Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009247.1 Hibiscus syriacus cultivar Beakdansim tig00112888_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: 1479039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:933466 original size:45 final size:45
Alignment explanation
Indices: 933416--933537 Score: 106
Period size: 45 Copynumber: 2.7 Consensus size: 45
933406 AGACATCCCG
*
933416 TTTCTTAATATTAAAAAATAAATAAATATTTA-AAATATGATTATT
1 TTTCTTAATATTAAAAAATAAATAAATATTTATAAATAGGATT-TT
* * * * *
933461 TTTCTTAAAAGTAATTTATATAAAATTAA-ATTTATAAATAGGATTTT
1 TTTCTTAATATTAA--AAAAT-AAATAAATATTTATAAATAGGATTTT
* *
933508 TAT-TTAATATATAAAAAATAAGTAAATATT
1 TTTCTTAATAT-TAAAAAATAAATAAATATT
933538 ATTTATTATA
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
44 5 0.09
45 18 0.31
46 5 0.09
47 15 0.26
48 15 0.26
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (45 bp):
TTTCTTAATATTAAAAAATAAATAAATATTTATAAATAGGATTTT
Found at i:933623 original size:22 final size:22
Alignment explanation
Indices: 933581--933626 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
933571 TAATAATAAT
*
933581 AACAATAATAATTAAATATATA
1 AACAATAAAAATTAAATATATA
933603 AACATATAAAAATTAAA-ATATA
1 AACA-ATAAAAATTAAATATATA
933625 AA
1 AA
933627 TAAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
AACAATAAAAATTAAATATATA
Found at i:934991 original size:3 final size:3
Alignment explanation
Indices: 934983--935061 Score: 69
Period size: 3 Copynumber: 27.3 Consensus size: 3
934973 GAAATGTAAA
*
934983 AAT AAT AAT AAT AAT AAT AA- ATAT AAT -AT AAT AAT AA- AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * *
935026 AAT AAT AGT -AT AAAT GA- AAT AAT ATT AAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
935062 TAAAAAACAC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
2 7 0.11
3 51 0.84
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:935064 original size:17 final size:17
Alignment explanation
Indices: 934983--935064 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
934973 GAAATGTAAA
934983 AATAATAATAATAATAAT
1 AATAATAAT-ATAATAAT
935001 AA-ATATAATATAATAAT
1 AATA-ATAATATAATAAT
935018 AA-AATAA-A-AATAAT
1 AATAATAATATAATAAT
*
935032 AGTATAAATGAA-ATAATATT
1 A--AT-AAT-AATATAATAAT
935052 AATAATAATATAA
1 AATAATAATATAA
935065 AAAACACAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
16 7 0.13
17 19 0.35
18 12 0.22
19 3 0.05
20 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AATAATAATATAATAAT
Found at i:939094 original size:29 final size:30
Alignment explanation
Indices: 939059--939122 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
939049 TTTATATTTC
* *
939059 TTATAAAATTACTATACAAAA-TAATATAT
1 TTATAAAAATAATATACAAAACTAATATAT
**
939088 TTATAAAAATAATATGTAAAACTAATATAT
1 TTATAAAAATAATATACAAAACTAATATAT
939118 TTATA
1 TTATA
939123 TTGCAGAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (30 bp):
TTATAAAAATAATATACAAAACTAATATAT
Found at i:940373 original size:253 final size:253
Alignment explanation
Indices: 939960--940547 Score: 903
Period size: 253 Copynumber: 2.3 Consensus size: 253
939950 ATATATTCGG
* *
939960 GTCGGATCGTGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATA-T----TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAA
* * *
940024 ACCGGACCGACCCGAAAATATATTTATTCAGGTCGGGTCGGATTAAGTCATTGTTTTTATTAAAT
61 ACCGGACCGACCCGAAAATATATTAATTCAGGTCGGGTCGGATTAAATCACTGTTTTTATTAAAT
* * * *
940089 AAAAATATTTTTTGATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCCGGTCGG
126 AAAAATATTTTTTGATTATTTCGGGTCGGGTCGGATCGGATTTCTAATTAATATATTCCGGTCGA
940154 GTCAGATGAAACTTTATTTTGTTCGGGTCAGGTC-GGTTTTTTAAGTGTGATATTCGGGTCGA
191 GTCAGATGAAACTTTATTTTGTTCGGGTCAGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
940216 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGG
* * *
940281 ACCGATCCGAAAATATATATAATTCGGGTTGGGTCGGATTAAATCACTGTTTTTATTAAATAAAA
66 ACCGACCCGAAAATATAT-TAATTCAGGTCGGGTCGGATTAAATCACTGTTTTTATTAAATAAAA
*
940346 ATAATTTTTT-ATTATTTCGGGTCGGGTCGGATCGGATTTCTAATTAATATATTCGGGTCGAGTC
130 AT-ATTTTTTGATTATTTCGGGTCGGGTCGGATCGGATTTCTAATTAATATATTCCGGTCGAGTC
* *
940410 GGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
194 AGATGAAACTTTATTTTGTTCGGGTCAGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* * * * **
940470 GTAGGGTCGGGTTTTTTTAAGTGTAATATTCGAGTCGGGTTCAGGTTTAGGGTGAAAAAAACTAG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGG
940535 ACCGACCCGAAAA
66 ACCGACCCGAAAA
940548 AAAATATATA
Statistics
Matches: 306, Mismatches: 22, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
251 25 0.08
252 27 0.09
253 121 0.40
254 106 0.35
255 1 0.00
256 26 0.08
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (253 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGG
ACCGACCCGAAAATATATTAATTCAGGTCGGGTCGGATTAAATCACTGTTTTTATTAAATAAAAA
TATTTTTTGATTATTTCGGGTCGGGTCGGATCGGATTTCTAATTAATATATTCCGGTCGAGTCAG
ATGAAACTTTATTTTGTTCGGGTCAGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:941124 original size:18 final size:17
Alignment explanation
Indices: 941091--941133 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
941081 GGAATTGGAC
941091 TTCAATT-CTTACAGAT
1 TTCAATTCCTTACAGAT
941107 TTCAATTCCTTCACAGAT
1 TTCAATTCCTT-ACAGAT
*
941125 TCCAATTCC
1 TTCAATTCC
941134 CTCATAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 7 0.29
17 3 0.12
18 14 0.58
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (17 bp):
TTCAATTCCTTACAGAT
Found at i:943944 original size:60 final size:60
Alignment explanation
Indices: 943880--943994 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
943870 AATATGGTTA
* * * *
943880 TCATTCTAATTTAGT-CCTCAAA-TTTTTGAAAATTTTAATTTCATCCCCAAACTATGACAT
1 TCATTCTAAATTAATGCC-CAAACTTTTTGAAAATTTCAATTCCAT-CCCAAACTATGACAT
*
943940 TCATTCTAAATTAATGCCCAAACTTTTTGAACATTTCAATTCCATCCCAAACTAT
1 TCATTCTAAATTAATGCCCAAACTTTTTGAAAATTTCAATTCCATCCCAAACTAT
943995 ATGTATATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 27 0.56
61 21 0.44
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (60 bp):
TCATTCTAAATTAATGCCCAAACTTTTTGAAAATTTCAATTCCATCCCAAACTATGACAT
Found at i:945500 original size:21 final size:22
Alignment explanation
Indices: 945474--945516 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
945464 TAATTATTTA
945474 TTTTATTAAT-TATATTTAAAT
1 TTTTATTAATGTATATTTAAAT
* *
945495 TTTTATTTATGTTTATTTAAAT
1 TTTTATTAATGTATATTTAAAT
945517 AAGGGTGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTATTAATGTATATTTAAAT
Found at i:955785 original size:41 final size:41
Alignment explanation
Indices: 955589--955789 Score: 190
Period size: 41 Copynumber: 4.8 Consensus size: 41
955579 AAGTTTTTGA
* * * * *
955589 ACAAACACCGCAAAAGACCCTTTCTTTAGTGG-ATTTTGTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTT-TAT
* * *
955630 ACAAACGAACACCGCTAAAGACTCAG-ACTTTCGTGGCGTTTGTAT
1 ACAAACG----CCGCTAAAGACTC-GTACTTTAGTGGCATTTTTAT
* * * *
955675 AAAAACGCCGCTAAAGACACGTACTGTAGTAGCATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
* * *
955716 ACAAACGCCGATATATACTCGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
*
955757 ACAAACGCCGCTAAAGACTCGTAGTTTAGTGGC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGC
955790 GTTTGTATTT
Statistics
Matches: 127, Mismatches: 26, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
40 1 0.01
41 95 0.75
45 28 0.22
46 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
