Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 56
Found at i:2422440 original size:30 final size:29
Alignment explanation
Indices: 2422381--2422447 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
2422371 GTTACGATAT
* *
2422381 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
2422411 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
2422441 ATTTTTT
1 ATATTTT
2422448 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:2424297 original size:141 final size:136
Alignment explanation
Indices: 2424046--2424301 Score: 343
Period size: 140 Copynumber: 1.8 Consensus size: 136
2424036 CTGCCCTTCT
* **
2424046 GTTTCATTGAATCTTTTGTTAATTTTGCTTAATTTTGCATATTTTTATTGAGTGAAGATAAACAC
1 GTTTCATTGAATCTTTTGTTAATTTTGCTTAATTTTCCATATTTTTAACGAGTGAAGATAAACAC
*
2424111 TGAATTTAGTATTAGGATAGCTTGATTTTAATGGGTTTGATTTATTTTGACTGTTCCTTTTTTCT
66 TGAATTTAGTATTAGGATAACTTGATTTTAATGGGTTTGATTTATTTTGACTGTTCCTTTTTTCT
2424176 TCTCCC
131 TCTCCC
* **
2424182 GTTTCATTGAATCTTTTG-TAATTTTGCTTAATTTTCCATTCATATATGTTAACGAGTTATTATA
1 GTTTCATTGAATCTTTTGTTAATTTTGCTTAATTTTCCA-T-AT-T-T-TTAACGAGTGAAGATA
* * * * *
2424246 AACACTGGATTTAGTGTTAGGGTAACTTTGGTTTTGATGGGTTTGATTTATTTTGA
61 AACACTGAATTTAGTATTAGGATAAC-TTGATTTTAATGGGTTTGATTTATTTTGA
2424302 ATTTTGCTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
135 19 0.19
136 19 0.19
137 2 0.02
138 1 0.01
139 1 0.01
140 33 0.32
141 27 0.26
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (136 bp):
GTTTCATTGAATCTTTTGTTAATTTTGCTTAATTTTCCATATTTTTAACGAGTGAAGATAAACAC
TGAATTTAGTATTAGGATAACTTGATTTTAATGGGTTTGATTTATTTTGACTGTTCCTTTTTTCT
TCTCCC
Found at i:2424919 original size:20 final size:21
Alignment explanation
Indices: 2424894--2424933 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2424884 AATTTTTGGG
2424894 TCTGC-TTTGTTTCAATAAGT
1 TCTGCTTTTGTTTCAATAAGT
2424914 TCTGCTTTTGTTTCAATAAG
1 TCTGCTTTTGTTTCAATAAG
2424934 ACTTGAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (21 bp):
TCTGCTTTTGTTTCAATAAGT
Found at i:2430995 original size:21 final size:20
Alignment explanation
Indices: 2430971--2431224 Score: 314
Period size: 21 Copynumber: 12.2 Consensus size: 20
2430961 TACATATTTG
2430971 CGTTGCGATAG-TCCAAGTT
1 CGTTGCGATAGCTCCAAGTT
**
2430990 CGCGTTGCGAT-TTTCCAAGTT
1 --CGTTGCGATAGCTCCAAGTT
2431011 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
2431032 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
2431053 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
*
2431074 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAG-CTCCAAGTT
*
2431095 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAG-CTCCAAGTT
2431116 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
2431137 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
* *
2431158 CGTTGCGATAATCTCCAAATT
1 CGTTGCGAT-AGCTCCAAGTT
*
2431179 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAG-CTCCAAGTT
*
2431200 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAG-CTCCAAGTT
2431221 CGTT
1 CGTT
2431225 ATTGCATTTG
Statistics
Matches: 219, Mismatches: 9, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.04
20 1 0.00
21 208 0.95
22 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCTCCAAGTT
Found at i:2431049 original size:42 final size:42
Alignment explanation
Indices: 2430971--2431224 Score: 399
Period size: 42 Copynumber: 6.1 Consensus size: 42
2430961 TACATATTTG
*
2430971 CGTTGCGATAG--TCCAAGTTCGCGTTGCGAT--TTTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT--CGTTGCGATAGTCTCCAAGTT
2431011 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
*
2431053 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
*
2431095 CGTTGCGATAGTCTCCAACTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
* *
2431137 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAATCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
* *
2431179 CGTTGCGATAGTCTCCAACTTCGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
2431221 CGTT
1 CGTT
2431225 ATTGCATTTG
Statistics
Matches: 200, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
40 20 0.10
42 180 0.90
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (42 bp):
CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
Found at i:2431077 original size:63 final size:63
Alignment explanation
Indices: 2430971--2431224 Score: 399
Period size: 63 Copynumber: 4.1 Consensus size: 63
2430961 TACATATTTG
* *
2430971 CGTTGCGATAG--TCCAAGTTCGCGTTGCGAT--TTTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT--CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
2431032 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
* *
2431095 CGTTGCGATAGTCTCCAACTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
* * *
2431158 CGTTGCGATAATCTCCAAATTCGTTGCGATAGTCTCCAACTTCGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
2431221 CGTT
1 CGTT
2431225 ATTGCATTTG
Statistics
Matches: 181, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
61 20 0.11
63 161 0.89
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (63 bp):
CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAACTT
Found at i:2431950 original size:21 final size:21
Alignment explanation
Indices: 2431920--2432203 Score: 419
Period size: 21 Copynumber: 13.6 Consensus size: 21
2431910 TGCGATTTTG
* *
2431920 GACTAACGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
2431941 GACTATCGCAATGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
2431962 GACTATCGCAACGCACTTGGA
1 GACTATCGCAACGAACTTGGA
*
2431983 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
2432004 GACTATCGCAATGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
2432025 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
2432046 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
2432067 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
2432088 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
2432109 GACTATCACAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
2432130 GACTATCGCAACAAACTTGAA
1 GACTATCGCAACGAACTTGGA
*
2432151 GACTATCGCAACGCACTTGGA
1 GACTATCGCAACGAACTTGGA
2432172 GACTATCGCAACGAACTTGG-
1 GACTATCGCAACGAACTTGGA
*
2432192 GA-AATCGCAACG
1 GACTATCGCAACG
2432204 CGAAGTTGGA
Statistics
Matches: 242, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
19 9 0.04
20 2 0.01
21 231 0.95
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:2440466 original size:21 final size:21
Alignment explanation
Indices: 2440424--2440467 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2440414 CACTTGTTAG
* * * *
2440424 AGTCGGAAGAGAAGAGGGAGA
1 AGTCAGAAGAAAAAAGGAAGA
2440445 AGTCAGAAGAAAAAAGGAAGA
1 AGTCAGAAGAAAAAAGGAAGA
2440466 AG
1 AG
2440468 GAAGGAACAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.39, T:0.05
Consensus pattern (21 bp):
AGTCAGAAGAAAAAAGGAAGA
Found at i:2447821 original size:18 final size:18
Alignment explanation
Indices: 2447798--2447835 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2447788 TTAATTTTAT
2447798 TTTATAT-TAATTATAATA
1 TTTATATAT-ATTATAATA
*
2447816 TTTATATATATTATAGTA
1 TTTATATATATTATAATA
2447834 TT
1 TT
2447836 ATTATTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTATATATATTATAATA
Found at i:2447996 original size:2 final size:2
Alignment explanation
Indices: 2447989--2448027 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2447979 TTTATATTTT
2447989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2448028 TATTTTACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2448070 original size:68 final size:68
Alignment explanation
Indices: 2447924--2448083 Score: 171
Period size: 68 Copynumber: 2.3 Consensus size: 68
2447914 ATTTATATGT
* * * * * *
2447924 TATATTATATATATATATATATGTATGTATACATTTTATTTTATTTCTTAATATGTTTATATTTT
1 TATA-TATATATATATATATATATATATATACATATTATTTTACTTCTTAATATGTTTATATCTA
* *
2447989 TATA
65 CAAA
* *
2447993 TATATATATATATATATATATATATATATATATATTATTTTACTTCTTAATATTTTTTATAGTCT
1 TATATATATATATATATATATATATATATACATATTATTTTACTTCTTAATA-TGTTTATA-TCT
2448058 ACAAA
64 ACAAA
* *
2448063 T-TA-ATATATATGTAAATATAT
1 TATATATATATATATATATATAT
2448084 TTTCTTTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
68 59 0.77
69 13 0.17
70 5 0.06
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (68 bp):
TATATATATATATATATATATATATATATACATATTATTTTACTTCTTAATATGTTTATATCTAC
AAA
Found at i:2448291 original size:14 final size:13
Alignment explanation
Indices: 2448274--2448309 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
2448264 TGTTATTTAC
2448274 TTATTTTCTCTTCT
1 TTATTTTCT-TTCT
2448288 TTATTTTACTTTCT
1 TTATTTT-CTTTCT
2448302 TTATTTTC
1 TTATTTTC
2448310 AATTTATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.86
15 2 0.10
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTCTTTCT
Found at i:2449273 original size:4 final size:4
Alignment explanation
Indices: 2449266--2449291 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2449256 TCGTCATTTC
2449266 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2449292 TTATTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2451951 original size:24 final size:24
Alignment explanation
Indices: 2451924--2451971 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2451914 CGCAATGGAG
*
2451924 ATGACATGATATGGGGGAAATGAC
1 ATGACATGATACGGGGGAAATGAC
*
2451948 ATGATATGATACGGGGGAAATGAC
1 ATGACATGATACGGGGGAAATGAC
2451972 CAACTCCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (24 bp):
ATGACATGATACGGGGGAAATGAC
