Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_pilon, whole genome shotgun sequence
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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2754901 original size:61 final size:61
Alignment explanation
Indices: 2754786--2754904 Score: 150
Period size: 61 Copynumber: 2.0 Consensus size: 61
2754776 ACGCATTGCA
* * * * *
2754786 AACAACCTGTTGGAGCATTATAAGGACATATACCATTCAGTAGAGCATGGAACACGTTAAT
1 AACAACCTGTTGGAACATTATAAAGACATATACCATTCAGTACAACATGAAACACGTTAAT
** *
2754847 AACAACCTGTTGGAACATTATAAAGACATAT-CCACTTCTTTACAATATGAAACACGTT
1 AACAACCTGTTGGAACATTATAAAGACATATACCA-TTCAGTACAACATGAAACACGTT
2754905 GGGAGACATA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 3 0.06
61 46 0.94
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (61 bp):
AACAACCTGTTGGAACATTATAAAGACATATACCATTCAGTACAACATGAAACACGTTAAT
Found at i:2756393 original size:27 final size:29
Alignment explanation
Indices: 2756350--2756432 Score: 107
Period size: 30 Copynumber: 2.9 Consensus size: 29
2756340 AGCTGTCAAT
*
2756350 GTCTCCCAAATGCTCCACTAAGCT-TATA
1 GTCTTCCAAATGCTCCACTAAGCTGTATA
*
2756378 -TCTTCCAAATGCTCCACTAAGTTGTATA
1 GTCTTCCAAATGCTCCACTAAGCTGTATA
* *
2756406 TGTCTTCCAAGTGCTCCACCAAGCTGT
1 -GTCTTCCAAATGCTCCACTAAGCTGT
2756433 CCCAACGTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 21 0.45
28 4 0.09
30 22 0.47
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.31
Consensus pattern (29 bp):
GTCTTCCAAATGCTCCACTAAGCTGTATA
Found at i:2756414 original size:30 final size:29
Alignment explanation
Indices: 2756348--2756430 Score: 107
Period size: 27 Copynumber: 2.9 Consensus size: 29
2756338 TGAGCTGTCA
*
2756348 ATGTCTCCCAAATGCTCCACTAAGCTTAT
1 ATGTCTTCCAAATGCTCCACTAAGCTTAT
*
2756377 A--TCTTCCAAATGCTCCACTAAGTTGTAT
1 ATGTCTTCCAAATGCTCCACTAAGCT-TAT
* *
2756405 ATGTCTTCCAAGTGCTCCACCAAGCT
1 ATGTCTTCCAAATGCTCCACTAAGCT
2756431 GTCCCAACGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 21 0.46
28 4 0.09
29 1 0.02
30 20 0.43
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (29 bp):
ATGTCTTCCAAATGCTCCACTAAGCTTAT
Found at i:2763778 original size:21 final size:20
Alignment explanation
Indices: 2763754--2763797 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2763744 CTTTCCTTGG
2763754 CTTTGCTTTCTTTTTGACTTT
1 CTTTGCTTTCTTTTT-ACTTT
** *
2763775 CTTTTTTTTCTTTTTATTTT
1 CTTTGCTTTCTTTTTACTTT
2763795 CTT
1 CTT
2763798 CTTTTCTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (20 bp):
CTTTGCTTTCTTTTTACTTT
Found at i:2763795 original size:20 final size:22
Alignment explanation
Indices: 2763760--2763802 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2763750 TTGGCTTTGC
2763760 TTTCTTTTTGACTTTCTT-TTT
1 TTTCTTTTTGACTTTCTTCTTT
*
2763781 TTTCTTTTT-ATTTTCTTCTTT
1 TTTCTTTTTGACTTTCTTCTTT
2763802 T
1 T
2763803 CTGAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTGACTTTCTTCTTT
Found at i:2763802 original size:21 final size:21
Alignment explanation
Indices: 2763760--2763802 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2763750 TTGGCTTTGC
2763760 TTTCTTTTTGACTTTCTTTTT
1 TTTCTTTTTGACTTTCTTTTT
* *
2763781 TTTCTTTTT-ATTTTCTTCTT
1 TTTCTTTTTGACTTTCTTTTT
2763801 TT
1 TT
2763803 CTGAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTCTTTTTGACTTTCTTTTT
Found at i:2765918 original size:28 final size:26
Alignment explanation
Indices: 2765887--2765943 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
2765877 GAAAATCAGA
* *
2765887 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACT-CAAAAG-AAG
*
2765915 AAAGAAAATCCAGCACTCAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAGAAG
2765941 AAA
1 AAA
2765944 AAACAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 14 0.54
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAGAAAATCAAGCACTCAAAAGAAG
Found at i:2775992 original size:185 final size:185
Alignment explanation
Indices: 2775680--2776050 Score: 742
Period size: 185 Copynumber: 2.0 Consensus size: 185
2775670 GAGCTAGAAA
2775680 ATAGATGCATGCATGCAAATGAGCTAAAGAAACATGGATTTAAAGCTAGTGAGATGTAAACATAA
1 ATAGATGCATGCATGCAAATGAGCTAAAGAAACATGGATTTAAAGCTAGTGAGATGTAAACATAA
2775745 CATGAGCTAGAATAACATGACCTGAGTTAATGAATGAATGAATACATGTTGTCATGATATGTAAA
66 CATGAGCTAGAATAACATGACCTGAGTTAATGAATGAATGAATACATGTTGTCATGATATGTAAA
2775810 TGATATACAAACATAATTAATGAATCTAAAATGTATGTAAACATAATATAAAGCT
131 TGATATACAAACATAATTAATGAATCTAAAATGTATGTAAACATAATATAAAGCT
2775865 ATAGATGCATGCATGCAAATGAGCTAAAGAAACATGGATTTAAAGCTAGTGAGATGTAAACATAA
1 ATAGATGCATGCATGCAAATGAGCTAAAGAAACATGGATTTAAAGCTAGTGAGATGTAAACATAA
2775930 CATGAGCTAGAATAACATGACCTGAGTTAATGAATGAATGAATACATGTTGTCATGATATGTAAA
66 CATGAGCTAGAATAACATGACCTGAGTTAATGAATGAATGAATACATGTTGTCATGATATGTAAA
2775995 TGATATACAAACATAATTAATGAATCTAAAATGTATGTAAACATAATATAAAGCT
131 TGATATACAAACATAATTAATGAATCTAAAATGTATGTAAACATAATATAAAGCT
2776050 A
1 A
2776051 AGTAAAGATG
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
185 186 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.27
Consensus pattern (185 bp):
ATAGATGCATGCATGCAAATGAGCTAAAGAAACATGGATTTAAAGCTAGTGAGATGTAAACATAA
CATGAGCTAGAATAACATGACCTGAGTTAATGAATGAATGAATACATGTTGTCATGATATGTAAA
TGATATACAAACATAATTAATGAATCTAAAATGTATGTAAACATAATATAAAGCT
Found at i:2781613 original size:22 final size:22
Alignment explanation
Indices: 2781564--2781617 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2781554 AGCACCATGA
* * *
2781564 GTCCATGCAAATTGTAATATTC
1 GTCCATGCATATTGTAACATAC
* *
2781586 GGCCATGCATATTGTAACCTAC
1 GTCCATGCATATTGTAACATAC
2781608 GTCCATGCAT
1 GTCCATGCAT
2781618 GCATTTCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (22 bp):
GTCCATGCATATTGTAACATAC
Found at i:2784293 original size:16 final size:16
Alignment explanation
Indices: 2784275--2784306 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2784265 CTATGAACCA
2784275 TATAT-TTATA-TATT
1 TATATCTTATATTATT
2784289 TATATCTTATATTATT
1 TATATCTTATATTATT
2784305 TA
1 TA
2784307 GCTTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATCTTATATTATT
Found at i:2787875 original size:23 final size:25
Alignment explanation
Indices: 2787849--2787903 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
2787839 AAATCCAGCA
*
2787849 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGAACTCAAAGAGG
* *
2787872 AAGAAATTGAAAGAACTCAAAGAGG
1 AAGAAAATCAAAGAACTCAAAGAGG
2787897 AAGAAAA
1 AAGAAAA
2787904 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGAACTCAAAGAGG
Found at i:2789167 original size:24 final size:25
Alignment explanation
Indices: 2789121--2789175 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2789111 ACAGTTATGC
*
2789121 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
2789145 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
2789170 CA-TTGA
1 CACTTGA
2789176 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:2791770 original size:23 final size:25
Alignment explanation
Indices: 2791744--2791798 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
2791734 AAATCCAGCA
2791744 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
2791767 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
2791792 AAGAAAA
1 AAGAAAA
2791799 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:2793056 original size:24 final size:25
Alignment explanation