Found at i:959370 original size:185 final size:186
Alignment explanation
Indices: 959053--959446 Score: 620
Period size: 185 Copynumber: 2.1 Consensus size: 186
959043 ATTAAATTTT
959053 AAATATTAAATATATTATTATATATAACATACGGGCTCAGTCTAAACCATTTAAAACCCAATTAA
1 AAATATT-AA-ATA-TATTATATATAACATACGGGCTCAGTCTAAACCATTTAAAACCCAATTAA
959118 TAATTTAAGATCTAATAACTTTTAAACATAAATAAATATTAATTAATTAAAAAATTATATAAAAA
63 TAATTTAAGATCTAATAACTTTTAAACATAAATAAATATTAATTAATTAAAAAATTATATAAAAA
959183 -TTTTATTTTATAATTATATATTATTTAAATTAATT-GTAAACTATTTTTTTGAATTAAA
128 TTTTTATTTTATAATTATATATTATTTAAATTAATTAG-AAACTATTTTTTTGAATTAAA
* * *
959241 AAATATTAAATATATTATATATAACATATGGGTTCAG-CTCAAACCATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATACGGGCTCAGTCT-AAACCATTTAAAACCCAATTAATA
* *
959305 ATTTAAGATAC-AATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAAA
65 ATTTAAGAT-CTAATAACTTTTAAACATAAATAAATATTAATTAATT-AAAAAATTATATAAAAA
*
959368 TTTTTATTTTATAATTATATATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAA
128 TTTTTATTTTATAATTATATATTATTTAAATTAATTAGAAACTATTTTTTTGAATTAAA
*
959427 AAATATTAAAT-TTTTATATA
1 AAATATTAAATATATTATATA
959447 AATTAGAAAA
Statistics
Matches: 194, Mismatches: 7, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
184 2 0.01
185 100 0.52
186 82 0.42
187 3 0.02
188 7 0.04
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATACGGGCTCAGTCTAAACCATTTAAAACCCAATTAATAA
TTTAAGATCTAATAACTTTTAAACATAAATAAATATTAATTAATTAAAAAATTATATAAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTAGAAACTATTTTTTTGAATTAAA
Found at i:962662 original size:125 final size:125
Alignment explanation
Indices: 962524--962752 Score: 325
Period size: 126 Copynumber: 1.8 Consensus size: 125
962514 AAATATACAC
* * * * *
962524 ATAATTATATTGGTGTAGGTATGTTT-TGTATTTGCAAAGAAATAAAAAAGTGTAGCAAGTAACA
1 ATAATTATATTGGTGTAAGTATATTTCTGTATTTGCAAAAAAACAAAAAAGTATAGCAAGTAACA
* * * *
962588 CATACTTATACCGGTGTAAGTATGGTACATCTCCCAATATATTGGTACGTACCTAAAACAT
66 CACACTTACACCGATGAAAGTAT-GTACATCTCCCAATATATTGGTACGTACCTAAAACAT
* * *
962649 ATAATTATATTGGTGTAAGTATATTTCTGTATTTTCAAAAAAACAAATAAGTATAGCAATTAACA
1 ATAATTATATTGGTGTAAGTATATTTCTGTATTTGCAAAAAAACAAAAAAGTATAGCAAGTAACA
*
962714 CACACTTACACCGATGAAAGTATGTATATCTCCCAATAT
66 CACACTTACACCGATGAAAGTATGTACATCTCCCAATAT
962753 CTTAATACCT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
125 39 0.43
126 51 0.57
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (125 bp):
ATAATTATATTGGTGTAAGTATATTTCTGTATTTGCAAAAAAACAAAAAAGTATAGCAAGTAACA
CACACTTACACCGATGAAAGTATGTACATCTCCCAATATATTGGTACGTACCTAAAACAT
Found at i:965993 original size:3 final size:3
Alignment explanation
Indices: 965985--966025 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
965975 TTTCGTCTCG
*
965985 TTA TTA TTA TTA TTA TTA TTAA TTA CTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TT
966026 GTTTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:966951 original size:146 final size:143
Alignment explanation
Indices: 966466--966993 Score: 483
Period size: 145 Copynumber: 3.6 Consensus size: 143
966456 TCTCGCCGTT
* * * *
966466 GATCGGAATCTCCGATCACCATTCCGAACGGTCAAAAGTTGCACAAGACCATCACGGACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCACATGACCAACACGAACAACATA
* * * * *
966531 CTGAAAATTCAGGACGATCAGACGGTGTACGGTGGTGGATCGGAGAAAATAAGCCGACCGGTTTT
66 CTGAAAATTCAGGACGATCGGACGGTG-ACGGTGGTGAATCGGAGAAAAAAATCC-AACGGTTTT
*
966596 TGGCCTCTTGCCTGC
129 TGGCCTCTTGCCAGC
* * * * *
966611 GATCGGGATCTCCGATCAACATTCCGAATGGTCAAAAGTTTCACCA-GACCAGCACAAACAACAT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCA-CATGACCAACACGAACAACAT
* * ** * * *
966675 ACTGAAAATTCAGGACGATCCGACAGTGGACGACGG-CAGATCGGAGAAAATAAGTCAAACGGTT
65 ACTGAAAATTCAGGACGATCGGACGGT-GACGGTGGTGA-ATCGGAGAAAA-AAATCCAACGGTT
* * *
966739 TTTAGCCTTTTGCCGGC
127 TTTGGCCTCTTGCCAGC
* * * * * * * *
966756 GATCGGGATCTCCGATCAATACTT-CAAATGGTGAAAAGTTGTGTA-ATG-TCAACACGAACAGC
1 GATCGGAATCTCCGATCAACA-TTCCGAACGGTCAAAAG-T-TGCACATGACCAACACGAACAAC
* *
966818 ATACTGAAATTTCATGACGATCGGACGGTAGACGGTGGTGAATCGGAGAAAACAAATCCATACGG
63 ATACTGAAAATTCAGGACGATCGGACGGT-GACGGTGGTGAATCGGAGAAAA-AAATCCA-ACGG
* * *
966883 TTTTTGGCCTCTCGTCAGT
125 TTTTTGGCCTCTTGCCAGC
* * * * * *
966902 GATCGGAACCTCCGATCAATATTCCGAACGGTCAAAAATTGCGCGATG-TCAACACGAACAGCAT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCAC-ATGACCAACACGAACAACAT
* *
966966 ACTGAAATTTCAGGACAATCGGACGGTG
65 ACTGAAAATTCAGGACGATCGGACGGTG
966994 GCACGGCAGC
Statistics
Matches: 313, Mismatches: 57, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
144 2 0.01
145 209 0.67
146 100 0.32
147 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (143 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCACATGACCAACACGAACAACATA
CTGAAAATTCAGGACGATCGGACGGTGACGGTGGTGAATCGGAGAAAAAAATCCAACGGTTTTTG
GCCTCTTGCCAGC
Found at i:974269 original size:32 final size:32
Alignment explanation
Indices: 974233--974304 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
974223 GCATCGTTAA
974233 AGATTCAAAAACAAATATTGGGGCATATTTGG
1 AGATTCAAAAACAAATATTGGGGCATATTTGG
* *** *
974265 AGATTCAACATTGAATATTGGGGTATATTTGG
1 AGATTCAAAAACAAATATTGGGGCATATTTGG
*
974297 GGATTCAA
1 AGATTCAA
974305 CATCCTGATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (32 bp):
AGATTCAAAAACAAATATTGGGGCATATTTGG
Found at i:974305 original size:32 final size:32
Alignment explanation
Indices: 974246--974307 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
974236 TTCAAAAACA
974246 AATATTGGGGCATATTTGGAGATTCAACATTG
1 AATATTGGGGCATATTTGGAGATTCAACATTG
* *
974278 AATATTGGGGTATATTTGGGGATTCAACAT
1 AATATTGGGGCATATTTGGAGATTCAACAT
974308 CCTGATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (32 bp):
AATATTGGGGCATATTTGGAGATTCAACATTG
Found at i:974632 original size:43 final size:42
Alignment explanation
Indices: 974583--974706 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
974573 ACGAAGGCGC
**
974583 CATCCACGATTTCAACTCGACGACGGAGGATATCGTACCAATG
1 CATCCACGATTTCAACTC-ACGACGGAGGATATCGTACCAACA
* * * *
974626 GATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACT-CACGACGGAGGATATCGTACCAACA
* * *
974669 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAAC-TCACGACGGAGGATATCGTAC
974707 ACACAAGCAG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 65 0.97
44 2 0.03
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (42 bp):
CATCCACGATTTCAACTCACGACGGAGGATATCGTACCAACA
Found at i:974980 original size:43 final size:43
Alignment explanation
Indices: 974918--975041 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
974908 ACGAAGGCGC
*
974918 CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCAATG
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCAATA
* * * *
974961 GATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCATA
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCAATA
* ** * *
975004 CATCCACGGTTTCAACTTTATGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTAC
975042 ACACAAGCAG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCAATA
Found at i:975078 original size:335 final size:335
Alignment explanation
Indices: 974468--975225 Score: 1354
Period size: 335 Copynumber: 2.3 Consensus size: 335
974458 TGCAGCTTTT
*
974468 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAATAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
* *
