254 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
29749215 TCGGCCCAGT
29749225 AATATGA
1 AATATGA
29749232 AATATGA
1 AATATGA
29749239 AATATGA
1 AATATGA
29749246 AATATGA
1 AATATGA
29749253 AA
1 AA
29749255 AGGGCTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (7 bp):
AATATGA
Found at i:29751573 original size:42 final size:41
Alignment explanation
Indices: 29751452--29751606 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 41
29751442 TACTAAACCA
* *
29751452 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACG-AATCTCATATTG
* * *
29751494 ATGCCAATAGCCTAGCTATGGTCTTACACGAAATCTCATATTG
1 ATGCC-ATATCCCAGATATGGTCTTACACG-AATCTCATATTG
*
29751537 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATACTG
1 ATGCCATATCCCAGATATGGTCTTACACGAA-TCTCATATTG
*
29751579 ATGTCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
29751607 ATAAACTTAG
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.02
42 62 0.62
43 36 0.36
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAATCTCATATTG
Found at i:29751896 original size:39 final size:39
Alignment explanation
Indices: 29751846--29751924 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
29751836 TCCCCAAATC
*
29751846 TAGGTCTGAACCTCGTTTCTCTTGATCTATAATAGCAAA
1 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
*
29751885 TAGGTCCGAACCTTGTTTCTCTTGATCTATAATAGCAAA
1 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
29751924 T
1 T
29751925 TAAACTCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (39 bp):
TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
Found at i:29762114 original size:43 final size:42
Alignment explanation
Indices: 29762010--29762120 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 42
29762000 TTAGGTTATT
* *
29762010 GATATGTGATTACATGTAAAACCATGTCTGGGACATTGGCATC
1 GATATGTG-TTACATGTAAGACCATGTCTGGGACAGTGGCATC
* * *
29762053 GTTAATCGAT-TT-CGTGTAAGACCCTGTCTGGGACAGTGGCATC
1 GAT-AT-G-TGTTACATGTAAGACCATGTCTGGGACAGTGGCATC
29762096 GATATGTGTTAACATGTAAGACCAT
1 GATATGTGTT-ACATGTAAGACCAT
29762121 ATTTGGGATA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
40 1 0.02
41 3 0.06
42 2 0.04
43 42 0.78
44 4 0.07
45 1 0.02
46 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (42 bp):
GATATGTGTTACATGTAAGACCATGTCTGGGACAGTGGCATC
Found at i:29777537 original size:20 final size:20
Alignment explanation
Indices: 29777503--29777540 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29777493 TCAACATCCC
29777503 ATATTTAAACTATCACATGA
1 ATATTTAAACTATCACATGA
29777523 ATATTATAAAC-ATCACAT
1 ATATT-TAAACTATCACAT
29777541 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:29778163 original size:40 final size:41
Alignment explanation
Indices: 29778116--29778212 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
29778106 TATCTTGGTA
* *
29778116 TCGCACACTTAGTGCC-TCATATAGTCGAAGCTA-TTTCAAC
1 TCGCACACTTAGTGCCAT-ATATAGCCAAAGCTATTTTCAAC
* * *
29778156 TCGCACACTTAGTGCCATTTGTAGCCAAAGCTATTTTGAAC
1 TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTTCAAC
29778197 -CGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
29778213 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:29778452 original size:18 final size:18
Alignment explanation
Indices: 29778429--29778466 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29778419 TTCAAAATTA
29778429 ACCCTTTTAATCACCAAC
1 ACCCTTTTAATCACCAAC
29778447 ACCCTTTTAATCACCAAC
1 ACCCTTTTAATCACCAAC
29778465 AC
1 AC
29778467 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:29779718 original size:32 final size:32
Alignment explanation
Indices: 29779682--29779746 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
29779672 TGAATAACAT
29779682 AGTATCAGTACAATCTGGG-CCAAGCCCTATTC
1 AGTATCAGTACAATCTGGGTCC-AGCCCTATTC
* *
29779714 AGTATCAGTACAGTCTGGGTGCAGCCCTATTC
1 AGTATCAGTACAATCTGGGTCCAGCCCTATTC
29779746 A
1 A
29779747 ATAGCAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (32 bp):
AGTATCAGTACAATCTGGGTCCAGCCCTATTC
Found at i:29791554 original size:31 final size:31
Alignment explanation
Indices: 29791514--29791597 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
29791504 TAAGTCTCGA
*
29791514 CATAT-ACTGGGCCGAAGCCTTTTCCTAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
29791544 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
29791575 CATATCACTTGGTCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
29791598 ACTGTAAGCG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:29791845 original size:25 final size:25
Alignment explanation
Indices: 29791817--29791886 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
29791807 CTCTTTTAAT
* *
29791817 AACTGGGGCAAATCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
29791842 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
29791867 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
29791887 AGTACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:29792730 original size:27 final size:27
Alignment explanation
Indices: 29792695--29792751 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
29792685 GGGCATATTC
* *
29792695 GTCATTTTATCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
*
29792722 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
29792749 GTC
1 GTC
29792752 TTTTTACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Done.