Indices: 2793010--2793064 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2793000 ACAGTTATGC
*
2793010 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
2793034 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
2793059 CA-TTGA
1 CACTTGA
2793065 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:2799156 original size:13 final size:13
Alignment explanation
Indices: 2799148--2799200 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2799138 ACTTCTCTTT
2799148 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
*
2799161 TTCTTTTCTGATTTTT
1 TTCTTTTC---TTTTC
*
2799177 TTCTCTTCTTTTC
1 TTCTTTTCTTTTC
*
2799190 GTCTTTTCTTT
1 TTCTTTTCTTT
2799201 CTTTTTGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 21 0.66
16 11 0.34
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.74
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:2799196 original size:21 final size:21
Alignment explanation
Indices: 2799143--2799202 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
2799133 TTTGAACTTC
2799143 TCTTTT-TCTTTTCTTT-TCT
1 TCTTTTCTCTTTTCTTTCTCT
*
2799162 TCTTTTCTGATTTT-TTTCTCT
1 TCTTTTCT-CTTTTCTTTCTCT
2799183 TCTTTTCGTCTTTTCTTTCT
1 TCTTTTC-TCTTTTCTTTCT
2799203 TTTTGCACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 18 0.53
22 6 0.18
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.73
Consensus pattern (21 bp):
TCTTTTCTCTTTTCTTTCTCT
Found at i:2799205 original size:29 final size:30
Alignment explanation
Indices: 2799140--2799206 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
2799130 CTTTTTGAAC
* *
2799140 TTCTCTTTTTCTTTTCTTTTCTTCTTTTCTG
1 TTCT-TTTTTCTCTTCTTTTCGTCTTTTCTG
*
2799171 AT-TTTTTTCTCTTCTTTTCGTCTTTTCT-
1 TTCTTTTTTCTCTTCTTTTCGTCTTTTCTG
2799199 TTCTTTTT
1 TTCTTTTT
2799207 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 28 0.90
30 1 0.03
31 1 0.03
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (30 bp):
TTCTTTTTTCTCTTCTTTTCGTCTTTTCTG
Found at i:2815439 original size:11 final size:11
Alignment explanation
Indices: 2815425--2815472 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
2815415 GAAATTTTGG
*
2815425 CTTTTTTGGCT
1 CTTTTTTTGCT
2815436 CTTTTTTTG--
1 CTTTTTTTGCT
2815445 -TTTTTTTGCT
1 CTTTTTTTGCT
*
2815455 TTTTTTTTGC-
1 CTTTTTTTGCT
2815465 CTTTTTTT
1 CTTTTTTT
2815473 TTTGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 8 0.25
10 7 0.22
11 17 0.53
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.77
Consensus pattern (11 bp):
CTTTTTTTGCT
Found at i:2815448 original size:19 final size:19
Alignment explanation
Indices: 2815426--2815463 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2815416 AAATTTTGGC
2815426 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGCTCTTTTTTTG
* *
2815445 TTTTTTTGCTTTTTTTTTG
1 TTTTTTGGCTCTTTTTTTG
2815464 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (19 bp):
TTTTTTGGCTCTTTTTTTG
Found at i:2815460 original size:12 final size:12
Alignment explanation
Indices: 2815445--2815474 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2815435 TCTTTTTTTG
2815445 TTTTTTTG-CTT
1 TTTTTTTGCCTT
2815456 TTTTTTTGCCTT
1 TTTTTTTGCCTT
2815468 TTTTTTT
1 TTTTTTT
2815475 TGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:2815469 original size:19 final size:20
Alignment explanation
Indices: 2815427--2815470 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2815417 AATTTTGGCT
*
2815427 TTTTTGGCTCTTTTTTTG-T
1 TTTTTGGCTCTTTTTTTGCC
* *
2815446 TTTTTTGCTTTTTTTTTGCC
1 TTTTTGGCTCTTTTTTTGCC
2815466 TTTTT
1 TTTTT
2815471 TTTTTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (20 bp):
TTTTTGGCTCTTTTTTTGCC
Found at i:2819958 original size:25 final size:25
Alignment explanation
Indices: 2819908--2819963 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2819898 TTCTTTGTTT
* *
2819908 TTTTC-TTCTTTTTGAGTGCTAGAA
1 TTTTCTTTCTTTTGGAGTGCTACAA
2819932 TTTTCTTTCTTTTGGAGTGC-ATCAA
1 TTTTCTTTCTTTTGGAGTGCTA-CAA
2819957 -TTTCTTT
1 TTTTCTTT
2819964 TCTGATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (25 bp):
TTTTCTTTCTTTTGGAGTGCTACAA
Found at i:2827254 original size:193 final size:192
Alignment explanation
Indices: 2826927--2827312 Score: 747
Period size: 193 Copynumber: 2.0 Consensus size: 192
2826917 ACATTAAGAT
2826927 CAAAATTCCTCAATTCCAAGGAAAGACTGATCCTGAAGCCTATCTTGATGGGAAAGCAAGTGGAA
1 CAAAATTCCTCAATTCCAAGGAAAGACTGATCCTGAAGCCTATCTTGATGGGAAAGCAAGTGGAA
2826992 CATGTTTTTAGTTGCCATAACTATTCCGAGATGAAGAAAGTAAGATTGGCAGCCATGGAGTTTAT
66 CATGTTTTTAGTTGCCATAACTATTCCGAGATGAAGAAAGTAAGATTGGCAGCCATGGAGTTTAT
2827057 AGACTATGCCTTAATATGGTGGGATCAAC-TACCCTTAACCGAAGGAGGAATGGAGAACGAC
131 AGACTATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAC
2827118 CAAAATTCCTCAATTCCAAGGAAAGACTGATCCTGAAGCCTATCTTGAATGGGAAAGCAAAGTGG
1 CAAAATTCCTCAATTCCAAGGAAAGACTGATCCTGAAGCCTATCTTG-ATGGGAAAGC-AAGTGG
2827183 AACATGTTTTTAGTTGCCATAACTATTCCGAGATGAAGAAAGTAAGATTGGCAGCCATGGAGTTT
64 AACATGTTTTTAGTTGCCATAACTATTCCGAGATGAAGAAAGTAAGATTGGCAGCCATGGAGTTT
2827248 ATAGACTATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAC
129 ATAGACTATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAC
2827312 C
1 C
2827313 GGTCTCACTT
Statistics
Matches: 192, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
191 47 0.24
192 10 0.05
193 102 0.53
194 33 0.17
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (192 bp):
CAAAATTCCTCAATTCCAAGGAAAGACTGATCCTGAAGCCTATCTTGATGGGAAAGCAAGTGGAA
CATGTTTTTAGTTGCCATAACTATTCCGAGATGAAGAAAGTAAGATTGGCAGCCATGGAGTTTAT
AGACTATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAC
Found at i:2828760 original size:32 final size:32
Alignment explanation
Indices: 2828719--2828785 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
2828709 TGATCATGCC
2828719 TATTGGAGTATTAAAAGACACCACTTTTGGGA
1 TATTGGAGTATTAAAAGACACCACTTTTGGGA
2828751 TATTGGAGTATTAAAAGACACCACTTTTGGGA
1 TATTGGAGTATTAAAAGACACCACTTTTGGGA
2828783 TAT
1 TAT
2828786 CAAGGGACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (32 bp):
TATTGGAGTATTAAAAGACACCACTTTTGGGA
Found at i:2833656 original size:15 final size:17
Alignment explanation
Indices: 2833636--2833673 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2833626 AACCATATAT
*
2833636 TTATATT-TTTAA-TTC
1 TTATATTATTTAACTTA
2833651 TTATATTATTTAACTTA
1 TTATATTATTTAACTTA
2833668 TTATAT
1 TTATAT
2833674 GCTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 5 0.25
17 8 0.40
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATTATTTAACTTA
Found at i:2834876 original size:9 final size:10
Alignment explanation
Indices: 2834862--2834901 Score: 57
Period size: 9 Copynumber: 4.2 Consensus size: 10
2834852 ATTTTATGCA
2834862 TGGATGA-TT
1 TGGATGAGTT
2834871 TGGATGAGTT
1 TGGATGAGTT
*
2834881 TGAATGA-TT
1 TGGATGAGTT
2834890 TGGATGAGTT
1 TGGATGAGTT
2834900 TG
1 TG
2834902 AGCCAAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 15 0.56
10 12 0.44
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (10 bp):
TGGATGAGTT
Found at i:2834889 original size:19 final size:19
Alignment explanation
Indices: 2834865--2834902 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2834855 TTATGCATGG
2834865 ATGATTTGGATGAGTTTGA
1 ATGATTTGGATGAGTTTGA
2834884 ATGATTTGGATGAGTTTGA
1 ATGATTTGGATGAGTTTGA