974533 TTCACGACGAAGCATATTCAAATCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
* *
974598 CTCGACGACGGAGGATATCGTACCAATGGATCCACAATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGAAGGATATCGTACCAATGGATCCACAATTTCAACTCCACGACGGAGGATATCGTG
974663 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
974728 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
*
974793 TTCCAGTTTC
326 TTCCAATTTC
* * *
974803 AGAGCCAATTTTAACTTCACGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
*
974868 TTCACGACGAAGGATATTTAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
*
974933 CTCCACGACGAAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGAAGGATATCGTACCAATGGATCCACAATTTCAACTCCACGACGGAGGATATCGTG
* * *
974998 CCCATACATCCACGGTTTCAACTTTATGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
975063 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
*
975128 TTCCAATTTT
326 TTCCAATTTC
* * *
975138 AGAGTCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAACACAAGCTTGGATTTTAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
975203 TTCACGACGAAGGATATTCAAGT
66 TTCACGACGAAGGATATTCAAGT
975226 TAAGCCTTCA
Statistics
Matches: 401, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
335 401 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (335 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACAGCACAAGCTTGGATTTCAAC
TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
CTCCACGACGAAGGATATCGTACCAATGGATCCACAATTTCAACTCCACGACGGAGGATATCGTG
CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
TTCCAATTTC
Found at i:975523 original size:42 final size:41
Alignment explanation
Indices: 975471--975584 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
975461 TCCAAAATTC
* * *
975471 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG
* * * * *
975512 CTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGTAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG
* * *
975554 ATAAGTCCTTTGGGCCATCAATAAGACCTTT
1 ATAAATCCTTCGGGCCATCAGTAAG-CCTTT
975585 GGGCAGGATG
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
41 18 0.32
42 38 0.68
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG
Found at i:976061 original size:134 final size:134
Alignment explanation
Indices: 975679--976202 Score: 786
Period size: 134 Copynumber: 3.9 Consensus size: 134
975669 GTCCCAATTC
* * * *
975679 AATGGATCAACTCATCCATATCTGATATTCCCTTCAGAATAAGCGGAATATAT-TTATCTCTTTC
1 AATGGATCAACTCATCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCAT-TCTCTTTC
*
975743 AAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCATGATTCAATCTTCCCTGAGTGAC
65 AAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGAC
975808 AGCGG
130 AGCGG
* * * * *
975813 AATGGATCAACTCATTCAAATCTGATATTCCCTTCGGAAGAAGCGGAATAGATCATT-T-TTTCA
1 AATGGATCAACTCATCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCATTCTCTTTCA
* * *
975876 AGATTTGATATTCCTTGAGTGACAGCGGAACAAGTCTACCATGATTCAATCTTCACTGAGTGACA
66 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACA
*
975941 GCAG
131 GCGG
* * * *
975945 AATGGATCAACTCATCCAGATCTGATATTCCCTTCAAAAGATGTGGAACAAATCATTCTCTTTCA
1 AATGGATCAACTCATCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCATTCTCTTTCA
976010 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACA
66 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACA
976075 GCGG
131 GCGG
* * * * *
976079 AATGGTTCAACACATCCAGATCTGACATTCCCTTCAGAAGAAGAGGAACATATCACTCTCTTTCA
1 AATGGATCAACTCATCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCATTCTCTTTCA
*
976144 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTCC-CAGATTCAATCTTCCCTGA
66 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCAC-GATTCAATCTTCCCTGA
976203 AGAACAGTTA
Statistics
Matches: 356, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
132 120 0.34
133 3 0.01
134 232 0.65
135 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (134 bp):
AATGGATCAACTCATCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCATTCTCTTTCA
AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACA
GCGG
Found at i:977226 original size:145 final size:145
Alignment explanation
Indices: 976871--977407 Score: 417
Period size: 145 Copynumber: 3.7 Consensus size: 145
976861 TCTCGCCGTT
* * * * * *
976871 GATCGGAATTTCCGATCACCATTCCGAACGGTCAAAAGTTGCACAAGATCATCACGAACAACATA
1 GATCGGGATCTCCGATCAACATTCCAAACGATCAAAAGTTGCACAAGATCAACACGAACAACATA
* * * * * ** * *
976936 CTAAAAATTCAGGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAATAAGCCTAACGGTTTT
66 CTGAAAATTTAGGACGATCGGACAGTGGACGACGGCAGATCGGAGAAAATAAGCCAAACGGATTT
* *
977001 TGGCCTCTTGCCTGC
131 TAGCCTCTTGCCGGC
* * * * * *
977016 GATCGGGATCTCCGATCAACATTCCAAATGGTCAAAAGTTGCACGAGACCAGCACAAACAACATA
1 GATCGGGATCTCCGATCAACATTCCAAACGATCAAAAGTTGCACAAGATCAACACGAACAACATA
*
977081 CTGAAAATTTAGGACGATCGGACAGTGGACGACGGCAGATCGGAGAAAATAAGTCAAACGGATTT
66 CTGAAAATTTAGGACGATCGGACAGTGGACGACGGCAGATCGGAGAAAATAAGCCAAACGGATTT
* * *
977146 TAGCTTTTTTCCGGC
131 TAGCCTCTTGCCGGC
* * *** * *
977161 GATCGGGATCTCCGATCAATACTT-CAAACGATGAAAAGTTGTGTAATATCAACACGAACATCAT
1 GATCGGGATCTCCGATCAACA-TTCCAAACGATCAAAAGTTGCACAAGATCAACACGAACAACAT
* * * * ** * * *
977225 ACTG-AAATTTCATGACAATCGGACGGTAGAC-A-GTGGTGAATCGGAGAAAACAAATCCAGACG
65 ACTGAAAATTT-AGGACGATCGGACAGTGGACGACG-GCAG-ATCGGAGAAAA-TAAGCCAAACG
* * * * *
977287 GTTTTTGGCCTCTCGTCGGT
126 GATTTTAGCCTCTTGCCGGC
* * * * * * * *
977307 GATC-GGAACTTCCGATCAATATTCCGAACGGTCAAAAATTGCGCGATG-TCAACACGAACAGCA
1 GATCGGGATC-TCCGATCAACATTCCAAACGATCAAAAGTTGCAC-AAGATCAACACGAACAACA
* *
977370 TACTG-AAATTTCAGGACAATCGGACGGTGG-C-ACGGCAG
64 TACTGAAAATTT-AGGACGATCGGACAGTGGACGACGGCAG
977408 CGCAGTAACA
Statistics
Matches: 314, Mismatches: 69, Indels: 18
0.78 0.17 0.04
Matches are distributed among these distances:
143 1 0.00
144 9 0.03
145 210 0.67
146 93 0.30
147 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (145 bp):
GATCGGGATCTCCGATCAACATTCCAAACGATCAAAAGTTGCACAAGATCAACACGAACAACATA
CTGAAAATTTAGGACGATCGGACAGTGGACGACGGCAGATCGGAGAAAATAAGCCAAACGGATTT
TAGCCTCTTGCCGGC
Found at i:982505 original size:2 final size:2
Alignment explanation
Indices: 982500--982525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
982490 TATTAATTTA
982500 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
982526 CATTCTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:984816 original size:20 final size:19
Alignment explanation
Indices: 984773--984808 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
984763 TAATAAAAGA
*
984773 TTCACAATTTTTATCATTC
1 TTCACAATCTTTATCATTC
984792 TTCACAATCTTT-TCATT
1 TTCACAATCTTTATCATT
984809 TCCTTCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (19 bp):
TTCACAATCTTTATCATTC
Found at i:989802 original size:59 final size:58
Alignment explanation
Indices: 989739--990174 Score: 280
Period size: 59 Copynumber: 7.4 Consensus size: 58
989729 TACCAAATGA
* * * * *
989739 CACTGTGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAG
1 CACTTTGTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGATGG-G
** **
989798 CACTGAGTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGAT-GGG
* * * * * * * **
989856 CATTTTATGTACTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTTCAGATAAAG
1 CACTTTGTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGAT-GGG
** ** *
989915 CACTAAAG-GTGCTACAAA-GATAAGGAAATCATATTGAAAATATGGATTTTCAGATAGGG