Found at i:2458379 original size:15 final size:16
Alignment explanation
Indices: 2458359--2458389 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2458349 CCTAAGTTGA
2458359 AAAAAAAGA-AAAAAC
1 AAAAAAAGAGAAAAAC
2458374 AAAAAAAGAGAAAAAC
1 AAAAAAAGAGAAAAAC
2458390 GTTTAGGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAC
Found at i:2458456 original size:68 final size:68
Alignment explanation
Indices: 2458324--2458456 Score: 164
Period size: 68 Copynumber: 2.0 Consensus size: 68
2458314 AATACTTCGC
* * * * *
2458324 TTAGGATGAAAACCCGAGAAGGTATCCTAAGTTGAAAAAAAAGAAAAAACAAAAAAAGAGAAAAA
1 TTAGGATGAAAACCCGAGAAGGCACCCTAAATTGAAAAAAAAGAAAAAACAAAAAAAAACAAAAA
2458389 CGT
66 CGT
*
2458392 TTAGGGTGAAAACCCGA-AAGGGCACCCTAAATTG-AAAAAAAGAAAAGAA-AAACAAAAAACAA
1 TTAGGATGAAAACCCGAGAA-GGCACCCTAAATTGAAAAAAAAGAAAA-AACAAA-AAAAAACAA
2458454 AAA
63 AAA
2458457 AAGAGAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
67 17 0.30
68 39 0.70
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.11
Consensus pattern (68 bp):
TTAGGATGAAAACCCGAGAAGGCACCCTAAATTGAAAAAAAAGAAAAAACAAAAAAAAACAAAAA
CGT
Found at i:2458484 original size:78 final size:79
Alignment explanation
Indices: 2458361--2458516 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 79
2458351 TAAGTTGAAA
* * *
2458361 AAAAAGAAAAAACAAAAAAAGAGAAAAACGTTTAGGGTGAAAACCCGAAAGGGCACCCTAAATTG
1 AAAAACAAAAAACAAAAAAAGAGAAAAACGTTTAGGGTGAAAACCCGAAAAGACACCCTAAATTG
2458426 AAAAAA-AGAAAAG
66 AAAAAAGAGAAAAG
* *
2458439 AAAAACAAAAAACAAAAAAAGAGAAAAATGTTTAGGGTGAAAACCCGAAAAGACGCCCTAAATTG
1 AAAAACAAAAAACAAAAAAAGAGAAAAACGTTTAGGGTGAAAACCCGAAAAGACACCCTAAATTG
2458504 AAAAAAGAGAAAA
66 AAAAAAGAGAAAA
2458517 AGAACCAAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
78 66 0.92
79 6 0.08
ACGTcount: A:0.61, C:0.12, G:0.18, T:0.10
Consensus pattern (79 bp):
AAAAACAAAAAACAAAAAAAGAGAAAAACGTTTAGGGTGAAAACCCGAAAAGACACCCTAAATTG
AAAAAAGAGAAAAG
Found at i:2461863 original size:57 final size:57
Alignment explanation
Indices: 2461779--2461900 Score: 151
Period size: 57 Copynumber: 2.1 Consensus size: 57
2461769 TATTTATTTA
*
2461779 TTTTATTTATATGTTATATTATATATATATATACATTTTATTTTA-TTGCTTAATATGT
1 TTTTATTTATATGTTATATTATATATATATATACATATTATTTTACTT-CTTAATAT-T
* * *
2461837 TTTTATTTTTAT-TTATA-TATTTTATATATATATATATTATTTTACTTCTTAATATT
1 TTTTATTTATATGTTATATTA-TATATATATATACATATTATTTTACTTCTTAATATT
2461893 TTTATATT
1 TTT-TATT
2461901 CTACAAGTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
56 6 0.11
57 38 0.67
58 13 0.23
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (57 bp):
TTTTATTTATATGTTATATTATATATATATATACATATTATTTTACTTCTTAATATT
Found at i:2461971 original size:11 final size:10
Alignment explanation
Indices: 2461952--2461987 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2461942 CTTTCCCCTC
2461952 ATTTTTATTT
1 ATTTTTATTT
2461962 ATTATTTATTT
1 ATT-TTTATTT
2461973 ATTTTTATTT
1 ATTTTTATTT
2461983 -TTTTT
1 ATTTTT
2461988 CGTATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.20
10 10 0.40
11 10 0.40
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:2468845 original size:9 final size:10
Alignment explanation
Indices: 2468824--2468854 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2468814 AGAACCTTTG
2468824 TTTTCATGTT
1 TTTTCATGTT
2468834 TTTTCATGTT
1 TTTTCATGTT
2468844 TTTTCAT-TT
1 TTTTCATGTT
2468853 TT
1 TT
2468855 ATTTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (10 bp):
TTTTCATGTT
Found at i:2476082 original size:17 final size:15
Alignment explanation
Indices: 2476045--2476075 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2476035 GATGTCTTTT
*
2476045 AAAATAATTTTAAGG
1 AAAATTATTTTAAGG
2476060 AAAATTATTTTAAGG
1 AAAATTATTTTAAGG
2476075 A
1 A
2476076 CAAAATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (15 bp):
AAAATTATTTTAAGG
Found at i:2476499 original size:19 final size:19
Alignment explanation
Indices: 2476477--2476523 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2476467 TATGAATGCA
* *
2476477 ACAATAATAAATGATATAT
1 ACAAAAATAAATGAAATAT
*
2476496 ACAAAAATGAATGAAATAT
1 ACAAAAATAAATGAAATAT
*
2476515 -CAAATATAA
1 ACAAAAATAA
2476524 TATCACAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (19 bp):
ACAAAAATAAATGAAATAT
Found at i:2479101 original size:17 final size:18
Alignment explanation
Indices: 2479081--2479123 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2479071 GTTAGTTAGC
*
2479081 TTAATTAACTAA-TTTAA
1 TTAATGAACTAACTTTAA
2479098 TTAATGAACTAACTTT-A
1 TTAATGAACTAACTTTAA
2479115 TTGAATGAA
1 TT-AATGAA
2479124 TTAAGGTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TTAATGAACTAACTTTAA
Found at i:2479177 original size:17 final size:17
Alignment explanation
Indices: 2479151--2479194 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2479141 AGTAGCTTAC
* *
2479151 TAAATCAACTAAGTTCA
1 TAAATGAACTAACTTCA
*
2479168 TAAATGAACT-ACTTCC
1 TAAATGAACTAACTTCA
2479184 TAAATGAACTA
1 TAAATGAACTA
2479195 GAAGCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (17 bp):
TAAATGAACTAACTTCA
Found at i:2479189 original size:16 final size:16
Alignment explanation
Indices: 2479136--2479194 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
2479126 AAGGTGCATG
* *
2479136 AATGAAGTAGCTTACTA
1 AATGAACTA-CTTCCTA
* * *
2479153 AATCAACTAAGTTCATA
1 AATGAACT-ACTTCCTA
2479170 AATGAACTACTTCCTA
1 AATGAACTACTTCCTA
2479186 AATGAACTA
1 AATGAACTA
2479195 GAAGCTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
16 15 0.45
17 17 0.52
18 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (16 bp):
AATGAACTACTTCCTA
Found at i:2481328 original size:45 final size:45
Alignment explanation
Indices: 2481279--2481378 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
2481269 TGGGTTTGGA
*
2481279 AATGGCTTTGCAAATTGTTG-GGCATTCTATTTTGCTAGTTTCGAC
1 AATGGCTTTGCAAATTGTCGAGGCATTC-ATTTTGCTAGTTTCGAC
* * * *
2481324 AATGGCTTTGCGAATTGTCGAGGTATTCCTTTTGCTGGTTTCGAC
1 AATGGCTTTGCAAATTGTCGAGGCATTCATTTTGCTAGTTTCGAC
2481369 AATGGCTTTG
1 AATGGCTTTG
2481379 AATTATTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (45 bp):
AATGGCTTTGCAAATTGTCGAGGCATTCATTTTGCTAGTTTCGAC
Found at i:2482684 original size:18 final size:18
Alignment explanation
Indices: 2482661--2482699 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2482651 TATGAATGGA
* *
2482661 GTTGCCATGGCAAGTGGT
1 GTTGCCACGACAAGTGGT
2482679 GTTGCCACGACAAGTGGT
1 GTTGCCACGACAAGTGGT
2482697 GTT
1 GTT
2482700 TCCGTGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.28
Consensus pattern (18 bp):
GTTGCCACGACAAGTGGT
Found at i:2485166 original size:3 final size:3
Alignment explanation
Indices: 2485135--2485203 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
2485125 ATTAGCATGC
* *
2485135 AAT AA- AAT AA- AAT AAT ATT AAT ACA- AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
*
2485178 AAT AAAT AAC AAT AAT AAT AAAT AAT
1 AAT -AAT AAT AAT AAT AAT -AAT AAT
2485204 GAAAAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
2 5 0.09
3 42 0.78
4 7 0.13
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2485191 original size:16 final size:16
Alignment explanation
Indices: 2485160--2485202 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2485150 TATTAATACA
*
2485160 AATAAT-AATAATAAT
1 AATAATAAATAACAAT
*
2485175 AGTAATAAATAACAAT
1 AATAATAAATAACAAT
2485191 AATAATAAATAA
1 AATAATAAATAA
2485203 TGAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AATAATAAATAACAAT
Found at i:2485887 original size:124 final size:123
Alignment explanation
Indices: 2485568--2485887 Score: 306
Period size: 124 Copynumber: 2.6 Consensus size: 123
2485558 TATAGTGAAG
* * * * * *
2485568 ATCTCACTCTTTCCTCTGAAAGACTTTGAGTCATGGGACGATCTTAC-TCATTCTTCTAAAGGAT
1 ATCTCACTATTTCCTTTGAAAGACATTGAGTCGTGGAACGATCTTACTTC-TTCCTC-AAAGGAT
* * * * *
2485632 GCTAAATCGTAATTGGTTGGTGATCCACTCCTTTTACTGAATGACGTTGAATATGGTGACA
64 GCTAAGTAGTAATTAG-TGGTGATCCACTCCTTTTACTGAATGACGCTAAATATGGTGACA
* ** * * * *
2485693 ATCTCACTATTT-CTTCTGAAATACGCTGAGTTGTGGAACGATCTTACTCCTTCCTCTTAAGGAC
1 ATCTCACTATTTCCTT-TGAAAGACATTGAGTCGTGGAACGATCTTACTTCTTCCTC-AAAGGAT
* * * * *
2485757 GTTAAGTAGTAATTCAG-GGTGATCCACT-CTTTTGGCTGAATGATGCTAAATCTGGTGACG
64 GCTAAGTAGTAATT-AGTGGTGATCCACTCCTTTT-ACTGAATGACGCTAAATATGGTGACA
* * *
2485817 GTCTCACTTTTTCCTTTGAAAGACATTGAGTCGTGGAACAATCTTACTTCTTCCTCAGAAGGATG
1 ATCTCACTATTTCCTTTGAAAGACATTGAGTCGTGGAACGATCTTACTTCTTCCTCA-AAGGATG
2485882 CTAAGT
65 CTAAGT
2485888 CATATTTGAA
Statistics
Matches: 156, Mismatches: 33, Indels: 13
0.77 0.16 0.06
Matches are distributed among these distances:
123 5 0.03
124 88 0.56
125 61 0.39
126 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (123 bp):
ATCTCACTATTTCCTTTGAAAGACATTGAGTCGTGGAACGATCTTACTTCTTCCTCAAAGGATGC
TAAGTAGTAATTAGTGGTGATCCACTCCTTTTACTGAATGACGCTAAATATGGTGACA
Found at i:2486246 original size:50 final size:50
Alignment explanation
Indices: 2486192--2486386 Score: 225
Period size: 50 Copynumber: 3.9 Consensus size: 50
2486182 TTTGTTGAAC
* *
2486192 AATGATATCACAT-AAAAGTTGACTCCTCTCCACGAGAAAGTCAAGTTGTG
1 AATGACATCA-ATGAAAAGTTGACTCCTCTCCACGAGAAAGTCAAGTTGAG
* * * *
2486242 AATGACATCACTGAAAAGTTGACTCCTCTTCGCAAGAAAGTCAAGTTGAG
1 AATGACATCAATGAAAAGTTGACTCCTCTCCACGAGAAAGTCAAGTTGAG
* * *
2486292 AATGACAT-AATCGAAAAATTAACTCCTCTTCGA-GAGAAAGTCAAGTTGAG
1 AATGACATCAAT-GAAAAGTTGACTCCTC-TCCACGAGAAAGTCAAGTTGAG
* * * *
2486342 AATGACATCATTGAAAAGTTGATTCCTCTTCGCGAGAAAGTCAAG
1 AATGACATCAATGAAAAGTTGACTCCTCTCCACGAGAAAGTCAAG