2834903 GCCAAGGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
ATGATTTGGATGAGTTTGA
Found at i:2841930 original size:18 final size:18
Alignment explanation
Indices: 2841909--2841946 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2841899 CCTTACACAC
2841909 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
2841927 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
2841945 TT
1 TT
2841947 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:2841930 original size:134 final size:134
Alignment explanation
Indices: 2841664--2841931 Score: 520
Period size: 135 Copynumber: 2.0 Consensus size: 134
2841654 GCTCATATAT
2841664 ATCTAGTGGGTCACGTTCCATACCCTACCATTTCGATTCCAATTTTTTTATATTGTTGGTTCTTA
1 ATCTAGTGGGTCACGTTCCATACCCTACCATTTCGATTCCAATTTTTTTATATTGTTGGTTCTTA
2841729 GCTCCAAATAGCTAACGGGTCACAATCCGCTTTATCCTTACACACTTTGCCACAACAACACCCAT
66 GCTCCAAATAGCTAACGGGTCACAATCCGCTTTATCCTTACACACTTTGCCACAACAACACCCAT
2841794 TTGC
131 TTGC
2841798 ATCTAGTGGGTCACGTTCCATACCCTACCATTTCGATTCCAATTTTTTTTATATTGTTGGTTCTT
1 ATCTAGTGGGTCACGTTCCATACCCTACCATTTCGATTCCAA-TTTTTTTATATTGTTGGTTCTT
2841863 AGCTCCAAATAGCTAACGGGTCACAATCCGCTTTATCCTTACACACTTTGCCACAACAACA-CCA
65 AGCTCCAAATAGCTAACGGGTCACAATCCGCTTTATCCTTACACACTTTGCCACAACAACACCCA
2841927 TTTGC
130 TTTGC
2841932 CACGACAACG
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
134 50 0.38
135 83 0.62
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.35
Consensus pattern (134 bp):
ATCTAGTGGGTCACGTTCCATACCCTACCATTTCGATTCCAATTTTTTTATATTGTTGGTTCTTA
GCTCCAAATAGCTAACGGGTCACAATCCGCTTTATCCTTACACACTTTGCCACAACAACACCCAT
TTGC
Found at i:2842701 original size:15 final size:15
Alignment explanation
Indices: 2842681--2842717 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2842671 TTTGATATCA
2842681 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
*
2842696 TTTCTTACCATTTCC
1 TTTCTTTCCATTTCC
2842711 TTTCTTT
1 TTTCTTT
2842718 TTCTGTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.30, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:2844131 original size:59 final size:58
Alignment explanation
Indices: 2844019--2844134 Score: 205
Period size: 59 Copynumber: 2.0 Consensus size: 58
2844009 ACGCATGCGA
*
2844019 AAAGGAAATCAGGAAATGTATTTCCTCTAGTAGTCTTTACTTATTTTAATGTATAAGT
1 AAAGGAAATCAAGAAATGTATTTCCTCTAGTAGTCTTTACTTATTTTAATGTATAAGT
*
2844077 AAAGGAAATCAAGAAATGTCTTTCCTCTCAGTAGTCTTTACTTATTTTAATGTATAAG
1 AAAGGAAATCAAGAAATGTATTTCCTCT-AGTAGTCTTTACTTATTTTAATGTATAAG
2844135 GAGCATTTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 26 0.47
59 29 0.53
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (58 bp):
AAAGGAAATCAAGAAATGTATTTCCTCTAGTAGTCTTTACTTATTTTAATGTATAAGT
Found at i:2844565 original size:11 final size:11
Alignment explanation
Indices: 2844549--2844581 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2844539 AAATTAGTAT
2844549 CTCAAAGAAGA
1 CTCAAAGAAGA
2844560 CTCAAAGAAGA
1 CTCAAAGAAGA
*
2844571 CTTAAAGAAGA
1 CTCAAAGAAGA
2844582 ACCAATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (11 bp):
CTCAAAGAAGA
Found at i:2845369 original size:43 final size:47
Alignment explanation
Indices: 2845321--2845426 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 47
2845311 ATAACTAGAG
*
2845321 AATAAAATAATAATAAACTAAACATA-TTTTAA-C-T-C-TAATTCCT
1 AATAAAATAATAAT-AACTAAAAATATTTTTAACCGTCCTTAATTCCT
2845364 AATAAAATAATAATAACTAAAAATATTGTTTTAACCCGTCCTTAATTCCT
1 AATAAAATAATAATAACTAAAAATA-T-TTTTAA-CCGTCCTTAATTCCT
2845414 AATAAAATAATAA
1 AATAAAATAATAA
2845427 ATCTAATCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
42 10 0.19
43 14 0.26
45 6 0.11
47 1 0.02
48 1 0.02
49 1 0.02
50 21 0.39
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (47 bp):
AATAAAATAATAATAACTAAAAATATTTTTAACCGTCCTTAATTCCT
Found at i:2848287 original size:24 final size:21
Alignment explanation
Indices: 2848252--2848294 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2848242 GGCTCATTCT
*
2848252 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2848275 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2848295 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2852287 original size:24 final size:21
Alignment explanation
Indices: 2852252--2852294 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2852242 GGCTCATTCT
*
2852252 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2852275 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2852295 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2853534 original size:5 final size:5
Alignment explanation
Indices: 2853501--2853532 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2853491 CTTCAACTTC
2853501 TTTCT TTTCT TTTCT TTTCT TTTCT TTT-T TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
2853533 TTGTGCTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:2854834 original size:24 final size:21
Alignment explanation
Indices: 2854799--2854841 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2854789 GGCTCATTCT
*
2854799 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2854822 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2854842 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2856063 original size:10 final size:10
Alignment explanation
Indices: 2856048--2856081 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2856038 CTTCAACTTC
2856048 TTTCTTTTTT
1 TTTCTTTTTT
*
2856058 TTTCTTTGTT
1 TTTCTTTTTT
2856068 TTTCTTCTTTT
1 TTTCTT-TTTT
2856079 TTT
1 TTT
2856082 TGTGCTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:2859844 original size:33 final size:33
Alignment explanation
Indices: 2859765--2859868 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2859755 ATACAATCTG
* *
2859765 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2859801 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2859834 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2859867 TC
1 TC
2859869 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2864319 original size:33 final size:33
Alignment explanation
Indices: 2864240--2864319 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
2864230 ATACAATCTG
* *
2864240 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCA-TATCACGCCAATAACATCACC--AT
2864276 TCCATCACCATATCACGCCAATAACATCATCC-T
1 TCCATCACCATATCACGCCAATAACATCA-CCAT
*
2864309 TCCATTACCAT
1 TCCATCACCAT
2864320 TTCATCACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 11 0.28
35 17 0.43
36 12 0.30
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCACCAT
Found at i:2870332 original size:19 final size:19
Alignment explanation
Indices: 2870308--2870346 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2870298 TCGAATGTAT
2870308 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2870327 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2870346 T
1 T
2870347 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2870471 original size:64 final size:65
Alignment explanation
Indices: 2870294--2870456 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
2870284 GAATTAATTG
* * * * *
2870294 AACATCGAATGTATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* * ** **
2870359 AACATCGAATGCATTTGATGCATCGATGCATAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
2870422 A
65 A
2870423 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
