Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 29
Found at i:2253066 original size:108 final size:109
Alignment explanation
Indices: 2252935--2253176 Score: 312
Period size: 110 Copynumber: 2.2 Consensus size: 109
2252925 ACTATATATG
* * * * * * * *
2252935 ACCAAAATGTAAAAACACACTAAACTTAAA-AGACTAAATAGTGAAT-AACCCAATAAATACATA
1 ACCAAAATGTAAAAACACGCTAAAATTAAAGAGAATAAACAGAGAATAAACCAAAAAAATACACA
2252998 ACATGCAAGGAAAAGGAAAAATAACGATTTTATTC-CTCAAAGATGA
66 ACATGCAAGGAAAAGGAAAAATAACGATTTTA-TCACT-AAAGAT-A
* *
2253044 A-CATAATGTAAAAACACGCTAAAATTAAAGGGAATAAACAGAGAATAAACCAAAAAAATACACA
1 ACCAAAATGTAAAAACACGCTAAAATTAAAGAGAATAAACAGAGAATAAACCAAAAAAATACACA
* * *
2253108 ATATGCAAGGAAAAGGGAAAATAACGATTTTATCACTAAAGGTA
66 ACATGCAAGGAAAAGGAAAAATAACGATTTTATCACTAAAGATA
2253152 ACCAAAATGTAAAAACACGCTAAAA
1 ACCAAAATGTAAAAACACGCTAAAA
2253177 CTAGGGGAAC
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
108 27 0.23
109 42 0.37
110 46 0.40
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.18
Consensus pattern (109 bp):
ACCAAAATGTAAAAACACGCTAAAATTAAAGAGAATAAACAGAGAATAAACCAAAAAAATACACA
ACATGCAAGGAAAAGGAAAAATAACGATTTTATCACTAAAGATA
Found at i:2254713 original size:139 final size:139
Alignment explanation
Indices: 2254443--2255077 Score: 844
Period size: 139 Copynumber: 4.6 Consensus size: 139
2254433 GGGCTAAGGA
* * * * *
2254443 TGAACAAGTTTTTCTCATTATGAACTTTTTCTCCTTCATCGG-TGAGTTCTGCTCATTATGAACT
1 TGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* * * * * *
2254507 ATCC-TTGAAAATATAAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGTGATGAATCG
66 CTCCACTGGAAATGTTAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGCGATGAATCG
*
2254571 AGCTAAACT
131 AGCTAAAGT
* * * *
2254580 TGAACAAGTTCTTATCATTATGAACTTATTCTCCCTTATAGGATTAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* * * * * * * * * *
2254645 CTCTACTAGAAATGTTGATCCCTCTAGTGAGGTGTCAATAATTAAAATCCATATGCAATGAATCG
66 CTCCACTGGAAATGTTAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGCGATGAATCG
*
2254710 AGCTAAGGT
131 AGCTAAAGT
*
2254719 TGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCCGATGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* *
2254784 CTCCACTGGAGATGTTAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGCGATGAATTG
66 CTCCACTGGAAATGTTAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGCGATGAATCG
2254849 AGCTAAAGT
131 AGCTAAAGT
* * * * *
2254858 TGGACAAGTT-TGTCTCATTATGTACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATCATGAAT
1 TGAACAAGTTCT-TATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAAC
* *
2254922 TCTCCACTGGAAATGTTAATCCCTTGAGTGAGGCATCACTGATTCAACTCCATATGCGATGAATC
65 TCTCCACTGGAAATGTTAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGCGATGAATC
* *
2254987 AAGCTAAGGT
130 GAGCTAAAGT
* * * *
2254997 TGAACAAGTTCTTGTCATTATAAACTTCTTCTCCCTCATCAGATGAGTTATTCTCATTATGAACT
1 TGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
*
2255062 CTCCAGTGGAAATGTT
66 CTCCACTGGAAATGTT
2255078 GATTGGTTTA
Statistics
Matches: 429, Mismatches: 65, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
137 36 0.08
138 23 0.05
139 369 0.86
140 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (139 bp):
TGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
CTCCACTGGAAATGTTAATCCCTCGAGTGAGGCGTCACTGATTCAACTCCATATGCGATGAATCG
AGCTAAAGT
Found at i:2265539 original size:17 final size:18
Alignment explanation
Indices: 2265508--2265544 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
2265498 TTCTACGTAC
2265508 GAGGTGCCGAAAGATCTT
1 GAGGTGCCGAAAGATCTT
2265526 GAGGTGCC-AAAGATCTT
1 GAGGTGCCGAAAGATCTT
2265543 GA
1 GA
2265545 ATTGCCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (18 bp):
GAGGTGCCGAAAGATCTT
Found at i:2265550 original size:17 final size:18
Alignment explanation
Indices: 2265511--2265550 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2265501 TACGTACGAG
*
2265511 GTGCCGAAAGATCTTGAG
1 GTGCCGAAAGATCTTGAA
2265529 GTGCC-AAAGATCTTGAA
1 GTGCCGAAAGATCTTGAA
*
2265546 TTGCC
1 GTGCC
2265551 TTGACTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (18 bp):
GTGCCGAAAGATCTTGAA
Found at i:2274944 original size:32 final size:30
Alignment explanation
Indices: 2274886--2274944 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
2274876 AATTAAAATG
2274886 AATTAAAATTTAATGACTAAATCAAAACAA
1 AATTAAAATTTAATGACTAAATCAAAACAA
2274916 AATTAAAAATGTTAATGAC-AAATGCAAAA
1 AATT-AAAAT-TTAATGACTAAAT-CAAAA
2274945 ACACACGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.15
31 9 0.35
32 13 0.50
ACGTcount: A:0.59, C:0.08, G:0.07, T:0.25
Consensus pattern (30 bp):
AATTAAAATTTAATGACTAAATCAAAACAA
Found at i:2283327 original size:42 final size:42
Alignment explanation
Indices: 2283223--2283328 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 42
2283213 AAGAATTTTT
*
2283223 TATATTATTTAATTA-TAAAAATTATAAAAATTATTATAAAA
1 TATATTATTTAATTATTTAAAATTATAAAAATTATTATAAAA
* *
2283264 TATATTAAATTAATTGTTTAAAA-TATAATAAA-TATT-TAAAA
1 TATATT-ATTTAATTATTTAAAATTATAA-AAATTATTATAAAA
2283305 TATATTATTTTAATTAATTTAAAA
1 TATATTA-TTTAATT-ATTTAAAA
2283329 ATTTTGGGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.02
41 23 0.42
42 23 0.42
43 8 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (42 bp):
TATATTATTTAATTATTTAAAATTATAAAAATTATTATAAAA
Found at i:2300000 original size:25 final size:24
Alignment explanation
Indices: 2299970--2300022 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
2299960 TATAACAAAT
*
2299970 TTAATTT-ATGCATTTATAAATTTTG
1 TTAATTTCA-GCATTTATAAA-GTTG
*
2299995 TTAATTTCAGTATTTATAAAGTTG
1 TTAATTTCAGCATTTATAAAGTTG
2300019 TTAA
1 TTAA
2300023 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 17 0.68
26 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTTCAGCATTTATAAAGTTG
Found at i:2300076 original size:2 final size:2
Alignment explanation
Indices: 2300069--2300108 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2300059 AAATTATGTT
2300069 TA TA TA TA TA 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
2300109 AAATTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2304864 original size:36 final size:35
Alignment explanation
Indices: 2304778--2304881 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 35
2304768 GAAGTCTCTG
* * * *
2304778 CAGGTTCAGCTCGATCAAACTGGTTATTCCTTATA
1 CAGGTTCAGCTTGATCAAACTAGTAATTCCTTAAA
*
2304813 TAGGTTCAGAC-TGATCAAACTAGTAATTCCTTACAA
1 CAGGTTCAG-CTTGATCAAACTAGTAATTCCTTA-AA
* *
2304849 CAGGTTTAGCTTGATCAAATTAGTAATTCCTTA
1 CAGGTTCAGCTTGATCAAACTAGTAATTCCTTA
2304882 TGTACCCTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
35 28 0.48
36 30 0.52
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (35 bp):
CAGGTTCAGCTTGATCAAACTAGTAATTCCTTAAA
Found at i:2305201 original size:16 final size:13
Alignment explanation
Indices: 2305168--2305210 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 13
2305158 TTTTACTATG
2305168 GTTTTAAAAATAT
1 GTTTTAAAAATAT
2305181 GTTTTAAACAATTACT
1 GTTTTAAA-AA-TA-T
2305197 GTTTTAAAAGATAT
1 GTTTTAAAA-ATAT
2305211 ATGTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
15 5 0.19
16 10 0.38
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (13 bp):
GTTTTAAAAATAT
Found at i:2306734 original size:25 final size:25
Alignment explanation
Indices: 2306706--2306758 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
2306696 CTGGATCGGT
2306706 CCGAACC-ATGTCAACTCGACATAAC
1 CCGAACCGA-GTCAACTCGACATAAC
*
2306731 CCGAACCGAGTCAACTCGACCTAAC
1 CCGAACCGAGTCAACTCGACATAAC
2306756 CCG
1 CCG
2306759 TTTACTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.32, C:0.40, G:0.15, T:0.13
Consensus pattern (25 bp):
CCGAACCGAGTCAACTCGACATAAC
Found at i:2310219 original size:36 final size:35
Alignment explanation
Indices: 2310129--2310223 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 35
2310119 CTGCAAGTTT
2310129 AGCTCGATCAAACTGGTAATTCCTTATATAGGTTC
1 AGCTCGATCAAACTGGTAATTCCTTATATAGGTTC
* *
2310164 AGAC-CGATCGAACTAGTAATTCCTTATGGA-AGGTTC
1 AG-CTCGATCAAACTGGTAATTCCTTAT--ATAGGTTC
*
2310200 AGCTTGATCAAACTGGTAATTCCT
1 AGCTCGATCAAACTGGTAATTCCT
2310224 AAGGAACTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 24 0.47
36 26 0.51
37 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (35 bp):
AGCTCGATCAAACTGGTAATTCCTTATATAGGTTC
Found at i:2318768 original size:20 final size:20
Alignment explanation
Indices: 2318731--2318769 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2318721 AGTATTCCTC
* *
2318731 GGTAATGTGACGTCTTCCCT
1 GGTAATGTGACATATTCCCT
2318751 GGTAATGTGACATATTCCC
1 GGTAATGTGACATATTCCC
2318770 CCTACTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
GGTAATGTGACATATTCCCT
Found at i:2320810 original size:19 final size:18
Alignment explanation
Indices: 2320785--2320836 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
2320775 ATATTATAAT
2320785 TTTTTTTGTTATTTTT-C
1 TTTTTTTGTTATTTTTAC
*
2320802 TGATTTTTTATT-TTTTTAC
1 T--TTTTTTGTTATTTTTAC
2320821 TTTCTTTTGTTATTTT
1 TTT-TTTTGTTATTTT
2320837 CTTTTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 14 0.50
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTTTGTTATTTTTAC
Found at i:2321439 original size:132 final size:132
Alignment explanation
Indices: 2321198--2321464 Score: 507
Period size: 132 Copynumber: 2.0 Consensus size: 132
2321188 ACCACATGTA