2486387 AATGGCATAA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 4 0.03
50 113 0.94
51 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (50 bp):
AATGACATCAATGAAAAGTTGACTCCTCTCCACGAGAAAGTCAAGTTGAG
Found at i:2486414 original size:45 final size:45
Alignment explanation
Indices: 2486198--2486521 Score: 190
Period size: 50 Copynumber: 6.9 Consensus size: 45
2486188 GAACAATGAT
* * *
2486198 ATCACATAAAAG-TTGACTCCTCTCCACGAGAAAGTCAAGTTGTGAATGAC
1 ATCAC-TAAAAGATTGACTCCTCTTCGCGAGAAAGTCAA-----GAATGGC
* *
2486248 ATCACTGAAAAG-TTGACTCCTCTTCGCAAGAAAGTCAAGTTGAGAATGAC
1 ATCACT-AAAAGATTGACTCCTCTTCGCGAGAAAGTC-A----AGAATGGC
* * * * *
2486298 ATAATCGAAAA-ATTAACTCCTCTTCGAGAGAAAGTCAAGTTGAGAATGAC
1 ATCA-CTAAAAGATTGACTCCTCTTCGCGAGAAAGTC-A----AGAATGGC
* *
2486348 ATCATTGAAAAG-TTGATTCCTCTTCGCGAGAAAGTCAAGAATGGC
1 ATCACT-AAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGC
* ** * * *
2486393 ATAACTAAAAGGCTAACTCCTCTTCCCGAGAAAGTCAATAA-GGAC
1 ATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGG-C
* * * * *
2486438 TTCACTAAAAGATTGACTCCTCTTTGCTAGAAAGTTAAGAATGAC
1 ATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGC
** * *
2486483 ATCACTATCATATTGACTCCTCTTCGCAAGAAAGTCAAG
1 ATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAG
2486522 TTGATTATGG
Statistics
Matches: 221, Mismatches: 40, Indels: 31
0.76 0.14 0.11
Matches are distributed among these distances:
44 7 0.03
45 100 0.45
46 1 0.00
49 2 0.01
50 108 0.49
51 2 0.01
55 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (45 bp):
ATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGC
Found at i:2488187 original size:26 final size:26
Alignment explanation
Indices: 2488130--2488202 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
2488120 AAAATGATTT
2488130 ATGAAA-AAGTTTTGAAAAATG-CTCG
1 ATGAAAGAA-TTTTGAAAAATGTCTCG
* *
2488155 ATAAAAGAATTTTTGAAAGATGTCT-G
1 ATGAAAGAA-TTTTGAAAAATGTCTCG
2488181 ATGAAAGAATTTTGAAAAATGT
1 ATGAAAGAATTTTGAAAAATGT
2488203 TATCCTGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 17 0.41
26 22 0.54
27 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (26 bp):
ATGAAAGAATTTTGAAAAATGTCTCG
Found at i:2488538 original size:19 final size:19
Alignment explanation
Indices: 2488502--2488552 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2488492 ATTAATTAAA
2488502 CATCGAATGCA-T-TCCATG
1 CATCG-ATGCACTCTCCATG
2488520 CA-CTGATGCACTCTCCATG
1 CATC-GATGCACTCTCCATG
2488539 CATCGATGCACTCT
1 CATCGATGCACTCT
2488553 GAATATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 18 0.62
20 1 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCCATG
Found at i:2488568 original size:65 final size:64
Alignment explanation
Indices: 2488451--2488660 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 64
2488441 TATTCAAAGG
* **
2488451 CATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATGAAT-TAATT-AAACATCGAATGCA
1 CATGCATCGATGCA-CAAG-CCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCA
*
2488513 TTC
62 TTT
*** *
2488516 CATGCA-CTGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCAT
1 CATGCATC-GATGCACAAGCCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCAT
2488579 TT
63 TT
* **
2488581 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
2488645 CATGCATCGATGCACA
1 CATGCATCGATGCACA
2488661 CTTGGTGCAC
Statistics
Matches: 123, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
63 6 0.05
64 54 0.44
65 62 0.50
66 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:2488675 original size:64 final size:64
Alignment explanation
Indices: 2488451--2488680 Score: 227
Period size: 64 Copynumber: 3.6 Consensus size: 64
2488441 TATTCAAAGG
* * *
2488451 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--AAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
2488513 TTC
62 TTT
* *
2488516 CATGCA-CTGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 CATGCATC-GATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATT
2488580 T
64 T
* ** **
2488581 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
2488645 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
2488681 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
63 6 0.04
64 70 0.50
65 62 0.45
66 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:2494468 original size:20 final size:21
Alignment explanation
Indices: 2494439--2494494 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2494429 TTTGTGCTTC
*
2494439 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
2494459 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
2494481 ATGCATCGATGCAT
1 ATGCATCGATGCAT
2494495 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:2496062 original size:21 final size:21
Alignment explanation
Indices: 2496020--2496063 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2496010 ACCCCGGGAG
*
2496020 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
2496041 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
2496062 CT
1 CT
2496064 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:2497115 original size:19 final size:19
Alignment explanation
Indices: 2497091--2497129 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2497081 TCGAATGCAT
2497091 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2497110 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2497129 T
1 T
2497130 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:2497123 original size:64 final size:64
Alignment explanation
Indices: 2497028--2497236 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
2497018 TATTCAAAGG
*
2497028 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATT-AAACATCGAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC-ATGAATTATTTCAAACATCGAATGCAT
*
2497091 TC
63 TT
2497093 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCAT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCATGAATTA-TTTC-AAACATCGAATGCAT
2497156 TT
63 TT
* * *** * *
2497158 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATT-TTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCATG-AATTATTTCAAACATCGAATGCATTT
*
2497222 CATGCATCGATGCAC
1 CATGCACCGATGCAC
2497237 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
62 2 0.02
63 6 0.05
64 49 0.39
65 65 0.52
66 3 0.02
67 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCATGAATTATTTCAAACATCGAATGCATTT
Found at i:2497252 original size:64 final size:64
Alignment explanation
Indices: 2497028--2497257 Score: 234
Period size: 64 Copynumber: 3.6 Consensus size: 64
2497018 TATTCAAAGG
* * *
2497028 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--AAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
2497090 TTC
62 TTT
* * *
2497093 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
2497158 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
2497222 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
2497258 AGTGTTCCAA
Statistics
Matches: 140, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.49
65 65 0.46
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:2503113 original size:3 final size:3
Alignment explanation
Indices: 2503092--2503149 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
2503082 AATAAAACAA
* ** *
2503092 AAT AAT ATT AAT ACG AAT AAT AAT AAT AAT -AT AAT AAAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
2503137 AAT AAT AAAT AAT
1 AAT AAT -AAT AAT
2503150 GAAAAATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2503154 original size:20 final size:21
Alignment explanation
Indices: 2503082--2503158 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 21
2503072 AATGGCTTGT
*
2503082 AATAAAACAAAATAATATTAATA
1 AATAAAA-ATAATAATA-TAATA
*
2503105 CGAATAATAATAATAATATAATA
1 --AATAAAAATAATAATATAATA
2503128 AATAAAAATAATAATA-AAT-
1 AATAAAAATAATAATATAATA
2503147 AATGAAAAATAA
1 AAT-AAAAATAA
2503159 ACCCAGACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.06
20 11 0.23
21 15 0.31
23 5 0.10
24 8 0.17
25 6 0.12
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (21 bp):
AATAAAAATAATAATATAATA
Found at i:2509183 original size:2 final size:2
Alignment explanation
Indices: 2509145--2509173 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2509135 TTTGAAATTT
2509145 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2509174 CTTCTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2510379 original size:15 final size:15
Alignment explanation
Indices: 2510361--2510393 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2510351 AAATTCTAAA
2510361 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
2510376 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
2510391 TAT
1 TAT
2510394 ATCTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2513971 original size:7 final size:7
Alignment explanation
Indices: 2513959--2514010 Score: 104
Period size: 7 Copynumber: 7.4 Consensus size: 7
2513949 AGTTAGAGGT
2513959 GAAACGA
1 GAAACGA
2513966 GAAACGA
1 GAAACGA
2513973 GAAACGA
1 GAAACGA
2513980 GAAACGA
1 GAAACGA
2513987 GAAACGA
1 GAAACGA
2513994 GAAACGA
1 GAAACGA
2514001 GAAACGA
1 GAAACGA
2514008 GAA
1 GAA
2514011 GCTCTCCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAACGA
Found at i:2514492 original size:14 final size:14
Alignment explanation
Indices: 2514474--2514516 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2514464 CATATTAAAT
2514474 AATAAATATAATTA
1 AATAAATATAATTA
* *
2514488 TATAACTATAATTA
1 AATAAATATAATTA
* *
2514502 AAAAAATAAAATTA
1 AATAAATATAATTA
2514516 A
1 A