2870457 TGGTGCACCG
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 35 0.43
65 47 0.57
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2876282 original size:20 final size:21
Alignment explanation
Indices: 2876253--2876308 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2876243 TTTGTGCTTC
*
2876253 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
2876273 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
2876295 ATGCATCGATGCAT
1 ATGCATCGATGCAT
2876309 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:2877035 original size:21 final size:21
Alignment explanation
Indices: 2877011--2877074 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2877001 AAAACCGTCC
2877011 TCCCGTTCCTCAACATCCTAA
1 TCCCGTTCCTCAACATCCTAA
** *
2877032 TCCCGTTCCTCCTCAACCTAA
1 TCCCGTTCCTCAACATCCTAA
* *
2877053 TCCTGATCCTCAAGC-TCCTAA
1 TCCCGTTCCTCAA-CATCCTAA
2877074 T
1 T
2877075 GGCTTATTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.42, G:0.06, T:0.30
Consensus pattern (21 bp):
TCCCGTTCCTCAACATCCTAA
Found at i:2877897 original size:21 final size:21
Alignment explanation
Indices: 2877871--2877914 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2877861 ACTCCGGGAG
*
2877871 CTAGTTCTTCTCGAGCTGCTC
1 CTAGTTCTTCTCGAGCTCCTC
*
2877892 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCTCGAGCTCCTC
2877913 CT
1 CT
2877915 CCAGCTCCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.36, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCTCGAGCTCCTC
Found at i:2878933 original size:19 final size:19
Alignment explanation
Indices: 2878909--2878947 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2878899 TCGAATGCAT
2878909 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2878928 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2878947 T
1 T
2878948 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2878966 original size:65 final size:65
Alignment explanation
Indices: 2878895--2879054 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
2878885 GAATTAATTG
* * ** *
2878895 AACATCGAATGCATTCCATGCACCGATGCACT-CTCCATGCATCGATGCACTCTGAATA-TTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACTAAGCCATGCATCGATGCAC-CAGAATATTTTTC
2878958 A
65 A
* **
2878959 AAGCATCGAATGCATTTGATGCATCGATGCA-TAAGCCATGCATCGATGCACCAGGCTATTTTTC
1 AA-CATCGAATGCATTTCATGCATCGATGCACTAAGCCATGCATCGATGCACCAGAATATTTTTC
2879023 A
65 A
2879024 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
2879055 ACTTGGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 34 0.41
65 49 0.59
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACTAAGCCATGCATCGATGCACCAGAATATTTTTCA
Found at i:2898092 original size:9 final size:9
Alignment explanation
Indices: 2898078--2898104 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2898068 TAATAACTCG
2898078 GATATTTCT
1 GATATTTCT
2898087 GATATTTCT
1 GATATTTCT
2898096 GATATTTCT
1 GATATTTCT
2898105 ACTCATACTT
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:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:2902960 original size:30 final size:31
Alignment explanation
Indices: 2902908--2902967 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2902898 CTTAGCTTTA
**
2902908 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
2902938 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2902968 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2903488 original size:10 final size:10
Alignment explanation
Indices: 2903475--2903513 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
2903465 TGGACTAAAG
2903475 GTAGCTGGAA
1 GTAGCTGGAA
2903485 GTAGCTGGAA
1 GTAGCTGGAA
2903495 GTAGCTGGGAGA
1 GTAGCT-GGA-A
2903507 GTAGCTG
1 GTAGCTG
2903514 AGGAGCTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.59
11 4 0.15
12 7 0.26
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.21
Consensus pattern (10 bp):
GTAGCTGGAA
Found at i:2903917 original size:19 final size:20
Alignment explanation
Indices: 2903887--2903937 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2903877 CAGCCAAGAG
* *
2903887 CATGTATCTTCATTAAA-AT
1 CATGTATTTTCATAAAACAT
*
2903906 CTTGTATTTTCATAAAACAT
1 CATGTATTTTCATAAAACAT
2903926 CATGTATTTTCA
1 CATGTATTTTCA
2903938 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATAAAACAT
Found at i:2907763 original size:10 final size:10
Alignment explanation
Indices: 2907750--2907788 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
2907740 TGGACTAAAG
2907750 GTAGCTGGAA
1 GTAGCTGGAA
2907760 GTAGCTGGAA
1 GTAGCTGGAA
2907770 GTAGCTGGGAGA
1 GTAGCT-GGA-A
2907782 GTAGCTG
1 GTAGCTG
2907789 AGGAGCTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.59
11 4 0.15
12 7 0.26
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.21
Consensus pattern (10 bp):
GTAGCTGGAA
Found at i:2908186 original size:19 final size:20
Alignment explanation
Indices: 2908162--2908208 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2908152 CAGCCAAGAG
*
2908162 CATGTATCTTCAT-TAAAAT
1 CATGTATCTTCATAAAAAAT
*
2908181 CATGTATTTTCATCAAAAAAT
1 CATGTATCTTCAT-AAAAAAT
2908202 CATGTAT
1 CATGTAT
2908209 TGTCAAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (20 bp):
CATGTATCTTCATAAAAAAT
Found at i:2915181 original size:24 final size:23
Alignment explanation
Indices: 2915154--2915200 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2915144 GTGTTACAAC
2915154 AAAAAAGCAACAAGAA-AAAAGAAG
1 AAAAAAG-AA-AAGAAGAAAAGAAG
2915178 AAAAAAGAAAAGAATGAAAAGAA
1 AAAAAAGAAAAGAA-GAAAAGAA
2915201 AAAGACTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 14 0.67
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAGAAGAAAAGAAG
Found at i:2931009 original size:16 final size:17
Alignment explanation
Indices: 2930979--2931013 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2930969 TCTCTATTCC
2930979 TTCATTTCATTTTTTAA
1 TTCATTTCATTTTTTAA
2930996 TTCATTTC-TTTTTTAA
1 TTCATTTCATTTTTTAA
2931012 TT
1 TT
2931014 TTATTATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCATTTCATTTTTTAA
Found at i:2942499 original size:26 final size:26
Alignment explanation
Indices: 2942463--2942531 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
2942453 AAATGATCCG
2942463 TATGCAAGGCACATGGGGGCTGGTCA
1 TATGCAAGGCACATGGGGGCTGGTCA
2942489 TATGCAAGGCACATGGGGGCTGGTCA
1 TATGCAAGGCACATGGGGGCTGGTCA
2942515 TATGCAAGGCACATGGG
1 TATGCAAGGCACATGGG
2942532 TGTTCTAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.38, T:0.19
Consensus pattern (26 bp):
TATGCAAGGCACATGGGGGCTGGTCA
Found at i:2944278 original size:24 final size:21
Alignment explanation
Indices: 2944243--2944285 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2944233 AGCTCATTCT
*
2944243 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2944266 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2944286 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2945541 original size:24 final size:24
Alignment explanation
Indices: 2945513--2945568 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2945503 CTTCTCTTTT
*
2945513 CTTTTATTCTTTTTGAGTG-TTGGA
1 CTTTTATTCTTTTGGAGTGCTT-GA
* *
2945537 TTTTTCTTCTTTTGGAGTGCTTGA
1 CTTTTATTCTTTTGGAGTGCTTGA
2945561 CTTTTATT
1 CTTTTATT
2945569 TGTTGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.61
