Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 35
Found at i:3253880 original size:2 final size:2
Alignment explanation
Indices: 3253873--3253900 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3253863 GCTTGTGGTC
3253873 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
3253901 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3264454 original size:257 final size:257
Alignment explanation
Indices: 3263962--3264967 Score: 1275
Period size: 257 Copynumber: 3.9 Consensus size: 257
3263952 GTGATTTTCA
* * * * * *
3263962 AAAAATGAGAAAGTTATTTCCAAAGTATCTCATTTAAATATTTT-ATGAAAATAAAATTTTTGAA
1 AAAAATGAGAAAGTGATTTTCAAAGTTTCCCATTT-AATATTTTCA-GAAAATGAAATCTTTGAA
* * **
3264026 GAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTTTTTC
64 AAGTAAGAAAGCGATTTCCAAAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
* * * ** *
3264091 GGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATACTTTGGGTTGTCTATCAGTCTTTTGAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCTTTCGAG
* *
3264156 TAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTATGATGTTTTCACATGAATTTG
194 TAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAAGATGTTTTCACATGAATTTG
* *
3264220 ACAAACGAGAAAGTGATTTTCAAAGTTTCCCATTTAATATTTTCAGAAAATGAAATCTTTGAAAA
1 AAAAATGAGAAAGTGATTTTCAAAGTTTCCCATTTAATATTTTCAGAAAATGAAATCTTTGAAAA
* *
3264285 GTAAGAAAGCGATTTCTAGAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
66 GTAAGAAAGCGATTTCCAAAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
* * * * * * * *
3264350 GCCATCATTAAGCCTTTCAAGCATCATGATTAAATCCTTCGAGTCATATGTAAGTCTTTCGAGTA
131 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCTTTCGAGTA
* * * *
3264415 AGATGATAAGTACTTGGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTTACATGAATTTG
196 AGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAAGATGTTTTCACATGAATTTG
* * * * *
3264477 AAAAATTG-GAAAGCGATTTTC-AAGTTTACTATTTAATATTTTCAGAAAATGAAATTTTTGAAG
1 AAAAA-TGAGAAAGTGATTTTCAAAGTTTCCCATTTAATATTTTCAGAAAATGAAATCTTTGAAA
* * * * * * *
3264540 AGTAAGAAAGTGATTTCCAAAGCTTCTTACCCAGTAAACTATTTCTAAAATTGGTAATTCCTTTG
65 AGTAAGAAAGCGATTTCCAAAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCG
* * * *
3264605 GGCCATCAATAAGTCTTTCGATCATGATGATTAAATCTTTCGGGGTCATCCATCAGTCTTTCGAG
130 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-GGGTCATCTATCAGTCTTTCGAG
* * * * * *
3264670 GAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGAT-TCTTTCATATGATGTTT
194 TAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAAGATGT-TTTCACATGA--ATT
3264734 GTG
256 -TG
* * * * *
3264737 AAAAATGAGAAAAGTAATTTTCAAAGTTTCTCACTTAATATTTTCATAAAATGAAACCTTTGAAA
1 AAAAATGAG-AAAGTGATTTTCAAAGTTTCCCATTTAATATTTTCAGAAAATGAAATCTTTGAAA
* *
3264802 AGTAAGAAAGCGATTTCCAAAGTTT-ATTATCTAGTAAACTATTTCCAAAATTTGTAAGTCCTTC
65 AGTAAGAAAGCGATTTCCAAAGTTTCA-TACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
* *
3264866 GGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCAAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCTTTCGAG
* * *
3264931 CAAGATGATAAGTCCTTCGGGCCAACTATAAGACCTT
194 TAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTT
3264968 TGGGCACGAT
Statistics
Matches: 640, Mismatches: 97, Indels: 19
0.85 0.13 0.03
Matches are distributed among these distances:
256 130 0.20
257 275 0.43
258 31 0.05
259 4 0.01
260 8 0.01
261 65 0.10
262 127 0.20
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (257 bp):
AAAAATGAGAAAGTGATTTTCAAAGTTTCCCATTTAATATTTTCAGAAAATGAAATCTTTGAAAA
GTAAGAAAGCGATTTCCAAAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCTTTCGAGTA
AGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAAGATGTTTTCACATGAATTTG
Found at i:3264907 original size:42 final size:41
Alignment explanation
Indices: 3264860--3264954 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 41
3264850 AATTTGTAAG
* *
3264860 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGA-TAAA
* * * *
3264902 TCCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATAAA
3264943 TCCTTCGGGCCA
1 TCCTTCGGGCCA
3264955 ACTATAAGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 14 0.30
42 32 0.70
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:3265619 original size:134 final size:134
Alignment explanation
Indices: 3265418--3265664 Score: 314
Period size: 134 Copynumber: 1.8 Consensus size: 134
3265408 CAAATCGATC
* * * ** * * *
3265418 TCGATTCAATTTTCCCTGAAGAGAAACGAAGTGGATTAAATTTTTCTTGAGTCTGATCTCCCCTA
1 TCGACTCAATCTTCCCTGAAGAGAAACGAAGTGGATGAAAACTTTATCGAGTCTGATCTACCCTA
* * * * **
3265483 AAGAGTAGCGGATCATATTATTTTTCTTTTAGATTTGGTCTTCCTGAAGAGCAACGAAGCAAATC
66 AAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGGTAATCCTGAAGAGCAACGAAGCAAATC
3265548 AAGT
131 AAGT
* * * *
3265552 TCGACTCAATCTTCCCTGAAGAGCAGCGAAGTTGATGAAAACTTTATCGAGTTTGATCTACCCTA
1 TCGACTCAATCTTCCCTGAAGAGAAACGAAGTGGATGAAAACTTTATCGAGTCTGATCTACCCTA
* *
3265617 AAGATTAGCGGAGCAGATTCTTCTTCTTTCAGATTTGGTAATCCTGAA
66 AAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGGTAATCCTGAA
3265665 AAGATGGAGC
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
134 93 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (134 bp):
TCGACTCAATCTTCCCTGAAGAGAAACGAAGTGGATGAAAACTTTATCGAGTCTGATCTACCCTA
AAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGGTAATCCTGAAGAGCAACGAAGCAAATC
AAGT
Found at i:3267812 original size:19 final size:19
Alignment explanation
Indices: 3267790--3267826 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3267780 AAATTTGTTG
*
3267790 TTTTAATTAAAATTAAAAT
1 TTTTAATTAAAATGAAAAT
3267809 TTTTAATTAAAATGAAAA
1 TTTTAATTAAAATGAAAA
3267827 AAGGTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTAATTAAAATGAAAAT
Found at i:3269506 original size:237 final size:244
Alignment explanation
Indices: 3269080--3270012 Score: 816
Period size: 237 Copynumber: 3.7 Consensus size: 244
3269070 GCGATTTTCA
* * * * *
3269080 AAAAAT-GAGAAAGCGATTTCCAAAGTATCTCATTTAA-ATATTTTCTGAAAATAAAATTTTTGA
1 AAAAATCGAGAAAGCGATTTTCAAAGTTTCCCATTTAATAT-TTTTCAGAAAATGAAATTTTTGA
* **
3269143 AGAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATATCCAAAATTGGTAAGTTTTT
65 AGAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
* * * * * * * ** * *
3269208 CGGGTCATCAGTAAGTCATTCGAGCATGATGAATAAATACTTTGGGTTGTCTATCAG-TC-T-T-
130 CGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATATATAAGTTCATATA
*
3269269 T-C-GGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATTTG
195 TACTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTG
* * *
3269317 ACAAA-CGAGAAAGTGATTTTCAAAGTTTCCCATTTAATATTTTTCAGAAAATGAAATCTTTGAA
1 AAAAATCGAGAAAGCGATTTTCAAAGTTTCCCATTTAATATTTTTCAGAAAATGAAATTTTTGAA
* * * *
3269381 AAGTAAGAAAGCGATTTCTAGAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
66 GAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
* * * * *
3269446 GGGCCATCATTAAGCCTTTCAAGCATCATGATTAAATCCTTCGAGTCATATGTAAGTCTTTCGAG
131 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATATATAAG---TTC---
3269511 TAAGATGATAAGTACTTGGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTG
190 ----AT-AT-A-TAC-T-GGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTG
* * *
3269575 AAAAATTG-GAAAGCGATTTTC-AAGTTTACTATTTAATA-TTTTCAGAAAATGAAATTTTTGAA
1 AAAAATCGAGAAAGCGATTTTCAAAGTTTCCCATTTAATATTTTTCAGAAAATGAAATTTTTGAA
* * * * * *
3269637 GAGTAAGAAAGTGATTTCCAAAGCTTCTTACCCAGTAAACTATTTCTAAAATTGGTAACTCCTTT
66 GAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
* * * ** *
3269702 GGGCCATCAATAAGTCTTTCGATCATGATGATTAAATCTTTCGGGGTCATCCATCAGTCTTTCGA
131 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTC-GAGTCATATATAAG---TTC--
* * * * * * * *
3269767 GGAAGATGATAAGTCCTTCGGGCCATCTATAAGATCTTTGGGCAAGAT-TCTTTCATATGATGTT
190 -----AT-AT-A-TAC-T-GGGCCATCCATAAGACCTTCGGGTAGGATGT-TTTCACATGA--AT
3269831 TGTG
242 T-TG
* * * * * **
3269835 AAAAAT-AAGAAAAGCAATTTTCAAAGTTTCTCACTTAATA-TTTTCATAAAATGAAACCTTTGA
1 AAAAATCGAG-AAAGCGATTTTCAAAGTTTCCCATTTAATATTTTTCAGAAAATGAAATTTTTGA
* * * *
3269898 AAAGTAAGAAAGCGATTTCCAAAGTTTATTATCTAGTAAACTATTTCCAAAATTTGTAAGTCCTT
65 AGAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
* *
3269963 CGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCAT
130 CGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCAT
3270013 CTGTCAGTCT
Statistics
Matches: 574, Mismatches: 90, Indels: 40
0.82 0.13 0.06
Matches are distributed among these distances:
237 151 0.26
238 2 0.00
241 2 0.00
249 1 0.00
251 1 0.00
254 1 0.00
255 1 0.00
256 115 0.20
257 81 0.14
258 61 0.11
259 3 0.01
260 9 0.02
261 18 0.03
262 128 0.22
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (244 bp):
AAAAATCGAGAAAGCGATTTTCAAAGTTTCCCATTTAATATTTTTCAGAAAATGAAATTTTTGAA
GAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATATATAAGTTCATATAT
ACTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTG
Found at i:3269735 original size:256 final size:255
Alignment explanation
Indices: 3269263--3270065 Score: 1000
Period size: 262 Copynumber: 3.1 Consensus size: 255
3269253 GTTGTCTATC
* * *
3269263 AGTCTTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGACAAA-CGAGA
1 AGTC-TTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAATAG-GA
* *
3269327 AAGTGATTTTCAAAGTTTCCCATTTAATATTTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAG
64 AAGCGATTTTCAAAGTTT-CTATTTAATA-TTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAG
* * * *
3269392 CGATTTCTAGAGTTTCATACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCATT
127 CGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAAT
* * * * * * *
3269457 AAGCCTTTCAAGCATCATGATTAAATCCTTCGAGTCATATGTAAGTCTTTCGAGTAAGATGATA
192 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATA
* *
3269521 AGTACTTGGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAATTGGAA
1 AGT-CTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAATAGGAA
* * *
3269586 AGCGATTTTC-AAGTTTACTATTTAATATTTTCAGAAAATGAAATTTTTGAAGAGTAAGAAAGTG
65 AGCGATTTTCAAAGTTT-CTATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAGCG
* * * * *
3269650 ATTTCCAAAGCTTCTTACCCAGTAAACTATTTCTAAAATTGGTAACTCCTTTGGGCCATCAATAA
129 ATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAATAA
* * ** *
3269715 GTCTTTCGATCATGATGATTAAATCTTTCGGGGTCATCCATCAGTCTTTCGAGGAAGATGATA
194 GTCTTTCGAGCATGATGATTAAATCCTTC-GGGTCATCTGTCAGTCTTTCGAGCAAGATGATA
* * * * * * *
3269778 AGTCCTTCGGGCCATCTATAAGATCTTTGGGCAAGAT-TCTTTCATATGATGTTTGTGAAAAATA
1 AGT-CTTCGGGCCATCCATAAGACCTTCGGGTAGGATGT-TTTCACATGA--ATT-TGAAAAAT-
* * * * *
3269842 AGAAAAGCAATTTTCAAAGTTTCTCACTTAATATTTTCATAAAATGAAACCTTTGAAAAGTAAGA
60 AGGAAAGCGATTTTCAAAGTTTCT-ATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGA
* * *
3269907 AAGCGATTTCCAAAGTTTATTATCTAGTAAACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATC
124 AAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATC
* *
3269972 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGA
189 AATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGA
3270037 TA
254 TA
* *
3270039 AGTCATTCGGGCCAACTATAAGACCTT
1 AGTC-TTCGGGCCATCCATAAGACCTT
3270066 TGGGAACGAT
Statistics
Matches: 469, Mismatches: 65, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
256 115 0.25
257 81 0.17
258 66 0.14
259 4 0.01
260 9 0.02
261 66 0.14
262 128 0.27
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (255 bp):
AGTCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAATAGGAAA
GCGATTTTCAAAGTTTCTATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAGCGAT
TTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAATAAGT
CTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATA
Found at i:3270005 original size:42 final size:41
Alignment explanation
Indices: 3269958--3270052 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
3269948 AATTTGTAAG
* *
3269958 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGA-TAAA