2514517 GGCTTAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAATATAATTA
Found at i:2515430 original size:24 final size:24
Alignment explanation
Indices: 2515385--2515431 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2515375 TTTTTTAATA
* *
2515385 TAATAATATTACATATTTAATTAT
1 TAATAATATTACACATTAAATTAT
* *
2515409 TAATAATTTTATACATTAAATTA
1 TAATAATATTACACATTAAATTA
2515432 AACTAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAATATTACACATTAAATTAT
Found at i:2515508 original size:21 final size:22
Alignment explanation
Indices: 2515464--2515523 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
2515454 ACACTCAATG
2515464 TATG-TTTAATAATTAATATAA
1 TATGTTTTAATAATTAATATAA
2515485 TAT-TTTTAATAATATAAGT-T-A
1 TATGTTTTAATAAT-TAA-TATAA
*
2515506 TATGTTTT-TTAATTAATA
1 TATGTTTTAATAATTAATA
2515524 ATTTGAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 20 0.61
22 8 0.24
23 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TATGTTTTAATAATTAATATAA
Found at i:2517078 original size:28 final size:28
Alignment explanation
Indices: 2517046--2517099 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2517036 TCACTTAGCT
* *
2517046 AAACCATCCTCCCTGGCATTGGCACTCC
1 AAACCATCCACCCTAGCATTGGCACTCC
2517074 AAACCATCCACCCTAGCATTGGCACT
1 AAACCATCCACCCTAGCATTGGCACT
2517100 TCGACGAACA
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:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (28 bp):
AAACCATCCACCCTAGCATTGGCACTCC
Found at i:2519834 original size:36 final size:36
Alignment explanation
Indices: 2519794--2519866 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2519784 AGTTCTGGAA
*
2519794 TTAAGTGATAAAAGAATTAGCCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
2519830 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
2519866 T
1 T
2519867 ATAATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
Found at i:2520024 original size:17 final size:18
Alignment explanation
Indices: 2520002--2520035 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2519992 TGAAAAGAAT
2520002 TATTGATATG-ATAAAAC
1 TATTGATATGCATAAAAC
*
2520019 TATTGATGTGCATAAAA
1 TATTGATATGCATAAAA
2520036 AATGTTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (18 bp):
TATTGATATGCATAAAAC
Found at i:2522019 original size:43 final size:43
Alignment explanation
Indices: 2521958--2522249 Score: 471
Period size: 43 Copynumber: 6.8 Consensus size: 43
2521948 TTAATTACCG
* *
2521958 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAACC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
2522001 TTACAGTTCCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
2522044 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
2522087 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
2522130 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
2522173 TTACAGTT-TCCCAGGTTCCTTTGTTGTGTGCAATGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
2522215 TTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
1 TTACAGTTCCCCCAGGTC-CCTTTGCTGTGTGCAAG
2522250 TATAAGACCT
Statistics
Matches: 233, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
42 38 0.16
43 195 0.84
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2524200 original size:93 final size:92
Alignment explanation
Indices: 2523998--2524281 Score: 293
Period size: 93 Copynumber: 3.2 Consensus size: 92
2523988 ACAAAATGAA
* * * * *
2523998 ACTTTAGCGGCGTTTTTTAAACAAATGCCACAATAGAGTAGTAATTAGGGTTGTTTATTATGAAA
1 ACTTTAGCGGCGTTTTTTAAACAAA-CCCATAATAGAGTAGTAATTAGGGTTGTTTATTGTGGAG
** *
2524063 TTTTTCAACAAACATCGCGATAAAGAAT
65 TTTTTCAACAAACGCCGTGATAAAGAAT
* *
2524091 ACTTTAGCGGCATTTTTTAAACAAACACCATAATAGAGTAGTAATTAGGGTTGTTTATTGTGGTG
1 ACTTTAGCGGCGTTTTTTAAACAAAC-CCATAATAGAGTAGTAATTAGGGTTGTTTATTGTGGAG
* * *
2524156 TTTTTCAATAAATGCCGTAATAAAGAAT
65 TTTTTCAACAAACGCCGTGATAAAGAAT
* ** * *
2524184 ACTTTAGCGGTGTTTTTTGCACAAACGC-T-ATA-A-TAG----T---GTTGTTTATTGTGGCGT
1 ACTTTAGCGGCGTTTTTTAAACAAACCCATAATAGAGTAGTAATTAGGGTTGTTTATTGTGGAGT
2524238 TTTTCAACAAACGCCGTGATAAAGAAT
66 TTTTCAACAAACGCCGTGATAAAGAAT
* *
2524265 ACTTTAGCAGTGTTTTT
1 ACTTTAGCGGCGTTTTT
2524282 AGCATAAATG
Statistics
Matches: 167, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
81 56 0.34
84 1 0.01
88 3 0.02
89 1 0.01
90 3 0.02
91 1 0.01
92 1 0.01
93 101 0.60
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (92 bp):
ACTTTAGCGGCGTTTTTTAAACAAACCCATAATAGAGTAGTAATTAGGGTTGTTTATTGTGGAGT
TTTTCAACAAACGCCGTGATAAAGAAT
Found at i:2528554 original size:21 final size:21
Alignment explanation
Indices: 2528521--2528590 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
2528511 AGCCGAAAAT
*
2528521 GAAGC-GAGAGAAGCAGAGAGA
1 GAAGCAGAG-GAAGCACAGAGA
* * *
2528542 GAAGCAGTGGAAGAACAAAGA
1 GAAGCAGAGGAAGCACAGAGA
*
2528563 GAAGCAGAGGTAGCACAGAGA
1 GAAGCAGAGGAAGCACAGAGA
2528584 GAAGCAG
1 GAAGCAG
2528591 CATATCAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 38 0.95
22 2 0.05
ACGTcount: A:0.47, C:0.11, G:0.39, T:0.03
Consensus pattern (21 bp):
GAAGCAGAGGAAGCACAGAGA
Found at i:2529077 original size:84 final size:85
Alignment explanation
Indices: 2528989--2529153 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 85
2528979 AATTTAGATA
* * * *
2528989 TTTTGCGGCGTTTGTA-AAAAAACGCCGCTATATACCATACCTTTTGCGGCGTTTGTAT-GAAAA
1 TTTTGCGGAGTTTGTATAAAAAACGCCGCTATATAACAGA-CTTTTGCGGCGTCTGTATCGAAAA
2529052 ATGCCAC-ATAATATCTAAATT
65 ATGCCACTA-AATATCTAAATT
* * **
2529073 TTTTGTGGAGTTTTTATGTAAAACGCCGCTATATAACAGACTTTTGCGGCGTCTGTATCCGAAAA
1 TTTTGCGGAGTTTGTATAAAAAACGCCGCTATATAACAGACTTTTGCGGCGTCTGTAT-CGAAAA
2529138 ATGCCACTAAATATCT
65 ATGCCACTAAATATCT
2529154 TAACCATTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 30 0.43
85 19 0.28
86 19 0.28
87 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (85 bp):
TTTTGCGGAGTTTGTATAAAAAACGCCGCTATATAACAGACTTTTGCGGCGTCTGTATCGAAAAA
TGCCACTAAATATCTAAATT
Found at i:2529173 original size:84 final size:84
Alignment explanation
Indices: 2529006--2529223 Score: 212
Period size: 85 Copynumber: 2.6 Consensus size: 84
2528996 GCGTTTGTAA
* *
2529006 AAAAACGCCGCTATATACCATACCTTTTGCGGCGTTTGTAT--GAAAAATGCCACATAATATCTA
1 AAAAACGCCGCTATATAACAGA-CTTTTGCGGCGTTTGTATCCGAAAAATGCCACATAATATCTA
*** *
2529069 AATTTTTTGTGGAGTTTTTAT
65 AACCATTTGTCGAG-TTTTAT
* *
2529090 GTAAAACGCCGCTATATAACAGACTTTTGCGGCGTCTGTATCCGAAAAATGCCAC-TAAATATCT
1 -AAAAACGCCGCTATATAACAGACTTTTGCGGCGTTTGTATCCGAAAAATGCCACAT-AATATCT
*
2529154 TAACCATTTG-CGACG-TTTAT
64 AAACCATTTGTCGA-GTTTTAT
* * ** *
2529174 AAAAACGCTGCTATAGATGTAGACATTTTGCGGCGTTTGTATCCAAAAAA
1 AAAAACGCCGCTATATA-ACAGAC-TTTTGCGGCGTTTGTATCCGAAAAA
2529224 ACACCGTTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
83 14 0.13
84 26 0.23
85 45 0.41
86 26 0.23
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (84 bp):
AAAAACGCCGCTATATAACAGACTTTTGCGGCGTTTGTATCCGAAAAATGCCACATAATATCTAA
ACCATTTGTCGAGTTTTAT
Found at i:2531561 original size:2 final size:2
Alignment explanation
Indices: 2531554--2531590 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2531544 CTAACCCGAA
2531554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2531591 ATTTAGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2531843 original size:19 final size:19
Alignment explanation
Indices: 2531818--2531894 Score: 109
Period size: 19 Copynumber: 4.1 Consensus size: 19
2531808 TATGCATTGG
2531818 GCTATGAATTTGAAAATAA
1 GCTATGAATTTGAAAATAA
*
2531837 ACTATGAATTTGAAAATAA
1 GCTATGAATTTGAAAATAA
* * *
2531856 GCTATGAATCTGACAGTAA
1 GCTATGAATTTGAAAATAA
*
2531875 GCTATGAGTTTGAAAATAA
1 GCTATGAATTTGAAAATAA
2531894 G
1 G
2531895 TAATTAATCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (19 bp):
GCTATGAATTTGAAAATAA
Found at i:2531880 original size:38 final size:38
Alignment explanation
Indices: 2531818--2531912 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
2531808 TATGCATTGG
*
2531818 GCTATGAATTTGAAAATAAACTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAAACTATGAATTTGAAAATAA
* * * *
2531856 GCTATGAATCTGACAGTAAGCTATGAGTTTGAAAATAA
1 GCTATGAATCTGAAAATAAACTATGAATTTGAAAATAA
* *
2531894 G-TAATTAATCTGGAAATAA
1 GCT-ATGAATCTGAAAATAA
2531913 GTTATGGTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 1 0.02
38 46 0.98
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (38 bp):
GCTATGAATCTGAAAATAAACTATGAATTTGAAAATAA
Found at i:2531983 original size:12 final size:12
Alignment explanation
Indices: 2531956--2531999 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2531946 AAGTATTTAT
*
2531956 TATGAACATGGAA
1 TATGAAAAT-GAA
2531969 TATGAAAATGAA
1 TATGAAAATGAA
**
2531981 TATGTGAATGAA
1 TATGAAAATGAA
2531993 TATGAAA
1 TATGAAA
2532000 GTGGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.27
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:2533973 original size:20 final size:20
Alignment explanation
Indices: 2533950--2533998 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2533940 TTGAGTGGGG
* *
2533950 TATCAATACT-TAAGAGGCGA
1 TATCAATACTGTAAGA-CCAA
*
2533970 TATCGATACTGTAAGACCAA
1 TATCAATACTGTAAGACCAA
2533990 TATCAATAC
1 TATCAATAC
2533999 CATAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (20 bp):
TATCAATACTGTAAGACCAA
Found at i:2542742 original size:27 final size:26
Alignment explanation
Indices: 2542676--2542742 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
2542666 ATTTAAGTAT
*
2542676 ATTTATTATTAAAATAGTAATATAAA
1 ATTTATTATTAAAATAGTAAAATAAA
*
2542702 ACTTT-TTCGA-TAAAATATTAAAAGTAAA