Consensus pattern (24 bp):
CTTTTATTCTTTTGGAGTGCTTGA
Found at i:2947489 original size:11 final size:11
Alignment explanation
Indices: 2947473--2947511 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2947463 AATTTGGTGA
2947473 TGATATAGGCG
1 TGATATAGGCG
*
2947484 TGATAT-GGTG
1 TGATATAGGCG
2947494 ATGATATAGGCG
1 -TGATATAGGCG
2947506 TGATAT
1 TGATAT
2947512 GGTGATGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.33
Consensus pattern (11 bp):
TGATATAGGCG
Found at i:2947495 original size:22 final size:22
Alignment explanation
Indices: 2947467--2947518 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
2947457 TTTGAGAATT
2947467 TGGTGATGATATAGGCGTGATA
1 TGGTGATGATATAGGCGTGATA
2947489 TGGTGATGATATAGGCGTGATA
1 TGGTGATGATATAGGCGTGATA
2947511 TGGTGATG
1 TGGTGATG
2947519 GAAATATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.04, G:0.38, T:0.33
Consensus pattern (22 bp):
TGGTGATGATATAGGCGTGATA
Found at i:2947526 original size:36 final size:37
Alignment explanation
Indices: 2947486--2947569 Score: 127
Period size: 36 Copynumber: 2.3 Consensus size: 37
2947476 TATAGGCGTG
*
2947486 ATATGGTGATGATATAGGCGTGAT-ATGG-TGATGGAA
1 ATATGGTGATGATATAGGCGTGATAATGGAAGATGG-A
2947522 ATATGGTGATGATATAGGCGTGATAATGGAAGATGGA
1 ATATGGTGATGATATAGGCGTGATAATGGAAGATGGA
*
2947559 TTATGGTGATG
1 ATATGGTGATG
2947570 GAAATAGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 24 0.55
37 15 0.34
38 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (37 bp):
ATATGGTGATGATATAGGCGTGATAATGGAAGATGGA
Found at i:2947531 original size:22 final size:22
Alignment explanation
Indices: 2947467--2947524 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2947457 TTTGAGAATT
*
2947467 TGGTGATGATATAGGCGTGATA
1 TGGTGATGAAATAGGCGTGATA
*
2947489 TGGTGATGATATAGGCGTGATA
1 TGGTGATGAAATAGGCGTGATA
2947511 TGGTGATGGAAATA
1 TGGTGAT-GAAATA
2947525 TGGTGATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.31
Consensus pattern (22 bp):
TGGTGATGAAATAGGCGTGATA
Found at i:2963103 original size:24 final size:23
Alignment explanation
Indices: 2963071--2963130 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
2963061 AGGTACAAAT
*
2963071 GCCTTACATCAAGTGGCATCAGAA
1 GCCTTACATCAAGTGACATCAG-A
*
2963095 GCCTTACATCAAGTGATATCAGA
1 GCCTTACATCAAGTGACATCAGA
*
2963118 GCCATACATCAAG
1 GCCTTACATCAAG
2963131 CGGTAATCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (23 bp):
GCCTTACATCAAGTGACATCAGA
Found at i:2963139 original size:24 final size:23
Alignment explanation
Indices: 2963075--2963142 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
2963065 ACAAATGCCT
* *
2963075 TACATCAAGTGGCATCAGAAGCCT
1 TACATCAAGTGGTATCAG-AGCCA
*
2963099 TACATCAAGTGATATCAGAGCCA
1 TACATCAAGTGGTATCAGAGCCA
*
2963122 TACATCAAGCGGTAATCAGAG
1 TACATCAAGTGGT-ATCAGAG
2963143 ATTTGGTGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 15 0.39
24 23 0.61
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (23 bp):
TACATCAAGTGGTATCAGAGCCA
Found at i:2979164 original size:18 final size:17
Alignment explanation
Indices: 2979141--2979184 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2979131 TAATGTAATG
2979141 GAATAAGAAAAGATGAAA
1 GAATAAGAAAA-ATGAAA
2979159 GAATAAG-AAAATGAAA
1 GAATAAGAAAAATGAAA
*
2979175 TAATAAGAAA
1 GAATAAGAAA
2979185 GTGAAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 12 0.50
17 5 0.21
18 7 0.29
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (17 bp):
GAATAAGAAAAATGAAA
Found at i:2979174 original size:16 final size:16
Alignment explanation
Indices: 2979141--2979189 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
2979131 TAATGTAATG
2979141 GAATAAGAAAAGATGAAA
1 GAATAAG-AAA-ATGAAA
2979159 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* *
2979175 TAATAAGAAAGTGAA
1 GAATAAGAAAATGAA
2979190 GATAACTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.66
17 3 0.10
18 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.14
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:2997934 original size:23 final size:24
Alignment explanation
Indices: 2997884--2997938 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
2997874 TTTTCTTTGC
*
2997884 TTTTTC-TTCTTTTCAGTGCTGGA
1 TTTTTCTTTCTTTTCAGTGCTGCA
* *
2997907 TTTTTCTTTCTTTTGAGTGCTTCA
1 TTTTTCTTTCTTTTCAGTGCTGCA
2997931 -TTTTCTTT
1 TTTTTCTTT
2997939 TATGATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.07, C:0.16, G:0.13, T:0.64
Consensus pattern (24 bp):
TTTTTCTTTCTTTTCAGTGCTGCA
Found at i:3003448 original size:15 final size:16
Alignment explanation
Indices: 3003421--3003457 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3003411 CTTTATTATC
3003421 TTATTTCATCTTTCAT
1 TTATTTCATCTTTCAT
*
3003437 TTATTT-ATCTTTTAT
1 TTATTTCATCTTTCAT
3003452 TTATTT
1 TTATTT
3003458 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCAT
Found at i:3003459 original size:16 final size:16
Alignment explanation
Indices: 3003416--3003460 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
3003406 GATTTCTTTA
*
3003416 TTATCTTATTTCATCTT
1 TTAT-TTATTTTATCTT
*
3003433 TCATTTA-TTTATCTT
1 TTATTTATTTTATCTT
3003448 TTATTTATTTTAT
1 TTATTTATTTTAT
3003461 TCTAATCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 13 0.54
16 8 0.33
17 3 0.12
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTATTTTATCTT
Found at i:3010639 original size:389 final size:389
Alignment explanation
Indices: 3009922--3011088 Score: 2228
Period size: 389 Copynumber: 3.0 Consensus size: 389
3009912 TGTGATCCTA
3009922 CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGTTCTTCCAAGATGATTCTAAGGG
1 CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGTTCTTCCAAGATGATTCTAAGGG
*
3009987 AGTCTTGCCTTATTTTATTAATTATTTACTTATTTATGCATTACATGTCAGGTGAATATGTTTAT
66 AGTCTTGCCTTATTTTATTATTTATTTACTTATTTATGCATTACATGTCAGGTGAATATGTTTAT
3010052 CTTATTCTTAATTATGCTTGAATGTTATATGCTGTCATTTATATGTATAATATATGATATTCATG
131 CTTATTCTTAATTATGCTTGAATGTTATATGCTGTCATTTATATGTATAATATATGATATTCATG
3010117 TATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATTCATCGTTAGCTCAT
196 TATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATTCATCGTTAGCTCAT
3010182 TTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
261 TTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
3010247 TTTGTTTACATACTTTGTCTAGGGTCATTGAATGCTAAGAAGACTAAAGGCAATTGAAGAGTTG
326 TTTGTTTACATACTTTGTCTAGGGTCATTGAATGCTAAGAAGACTAAAGGCAATTGAAGAGTTG
*
3010311 CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGCTCTTCCAAGATGATTCTAAGGG
1 CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGTTCTTCCAAGATGATTCTAAGGG
*
3010376 AGTCTTGCCTTATTTTATTATTTATTTACTTATTTATGCATTACATGTTAGGTGAATATGTTTAT
66 AGTCTTGCCTTATTTTATTATTTATTTACTTATTTATGCATTACATGTCAGGTGAATATGTTTAT
3010441 CTTATTCTTAATTATGCTTGAATGTTATATGCTGTCATTTATATGTATAATATATGATATTCATG
131 CTTATTCTTAATTATGCTTGAATGTTATATGCTGTCATTTATATGTATAATATATGATATTCATG
*
3010506 TATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCGTATGCATTCATCGTTAGCTCAT
196 TATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATTCATCGTTAGCTCAT
*
3010571 TTGCATTATTAAAATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
261 TTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
*
3010636 TTTGTTTACATACTTTGTCTAGGGTCATTGAATGCTAAGAAGACTAAAGGCAATTGAAGAGTTA