* * * *
3270000 TCCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATAAA
*
3270041 TCATTCGGGCCA
1 TCCTTCGGGCCA
3270053 ACTATAAGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:3270742 original size:134 final size:134
Alignment explanation
Indices: 3270512--3270757 Score: 321
Period size: 134 Copynumber: 1.8 Consensus size: 134
3270502 AAATCGATCC
* * *** *
3270512 CGATTCAATCTTCTCTGAAGAGCAACAAAGTGGATTAATTTTTTCTCGAGTCTGGTATCCCCTAA
1 CGATTCAATCTTCCCTGAAGAGCAACAAAGTGGATGAAAACTTTCTCGAGTCTGATATCCCCTAA
* * ** * *
3270577 AGAGTGGTGGAGTGTATTCTTTTTCTTTCAGATCTGGTCTTCCTGAAGAGTAGCGAAGCAAATCA
66 AGAGTAGCGGAGCATATTCTTCTTCTTTCAGATCTGGTATTCCTGAAGAGTAGCGAAGCAAATCA
3270642 AGTT
131 AGTT
* * * * * *
3270646 CGATTCAATGTTCCCTGAAGAGCAGCGAAGTTGATGAAAACTTTCTCGAGTTTGATCTCCCCTAA
1 CGATTCAATCTTCCCTGAAGAGCAACAAAGTGGATGAAAACTTTCTCGAGTCTGATATCCCCTAA
*
3270711 AGAGTAGCGGAGCATATTCTTCTTCTTTCAGATTTGGTATTCCTGAA
66 AGAGTAGCGGAGCATATTCTTCTTCTTTCAGATCTGGTATTCCTGAA
3270758 AAGATGGAAC
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
134 93 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (134 bp):
CGATTCAATCTTCCCTGAAGAGCAACAAAGTGGATGAAAACTTTCTCGAGTCTGATATCCCCTAA
AGAGTAGCGGAGCATATTCTTCTTCTTTCAGATCTGGTATTCCTGAAGAGTAGCGAAGCAAATCA
AGTT
Found at i:3274187 original size:27 final size:27
Alignment explanation
Indices: 3274141--3274208 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
3274131 TGTACATTCA
* ** **
3274141 ACATTTGCATATTTTCATTTTGTATTT
1 ACATTCGCATATTTGAATTTTACATTT
3274168 ACATTCGCATATTTGAATTTTACATTT
1 ACATTCGCATATTTGAATTTTACATTT
* *
3274195 GCATTCACATATTT
1 ACATTCGCATATTT
3274209 ACATATGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.51
Consensus pattern (27 bp):
ACATTCGCATATTTGAATTTTACATTT
Found at i:3277341 original size:27 final size:27
Alignment explanation
Indices: 3277309--3277375 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
3277299 CAACAAAATT
3277309 AAATGTAATTAAAAAGAACCAGGATTA
1 AAATGTAATTAAAAAGAACCAGGATTA
3277336 AAATGTAATTAAAAAGAACCAGGATTA
1 AAATGTAATTAAAAAGAACCAGGATTA
3277363 AAATGTAA-TAAAA
1 AAATGTAATTAAAA
3277376 TAAACAAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 5 0.12
27 35 0.88
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.22
Consensus pattern (27 bp):
AAATGTAATTAAAAAGAACCAGGATTA
Found at i:3279518 original size:5 final size:5
Alignment explanation
Indices: 3279508--3279534 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3279498 TAGGAGGGGA
3279508 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
3279535 CTAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3280923 original size:15 final size:15
Alignment explanation
Indices: 3280903--3280934 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3280893 GTAACACCCC
3280903 ATATGTTGGGTTAGG
1 ATATGTTGGGTTAGG
3280918 ATATGTTGGGTTAGG
1 ATATGTTGGGTTAGG
3280933 AT
1 AT
3280935 TTTCTGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.41
Consensus pattern (15 bp):
ATATGTTGGGTTAGG
Found at i:3284080 original size:26 final size:26
Alignment explanation
Indices: 3284051--3284112 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
3284041 ATATATAAAA
3284051 TTTTGAAAACATATATAATATATAGT
1 TTTTGAAAACATATATAATATATAGT
3284077 TTTTGAAAACATATATAATATATAGT
1 TTTTGAAAACATATATAATATATAGT
3284103 TTTTGAAAAC
1 TTTTGAAAAC
3284113 GTTTTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTTGAAAACATATATAATATATAGT
Found at i:3284120 original size:37 final size:37
Alignment explanation
Indices: 3284077--3284351 Score: 236
Period size: 37 Copynumber: 7.9 Consensus size: 37
3284067 AATATATAGT
*
3284077 TTTTGAAAACATATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* *
3284114 TTTTGAAAACATATATATAATATATAG-TTTCGAAAATA
1 TTTTGAAAAC--ATATATAATATATAGTTTTTGAAAACA
* * *
3284152 TTTTCAAAATATATATAATATATAGTGTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
3284189 TTTTGAAAACATATATATAATATATAGTTTTTG-AAA-A
1 TTTTGAAAAC--ATATATAATATATAGTTTTTGAAAACA
* *
3284226 ---T------ATATATAATATATATTTTTTGAAAATA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* *
3284254 TTTT-----C--A-AT-ATATATAGTTTTTGAACATA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
3284282 TTTTG--AATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* *
3284317 TTTTGAAAATATATATAATATATAGTTTTTAAAAA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAA
3284352 AATATTTATA
Statistics
Matches: 200, Mismatches: 18, Indels: 40
0.78 0.07 0.16
Matches are distributed among these distances:
26 20 0.10
27 3 0.01
28 23 0.12
29 2 0.01
30 1 0.00
31 1 0.00
33 1 0.00
34 3 0.01
35 23 0.12
36 15 0.08
37 54 0.27
38 19 0.09
39 35 0.17
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
Found at i:3284141 original size:39 final size:39
Alignment explanation
Indices: 3284077--3284225 Score: 218
Period size: 39 Copynumber: 3.9 Consensus size: 39
3284067 AATATATAGT
*
3284077 TTTTGAAAAC--ATATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
* *
3284114 TTTTGAAAACATATATATAATATATAG-TTTCGAAAATA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
* *
3284152 TTTT-CAAA-ATATATATAATATATAGTGTTTGAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
3284189 TTTTGAAAACATATATATAATATATAGTTTTTGAAAA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAA
3284226 TATATATAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
36 17 0.17
37 25 0.26
38 15 0.15
39 41 0.42
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.41
Consensus pattern (39 bp):
TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
Found at i:3284172 original size:75 final size:76
Alignment explanation
Indices: 3284077--3284228 Score: 252
Period size: 75 Copynumber: 2.0 Consensus size: 76
3284067 AATATATAGT
* * *
3284077 TTTTGAAAACATATATAATATATAGTTTTTGAAAACGTTTTGAAAACATATATATAATATATAG-
1 TTTTCAAAACATATATAATATATAGTGTTTGAAAACATTTTGAAAACATATATATAATATATAGT
3284141 TTTCGAAAATA
66 TTTCGAAAATA
*
3284152 TTTTCAAAATATATATAATATATAGTGTTTGAAAACATTTTGAAAACATATATATAATATATAGT
1 TTTTCAAAACATATATAATATATAGTGTTTGAAAACATTTTGAAAACATATATATAATATATAGT
*
3284217 TTTTGAAAATA
66 TTTCGAAAATA
3284228 T
1 T
3284229 ATATAATATA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
75 60 0.85
76 11 0.15
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (76 bp):
TTTTCAAAACATATATAATATATAGTGTTTGAAAACATTTTGAAAACATATATATAATATATAGT
TTTCGAAAATA
Found at i:3284220 original size:28 final size:28
Alignment explanation
Indices: 3284189--3284317 Score: 113
Period size: 28 Copynumber: 4.4 Consensus size: 28
3284179 TTTGAAAACA
3284189 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGT
*
3284217 TTTTG-AAA-ATATATATAATATATATT
1 TTTTGAAAACATATATATAATATATAGT
* *
3284243 TTTTGAAAATAT-TTTCA-ATATATATAGT
1 TTTTGAAAACATATAT-ATA-ATATATAGT
*
3284271 TTTTGAACATATTTTGAATATATATAATATATAGT
1 TTTTGAA-A-A-----CATATATATAATATATAGT
3284306 TTTTGAAAACAT
1 TTTTGAAAACAT
3284318 TTTGAAAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
26 22 0.27
27 9 0.11
28 25 0.30
29 1 0.01
30 1 0.01
33 1 0.01
34 1 0.01
35 19 0.23
36 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATAGT
Found at i:3284235 original size:26 final size:26
Alignment explanation
Indices: 3284189--3284282 Score: 109
Period size: 26 Copynumber: 3.5 Consensus size: 26
3284179 TTTGAAAACA
3284189 TTTTGAAAACATATATATAATATATAGT
1 TTTTG-AAA-ATATATATAATATATAGT
*
3284217 TTTTGAAAATATATATAATATATATT
1 TTTTGAAAATATATATAATATATAGT
*
3284243 TTTTGAAAATAT-TTTCAATATATATAGT
1 TTTTGAAAATATATAT--A-ATATATAGT
*
3284271 TTTTGAACATAT
1 TTTTGAAAATAT
3284283 TTTGAATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
25 2 0.03
26 29 0.49
27 4 0.07
28 24 0.41
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:3284237 original size:65 final size:64
Alignment explanation
Indices: 3284152--3284367 Score: 228
Period size: 65 Copynumber: 3.4 Consensus size: 64
3284142 TTCGAAAATA
* *
3284152 TTTTCAAAATATATATAATATATAGTGTTTGAAAACATTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAA-ATATATATAATATATAGT
* * * * * *
3284217 TTTTGAAAATATATATAATATATATTTTTTGAAAATATTTT---CAATATATATAGTTTTTGAAC
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAATATATATAATATAT--A-
*
3284279 AT
63 GT
3284281 ATTTTG--AATATATATAATATATAGTTTTTGAAAACATTTTG-AAAATATATATAATATATAGT
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAATATATATAATATATAGT
* * *
3284343 TTTTAAAAAAATATTTATATATATA
1 TTTTGAAAATATATATA-ATATATA
3284368 TTATATATTA
Statistics
Matches: 123, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
61 16 0.13
62 2 0.02
63 42 0.34
64 8 0.07
65 55 0.45
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (64 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAATATATATAATATATAGT
Found at i:3284291 original size:26 final size:25
Alignment explanation
Indices: 3284206--3284294 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 25
3284196 AACATATATA
*
3284206 TAATATATAGTTTTTGAAAATATATA
1 TAATATATAGTTTTTGAAAATAT-TT
*
3284232 TAATATATATTTTTTGAAAATATTT
1 TAATATATAGTTTTTGAAAATATTT
*
3284257 TCAATATATATAGTTTTTGAACATATTT
1 T--A-ATATATAGTTTTTGAAAATATTT
3284285 TGAATATATA
1 T-AATATATA
3284295 TAATATATAG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
25 2 0.04
26 29 0.53
27 2 0.04
28 22 0.40
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (25 bp):
TAATATATAGTTTTTGAAAATATTT
Found at i:3284374 original size:7 final size:7
Alignment explanation
Indices: 3284353--3284423 Score: 56
Period size: 7 Copynumber: 10.0 Consensus size: 7
3284343 TTTTAAAAAA
3284353 ATATT-T
1 ATATTAT
3284359 ATA-TAT
1 ATATTAT
3284365 ATATTAT
1 ATATTAT
3284372 ATATTAT
1 ATATTAT
*
3284379 ATTTATATT
1 ATAT-TA-T
3284388 ATATTAT
1 ATATTAT
*
3284395 TTATTAT
1 ATATTAT
*
3284402 ATTATTGT
1 A-TATTAT
*
3284410 AAATTAT
1 ATATTAT
*
3284417 TTATTAT
1 ATATTAT
3284424 TTTCATTTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
5 1 0.02
6 7 0.14
7 29 0.57
8 10 0.20
9 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (7 bp):
ATATTAT
Found at i:3284394 original size:23 final size:24
Alignment explanation
Indices: 3284353--3284404 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
3284343 TTTTAAAAAA
3284353 ATATTTATATATATATTATATATT
1 ATATTTATATATATATTATATATT
*
3284377 ATATTTATAT-TATATTATTTATT
1 ATATTTATATATATATTATATATT
3284400 ATATT
1 ATATT
3284405 ATTGTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTTATATATATATTATATATT
Found at i:3284487 original size:13 final size:13
Alignment explanation
Indices: 3284471--3284508 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3284461 CCAAATAAGG
3284471 AGTCCAAGATCCA
1 AGTCCAAGATCCA
* *
3284484 AGTCCAAGGTTCA
1 AGTCCAAGATCCA
3284497 AGTCCAA-ATCCA
1 AGTCCAAGATCCA
3284509 GAAGGGATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (13 bp):
AGTCCAAGATCCA
Found at i:3285642 original size:13 final size:13
Alignment explanation
Indices: 3285624--3285658 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3285614 TCCTACATTT
3285624 TTATTTATTTTTA
1 TTATTTATTTTTA
3285637 TTATTTA-TTTTA
1 TTATTTATTTTTA
3285649 TT-TTTATTTT
1 TTATTTATTTT
3285659 AATTTAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 10 0.48
13 7 0.33
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTATTTTTA
Found at i:3285650 original size:18 final size:17
Alignment explanation
Indices: 3285623--3285656 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3285613 ATCCTACATT
3285623 TTTATTTATTTTTATTA
1 TTTATTTATTTTTATTA
3285640 TTTATTTTATTTTTATT
1 TTTA-TTTATTTTTATT
3285657 TTAATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTTTATTA
Found at i:3302289 original size:123 final size:123
Alignment explanation
Indices: 3302070--3302342 Score: 361
Period size: 123 Copynumber: 2.2 Consensus size: 123
3302060 TTCTTATAGT
* * *