2321198 CTAATATTTTCATCGCTGCTTAAATTGATGGTAATGTAGAGATAATACTGTAGATGAATTATTCT
1 CTAATATTTTCATCGCTGCTTAAATTGATGGTAATGTAGAGATAATACTGTAGATGAATTATTCT
* *
2321263 TTCATCTTTAGAGTGGAGATAGAGATGCTGTAGAGTAGATATGAGGACTGGAGATGGTCTGAGAA
66 TTCATCTTTAGAGTGGAGATAGAGATGCTGTAGAGTAGAGATGAGGACTAGAGATGGTCTGAGAA
2321328 CC
131 CC
*
2321330 CTAATATTTTCATCGCTGCTTAAATTGATGGTAATGTAGAGATAATACTGTATATGAATTATTCT
1 CTAATATTTTCATCGCTGCTTAAATTGATGGTAATGTAGAGATAATACTGTAGATGAATTATTCT
2321395 TTCATCTTTAGAGTGGAGATAGAGATGCTGTAGAGTAGAGATGAGGACTAGAGATGGTCTGAGAA
66 TTCATCTTTAGAGTGGAGATAGAGATGCTGTAGAGTAGAGATGAGGACTAGAGATGGTCTGAGAA
2321460 CC
131 CC
2321462 CTA
1 CTA
2321465 GCCTCCTTAA
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 132 1.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (132 bp):
CTAATATTTTCATCGCTGCTTAAATTGATGGTAATGTAGAGATAATACTGTAGATGAATTATTCT
TTCATCTTTAGAGTGGAGATAGAGATGCTGTAGAGTAGAGATGAGGACTAGAGATGGTCTGAGAA
CC
Found at i:2342486 original size:22 final size:22
Alignment explanation
Indices: 2342461--2342504 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2342451 AAAAAGATTA
2342461 ATATATAATTTA-TAAAAATATG
1 ATATAT-ATTTATTAAAAATATG
*
2342483 ATATGTATTTATTTAAAAATAT
1 ATATATATTTA-TTAAAAATAT
2342505 CAGAAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATATATTTATTAAAAATATG
Found at i:2346928 original size:19 final size:20
Alignment explanation
Indices: 2346906--2346949 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2346896 GAGAAAAGGT
2346906 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
2346925 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
2346945 AAAAG
1 AAAAG
2346950 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:2354418 original size:3 final size:3
Alignment explanation
Indices: 2354412--2354484 Score: 60
Period size: 3 Copynumber: 24.7 Consensus size: 3
2354402 TAATATTTAT
* * * * *
2354412 TAA TAA TAA -AA TAA TAA TAA TAA TTA TTA TTA TTA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2354459 TAA TAA TGA TAA TTA T-A TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA
2354485 TTCTAATGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:2354429 original size:27 final size:27
Alignment explanation
Indices: 2354399--2354462 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
2354389 ATGTAATATG
*
2354399 TAATAATATTTATTAATAATAAAATAA
1 TAATAATAATTATTAATAATAAAATAA
* * *
2354426 TAATAATAATTATTATTATTATAATAA
1 TAATAATAATTATTAATAATAAAATAA
*
2354453 TAATTATAAT
1 TAATAATAAT
2354463 AATGATAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATAATAATTATTAATAATAAAATAA
Found at i:2354470 original size:21 final size:21
Alignment explanation
Indices: 2354412--2354484 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
2354402 TAATATTTAT
*
2354412 TAATAATAA-AATAATAATAA
1 TAATTATAATAATAATAATAA
* * *
2354432 TAATTATTATTATTATAATAA
1 TAATTATAATAATAATAATAA
* *
2354453 TAATTATAATAATGATAATTA
1 TAATTATAATAATAATAATAA
2354474 T-ATATATAATA
1 TAAT-TATAATA
2354485 TTCTAATGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
20 9 0.21
21 34 0.79
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
TAATTATAATAATAATAATAA
Found at i:2355083 original size:113 final size:114
Alignment explanation
Indices: 2354932--2355503 Score: 600
Period size: 113 Copynumber: 4.8 Consensus size: 114
2354922 TAGAGTCATG
*
2354932 AAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
2354997 TTATGAAC-TTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAAC
66 TTATGAACTTTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAAC
* *
2355045 AAAAAGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * **
2355110 TTATGAACTTTCTCTGAAAAAATTTGATGTTGATCTATCTACTTCTG-TGATAGAGTCATGC
66 TTATGAACTTTCTCT--AGAAA----A-GTTGATCCATCGA---ATGATG--A-ATTCAAAC
*
2355171 -AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
2355235 TTATGAAC-TTCTCTGGAGAAGTTGATCCATCGAATGATGAATTCAAAC
66 TTATGAACTTTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAAC
* *
2355283 AAAAAGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *** * **
2355348 TTATGAACTTTCTCTGGAAAAAAATTGATGTTGATCTATCTCCTTCTTTGAT-AGAGTCATGC
66 TTATGAACTTTCTCT----AGAAA---A-GTTGATCCA--T-C--GAATGATGA-ATTCAAAC
* *
2355410 -AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCA
1 AAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
2355474 TTATGAACTCT-TCTGGAAATGTTGATCCAT
66 TTATGAACTTTCTCTAGAAAAGTTGATCCAT
2355504 TGTGATGGAT
Statistics
Matches: 384, Mismatches: 44, Indels: 60
0.79 0.09 0.12
Matches are distributed among these distances:
112 5 0.01
113 140 0.36
114 14 0.04
115 3 0.01
116 4 0.01
117 19 0.05
118 3 0.01
120 1 0.00
121 15 0.04
122 10 0.03
123 2 0.01
124 9 0.02
125 74 0.19
126 76 0.20
127 9 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
AAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTAGAAAAGTTGATCCATCGAATGATGAATTCAAAC
Found at i:2355124 original size:238 final size:238
Alignment explanation
Indices: 2354817--2355503 Score: 1188
Period size: 238 Copynumber: 2.9 Consensus size: 238
2354807 ATACAAGAGG
** * *
2354817 TTGAACAAGCTCTTCTCATTATGAACTTCTTGCAT-C-T-TT-AGATGAGTTCTTCTTATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCTT-CTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
2354878 ATTTTCTCTGGAAAAAATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGAAAAAGGTTGA
65 ACTTTCTCTGGAAAAAATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGA
2354943 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
130 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
*
2355008 TCTAGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGT
195 TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGT
2355052 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
2355117 CTTTCTCT-GAAAAAATTTGATGTTGATCTATCTACTTCTGTGATAGAGTCATGCAAAAGGTTGA
66 CTTTCTCTGGAAAAAA-TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGA
2355181 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
130 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
*
2355246 TCTGGAGAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGT
195 TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGT
2355290 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
2355355 CTTTCTCTGGAAAAAAATTGATGTTGATCTATCTCCTTCTTTGATAGAGTCATGCAAAAGGTTGA
66 CTTTCTCTGG-AAAAAATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGA
*
2355420 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAAC-TC
130 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
*
2355484 TTCTGGAAATGTTGATCCAT
195 -TCTGGAAAAGTTGATCCAT
2355504 TGTGATGGAT
Statistics
Matches: 430, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
234 2 0.00
235 30 0.07
236 1 0.00
237 9 0.02
238 257 0.60
239 125 0.29
240 6 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (238 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAAATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAA
CAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCT
CTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGT
Found at i:2357075 original size:11 final size:10
Alignment explanation
Indices: 2357061--2357091 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
2357051 TTTTTCAACA
2357061 TTTTTTTTCT
1 TTTTTTTTCT
2357071 TTTTTTTTCT
1 TTTTTTTTCT
2357081 TTTTTTTTCT
1 TTTTTTTTCT
2357091 T
1 T
2357092 CAAGCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:2364444 original size:15 final size:15
Alignment explanation
Indices: 2364421--2364452 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2364411 TGCAATGAAT
2364421 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2364436 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2364451 AA
1 AA
2364453 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2367813 original size:23 final size:23
Alignment explanation
Indices: 2367769--2367819 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2367759 GCATTAATAG
*
2367769 AATAATATAAATATTATGAAAAT
1 AATAATATAAATATTATGAAAAA
* *
2367792 AATAAGTATATATATT-TTAAAAA
1 AATAA-TATAAATATTATGAAAAA
2367815 AATAA
1 AATAA
2367820 AAATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
AATAATATAAATATTATGAAAAA
Found at i:2368611 original size:2 final size:2
Alignment explanation
Indices: 2368604--2368659 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
2368594 CATAAAATAA
* *
2368604 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT ACT AA AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
2368646 -T AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2368660 AAATAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2373611 original size:24 final size:24
Alignment explanation
Indices: 2373584--2373633 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2373574 ACAAACAACA
*
2373584 ACAATAGATTGGCGGCCAATAGCG
1 ACAATAGAGTGGCGGCCAATAGCG
*
2373608 ACAATAGAGTGGCGGTCAATAGCG
1 ACAATAGAGTGGCGGCCAATAGCG
2373632 AC
1 AC
2373634 GAATTCGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.30, T:0.16
Consensus pattern (24 bp):
ACAATAGAGTGGCGGCCAATAGCG
Found at i:2381118 original size:22 final size:22
Alignment explanation
Indices: 2381046--2381107 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
2381036 GCTACAGTAC
*
2381046 GAGATGAACTCGTCACCTTGAG
1 GAGACGAACTCGTCACCTTGAG
*
2381068 GAAACGAACTCGTCACCTTGAG
1 GAGACGAACTCGTCACCTTGAG