1 A-TTTATT--ATTAAAATAGTAAAA-TAAA
2542730 ATTTATTATTAAA
1 ATTTATTATTAAA
2542743 TAATTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
26 4 0.12
27 21 0.64
28 8 0.24
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTTATTATTAAAATAGTAAAATAAA
Found at i:2556660 original size:21 final size:21
Alignment explanation
Indices: 2556634--2556673 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2556624 CCCGTTTACT
*
2556634 GCGATTGTGGCCACAGCGGGC
1 GCGATTGTGACCACAGCGGGC
2556655 GCGATTGTGACCACAGCGG
1 GCGATTGTGACCACAGCGG
2556674 ATATATCGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.40, T:0.15
Consensus pattern (21 bp):
GCGATTGTGACCACAGCGGGC
Found at i:2558916 original size:26 final size:26
Alignment explanation
Indices: 2558865--2558916 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2558855 TTTGTTTTTC
* * * *
2558865 TAAAATTTTATAAGTTTATGTTCTCT
1 TAAAACTTTATAAATTTATCTCCTCT
2558891 TAAAACTTTATAAATTTATCTCCTCT
1 TAAAACTTTATAAATTTATCTCCTCT
2558917 AACATAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (26 bp):
TAAAACTTTATAAATTTATCTCCTCT
Found at i:2561700 original size:12 final size:12
Alignment explanation
Indices: 2561671--2561748 Score: 77
Period size: 12 Copynumber: 6.5 Consensus size: 12
2561661 AAACAGAGAT
* *
2561671 ATCAGAAATCAA
1 ATCAGAATTCAG
*
2561683 AACAGAATTCAG
1 ATCAGAATTCAG
2561695 ATCAG-ATATCAG
1 ATCAGAAT-TCAG
*
2561707 AACAGAATTCAG
1 ATCAGAATTCAG
* *
2561719 ATCAGAAATCAT
1 ATCAGAATTCAG
*
2561731 AACAGAATTCAG
1 ATCAGAATTCAG
2561743 ATCAGA
1 ATCAGA
2561749 GATCATAATA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
11 2 0.04
12 48 0.92
13 2 0.04
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (12 bp):
ATCAGAATTCAG
Found at i:2561705 original size:24 final size:24
Alignment explanation
Indices: 2561671--2561779 Score: 155
Period size: 24 Copynumber: 4.5 Consensus size: 24
2561661 AAACAGAGAT
*
2561671 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* *
2561695 ATCAGATATCAGAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
2561719 ATCAGAAATCATAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
2561743 ATCAGAGATCATAATAGAATTCAA
1 ATCAGAAATCATAACAGAATTCAG
*
2561767 ATCGGAAATCATA
1 ATCAGAAATCATA
2561780 TAAAATATTC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:2566518 original size:3 final size:3
Alignment explanation
Indices: 2566510--2566556 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2566500 TATGAAATGC
2566510 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2566557 ATGTTATGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2566942 original size:12 final size:12
Alignment explanation
Indices: 2566923--2566962 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2566913 GCATTGTAGC
2566923 ACTGTTCATGGT
1 ACTGTTCATGGT
*
2566935 ATTGTTCAT--T
1 ACTGTTCATGGT
2566945 ACTGTTCATGGT
1 ACTGTTCATGGT
2566957 ACTGTT
1 ACTGTT
2566963 TATATCGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:2568429 original size:24 final size:24
Alignment explanation
Indices: 2568402--2568496 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
2568392 AAACGGAGAT
*
2568402 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
2568426 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
2568450 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
2568474 ATCAGAGATCATAATAGAATTCA
1 ATCAGAAATCAGAACAGAATTCA
2568497 AGTCGGAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:2568431 original size:12 final size:12
Alignment explanation
Indices: 2568402--2568479 Score: 68
Period size: 12 Copynumber: 6.5 Consensus size: 12
2568392 AAACGGAGAT
* *
2568402 ATCAGAAATCAA
1 ATCAGAATTCAG
*
2568414 AACAGAATTCAG
1 ATCAGAATTCAG
2568426 ATCAG-ATATCAG
1 ATCAGAAT-TCAG
* *
2568438 AACAGAATCCAG
1 ATCAGAATTCAG
*
2568450 ATCAGAAATCAG
1 ATCAGAATTCAG
* *
2568462 AACATAATTCAG
1 ATCAGAATTCAG
2568474 ATCAGA
1 ATCAGA
2568480 GATCATAATA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
11 2 0.04
12 46 0.92
13 2 0.04
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (12 bp):
ATCAGAATTCAG
Found at i:2568702 original size:19 final size:20
Alignment explanation
Indices: 2568675--2568713 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2568665 ATACAATGTC
2568675 GGAAATTAGAATCA-CTGTT
1 GGAAATTAGAATCATCTGTT
*
2568694 GGAAGTTAGAATCATCTGTT
1 GGAAATTAGAATCATCTGTT
2568714 ATTCAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
GGAAATTAGAATCATCTGTT
Found at i:2571861 original size:17 final size:18
Alignment explanation
Indices: 2571836--2571875 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2571826 TTTCCTAAAA
*
2571836 ATTTAAAATTATT-ATAT
1 ATTTTAAATTATTAATAT
*
2571853 ATTTTAAATTTTTAATAT
1 ATTTTAAATTATTAATAT
2571871 ATTTT
1 ATTTT
2571876 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAAATTATTAATAT
Found at i:2574150 original size:25 final size:25
Alignment explanation
Indices: 2574116--2574173 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
2574106 ATAATAATAC
2574116 AATAATTCAGAGTGATTAAAACATG
1 AATAATTCAGAGTGATTAAAACATG
2574141 AATAATTCAGAGTGATTAAAACATG
1 AATAATTCAGAGTGATTAAAACATG
2574166 AATAATTC
1 AATAATTC
2574174 GAAAGTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (25 bp):
AATAATTCAGAGTGATTAAAACATG
Found at i:2574203 original size:21 final size:21
Alignment explanation
Indices: 2574174--2574224 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2574164 TGAATAATTC
2574174 GAAAGTTTAGTGAGTAAATTAG
1 GAAA-TTTAGTGAGTAAATTAG
2574196 GAAATTTAGTGAGTAAATTAG
1 GAAATTTAGTGAGTAAATTAG
*
2574217 TAAATTTA
1 GAAATTTA
2574225 AAAATACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (21 bp):
GAAATTTAGTGAGTAAATTAG
Found at i:2575073 original size:30 final size:30
Alignment explanation
Indices: 2575016--2575088 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
2575006 GGATTAATTT
* * *
2575016 TTAATTTTACCTCTAAATTTTAGATAAAATA
1 TTAATTTAACC-CTAAACTTTAAATAAAATA
2575047 TTAATTTAACCCTAAACTTTAAATAAAATA
1 TTAATTTAACCCTAAACTTTAAATAAAATA
*
2575077 TTATTTTAACCC
1 TTAATTTAACCC
2575089 ATATCAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 28 0.74
31 10 0.26
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.42
Consensus pattern (30 bp):
TTAATTTAACCCTAAACTTTAAATAAAATA
Found at i:2579137 original size:25 final size:25
Alignment explanation
Indices: 2579105--2579161 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
2579095 AAATTGAAAT
*
2579105 AAAATCATTACTTTACATAAAATAA
1 AAAATCATTACTTCACATAAAATAA
2579130 AAAATCATTACTTCACATAAAATAA
1 AAAATCATTACTTCACATAAAATAA
*
2579155 AACATCA
1 AAAATCA
2579162 CAGCATTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATCATTACTTCACATAAAATAA
Found at i:2581069 original size:12 final size:12
Alignment explanation
Indices: 2581054--2581079 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2581044 TTTAGAATAT
2581054 TTCATATAATCA
1 TTCATATAATCA
2581066 TTCATATAATCA
1 TTCATATAATCA
2581078 TT
1 TT
2581080 GATAACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (12 bp):
TTCATATAATCA
Found at i:2581317 original size:79 final size:79
Alignment explanation
Indices: 2581186--2581345 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 79
2581176 TATTTAACTA
*
2581186 TTAAGTAATCATCACATAATTAGTTCTTACTTATCATTATAACGTAATATGTGAGATAAATATGT
1 TTAAGTAATCATCACATAATTAGTTATTACTTATCATTATAACGTAATATGTGAGATAAATATGT
2581251 AATATTTAATTTTT
66 AATATTTAATTTTT
2581265 TTAAGTAATCATCACATAATTAGTTATTACTTATCATTATAACGTAATATGTGAGATAAATATGT
1 TTAAGTAATCATCACATAATTAGTTATTACTTATCATTATAACGTAATATGTGAGATAAATATGT
2581330 AATATTTAATTTTT
66 AATATTTAATTTTT
2581344 TT
1 TT
2581346 TCTCGTAATT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (79 bp):
TTAAGTAATCATCACATAATTAGTTATTACTTATCATTATAACGTAATATGTGAGATAAATATGT
AATATTTAATTTTT
Found at i:2581517 original size:2 final size:2
Alignment explanation
Indices: 2581510--2581605 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
2581500 TAAAAATTGA
2581510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2581552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2581594 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2581606 GAAATTACAC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2587334 original size:2 final size:2
Alignment explanation
Indices: 2587327--2587384 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
2587317 CATTTCTAAC
* * * *
2587327 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AC AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2587369 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2587385 GTTTGTTGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2587384 original size:20 final size:20
Alignment explanation
Indices: 2587327--2587375 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
2587317 CATTTCTAAC
2587327 ATATATATACATACATATAT
1 ATATATATACATACATATAT
2587347 ATATATATACATACATATAT
1 ATATATATACATACATATAT
2587367 ATATATATA
1 ATATATATA
2587376 TATATATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATATATACATACATATAT
Found at i:2588128 original size:21 final size:21
Alignment explanation
Indices: 2588102--2588146 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2588092 GATTTCTGGG
* *
2588102 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2588123 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2588144 CAA
1 CAA
2588147 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2589893 original size:23 final size:22
Alignment explanation