3302070 CAATTTCAACTTCACAATGAAAGATATTGAACTCAACGCAATGCAAATTACAAGATTAGATTTCA
1 CAATTTCAACTTCATAAAGAAAGATATTAAACTCAACGCAATGCAAATTACAAGATTAGATTTCA
* *
3302135 ACTTCACAAAGAAGGACATTCAATTCAAAGCTCAACTTCACAGCAAAGGAGCCATCTA
66 ACTTCACAAAGAAGGACATCCAATTCAAAGCTCAACTTCACAGCAAAGGAGCCATCCA
* ** * * *
3302193 CAATTTCAACTTCATAAAGAAAGATATTAAACTTGAA-GTGATGCAATTTACAATATTGGATTTC
1 CAATTTCAACTTCATAAAGAAAGATATTAAAC-TCAACGCAATGCAAATTACAAGATTAGATTTC
* * *
3302257 AACTTCACAACGAAGGACATCCAATAT-AAAGCTCAACTTCACAGCGAATGAGCCATCCA
65 AACTTCACAAAGAAGGACATCCAAT-TCAAAGCTCAACTTCACAGCAAAGGAGCCATCCA
* * *
3302316 CGATTTCAACTTCATGAAGAAGGATAT
1 CAATTTCAACTTCATAAAGAAAGATAT
3302343 CGTATAGATT
Statistics
Matches: 131, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
123 127 0.97
124 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (123 bp):
CAATTTCAACTTCATAAAGAAAGATATTAAACTCAACGCAATGCAAATTACAAGATTAGATTTCA
ACTTCACAAAGAAGGACATCCAATTCAAAGCTCAACTTCACAGCAAAGGAGCCATCCA
Found at i:3302965 original size:37 final size:37
Alignment explanation
Indices: 3302917--3303248 Score: 375
Period size: 37 Copynumber: 9.1 Consensus size: 37
3302907 TATATATACA
* * *
3302917 ATTTTGAAAACATATATAATATATAGTTTTTGAATAT
1 ATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
* *
3302954 GTTTTAAAAACATATATAATATATAG-TTTTGAAAAT
1 ATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
*
3302990 ATTTTGAAAATATATAT-A-ATATAGTTTTTGAAAACT
1 ATTTTAAAAATATATATAATATATAGTTTTTGAAAA-T
*
3303026 TTTTTGAAAACATATATATAATATATA-TATTTTGAAAAT
1 ATTTT-AAAA-ATATATATAATATATAGT-TTTTGAAAAT
3303065 ATTTTGAAAAA-ATATATAATATATAGTTTTTGAAAAT
1 ATTTT-AAAAATATATATAATATATAGTTTTTGAAAAT
* *
3303102 ATTTT--GAA-A-ATAT-ATAT-T-GTTTTTGAAAAC
1 ATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
*
3303132 ATTTTGAAAATATAAATATAATATATAGTTTTTGAAAAT
1 ATTTT-AAAA-ATATATATAATATATAGTTTTTGAAAAT
*
3303171 ATTTTGAAAATATATATAATATATAGTTTTTG-AAAT
1 ATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
* * *
3303207 CATTTTGAAAATATATATATTATATAGTTTTTAAAAAT
1 -ATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
3303245 ATTT
1 ATTT
3303249 ATATATTATA
Statistics
Matches: 259, Mismatches: 17, Indels: 38
0.82 0.05 0.12
Matches are distributed among these distances:
30 16 0.06
31 1 0.00
32 4 0.02
33 5 0.02
34 10 0.04
35 11 0.04
36 36 0.14
37 116 0.45
38 18 0.07
39 28 0.11
40 14 0.05
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
ATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
Found at i:3302996 original size:11 final size:11
Alignment explanation
Indices: 3302980--3303114 Score: 58
Period size: 11 Copynumber: 11.1 Consensus size: 11
3302970 TAATATATAG
3302980 TTTTGAAAATA
1 TTTTGAAAATA
3302991 TTTTGAAAATA
1 TTTTGAAAATA
* *
3303002 TATAT-AATATA
1 T-TTTGAAAATA
*
3303013 GTTTTTGAAAACTT
1 --TTTTGAAAA-TA
3303027 TTTTGAAAACATA
1 TTTTG-AAA-ATA
* *
3303040 TATATAATATATATA
1 T-TTTGA-A-A-ATA
3303055 TTTTGAAAATA
1 TTTTGAAAATA
*
3303066 TTTTGAAAAAA
1 TTTTGAAAATA
*
3303077 TATAT-AATATATA
1 T-TTTGAA-A-ATA
3303090 GTTTTTGAAAATA
1 --TTTTGAAAATA
3303103 TTTTGAAAATA
1 TTTTGAAAATA
3303114 T
1 T
3303115 ATATTGTTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
11 45 0.48
12 13 0.14
13 16 0.17
14 11 0.12
15 8 0.09
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:3303124 original size:30 final size:30
Alignment explanation
Indices: 3303083--3303187 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
3303073 AAAATATATA
*
3303083 ATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATTGTTTTTGAAAATATTTTGAAAAT
*
3303113 ATATATTGTTTTTGAAAACATTTTGAAAATATAAAT
1 ATATATTGTTTTTGAAAATATTTTG-----A-AAAT
3303149 ATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 AT-ATAT-T-GTTTTTGAAAATATTTTGAAAAT
3303182 ATATAT
1 ATATAT
3303188 AATATATAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
30 23 0.37
32 4 0.06
33 6 0.10
34 1 0.02
35 1 0.02
36 6 0.10
37 4 0.06
38 1 0.02
39 17 0.27
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.46
Consensus pattern (30 bp):
ATATATTGTTTTTGAAAATATTTTGAAAAT
Found at i:3303167 original size:106 final size:108
Alignment explanation
Indices: 3302917--3303226 Score: 447
Period size: 106 Copynumber: 2.9 Consensus size: 108
3302907 TATATATACA
* *
3302917 ATTTTGAAAACAT-ATATAATATATAGTTTTTGAATATGTTTT-AAAAACATATATAATATATAG
1 ATTTTGAAAACATAATATAATATATAGTTTTTGAAAATATTTTGAAAAA-ATATATAATATATAG
3302980 -TTTTGAAAATATTTTGAAAATATATATAATATAGTTTTTGAAAACT
65 TTTTTGAAAATATTTTG-AAA-ATATAT-ATATAGTTTTTGAAAACT
*
3303026 TTTTTGAAAACATATATATAATATATA-TATTTTGAAAATATTTTGAAAAAATATATAATATATA
1 ATTTTGAAAACATA-ATATAATATATAGT-TTTTGAAAATATTTTGAAAAAATATATAATATATA
3303090 GTTTTTGAAAATATTTTGAAAATATATAT-T-GTTTTTGAAAAC-
64 GTTTTTGAAAATATTTTGAAAATATATATATAGTTTTTGAAAACT
* *
3303132 ATTTTGAAAATATAAATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAG
1 ATTTTGAAAACAT-AATATAATATATAGTTTTTGAAAATATTTTGAAAAAATATATAATATATAG
3303197 TTTTTG-AAATCATTTTGAAAATATATATAT
65 TTTTTGAAAAT-ATTTTGAAAATATATATAT
3303227 TATATAGTTT
Statistics
Matches: 186, Mismatches: 6, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
105 4 0.02
106 81 0.44
107 15 0.08
108 1 0.01
109 14 0.08
110 7 0.04
111 43 0.23
112 21 0.11
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (108 bp):
ATTTTGAAAACATAATATAATATATAGTTTTTGAAAATATTTTGAAAAAATATATAATATATAGT
TTTTGAAAATATTTTGAAAATATATATATAGTTTTTGAAAACT
Found at i:3303278 original size:22 final size:22
Alignment explanation
Indices: 3303244--3303296 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
3303234 TTTTTAAAAA
*
3303244 TATTTA-TATATTATAGCATAT
1 TATTTATTATATTATAGCAAAT
* *
3303265 TATTTATTATATTATTGTAAAT
1 TATTTATTATATTATAGCAAAT
3303287 TATTTATTAT
1 TATTTATTAT
3303297 TTTCATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (22 bp):
TATTTATTATATTATAGCAAAT
Found at i:3305171 original size:26 final size:27
Alignment explanation
Indices: 3305142--3305193 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3305132 TTTGAAATCA
*
3305142 TTTTGAAAATA-TATATATTATATAGT
1 TTTTAAAAATATTATATATTATATAGT
3305168 TTTTAAAAATATTTATATATTATATA
1 TTTTAAAAATA-TTATATATTATATA
3305194 TTATAGCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
28 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTTAAAAATATTATATATTATATAGT
Found at i:3305192 original size:7 final size:7
Alignment explanation
Indices: 3305176--3305236 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
3305166 GTTTTTAAAA
3305176 ATAT-TT
1 ATATATT
3305182 ATATATT
1 ATATATT
3305189 ATATATT
1 ATATATT
3305196 ATAGCATATT
1 AT---ATATT
*
3305206 ATTTATT
1 ATATATT
3305213 ATATTATT
1 ATA-TATT
*
3305221 ATAAATT
1 ATATATT
*
3305228 ATTTATT
1 ATATATT
3305235 AT
1 AT
3305237 TTTCATTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
6 4 0.09
7 27 0.60
8 7 0.16
10 7 0.16
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:3305194 original size:37 final size:37
Alignment explanation
Indices: 3304918--3305181 Score: 347
Period size: 37 Copynumber: 7.1 Consensus size: 37
3304908 ATATATACAA
* *
3304918 TTTGAAAACATATATAATATATAGTTTTTGAAAATGT
1 TTTGAAAATATATATAATATATAGTTTTTGAAAATAT
3304955 TTTGAAAATATATATAATATATAG-TTTTGAAAATATTTT
1 TTTGAAAATATATATAATATATAGTTTTTGAAAATA---T
* *
3304994 TTTGAAAATATATAT-A-ATATAGTTTTTTAAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTGAAAATA-T
* * *
3305030 TTTGAAGACATATATGTAATATATAATTTTTGACAATAT
1 TTTGAA-A-ATATATATAATATATAGTTTTTGAAAATAT
*
3305069 TTTGAAAAAATATATAATATATAGTTTTTGAAAATAT
1 TTTGAAAATATATATAATATATAGTTTTTGAAAATAT
3305106 TTTGAAAATATATATAATATATAGTTTTTG-AAATCAT
1 TTTGAAAATATATATAATATATAGTTTTTGAAAAT-AT
* *
3305143 TTTGAAAATATATATATTATATAGTTTTTAAAAATAT
1 TTTGAAAATATATATAATATATAGTTTTTGAAAATAT
3305180 TT
1 TT
3305182 ATATATTATA
Statistics
Matches: 201, Mismatches: 16, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
36 22 0.11
37 119 0.59
38 22 0.11
39 24 0.12
40 14 0.07
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (37 bp):
TTTGAAAATATATATAATATATAGTTTTTGAAAATAT
Found at i:3305218 original size:22 final size:22
Alignment explanation
Indices: 3305190--3305236 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3305180 TTATATATTA
*
3305190 TATATTA-TAGCATATTATTTAT
1 TATATTATTA-CAAATTATTTAT
*
3305212 TATATTATTATAAATTATTTAT
1 TATATTATTACAAATTATTTAT
3305234 TAT
1 TAT
3305237 TTTCATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATATTATTACAAATTATTTAT
Found at i:3305270 original size:16 final size:18
Alignment explanation
Indices: 3305233--3305271 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
3305223 AAATTATTTA
3305233 TTATTTTCATTTTCTTTC
1 TTATTTTCATTTTCTTTC
3305251 -TATTTT-ATTTT-TTTC
1 TTATTTTCATTTTCTTTC
3305266 TTATTT
1 TTATTT
3305272 GGTCCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATTTTCATTTTCTTTC
Found at i:3306890 original size:37 final size:37
Alignment explanation
Indices: 3306847--3307180 Score: 422
Period size: 37 Copynumber: 9.1 Consensus size: 37
3306837 TATATATACA
*
3306847 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3306884 GTTTTGAAAACATATATAATATATAG-TTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3306920 ATTTTGAATATATATAT-A-ATATAGTTTTTGAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
3306955 ATTTTTGAAAACATATATATAATATATA-TATTTTGAAAAT
1 A-TTTTG-AAA-ATATATATAATATATAGT-TTTTGAAAAT
*
3306995 ATTTTGAAAAAATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
*
3307032 ATTTTG--AA-A-ATAT-ATAT-T-GTTTTTGAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
3307062 ATTTTGAAAATATAAATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATAT--ATATAATATATAGTTTTTGAAAAT
3307101 ATTTTGAAAATATATATAATATATAGTTTTTG-AAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3307137 CATTTTGAATATATATATATATTATATAGTTTTTAAAAAT
1 -ATTTTGAA-A-ATATATATAATATATAGTTTTTGAAAAT
3307177 ATTT
1 ATTT
3307181 ATATATTATA
Statistics
Matches: 264, Mismatches: 12, Indels: 40
0.84 0.04 0.13
Matches are distributed among these distances:
30 17 0.06
31 1 0.00
32 6 0.02
33 5 0.02
34 7 0.03
35 13 0.05
36 37 0.14
37 89 0.34
38 14 0.05
39 56 0.21
40 19 0.07
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (37 bp):
ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
Found at i:3306961 original size:12 final size:12
Alignment explanation
Indices: 3306944--3306968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3306934 TATAATATAG
3306944 TTTTTGAAAACA
1 TTTTTGAAAACA
3306956 TTTTTGAAAACA
1 TTTTTGAAAACA
3306968 T
1 T
3306969 ATATATAATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:3307054 original size:30 final size:30
Alignment explanation
Indices: 3307013--3307117 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
3307003 AAAATATATA
*
3307013 ATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATTGTTTTTGAAAATATTTTGAAAAT
*
3307043 ATATATTGTTTTTGAAAACATTTTGAAAATATAAAT
1 ATATATTGTTTTTGAAAATATTTTG-----A-AAAT
3307079 ATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 AT-ATAT-T-GTTTTTGAAAATATTTTGAAAAT
3307112 ATATAT
1 ATATAT
3307118 AATATATAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
30 23 0.37
32 4 0.06
33 6 0.10
34 1 0.02
35 1 0.02
36 6 0.10
37 4 0.06
38 1 0.02
39 17 0.27
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.46
Consensus pattern (30 bp):
ATATATTGTTTTTGAAAATATTTTGAAAAT
Found at i:3307105 original size:106 final size:107
Alignment explanation
Indices: 3306847--3307157 Score: 463
Period size: 106 Copynumber: 2.9 Consensus size: 107
3306837 TATATATACA
* *
3306847 ATTTTGAAAACAT-ATATAATATATAGTTTTTGAAAATGTTTTGAAAACATATATAATATATAG-
1 ATTTTGAAAACATAATATAATATATAGTTTTTGAAAATATTTTGAAAAAATATATAATATATAGT
3306910 TTTTGAAAATATTTTGAATATATATATAATATAGTTTTTGAAAAC
66 TTTTGAAAATATTTTGAA-A-ATATAT-ATATAGTTTTTGAAAAC
3306955 ATTTTTGAAAACATATATATAATATATA-TATTTTGAAAATATTTTGAAAAAATATATAATATAT
1 A-TTTTGAAAACATA-ATATAATATATAGT-TTTTGAAAATATTTTGAAAAAATATATAATATAT