326 TTTGTTTACATACTTTGTCTAGGGTCATTGAATGCTAAGAAGACTAAAGGCAATTGAAGAGTTG
3010700 CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGTTCTTCCAAGATGATTCTAAGGG
1 CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGTTCTTCCAAGATGATTCTAAGGG
3010765 AGTCTTGCCTTATTTTATTATTTATTTACTTATTTATGCATTACATGTCAGGTGAATATGTTTAT
66 AGTCTTGCCTTATTTTATTATTTATTTACTTATTTATGCATTACATGTCAGGTGAATATGTTTAT
*
3010830 CTTATTCTTAATTATGCTTGAATGTTATATGATGTCATTTATATGTATAATATATGATATTCATG
131 CTTATTCTTAATTATGCTTGAATGTTATATGCTGTCATTTATATGTATAATATATGATATTCATG
* * *
3010895 CATGACTTATAAATTCACATCTTTATATAACTCATTCAATGCATATGCATTCATAGTTAGCTCAT
196 TATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATTCATCGTTAGCTCAT
3010960 TTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
261 TTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
3011025 TTTGTTTACATACTTTGTCTAGGGTCATT-AGATGCTAAGAAGACTAAAGGCAATTGAAGAGTTG
326 TTTGTTTACATACTTTGTCTAGGGTCATTGA-ATGCTAAGAAGACTAAAGGCAATTGAAGAGTTG
3011089 GTTGGACAGT
Statistics
Matches: 762, Mismatches: 15, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
388 1 0.00
389 761 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (389 bp):
CCGACCACCAAGTTCAAACAAAACATGCTCACAACTTTGAAGTTCTTCCAAGATGATTCTAAGGG
AGTCTTGCCTTATTTTATTATTTATTTACTTATTTATGCATTACATGTCAGGTGAATATGTTTAT
CTTATTCTTAATTATGCTTGAATGTTATATGCTGTCATTTATATGTATAATATATGATATTCATG
TATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATTCATCGTTAGCTCAT
TTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAATTCCTATCTAATTA
TTTGTTTACATACTTTGTCTAGGGTCATTGAATGCTAAGAAGACTAAAGGCAATTGAAGAGTTG
Found at i:3019361 original size:11 final size:10
Alignment explanation
Indices: 3019322--3019375 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
3019312 TTTTGAATTC
3019322 TTTTTCTT-T
1 TTTTTCTTCT
3019331 TCTTTTCTTCT
1 T-TTTTCTTCT
3019342 TTTCTTCTTC-
1 TTT-TTCTTCT
*
3019352 TTTTT-GTCT
1 TTTTTCTTCT
3019361 TTTTTCTTTCT
1 TTTTTC-TTCT
3019372 TTTT
1 TTTT
3019376 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 2 0.05
9 8 0.22
10 12 0.32
11 15 0.41
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:3019376 original size:19 final size:19
Alignment explanation
Indices: 3019322--3019376 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
3019312 TTTTGAATTC
3019322 TTTTTCTTTTCTTTTCT-TCT
1 TTTTTC-TTTCTTTT-TGTCT
3019342 TTTCTTC-TTCTTTTTGTCT
1 TTT-TTCTTTCTTTTTGTCT
3019361 TTTTTCTTTCTTTTTG
1 TTTTTCTTTCTTTTTG
3019377 CACTCCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.12
19 22 0.69
20 3 0.09
21 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTGTCT
Found at i:3023509 original size:22 final size:24
Alignment explanation
Indices: 3023476--3023528 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3023466 ATAAGGGAGA
3023476 TATTTTGATTTC-TTTA-TTATCT
1 TATTTTGATTTCATTTATTTATCT
3023498 TATTTT-ATTTTCAATTTATTTATCT
1 TATTTTGA-TTTC-ATTTATTTATCT
*
3023523 TTTTTT
1 TATTTT
3023529 TTATTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 10 0.38
24 4 0.15
25 11 0.42
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.72
Consensus pattern (24 bp):
TATTTTGATTTCATTTATTTATCT
Found at i:3023895 original size:18 final size:18
Alignment explanation
Indices: 3023872--3023926 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
3023862 ATATTTTTTT
*
3023872 CAAAAAAACAAAAAAAGG
1 CAAAAAAACAAAAAAAGC
3023890 C---AAAA-AAAAAAAGC
1 CAAAAAAACAAAAAAAGC
*
3023904 CAAAAAAGCAAAAAAAGC
1 CAAAAAAACAAAAAAAGC
3023922 CAAAA
1 CAAAA
3023927 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 9 0.29
15 4 0.13
17 3 0.10
18 15 0.48
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAGC
Found at i:3023900 original size:14 final size:14
Alignment explanation
Indices: 3023876--3023910 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3023866 TTTTTTCAAA
*
3023876 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGCC
3023891 AAAAAAAAAAAGCC
1 AAAAAAAAAAAGCC
3023905 AAAAAA
1 AAAAAA
3023911 GCAAAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGCC
Found at i:3023901 original size:22 final size:22
Alignment explanation
Indices: 3023873--3023919 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
3023863 TATTTTTTTC
3023873 AAAAAAA-CAAAAAAAGGCAAAA
1 AAAAAAAGCAAAAAAA-GCAAAA
*
3023895 AAAAAAAGCCAAAAAAGCAAAA
1 AAAAAAAGCAAAAAAAGCAAAA
3023917 AAA
1 AAA
3023920 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.81, C:0.11, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAAAAGCAAAAAAAGCAAAA
Found at i:3023908 original size:9 final size:9
Alignment explanation
Indices: 3023896--3023926 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3023886 AAGGCAAAAA
3023896 AAAAAAGCC
1 AAAAAAGCC
*
3023905 AAAAAAGCA
1 AAAAAAGCC
3023914 AAAAAAGCC
1 AAAAAAGCC
3023923 AAAA
1 AAAA
3023927 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAGCC
Found at i:3029626 original size:16 final size:16
Alignment explanation
Indices: 3029593--3029641 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3029583 TAAGGTAATG
3029593 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
3029611 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* *
3029627 TAATAAGAAAGTGAA
1 GAATAAGAAAATGAA
3029642 GATAACTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.66
17 1 0.03
18 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:3029744 original size:54 final size:54
Alignment explanation
Indices: 3029681--3029791 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
3029671 ACTATCTTTC
3029681 TTCACAAGAAACAACAAGGATACCTCCTTCTAGTTTGTTTTTAGGCATATTATT
1 TTCACAAGAAACAACAAGGATACCTCCTTCTAGTTTGTTTTTAGGCATATTATT
*
3029735 TTCACAAGAAACAACAAGGATACCTCCTTCTAGTTTGTTTTTGGGCATATTATT
1 TTCACAAGAAACAACAAGGATACCTCCTTCTAGTTTGTTTTTAGGCATATTATT
3029789 TTC
1 TTC
3029792 TTCTTCTCTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (54 bp):
TTCACAAGAAACAACAAGGATACCTCCTTCTAGTTTGTTTTTAGGCATATTATT
Found at i:3029852 original size:14 final size:16
Alignment explanation
Indices: 3029828--3029859 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3029818 CTTTCTTCAC
3029828 TTTTCTTTTTC-TTCT
1 TTTTCTTTTTCTTTCT
3029843 TTTTC-TTTTCTTTCT
1 TTTTCTTTTTCTTTCT
3029858 TT
1 TT
3029860 GACACTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTTCTTTCT
Found at i:3049884 original size:35 final size:37
Alignment explanation
Indices: 3049838--3049917 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
3049828 TTTGAGAATT
*
3049838 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
3049873 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
3049910 TGGTGATG
1 TGGTGATG
3049918 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:3055542 original size:35 final size:37
Alignment explanation
Indices: 3055496--3055574 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
3055486 TTTGAGAATT
*
3055496 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
3055531 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
3055568 TGGTGAT
1 TGGTGAT
3055575 AGAAATAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:3061070 original size:25 final size:25
Alignment explanation
Indices: 3061035--3061097 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
3061025 TTTCATCATC
3061035 AACCATCATCAATATCCTTCAACAA
1 AACCATCATCAATATCCTTCAACAA
* * *