1 CACT-TTGTGTGCTA-AAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGAT-GGG
* * * * * **
989974 CATTTTATGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAG
1 CACTTTGTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGAT-GGG
** * * * *
990033 CACTAAGGGTGCTACAAA-GATAAGGAAATCATACT-AATGGTATGGATTTTCACATAGGG
1 CACTTTGTGTGCTA-AAATGATAAGGAAATCATATTGAAT-GTATGGATTTCCAGAT-GGG
* ** * * **
990092 CA-TTTCATGTGCTAAAATGATAACAAAATCATACT-AATGGTATGAATTT-TTGAATAGGG
1 CACTTT-GTGTGCTAAAATGATAAGGAAATCATATTGAAT-GTATGGATTTCCAG-AT-GGG
990151 CA-TTTCGTGTGCTAAAATGA-AAGG
1 CACTTT-GTGTGCTAAAATGATAAGG
990175 GGAAGCATAC
Statistics
Matches: 296, Mismatches: 70, Indels: 23
0.76 0.18 0.06
Matches are distributed among these distances:
58 55 0.19
59 235 0.79
60 6 0.02
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.30
Consensus pattern (58 bp):
CACTTTGTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGATGGG
Found at i:989979 original size:118 final size:118
Alignment explanation
Indices: 989746--990110 Score: 529
Period size: 118 Copynumber: 3.1 Consensus size: 118
989736 TGACACTGTG
* * * * * ** *
989746 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACT-GAGTGTGC
1 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAAG-GTGC
* *
989810 TA-AATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
65 TACAAAGATAAGGAAATCATATTGAAAATATGGATTTTCAGATAGGGCATTTTA
* *
989863 TGTACTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTTCAGATAAAGCACTAAAGGTGCT
1 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAAGGTGCT
989928 ACAAAGATAAGGAAATCATATTGAAAATATGGATTTTCAGATAGGGCATTTTA
66 ACAAAGATAAGGAAATCATATTGAAAATATGGATTTTCAGATAGGGCATTTTA
*
989981 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
1 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAAGGTGCT
* ** * *
990046 ACAAAGATAAGGAAATCATACT-AATGGTATGGATTTTCACATAGGGCATTTCA
66 ACAAAGATAAGGAAATCATATTGAA-AATATGGATTTTCAGATAGGGCATTTTA
990099 TGTGCTAAAATG
1 TGTGCTAAAATG
990111 ATAACAAAAT
Statistics
Matches: 225, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
117 55 0.24
118 170 0.76
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (118 bp):
TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAAGGTGCT
ACAAAGATAAGGAAATCATATTGAAAATATGGATTTTCAGATAGGGCATTTTA
Found at i:990362 original size:44 final size:44
Alignment explanation
Indices: 990302--990411 Score: 141
Period size: 44 Copynumber: 2.5 Consensus size: 44
990292 TAAATAAGGT
* *
990302 TAATGGCAAGTATATTGGTAAAATAAGCTT-TCGAGCTTATGGAA
1 TAATGGTAAGTATATTGATAAAATAAGCTTAT-GAGCTTATGGAA
* *
990346 TAATGGTAAGTGTATTGATAAAATAAGCTTATGAGCTTATGGGA
1 TAATGGTAAGTATATTGATAAAATAAGCTTATGAGCTTATGGAA
* *
990390 TAAATGGTAAATTTATTGATAA
1 T-AATGGTAAGTATATTGATAA
990412 GAAATGTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
44 39 0.67
45 19 0.33
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (44 bp):
TAATGGTAAGTATATTGATAAAATAAGCTTATGAGCTTATGGAA
Found at i:994877 original size:21 final size:20
Alignment explanation
Indices: 994837--994895 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
994827 AACAGAATGT
994837 CAAGGGGGTACAGATTCCCC
1 CAAGGGGGTACAGATTCCCC
*
994857 CAAGGGGGTACTGATTCCCC
1 CAAGGGGGTACAGATTCCCC
* * *
994877 CCAGGGGGAATAGATTCCC
1 CAAGGGGGTACAGATTCCC
994896 TCTTCTCAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.17
Consensus pattern (20 bp):
CAAGGGGGTACAGATTCCCC
Found at i:995925 original size:30 final size:30
Alignment explanation
Indices: 995889--995961 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
995879 CCCGAAGGAC
* *
995889 CTATCCAGAGGTCATAGAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCCTCGGTAA
995919 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCCTCGGTAA
*
995949 CTATCCATAGGTC
1 CTATCCAAAGGTC
995962 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAAAGGTCATAAAGATCCTCGGTAA
Found at i:995978 original size:30 final size:30
Alignment explanation
Indices: 995889--995988 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
995879 CCCGAAGGAC
* * * * *
995889 CTATCCAGAGGTCATAGAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAA
* * * *
995919 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAA
* *
995949 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGAACCTAGGT-AA
*
995980 CTGTCCATA
1 CTATCCATA
995989 TGTTCCTTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
30 50 0.83
31 10 0.17
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTAGGTAA
Found at i:996813 original size:19 final size:19
Alignment explanation
Indices: 996789--996838 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
996779 TAAGCAGGTA
996789 CATCGATGCACTCCTTATG
1 CATCGATGCACTCCTTATG
996808 CATCGATGCACTCCTTATG
1 CATCGATGCACTCCTTATG
996827 CATCGATGCACT
1 CATCGATGCACT
996839 AATTGCATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (19 bp):
CATCGATGCACTCCTTATG
Found at i:1003311 original size:22 final size:22
Alignment explanation
Indices: 1003286--1003329 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1003276 GAATATGTGG
* *
1003286 TTTAAATTTAATAAAAAATTAA
1 TTTAAAATGAATAAAAAATTAA
*
1003308 TTTAAAATGAATGAAAAATTAA
1 TTTAAAATGAATAAAAAATTAA
1003330 AAGAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
TTTAAAATGAATAAAAAATTAA
Found at i:1003331 original size:17 final size:17
Alignment explanation
Indices: 1003309--1003347 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1003299 AAAAATTAAT
*
1003309 TTAAAATGAATGA-AAAA
1 TTAAAA-GAATAATAAAA
1003326 TTAAAAGAATAATAAAA
1 TTAAAAGAATAATAAAA
1003343 TTAAA
1 TTAAA
1003348 CACTAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (17 bp):
TTAAAAGAATAATAAAA
Found at i:1008886 original size:127 final size:127
Alignment explanation
Indices: 1008641--1008893 Score: 427
Period size: 126 Copynumber: 2.0 Consensus size: 127
1008631 AGTGCATGGT
*
1008641 GGACATTATTATGCATTTATCAGACCGGCACTTTCTGATCAATGGTACAGATCATACCAATGCAT
1 GGACATTATCATGCATTTATCAGACCGGCACTTTCTGATCAATGGTACAGATCATACCAATGCAT
*
1008706 AAAATTTATACTATGCAGAAAATAAATAAATAAAAAGAAGAAATAGGTTATTAATTATTGTC
66 AAAATTTATACTATGCAAAAAATAAATAAATAAAAAGAAGAAATAGGTTATTAATTATTGTC
* * * *
1008768 GGACATTATCATGCA-TTATCAGGCTGGCATTTTCTGATCAATGGTACAGATCATATCAATGCAT
1 GGACATTATCATGCATTTATCAGACCGGCACTTTCTGATCAATGGTACAGATCATACCAATGCAT
*
1008832 AATATTTATACTATGCAAAAAAATAAATAAATAAAAAGAAGAAATAGGTTATTAATTATTGT
66 AAAATTTATACTATGC-AAAAAATAAATAAATAAAAAGAAGAAATAGGTTATTAATTATTGT
1008894 TGAAAAAAGG
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
126 60 0.51
127 58 0.49
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (127 bp):
GGACATTATCATGCATTTATCAGACCGGCACTTTCTGATCAATGGTACAGATCATACCAATGCAT
AAAATTTATACTATGCAAAAAATAAATAAATAAAAAGAAGAAATAGGTTATTAATTATTGTC
Found at i:1011240 original size:37 final size:39
Alignment explanation
Indices: 1011164--1011244 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
1011154 ACCCTTTCAT
* * *
1011164 TAAATTTTTTTATATTTTCAATTTTGTAAAAACATTATA
1 TAAATTTTATTATATTTTAAATTTTGTAAAAACAATATA
*
1011203 TAAATTTTATTA-A-TTTAAATTTTTTAAAGAA-AATATA
1 TAAATTTTATTATATTTTAAATTTTGTAAA-AACAATATA
1011240 TAAAT
1 TAAAT
1011245 ATTTTCCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 23 0.62
38 3 0.08
39 11 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (39 bp):
TAAATTTTATTATATTTTAAATTTTGTAAAAACAATATA
Found at i:1011419 original size:18 final size:19