3307019 AGTTTTTGAAAATATTTTGAAAATATATAT-T-GTTTTTGAAAAC
63 AGTTTTTGAAAATATTTTGAAAATATATATATAGTTTTTGAAAAC
* *
3307062 ATTTTGAAAATATAAATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAG
1 ATTTTGAAAACAT-AATATAATATATAGTTTTTGAAAATATTTTGAAAAAATATATAATATATAG
*
3307127 TTTTTG-AAATCATTTTGAATATATATATATA
65 TTTTTGAAAAT-ATTTTGAAAATATATATATA
3307158 TTATATAGTT
Statistics
Matches: 188, Mismatches: 5, Indels: 20
0.88 0.02 0.09
Matches are distributed among these distances:
105 4 0.02
106 80 0.43
107 16 0.09
108 2 0.01
109 14 0.07
110 7 0.04
111 47 0.25
112 18 0.10
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (107 bp):
ATTTTGAAAACATAATATAATATATAGTTTTTGAAAATATTTTGAAAAAATATATAATATATAGT
TTTTGAAAATATTTTGAAAATATATATATAGTTTTTGAAAAC
Found at i:3307220 original size:22 final size:22
Alignment explanation
Indices: 3307176--3307228 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
3307166 TTTTTAAAAA
*
3307176 TATTTA-TATATTATAGCATAT
1 TATTTATTATATTATAGCAAAT
* *
3307197 TATTTATTATATTATTGTAAAT
1 TATTTATTATATTATAGCAAAT
*
3307219 TATTTTTTAT
1 TATTTATTAT
3307229 TTTCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TATTTATTATATTATAGCAAAT
Found at i:3307239 original size:15 final size:14
Alignment explanation
Indices: 3307221--3307254 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3307211 TTGTAAATTA
3307221 TTTTTTATTTTCATT
1 TTTTTTATTTT-ATT
*
3307236 TTTTCTATTTTATT
1 TTTTTTATTTTATT
3307250 TTTTT
1 TTTTT
3307255 GTTATTTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:3307250 original size:14 final size:14
Alignment explanation
Indices: 3307221--3307254 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3307211 TTGTAAATTA
3307221 TTTTTTATTTTCAT
1 TTTTTTATTTTCAT
3307235 TTTTTCTATTTT-AT
1 TTTTT-TATTTTCAT
3307249 TTTTTT
1 TTTTTT
3307255 GTTATTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 12 0.63
15 6 0.32
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTATTTTCAT
Found at i:3308890 original size:37 final size:37
Alignment explanation
Indices: 3308847--3309112 Score: 335
Period size: 37 Copynumber: 7.1 Consensus size: 37
3308837 TATATATACA
*
3308847 ATTTTGAAAACATATATAATATATAGTTTTTGAAAA-
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
3308883 AGTTTTGAAAATATATATAATATATAG-TTTTGAAAAT
1 A-TTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3308920 ATTTTTTTGAAAATATATAT-A-ATATAGTTTTTTAAAAC
1 A---TTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3308958 ATTTTTGAAGACATATATGTAATATATATTTTTTGAAAAT
1 A-TTTTGAA-A-ATATATATAATATATAGTTTTTGAAAAT
*
3308998 ATTTTGAAAAAATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3309035 ATTTTGAAAATATGTATAATATAGAGTTTTTG-AAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
3309071 CATTTTGAAAATATATATATTATATAGTTTTTAAAAAT
1 -ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
3309109 ATTT
1 ATTT
3309113 ATATATTATT
Statistics
Matches: 201, Mismatches: 18, Indels: 21
0.84 0.08 0.09
Matches are distributed among these distances:
36 22 0.11
37 118 0.59
38 22 0.11
39 24 0.12
40 15 0.07
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (37 bp):
ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
Found at i:3309002 original size:11 final size:11
Alignment explanation
Indices: 3308988--3309047 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
3308978 AATATATATT
3308988 TTTTGAAAATA
1 TTTTGAAAATA
*
3308999 TTTTGAAAAAA
1 TTTTGAAAATA
*
3309010 TATAT-AATATATA
1 T-TTTGAA-A-ATA
3309023 GTTTTTGAAAATA
1 --TTTTGAAAATA
3309036 TTTTGAAAATA
1 TTTTGAAAATA
3309047 T
1 T
3309048 GTATAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 25 0.64
12 3 0.08
13 5 0.13
14 3 0.08
15 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:3310928 original size:11 final size:11
Alignment explanation
Indices: 3310914--3310984 Score: 63
Period size: 11 Copynumber: 6.1 Consensus size: 11
3310904 AATATATATT
3310914 TTTTGAAAATA
1 TTTTGAAAATA
*
3310925 TTTTGAAAAAA
1 TTTTGAAAATA
*
3310936 TATAT-AATATATA
1 T-TTTGAA-A-ATA
3310949 GTTTTTGAAAATA
1 --TTTTGAAAATA
*
3310962 TTTTGAAAACA
1 TTTTGAAAATA
3310973 TTTTGAAAATA
1 TTTTGAAAATA
3310984 T
1 T
3310985 ATATAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 34 0.71
12 3 0.06
13 5 0.10
14 3 0.06
15 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:3310966 original size:48 final size:48
Alignment explanation
Indices: 3310914--3311021 Score: 182
Period size: 48 Copynumber: 2.2 Consensus size: 48
3310904 AATATATATT
3310914 TTTTGAAAATATTTTGAAAAAATATATAATATATAGTTTTTGAAAAT-A
1 TTTTGAAAATATTTTGAAAAAATATATAATATATAGTTTTTG-AAATCA
* *
3310962 TTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAATCA
1 TTTTGAAAATATTTTGAAAAAATATATAATATATAGTTTTTGAAATCA
3311010 TTTTGAAAATAT
1 TTTTGAAAATAT
3311022 ATATATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 4 0.07
48 52 0.93
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (48 bp):
TTTTGAAAATATTTTGAAAAAATATATAATATATAGTTTTTGAAATCA
Found at i:3310985 original size:37 final size:37
Alignment explanation
Indices: 3310776--3310973 Score: 285
Period size: 37 Copynumber: 5.4 Consensus size: 37
3310766 TATATATACA
3310776 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
*
3310813 GTTTTGAAAACATATATAATATATAG-TTTTGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
* * * *
3310849 ATTTTGAATATATATAT-A-ATATAGTTTTTTAAAAC
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
*
3310884 ATTTTTGAAAACATATATATAATATATATTTTTTGAAAAT
1 A-TTTTGAAAAC--ATATATAATATATAGTTTTTGAAAAT
*
3310924 ATTTTGAAAAAATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
3310961 ATTTTGAAAACAT
1 ATTTTGAAAACAT
3310974 TTTGAAAATA
Statistics
Matches: 141, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
34 6 0.04
35 10 0.07
36 32 0.23
37 62 0.44
38 6 0.04
39 10 0.07
40 15 0.11
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
Found at i:3311003 original size:37 final size:36
Alignment explanation
Indices: 3310962--3311031 Score: 122
Period size: 37 Copynumber: 1.9 Consensus size: 36
3310952 TTTGAAAATA
3310962 TTTTGAAAACATTTTGAAAATATATATAATATATAGT
1 TTTTGAAAACATTTTGAAAATATATAT-ATATATAGT
*
3310999 TTTTGAAATCATTTTGAAAATATATATATATAT
1 TTTTGAAAACATTTTGAAAATATATATATATAT
3311032 TATATAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (36 bp):
TTTTGAAAACATTTTGAAAATATATATATATATAGT
Found at i:3311066 original size:30 final size:30
Alignment explanation
Indices: 3311010--3311065 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
3311000 TTTGAAATCA
*
3311010 TTTTGAAAATATATATATATATTATATAGT
1 TTTTAAAAATATATATATATATTATATAGT
3311040 TTTTAAAAATAT-T-TATATATTATATA
1 TTTTAAAAATATATATATATATTATATA
3311066 TTATAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 1 0.04
30 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (30 bp):
TTTTAAAAATATATATATATATTATATAGT
Found at i:3312763 original size:37 final size:37
Alignment explanation
Indices: 3312720--3312985 Score: 360
Period size: 37 Copynumber: 7.1 Consensus size: 37
3312710 TATATATACA
*
3312720 ATTTTGAAAACATATATAATATATAGTTTATGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
*
3312757 GTTTTGAAAACATATATAATATATAG-TTTTGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
* * *
3312793 ATTTTGAAAATATATATAATATA-ATTTTTTCAAACAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAA-AT
*
3312830 -TTTTGAAAACATATATATAATATATATTTTTTGAAAAT
1 ATTTTGAAAAC--ATATATAATATATAGTTTTTGAAAAT
*
3312868 ATTTTGAAAAAATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
*
3312905 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
*
3312942 CATTTTG-AAACTATATATATATTATATAGTTTTTAAAAAT
1 -ATTTTGAAAAC-ATATATA-A-TATATAGTTTTTGAAAAT
3312982 ATTT
1 ATTT
3312986 ATATATTATA
Statistics
Matches: 206, Mismatches: 13, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
35 1 0.00
36 46 0.22
37 91 0.44
38 27 0.13
39 24 0.12
40 17 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
Found at i:3312872 original size:11 final size:11
Alignment explanation
Indices: 3312858--3312917 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
3312848 AATATATATT
3312858 TTTTGAAAATA
1 TTTTGAAAATA
*
3312869 TTTTGAAAAAA
1 TTTTGAAAATA
*
3312880 TATAT-AATATATA
1 T-TTTGAA-A-ATA
3312893 GTTTTTGAAAATA
1 --TTTTGAAAATA
3312906 TTTTGAAAATA
1 TTTTGAAAATA
3312917 T
1 T
3312918 ATATAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 25 0.64
12 3 0.08
13 5 0.13
14 3 0.08
15 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:3312996 original size:75 final size:73
Alignment explanation
Indices: 3312720--3313002 Score: 306
Period size: 75 Copynumber: 3.8 Consensus size: 73
3312710 TATATATACA
* * * * *
3312720 ATTTTGAAAACATATATAATATATAGTTTATGAAAATGTTT-TGAAAACATATATAATATATAG-
1 ATTTTGAAAATATATATAATATATAGTTTTTAAAAATATTTAT--AAATATATATAATATATAGT
3312783 TTTTGAAAAT
64 TTTTGAAAAT
* * * * *
3312793 ATTTTGAAAATATATATAATATA-ATTTTTTCAAACATTTTTGAAAACATATATATAATATATAT
1 ATTTTGAAAATATATATAATATATAGTTTTT-AAAAATATTT-ATAA-ATATATATAATATATAG
3312857 TTTTTGAAAAT
63 TTTTTGAAAAT
* *
3312868 ATTTTGAAAAAATATATAATATATAGTTTTTGAAAATATTT-TGAAAATATATATAATATATAGT
1 ATTTTGAAAATATATATAATATATAGTTTTTAAAAATATTTAT--AAATATATATAATATATAGT
3312932 TTTTGAAAAT
64 TTTTGAAAAT
* * *
3312942 CATTTTGAAACTATATATATATTATATAGTTTTTAAAAATATTTATATAT-TATATATTATA
1 -ATTTTGAAA--ATATATATAATATATAGTTTTTAAAAATATTTATAAATATATATAATATA
3313003 ACATATTATT
Statistics
Matches: 177, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
72 5 0.03
73 31 0.18
74 42 0.24
75 60 0.34
76 9 0.05
77 29 0.16
78 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (73 bp):
ATTTTGAAAATATATATAATATATAGTTTTTAAAAATATTTATAAATATATATAATATATAGTTT
TTGAAAAT
Found at i:3313032 original size:22 final size:23
Alignment explanation
Indices: 3313007--3313049 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3312997 ATTATAACAT
3313007 ATTATTTATTATATT-ATTTTAA
1 ATTATTTATTATATTCATTTTAA
*
3313029 ATTATTTATTATTTTCATTTT
1 ATTATTTATTATATTCATTTT
3313050 CTTTCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTATTTATTATATTCATTTTAA
Found at i:3313074 original size:16 final size:18
Alignment explanation
Indices: 3313037--3313075 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
3313027 AAATTATTTA
3313037 TTATTTTCATTTTCTTTC
1 TTATTTTCATTTTCTTTC
3313055 -TATTTT-ATTTT-TTTC
1 TTATTTTCATTTTCTTTC
3313070 TTATTT
1 TTATTT
3313076 GGTCCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATTTTCATTTTCTTTC
Found at i:3315019 original size:23 final size:23
Alignment explanation
Indices: 3314990--3315034 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3314980 TAATATATAA
*
3314990 AAATAATATTTTGGATTAATTTG
1 AAATAATATTTTAGATTAATTTG
* *
3315013 AAATAATTTTTTAGATTTATTT
1 AAATAATATTTTAGATTAATTT
3315035 TTTTCAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (23 bp):
AAATAATATTTTAGATTAATTTG
Found at i:3316094 original size:17 final size:17
Alignment explanation
Indices: 3316074--3316112 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3316064 CCCAAGTTTT
*
3316074 ATTTTGAGATTTACGAC
1 ATTTTGAGATTTACAAC
3316091 ATTTTGAGATTTACAAC
1 ATTTTGAGATTTACAAC
3316108 ATTTT
1 ATTTT
3316113 TTATAGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (17 bp):
ATTTTGAGATTTACAAC
Found at i:3317532 original size:132 final size:132
Alignment explanation
Indices: 3317307--3317554 Score: 363
Period size: 132 Copynumber: 1.9 Consensus size: 132
3317297 GGTGCATTAC
* *
3317307 TTTGCCTTTGAGAAATGCACGTCTTTCTGATATAAAGTGATATATCAACACTGAAAAATTTTCTA
1 TTTGCCTATGAAAAATGCACGTCTTTCTGATATAAAGTGATATATCAACACTGAAAAATTTTCTA
*
3317372 TAAAGAGTTGATATATCACTGAGAAGTTGCTAAAGATGAGAAATTGGGCACTTAAATGGTGTGTT
66 TAAAGAGTTGATATATCACTGAAAAGTTGCTAAAGATGAGAAATTGGGCACTTAAATGGTGTGTT
3317437 GT
131 GT
* * * * *
3317439 TTTGCCTATGAAAAATGCACGTTTTTCTGATATGAATTGATATCTCAACACTGAAAAGTTTTCTG