3061060 GACCATTATCAACATCCTTCAACAA
1 AACCATCATCAATATCCTTCAACAA
3061085 AACCATCATCAAT
1 AACCATCATCAAT
3061098 TCCATAATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.43, C:0.32, G:0.02, T:0.24
Consensus pattern (25 bp):
AACCATCATCAATATCCTTCAACAA
Found at i:3068404 original size:11 final size:11
Alignment explanation
Indices: 3068390--3068426 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3068380 AAATTTTAAC
3068390 TTTTTTGTTTT
1 TTTTTTGTTTT
**
3068401 TTTTTTGCCTT
1 TTTTTTGTTTT
3068412 TTTTTTGTTTT
1 TTTTTTGTTTT
3068423 TTTT
1 TTTT
3068427 GGAAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:3068406 original size:20 final size:20
Alignment explanation
Indices: 3068383--3068426 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3068373 TTTTTTGAAA
3068383 TTTTAACTTTTTTGTT-TTTT
1 TTTTAACTTTTTT-TTGTTTT
**
3068403 TTTTGCCTTTTTTTTGTTTT
1 TTTTAACTTTTTTTTGTTTT
3068423 TTTT
1 TTTT
3068427 GGAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.82
Consensus pattern (20 bp):
TTTTAACTTTTTTTTGTTTT
Found at i:3068427 original size:20 final size:20
Alignment explanation
Indices: 3068389--3068427 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3068379 GAAATTTTAA
3068389 CTTTTTTGTTTTTTTTTTGC
1 CTTTTTTGTTTTTTTTTTGC
3068409 CTTTTTT-TTGTTTTTTTTG
1 CTTTTTTGTT-TTTTTTTTG
3068428 GAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (20 bp):
CTTTTTTGTTTTTTTTTTGC
Found at i:3069198 original size:15 final size:17
Alignment explanation
Indices: 3069173--3069206 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3069163 TAAAGGTCCT
3069173 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
3069189 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
3069205 AA
1 AA
3069207 CATATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:3070354 original size:24 final size:24
Alignment explanation
Indices: 3070327--3070376 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3070317 ATCAGCAAAC
* *
3070327 AATTTGAAGCACTCCAAAAGAAGA
1 AATTTCAAGCACTCAAAAAGAAGA
*
3070351 AATTTCCAGCACTCAAAAAGAAGA
1 AATTTCAAGCACTCAAAAAGAAGA
3070375 AA
1 AA
3070377 AGCAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (24 bp):
AATTTCAAGCACTCAAAAAGAAGA
Found at i:3076331 original size:13 final size:13
Alignment explanation
Indices: 3076297--3076352 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
3076287 TTGGAGTGCA
3076297 AAAAGAAAAGAAA-
1 AAAAGAAAA-AAAG
3076310 AAATCAGAAAAAAAG
1 AAA--AGAAAAAAAG
*
3076325 AAAAGAAGAAAAG
1 AAAAGAAAAAAAG
*
3076338 AAAAGAAAAAGAG
1 AAAAGAAAAAAAG
3076351 AA
1 AA
3076353 GTTCAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 25 0.68
14 3 0.08
15 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:3083072 original size:19 final size:20
Alignment explanation
Indices: 3083031--3083081 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3083021 GAAACCCCTT
*
3083031 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
3083051 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3083070 TGAAGATACATG
1 TGAAAATACATG
3083082 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3087271 original size:19 final size:20
Alignment explanation
Indices: 3087230--3087280 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3087220 GAAACCCCTT
*
3087230 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
3087250 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3087269 TGAAGATACATG
1 TGAAAATACATG
3087281 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3088253 original size:22 final size:20
Alignment explanation
Indices: 3088209--3088253 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
3088199 AAATGAAATG
*
3088209 AAAACATAATAAATTAATCT
1 AAAACATAATAAATTAATAT
*
3088229 AAAACATATGTAAATATAATAT
1 AAAACATA-ATAAAT-TAATAT
3088251 AAA
1 AAA
3088254 GCTAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAACATAATAAATTAATAT
Found at i:3089816 original size:6 final size:6
Alignment explanation
Indices: 3089807--3089865 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
3089797 CTCTTTTGAA
* * * *
3089807 TTTCTT TTTC-T TTTC-T TTTCTT TTTCTA ATTCTT CTT-TT TGTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
3089852 TTTC-T TTTCTT TTT
1 TTTCTT TTTCTT TTT
3089866 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
5 18 0.42
6 25 0.58
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:3089821 original size:11 final size:11
Alignment explanation
Indices: 3089807--3089865 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
3089797 CTCTTTTGAA
3089807 TTTCTTTT-TCT
1 TTTCTTTTCT-T
3089818 TTTCTTTTCTT
1 TTTCTTTTCTT
*
3089829 TTTCTAATTCTT
1 TTTCT-TTTCTT
*
3089841 CTTT-TTGTCTT
1 -TTTCTTTTCTT
3089852 TTTCTTTTCTT
1 TTTCTTTTCTT
3089863 TTT
1 TTT
3089866 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 3 0.08
11 27 0.68
12 7 0.17
13 3 0.08
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:3090149 original size:17 final size:19
Alignment explanation
Indices: 3090117--3090161 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
3090107 AAGAATAAGT
3090117 GAAAT-AATA-AAGAT-AA
1 GAAATGAATAGAAGATAAA
3090133 GAAATGAATAGAA-ATAAA
1 GAAATGAATAGAAGATAAA
3090151 GAAATG-ATAGA
1 GAAATGAATAGA
3090162 GATGGCTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (19 bp):
GAAATGAATAGAAGATAAA
Found at i:3090625 original size:19 final size:20
Alignment explanation
Indices: 3090581--3090635 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 20
3090571 GAAACCCCTT
3090581 TGAAAATACATGATTTTTAAAA
1 TGAAAATACATGA-TTTT-AAA
3090603 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
3090622 TGAAGATACATGAT
1 TGAAAATACATGAT
3090636 GGTTCAGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 15 0.47
21 4 0.12
22 13 0.41
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3090678 original size:80 final size:79
Alignment explanation
Indices: 3090545--3090712 Score: 291
Period size: 80 Copynumber: 2.1 Consensus size: 79
3090535 TAGGCCGAAT
*
3090545 AGATACATGATGGTTCGGCTATGGATGAAACCCCTTTGAAAATACATGATTTTTAAAATGAAAAT
1 AGATACATGATGGTTCAGCTATGGATGAAACCCCTTTGAAAATACATGATTTTT-AAATGAAAAT
*
3090610 ACATGATTTTAATGA
65 ACACGATTTTAATGA
*
3090625 AGATACATGATGGTTCAGCTATGGATGAAACCTCTTTGAAAATACATGATTTTTAAATGAAAATA
1 AGATACATGATGGTTCAGCTATGGATGAAACCCCTTTGAAAATACATGATTTTTAAATGAAAATA
3090690 CACGATTTTAATGA
66 CACGATTTTAATGA
*
3090704 ATATACATG
1 AGATACATG
3090713 CTCTTGGCTG
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
79 32 0.38
80 52 0.62
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (79 bp):
AGATACATGATGGTTCAGCTATGGATGAAACCCCTTTGAAAATACATGATTTTTAAATGAAAATA
CACGATTTTAATGA
Found at i:3090685 original size:21 final size:19
Alignment explanation
Indices: 3090661--3090712 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
3090651 GAAACCTCTT
3090661 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTT-AA
*
3090682 TGAAAATACACGATTTTAA
1 TGAAAATACATGATTTTAA
*
3090701 TGAATATACATG
1 TGAAAATACATG
3090713 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:3090704 original size:19 final size:21
Alignment explanation
Indices: 3090661--3090710 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3090651 GAAACCTCTT
*
3090661 TGAAAATACATGATTTTTAAA
1 TGAAAATACACGATTTTTAAA
3090682 TGAAAATACACGA-TTTT-AA