2381090 GAGACGAACTCGTCACCT
1 GAGACGAACTCGTCACCT
2381108 CAAGGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.19
Consensus pattern (22 bp):
GAGACGAACTCGTCACCTTGAG
Found at i:2381649 original size:28 final size:28
Alignment explanation
Indices: 2381615--2381709 Score: 181
Period size: 28 Copynumber: 3.4 Consensus size: 28
2381605 GAAAAATGTT
2381615 TTAAATATATGTATGAATTTGAGTTTAG
1 TTAAATATATGTATGAATTTGAGTTTAG
2381643 TTAAATATATGTATGAATTTGAGTTTAG
1 TTAAATATATGTATGAATTTGAGTTTAG
*
2381671 TTAAATATATGTATGAATTTGAGTTTAA
1 TTAAATATATGTATGAATTTGAGTTTAG
2381699 TTAAATATATG
1 TTAAATATATG
2381710 GTTATTGATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (28 bp):
TTAAATATATGTATGAATTTGAGTTTAG
Found at i:2385167 original size:19 final size:21
Alignment explanation
Indices: 2385145--2385191 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
2385135 TATTAACATC
2385145 CTTAAAAAATAA-TTT-ATTA
1 CTTAAAAAATAATTTTAATTA
* *
2385164 CTTAATAATTAATTTTAATTA
1 CTTAAAAAATAATTTTAATTA
2385185 CTTAAAA
1 CTTAAAA
2385192 GCAAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 10 0.43
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
CTTAAAAAATAATTTTAATTA
Found at i:2385346 original size:2 final size:2
Alignment explanation
Indices: 2385335--2385374 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2385325 TTAATTTATT
*
2385335 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2385375 TTGGTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2387988 original size:64 final size:65
Alignment explanation
Indices: 2387856--2388011 Score: 208
Period size: 64 Copynumber: 2.4 Consensus size: 65
2387846 TACACTAGGG
* * * * * *
2387856 GTGCATCGGTGCACTAATTACATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGGTTT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAATAACCCTGGAGTGCATCGATGCATAGTGT
* *
2387921 GTGCATCGGTACACAAAATGCATTCGATTTTTC-AATAAACCCT-GAGTGCATCGATGCATAGTG
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAT-AACCCTGGAGTGCATCGATGCATAGTG
2387984 T
65 T
*
2387985 GTGCATTGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
2388012 AATGGGGTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 47 0.59
65 33 0.41
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAATAACCCTGGAGTGCATCGATGCATAGTGT
Found at i:2390651 original size:23 final size:23
Alignment explanation
Indices: 2390617--2390696 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
2390607 CAAAGTAGAG
2390617 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGGAA
* * *
2390640 TGCATCGGTGCACCTTCATGG--
1 TGCATCGATGCACATTCAAGGAA
*
2390661 TGTATCGATGCACATTCAA-GAGA
1 TGCATCGATGCACATTCAAGGA-A
2390684 TGCATCGATGCAC
1 TGCATCGATGCAC
2390697 TGTCTAGTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
23 30 0.65
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGAA
Found at i:2390687 original size:44 final size:43
Alignment explanation
Indices: 2390615--2390715 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 43
2390605 TACAAAGTAG
* *
2390615 AGTGCATCGATGCACATTCAAGGAATGCATCGGTGCACCT-TCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCA-CTGTC-T
*
2390659 GGTGTATCGATGCACATTCAA-GAGATGCATCGATGCACTGTCT
1 AGTGTATCGATGCACATTCAAGGA-ATGCATCGATGCACTGTCT
2390702 AGTGTATCGATGCA
1 AGTGTATCGATGCA
2390716 TTATGCACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
43 18 0.35
44 33 0.65
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTGTCT
Found at i:2394572 original size:22 final size:21
Alignment explanation
Indices: 2394530--2394569 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2394520 AAGACTATTT
2394530 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
2394551 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
2394570 ATAAAGTCGT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:2396878 original size:26 final size:26
Alignment explanation
Indices: 2396849--2396906 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2396839 GTGTAATATT
* *
2396849 TATTTTAAATATAATTATAAAAATAA
1 TATTTAAAAAATAATTATAAAAATAA
* * *
2396875 TATTTAAAAAATATTTTTAGAAATAA
1 TATTTAAAAAATAATTATAAAAATAA
2396901 TATTTA
1 TATTTA
2396907 TTTTAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
TATTTAAAAAATAATTATAAAAATAA
Found at i:2396884 original size:13 final size:13
Alignment explanation
Indices: 2396852--2396906 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2396842 TAATATTTAT
*
2396852 TTTAAATATAAT-
1 TTTAAAAATAATA
*
2396864 TATAAAAATAATA
1 TTTAAAAATAATA
*
2396877 TTTAAAAA-ATATT
1 TTTAAAAATA-ATA
*
2396890 TTTAGAAATAATA
1 TTTAAAAATAATA
2396903 TTTA
1 TTTA
2396907 TTTTAATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
12 11 0.32
13 22 0.65
14 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TTTAAAAATAATA
Found at i:2397693 original size:19 final size:19
Alignment explanation
Indices: 2397669--2397713 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
2397659 ATAAAACCAT
2397669 TATAATATTAAAAATAAAA
1 TATAATATTAAAAATAAAA
2397688 TATAATA--AAAAATAAAA
1 TATAATATTAAAAATAAAA
*
2397705 AATAA-ATTA
1 TATAATATTA
2397714 GATTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 1 0.04
19 7 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TATAATATTAAAAATAAAA
Found at i:2402369 original size:29 final size:29
Alignment explanation
Indices: 2402314--2402372 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2402304 GAAAAGACTT
* * *
2402314 CTTTGTCTCTTCTCTATTCTACTTGTTGG
1 CTTTCTCTCTTCTCTATTATACATGTTGG
* *
2402343 CTTTCTCTCTTTTCTATTATGCATGTTGG
1 CTTTCTCTCTTCTCTATTATACATGTTGG
2402372 C
1 C
2402373 GTTTGGTTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (29 bp):
CTTTCTCTCTTCTCTATTATACATGTTGG
Found at i:2402788 original size:18 final size:20
Alignment explanation
Indices: 2402748--2402789 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2402738 TTTTATTAAA
2402748 ATAAAAATATTATTAATAATT
1 ATAAAAATATTATTAAT-ATT
2402769 ATAAAAATATTA-TAAT-TT
1 ATAAAAATATTATTAATATT
2402787 ATA
1 ATA
2402790 TTAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
20 4 0.19
21 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAAATATTATTAATATT
Found at i:2403996 original size:32 final size:32
Alignment explanation
Indices: 2403960--2404020 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2403950 GGGCACTTTT
2403960 AATAAGTACTGTAGC-AAGGATCCTAGTTAAAA
1 AATAAGTACTGTAGCGAA-GATCCTAGTTAAAA
* *
2403992 AATAAGTATTGTAGCGAAGATCTTAGTTA
1 AATAAGTACTGTAGCGAAGATCCTAGTTA
2404021 TGTGGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (32 bp):
AATAAGTACTGTAGCGAAGATCCTAGTTAAAA
Found at i:2406678 original size:28 final size:27
Alignment explanation
Indices: 2406630--2406692 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
2406620 TTATTTTTTT
*
2406630 ATTTTTAAAATCGTTCATGTTTGTTTAA
1 ATTTTTAAAATCGTTCATGTTTATTT-A
* *
2406658 ATTTTTAATATCGTAT-TTGTTTATTTA
1 ATTTTTAAAATCGT-TCATGTTTATTTA
*
2406685 TTTTTTAA
1 ATTTTTAA
2406693 GGTATTCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 8 0.27
28 21 0.70
29 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (27 bp):
ATTTTTAAAATCGTTCATGTTTATTTA
Found at i:2406791 original size:23 final size:23
Alignment explanation
Indices: 2406758--2406838 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
2406748 TATGTTTGCA
* *
2406758 AACATGATCATTTAGTGCTCCTG
1 AACATGTTCATTTAGCGCTCCTG
*
2406781 AACATGTTCATTTAGGGCTCCTG
1 AACATGTTCATTTAGCGCTCCTG
* *
2406804 AACATGTTCATTTAGCGATCTTG
1 AACATGTTCATTTAGCGCTCCTG
2406827 AACATGTT-ATTT
1 AACATGTTCATTT
2406839 TATATACTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 4 0.08
23 49 0.92
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (23 bp):
AACATGTTCATTTAGCGCTCCTG
Found at i:2416488 original size:30 final size:30
Alignment explanation
Indices: 2416454--2416521 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2416444 TTTATGTCCC
* *
2416454 TAATTAGCATTAATTATTCTTTAAATTCTT
1 TAATTAACATCAATTATTCTTTAAATTCTT
* *
2416484 TAATTAACATCCATTATTCTTTGAATTCTAT
1 TAATTAACATCAATTATTCTTTAAATTCT-T
*
2416515 GAATTAA
1 TAATTAA
2416522 TTTAACTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (30 bp):
TAATTAACATCAATTATTCTTTAAATTCTT
Found at i:2422743 original size:14 final size:14
Alignment explanation
Indices: 2422707--2422743 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2422697 TTCAATATTC
*
2422707 ATTCTTTACACCAT
1 ATTCTTTATACCAT
*
2422721 ATTCTTTATTCCAT
1 ATTCTTTATACCAT
2422735 ATTCTTTAT
1 ATTCTTTAT
2422744 CATTCACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTCTTTATACCAT
Found at i:2425158 original size:300 final size:303
Alignment explanation
Indices: 2424770--2425372 Score: 1185
Period size: 300 Copynumber: 2.0 Consensus size: 303
2424760 CGAACAATTG
2424770 AAAAAATTTAAAGATGTTGCATTTAGATATCTTCCCCCGATAGGACAATCAAATGGCCGATGCTC
1 AAAAAATTTAAAGATGTTGCATTTAGATATCTTCCCCCGATAGGACAATCAAATGGCCGATGCTC
2424835 TAGCTACGTTGGCTGCAATGTTTAAGGCAAATAGGGAAACAAACATGATGCTAATGGTGGAACAC
66 TAGCTACGTTGGCTGCAATGTTTAAGGCAAATAGGGAAACAAACATGATGCTAATGGTGGAACAC
2424900 ATGCAAATGGTTTATCTATGGCTAGG-AAATCATGAGATATAGTTACTATTGGGCCACGATGTAT
131 ATGCAAATGGTTTATCTATGGCTAGGAAAATCATGAGATATAGTTACTATTGGGCCACGATGTAT
2424964 ATAGATTGTGTCAATTATGTAAG-AAATGCCACAAATAGCATATAT-TAAGGATAAAATTCAGGC
196 ATAGATTGTGTCAATTATGTAAGAAAATGCCACAAATAGCATATATATAAGGATAAAATTCAGGC
2425027 ACCGTCTTTGCCTCTACATGTTATGATCTCACCTTAGCCGTTT