1 TTTGCCTATGAAAAATGCACGTCTTTCTGATATAAAGTGATATATCAACACTGAAAAATTTTCT-
* * * **
3317504 A-AATGAGTTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCAC
65 ATAAAGAGTTGATATATCACTGAAAAGTTGCTAAAGATGAGAAATTGGGCAC
3317555 ACTTAGATTT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
132 101 0.99
133 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (132 bp):
TTTGCCTATGAAAAATGCACGTCTTTCTGATATAAAGTGATATATCAACACTGAAAAATTTTCTA
TAAAGAGTTGATATATCACTGAAAAGTTGCTAAAGATGAGAAATTGGGCACTTAAATGGTGTGTT
GT
Found at i:3318816 original size:15 final size:15
Alignment explanation
Indices: 3318798--3318841 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
3318788 GATCTGGCCT
3318798 GATCAGACCCGACCC
1 GATCAGACCCGACCC
*
3318813 GATCCGACCCGACCC
1 GATCAGACCCGACCC
*
3318828 -A-CTGACCCGACCC
1 GATCAGACCCGACCC
3318841 G
1 G
3318842 TCTGTCCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 14 0.54
ACGTcount: A:0.23, C:0.50, G:0.20, T:0.07
Consensus pattern (15 bp):
GATCAGACCCGACCC
Found at i:3320313 original size:21 final size:20
Alignment explanation
Indices: 3320287--3320333 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3320277 AGGCTACTTC
3320287 AGAGGGACAAGGTTTTGATAT
1 AGAGGG-CAAGGTTTTGATAT
** *
3320308 AGAGGGTGATGTTTTGATAT
1 AGAGGGCAAGGTTTTGATAT
3320328 AGAGGG
1 AGAGGG
3320334 TGATGTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.30, C:0.02, G:0.38, T:0.30
Consensus pattern (20 bp):
AGAGGGCAAGGTTTTGATAT
Found at i:3320323 original size:20 final size:20
Alignment explanation
Indices: 3320298--3320341 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3320288 GAGGGACAAG
3320298 GTTTTGATATAGAGGGTGAT
1 GTTTTGATATAGAGGGTGAT
3320318 GTTTTGATATAGAGGGTGAT
1 GTTTTGATATAGAGGGTGAT
3320338 GTTT
1 GTTT
3320342 GGGAGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (20 bp):
GTTTTGATATAGAGGGTGAT
Found at i:3325202 original size:58 final size:57
Alignment explanation
Indices: 3325037--3325335 Score: 252
Period size: 58 Copynumber: 5.2 Consensus size: 57
3325027 TTATTTAATA
* * *
3325037 GAATTTATTTCCTTGAGAATCTTAAATGATTTTAACTTTGTATGA-AAA-AAAATATTT
1 GAATTTATTTCCTTGAGAATCTTAAATGATTCTAA-TTTGTAAGATAAATAAATTA-TT
* * * *
3325094 GAATTTATTTCCTTGAGTATCTTCAATGATTCCAACTTTGTAA-CTAAAATAAA-TATTT
1 GAATTTATTTCCTTGAGAATCTTAAATGATTCTAA-TTTGTAAGAT-AAATAAATTA-TT
*
3325152 GAATTTATTTCCTTGAGAATCTTAAATGATTCTAATTTCGTAAGATAAATAAATTATC
1 GAATTTATTTCCTTGAGAATCTTAAATGATTCTAATTT-GTAAGATAAATAAATTATT
* * * ** * * *
3325210 AAATTTATTTTCTTGAGAATCGTGGATAATTCT-ATCTTTTAAAAATAAATAAATTATT
1 GAATTTATTTCCTTGAGAATCTTAAATGATTCTAAT-TTGT-AAGATAAATAAATTATT
* * * * *
3325268 AAATTTATTTTCTTGAGAATCTTAAATTATTCTATTTTCTTAAAGGA-AAA-AAATTATT
1 GAATTTATTTCCTTGAGAATCTTAAATGATTCTAATTT-GT-AA-GATAAATAAATTATT
*
3325326 AAATTTATTT
1 GAATTTATTT
3325336 TTTAAGGAAT
Statistics
Matches: 205, Mismatches: 26, Indels: 21
0.81 0.10 0.08
Matches are distributed among these distances:
57 44 0.21
58 145 0.71
59 15 0.07
60 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (57 bp):
GAATTTATTTCCTTGAGAATCTTAAATGATTCTAATTTGTAAGATAAATAAATTATT
Found at i:3325276 original size:116 final size:114
Alignment explanation
Indices: 3325038--3325336 Score: 325
Period size: 116 Copynumber: 2.6 Consensus size: 114
3325028 TATTTAATAG
* * * *
3325038 AATTTATTTCCTTGAGAATCTTAAATGATTTTAACTTT-GTATGAAAAAAAATATTTGAATTTAT
1 AATTTATTTCCTTGAGAATCTTAAATGATTCTAA-TTTCGTAAGAAAAAAATTA-TTAAATTTAT
* * * * ** *
3325102 TTCCTTGAGTATCTTCAATGATTCCAACTTTGTAACTAAAATAAATATTTG
64 TTTCTTGAGAATCGTCAATAATTCCAACTTTGTAAAAAAAATAAATATTTA
*
3325153 AATTTATTTCCTTGAGAATCTTAAATGATTCTAATTTCGTAAGATAAATAAATTATCAAATTTAT
1 AATTTATTTCCTTGAGAATCTTAAATGATTCTAATTTCGTAAGA-AAA-AAATTATTAAATTTAT
** * *
3325218 TTTCTTGAGAATCGTGGATAATTCTATCTTT-TAAAAATAAATAAAT-TATTA
64 TTTCTTGAGAATCGTCAATAATTCCAACTTTGTAAAAA-AAATAAATAT-TTA
* * * *
3325269 AATTTATTTTCTTGAGAATCTTAAATTATTCTATTTTCTTAAAGGAAAAAAATTATTAAATTTAT
1 AATTTATTTCCTTGAGAATCTTAAATGATTCTAATTTCGT-AA-GAAAAAAATTATTAAATTTAT
3325334 TTT
64 TTT
3325337 TTAAGGAATC
Statistics
Matches: 156, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
114 3 0.02
115 43 0.28
116 98 0.63
117 10 0.06
118 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (114 bp):
AATTTATTTCCTTGAGAATCTTAAATGATTCTAATTTCGTAAGAAAAAAATTATTAAATTTATTT
TCTTGAGAATCGTCAATAATTCCAACTTTGTAAAAAAAATAAATATTTA
Found at i:3327181 original size:16 final size:16
Alignment explanation
Indices: 3327160--3327193 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3327150 CTGTTTTGGG
3327160 ACTTAACCGTC-CAACC
1 ACTTAACC-TCTCAACC
3327176 ACTTAACCTCTCAACC
1 ACTTAACCTCTCAACC
3327192 AC
1 AC
3327194 AGGGACCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.32, C:0.44, G:0.03, T:0.21
Consensus pattern (16 bp):
ACTTAACCTCTCAACC
Found at i:3328196 original size:16 final size:16
Alignment explanation
Indices: 3328171--3328201 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3328161 GTTTGGGCTT
3328171 GTGTAAGATGTAAAGA
1 GTGTAAGATGTAAAGA
*
3328187 GTGTATGATGTAAAG
1 GTGTAAGATGTAAAG
3328202 GGACTCTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (16 bp):
GTGTAAGATGTAAAGA
Found at i:3328928 original size:84 final size:84
Alignment explanation
Indices: 3328786--3329018 Score: 342
Period size: 84 Copynumber: 2.8 Consensus size: 84
3328776 CGGAGGACTT
* * * * * *
3328786 ATCATCTTGCTTGAAAGACTTA-TAAATGACCCAAAGGATTTCATCATCATGCTTGAAAGACTTA
1 ATCATCATGCTCGAAAGACTTACT-GATGGCCCTAAGGATTTCATCATCATGCTAGAAAGACTTA
* *
3328850 CAAATAACCCGAAGGATTTA
65 CAAATAACCCAAAGGATTAA
* *
3328870 ATCATTATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGATAGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGCTAGAAAGACTTAC
3328935 AAATAACCCAAAGGATTAA
66 AAATAACCCAAAGGATTAA
* *
3328954 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGCTCGAAAGGCTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGCTAGAAAGACTTAC
3329019 TGATGGCACT
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
84 133 0.99
85 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (84 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGCTAGAAAGACTTAC
AAATAACCCAAAGGATTAA
Found at i:3329011 original size:126 final size:126
Alignment explanation
Indices: 3328798--3329025 Score: 339
Period size: 126 Copynumber: 1.8 Consensus size: 126
3328788 CATCTTGCTT
* * ** *
3328798 GAAAGACTTATAAATGACCCAAAGGATTTCATCATCATGCTTGAAAGACTTACAAATAACCCGAA
1 GAAAGACTTACAAATAACCCAAAGGATTAAATCATCATGCTCGAAAGACTTACAAATAACCCGAA
*
3328863 GGATTTAATCATTATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGATA
66 GGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGATA
** ** *
3328924 GAAAGACTTACAAATAACCCAAAGGATTAAATCATCATGCTCGAAAGACTTACTGATGGCCCTAA
1 GAAAGACTTACAAATAACCCAAAGGATTAAATCATCATGCTCGAAAGACTTACAAATAACCCGAA
* *
3328989 GGATTTCATCATCATGCTCGAAAGGCTTACTGATGGC
66 GGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
3329026 ACTTACTGAT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 89 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (126 bp):
GAAAGACTTACAAATAACCCAAAGGATTAAATCATCATGCTCGAAAGACTTACAAATAACCCGAA
GGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTCATCATCATGATA
Found at i:3329018 original size:42 final size:42
Alignment explanation
Indices: 3328786--3329025 Score: 257
Period size: 42 Copynumber: 5.7 Consensus size: 42
3328776 CGGAGGACTT
* * * * *
3328786 ATCATCTTGCTTGAAAGACTTA-TAAATGACCCAAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACT-GATGGCCCTAAGGATTTC
* ** ** * *
3328828 ATCATCATGCTTGAAAGACTTACAAATAACCCGAAGGATTTA
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
*
3328870 ATCATTATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
* * ** ** * **
3328912 ATCATCATGATAGAAAGACTTACAAATAACCCAAAGGATTAA
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
3328954 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
*
3328996 ATCATCATGCTCGAAAGGCTTACTGATGGC
1 ATCATCATGCTCGAAAGACTTACTGATGGC
3329026 ACTTACTGAT
Statistics
Matches: 164, Mismatches: 33, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
42 164 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTC
Found at i:3329080 original size:36 final size:36
Alignment explanation
Indices: 3329040--3329217 Score: 257
Period size: 36 Copynumber: 4.9 Consensus size: 36
3329030 ACTGATGGAT
* * * *
3329040 TTGCTTCATTACTCTTCCGTGGAGACTTAAGATTGA
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA
3329076 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA
* *
3329112 TTGTTTCACTACTCTTTGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA
* * * *
3329148 TTTCTTCACTACTCTTTGGTGAAGACTTAAGATGGA
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA
3329184 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 -TTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
3329218 GGCCCGAAGG
Statistics
Matches: 128, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 98 0.77
37 30 0.23
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA
Found at i:3329326 original size:42 final size:41
Alignment explanation
Indices: 3329278--3329375 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
3329268 TTACGGACGG
* *
3329278 CCCGAAGGACTTATCATCTTGCTCAAAAAGGCTTACAAATGA
1 CCCGAAGGACTTATCATCATGCTC-AAAAGACTTACAAATGA
* * * * *
3329320 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAGTGG
1 CCCGAAGGACTT-ATCATCATGCTCAAAAGACTTACAAATGA
*
3329362 CCCGAATGACTTAT
1 CCCGAAGGACTTAT
3329376 AAATTTTAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.04
42 33 0.72
43 11 0.24
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (41 bp):
CCCGAAGGACTTATCATCATGCTCAAAAGACTTACAAATGA
Found at i:3334712 original size:90 final size:89
Alignment explanation
Indices: 3334555--3334731 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
3334545 CCTAACACAC
*
3334555 CCTTTTATAGCCAAGTTACCCTAATCCTATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
3334620 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
3334644 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
3334709 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
3334732 TTCGGGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 33 0.40
90 50 0.60
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:3335113 original size:37 final size:37
Alignment explanation
Indices: 3335063--3335142 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
3335053 TTGTTTCTTG
*
3335063 ATATCTATAGTAGACTGTAATTAACGAATAGTTTATA
1 ATATCTAGAGTAGACTGTAATTAACGAATAGTTTATA
*
3335100 ATATCTAGAGTAGACTGTAATTAACGAATAGTTTATG
1 ATATCTAGAGTAGACTGTAATTAACGAATAGTTTATA
3335137 ATATCT
1 ATATCT
3335143 CATATCAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (37 bp):
ATATCTAGAGTAGACTGTAATTAACGAATAGTTTATA
Found at i:3341431 original size:20 final size:20
Alignment explanation
Indices: 3341406--3341492 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 20
3341396 TATTATTTCA
3341406 AATTAATTAAATATATATTT
1 AATTAATTAAATATATATTT
* *
3341426 AATTAATTGAAATTAAATATTCG
1 AATTAATT-AAA-TATATATT-T
* *
3341449 AGATTAATAAAACATATATTT
1 A-ATTAATTAAATATATATTT
*
3341470 AATTAACTATAGATATATATTT
1 AATTAA-T-TAAATATATATTT
3341492 A
1 A
3341493 GTAACGTACA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
20 13 0.25
21 5 0.10
22 24 0.46
23 4 0.08
24 6 0.12
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (20 bp):
AATTAATTAAATATATATTT
Found at i:3341741 original size:18 final size:18
Alignment explanation
Indices: 3341718--3341766 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3341708 CCTTTATATC
3341718 TAGAATAGGCACAAATCT
1 TAGAATAGGCACAAATCT
*
3341736 TAGAATAGGCACAAGTCT
1 TAGAATAGGCACAAATCT
* *
3341754 TGGAATAGTCACA
1 TAGAATAGGCACA
3341767 CTTGTATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (18 bp):
TAGAATAGGCACAAATCT