Indices: 2589834--2589900 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
2589824 TATGGACATC
*
2589834 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2589856 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2589878 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
2589901 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:2592998 original size:21 final size:21
Alignment explanation
Indices: 2592972--2593016 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2592962 GATTTCTGGG
* *
2592972 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2592993 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2593014 CAA
1 CAA
2593017 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2594766 original size:23 final size:22
Alignment explanation
Indices: 2594707--2594773 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
2594697 TATGGACATC
*
2594707 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2594729 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2594751 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
2594774 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:2598863 original size:35 final size:35
Alignment explanation
Indices: 2598815--2598882 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2598805 CAGCCTGCCT
* * *
2598815 CGGAGGATTACGATTCGATGTCACTTGGGTTCTAG
1 CGGAGGATGACGATTCAATATCACTTGGGTTCTAG
*
2598850 CGGAGGATGACGATTCAATATCGCTTGGGTTCT
1 CGGAGGATGACGATTCAATATCACTTGGGTTCT
2598883 GGGATGGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.31
Consensus pattern (35 bp):
CGGAGGATGACGATTCAATATCACTTGGGTTCTAG
Found at i:2599802 original size:7 final size:7
Alignment explanation
Indices: 2599790--2599824 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2599780 GTTGTGATAG
2599790 ACTCTTC
1 ACTCTTC
2599797 ACTCTTC
1 ACTCTTC
2599804 ACTCTTC
1 ACTCTTC
* *
2599811 ATTCTCC
1 ACTCTTC
2599818 ACTCTTC
1 ACTCTTC
2599825 TTTTAACTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
ACTCTTC
Found at i:2601722 original size:18 final size:18
Alignment explanation
Indices: 2601675--2601724 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
2601665 ATTTTAATTT
2601675 ATTTATTATTTTAATTAAA
1 ATTTA-TATTTTAATTAAA
* *
2601694 CTTAAATATTTTAATTAAA
1 ATT-TATATTTTAATTAAA
2601713 ATTTATATTTTA
1 ATTTATATTTTA
2601725 TTTGAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATATTTTAATTAAA
Found at i:2603628 original size:15 final size:17
Alignment explanation
Indices: 2603599--2603631 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2603589 AAATATTATT
2603599 TTATTATTTATTATAAA
1 TTATTATTTATTATAAA
2603616 TTATT-TTTA-TATAAA
1 TTATTATTTATTATAAA
2603631 T
1 T
2603632 AATAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTATTTATTATAAA
Found at i:2603639 original size:25 final size:25
Alignment explanation
Indices: 2603579--2603641 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
2603569 TTTCAAATTT
*
2603579 AATAATAATAAAATATTATTTTATT
1 AATAATAATAAAATATTATTTTATA
* * * *
2603604 ATTTATTATAAATTATT-TTTATATA
1 AATAATAATAAAATATTATTT-TATA
2603629 AATAATAATAAAA
1 AATAATAATAAAA
2603642 ATTCACATTA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATAATAATAAAATATTATTTTATA
Found at i:2611299 original size:3 final size:3
Alignment explanation
Indices: 2611293--2611365 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
2611283 TTTTTTTTTT
2611293 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
2611341 GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG G
2611366 GGGGGGGGGC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:2612512 original size:17 final size:17
Alignment explanation
Indices: 2612478--2612527 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
2612468 CTATGCAAAT
2612478 AAAAA-TTAAAATATTA
1 AAAAATTTAAAATATTA
2612494 AAAAATTTAAAAT-TCTA
1 AAAAATTTAAAATAT-TA
*
2612511 AAACATTTTAAAA-ATTA
1 AAA-AATTTAAAATATTA
2612528 TTTATTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.21
17 14 0.48
18 9 0.31
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTTAAAATATTA
Found at i:2612597 original size:18 final size:18
Alignment explanation
Indices: 2612563--2612598 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2612553 TACTAAATAT
2612563 TATTATAAAATTGTTAAA
1 TATTATAAAATTGTTAAA
2612581 TATTACTAAAATT-TTAAA
1 TATTA-TAAAATTGTTAAA
2612599 AACCTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTATAAAATTGTTAAA
Found at i:2612998 original size:21 final size:21
Alignment explanation
Indices: 2612961--2613011 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2612951 GTATTTTAAA
* *
2612961 AATATTTTT-ACTAATTATTT
1 AATATTTTTAAATAATTATGT
*
2612981 AATATTTTTAAATGATTATGT
1 AATATTTTTAAATAATTATGT
*
2613002 GATATTTTTA
1 AATATTTTTA
2613012 TATTTCTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
AATATTTTTAAATAATTATGT
Found at i:2613310 original size:2 final size:2
Alignment explanation
Indices: 2613303--2613343 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2613293 TTATTTTATT
2613303 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2613344 GGAAAATGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2613477 original size:20 final size:21
Alignment explanation
Indices: 2613431--2613478 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2613421 ATTGAGTATT
*
2613431 TGAATTAAATAATATTAATTA
1 TGAATAAAATAATATTAATTA
*
2613452 TAAATAAAATAA-ATTAAGTTA
1 TGAATAAAATAATATTAA-TTA
2613473 -GAATAA
1 TGAATAA
2613479 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (21 bp):
TGAATAAAATAATATTAATTA
Found at i:2615020 original size:23 final size:23
Alignment explanation
Indices: 2614994--2615050 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
2614984 ATCAAGTATA
*
2614994 ATAATATAATAGGTAACGCTTAT
1 ATAATATAATAGATAACGCTTAT
* *
2615017 ATAATGTAATAGATAGCGCTTAT
1 ATAATATAATAGATAACGCTTAT
*
2615040 ATAATAAAATA
1 ATAATATAATA
2615051 TGTTAATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGATAACGCTTAT
Found at i:2615178 original size:23 final size:23
Alignment explanation
Indices: 2615152--2615201 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2615142 ATCAAACACA
*
2615152 ATAACATATTAGGTAGCGCTTAG
1 ATAACATAATAGGTAGCGCTTAG
* *
2615175 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAG
2615198 ATAA
1 ATAA
2615202 TAAAATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAG
Found at i:2615208 original size:23 final size:23
Alignment explanation
Indices: 2615152--2615208 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
2615142 ATCAAACACA
* *
2615152 ATAACATATTAGGTAGCGCTTAG
1 ATAACAAAATAGGTAGCGCTTAG
** *
2615175 ATAACGTAATAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCTTAG
*
2615198 ATAATAAAATA
1 ATAACAAAATA
2615209 TGTTAATTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCGCTTAG
Found at i:2615272 original size:158 final size:158
Alignment explanation
Indices: 2614993--2615331 Score: 545
Period size: 158 Copynumber: 2.1 Consensus size: 158
2614983 AATCAAGTAT
* * * * *
2614993 AATAATATAATAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATATGTTAAT
1 AATAACATATTAGGTAGCGCTTAGATAACGTAATAGATAGCGCTTATATAATAAAATATGTTAAT
* *
2615058 TACTTAATTTGTTATTACAACATATTAGGTAAACACTTAAAATGTTACCAAGGATAACATAACCG
66 TACTTAATTTATTATTACAACATATTAGGTAAACACTTAAAATGTTACCAAGGATAACATAACCA
* *
2615123 GTTAATTAATGGAAACATTATCAAACAC
131 ATTAATTAATAGAAACATTATCAAACAC
*
2615151 AATAACATATTAGGTAGCGCTTAGATAACGTAATAGGTAGCGCTTATATAATAAAATATGTTAAT
1 AATAACATATTAGGTAGCGCTTAGATAACGTAATAGATAGCGCTTATATAATAAAATATGTTAAT
* *
2615216 TACTTAATTTATTATTACAACATATTAGGTAAAC-GTCTAAAATGTTACCAAGGATAATATAACC
66 TACTTAATTTATTATTACAACATATTAGGTAAACACT-TAAAATGTTACCAAGGATAACATAACC
*
2615280 AATTAATTACTAGAAACATTATCAAACAC
130 AATTAATTAATAGAAACATTATCAAACAC
2615309 AATAACATATTAGGTAGCGCTTA
1 AATAACATATTAGGTAGCGCTTA
2615332 TATTAGGTAA
Statistics
Matches: 167, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
157 1 0.01
158 166 0.99
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (158 bp):
AATAACATATTAGGTAGCGCTTAGATAACGTAATAGATAGCGCTTATATAATAAAATATGTTAAT
TACTTAATTTATTATTACAACATATTAGGTAAACACTTAAAATGTTACCAAGGATAACATAACCA
ATTAATTAATAGAAACATTATCAAACAC
Found at i:2615350 original size:94 final size:94
Alignment explanation
Indices: 2615237--2615426 Score: 292
Period size: 94 Copynumber: 2.0 Consensus size: 94
2615227 TTATTACAAC
** *
2615237 ATATTAGGTAAACGTCTAAAATGTTACCAAGGATAATATAACCAATTAATTACTAG-AAACATTA
1 ATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAACCAATTAATTACT-GTAAACATTA
*
2615301 TCAAACACAATAACATATTAGGTAGCGCTT
65 TCAAACACAATAACATATTAGGTAGAGCTT
**
2615331 ATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGTAAACATTAT
1 ATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAACCAATTAATTACTGTAAACATTAT
* *
2615396 CAAGCATAATAACATATTAGGTAGAGCTT
66 CAAACACAATAACATATTAGGTAGAGCTT
2615425 AT
1 AT
2615427 GTAACATAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 1 0.01
94 86 0.99
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (94 bp):
ATATTAGGTAAACACCTAAAATGTTACCAAGGATAACATAACCAATTAATTACTGTAAACATTAT
CAAACACAATAACATATTAGGTAGAGCTT
Found at i:2617951 original size:21 final size:21
Alignment explanation
Indices: 2617927--2617966 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2617917 CATGCGTAAT
2617927 TTTAAAAAATATCGATACAAA
1 TTTAAAAAATATCGATACAAA
* *
2617948 TTTAAAAAGTGTCGATACA
1 TTTAAAAAATATCGATACA