261 ACCGTCTTTGCCTCTACATGTTATGATCTCACCTTAGCCGTTT
2425070 AAAAAATTTAAAGATGTTGCATTTAGATATCTTCCCCCGATAGGACAATCAAATGGCCGATGCTC
1 AAAAAATTTAAAGATGTTGCATTTAGATATCTTCCCCCGATAGGACAATCAAATGGCCGATGCTC
2425135 TAGCTACGTTGGCTGCAATGTTTAAGGCAAATAGGGAAACAAACATGATGCTAATGGTGGAACAC
66 TAGCTACGTTGGCTGCAATGTTTAAGGCAAATAGGGAAACAAACATGATGCTAATGGTGGAACAC
2425200 ATGCAAATGGTTTATCTATGGCTAGGAAAATCATGAGATATAGTTACTATTGGGCCACGATGTAT
131 ATGCAAATGGTTTATCTATGGCTAGGAAAATCATGAGATATAGTTACTATTGGGCCACGATGTAT
2425265 ATAGATTGTGTCAATTATGTAAGAAAATGCCACAAATAGCATATATATAAGGATAAAATTCAGGC
196 ATAGATTGTGTCAATTATGTAAGAAAATGCCACAAATAGCATATATATAAGGATAAAATTCAGGC
2425330 ACCGTCTTTGCCTCTACATGTTATGATCTCACCTTAGCCGTTT
261 ACCGTCTTTGCCTCTACATGTTATGATCTCACCTTAGCCGTTT
2425373 TCTATCTAGG
Statistics
Matches: 300, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
300 156 0.52
301 61 0.20
302 22 0.07
303 61 0.20
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (303 bp):
AAAAAATTTAAAGATGTTGCATTTAGATATCTTCCCCCGATAGGACAATCAAATGGCCGATGCTC
TAGCTACGTTGGCTGCAATGTTTAAGGCAAATAGGGAAACAAACATGATGCTAATGGTGGAACAC
ATGCAAATGGTTTATCTATGGCTAGGAAAATCATGAGATATAGTTACTATTGGGCCACGATGTAT
ATAGATTGTGTCAATTATGTAAGAAAATGCCACAAATAGCATATATATAAGGATAAAATTCAGGC
ACCGTCTTTGCCTCTACATGTTATGATCTCACCTTAGCCGTTT
Found at i:2426710 original size:12 final size:12
Alignment explanation
Indices: 2426695--2426719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2426685 CAATAACCCA
2426695 AATGATAAAATG
1 AATGATAAAATG
2426707 AATGATAAAATG
1 AATGATAAAATG
2426719 A
1 A
2426720 CAATAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AATGATAAAATG
Found at i:2427671 original size:22 final size:24
Alignment explanation
Indices: 2427628--2427673 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2427618 AATTTTTAAC
*
2427628 CATTATTATAATATTATTATAAAA
1 CATTATTATAATATTATCATAAAA
*
2427652 CATTATTATTAT-TTA-CATAAAA
1 CATTATTATAATATTATCATAAAA
2427674 ACTTGGGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (24 bp):
CATTATTATAATATTATCATAAAA
Found at i:2436772 original size:43 final size:42
Alignment explanation
Indices: 2436710--2436970 Score: 222
Period size: 43 Copynumber: 6.0 Consensus size: 42
2436700 TTTTTGGTTT
* *
2436710 TCTCACTTTTTTATCTTTATAATTGAGGCCCTAATTTTTTCAA
1 TCTCAC-TTTTTACCTTTATAATTGAGTCCCTAATTTTTTCAA
* * * *
2436753 TCTCACTCTTTTACATTTATGATTGATGACCCTAA-CTTTTCTAA
1 TCTCACT-TTTTACCTTTATAATTGA-GTCCCTAATTTTTTC-AA
* * *
2436797 TCTCACGTTTTACCTTTTATAATTGA-TCTCCTAATTTTTTTAG
1 TCTCACTTTTTACC-TTTATAATTGAGTC-CCTAATTTTTTCAA
* * * * *
2436840 TCACACTTTCTACCTTTATAATTCAGATTCCTAATTTTTT-GA
1 TCTCACTTTTTACCTTTATAATTGAG-TCCCTAATTTTTTCAA
* * *
2436882 CCTCACTTTTTACCTTTATAATGGAGATTCCTAATTTTTTCAA
1 TCTCACTTTTTACCTTTATAATTGAG-TCCCTAATTTTTTCAA
* * * *
2436925 TCTCATTTTTTTACTTTTATAATTGAGGCCCTTAATTGTTTCAA
1 TCTCA-CTTTTTACCTTTATAATTGAGTCCC-TAATTTTTTCAA
2436969 TC
1 TC
2436971 ATATTTTTTT
Statistics
Matches: 175, Mismatches: 32, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
42 47 0.27
43 67 0.38
44 61 0.35
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (42 bp):
TCTCACTTTTTACCTTTATAATTGAGTCCCTAATTTTTTCAA
Found at i:2436786 original size:44 final size:42
Alignment explanation
Indices: 2436672--2436970 Score: 228
Period size: 44 Copynumber: 6.9 Consensus size: 42
2436662 TTCTTCAATT
* * **
2436672 TTTTTATCTTTATAATTGATACCTCTAATTTTTGGT-TTTCTCAC
1 TTTTTACCTTTATAATTGAGACC-CTAATTTTT--TCAATCTCAC
* *
2436716 TTTTTTATCTTTATAATTGAGGCCCTAATTTTTTCAATCTCAC
1 -TTTTTACCTTTATAATTGAGACCCTAATTTTTTCAATCTCAC
* * *
2436759 TCTTTTACATTTATGATTGATGACCCTAA-CTTTTCTAATCTCAC
1 T-TTTTACCTTTATAATTGA-GACCCTAATTTTTTC-AATCTCAC
* * * * *
2436803 GTTTTACCTTTTATAATTGA-TCTCCTAATTTTTTTAGTCACAC
1 TTTTTACC-TTTATAATTGAGAC-CCTAATTTTTTCAATCTCAC
* * * * *
2436846 TTTCTACCTTTATAATTCAGATTCCTAATTTTTT-GACCTCAC
1 TTTTTACCTTTATAATTGAGA-CCCTAATTTTTTCAATCTCAC
* * *
2436888 TTTTTACCTTTATAATGGAGATTCCTAATTTTTTCAATCTCATT
1 TTTTTACCTTTATAATTGAGA-CCCTAATTTTTTCAATCTCA-C
* * *
2436932 TTTTTACTTTTATAATTGAGGCCCTTAATTGTTTCAATC
1 TTTTTACCTTTATAATTGAGACCC-TAATTTTTTCAATC
2436971 ATATTTTTTT
Statistics
Matches: 205, Mismatches: 37, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
42 48 0.23
43 67 0.33
44 69 0.34
45 21 0.10
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (42 bp):
TTTTTACCTTTATAATTGAGACCCTAATTTTTTCAATCTCAC
Found at i:2436878 original size:42 final size:41
Alignment explanation
Indices: 2436807--2436921 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 41
2436797 TCTCACGTTT
* *
2436807 TACCTTTTATAATT-GATCTCCTAATTTTTTTAGTCACACTTTC
1 TACC-TTTATAATTAGAT-TCCTAATTTTTTGA-CCACACTTTC
* *
2436850 TACCTTTATAATTCAGATTCCTAATTTTTTGACCTCACTTTT
1 TACCTTTATAATT-AGATTCCTAATTTTTTGACCACACTTTC
*
2436892 TACCTTTATAATGGAGATTCCTAATTTTTT
1 TACCTTTATAAT-TAGATTCCTAATTTTTT
2436922 CAATCTCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 44 0.69
43 17 0.27
44 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.50
Consensus pattern (41 bp):
TACCTTTATAATTAGATTCCTAATTTTTTGACCACACTTTC
Found at i:2437006 original size:45 final size:43
Alignment explanation
Indices: 2436710--2437006 Score: 124
Period size: 43 Copynumber: 6.8 Consensus size: 43
2436700 TTTTTGGTTT
* ** *
2436710 TCTCACTTTTTTA-TCTTTATAATTGAGGCCCTAATTTTTTCAA
1 TCTCATTTTTTTACT-TTTATAATTGAAACCCTAATTGTTTCAA
* * * * * *
2436753 TCTCACTCTTTTACATTTATGATTGATGACCCTAACT-TTTCTAA
1 TCTCATTTTTTTACTTTTATAATTGA-AACCCTAATTGTTTC-AA
** * * * *
2436797 TCTCA-CGTTTTACCTTTTATAATTG-ATCTCCTAATTTTTTTAG
1 TCTCATTTTTTTA-CTTTTATAATTGAAAC-CCTAATTGTTTCAA
* * * * * ** **
2436840 TCACA-CTTTCTACCTTTATAATTCAGATTCCTAATT-TTTTGA
1 TCTCATTTTTTTACTTTTATAATTGA-AACCCTAATTGTTTCAA
* * * * ** *
2436882 CCTCA-CTTTTTACCTTTATAATGGAGATTCCTAATTTTTTCAA
1 TCTCATTTTTTTACTTTTATAATTGA-AACCCTAATTGTTTCAA
**
2436925 TCTCATTTTTTTACTTTTATAATTGAGGCCCTTAATTGTTTCAA
1 TCTCATTTTTTTACTTTTATAATTGAAACCC-TAATTGTTTCAA
*
2436969 TCAT-ATTTTTTTTACTTTTATAATTTAAACCTCTAATT
1 TC-TCA-TTTTTTTACTTTTATAATTGAAACC-CTAATT
2437007 TAATCATTTT
Statistics
Matches: 200, Mismatches: 40, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
42 46 0.23
43 64 0.32
44 61 0.31
45 28 0.14
46 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.51
Consensus pattern (43 bp):
TCTCATTTTTTTACTTTTATAATTGAAACCCTAATTGTTTCAA
Found at i:2445215 original size:41 final size:41
Alignment explanation
Indices: 2445164--2445355 Score: 115
Period size: 41 Copynumber: 4.7 Consensus size: 41
2445154 TGTTTTTTCA
* *
2445164 ACAAATGCCGCAATAGAGAAGTACTTTAGCGGCGTTTTTAT
1 ACAAACGCCGCAATAGAGAAGTACTATAGCGGCGTTTTTAT
* ** * *
2445205 ACAAACGCCGCGATAGTATCA-T-CTATAGTGGTGTTTTT-T
1 ACAAACGCCGCAATAG-AGAAGTACTATAGCGGCGTTTTTAT
* * * * **
2445244 CAACAAATGCCGCAACAGAGTAGTACTTTAGCGGAATTTTTAT
1 --ACAAACGCCGCAATAGAGAAGTACTATAGCGGCGTTTTTAT
* * * *
2445287 AGAAACTCCGCAATAGAGTTAA-T-CTATAGTGGCGTTTTTCT
1 ACAAACGCCGCAATAGAG--AAGTACTATAGCGGCGTTTTTAT
* * * *
2445328 ACAATCGCCACAATAAAGTAGTACTATA
1 ACAAACGCCGCAATAGAGAAGTACTATA
2445356 AAAATGACGT
Statistics
Matches: 109, Mismatches: 32, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
39 2 0.02
40 16 0.15
41 74 0.68
42 15 0.14
43 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
ACAAACGCCGCAATAGAGAAGTACTATAGCGGCGTTTTTAT
Found at i:2445348 original size:82 final size:82
Alignment explanation
Indices: 2445155--2445352 Score: 240
Period size: 82 Copynumber: 2.4 Consensus size: 82
2445145 CTTTAATGAT
* ** *
2445155 GTTTTTTCAACAAATGCCGCAATAGAGAAGTACTTTAGCGGCGTTTTTATACAAACGCCGCGATA
1 GTTTTTTCAACAAATGCCGCAATAGAGTAGTACTTTAGCGGAATTTTTATACAAACGCCGCAATA
* *
2445220 GTATCATCTATAGTGGT
66 GTATAATCTATAGTGGC
* * *
2445237 GTTTTTTCAACAAATGCCGCAACAGAGTAGTACTTTAGCGGAATTTTTATAGAAACTCCGCAATA
1 GTTTTTTCAACAAATGCCGCAATAGAGTAGTACTTTAGCGGAATTTTTATACAAACGCCGCAATA
2445302 G-AGTTAATCTATAGTGGC
66 GTA--TAATCTATAGTGGC
* * *
2445320 G-TTTTTCTAC-AATCGCCACAATAAAGTAGTACT
1 GTTTTTTCAACAAAT-GCCGCAATAGAGTAGTACT
2445353 ATAAAAATGA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
81 4 0.04
82 83 0.83
83 13 0.13
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (82 bp):
GTTTTTTCAACAAATGCCGCAATAGAGTAGTACTTTAGCGGAATTTTTATACAAACGCCGCAATA
GTATAATCTATAGTGGC
Found at i:2445876 original size:28 final size:28
Alignment explanation
Indices: 2445843--2445904 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
2445833 CAACAAGAAG
2445843 AACCGTATCCAAGTCTCCAATACCCAGA
1 AACCGTATCCAAGTCTCCAATACCCAGA
2445871 AACCGTATCCAAGTCTCCAATACCCAGA
1 AACCGTATCCAAGTCTCCAATACCCAGA
2445899 AACCGT
1 AACCGT
2445905 TTGACTTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.35, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCGTATCCAAGTCTCCAATACCCAGA
Found at i:2446655 original size:42 final size:42
Alignment explanation
Indices: 2446608--2446721 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 42
2446598 CATCGAAATG
* * * *
2446608 TCGTGTTTGTTTCATGTAATTTGTTTTTCGGAAAATGTTTTC
1 TCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
2446650 TCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
1 TCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
* *
2446692 CCGTGTTTGTTTCACGTAATTCATTTTCCG
1 TCGTGTTTGTTTCACGTAATTCGTTTTCCG
2446722 GAACGTAGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.50
Consensus pattern (42 bp):
TCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