Found at i:3342639 original size:16 final size:16
Alignment explanation
Indices: 3342614--3342644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3342604 GTTTGGGCTT
3342614 GTGTAAGATGTAAAGA
1 GTGTAAGATGTAAAGA
*
3342630 GTGTATGATGTAAAG
1 GTGTAAGATGTAAAG
3342645 GGACTCTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (16 bp):
GTGTAAGATGTAAAGA
Found at i:3343444 original size:45 final size:44
Alignment explanation
Indices: 3343345--3343496 Score: 148
Period size: 45 Copynumber: 3.4 Consensus size: 44
3343335 TATCCAAGGT
*
3343345 TTTTGATTATTGGATTGTCAAAAGTAAAATCAAAT-AAGTA-ATTTC
1 TTTTGATTATTGG-TTGTCAAAAGTAAAATCAAATGAA-TAGA-TCC
* *
3343390 TTTTTATTATTGTGTTGTCAAAAGTAAAATCAAATGATTAGATCC
1 TTTTGATTATTG-GTTGTCAAAAGTAAAATCAAATGAATAGATCC
* * * * *
3343435 TTTAGATTATTGGGTTG-CGGAAATTAAAATCAAAGGAATAGTTCC
1 TTTTGATTATT-GGTTGTC-AAAAGTAAAATCAAATGAATAGATCC
3343480 TTTTGATTATTAGGTTG
1 TTTTGATTATT-GGTTG
3343497 CTAAACTTAA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.01
45 85 0.94
46 4 0.04
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (44 bp):
TTTTGATTATTGGTTGTCAAAAGTAAAATCAAATGAATAGATCC
Found at i:3343712 original size:58 final size:57
Alignment explanation
Indices: 3343640--3344046 Score: 417
Period size: 58 Copynumber: 7.0 Consensus size: 57
3343630 AATCTTGTGT
* * *
3343640 TGATTCTAACTTTGTAAGGGAATTAAATTGTTTAATTTATTTACTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTT-CTTGAGAATCTTAAA
* * *
3343698 TGATTCTGACTTTGTAAGGAAAATAAATCGTTGAATTTATTTCCTCGAGAATC-TAGAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTT-CTTGAGAATCTTA-AA
* * *
3343756 TTATTCTAACTTTGTTAGGAAAATAAATTGTTTAATTTATTTCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTT-CTTGAGAATCTTAAA
* * * * *
3343814 TGATTTTAACTTTTTTTA-GAAAATAAATAGTTGAATTTATTTCTTTGAGAATCTTCAA
1 TGATTCTAAC-TTTGTAAGGAAAATAAATTGTTGAATTTATTTC-TTGAGAATCTTAAA
* * *
3343872 TGATTCTAACTTTGTAACGAAAATATATAGTTGAATTTATTTTCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTA-TTTCTTGAGAATCTTAAA
* * * * * * *
3343930 TGGTTTTAACTTTGTAA-GATAAATAAATTATCGAATTTATTTTCTTGATAATCGTAGA
1 TGATTCTAACTTTGTAAGGA-AAATAAATTGTTGAATTTA-TTTCTTGAGAATCTTAAA
** * * * *
3343988 TGATTCTATTTTCTTTAAGG-AAATAAATTGTTAAATTTGGTTTCTCGAGAATCTTAAA
1 TGATTCTAACTT-TGTAAGGAAAATAAATTGTTGAATTT-ATTTCTTGAGAATCTTAAA
3344046 T
1 T
3344047 AAAAAAAATT
Statistics
Matches: 293, Mismatches: 46, Indels: 20
0.82 0.13 0.06
Matches are distributed among these distances:
57 10 0.03
58 266 0.91
59 16 0.05
60 1 0.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (57 bp):
TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCTTGAGAATCTTAAA
Found at i:3343806 original size:116 final size:114
Alignment explanation
Indices: 3343640--3344046 Score: 460
Period size: 116 Copynumber: 3.5 Consensus size: 114
3343630 AATCTTGTGT
* * *
3343640 TGATTCTAACTTTGTAAGGGAATTAAATTGTTTAATTTATTTACTTGAGAATCTTAAATGATTCT
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTTAATTTATTT-CTTGAGAATCTTAAATGATTTT
* * *
3343705 GACTTTGTAAGGAAAATAAATCGTTGAATTTATTTCCTCGAGAATCTAGAA
65 AACTTTGTAA-GAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTAGAA
* *
3343756 TTATTCTAACTTTGTTAGGAAAATAAATTGTTTAATTTATTTCCTTGAGAATCTTAAATGATTTT
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTTAATTTATTT-CTTGAGAATCTTAAATGATTTT
* * * **
3343821 AACTTTTTTTAGAAAATAAATAGTTGAATTTATTTCTTTGAGAATCTTCAA
65 AAC-TTTGTAAGAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTAGAA
* * * * *
3343872 TGATTCTAACTTTGTAACGAAAATATATAGTTGAATTTATTTTCTTGAGAATCTTAAATGGTTTT
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTTAATTTA-TTTCTTGAGAATCTTAAATGATTTT
* * *
3343937 AACTTTGTAAGATAAATAAATTA-TCGAATTTATTTTCTTGATAATCGTAG-A
65 AACTTTGTAAGA-AAATAAA-TAGTTGAATTTATTTCCTTGAGAATC-TAGAA
** * * * *
3343988 TGATTCTATTTTCTTTAAGG-AAATAAATTGTTAAATTTGGTTTCTCGAGAATCTTAAAT
1 TGATTCTAACTT-TGTAAGGAAAATAAATTGTTTAATTT-ATTTCTTGAGAATCTTAAAT
3344047 AAAAAAAATT
Statistics
Matches: 246, Mismatches: 38, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
115 7 0.03
116 223 0.91
117 16 0.07
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (114 bp):
TGATTCTAACTTTGTAAGGAAAATAAATTGTTTAATTTATTTCTTGAGAATCTTAAATGATTTTA
ACTTTGTAAGAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTAGAA
Found at i:3344194 original size:98 final size:98
Alignment explanation
Indices: 3344046--3344274 Score: 254
Period size: 98 Copynumber: 2.4 Consensus size: 98
3344036 GAATCTTAAA
* * * *
3344046 TAAAA-AAAATTAAATTGTTTAATTTA-TTTTCTTATGAATTTTTAATGATTCTATCTTGTAAAA
1 TAAAAGAAAA-TAAATAGTTGAATTTATTTTTCTTAAGAATTTATAATGATTCTATCTTGTAAAA
* *
3344109 GGAAATAAATCATCAG-ATTTATTTTCCTATTTTG
65 AGAAATAAATCAT-AGAATTTAGTTTCCTATTTTG
*
3344143 TAAAACGAAAATAAATAGTTGAATTTATTTTTC-TAAGAATCTTAT-ATGATTCTATTTTGTAAA
1 TAAAA-GAAAATAAATAGTTGAATTTATTTTTCTTAAGAAT-TTATAATGATTCTATCTTGTAAA
* ** *
3344206 AAGACATAAATTGTTGAATTTAGTTTCCTATTTTG
64 AAGAAATAAATCATAGAATTTAGTTTCCTATTTTG
* * *
3344241 TAAAAGAAAATCAATCGTAGAATTTA-TTTTCTTA
1 TAAAAGAAAATAAATAGTTGAATTTATTTTTCTTA
3344275 TTTTGTAAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
96 5 0.04
97 26 0.23
98 69 0.62
99 12 0.11
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (98 bp):
TAAAAGAAAATAAATAGTTGAATTTATTTTTCTTAAGAATTTATAATGATTCTATCTTGTAAAAA
GAAATAAATCATAGAATTTAGTTTCCTATTTTG
Found at i:3344264 original size:39 final size:39
Alignment explanation
Indices: 3344194--3344292 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
3344184 TTATATGATT
* * * *
3344194 CTATTTTGTAAAA-AGACATAAATTGTTGAATTTAGTTTC
1 CTATTTTGTAAAAGA-AAATCAATCGTAGAATTTAGTTTC
*
3344233 CTATTTTGTAAAAGAAAATCAATCGTAGAATTTATTTTC
1 CTATTTTGTAAAAGAAAATCAATCGTAGAATTTAGTTTC
* *
3344272 TTATTTTGTAAAAGGAAATCA
1 CTATTTTGTAAAAGAAAATCA
3344293 TTAGTTAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
39 51 0.98
40 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.41
Consensus pattern (39 bp):
CTATTTTGTAAAAGAAAATCAATCGTAGAATTTAGTTTC
Found at i:3344304 original size:39 final size:38
Alignment explanation
Indices: 3344194--3344314 Score: 118
Period size: 39 Copynumber: 3.1 Consensus size: 38
3344184 TTATATGATT
* * * * *
3344194 CTATTTTGTAAAAAGACATAAATTGTTGAATTTAGTTTC
1 CTATTTTGTAAAAGGAAAT-CATTGTTAAATTTATTTTC
* *
3344233 CTATTTTGTAAAAGAAAATCAATCG-TAGAATTTATTTTC
1 CTATTTTGTAAAAGGAAATC-ATTGTTA-AATTTATTTTC
*
3344272 TTATTTTGTAAAAGGAAATCATTAGTTAAATTTTATTTTC
1 CTATTTTGTAAAAGGAAATCATT-GTTAAA-TTTATTTTC
3344312 CTA
1 CTA
3344315 CGAATCTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
38 3 0.05
39 50 0.76
40 13 0.20
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (38 bp):
CTATTTTGTAAAAGGAAATCATTGTTAAATTTATTTTC
Found at i:3344421 original size:136 final size:136
Alignment explanation
Indices: 3344101--3344449 Score: 377
Period size: 137 Copynumber: 2.6 Consensus size: 136
3344091 TGATTCTATC
* *
3344101 TTGTAAAAGGAAATAAATCATCA-GATTTATTTTCCTATTTTGTAAAACGAAAATAAATAGTTGA
1 TTGTAAAAGGAAATAAATCAT-AGGATTTATTTTCTTATTTTGTAAAA-GAAAATAAATAGTTAA
* * * * * *** *
3344165 ATTTATTTTTCTAAGAATCTTATATGATTCTATTTTGTAAAAAGACATAAATTGTTGAATTTAGT
64 ATTTATTTTCCTAAGAATCTTATATGATTCGATTATATAAAAAGAAATAAACCATAGAATTTAGT
*
3344230 TTCCTATT
129 TTCCTACT
* * * * * * *
3344238 TTGTAAAAGAAAATCAATCGTAGAATTTATTTTCTTATTTTGTAAAAGGAAATCATTAGTTAAAT
1 TTGTAAAAGGAAATAAATCATAGGATTTATTTTCTTATTTTGTAAAAGAAAATAAATAGTTAAA-
* *
3344303 TTTATTTTCCTACGAATCTTATATGATTCCGA-TATAT-AAAAGAAAATAAACCATAGAATTTAT
65 TTTATTTTCCTAAGAATCTTATATGATT-CGATTATATAAAAAG-AAATAAACCATAGAATTTAG
3344366 TTTCCT-CT
128 TTTCCTACT
* * *
3344374 TTGTAAAAGGTAATAAATCATTGGATTTATTTTTTTATTTTGTAAAAGAAAATAAA-ACG-TATA
1 TTGTAAAAGGAAATAAATCATAGGATTTATTTTCTTATTTTGTAAAAGAAAATAAATA-GTTA-A
3344437 ATTTATTTTCCTA
64 ATTTATTTTCCTA
3344450 TTTTGTAAAA
Statistics
Matches: 175, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
135 15 0.09
136 69 0.39
137 89 0.51
138 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (136 bp):
TTGTAAAAGGAAATAAATCATAGGATTTATTTTCTTATTTTGTAAAAGAAAATAAATAGTTAAAT
TTATTTTCCTAAGAATCTTATATGATTCGATTATATAAAAAGAAATAAACCATAGAATTTAGTTT
CCTACT
Found at i:3344428 original size:39 final size:39
Alignment explanation
Indices: 3344339--3344653 Score: 194
Period size: 39 Copynumber: 8.4 Consensus size: 39
3344329 TTCCGATATA
* * * *
3344339 TAAAAGAAAATAAACCATAGAATTTATTTTCCT-CTTTG
1 TAAAAGAAAATAAATCATTGAATTTATTTTTCTATTTTG
** * *
3344377 TAAAAGGTAATAAATCATTGGATTTATTTTTTTATTTTG
1 TAAAAGAAAATAAATCATTGAATTTATTTTTCTATTTTG
* * *
3344416 TAAAAGAAAATAAAACGTAT-AATTTATTTTCCTATTTTG
1 TAAAAGAAAATAAATCAT-TGAATTTATTTTTCTATTTTG
* ** * *
3344455 TAAAAGTAAATAAATCCCTGGATTTATTTTTCTAATTTG
1 TAAAAGAAAATAAATCATTGAATTTATTTTTCTATTTTG
** * * *
3344494 TTGAAGGAAATAAATCATTGTATTTA-TTTTGTATTTTG
1 TAAAAGAAAATAAATCATTGAATTTATTTTTCTATTTTG
* * * *
3344532 TAAAATG-AAATAAATCGTTGCATTTA-TTTTC-ATGTTC
1 TAAAA-GAAAATAAATCATTGAATTTATTTTTCTATTTTG
* * *
3344569 T---AGAAAATAAATC------CTTATTTTCCTATTTTT
1 TAAAAGAAAATAAATCATTGAATTTATTTTTCTATTTTG
* * * *
3344599 TAAAAAAGAAATAAATCACTAAATTTA-TTTTCTTGTTTTG
1 TAAAAGA-AAATAAATCATTGAATTTATTTTTC-TATTTTG
3344639 TAAAAGAAAATAAAT
1 TAAAAGAAAATAAAT
3344654 TAGTTGATTG
Statistics
Matches: 212, Mismatches: 47, Indels: 35
0.72 0.16 0.12
Matches are distributed among these distances:
28 3 0.01
29 4 0.02
30 5 0.02
33 3 0.01
34 19 0.09
37 5 0.02
38 61 0.29
39 97 0.46
40 15 0.07
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (39 bp):
TAAAAGAAAATAAATCATTGAATTTATTTTTCTATTTTG
Found at i:3344485 original size:77 final size:78
Alignment explanation
Indices: 3344339--3344561 Score: 240
Period size: 77 Copynumber: 2.9 Consensus size: 78
3344329 TTCCGATATA
* * *
3344339 TAAAAGAAAATAAACCATAGAATTTATTTTCCT-CTTTGTAAAAGGT-AATAAATCATTGGATTT
1 TAAAAGAAAATAAAACATATAATTTATTTTCCTATTTTGTAAAA-GTAAATAAATCATTGGATTT
* *
3344402 ATTTTTTTATTTTG
65 ATTTTTCTAATTTG
* **
3344416 TAAAAGAAAATAAAACGTATAATTTATTTTCCTATTTTGTAAAAGTAAATAAATCCCTGGATTTA
1 TAAAAGAAAATAAAACATATAATTTATTTTCCTATTTTGTAAAAGTAAATAAATCATTGGATTTA
3344481 TTTTTCTAATTTG
66 TTTTTCTAATTTG
** * * * * * *
3344494 TTGAAGGAAATAAATCAT-TGTATTTATTTT-GTATTTTGTAAAA-TGAAATAAATCGTTGCATT
1 TAAAAGAAAATAAAACATAT-AATTTATTTTCCTATTTTGTAAAAGT-AAATAAATCATTGGATT
3344556 TATTTT
64 TATTTT
3344562 CATGTTCTAG
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
76 1 0.01
77 65 0.52
78 58 0.47
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (78 bp):
TAAAAGAAAATAAAACATATAATTTATTTTCCTATTTTGTAAAAGTAAATAAATCATTGGATTTA
TTTTTCTAATTTG
Found at i:3345351 original size:20 final size:20
Alignment explanation
Indices: 3345326--3345369 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3345316 TTTCATTGGA
3345326 TATATAGATTATAGCAAGGC
1 TATATAGATTATAGCAAGGC
3345346 TATATAGATTATAGCAAGGC
1 TATATAGATTATAGCAAGGC
3345366 -ATAT
1 TATAT
3345370 CGATATATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
TATATAGATTATAGCAAGGC
Found at i:3352916 original size:11 final size:11
Alignment explanation
Indices: 3352897--3352943 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
3352887 TATTCAAGAT
*
3352897 AAAGAAAAGAGA
1 AAAG-AAAGAAA
3352909 AAAGAAAGAAA
1 AAAGAAAGAAA
3352920 AAAGAAAGAAA
1 AAAGAAAGAAA
3352931 AAAG-AAGAAA
1 AAAGAAAGAAA
3352941 AAA
1 AAA
3352944 TAGAATAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 9 0.26
11 21 0.62
12 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:3352918 original size:16 final size:15
Alignment explanation
Indices: 3352897--3352940 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3352887 TATTCAAGAT
*
3352897 AAAGAAAAGAGAAAAG
1 AAAGAAAAAAG-AAAG
3352913 AAAGAAAAAAGAAAG
1 AAAGAAAAAAGAAAG
*
3352928 AAA-AAAGAAGAAA
1 AAAGAAAAAAGAAA
3352941 AAATAGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 9 0.35
15 7 0.27
16 10 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAG
Found at i:3355488 original size:25 final size:25
Alignment explanation
Indices: 3355454--3355504 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3355444 ATATCACCTT
3355454 TGAGATTGTTTCTCTCGAAAAAAAG
1 TGAGATTGTTTCTCTCGAAAAAAAG
*
3355479 TGAGATTGTTTCTCTCGAAACAAAG
1 TGAGATTGTTTCTCTCGAAAAAAAG
3355504 T
1 T
3355505 TTTGTCTCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (25 bp):
TGAGATTGTTTCTCTCGAAAAAAAG
Found at i:3355689 original size:66 final size:67
Alignment explanation
Indices: 3355614--3355768 Score: 195
Period size: 67 Copynumber: 2.3 Consensus size: 67
3355604 ATTTTGTCTT
* *
3355614 GCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATT-TTTCTCTCCAAATAATGTGTCATC
1 GCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTATTTCTCTCCAAACAAAGTGTCATC
3355678 TC
66 TC
* * * * * ** * *
3355680 GCTTTAGACAGTTTCTCTTAAAATATAAGCCTTTGAGATTATTTCTCTTGAAACAAAGTTTCGTC
1 GCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTATTTCTCTCCAAACAAAGTGTCATC
3355745 TC
66 TC
*
3355747 GCTTGAGACAGTTTCCCTTGAA
1 GCTTGAGACAGTTTCTCTTGAA
3355769 GCCCAAATTC
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
66 35 0.47
67 39 0.53
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (67 bp):
GCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTATTTCTCTCCAAACAAAGTGTCATC
TC
Found at i:3355759 original size:67 final size:66
Alignment explanation
Indices: 3355609--3355761 Score: 189
Period size: 66 Copynumber: 2.3 Consensus size: 66
3355599 AATAAATTTT
* * * *
3355609 GTCTTGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTTTTCTCTCCAAATAATGTGT
1 GTCTCGCTTGAGACAGTTTCTCTTAAAACATAAACATTTGAGATTTTTCTCTCCAAACAAAGTGT
3355674 C
66 C
* * * * * ** *
3355675 ATCTCGCTTTAGACAGTTTCTCTTAAAATATAAGCCTTTGAGATTATTTCTCTTGAAACAAAGTT
1 GTCTCGCTTGAGACAGTTTCTCTTAAAACATAAACATTTGAGATT-TTTCTCTCCAAACAAAGTG
3355740 TC
65 TC
3355742 GTCTCGCTTGAGACAGTTTC
1 GTCTCGCTTGAGACAGTTTC
3355762 CCTTGAAGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
66 38 0.53
67 34 0.47
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (66 bp):
GTCTCGCTTGAGACAGTTTCTCTTAAAACATAAACATTTGAGATTTTTCTCTCCAAACAAAGTGT
C
Found at i:3357031 original size:5 final size:5
Alignment explanation
Indices: 3357021--3357045 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3357011 CAACATCAAC
3357021 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
3357046 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3362737 original size:46 final size:46
Alignment explanation
Indices: 3362670--3362761 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
3362660 AACCTGAAAT
* * *
3362670 CAGGTTTAAAAGAAAGGTTATTTGTAGTAGGTATACAGACTTAATA
1 CAGGTTGAAAAGAAAGCTTATTTGTAGTAGGTAAACAGACTTAATA
3362716 CAGGTTGAAAAGAAAGCTTATTTGTAGTAGGTAAACAGACTTAATA
1 CAGGTTGAAAAGAAAGCTTATTTGTAGTAGGTAAACAGACTTAATA
3362762 GAGCCTAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (46 bp):
CAGGTTGAAAAGAAAGCTTATTTGTAGTAGGTAAACAGACTTAATA
Found at i:3375373 original size:20 final size:20
Alignment explanation
Indices: 3375345--3375393 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3375335 TCACTTGTGA
*
3375345 TCGTACAACGTCATGCATGC
1 TCGTGCAACGTCATGCATGC
3375365 TCGTGCAACGTCATGCATGC
1 TCGTGCAACGTCATGCATGC
*
3375385 TCATGCAAC
1 TCGTGCAAC
3375394 TTTATGCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGTGCAACGTCATGCATGC
Found at i:3375468 original size:31 final size:31
Alignment explanation
Indices: 3375430--3375495 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
3375420 TTCTAGAAGA
*
3375430 TAGTCTAGAAGTTAGGTTGTTATAAGTTTGT
1 TAGTCTAGAAGTTAGGTTATTATAAGTTTGT
3375461 TAGTCTAGAAGTTAGGTTATTATAAGTTTGT
1 TAGTCTAGAAGTTAGGTTATTATAAGTTTGT
3375492 TAGT
1 TAGT
3375496 GTAGCAGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.45
Consensus pattern (31 bp):
TAGTCTAGAAGTTAGGTTATTATAAGTTTGT
Found at i:3379994 original size:20 final size:20
Alignment explanation
Indices: 3379971--3380026 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3379961 CGTGTGCTCG
3379971 TGCAACGTCATGCATGCTTA
1 TGCAACGTCATGCATGCTTA
3379991 TGCAACGTCATGCATGCTTA
1 TGCAACGTCATGCATGCTTA
* *
3380011 TGCAACTTTATGCATG
1 TGCAACGTCATGCATG
3380027 TCCATGCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (20 bp):
TGCAACGTCATGCATGCTTA
Found at i:3381202 original size:3 final size:3
Alignment explanation
Indices: 3381194--3381255 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
3381184 TTATATTTAT
3381194 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
*
3381242 TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TT
3381256 TGCTATTAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3381585 original size:46 final size:45
Alignment explanation
Indices: 3381385--3381658 Score: 154
Period size: 43 Copynumber: 6.2 Consensus size: 45
3381375 TTTTTTATCC
* * * *
3381385 TTATAATTGATGTCTCTAATTTTTGT-AATCCTATTTTTCT-C-T
1 TTATAATTGAGGTCTCTAATTTTTTTCAATCCCATTTTTTTACTT
* * * *
3381427 TTATAATGGAGG-CCCTTAATTTTATTCAATCCCATTTTTTTTACAT
1 TTATAATTGAGGTCTC-TAATTTTTTTCAATCCCA-TTTTTTTACTT
* * ** * *
3381473 TTATAATTGATGATC-CTAA-GTTTTTCAATCCCA-CCTTGTACCT
1 TTATAATTGA-GGTCTCTAATTTTTTTCAATCCCATTTTTTTACTT
* * * ** *
3381516 TTATAATTAAGCTCATGTTTTTTTTTTCAATCTCATTTTTTTACTT
1 TTATAATTGAGGTC-TCTAATTTTTTTCAATCCCATTTTTTTACTT
* * *
3381562 TTATAATTGAGGTCTCTAATTTTTTT-AAACCCA-ATTTTTACTC
1 TTATAATTGAGGTCTCTAATTTTTTTCAATCCCATTTTTTTACTT
* * * * * * * *
3381605 ATATAATTTAGGCCCCTAATGTTTTTCAATCTCA-CTTTTTACCT
1 TTATAATTGAGGTCTCTAATTTTTTTCAATCCCATTTTTTTACTT
*
3381649 TTAAAATTGA
1 TTATAATTGA
3381659 TGGCCCTTTT
Statistics
Matches: 172, Mismatches: 48, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
41 2 0.01
42 21 0.12
43 50 0.29
44 31 0.18
45 34 0.20
46 31 0.18
47 2 0.01
48 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (45 bp):
TTATAATTGAGGTCTCTAATTTTTTTCAATCCCATTTTTTTACTT
Found at i:3381610 original size:89 final size:90
Alignment explanation
Indices: 3381446--3381612 Score: 196
Period size: 89 Copynumber: 1.9 Consensus size: 90
3381436 AGGCCCTTAA
* *
3381446 TTTTATTCAATCCCATTTTTTTTACATTTATAATTGATGATCCTAAGTTTTTCAATCCCACCTTG
1 TTTTATTCAATCCCATTTTTTTTACATTTATAATTGATGATCCTAAGTTTTTCAAACCCAACTTG
*
3381511 TACCTTTATAATTAAGCTCATGTTT
66 TACCTATATAATTAAGCTCATGTTT
* * * * * * *
3381536 TTTTTTTCAATCTCA-TTTTTTTACTTTTATAATTGA-GGTCTCTAATTTTTTTAAACCCAATTT
1 TTTTATTCAATCCCATTTTTTTTACATTTATAATTGATGATC-CTAAGTTTTTCAAACCCAACTT
*
3381599 TTA-CTCATATAATT
65 GTACCT-ATATAATT
3381613 TAGGCCCCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
88 5 0.08
89 46 0.72
90 13 0.20
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (90 bp):
TTTTATTCAATCCCATTTTTTTTACATTTATAATTGATGATCCTAAGTTTTTCAAACCCAACTTG
TACCTATATAATTAAGCTCATGTTT
Found at i:3381646 original size:44 final size:43
Alignment explanation
Indices: 3381537--3381646 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 43
3381527 CTCATGTTTT
* ** * *
3381537 TTTTTTCAATCTCATTTTTTTACTTTTATAATTGAGGTCTCTAA
1 TTTTTTCAATCTCA-ATTTTTACTCATATAATTGAGGCCCCTAA
* * * *
3381581 TTTTTTTAAACCCAATTTTTACTCATATAATTTAGGCCCCTAA
1 TTTTTTCAATCTCAATTTTTACTCATATAATTGAGGCCCCTAA
*
3381624 TGTTTTTCAATCTCACTTTTTAC
1 T-TTTTTCAATCTCAATTTTTAC
3381647 CTTTAAAATT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
43 24 0.46
44 28 0.54
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (43 bp):
TTTTTTCAATCTCAATTTTTACTCATATAATTGAGGCCCCTAA
Found at i:3383798 original size:21 final size:22
Alignment explanation
Indices: 3383774--3383815 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3383764 TTCCATAATC
*
3383774 AAATCCT-AAAACATTAAGCAA
1 AAATCCTAAAAACACTAAGCAA
*
3383795 AAATGCTAAAAACACTAAGCA
1 AAATCCTAAAAACACTAAGCA
3383816 TTTTCGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATCCTAAAAACACTAAGCAA
Found at i:3385534 original size:16 final size:16
Alignment explanation
Indices: 3385513--3385548 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3385503 AAGTCTAATG
3385513 ATCTCAGAAATGTACA
1 ATCTCAGAAATGTACA
3385529 ATCTCAGAAATGTACA
1 ATCTCAGAAATGTACA
3385545 ATCT
1 ATCT
3385549 AGCTAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (16 bp):
ATCTCAGAAATGTACA
Found at i:3397779 original size:25 final size:24
Alignment explanation
Indices: 3397733--3397785 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
3397723 GAAAAATGAC
* *
3397733 AGAAGAAGAAAAAGCAAGTGAAAG
1 AGAAGAAGAAAAAGCAAATGAAAA
* *
3397757 AGAAGAGAGGAAAAGGAAATGAAAA
1 AGAAGA-AGAAAAAGCAAATGAAAA
3397782 AGAA
1 AGAA
3397786 AGAAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04
Consensus pattern (24 bp):
AGAAGAAGAAAAAGCAAATGAAAA
Found at i:3401523 original size:81 final size:81
Alignment explanation
Indices: 3401434--3401844 Score: 468
Period size: 81 Copynumber: 5.1 Consensus size: 81
3401424 GCTTTAAATA
* * * *
3401434 AAAGATTAATTGCATAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAAATGAAAGGC
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGC
* * *
3401499 TAAATTCCTTTAATTT
66 TAAATGCCTTTGAGTT
* * * * *
3401515 AAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATTG-CAATTTGATGAAAGG
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTA-TGCCAGTTAGATGAAAGG
* * *
3401579 TTAAATTCATTTGAGTT
65 CTAAATGCCTTTGAGTT
* * * * ** * *
3401596 AAAGATTAGTTGCTTAGCTATGCATTTGACAAAAAAGTGTCAATTATGTTAGTTAGATGAACGGT
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGC
*
3401661 TAAATGCCTCTGAG-T
66 TAAATGCCTTTGAGTT
* *
3401676 AAATGATTAATTGCCTAGCTGTGCATTTGACA-AAAAGGTGTCAATTATGCCAATTAGATGAAAT
1 AAA-GATTAATTGCCTAGCTGTGCATTTGACAGAAAA-GTGTCAATTATGCCAGTTAGATGAAAG
3401740 GCTAAATGCCTTTGAGTT
64 GCTAAATGCCTTTGAGTT
* ** * *
3401758 AAAGATTAAATGCCTAGCTGTGCATTTTGGTAGAAAAGTGTCAATGATGCAAGTTAGATGAAAGG
1 AAAGATTAATTGCCTAGCTGTGCA-TTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGG
* *
3401823 CTAAATGCCTTTGGGTA
65 CTAAATGCCTTTGAGTT
3401840 AAAGA
1 AAAGA
3401845 CTAAATACTT
Statistics
Matches: 280, Mismatches: 43, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
80 10 0.04
81 211 0.75
82 55 0.20
83 4 0.01
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (81 bp):
AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGC
TAAATGCCTTTGAGTT
Found at i:3405580 original size:33 final size:33
Alignment explanation
Indices: 3405538--3405620 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
3405528 TATGGGTTAG
*
3405538 AAAGCATGTTTGGGTAGGATTGCTATTTATTTA
1 AAAGCATGTTTGGGTAGGATTGCTATTTATTAA
3405571 AAAGCATGTTTGGGTAGGATTGCTATTTATTAA
1 AAAGCATGTTTGGGTAGGATTGCTATTTATTAA
3405604 AAAGCATGTTTGGGTAG
1 AAAGCATGTTTGGGTAG
3405621 CTATCATGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.39
Consensus pattern (33 bp):
AAAGCATGTTTGGGTAGGATTGCTATTTATTAA
Found at i:3413243 original size:31 final size:31
Alignment explanation
Indices: 3413205--3413271 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
3413195 AGAGGAATTG
*
3413205 AGATCGATTCGGACAAAGTAAAGGTCATTCA
1 AGATCGATCCGGACAAAGTAAAGGTCATTCA
3413236 AGATCGATCCGGACAAAGTAAAGGTCATTCA
1 AGATCGATCCGGACAAAGTAAAGGTCATTCA
3413267 AGATC
1 AGATC
3413272 TTCCGCCATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (31 bp):
AGATCGATCCGGACAAAGTAAAGGTCATTCA
Found at i:3414365 original size:24 final size:24
Alignment explanation
Indices: 3414320--3414383 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 24
3414310 CGGAACAGAT
* * **
3414320 ATCAAAACAAAATCCATATCATAA
1 ATCAGAACAAAATTCAGGTCATAA
* **
3414344 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAAAATTCAGGTCATAA
*
3414368 ATCATAACAAAATTCA
1 ATCAGAACAAAATTCA
3414384 AGTAGGAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (24 bp):
ATCAGAACAAAATTCAGGTCATAA
Found at i:3419017 original size:24 final size:24
Alignment explanation
Indices: 3418976--3419044 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
3418966 ACAGAGATAT