Alignment explanation
Indices: 1011396--1011438 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1011386 TAGTAATCCT
1011396 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
* *
1011414 ATTCCCACTTGTAATCTTAT
1 ATT-CCACTGGTAATCTTAC
1011434 ATTCC
1 ATTCC
1011439 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:1018603 original size:21 final size:21
Alignment explanation
Indices: 1018579--1018631 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1018569 AAACCTACTA
**
1018579 AAAATCCTACAGCCACTGTTG
1 AAAATCCTACAGCCACTGCAG
* *
1018600 AAAATCCTACAGTCATTGCAG
1 AAAATCCTACAGCCACTGCAG
1018621 AAAATCCTACA
1 AAAATCCTACA
1018632 ACCGCTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (21 bp):
AAAATCCTACAGCCACTGCAG
Found at i:1024868 original size:17 final size:17
Alignment explanation
Indices: 1024846--1024886 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1024836 TCCCATTTAT
*
1024846 CATTTAAATTTAAAATA
1 CATTTAAATTTAAAACA
1024863 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1024880 CATTTAA
1 CATTTAA
1024887 CACTTCTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (17 bp):
CATTTAAATTTAAAACA
Found at i:1033534 original size:19 final size:19
Alignment explanation
Indices: 1033510--1033555 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1033500 ATGAGACGGT
1033510 AAGTTTAACTCAACAAATA
1 AAGTTTAACTCAACAAATA
1033529 AAGTTTAACTCAACAAATA
1 AAGTTTAACTCAACAAATA
1033548 AAGTTTAA
1 AAGTTTAA
1033556 TATTTTTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (19 bp):
AAGTTTAACTCAACAAATA
Found at i:1038809 original size:25 final size:25
Alignment explanation
Indices: 1038781--1038828 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1038771 AGATATAGTA
*
1038781 TTGCACTCGAAAGTGCCTCGTAGGG
1 TTGCACTCGAAAGTGCATCGTAGGG
*
1038806 TTGCACTCGTAAGTGCATCGTAG
1 TTGCACTCGAAAGTGCATCGTAG
1038829 AATTTCACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (25 bp):
TTGCACTCGAAAGTGCATCGTAGGG
Found at i:1039967 original size:12 final size:12
Alignment explanation
Indices: 1039934--1039967 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1039924 ATATTCTCTT
1039934 ATTTCCAAATTC
1 ATTTCCAAATTC
*
1039946 ATCATCCAAATTC
1 AT-TTCCAAATTC
1039959 ATTTCCAAA
1 ATTTCCAAA
1039968 CAATTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTTCCAAATTC
Found at i:1040806 original size:25 final size:25
Alignment explanation
Indices: 1040778--1040830 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1040768 AATTCATTTC
*
1040778 CAAACAATTTTCAACCATTCTTAAT
1 CAAACAATTTTCAACCATTCTCAAT
1040803 CAAACAATTTTCAACCATTCTCAAT
1 CAAACAATTTTCAACCATTCTCAAT
1040828 CAA
1 CAA
1040831 TCACAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (25 bp):
CAAACAATTTTCAACCATTCTCAAT
Found at i:1043308 original size:18 final size:18
Alignment explanation
Indices: 1043285--1043353 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
1043275 TGAATATTTA
1043285 TCCCGAAAGACCACTATG
1 TCCCGAAAGACCACTATG
* *
1043303 TCCCGAAGGACCACTGGTTG
1 TCCCGAAAGACCACT--ATG
*
1043323 TTCCG-AAGAACCACTATG
1 TCCCGAAAG-ACCACTATG
*
1043341 TCCCGAAGGACCA
1 TCCCGAAAGACCA
1043354 TTGTATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
18 24 0.60
19 4 0.10
20 12 0.30
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.17
Consensus pattern (18 bp):
TCCCGAAAGACCACTATG
Found at i:1046998 original size:20 final size:20
Alignment explanation
Indices: 1046973--1047029 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1046963 AAAAACCTTT
1046973 AGTATCGATACTCTTATGGA
1 AGTATCGATACTCTTATGGA
1046993 AGTATCGATACTCTTATGGA
1 AGTATCGATACTCTTATGGA
*
1047013 AGTATCGGTACTCTTAT
1 AGTATCGATACTCTTAT
1047030 AGGTGGGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTCTTATGGA
Found at i:1048537 original size:31 final size:30
Alignment explanation
Indices: 1048519--1048622 Score: 140
Period size: 31 Copynumber: 3.4 Consensus size: 30
1048509 GTTCCGAAGA
*
1048519 ACATAGGTAACGTGTCCATATATC-CTGAAGG
1 ACATAGGTAAC-TGTCCATATATCTC-GAAAG
1048550 ACATAGGTAAACTGTCCATATATCTCGAAAG
1 ACATAGGT-AACTGTCCATATATCTCGAAAG
1048581 ACATAGGTAATCTGTCCATA-ATTCTCGAAAG
1 ACATAGGTAA-CTGTCCATATA-TCTCGAAAG
1048612 ACATAGGTAAC
1 ACATAGGTAAC
1048623 CTCGACTCTT
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
30 4 0.06
31 60 0.88
32 4 0.06
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (30 bp):
ACATAGGTAACTGTCCATATATCTCGAAAG
Found at i:1048752 original size:21 final size:21
Alignment explanation
Indices: 1048694--1048753 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
1048684 TTTTATCTTT
*
1048694 TCACATATTCATATAAACATA
1 TCACATATTCATATAAGCATA
1048715 TCACATATTCATATAAGCATA
1 TCACATATTCATATAAGCATA
1048736 TCACATATTCATATAAGC
1 TCACATATTCATATAAGC
1048754 TCATAGTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (21 bp):
TCACATATTCATATAAGCATA
Found at i:1050856 original size:18 final size:18
Alignment explanation
Indices: 1050830--1050868 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1050820 GAGAGTTATC
1050830 ATTACTTGTATAAA-CCTT
1 ATTACTTGTA-AAATCCTT
*
1050848 ATTATTTGTAAAATCCTT
1 ATTACTTGTAAAATCCTT
1050866 ATT
1 ATT
1050869 CGAATCACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTACTTGTAAAATCCTT
Found at i:1058970 original size:21 final size:21
Alignment explanation
Indices: 1058944--1058983 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1058934 CCCCCTTTGA
*
1058944 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1058965 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1058984 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1062446 original size:31 final size:31
Alignment explanation
Indices: 1062398--1062483 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
1062388 TAACTCAACA
* *
1062398 ATATGTCCCAAAGTACATAGGTAAACTATCC
1 ATATGTCTCAAAATACATAGGTAAACTATCC
* * *
1062429 ATATGTCTCGAAATACATAGGTAATCTGTCC
1 ATATGTCTCAAAATACATAGGTAAACTATCC
*
1062460 ATATGTCTCAAAAGACATAGGTAA
1 ATATGTCTCAAAATACATAGGTAA
1062484 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (31 bp):
ATATGTCTCAAAATACATAGGTAAACTATCC
Found at i:1062615 original size:21 final size:21
Alignment explanation
Indices: 1062559--1062616 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1062549 TTATCTTTTA
*
1062559 ACATATTCATATAAACATATC
1 ACATATTCATATAAGCATATC
1062580 ACATATTCATATAAGCATATC
1 ACATATTCATATAAGCATATC
1062601 ACATATTCATATAAGC
1 ACATATTCATATAAGC
1062617 TCATAGCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (21 bp):
ACATATTCATATAAGCATATC
Found at i:1069100 original size:3 final size:3
Alignment explanation
Indices: 1069089--1069121 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1069079 AGTAAAACGT
*
1069089 ATG AT- ATG ATG ATG ATG ATG ATG ATG ATA ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1069122 GTGGCTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1072569 original size:2 final size:2
Alignment explanation
Indices: 1072562--1072590 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1072552 AGATAAAGAA
1072562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1072591 CAGTAATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1075455 original size:41 final size:41
Alignment explanation
Indices: 1075314--1075595 Score: 132
Period size: 41 Copynumber: 6.9 Consensus size: 41
1075304 CAAAATGGTA
* * * *