Found at i:2447062 original size:26 final size:26
Alignment explanation
Indices: 2447012--2447089 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 26
2447002 ATAATATAAG
* *
2447012 ATATTATAATTTTTATTT-TA-ATAAT
1 ATATAATAATTTTT-TTTATATTTAAT
2447037 ATATAATAATTTTTTTTATATTTAAT
1 ATATAATAATTTTTTTTATATTTAAT
*
2447063 A-ATGAATAATATTATTTATATATTTAA
1 ATAT-AATAAT-TT-TTTTTATATTTAA
2447090 ATAATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
24 3 0.07
25 17 0.38
26 11 0.24
27 2 0.04
28 12 0.27
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATAATAATTTTTTTTATATTTAAT
Found at i:2447063 original size:29 final size:28
Alignment explanation
Indices: 2447020--2447096 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 28
2447010 AGATATTATA
2447020 ATTTTTAT-TTTAATAATATATAATAATT
1 ATTTTTATATTTAATAATATATAAT-ATT
*
2447048 TTTTTTATATTTAATAATGA-ATAATATT
1 ATTTTTATATTTAATAAT-ATATAATATT
*
2447076 ATTTATATATTTAAATAATAT
1 ATTTTTATATTT-AATAATAT
2447097 TTTAGTAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 21 0.50
29 20 0.48
30 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
ATTTTTATATTTAATAATATATAATATT
Found at i:2447224 original size:90 final size:86
Alignment explanation
Indices: 2447112--2447281 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
2447102 TAAAGATATT
* * * * * *
2447112 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
2447175 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
2447200 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
2447265 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
2447282 AAATAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 19 0.27
89 8 0.11
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:2447483 original size:20 final size:20
Alignment explanation
Indices: 2447425--2447474 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2447415 TTTTCAGATG
2447425 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2447445 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2447465 TTTTCCAGAA
1 TTTTCCAGAA
2447475 TTAAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2447499 original size:15 final size:15
Alignment explanation
Indices: 2447457--2447531 Score: 80
Period size: 15 Copynumber: 5.1 Consensus size: 15
2447447 TTCCAGAAAT
*
2447457 GTAATTCATTTTCCA
1 GTAATTCATATTCCA
* *
2447472 G-AATTAAAATTCCA
1 GTAATTCATATTCCA
*
2447486 GTAATTCATTTTCCA
1 GTAATTCATATTCCA
* *
2447501 GTAACTCAAATTCCA
1 GTAATTCATATTCCA
*
2447516 GTAATTCAGATTCCA
1 GTAATTCATATTCCA
2447531 G
1 G
2447532 ATTCATTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
14 11 0.23
15 37 0.77
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (15 bp):
GTAATTCATATTCCA
Found at i:2447514 original size:30 final size:29
Alignment explanation
Indices: 2447457--2447532 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
2447447 TTCCAGAAAT
*
2447457 GTAATTCATTTTCCAGAATTAAAATTCCA
1 GTAATTCATTTTCCAGAACTAAAATTCCA
*
2447486 GTAATTCATTTTCCAGTAACTCAAATTCCA
1 GTAATTCATTTTCCAG-AACTAAAATTCCA
**
2447516 GTAATTCAGATTCCAGA
1 GTAATTCATTTTCCAGA
2447533 TTCATTTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 17 0.40
30 25 0.60
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAACTAAAATTCCA
Found at i:2455922 original size:11 final size:11
Alignment explanation
Indices: 2455900--2455933 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
2455890 GTTTGATGCT
2455900 TTCTCT-TTGA
1 TTCTCTCTTGA
2455910 TTCTCTCTTGA
1 TTCTCTCTTGA
2455921 TTCTCTCTTGA
1 TTCTCTCTTGA
2455932 TT
1 TT
2455934 GTTGTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.09, C:0.24, G:0.09, T:0.59
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:2458978 original size:23 final size:22
Alignment explanation
Indices: 2458948--2459034 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 22
2458938 GCATGGCCTT
2458948 GTGCATCGATGCACATTCAGGGA
1 GTGCATCGATGCACATTCA-GGA
* *
2458971 GTGCATCGGTGCATC-TTCATGA
1 GTGCATCGATGCA-CATTCAGGA
* *
2458993 -TGTATCGATGTACATTCAAAGGA
1 GTGCATCGATGCACATTC--AGGA
*
2459016 ATGCATCGATGCACTATTC
1 GTGCATCGATGCAC-ATTC
2459035 GGTGTATCGA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
22 2 0.04
23 19 0.38
24 12 0.24
25 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:2463382 original size:22 final size:22
Alignment explanation
Indices: 2463356--2463404 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2463346 TTGGCTCGTC
2463356 TCTTTTCTCGAGGTCTTCCTCT
1 TCTTTTCTCGAGGTCTTCCTCT
2463378 TCTTTTCTCGAGGTCTTCCTCT
1 TCTTTTCTCGAGGTCTTCCTCT
2463400 TCTTT
1 TCTTT
2463405 AAGCATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.04, C:0.31, G:0.12, T:0.53
Consensus pattern (22 bp):
TCTTTTCTCGAGGTCTTCCTCT
Found at i:2464922 original size:64 final size:63
Alignment explanation
Indices: 2464835--2464990 Score: 201
Period size: 64 Copynumber: 2.5 Consensus size: 63
2464825 GTGCACTAAG
* * * *
2464835 AGTGCATCGATGAATTAAATGCATTCGATG-TTTCA-AACAAGTCTGAGT-TCATCGATGCATGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCTGAGTGT-ATCAATGCATGG
2464897 T
63 T
* *
2464898 CTGTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGTATCAATGCATGGT
1 -AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGTATCAATGCATGGT
2464962 AGTGCATCGATGCATAAAATGCATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
2464991 ATGGTGAGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
63 27 0.33
64 44 0.54
65 8 0.10
66 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGTATCAATGCATGGT
Found at i:2464974 original size:18 final size:18
Alignment explanation
Indices: 2464953--2465011 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
2464943 GAGTGTATCA
2464953 ATGCATGGTAGTGCATCG
1 ATGCATGGTAGTGCATCG
** *
2464971 ATGCAT-AAAATGCATTCG
1 ATGCATGGTAGTGCA-TCG
2464989 AT--ATGGTGAGTGCATCG
1 ATGCATGGT-AGTGCATCG
2465006 ATGCAT
1 ATGCAT
2465012 CAATGAGTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
16 2 0.07
17 10 0.33
18 16 0.53
19 2 0.07
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (18 bp):
ATGCATGGTAGTGCATCG
Found at i:2465020 original size:20 final size:20
Alignment explanation
Indices: 2464995--2465032 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2464985 TTCGATATGG
2464995 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
2465015 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
2465033 CCTTCTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:2474055 original size:29 final size:29
Alignment explanation
Indices: 2474014--2474069 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
2474004 TATCTTTTTT
*
2474014 TTTCGAAAAAATTACTAAAATAGCACCCA
1 TTTCGAAAAAATTACCAAAATAGCACCCA
** * *
2474043 TTTCGAATTAATTCCCAGAATAGCACC
1 TTTCGAAAAAATTACCAAAATAGCACC
2474070 AAAACCAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (29 bp):
TTTCGAAAAAATTACCAAAATAGCACCCA
Found at i:2474156 original size:18 final size:18
Alignment explanation
Indices: 2474133--2474207 Score: 114
Period size: 18 Copynumber: 4.0 Consensus size: 18
2474123 TCGGGTCAAC
2474133 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
2474151 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
2474169 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
2474187 GGTAAACGGGTAAACGGGTCG
1 GGT---CGGGTAAACGGGTCG
2474208 TGACCGGTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
18 37 0.71
21 15 0.29
ACGTcount: A:0.20, C:0.16, G:0.47, T:0.17
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:2474183 original size:13 final size:13
Alignment explanation
Indices: 2474117--2474197 Score: 68
Period size: 13 Copynumber: 6.5 Consensus size: 13
2474107 GTTAACGGTC
*
2474117 AACGGGTCGGGTC
1 AACGGGTCGGGTA
2474130 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
2474142 AACGGGTCGGGT-
1 AACGGGTCGGGTA
*
2474154 --CGGGTAAACTGGT-
1 AACGGGT---CGGGTA
2474167 --CGGGTCGGGTA
1 AACGGGTCGGGTA
2474178 AACGGGTCGGGTA
1 AACGGGTCGGGTA
2474191 AACGGGT
1 AACGGGT
2474198 AAACGGGTCG
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 9 0.16
12 11 0.19
13 38 0.66
ACGTcount: A:0.20, C:0.17, G:0.46, T:0.17
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:2474230 original size:10 final size:10
Alignment explanation
Indices: 2474210--2474245 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
2474200 ACGGGTCGTG
2474210 ACCGGTC-AA
1 ACCGGTCAAA
2474219 ACCGGTCAAA
1 ACCGGTCAAA
2474229 ACCGGTTCAAA
1 ACCGG-TCAAA
2474240 ACCGGT
1 ACCGGT
2474246 TTCCAGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:2478733 original size:263 final size:264
Alignment explanation
Indices: 2478266--2478794 Score: 1051
Period size: 263 Copynumber: 2.0 Consensus size: 264
2478256 ATCTTTATAC
2478266 TTAATGCGTACTGTTCATATTTGACTTGCACATTTATGTATGTGAACCTCATAAAATAATATAGA
1 TTAATGCGTACTGTTCATATTTGACTTGCACATTTATGTATGTGAACCTCATAAAATAATATAGA
2478331 ATAAATGTACACTATTGAATTTTATAAGCTAAACGTCCAGATTGCTTTTGTGTGCATGTTACAAG
66 ATAAATGTACACTATTGAATTTTATAAGCTAAACGTCCAGATTGCTTTTGTGTGCATGTTACAAG
2478396 TTTCTTTATTCATTAGAGGATATCAACATTAATGGAAGAGTCTCAATGAATCATTTGAGTACGAT
131 TTTCTTTATTCATTAGAGGATATCAACATTAATGGAAGAGTCTCAATGAATCATTTGAGTACGAT
2478461 AAATGATTACTTATGTGGACATATAAATATTGAAATATTTTAGTTAAGATTGTAAA-TTATTTGT
196 AAATGATTACTTATGTGGACATATAAATATTGAAATATTTTAGTTAAGATTGTAAATTTATTTGT
2478525 ACAT
261 ACAT