* *
3418976 CAGAAATCAAAACAGAATTCAGAA
1 CAGATATCAAAACAGAATCCAGAA
* * * *
3419000 CATATATCATAACTGAATCCAGAT
1 CAGATATCAAAACAGAATCCAGAA
* *
3419024 CAGATATCAGAACACAATCCA
1 CAGATATCAAAACAGAATCCA
3419045 TGTCTTGTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (24 bp):
CAGATATCAAAACAGAATCCAGAA
Found at i:3427368 original size:105 final size:105
Alignment explanation
Indices: 3427225--3427735 Score: 740
Period size: 105 Copynumber: 4.9 Consensus size: 105
3427215 AACTATGATC
3427225 CACCA-AAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAA
1 CACCACAA-AAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAA
*
3427289 GGAGAAAGTTCATAATGAGAAGAACTTGTTACTTTCAAATT
65 GGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATT
* * * *
3427330 CACCGCAAAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCCTAAAG
1 CACCACAAAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAG
* * *
3427395 GAGAAAGTTCTTAATGAGAAGAACATGTTCCTTTCGAA-T
66 GAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATT
* *
3427434 CTACCACAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAA
1 C-ACCACAAAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAA
*
3427499 GGAGAAAGTTCATAATGAAAAGAACTTGTTCCTTTCAAATT
65 GGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATT
* * * * *
3427540 CACCACAGAATGAGGTGAATCTACATTTACAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAG
1 CACCACAAAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAG
*
3427605 GAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATA
66 GAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATT
* * * * * * *
3427645 CACCGCATAAGGAGGTCAACCATCATTTCCAAAAGAGTTCATAATGAGAATAACTCGAT-GTAAA
1 CACCACAAAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCG-TCTTAAA
* *
3427709 GGAGGAAGTTAATAATGAGAAGAACTT
65 GGAGAAAGTTCATAATGAGAAGAACTT
3427736 ACTCAACTCT
Statistics
Matches: 366, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
104 2 0.01
105 359 0.98
106 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (105 bp):
CACCACAAAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAG
GAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATT
Found at i:3431300 original size:19 final size:19
Alignment explanation
Indices: 3431276--3431321 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3431266 TCCAATGTGG
3431276 CGAGACTGGTCACTTTACC
1 CGAGACTGGTCACTTTACC
3431295 CGAGACTGGTCACTTTACC
1 CGAGACTGGTCACTTTACC
*
3431314 CGAAACTG
1 CGAGACTG
3431322 TCCAAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (19 bp):
CGAGACTGGTCACTTTACC
Found at i:3436449 original size:26 final size:26
Alignment explanation
Indices: 3436420--3436473 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3436410 ATGTTCTTGG
3436420 AAGATTTAAGATATTTTAAGAAGCTA
1 AAGATTTAAGATATTTTAAGAAGCTA
3436446 AAGATTTAAGATATTTTAAGAAGCTA
1 AAGATTTAAGATATTTTAAGAAGCTA
3436472 AA
1 AA
3436474 TGAAGGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (26 bp):
AAGATTTAAGATATTTTAAGAAGCTA
Found at i:3437635 original size:80 final size:81
Alignment explanation
Indices: 3437206--3437646 Score: 627
Period size: 81 Copynumber: 5.5 Consensus size: 81
3437196 CTGTTTTAAA
* *
3437206 TAAAAGATTAATTTCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT-ACCAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAATGTGTCAATTATGA-CAGTTAGATGAAA
3437270 GGCTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* *
3437287 TAAAA-ATTAATTGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATGACAGTTATATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAATGTGTCAATTATGACAGTTAGATGAAAG
3437351 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
3437367 TTAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAGGTGTCAATTTTGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAATGTGTCAATTATGACAGTTAGATGAAAG
**
3437432 TTTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * *
3437448 TTAAAGATTAATTGCCTAGTTGTGCATTTGAAAGAAATGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAATGTGTCAATTATGACAGTTAGATGAAAG
*
3437513 GCTAAATTCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
3437529 TAAAAGATTAATTGCCTAGCTCTGCATTTGACATAAAGGTGTCAATTATG-CAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAATGTGTCAATTATGACAGTTAGATGAAAG
*
3437593 GCTAAATGCCTTTGAA
66 GCTAAATGCCTTTGAG
* * * * *
3437609 TAAAAGACTAAATGCTTAACGGTGCATTTTGACATAAA
1 TAAAAGATTAATTGCCTAGCTGTGCA-TTTGACATAAA
3437647 CGATAGCATT
Statistics
Matches: 322, Mismatches: 35, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
80 121 0.38
81 201 0.62
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAATGTGTCAATTATGACAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:3437636 original size:242 final size:243
Alignment explanation
Indices: 3437208--3437646 Score: 702
Period size: 242 Copynumber: 1.8 Consensus size: 243
3437198 GTTTTAAATA
* *
3437208 AAAGATTAATTTCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATACCAGTTAGATGAAAGGC
1 AAAGATTAATTGCCTAGCTGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGATGAAAGGC
* * *
3437273 TAAATGCCTTTGAGTAAAAATTAATTGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATGAC
66 TAAATGCCTTTGAGTAAAAATTAATTGCCTAGCTCTGCATTTGACATAAAGGTGTCAATTATGAC
* * * * * * *
3437338 AGTTATATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTGCA-TTTGACATA
131 AGTTAGATGAAAGGCTAAATGCCTTTGAATAAAAGACTAAATGCCTAACGGTGCATTTTGACATA
3437402 AAGGTGTCAATTTTGCCAGTTAGATGAAAGTTTAAATGCCTTTGAGTT
196 AAGGTGTCAATTTTGCCAGTTAGATGAAAGTTTAAATGCCTTTGAGTT
* **
3437450 AAAGATTAATTGCCTAGTTGTGCATTTGAAAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGC
1 AAAGATTAATTGCCTAGCTGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGATGAAAGGC
*
3437515 TAAATTCCTTTGAGTAAAAGATTAATTGCCTAGCTCTGCATTTGACATAAAGGTGTCAATTATG-
66 TAAATGCCTTTGAGTAAAA-ATTAATTGCCTAGCTCTGCATTTGACATAAAGGTGTCAATTATGA
*
3437579 CAGTTAGATGAAAGGCTAAATGCCTTTGAATAAAAGACTAAATGCTTAACGGTGCATTTTGACAT
130 CAGTTAGATGAAAGGCTAAATGCCTTTGAATAAAAGACTAAATGCCTAACGGTGCATTTTGACAT
3437644 AAA
195 AAA
3437647 CGATAGCATT
Statistics
Matches: 178, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
242 126 0.71
243 52 0.29
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (243 bp):
AAAGATTAATTGCCTAGCTGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGATGAAAGGC
TAAATGCCTTTGAGTAAAAATTAATTGCCTAGCTCTGCATTTGACATAAAGGTGTCAATTATGAC
AGTTAGATGAAAGGCTAAATGCCTTTGAATAAAAGACTAAATGCCTAACGGTGCATTTTGACATA
AAGGTGTCAATTTTGCCAGTTAGATGAAAGTTTAAATGCCTTTGAGTT
Found at i:3439053 original size:55 final size:55
Alignment explanation
Indices: 3438643--3439035 Score: 520
Period size: 55 Copynumber: 7.1 Consensus size: 55
3438633 CTATAATAAG
* * * * ** *
3438643 GAAATTTATACACCTAGTATGAATTTCCT-AGTTTTGTACATAAAGTGCCAATACA
1 GAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACA
* * * * *
3438698 TAAATTCATTCACTTAGTATGAATTTATTAAGTTCACACATAAAGTGCCCATACG
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
* * * *
3438753 GAAATTTATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCTCATACG
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
*
3438808 GAAATTCATCCACTTAGTATGAATTTCTTATGTTTACACATAAAGTGCCCATACA
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
* * *
3438863 GAAATTCATCCACTCAGTACGAATTTCGTAAGTTTACACATAAAGTGCCCATAC-
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
3438917 GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
1 G-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
** ** * *
3438973 GAAATTCATAAACAAATTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACT
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
3439028 GAAATTCA
1 GAAATTCA
3439036 AAAATAAATT
Statistics
Matches: 299, Mismatches: 36, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
54 1 0.00
55 295 0.99
56 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (55 bp):
GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
Found at i:3445416 original size:55 final size:55
Alignment explanation
Indices: 3445016--3445394 Score: 480
Period size: 55 Copynumber: 6.9 Consensus size: 55
3445006 AAAATTTATA
* * * * * * *
3445016 TAGTATGAATTTATT-AGTTTTGCATATAAAATGC-CTATACAGAAATCCATTCACT
1 TAGTATGAATTTCTTAAG-TTTACACATAAAGTGCTC-ATACGGAAATTCATCCACT
* * *
3445071 TAGTATGATTTTCTTAAGTTCACATATAAAGTGCTCATACGGAAATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGGAAATTCATCCACT
* * **
3445126 TAGTATGAATTTCTTAAGTTCACACATAAAGAGC-CAATACTAAAATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTC-ATACGGAAATTCATCCACT
* * *
3445181 TTGTATGAATTTCTTAAGTTTACACATAAAGTACCCATACGGAAATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGGAAATTCATCCACT
* * * *
3445236 TTGTATGAATTTCGTAAGTTTACACATAAAGTGCCCATATAGG-AATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATA-CGGAAATTCATCCACT
*
3445291 TAGTATGAATTTCTTAAGTTTACACATAAAGTG-TCGTACGGAAATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGGAAATTCATCCACT
*
3445345 TAGTATTAATTTCTTAAGTTTACACATAAAGTGCTCATACGGAAATTCAT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGGAAATTCAT
3445395 AAACAAATTA
Statistics
Matches: 288, Mismatches: 29, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
53 2 0.01
54 48 0.17
55 232 0.81
56 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (55 bp):
TAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGGAAATTCATCCACT
Found at i:3445819 original size:19 final size:21
Alignment explanation
Indices: 3445776--3445829 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 21
3445766 TACCCCTACC
*
3445776 ATGGTATCAATACTACTATACT
1 ATGGTATCGATACTACTATA-T
3445798 ATGGTATCGATACT-CTAT-T
1 ATGGTATCGATACTACTATAT
3445817 ATGGTATCGATAC
1 ATGGTATCGATAC
3445830 CATTTTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 14 0.45
21 4 0.13
22 13 0.42
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
ATGGTATCGATACTACTATAT
Found at i:3449175 original size:21 final size:21
Alignment explanation
Indices: 3449133--3449171 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3449123 TATCAAGGCC
*
3449133 TTTGTTGAAGTCATGAAATCT
1 TTTGTTGAAGCCATGAAATCT
*
3449154 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAAGCCATGAAAT
3449172 TCTTGCAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (21 bp):
TTTGTTGAAGCCATGAAATCT
Found at i:3450385 original size:42 final size:41
Alignment explanation
Indices: 3450334--3450414 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
3450324 GACGAGAAAA
3450334 AATTCAAGAGTAA-ACAAATAAAAATTGCTAAGGAAAAAATT
1 AATTCAAGAGTAAGA-AAATAAAAATTGCTAAGGAAAAAATT
* *
3450375 AATTGCAAGAGTAAGAAAATAAAAGTTGTTAAGGAAAAAA
1 AATT-CAAGAGTAAGAAAATAAAAATTGCTAAGGAAAAAA
3450415 ATGTTCGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 4 0.11
42 31 0.86
43 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (41 bp):
AATTCAAGAGTAAGAAAATAAAAATTGCTAAGGAAAAAATT
Found at i:3454783 original size:16 final size:17
Alignment explanation
Indices: 3454757--3454788 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3454747 GGGTATTGTA
3454757 ATTATTATTATAATAAT
1 ATTATTATTATAATAAT
3454774 ATTA-TATTATAATAA
1 ATTATTATTATAATAA
3454789 AAATGTCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTATTATAATAAT
Found at i:3455438 original size:20 final size:20
Alignment explanation
Indices: 3455412--3455533 Score: 118
Period size: 20 Copynumber: 6.1 Consensus size: 20
3455402 AGATTGACAG
*
3455412 ATAACCCAAAGGATTTACAA
1 ATAACCCAAAGGTTTTACAA
* * *
3455432 ATTACCCGAAGGCTTTACAA
1 ATAACCCAAAGGTTTTACAA
**
3455452 ATAACCCAGTGGTTTTACAA
1 ATAACCCAAAGGTTTTACAA
* **
3455472 ATAACTCGGAGGTTTTACAA
1 ATAACCCAAAGGTTTTACAA
**
3455492 ATAACCCGGAGGTTTTACAA
1 ATAACCCAAAGGTTTTACAA
* * *
3455512 ATTACCCAAATGCTTTACAA
1 ATAACCCAAAGGTTTTACAA
3455532 AT
1 AT
3455534 CCTTGGGAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
ATAACCCAAAGGTTTTACAA
Done.