2617967 TTATGTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTAAAAAATATCGATACAAA
Found at i:2620672 original size:199 final size:199
Alignment explanation
Indices: 2620306--2621065 Score: 1073
Period size: 198 Copynumber: 3.8 Consensus size: 199
2620296 GTAAATTAAG
* * * * * *
2620306 GTATCGACACAAATTTGAAAAGCGTCGATACATTATTTTGACCTATTCTCTCATAAAACC-GATA
1 GTATCGACAC-AATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAAT-TAACCTGATA
* * * ** *
2620370 TATTTCTACCGATTACATTGTAAATTTACCTATTATATTATAATTATCCATTTTGATGTTTTTGG
64 TATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* *
2620435 GGTCGATAATTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTCATTCATACTGGA
129 GGTCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTCATTCATTCTGGA
2620500 CAAAAA
194 CAAAAA
* * *
2620506 GTATCGACACAATTTTAAAAGTGTTGATACATTATGTTGACGTATTTTCTAATTAACCTG-TATA
1 GTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCTGATATA
* * * *
2620570 TTTCTACAGGTTACATTATACATTTACCTATTACATTATAATTATCGGTTTCCGATGTTTTTAGG
66 TTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTT-CGATGTTTTTGGG
* * * * *
2620635 GTTGATACTTTTAATAAATGTATCGGCACTTTATGCGTGCACCTCGTTTGACATTTATTCTGGGC
130 GTCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTCATTCATTCTGGAC
2620700 AAAAA
195 AAAAA
*
2620705 GTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATT-ATCTGATATA
1 GTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCTGATATA
* *
2620769 TTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATGATTGGTTTCGATGTTTTTGGGG
66 TTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGG
* *
2620834 TCGATACTTTTAATAAATGTATCGACACTTTACGCGTGCACCTCGTTTGTGATTCATTCTGGACA
131 TCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTCATTCATTCTGGACA
2620899 AAAA
196 AAAA
* * * *
2620903 GTATCAACACAATTTAAAAAGTGTCGATACATTATGTTAACCTAATTTCTAATTAACCAG-TATA
1 GTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCTGATATA
* *
2620967 TTTCTACTGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTTTTGGGA
66 TTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGG
* * *
2621032 TTGATACAATTTTAA-AAAT-TATTGATACTTTATG
131 TCGATAC--TTTTAATAAATGTATCGACACTTTATG
2621066 TTTACCTATT
Statistics
Matches: 500, Mismatches: 54, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
198 265 0.53
199 219 0.44
200 16 0.03
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (199 bp):
GTATCGACACAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCTGATATA
TTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGG
TCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTCATTCATTCTGGACA
AAAA
Found at i:2622646 original size:394 final size:398
Alignment explanation
Indices: 2621906--2622705 Score: 1239
Period size: 394 Copynumber: 2.0 Consensus size: 398
2621896 TGTCATGTAC
* *
2621906 GTCTATTGTCATTGCACCGGTAGAATTTTACCGTTTACATTGATAATTTAGCAAAGTATCGACAG
1 GTCTATTATCATTGCACCAGTAGAATTTTACCGTTTACATTGATAATTTAGCAAAGTATCGACAG
**
2621971 TTTATACACGAGTACCCTTCAATTATTTTTGTTATTATTACAAGTTGTAGCCCTCAATTATCGGG
66 TTTATACACGAGTACCCTTCAATTATTTTTGTTATTATTACAAGTTGTAGCCCTCAATTATCAAG
* * * *
2622036 ATTTTTGGTTGCCCATTGTTACATTTCCCGTATACCATCTAGATTATACGTCCGAACCATTTCTG
131 ATTTTTAGTTACCCATTGTTACATTTCCCGTATACCATCCAGATCATACGTCCG-A--A----T-
* *
2622101 ACGCTTTAACTGTTTGAGAACCAAATGCATCACCGTTGAGATTTTAAATTTGCAGCTGCTTTTAC
188 ACGCTTTAACTGTTTGAGAACCAAATGCATCACCGTTGAGATTTTAAATCTGCAGCTGCTCTTAC
*
2622166 ATCAAGTATGTTTCACTAAGACGGTTTCAATTTAGGGTTAACCTATCTCAATAAGCTAGATGAAA
253 ATCAAGTATGTTTCACTAAGACGGTTTCAATTTAAGGTTAACCTATCTCAATAAGCTAGATGAAA
* *
2622231 TGGATAATATCCGAAAGGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACCAAAAATTAGGA
318 TGGATAATATCCGAAAGGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACAAAAAATTACGA
2622296 TGGTCGGGATTTCCCT
383 TGGTCGGGATTTCCCT
** *
2622312 GTCTATTATCATTGCACCAGTAGAATTTTACCGTTTACATTTTTAATTTAGCAAAGTATCGATAG
1 GTCTATTATCATTGCACCAGTAGAATTTTACCGTTTACATTGATAATTTAGCAAAGTATCGACAG
* *
2622377 TTTATACACGTGTACCCTTCAATTATTTTT-TTATTATTACAAGTTGTAGCCCTCAATTATCAAT
66 TTTATACACGAGTACCCTTCAATTATTTTTGTTATTATTACAAGTTGTAGCCCTCAATTATCAAG
* *
2622441 ATTTTTAGTTACCCTTTGTTACATTTCCCGTATACCA-CCAGATCATACGTCTG-A-ACGCTTTA
131 ATTTTTAGTTACCCATTGTTACATTTCCCGTATACCATCCAGATCATACGTCCGAATACGCTTTA
* *
2622503 ACTGTTTGATAACCAAATGCATCATCGTTGAGATTTTAAATCTGCAGCTGCTCTTACATCAAGTA
196 ACTGTTTGAGAACCAAATGCATCACCGTTGAGATTTTAAATCTGCAGCTGCTCTTACATCAAGTA
* * * * *
2622568 TGTTTCACTAAGATGGTTTCAGTTTAAGGTTAACCTATCTCGATTAGCTGGATGAAATGGATAAT
261 TGTTTCACTAAGACGGTTTCAATTTAAGGTTAACCTATCTCAATAAGCTAGATGAAATGGATAAT
* *
2622633 ATCCGAAAGGCATTCTTCTGATATCCAATCTTCCTGCTTGTTAACAAAAAATTACGATGGTCGGG
326 ATCCGAAAGGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACAAAAAATTACGATGGTCGGG
2622698 ATTTCCCT
391 ATTTCCCT
2622706 CGCGTTTAAA
Statistics
Matches: 365, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
394 197 0.54
400 1 0.00
404 13 0.04
405 65 0.18
406 89 0.24
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (398 bp):
GTCTATTATCATTGCACCAGTAGAATTTTACCGTTTACATTGATAATTTAGCAAAGTATCGACAG
TTTATACACGAGTACCCTTCAATTATTTTTGTTATTATTACAAGTTGTAGCCCTCAATTATCAAG
ATTTTTAGTTACCCATTGTTACATTTCCCGTATACCATCCAGATCATACGTCCGAATACGCTTTA
ACTGTTTGAGAACCAAATGCATCACCGTTGAGATTTTAAATCTGCAGCTGCTCTTACATCAAGTA
TGTTTCACTAAGACGGTTTCAATTTAAGGTTAACCTATCTCAATAAGCTAGATGAAATGGATAAT
ATCCGAAAGGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACAAAAAATTACGATGGTCGGG
ATTTCCCT
Found at i:2622929 original size:24 final size:24
Alignment explanation
Indices: 2622910--2622958 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2622900 CGAAATTTAT
2622910 ATTAAAATTAAAACTCAAATTGAA
1 ATTAAAATTAAAACTCAAATTGAA
* * *
2622934 ATTTAAATTCAAACTCGAATT-AA
1 ATTAAAATTAAAACTCAAATTGAA
2622957 AT
1 AT
2622959 ATGAAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTAAAATTAAAACTCAAATTGAA
Found at i:2622965 original size:24 final size:24
Alignment explanation
Indices: 2622914--2622965 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2622904 ATTTATATTA
*
2622914 AAATTAAAACTCAAATTGAAATTT
1 AAATTAAAACTCAAATTGAAATTG
* *
2622938 AAATTCAAACTCGAATT-AAATATG
1 AAATTAAAACTCAAATTGAAAT-TG
2622962 AAAT
1 AAAT
2622966 GAACATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATTAAAACTCAAATTGAAATTG
Found at i:2624370 original size:3 final size:3
Alignment explanation
Indices: 2624362--2624394 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2624352 ACTTGTTTGG
2624362 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2624395 TACATCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:2626232 original size:199 final size:198
Alignment explanation
Indices: 2625892--2627256 Score: 1937
Period size: 199 Copynumber: 6.9 Consensus size: 198
2625882 CGTAATATAA
* * * *
2625892 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTAGGTAGACCTATTTTCTCTTAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-T
**
2625957 GAAATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
*
2626022 TTGGGATCGATACAATTTTACATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
2626087 GGAC
195 GGAC
*
2626091 AAAAAGTATCGACACAAATTTAAAAAGCGTCGATACATTATGTAGACCTATTTTCTCATAAAATA
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAT-
* * ** * *
2626156 GGTATATTTATATCAGTTACATCATAAATTTACCTATTACATTATAATTATTGGTTTCAATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
2626221 TTGGGATCGATACAATTTCAAATGTATCAACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
*
2626286 AGAC
195 GGAC
*
2626290 AAAAAGTACCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-T
*
2626355 GGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
2626420 TTAGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTCATTGGGCATTCATTCT
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
2626485 GGAC
195 GGAC
* * *
2626489 AAAACGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-T
*
2626554 GGTATATTTATACCGGTTACATTGTAAATTTACCCATTACATTATAATTATCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
2626619 TTGGGATCAATACATTTTTAAATGTATCGACACTTTATGCGTGAACCTCGTTGGGCATTCATTCT
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
2626684 GGAC
195 GGAC
* * * * * *
2626688 AAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTTGACTTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-T
* **
2626753 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
2626818 TTGGGATTGATAC--TTTAATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGTCATTCATT
130 TTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATT
*
2626881 CGGGAC
193 CTGGAC
* * * * * *
2626887 AAAATGTATCAACACAAATTTAGAAAGTGTCGATACATTATGTTGACATATTCTCTCATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-T
* * * * * * *
2626952 GGTATATTTATATCAGTTACATTGTAAAATTACCTATTATATTATAAGTATCAGTTTCAATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * ** * * *
2627017 TTGGAATCGATAC-TTTTAATAAATGTATCGACACTTTATGCATGCACCTAGTTTGTCATTCATT
130 TTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATT
*
2627081 CTGGAT
193 CTGGAC
* * * * *
2627087 AAAATGTATTGACACAAATTTAGAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAT-
* * *
2627152 GGTATATTTATACCGGTTACTTTGTAAATTTACTTATTACATTATAATTATTGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
*
2627217 TTTGGATCGATACAATTTTAAATGTATCGAC-CTTTTATGT
130 TTGGGATCGATACAATTTTAAATGTATCGACAC-TTTATGT
2627257 TGACCTATTT
Statistics
Matches: 1064, Mismatches: 94, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
197 3 0.00
198 2 0.00
199 877 0.82
200 179 0.17