2478529 TTAATGCGTACTGTTCATATTTGACTTGCACATTTATGTATGTGAACCTCATAAAATAATATAGA
1 TTAATGCGTACTGTTCATATTTGACTTGCACATTTATGTATGTGAACCTCATAAAATAATATAGA
2478594 ATAAATGTACACTATTGAATTTTATAAGCTAAACGTCCAGATTGCTTTTGTGTGCATGTTACAAG
66 ATAAATGTACACTATTGAATTTTATAAGCTAAACGTCCAGATTGCTTTTGTGTGCATGTTACAAG
2478659 TTTCTTTATTCATTAGAGGATATCAACATTAATGGAAGAGTCTCAATGAATCATTTGAGTACGAT
131 TTTCTTTATTCATTAGAGGATATCAACATTAATGGAAGAGTCTCAATGAATCATTTGAGTACGAT
2478724 AAATGATTACTTATGTGGACATATAAATATTGAAATATTTTAGTTAAGATTGTAAATTTATTTGT
196 AAATGATTACTTATGTGGACATATAAATATTGAAATATTTTAGTTAAGATTGTAAATTTATTTGT
2478789 ACAT
261 ACAT
2478793 TT
1 TT
2478795 TATTTTAATA
Statistics
Matches: 265, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
263 251 0.95
264 14 0.05
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (264 bp):
TTAATGCGTACTGTTCATATTTGACTTGCACATTTATGTATGTGAACCTCATAAAATAATATAGA
ATAAATGTACACTATTGAATTTTATAAGCTAAACGTCCAGATTGCTTTTGTGTGCATGTTACAAG
TTTCTTTATTCATTAGAGGATATCAACATTAATGGAAGAGTCTCAATGAATCATTTGAGTACGAT
AAATGATTACTTATGTGGACATATAAATATTGAAATATTTTAGTTAAGATTGTAAATTTATTTGT
ACAT
Found at i:2480272 original size:23 final size:24
Alignment explanation
Indices: 2480238--2480299 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
2480228 TTGTAGTCGA
*
2480238 AACTGCCACATAGAAT-TGCATCG
1 AACTGCCACATAGAATATGCACCG
* * *
2480261 AAGTGCTACATAGAATATGTACCG
1 AACTGCCACATAGAATATGCACCG
2480285 AACTGCCACATAGAA
1 AACTGCCACATAGAA
2480300 ATGTTCTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (24 bp):
AACTGCCACATAGAATATGCACCG
Found at i:2480295 original size:24 final size:24
Alignment explanation
Indices: 2480238--2480303 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
2480228 TTGTAGTCGA
* *
2480238 AACTGCCACATAGAAT-TGCATCG
1 AACTGCCACATAGAATATGTACCG
* *
2480261 AAGTGCTACATAGAATATGTACCG
1 AACTGCCACATAGAATATGTACCG
2480285 AACTGCCACATAGAA-ATGT
1 AACTGCCACATAGAATATGT
2480304 TCTGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (24 bp):
AACTGCCACATAGAATATGTACCG
Found at i:2480353 original size:23 final size:23
Alignment explanation
Indices: 2480318--2480392 Score: 123
Period size: 23 Copynumber: 3.2 Consensus size: 23
2480308 AAGAACCGTG
2480318 TAGAATTTGTCCCGAATGACCACA
1 TAGAA-TTGTCCCGAATGACCACA
*
2480342 TAGAATTGTCCCGAAGGACCACA
1 TAGAATTGTCCCGAATGACCACA
*
2480365 TAGAATTGTCCCGAATGACCGCA
1 TAGAATTGTCCCGAATGACCACA
2480388 TAGAA
1 TAGAA
2480393 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 43 0.90
24 5 0.10
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (23 bp):
TAGAATTGTCCCGAATGACCACA
Found at i:2480369 original size:47 final size:47
Alignment explanation
Indices: 2480243--2480392 Score: 137
Period size: 47 Copynumber: 3.2 Consensus size: 47
2480233 GTCGAAACTG
* * * *
2480243 CCACATAGAATTG-CATCGAAGTG-CTACATAGAATATGTACCGAACTG-
1 CCACATAGAATTGTC-CCGAAG-GACCACATAGAATTTGTCCCGAA-TGA
* * * * ***
2480290 CCACATAGAAATGTTCTGAAGAACCGTGTAGAATTTGTCCCGAATGA
1 CCACATAGAATTGTCCCGAAGGACCACATAGAATTTGTCCCGAATGA
2480337 CCACATAGAATTGTCCCGAAGGACCACATAGAA-TTGTCCCGAATGA
1 CCACATAGAATTGTCCCGAAGGACCACATAGAATTTGTCCCGAATGA
*
2480383 CCGCATAGAA
1 CCACATAGAA
2480393 CCCTCGACTC
Statistics
Matches: 81, Mismatches: 19, Indels: 7
0.76 0.18 0.07
Matches are distributed among these distances:
46 24 0.30
47 57 0.70
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (47 bp):
CCACATAGAATTGTCCCGAAGGACCACATAGAATTTGTCCCGAATGA
Found at i:2481155 original size:20 final size:20
Alignment explanation
Indices: 2481105--2481156 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2481095 TTCACCTTAT
*
2481105 AGTATCGATAATGTTCTTCC
1 AGTATCGATACTGTTCTTCC
2481125 AGTATCGATACTGTTCTTCC
1 AGTATCGATACTGTTCTTCC
*
2481145 AGTATCAATACT
1 AGTATCGATACT
2481157 CCAACACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTGTTCTTCC
Found at i:2488659 original size:13 final size:13
Alignment explanation
Indices: 2488638--2488668 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2488628 CCAGAAACAT
*
2488638 ATGAGGAGGGAAC
1 ATGATGAGGGAAC
2488651 ATGATGAGGGAAC
1 ATGATGAGGGAAC
2488664 ATGAT
1 ATGAT
2488669 AAGAAAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.16
Consensus pattern (13 bp):
ATGATGAGGGAAC
Found at i:2488948 original size:18 final size:18
Alignment explanation
Indices: 2488927--2488961 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2488917 TAAAAAAATG
2488927 AAAAGAAAGAA-AAAAGAA
1 AAAAGAAA-AATAAAAGAA
2488945 AAAAGAAAAATAAAAGA
1 AAAAGAAAAATAAAAGA
2488962 GAATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAATAAAAGAA
Found at i:2488953 original size:29 final size:29
Alignment explanation
Indices: 2488885--2488961 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
2488875 ATCATTCGCC
* *
2488885 TGAAGAAAGAAAA-AAAATAAAGAAAAAA
1 TGAAAAAAGAAAATAAAAGAAAGAAAAAA
**
2488913 TGATTAAA-AAAATGAAAAGAAAGAAAAAA
1 TGAAAAAAGAAAAT-AAAAGAAAGAAAAAA
2488942 -GAAAAAAGAAAAATAAAAGA
1 TGAAAAAAG-AAAATAAAAGA
2488962 GAATAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 20 0.50
30 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (29 bp):
TGAAAAAAGAAAATAAAAGAAAGAAAAAA
Found at i:2490720 original size:133 final size:132
Alignment explanation
Indices: 2490239--2490722 Score: 457
Period size: 133 Copynumber: 3.6 Consensus size: 132
2490229 GAAGACAAGA
* * * * * * * *** * *
2490239 GGAACAAATCTACCTCGATTTAATATTCCATGAAGAACAGTGGAATGAATCAACACTTCCAAAGC
1 GGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATGTTTCCAGATC
* * * * * * * *
2490304 TTATTTTCCTTGAAGAAG-AAGTAGAACAAATCCCTTCTTTCTAGATTTGATCTTCTCTGAGTAG
66 TGATTTTCC-TGAAGAAGCAA-CATAACAGACCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAG
2490368 CAGT
129 CAGT
* * ** ** * *
2490372 GAAACAAGTCTGCCTCGATTAAATCTTCTTTGAAGAATAGTGGCATGAATCAATGATTCTAGATC
1 GGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATGTTTCCAGATC
* * * * * * *
2490437 TGATTTTCCTTGAAGAAACAACATAATATATCCCCTCTTTCCAAATTTGATATTCCCTGAGTAGG
66 TGATTTTCC-TGAAGAAGCAACATAACAGACCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGC
2490502 AGT
130 AGT
* * *
2490505 GGAACAAGTTTGCCTCAATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATTTTTCCAGATC
1 GGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATGTTTCCAGATC
* * * *
2490570 TAATTTTCCCTGTAGAAGCAACGTAACAGACCCCCTCTTTCCAGATTTGATCTTCCCTGGGTAGC
66 TGATTTT-CCTGAAGAAGCAACATAACAGACCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGC
2490635 AGT
130 AGT
* * * * * * *
2490638 GGAACAAGTCTACCTCGATTCAATTTTCCCTAAAGAACAGTGAAATGAATAAATGTTTCCAAATT
1 GGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATGTTTCCAGATC
* *
2490703 TGATCTACACTGAAGAAGCA
66 TGATTTTC-CTGAAGAAGCA
2490723 GTGGAGCAGA
Statistics
Matches: 285, Mismatches: 63, Indels: 6
0.81 0.18 0.02
Matches are distributed among these distances:
132 1 0.00
133 280 0.98
134 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (132 bp):
GGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATGTTTCCAGATC
TGATTTTCCTGAAGAAGCAACATAACAGACCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGCA
GT
Found at i:2490948 original size:3 final size:3
Alignment explanation
Indices: 2490942--2491020 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
2490932 GTTGTTGTTG
2490942 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2490990 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2491021 TTCAAGTTAC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2492183 original size:109 final size:109
Alignment explanation
Indices: 2491959--2492174 Score: 265
Period size: 109 Copynumber: 2.0 Consensus size: 109
2491949 AACTCTCGAA
* * *
2491959 TGTTTTTGTATGTTAGTCACCTGTAAGGACCGAATCTGCTATTTACCCACTTTTAATGCATGCTT
1 TGTTTTTGCATGTTAGTCACCTGTAAGGACCGAATCTGCTATTTACCCACTTTTAATGCATGATA
* *
2492024 TATATTTTTTGGATATTTGTTGTTTAGTCTCCCATTGTTTAGTG
66 TATATTTTTGGGATATTTGTTGTTTAGTCTCCCATTATTTAGTG
* * ** * * *
2492068 TGTTTTTGCATGTTGGTCACCTGTAGGGATTGAAAT-TGTTATTTACCCATTTTGTTATGCATGA
1 TGTTTTTGCATGTTAGTCACCTGTAAGGACCG-AATCTGCTATTTACCCACTTT-TAATGCATGA
* * *
2492132 TATGTGTTTTTGGGATATTTGTTGTTTAGT-TCCCCTTATTTAG
64 TATATATTTTTGGGATATTTGTTGTTTAGTCTCCCATTATTTAG
2492175 GCTTTTTTTA
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
109 53 0.59
110 37 0.41
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (109 bp):
TGTTTTTGCATGTTAGTCACCTGTAAGGACCGAATCTGCTATTTACCCACTTTTAATGCATGATA
TATATTTTTGGGATATTTGTTGTTTAGTCTCCCATTATTTAGTG
Found at i:2492540 original size:22 final size:24
Alignment explanation
Indices: 2492515--2492567 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2492505 TTTTATTTTA
2492515 TTTTATTCA-TGTTTGCATGTTG-
1 TTTTATTCAGTGTTTGCATGTTGC
* *
2492537 TTTTATTTTAGTTTTTGCATGTTGC
1 TTTTA-TTCAGTGTTTGCATGTTGC
2492562 TTTTAT
1 TTTTAT
2492568 GTTATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 3 0.12
24 13 0.50
25 5 0.19
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.64
Consensus pattern (24 bp):
TTTTATTCAGTGTTTGCATGTTGC
Found at i:2492541 original size:32 final size:30
Alignment explanation
Indices: 2492508--2492581 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
2492498 TGATGGTTTT
* *
2492508 TATTTTATTTTATTCATGTTTGCATGTTGTTT
1 TATTTTATTTTATGCATG-TTGC-TGTTATTT
* *
2492540 TATTTTAGTTTT-TGCATGTTGCTTTTATGT
1 TATTTTA-TTTTATGCATGTTGCTGTTATTT
2492570 TATTTTATTTTA
1 TATTTTATTTTA
2492582 GTCACTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 4 0.11