1075314 ACTTTAGCGGTGTTTTTATACAAAACGCTGCAACAGAGTAGT
1 ACTTTAGCGGCGTTTTTATA-AAAACGCCGTAATAGAGTAGT
* * *
1075356 ACTTTAGCGGCATTTGTATAAAAATGCC--AATA-AG--GTT
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGTAATAGAGTAG-T
* * * *
1075393 CATCTATAGTGGCATTTTTTTTCAAAAAACGCCGTAATAGAGTAGT
1 -A-CTTTAGCGGC-GTTTTTAT--AAAAACGCCGTAATAGAGTAGT
* * * *
1075439 ACTTTAGCGGCGTTTTTATACAAATGCCGCAATTG-GT--T
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGTAATAGAGTAGT
** * * * * *
1075477 CATCCATAGTGGCGTTTCTA-AACAAACGTCGTGACAGAGTAGT
1 -A-CTTTAGCGGCGTTTTTATAA-AAACGCCGTAATAGAGTAGT
** * * * * *
1075520 ACTCCAGCGACGTTTTTATAGAAACGCCGCAAAATAGTAGT
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGTAATAGAGTAGT
* *
1075561 ACTTTAGCGGCGTTTTTACACAAACGCCGTAATAG
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGTAATAG
1075596 GGACTACAAC
Statistics
Matches: 171, Mismatches: 51, Indels: 37
0.66 0.20 0.14
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 4 0.02
39 13 0.08
40 28 0.16
41 73 0.43
42 27 0.16
43 7 0.04
44 12 0.07
45 3 0.02
46 1 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (41 bp):
ACTTTAGCGGCGTTTTTATAAAAACGCCGTAATAGAGTAGT
Found at i:1079116 original size:3 final size:3
Alignment explanation
Indices: 1079089--1079135 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
1079079 AAAATATTTC
1079089 ATT A-T ATT A-T ATT ATAT ATTT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT AT-T A-TT ATT ATT ATT ATT ATT ATT ATT ATT
1079133 ATT
1 ATT
1079136 TTTGTAGGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.15
3 28 0.72
4 4 0.10
5 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1079121 original size:20 final size:19
Alignment explanation
Indices: 1079093--1079135 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
1079083 TATTTCATTA
1079093 TATTATATTA-TATATTTAT
1 TATTATATTATTAT-TTTAT
1079112 TATTATTATTATTATTTTAT
1 TATTA-TATTATTATTTTAT
1079132 TATT
1 TATT
1079136 TTTGTAGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 14 0.64
21 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATATTATTATTTTAT
Found at i:1079135 original size:17 final size:18
Alignment explanation
Indices: 1079089--1079135 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
1079079 AAAATATTTC
1079089 ATTATATTA-TATTATAT
1 ATTATATTATTATTATAT
1079106 ATT-TATTATTATTAT-T
1 ATTATATTATTATTATAT
*
1079122 ATTATTTTATTATT
1 ATTATATTATTATT
1079136 TTTGTAGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTATATTATTATTATAT
Found at i:1079230 original size:33 final size:33
Alignment explanation
Indices: 1079185--1079255 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1079175 TTCAGAAAAT
* *
1079185 AAACCAATGTATTTGAGTCTTATTGAAACACTA
1 AAACCAACGTATTTAAGTCTTATTGAAACACTA
1079218 AAACCAACGTATTTAAGTCTTATTGAAACACTA
1 AAACCAACGTATTTAAGTCTTATTGAAACACTA
1079251 AAACC
1 AAACC
1079256 GAAGCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (33 bp):
AAACCAACGTATTTAAGTCTTATTGAAACACTA
Found at i:1079583 original size:26 final size:25
Alignment explanation
Indices: 1079554--1079616 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1079544 TTTTTATTTC
*
1079554 ATTTTTTATTTAT-TTACTTTATATAT
1 ATTTTTTATTTATCTTAATTT-TA-AT
* *
1079580 ATTTTTCATTTTCTCTTAATTTTAAT
1 ATTTTTTA-TTTATCTTAATTTTAAT
1079606 ATTTTTTATTT
1 ATTTTTTATTT
1079617 CTTTTTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 3 0.10
26 16 0.52
27 6 0.19
28 6 0.19
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTTTATTTATCTTAATTTTAAT
Found at i:1079670 original size:25 final size:26
Alignment explanation
Indices: 1079633--1079689 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1079623 ACATTGTTTT
* *
1079633 ATATATATATATATTCATTTTTTATTA
1 ATAT-TATATATATTAATATTTTATTA
1079660 ATATTAT-TATATTAATATTTTATTA
1 ATATTATATATATTAATATTTTATTA
*
1079685 TTATT
1 ATATT
1079690 CTTTTCTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 20 0.74
26 3 0.11
27 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATTATATATATTAATATTTTATTA
Found at i:1079674 original size:14 final size:14
Alignment explanation
Indices: 1079649--1079687 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1079639 ATATATATTC
1079649 ATTTT-TTATTAAT
1 ATTTTATTATTAAT
1079662 ATTATTA-TATTAAT
1 ATT-TTATTATTAAT
1079676 ATTTTATTATTA
1 ATTTTATTATTA
1079688 TTCTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTATTATTAAT
Found at i:1083597 original size:110 final size:110
Alignment explanation
Indices: 1083396--1083816 Score: 611
Period size: 110 Copynumber: 3.9 Consensus size: 110
1083386 TGATGGTAGT
* * *
1083396 AGCTTAACTTCACAACAAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCAAAGGGGCAGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
1083461 CAATTTCAACTTCACAGCGAATGATATTGGACAT-GAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACA
* *
1083506 AGCTCAACTTCATAGCAAAGGGGCAGCTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCAAAGGGGCAGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
1083571 CAATTTCAACTTCATAACGAAGGATATTAGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
*
1083616 AGCTCAACTTCACAGCGAAGGGGC-GACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAG
1 AGCTCAACTTCACAGCAAAGGGGCAG-CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAG
* *
1083680 TCAATTTTAACTTCATAGCGAAGGATATTGGACTCGAGACAACACA
65 TCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * * *
1083726 AGCTCAACTTCACAGCGAAGGGGCAGCTGGCTGTCAACAAATAACTTTCCAATTTC--T--GAGT
1 AGCTCAACTTCACAGCAAAGGGGCAGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
1083787 CAATTTTAACTTCACGGCGAAGGATATTGG
66 CAATTTCAACTTCACAGCGAAGGATATTGG
1083817 CCATGAAACA
Statistics
Matches: 287, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
106 32 0.11
108 1 0.00
109 2 0.01
110 251 0.87
111 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
AGCTCAACTTCACAGCAAAGGGGCAGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:1084175 original size:84 final size:83
Alignment explanation
Indices: 1083939--1084217 Score: 287
Period size: 84 Copynumber: 3.4 Consensus size: 83
1083929 AATCGTGCCC
* *
1083939 ACCAAAGGCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAGT
* *
1084004 CGAGAAGGG--CTATCTG
66 CGAGAAGGGTTATATGTG
* * * * * * ** * *
1084020 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGTAGCATAACTTAA-
*
1084084 GT-TAGAAGGGTTATATGTG
64 GTCGAGAAGGGTTATATGTG
* * * *
1084103 ACCAAAAGACCTTCGAGTTGGACTACGCTCAGCTCCAAGACATATCATTTGTAGTATAACTTAAG
1 ACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAG
* **
1084168 TCGAGAAGGGTTATCTGCCA
65 TCGAGAAGGGTTATATG-TG
*
1084188 ACCAAAGACCTTCGAGTTTGATTACGCTCA
1 ACCAAAGACCTTCGAGTTTGACTACGCTCA
1084218 TATCTGCCAA
Statistics
Matches: 156, Mismatches: 34, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
80 26 0.17
81 31 0.20
82 2 0.01
83 7 0.04
84 62 0.40
85 28 0.18
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAGT
CGAGAAGGGTTATATGTG
Found at i:1084365 original size:84 final size:83
Alignment explanation
Indices: 1084217--1084672 Score: 343
Period size: 84 Copynumber: 5.5 Consensus size: 83
1084207 GATTACGCTC
* * * * *
1084217 ATATCTG-CCAAAGACCCTT-GAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAACAT
1 ATATCTGACCAAAGA-CCTTCGAGTTCGACTACACTCAGC-TCGAAGGCACATCATTTGCAGCAT
**
1084280 AACTCAAGGATAGAAGGGTT
64 AACTCAAGGCGAGAAGGGTT
* * * * *