1 TGAAAATACACGATTTTTAAA
*
3090701 TGAATATACA
1 TGAAAATACA
3090711 TGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (21 bp):
TGAAAATACACGATTTTTAAA
Found at i:3095407 original size:16 final size:16
Alignment explanation
Indices: 3095389--3095420 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3095379 CTATGAACCA
3095389 TATAT-TTATA-TATT
1 TATATCTTATATTATT
3095403 TATATCTTATATTATT
1 TATATCTTATATTATT
3095419 TA
1 TA
3095421 GCTTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATCTTATATTATT
Found at i:3105169 original size:16 final size:17
Alignment explanation
Indices: 3105150--3105181 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3105140 TTTCATTCTT
3105150 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
3105166 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
3105182 ACTCTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:3106756 original size:2 final size:2
Alignment explanation
Indices: 3106739--3106782 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3106729 TCATAATAAC
*
3106739 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3106780 TA T
1 TA T
3106783 GAAAATAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3109255 original size:20 final size:21
Alignment explanation
Indices: 3109224--3109262 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3109214 GGTGGTGTGA
3109224 ATGATGGATGATAGAGTTGGC
1 ATGATGGATGATAGAGTTGGC
*
3109245 ATGAT-GATGATATAGTTG
1 ATGATGGATGATAGAGTTG
3109263 ATATGTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
ATGATGGATGATAGAGTTGGC
Found at i:3110354 original size:26 final size:25
Alignment explanation
Indices: 3110312--3110374 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
3110302 CTTGGCTTGC
3110312 TTTTCTCTTTTTGGAATCTTT-TTCT
1 TTTTCTCTTTTTGGAAT-TTTCTTCT
3110337 TTTTCTTCTTTTCT-GAATTTTCTTCT
1 TTTTC-TCTTTT-TGGAATTTTCTTCT
3110363 TTTGTC-CTTTTT
1 TTT-TCTCTTTTT
3110375 TTTGCACTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
24 1 0.03
25 13 0.38
26 17 0.50
27 3 0.09
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTTCTCTTTTTGGAATTTTCTTCT
Found at i:3110686 original size:19 final size:20
Alignment explanation
Indices: 3110629--3110678 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3110619 ATAATGGGTT
*
3110629 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
3110648 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
3110668 TAAG-AATGAAA
1 TAAGTAATGAAA
3110679 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:3114264 original size:8 final size:8
Alignment explanation
Indices: 3114251--3114278 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3114241 ATCTTTTTCT
3114251 TTTTCTTC
1 TTTTCTTC
3114259 TTTTCTTC
1 TTTTCTTC
3114267 TTTTCTTC
1 TTTTCTTC
3114275 TTTT
1 TTTT
3114279 GTCTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTC
Found at i:3114286 original size:16 final size:15
Alignment explanation
Indices: 3114242--3114286 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
3114232 CTTTTTGGAA
3114242 TCTTTTTCTTTTTCT
1 TCTTTTTCTTTTTCT
3114257 TC-TTTTCTTCTTTTCT
1 TCTTTTTC-T-TTTTCT
3114273 TCTTTTGTCTTTTT
1 TCTTTT-TCTTTTT
3114287 TTTTGCACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.19
15 3 0.12
16 12 0.46
17 4 0.15
18 2 0.08
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (15 bp):
TCTTTTTCTTTTTCT
Found at i:3114599 original size:19 final size:20
Alignment explanation
Indices: 3114542--3114591 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3114532 ATAATGGGTT
*
3114542 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
3114561 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
3114581 TAAG-AATGAAA
1 TAAGTAATGAAA
3114592 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:3118379 original size:19 final size:19
Alignment explanation
Indices: 3118355--3118409 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
3118345 AATTGGAGTG
3118355 CAAAAAGAAAGAAAAAAGA
1 CAAAAAGAAAGAAAAAAGA
3118374 CAAAAAG-AAGAAGAAAAGA
1 CAAAAAGAAAGAA-AAAAGA
3118393 -AGAAAAGAAAAGAAAAA
1 CA-AAAAG-AAAGAAAAA
3118410 GAATTCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.19
19 18 0.56
20 3 0.09
21 5 0.16
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (19 bp):
CAAAAAGAAAGAAAAAAGA
Found at i:3127561 original size:19 final size:20
Alignment explanation
Indices: 3127537--3127587 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3127527 CGGCCAAGAC
* *
3127537 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3127556 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3127576 CATGTATTTTCA
1 CATGTATTTTCA
3127588 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3137986 original size:19 final size:20
Alignment explanation
Indices: 3137962--3138012 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3137952 CGGCCAAGAG
* *
3137962 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3137981 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3138001 CATGTATTTTCA
1 CATGTATTTTCA
3138013 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3143167 original size:130 final size:131
Alignment explanation
Indices: 3142978--3143251 Score: 487
Period size: 130 Copynumber: 2.1 Consensus size: 131
3142968 TGTCACCTCT
3142978 TTGCATTTTGCTTTCTTTTTTTCCTTTCTTTAGTTTTTCTTCACTTGGAATCCCTTGTTGATGTT
1 TTGC-TTTTGCTTTCTTTTTTTCCTTTCTTTAGTTTTTCTTCACTTGGAATCCCTTGTTGATGTT
* * *
3143043 GTGATTAACTTGTTG-TTTTTTTTAGCACTTCTCTTTTTTATTTTCTTTTTATTGAATGGTAGGA
65 GGGATTAACTTGCTGATTTTTTTTAGCACTTCTCTTTTTGATTTTCTTTTTATTGAATGGTAGGA
3143107 TG
130 TG
3143109 TTGCTTTTGCTTTCTTTTTTTCCTTTCTTTAGTTTTTCTTCACTTGGAATCCCTTGTTGATGTTG
1 TTGCTTTTGCTTTCTTTTTTTCCTTTCTTTAGTTTTTCTTCACTTGGAATCCCTTGTTGATGTTG
*
3143174 GGATTAACTTGCTGATTTTTTTTTGCACTTCTCTTTTTGATTTTCTTTTTATTGAATGGTAGGAT
66 GGATTAACTTGCTGATTTTTTTTAGCACTTCTCTTTTTGATTTTCTTTTTATTGAATGGTAGGAT
3143239 G
131 G
*
3143240 TTACTTTTGCTT
1 TTGCTTTTGCTT
3143252 GTTATTGTTG
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
130 73 0.53
131 64 0.47
ACGTcount: A:0.12, C:0.14, G:0.15, T:0.58
Consensus pattern (131 bp):
TTGCTTTTGCTTTCTTTTTTTCCTTTCTTTAGTTTTTCTTCACTTGGAATCCCTTGTTGATGTTG
GGATTAACTTGCTGATTTTTTTTAGCACTTCTCTTTTTGATTTTCTTTTTATTGAATGGTAGGAT
G
Found at i:3148839 original size:23 final size:23
Alignment explanation
Indices: 3148794--3148839 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3148784 TTATACCTAT
*
3148794 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
3148817 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
3148840 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:3163353 original size:19 final size:20
Alignment explanation
Indices: 3163329--3163371 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3163319 AGCATTTATC
*
3163329 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
3163348 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
3163368 TTCA
1 TTCA
3163372 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:3166069 original size:13 final size:13
Alignment explanation
Indices: 3166047--3166076 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3166037 ACTAAACACC
3166047 TTTC-ACATACCT
1 TTTCAACATACCT
3166059 TTTCAACATACCT
1 TTTCAACATACCT
3166072 TTTCA
1 TTTCA
3166077 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Done.