30 12 0.33
31 4 0.11
32 12 0.33
33 4 0.11
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.66
Consensus pattern (30 bp):
TATTTTATTTTATGCATGTTGCTGTTATTT
Found at i:2492558 original size:24 final size:24
Alignment explanation
Indices: 2492526--2492575 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2492516 TTTATTCATG
*
2492526 TTTGCATGTTG-TTTTATTTTAGTT
1 TTTGCATGTTGCTTTTATGTTA-TT
2492550 TTTGCATGTTGCTTTTATGTTATT
1 TTTGCATGTTGCTTTTATGTTATT
2492574 TT
1 TT
2492576 ATTTTAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.12, C:0.06, G:0.16, T:0.66
Consensus pattern (24 bp):
TTTGCATGTTGCTTTTATGTTATT
Found at i:2492771 original size:30 final size:30
Alignment explanation
Indices: 2492737--2492796 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2492727 CTTTTGATTA
*
2492737 TTTTAAAATGAAAGTCTATCACATTAAGTG
1 TTTTAAAATGAAACTCTATCACATTAAGTG
*
2492767 TTTTAAAATGAAACTCTATCCCATTAAGTG
1 TTTTAAAATGAAACTCTATCACATTAAGTG
2492797 ACACGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (30 bp):
TTTTAAAATGAAACTCTATCACATTAAGTG
Found at i:2493324 original size:130 final size:131
Alignment explanation
Indices: 2493070--2493436 Score: 465
Period size: 130 Copynumber: 2.8 Consensus size: 131
2493060 TTAATATTGA
* * * * * *
2493070 AAATAGTAATATCTTTTCATATCGGTTGGAGCAATAAATGATTGTTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
** ** * *
2493135 TTATTCTTAATTGGAAATAATTAGATATTATTGTTTTCTTTC-GAATCAATATTGATTTTAGGA-
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCTGAATCAATATTGATTTTAAGAT
2493198 C
131 C
* *
2493199 AAAGTAGTGATATCTCTTCATTTCGATTGGAGTAATATATGATTGCTTTAAGGCATAAGAGGTCA
1 AAA-TAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCA
*
2493264 TTTATTCTCGATT-GAAATAATTAAATATTATCATTTTCTCTCTG-ATCAATATTGAGTTTTAAG
65 TTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCTGAATCAATATTGA-TTTTAAG
*
2493327 ATG
129 ATC
* * * * * * *
2493330 ACATAGTGACATCTCTTCATTACGATTGGAATAATAAATGACTGCTTTTAGGCATGAGTGGTCA-
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
*
2493394 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCT
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCT
2493437 TAGAATTATT
Statistics
Matches: 206, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
129 51 0.25
130 153 0.74
131 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCTGAATCAATATTGATTTTAAGAT
C
Found at i:2496478 original size:56 final size:56
Alignment explanation
Indices: 2496418--2496530 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 56
2496408 TTGAGATAAA
* *
2496418 TTGTCTCAAGTGAGATGAAA-AATTTCAAGGAAAAATATCTTAAGTGAGATAAAATT
1 TTGTCTCAAGTGAGA-CAAATAATTTCAAGGAAAAATATCTCAAGTGAGATAAAATT
* ** *
2496474 TTGTCTCGAGTGAGACAAATGTTTTCAAGGGAAAATATCTCAAGTGAGATAAAATT
1 TTGTCTCAAGTGAGACAAATAATTTCAAGGAAAAATATCTCAAGTGAGATAAAATT
2496530 T
1 T
2496531 ATTTTCAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 3 0.06
56 47 0.94
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (56 bp):
TTGTCTCAAGTGAGACAAATAATTTCAAGGAAAAATATCTCAAGTGAGATAAAATT
Found at i:2496520 original size:34 final size:34
Alignment explanation
Indices: 2496477--2496591 Score: 122
Period size: 34 Copynumber: 3.3 Consensus size: 34
2496467 TAAAATTTTG
* *
2496477 TCTCGAGTGAGACAAATGTTTTCAAGGGAAAATA
1 TCTCAAGTGAGACAAATATTTTCAAGGGAAAATA
* * *
2496511 TCTCAAGTGAGATAAAATTTATTTTCAAGAGAAAATG
1 TCTCAAGTGAGA-CAAA--TATTTTCAAGGGAAAATA
* * * *
2496548 TATCGAGTAAGACAAAAATTTTCAAGGGAAAATA
1 TCTCAAGTGAGACAAATATTTTCAAGGGAAAATA
2496582 TCTCAAGTGA
1 TCTCAAGTGA
2496592 AATGCAATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
34 33 0.52
35 3 0.05
36 3 0.05
37 24 0.38
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (34 bp):
TCTCAAGTGAGACAAATATTTTCAAGGGAAAATA
Found at i:2496601 original size:127 final size:128
Alignment explanation
Indices: 2496368--2496611 Score: 296
Period size: 127 Copynumber: 1.9 Consensus size: 128
2496358 GAGAAAGAGA
** ** * * * *
2496368 TTTTCAAGAGAATGTATCTCAAGTGAGATAAAATTTTGTTTTGAGATAAATTGTCTCAAGTGAGA
1 TTTTCAAGAGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAAATGTATCAAGTAAGA
* * *
2496433 TGAAAAATTTCAAGGAAAAATATCTTAAGTGAGATAAAA-TTTTGTCTCGAGTGAGACAAATG
66 TCAAAAATTTCAAGGAAAAATATCTCAAGTGAAATAAAATTTTTGTCTCGAGTGAGACAAATG
* *
2496495 TTTTCAAGGGAAAATATCTCAAGTGAGATAAAATTTAT-TTTCAAGAGAAAATGTATCGAGTAAG
1 TTTTCAAGAGAAAATATCTCAAGTGAGATAAAATTT-TGTTTCAAGAGAAAATGTATCAAGTAAG
* ** *
2496559 A-CAAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGCAATTTTTGTTTCGAG
65 ATCAAAAA-TTTCAAGGAAAAATATCTCAAGTGAAATAAAATTTTTGTCTCGAG
2496612 AGAAACTATC
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
126 5 0.05
127 80 0.82
128 12 0.12
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (128 bp):
TTTTCAAGAGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAAATGTATCAAGTAAGA
TCAAAAATTTCAAGGAAAAATATCTCAAGTGAAATAAAATTTTTGTCTCGAGTGAGACAAATG
Found at i:2496662 original size:72 final size:71
Alignment explanation
Indices: 2496477--2496777 Score: 268
Period size: 72 Copynumber: 4.2 Consensus size: 71
2496467 TAAAATTTTG
** ** *
2496477 TCTCGAGTGAGACAAATGTTTTCAAGGGAAAATATCTCAAGTGAGATAAAATTTAT-TTTCAAGA
1 TCTCGAGTGAGACAAA-AATTTCAAGGGAAAATATCTCAAGTGAGATGCAATTTTTGTTTCAAGA
*
2496541 GAAAATG
65 GAAAATA
* * * *
2496548 TATCGAGTAAGACAAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGCAATTTTTGTTTCGAGA
1 TCTCGAGTGAGACAAAAA-TTTCAAGGGAAAATATCTCAAGTGAGATGCAATTTTTGTTTCAAGA
*
2496613 GAAACTA
65 GAAAATA
* * *
2496620 TCTCGAGTGAGACGAAAAATTCCAAGAGAAAATATCTTAAGTGAGATGCAATTTTTGTTTCAAG-
1 TCTCGAGTGAGAC-AAAAATTTCAAGGGAAAATATCTCAAGTGAGATGCAATTTTTGTTTCAAGA
* * *
2496684 GAGATTG
65 GAAAATA
** * ***
2496691 TCTTAAGTGAGACAAAATTTGTTTTTGAGGAAAACTATCTCAAGTGAGAT--AATTTTTTTGTTT
1 TCTCGAGTGAGACAAAA-AT-TTCAAG-GGAAAA-TATCTCAAGTGAGATGCAA--TTTTTGTTT
* *
2496754 CAAAAGAAACTA
60 CAAGAGAAAATA
2496766 TCTCGAGTGAGA
1 TCTCGAGTGAGA
2496778 TGAATTTTAT
Statistics
Matches: 184, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
70 4 0.02
71 63 0.34
72 67 0.36
73 10 0.05
74 26 0.14
75 14 0.08
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Consensus pattern (71 bp):
TCTCGAGTGAGACAAAAATTTCAAGGGAAAATATCTCAAGTGAGATGCAATTTTTGTTTCAAGAG
AAAATA
Found at i:2496807 original size:36 final size:35
Alignment explanation
Indices: 2496713--2496816 Score: 120
Period size: 38 Copynumber: 2.9 Consensus size: 35
2496703 CAAAATTTGT
* * *
2496713 TTTTGAGGAAAACTATCTCAAGTGAGATAATTTTTT
1 TTTTAAGGAAAACTATCTCGAGTGAGATAA-TTTTA
*
2496749 TGTTTCAA-AAGAAACTATCTCGAGTGAGATGAATTTTA
1 T-TTT-AAGGA-AAACTATCTCGAGTGAGAT-AATTTTA
2496787 TTTTAAGGAAAACTATCTCGAGTGAGATAA
1 TTTTAAGGAAAACTATCTCGAGTGAGATAA
2496817 AATTTATATT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
35 2 0.03
36 22 0.38
37 8 0.14
38 24 0.41
39 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (35 bp):
TTTTAAGGAAAACTATCTCGAGTGAGATAATTTTA
Found at i:2496823 original size:36 final size:36
Alignment explanation
Indices: 2496696--2496823 Score: 123
Period size: 36 Copynumber: 3.5 Consensus size: 36
2496686 GATTGTCTTA
* * * *
2496696 AGTGAGACAAAATTTGTTTTTGAGGAAAACTATCTCA
1 AGTGAGATAAAATTT-ATTTTAAGGAAAACTATCTCG
** * *
2496733 AGTGAGATAATTTTTTTGTTTCAA-AAGAAACTATCTCG
1 AGTGAGATAAAATTTAT-TTT-AAGGA-AAACTATCTCG
* *
2496771 AGTGAGATGAATTTTATTTTAAGGAAAACTATCTCG
1 AGTGAGATAAAATTTATTTTAAGGAAAACTATCTCG
2496807 AGTGAGATAAAATTTAT
1 AGTGAGATAAAATTTAT
2496824 ATTTCGAGGG
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
36 30 0.40
37 20 0.27
38 25 0.33
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (36 bp):
AGTGAGATAAAATTTATTTTAAGGAAAACTATCTCG
Found at i:2505375 original size:26 final size:26
Alignment explanation
Indices: 2505346--2505405 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
2505336 GTATTTAGGG
2505346 AATTTCCAAGGGTACTGAACCCTAGA
1 AATTTCCAAGGGTACTGAACCCTAGA
2505372 AATTTCCAAGGGTACTGAACCCTAGA
1 AATTTCCAAGGGTACTGAACCCTAGA
2505398 AATTTCCA
1 AATTTCCA
2505406 CTATAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (26 bp):
AATTTCCAAGGGTACTGAACCCTAGA
Found at i:2513127 original size:21 final size:21
Alignment explanation
Indices: 2513089--2513130 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2513079 CTACGATAGG
* *
2513089 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACCACTTCATA
*
2513110 GGGTATCGATACTACTTCATA
1 GGGTATCGATACCACTTCATA
2513131 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (21 bp):
GGGTATCGATACCACTTCATA
Found at i:2513334 original size:29 final size:29
Alignment explanation
Indices: 2513313--2513370 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
2513303 AAACTTTGAA
2513313 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
2513342 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
2513371 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2513360 original size:30 final size:30
Alignment explanation
Indices: 2513313--2513372 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
2513303 AAACTTTGAA
2513313 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
2513342 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
2513373 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:2513535 original size:19 final size:21
Alignment explanation
Indices: 2513482--2513540 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
2513472 ATGTTTAATG