1084300 ATATATGACCAAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCATATCATTTGCAGCATA
1 ATATCTGACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCGAAGGCACATCATTTGCAGCATA
* *
1084365 ACTTAAGTCGAGAAGGGTT
65 ACTCAAGGCGAGAAGGGTT
* ** * * * ** *
1084384 ATCTGCCAACCAAAGACCTTCAACTTTGACTATGCTCAGCTCTAAGGCACATCATTTGCAGCATA
1 ATAT-CTGACCAAAGACCTTCGAGTTCGACTACACTCAGCTCGAAGGCACATCATTTGCAGCATA
* * *
1084449 GCTTAAGTCGAGAAGGG--
65 ACTCAAGGCGAGAAGGGTT
* * * * * * * ** *
1084466 CTATCTG-CAAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCACATCATTTATAACATA
1 ATATCTGACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCGAAGGCACATCATTTGCAGCATA
*
1084530 ACTCAAGGCTAGAAGGGTT
65 ACTCAAGGCGAGAAGGGTT
* * * * * * *
1084549 ATCTGTCAACAAAGACCTTCGAGTTTGACTCCACTCAGCTCAAAGGCACCATCATTTGCAGCATA
1 ATATCTGACCAAAGACCTTCGAGTTCGACTACACTCAGCTCGAAGGCA-CATCATTTGCAGCATA
* * *
1084614 GCTCAAGGCAATAAGGG--
65 ACTCAAGGCGAGAAGGGTT
* * * *
1084631 CTATCT-ACCAAAGACCTTCGAGTTCGATTCCATTCAGCTCGA
1 ATATCTGACCAAAGACCTTCGAGTTCGACTACACTCAGCTCGA
1084673 GGGCGTATCA
Statistics
Matches: 290, Mismatches: 74, Indels: 20
0.76 0.19 0.05
Matches are distributed among these distances:
80 23 0.08
81 65 0.22
82 5 0.02
83 16 0.06
84 157 0.54
85 24 0.08
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (83 bp):
ATATCTGACCAAAGACCTTCGAGTTCGACTACACTCAGCTCGAAGGCACATCATTTGCAGCATAA
CTCAAGGCGAGAAGGGTT
Found at i:1084368 original size:204 final size:204
Alignment explanation
Indices: 1084014--1084404 Score: 701
Period size: 204 Copynumber: 1.9 Consensus size: 204
1084004 CGAGAAGGGC
*
1084014 TATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAAC
1 TATCTGCCAAAGACCCTCGAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAACATAAC
* * *
1084079 TCAAGGTTAGAAGGGTTATATGTGACCAAAAGACCTTCGAGTTGGACTACGCTCAGCTCCAAGAC
66 TCAAGGATAGAAGGGTTATATATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGAC
* *
1084144 ATATCATTTGTAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
131 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
1084209 TTACGCTCA
196 TTACGCTCA
*
1084218 TATCTGCCAAAGACCCTTGAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAACATAAC
1 TATCTGCCAAAGACCCTCGAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAACATAAC
* *
1084283 TCAAGGATAGAAGGGTTATATATGACCAAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGC
66 TCAAGGATAGAAGGGTTATATATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGAC
1084348 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
131 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
1084405 AACTTTGACT
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
204 178 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (204 bp):
TATCTGCCAAAGACCCTCGAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAACATAAC
TCAAGGATAGAAGGGTTATATATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGAC
ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
TTACGCTCA
Found at i:1084532 original size:165 final size:164
Alignment explanation
Indices: 1084361--1084676 Score: 418
Period size: 165 Copynumber: 1.9 Consensus size: 164
1084351 TCATTTGCAG
* * **
1084361 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAACTTTGACTATGCTCAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCAACTTTGACTACACTCAGCTC
* * * * *
1084426 TAAGGCA-CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCAAAAGACCCTCAAGTT
65 AAAGGCACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTACAAAAGACCCTCAAGTT
1084490 CGATTACACTCAACTTCGAGGGCACATCATTTATAA
130 CGATTACACTCAAC-TCGAGGGCACATCATTTATAA
* * * * *
1084526 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGACTCCACTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTCAACTTTGACTACACTCAGCTCA
* * * *
1084591 AAGGCACCATCATTTGCAGCATAGCTCAAGGCAATAAGGGCTATCTACCAAAGACCTTCGAGTTC
66 AAGGCACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTACAAAAGACCCTCAAGTTC
* * *
1084656 GATTCCATTCAGCTCGAGGGC
131 GATTACACTCAACTCGAGGGC
1084677 GTATCAACCG
Statistics
Matches: 129, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
164 41 0.32
165 88 0.68
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (164 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTCAACTTTGACTACACTCAGCTCA
AAGGCACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTACAAAAGACCCTCAAGTTC
GATTACACTCAACTCGAGGGCACATCATTTATAA
Found at i:1085008 original size:5 final size:5
Alignment explanation
Indices: 1084998--1085048 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
1084988 GTCTACAAAA
*
1084998 ATATT ATATT ATATT ATATT ATATAT TTATT -TATT -TATT -TATT ATTATT
1 ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT A-TATT
1085047 AT
1 AT
1085049 TAATATATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
4 12 0.29
5 21 0.50
6 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
ATATT
Found at i:1085024 original size:12 final size:12
Alignment explanation
Indices: 1084998--1085057 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 12
1084988 GTCTACAAAA
1084998 ATATTATA-T-T
1 ATATTATATTAT
1085008 ATATTATATTAT
1 ATATTATATTAT
1085020 ATATT-TATT-T
1 ATATTATATTAT
1085030 AT-TTAT-TTAT
1 ATATTATATTAT
1085040 -TATTATTATTAAT
1 ATATTA-TATT-AT
1085053 ATATT
1 ATATT
1085058 TTTATTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
9 5 0.12
10 16 0.39
11 6 0.15
12 8 0.20
13 2 0.05
14 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:1085062 original size:31 final size:34
Alignment explanation
Indices: 1084999--1085070 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
1084989 TCTACAAAAA
*
1084999 TATTATATTATATTATATTATATATTTATTTATT
1 TATTATATTATATTATATAATATATTTATTTATT
1085033 TATT-TATTATTATTAT-TAATATA-TT-TTTATTT
1 TATTATATTA-TATTATATAATATATTTATTTA-TT
1085065 TATTAT
1 TATTAT
1085071 TTTTATAGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
31 4 0.12
32 8 0.24
33 12 0.35
34 10 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (34 bp):
TATTATATTATATTATATAATATATTTATTTATT
Found at i:1085071 original size:31 final size:31
Alignment explanation
Indices: 1084999--1085076 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
1084989 TCTACAAAAA
*
1084999 TATTATATTA-TATTA-TATTATATATTTAT
1 TATTTTATTATTATTATTATTATATATTTAT
1085028 T-TATTTATTTATTATTATTATTAATATATTT-T
1 TAT-TTTA-TTATTATTATTATT-ATATATTTAT
*
1085060 TATTTTATTATTTTTAT
1 TATTTTATTATTATTAT
1085077 AGGCCCAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 1 0.02
29 4 0.10
30 3 0.07
31 14 0.34
32 10 0.24
33 9 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
TATTTTATTATTATTATTATTATATATTTAT
Found at i:1085521 original size:26 final size:26
Alignment explanation
Indices: 1085456--1085524 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
1085446 CTTTTTATTT
*
1085456 TATTTTTTATTTATTTACTTTATATA
1 TATTTTTTATTTCTTTACTTTATATA
* *
1085482 TATTTTTCATTTTCTCTTAATTT-TA-A
1 TATTTTTTA-TTTCT-TTACTTTATATA
1085508 TATTTTTTTATTTCTTT
1 TA-TTTTTTATTTCTTT
1085525 TTACATTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 2 0.06
26 16 0.44
27 12 0.33
28 6 0.17
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (26 bp):
TATTTTTTATTTCTTTACTTTATATA
Found at i:1085569 original size:25 final size:25
Alignment explanation
Indices: 1085522--1085573 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1085512 TTTTTATTTC
1085522 TTTTTACATTGTTTTATATATATATA
1 TTTTTACATTGTTTTATATATAT-TA