201 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATG
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCTG
GAC
Found at i:2627329 original size:127 final size:127
Alignment explanation
Indices: 2627124--2627365 Score: 394
Period size: 127 Copynumber: 1.9 Consensus size: 127
2627114 TGTCGATACA
* * * * *
2627124 TTATGTTGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTACTTTGTAAATTTACTTAT
1 TTATGTTGACCTATTCTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
*
2627189 TACATTATAATTATTGGTTTCGATGTTTTTTGGATCGATACAATTTTAAATGTATCGACCTT
66 TACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGACCTT
* * * *
2627251 TTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTACCTGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTCTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
2627316 TACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAA
66 TACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAA
2627366 AATTATCGAT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
127 105 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (127 bp):
TTATGTTGACCTATTCTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGACCTT
Found at i:2627414 original size:127 final size:127
Alignment explanation
Indices: 2627123--2627436 Score: 368
Period size: 127 Copynumber: 2.5 Consensus size: 127
2627113 GTGTCGATAC
* * * * * * *
2627123 ATTATGTTGACCTATTCTCTCA-TAAAATCGGTATATTTATACCGGTTACTTTGTAAATTTACTT
1 ATTATGTTGACCTATTTTCTAATTAAAA-AGATATATTTATACCAGTTACATTGTAAATTTACCT
* *
2627187 ATTACATTATAATTATTGGTTTCGATGTTTTTTGGATCGATACAATTTTAAATGTATCGACCT
65 ATTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGAACT
* ** * *
2627250 TTTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTACCTGTTACATTGTAAATTTACCTA
1 ATTATGTTGACCTATTTTCTAATTAAAAAGATATATTTATACCAGTTACATTGTAAATTTACCTA
2627315 TTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAAAAT-TATCGATAC-
66 TTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTT--AAATGTATCGA-ACT
* * * * * *
2627378 ATTATGTTTA-CTAATTTTGTCATTAAAAAG-TGTATTTTTACCACTTACATTGTAAATTT
1 ATTATGTTGACCT-ATTTTCTAATTAAAAAGATATATTTATACCAGTTACATTGTAAATTT
2627437 TGCATATTAC
Statistics
Matches: 161, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
127 125 0.78
128 31 0.19
129 5 0.03
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (127 bp):
ATTATGTTGACCTATTTTCTAATTAAAAAGATATATTTATACCAGTTACATTGTAAATTTACCTA
TTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGAACT
Found at i:2630006 original size:67 final size:67
Alignment explanation
Indices: 2629894--2630020 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
2629884 AAGTATCAAC
2629894 ATGTATAAGAAACATGTACAACAACCTATTGCTAACTTTTATCATCTCATACATAATTACTCATA
1 ATGTATAAGAAACATGTACAACAACCTATTGCTAACTTTTATCATCTCATACATAATTACTCATA
2629959 CT
66 CT
* * *
2629961 ATGTATGAGAAACATGTACAACAATCTATTGCTAACTTTTTTCATCTCATACATAATTAC
1 ATGTATAAGAAACATGTACAACAACCTATTGCTAACTTTTATCATCTCATACATAATTAC
2630021 ATTCAGATAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (67 bp):
ATGTATAAGAAACATGTACAACAACCTATTGCTAACTTTTATCATCTCATACATAATTACTCATA
CT
Found at i:2632054 original size:18 final size:18
Alignment explanation
Indices: 2632008--2632055 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
2631998 TTCTTCATTA
* *
2632008 TCCTCTTCCTCTACTACC
1 TCCTCTACCTCCACTACC
* * *
2632026 TCCACTGCCTCCACTGCC
1 TCCTCTACCTCCACTACC
2632044 TCCTCTACCTCC
1 TCCTCTACCTCC
2632056 TTGCCAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.54, G:0.04, T:0.31
Consensus pattern (18 bp):
TCCTCTACCTCCACTACC
Found at i:2632479 original size:15 final size:15
Alignment explanation
Indices: 2632455--2632491 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2632445 GAATGGACAT
*
2632455 ATTCAACCCAATTGA
1 ATTCACCCCAATTGA
2632470 ATTCACCCCAATTGA
1 ATTCACCCCAATTGA
2632485 ATTCACC
1 ATTCACC
2632492 TTTCAAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.27
Consensus pattern (15 bp):
ATTCACCCCAATTGA
Found at i:2634635 original size:182 final size:182
Alignment explanation
Indices: 2634320--2635104 Score: 1180
Period size: 182 Copynumber: 4.3 Consensus size: 182
2634310 TACGCGTACT
* * * *
2634320 TATTAAAGTATCGACGCTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCAT-TTCGAGATC
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCATAAT-GATACC
* *
2634384 AGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGATAC
65 TGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
2634449 TTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
130 TTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
2634502 TGTTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACTGGTTTTTTCATAATGATACCT
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCATAATGATACCT
2634567 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
2634632 TTATAGGTGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * ** * *
2634684 TATTAAAGTGTCGACACTTTCAACATATTCTG-TAGATCTTTACCAGTTTTATCATAATGATACC
1 TATTAAAGTATCGACACTTTCAACATA-TCCGATAGCGCTTTACCGGTTTTGTCATAATGATACC
*
2634748 TGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
65 TGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
*** * *
2634813 TTTATAGGTTTTATTACTGCTTCTCTTATAATTTCCAAAAGTGTCGATACTTA
130 TTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
2634866 TATTAAAGTATCAACACTTTTAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGATACTT
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCATAATGATACCT
* * *
2634931 GTTTTGTAATATTTTTACCTGTTATATTGTTATAGATCGATATATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
2634996 TTATAAGCGCTATTACTGCTTCTGTTTTAAATTCCAAAAGTGTTGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
2635048 T-TTAAATGGTATCGACACATTCAACATATCCGGTAGTGATTTACCGGTTTTGTCATA
1 TATTAAA--GTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCATA
2635105 TTTTTACATG
Statistics
Matches: 549, Mismatches: 49, Indels: 9
0.90 0.08 0.01
Matches are distributed among these distances:
181 9 0.02
182 493 0.90
183 47 0.09
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCATAATGATACCT
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:2635235 original size:162 final size:163
Alignment explanation
Indices: 2634931--2635266 Score: 453
Period size: 162 Copynumber: 2.1 Consensus size: 163
2634921 AATGATACTT
* * * * *
2634931 GTTTTGTAATATTTTTACCTGTTATATTGTTATAGATCGATATATTTTTATAAAGTATCGACACT
1 GTTTTGTCATATTTTTACATGTTATAATGTTATAGAACGATACATTTTTATAAAGTATCGACACT
* * * * *
2634996 TTATAAGCGCTATTACTGCTTCTGTTTTAAATTCCAAAAGTGTTGATACTTATTTAAATGGTATC
66 TTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTAATTAAATGCTATC
*
2635061 GACACATTCAACATATCCGGTAGTGATTTACCG
131 GACACATTCAACATATCCGGTAGCGATTTACCG
* **
2635094 GTTTTGTCATATTTTTACATGTTATAATGTTATGGAACGATACATTTTTAT-TTGTATCGACACT
1 GTTTTGTCATATTTTTACATGTTATAATGTTATAGAACGATACATTTTTATAAAGTATCGACACT
* * *
2635158 TTATTAGTGCTATTACTGCTTCTCTTTTAAATTCTAAAACTGTCGATAC-TAATTACAAT-CTAA
66 TTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTAATTA-AATGCT-A
* * *
2635221 TCGATACTTTCAACATATCCGGTAGCGCTTTACCG
129 TCGACACATTCAACATATCCGGTAGCGATTTACCG
2635256 GTTTTGTCATA
1 GTTTTGTCATA
2635267 ACGAAACAAG
Statistics
Matches: 151, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
161 6 0.04
162 100 0.66
163 45 0.30
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (163 bp):
GTTTTGTCATATTTTTACATGTTATAATGTTATAGAACGATACATTTTTATAAAGTATCGACACT
TTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTAATTAAATGCTATC
GACACATTCAACATATCCGGTAGCGATTTACCG
Found at i:2644085 original size:90 final size:88
Alignment explanation
Indices: 2643967--2644140 Score: 303
Period size: 89 Copynumber: 2.0 Consensus size: 88
2643957 CTCAAATATT
* *
2643967 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
2644032 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
2644056 TTAAATTCTAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
2644121 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
2644141 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
89 41 0.51
90 40 0.49
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:2645582 original size:18 final size:18
Alignment explanation
Indices: 2645523--2645584 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
2645513 ATATTATAGA
*
2645523 AATTAAAATATAAACTAAT
1 AATTAAAATATTAAC-AAT
*
2645542 -ATTAAAAAAATT-A-AAT
1 AATT-AAAATATTAACAAT
*
2645558 AAATAAAATATTAACAAT
1 AATTAAAATATTAACAAT
2645576 AATTAAAAT
1 AATTAAAAT
2645585 TAAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
16 10 0.29
17 3 0.09
18 15 0.44
19 6 0.18
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTAAAATATTAACAAT
Found at i:2650592 original size:11 final size:11
Alignment explanation
Indices: 2650576--2650600 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2650566 AGCCTCAAAA
2650576 CATTGAGAATT
1 CATTGAGAATT
2650587 CATTGAGAATT
1 CATTGAGAATT
2650598 CAT
1 CAT
2650601 CATTCAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (11 bp):
CATTGAGAATT
Found at i:2658830 original size:15 final size:14
Alignment explanation
Indices: 2658799--2658837 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2658789 ATCTTTGGTG
2658799 AAATTCAATGTCTTTT
1 AAATTCAA-G-CTTTT
2658815 AAATGTCAAGCTTTT
1 AAAT-TCAAGCTTTT
2658830 AAATTCAA
1 AAATTCAA
2658838 ATTTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 5 0.23
17 4 0.18
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATTCAAGCTTTT
Done.