2513482 AAAAGGAT-ATCAATTGTTAC
1 AAAAGGATAATCAATTGTTAC
*
2513502 AAAAGGATACT-AATTGTTA-
1 AAAAGGATAATCAATTGTTAC
2513521 AAAA-GATAATCAATTGTTAC
1 AAAAGGATAATCAATTGTTAC
2513541 CAATTGTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.15
19 12 0.35
20 16 0.47
21 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (21 bp):
AAAAGGATAATCAATTGTTAC
Found at i:2515340 original size:20 final size:22
Alignment explanation
Indices: 2515315--2515354 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2515305 AGTTGTATAT
2515315 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
2515335 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
2515355 TCTGCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:2515410 original size:21 final size:21
Alignment explanation
Indices: 2515384--2515425 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2515374 TTACGATAGG
*
2515384 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCACTTCATA
*
2515405 GGGTATCGGTACTACTTCATA
1 GGGTATCGGTACCACTTCATA
2515426 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (21 bp):
GGGTATCGGTACCACTTCATA
Found at i:2515678 original size:30 final size:30
Alignment explanation
Indices: 2515630--2515686 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2515620 TTTGAATAAA
*
2515630 TTCAATTAAGTTCAAAAA-CATTTTGCAAG
1 TTCAATTAAGTCCAAAAACCATTTTGCAAG
2515659 TTCAATTCAAGTCCAAAAACCATTTTGC
1 TTCAATT-AAGTCCAAAAACCATTTTGC
2515687 CTTAAATTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (30 bp):
TTCAATTAAGTCCAAAAACCATTTTGCAAG
Found at i:2516117 original size:2 final size:2
Alignment explanation
Indices: 2516110--2516183 Score: 125
Period size: 2 Copynumber: 37.5 Consensus size: 2
2516100 ATATAATGTG
2516110 TA TA TA TA -A TGA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2516151 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 T
2516184 GCTATGTAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.03
2 65 0.94
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2516124 original size:8 final size:7
Alignment explanation
Indices: 2516086--2516182 Score: 85
Period size: 8 Copynumber: 13.6 Consensus size: 7
2516076 TATGTATATG
2516086 TATAATA
1 TATAATA
*
2516093 TGTAATAA
1 TATAAT-A
*
2516101 TATAATG
1 TATAATA
*
2516108 TGT-ATA
1 TATAATA
2516114 TATAATGA
1 TATAAT-A
2516122 TATAATA
1 TATAATA
2516129 TAT-ATA
1 TATAATA
2516135 TAT-ATA
1 TATAATA
2516141 TAT-ATA
1 TATAATA
2516147 TATATATA
1 TATA-ATA
2516155 TATATATA
1 TATA-ATA
2516163 TATATATA
1 TATA-ATA
2516171 TATATATA
1 TATA-ATA
2516179 TATA
1 TATA
2516183 TGCTATGTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
6 22 0.28
7 13 0.16
8 44 0.56
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (7 bp):
TATAATA
Found at i:2516271 original size:18 final size:18
Alignment explanation
Indices: 2516214--2516274 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
2516204 ATGTAACGGC
*
2516214 ATAATATATATACATTAT
1 ATAATATGTATACATTAT
*
2516232 ATAATTATAGTATACA--AC
1 ATAA-TAT-GTATACATTAT
*
2516250 ATAATATGTATATATTAT
1 ATAATATGTATACATTAT
2516268 ATAATAT
1 ATAATAT
2516275 AAACAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.17
17 3 0.09
18 17 0.49
19 3 0.09
20 6 0.17
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATAATATGTATACATTAT
Found at i:2517752 original size:27 final size:27
Alignment explanation
Indices: 2517721--2517785 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
2517711 TATAGAAAAC
* * *
2517721 AAATTTATTAATCTAGTGATTATAATT
1 AAATTTATTAATATAATAATTATAATT
2517748 AAATTTATTAATATAATAATTATAATT
1 AAATTTATTAATATAATAATTATAATT
2517775 AGTAATTTATT
1 A--AATTTATT
2517786 TTAAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 25 0.76
29 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
AAATTTATTAATATAATAATTATAATT
Found at i:2521454 original size:19 final size:20
Alignment explanation
Indices: 2521408--2521460 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
2521398 GTTATATAAA
2521408 ATATATTTT-TATTGTAATT
1 ATATATTTTATATTGTAATT
* *
2521427 ATATTTTTTAT-TTGTATTT
1 ATATATTTTATATTGTAATT
* *
2521446 TTATATTTTAAATTG
1 ATATATTTTATATTG
2521461 ATATAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (20 bp):
ATATATTTTATATTGTAATT
Found at i:2521482 original size:3 final size:3
Alignment explanation
Indices: 2521463--2521500 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
2521453 TTAAATTGAT
2521463 ATA ATTA ATA CATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
2521501 TTTTTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2522401 original size:14 final size:14
Alignment explanation
Indices: 2522382--2522408 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2522372 GTTCATTTAT
2522382 GTTCATTTATGTTC
1 GTTCATTTATGTTC
2522396 GTTCATTTATGTT
1 GTTCATTTATGTT
2522409 TGAACAGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:2528612 original size:21 final size:20
Alignment explanation
Indices: 2528588--2528626 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2528578 CAATCCCTTA
*
2528588 ATTTTACACGATAAACTATAC
1 ATTTAACAC-ATAAACTATAC
*
2528609 ATTTAACACTTAAACTAT
1 ATTTAACACATAAACTAT
2528627 TAGTTCTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTTAACACATAAACTATAC
Found at i:2528832 original size:21 final size:21
Alignment explanation
Indices: 2528789--2528832 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2528779 CACTCATATT
**
2528789 TTTAATTACTTAACTTTTTAA
1 TTTAATTACTTAACTTTCAAA
*
2528810 TTTAATTGCTTAACTTTCAAA
1 TTTAATTACTTAACTTTCAAA
2528831 TT
1 TT
2528833 ATTCTTAATT
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:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAATTACTTAACTTTCAAA
Found at i:2529913 original size:2 final size:2
Alignment explanation
Indices: 2529906--2529950 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2529896 TTAGGGACAT
2529906 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2529948 AG A
1 AG A
2529951 AAAAATTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2531063 original size:18 final size:19
Alignment explanation
Indices: 2531022--2531060 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
2531012 TTGGTTCACA
2531022 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAG-GG
2531042 GAATGTAAGATTACCAGGG
1 GAATGTAAGATTACCAGGG
2531061 AATAGGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.23
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGG
Found at i:2539196 original size:49 final size:49
Alignment explanation
Indices: 2539124--2539224 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
2539114 CTAAGTATTA
2539124 AGTTGATAAAAGAAATAAGGATTCTGTTAGAACCCATTTTGAATGGTAT
1 AGTTGATAAAAGAAATAAGGATTCTGTTAGAACCCATTTTGAATGGTAT
2539173 AGTTGATAAAAGAAATAAGGATTCTGTTAGAACCCATTTTGAATGGTAT
1 AGTTGATAAAAGAAATAAGGATTCTGTTAGAACCCATTTTGAATGGTAT
2539222 AGT
1 AGT
2539225 GGTGACAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.33
Consensus pattern (49 bp):
AGTTGATAAAAGAAATAAGGATTCTGTTAGAACCCATTTTGAATGGTAT
Found at i:2541336 original size:22 final size:23
Alignment explanation
Indices: 2541311--2541354 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2541301 AATTAAGTTT
2541311 TAATATTA-AAA-TAATTTCAAAA
1 TAATATTACAAAGT-ATTTCAAAA
*
2541333 TAATTTTACAAAGTATTTCAAA
1 TAATATTACAAAGTATTTCAAA
2541355 CAATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATATTACAAAGTATTTCAAAA
Found at i:2549387 original size:22 final size:21
Alignment explanation
Indices: 2549327--2549386 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
2549317 TTTTAGTGCA
2549327 AAGGGAATCGATACCCCCTTG
1 AAGGGAATCGATACCCCCTTG
*
2549348 AAGAGGAATCGATTCCCCCTTG
1 AAG-GGAATCGATACCCCCTTG
2549370 -AGGGAATCGATACCCCC
1 AAGGGAATCGATACCCCC
2549387 CACGGGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 14 0.39
21 5 0.14
22 17 0.47
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.18
Consensus pattern (21 bp):
AAGGGAATCGATACCCCCTTG
Found at i:2559931 original size:45 final size:47
Alignment explanation
Indices: 2559835--2559940 Score: 119
Period size: 45 Copynumber: 2.3 Consensus size: 47
2559825 AAACTTAGAG
*
2559835 TGAAAACCTGCAAAGGACGATCTAGGAAACAAAACGAGGGTTCAAGA
1 TGAAAACCTGTAAAGGACGATCTAGGAAACAAAACGAGGGTTCAAGA
* * * * *
2559882 TGAAAACCTGTAAAGGGC-ATCT-TGAAACCAAAGGA-GGTCTCAAGT
1 TGAAAACCTGTAAAGGACGATCTAGGAAACAAAACGAGGGT-TCAAGA
*
2559927 TGAAAACCCGTAAA
1 TGAAAACCTGTAAA
2559941 TGGTGACTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
44 3 0.06
45 28 0.55
46 4 0.08
47 16 0.31
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (47 bp):
TGAAAACCTGTAAAGGACGATCTAGGAAACAAAACGAGGGTTCAAGA
Found at i:2560037 original size:20 final size:20
Alignment explanation
Indices: 2560012--2560059 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2560002 ATTGATAAAG
2560012 GCATCAGATTGTGGTTGAAT
1 GCATCAGATTGTGGTTGAAT
*
2560032 GCATCATATTGTGGTTGAAT
1 GCATCAGATTGTGGTTGAAT
2560052 GCATCAGA
1 GCATCAGA
2560060 AGTTCAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (20 bp):
GCATCAGATTGTGGTTGAAT
Found at i:2562037 original size:2 final size:2
Alignment explanation
Indices: 2562030--2562070 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2562020 GTTACAAAAC
2562030 AT AT 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 AT AT A
2562071 ATTTTTATTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.