*
1085548 TTTTTTCATT-TTTTAT-TAATATTA
1 TTTTTACATTGTTTTATAT-ATATTA
1085572 TT
1 TT
1085574 ATATTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 10 0.42
26 9 0.38
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTACATTGTTTTATATATATTA
Found at i:1085580 original size:14 final size:14
Alignment explanation
Indices: 1085555--1085593 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1085545 ATATTTTTTC
1085555 ATTTT-TTATTAAT
1 ATTTTATTATTAAT
1085568 ATTATTA-TATTAAT
1 ATT-TTATTATTAAT
1085582 ATTTTATTATTA
1 ATTTTATTATTA
1085594 TTCTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTATTATTAAT
Found at i:1086754 original size:42 final size:43
Alignment explanation
Indices: 1086708--1086820 Score: 129
Period size: 43 Copynumber: 2.7 Consensus size: 43
1086698 ATGACCAACT
* * * *
1086708 TATTGCGGCGTTTCT-ACTAGATACGCCGCTATATATCAAATC
1 TATTGCGGCGTTTCTGACTACAAACGCCACTATATATCAAATA
* *
1086750 TATTGCGGCATTTGTGACTACAAACGCCACTATATATCAAATA
1 TATTGCGGCGTTTCTGACTACAAACGCCACTATATATCAAATA
* * * *
1086793 TATTGCAGCGTTTTTTAGTACAAACGCC
1 TATTGCGGCGTTTCTGACTACAAACGCC
1086821 GCAAAATGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
42 13 0.22
43 46 0.78
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (43 bp):
TATTGCGGCGTTTCTGACTACAAACGCCACTATATATCAAATA
Found at i:1088080 original size:21 final size:21
Alignment explanation
Indices: 1088056--1088100 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1088046 AATTTCAGGG
1088056 TATTCAAGTTACTATTTGAGT
1 TATTCAAGTTACTATTTGAGT
1088077 TATTCAAGTTACTATTTGAGT
1 TATTCAAGTTACTATTTGAGT
1088098 TAT
1 TAT
1088101 ATTTTATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (21 bp):
TATTCAAGTTACTATTTGAGT
Found at i:1089043 original size:18 final size:18
Alignment explanation
Indices: 1089020--1089054 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1089010 TGGGCAAAAG
1089020 TGTAGTGGAGCATGGGCT
1 TGTAGTGGAGCATGGGCT
1089038 TGTAGTGGAGCATGGGC
1 TGTAGTGGAGCATGGGC
1089055 ATAAAACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.46, T:0.26
Consensus pattern (18 bp):
TGTAGTGGAGCATGGGCT
Found at i:1090797 original size:3 final size:3
Alignment explanation
Indices: 1090789--1090860 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
1090779 ATTAATTTAT
* * * * * *
1090789 TTA TTA TTA TTA TAA TTA TAA ATA TTA TTA TTA TAA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1090837 ATA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1090861 AATACATTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1090830 original size:24 final size:24
Alignment explanation
Indices: 1090789--1090864 Score: 98
Period size: 24 Copynumber: 3.0 Consensus size: 24
1090779 ATTAATTTAT
*
1090789 TTATTATTATTATAATTATAAATA
1 TTATTATTATTATTATTATAAATA
*
1090813 TTATTATTATAATTATTATAAATAA
1 TTATTATTATTATTATTATAAAT-A
1090838 TAGTATTATTATTATTATTATTAAATA
1 T--TATTATTATTATTATTA-TAAATA
1090865 CATTAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 21 0.47
25 2 0.04
27 17 0.38
28 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
TTATTATTATTATTATTATAAATA
Found at i:1090869 original size:24 final size:25
Alignment explanation
Indices: 1090790--1090864 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 25
1090780 TTAATTTATT
* *
1090790 TATTATTATTATAATTA-TAAATAT
1 TATTATTATTATTATTATTAAATAG
* *
1090814 TATTATTATAATTATTATAAATAATAG
1 TATTATTATTATTATTAT-TA-AATAG
1090841 TATTATTATTATTATTATTAAATA
1 TATTATTATTATTATTATTAAATA
1090865 CATTAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
24 15 0.36
25 4 0.10
26 2 0.05
27 21 0.50
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
TATTATTATTATTATTATTAAATAG
Found at i:1091008 original size:19 final size:19
Alignment explanation
Indices: 1090984--1091029 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1090974 CCCGTATGCC
** *
1090984 GCCGCCTCAATGGTTTCCA
1 GCCGCCTCAACAGCTTCCA
1091003 GCCGCCTCAACAGCTTCCA
1 GCCGCCTCAACAGCTTCCA
1091022 GCCGCCTC
1 GCCGCCTC
1091030 TGCTGCCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.20
Consensus pattern (19 bp):
GCCGCCTCAACAGCTTCCA
Found at i:1102298 original size:40 final size:40
Alignment explanation
Indices: 1102253--1102328 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
1102243 TGAGCAGAGT
*
1102253 CCACAGCAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
* *
1102293 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTA
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTA
1102329 CATCTAAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
Found at i:1102748 original size:22 final size:22
Alignment explanation
Indices: 1102719--1102773 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1102709 ATCTACACTC
*
1102719 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
1102741 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
1102763 TTCAAAGATGA
1 TTCAAAGATGA
1102774 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:1103372 original size:114 final size:113
Alignment explanation
Indices: 1103175--1103857 Score: 1041
Period size: 114 Copynumber: 6.0 Consensus size: 113
1103165 GCAAAGATTC
* * *
1103175 AAATCCATCA-TTCGATGGATCA-GCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 AAATTCATCACTT-GATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
*
1103238 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
*
1103287 CAAA-TCTACCACTTGATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 -AAATTC-ATCACTTGATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
* *
1103351 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
64 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-CT
* *
1103402 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1103467 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-T
* * *
1103516 AATTTCATCCAATTGATGGATCATTCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 AAATTCAT-CACTTGATGGATCATTCATTACCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCA
* *
1103581 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
60 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-CT
* *
1103636 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1103701 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-T
* * *
1103750 AATTTCATCATTTGATGGATCA-ACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
*
1103814 GAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1103858 GTTTGATACT
Statistics
Matches: 530, Mismatches: 26, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
112 1 0.00
113 97 0.18
114 275 0.52
115 28 0.05
116 4 0.01
117 34 0.06
118 4 0.01
119 25 0.05
120 62 0.12
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AAATTCATCACTTGATGGATCATTCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
Found at i:1103659 original size:234 final size:229
Alignment explanation
Indices: 1103203--1103861 Score: 1139
Period size: 234 Copynumber: 2.9 Consensus size: 229
1103193 ATCAGCATTA
*
1103203 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
1103268 ATTTGTTCAACCTTTTGCTCAA-ATC-TACCACTTGATGGATCATTCATTACCAGAGAAGGTTCA
66 ACTTGTTCAACCTTTTGCTTAATTTCAT-CCAATTGATGGATCATTCATTACCAGAGAAGGTTCA
1103331 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
130 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
1103396 TTGTTTAAATTCATCACTTGATGGATCATTCTTTT
195 TTGTTTAAATTCATCACTTGATGGATCATTCTTTT
1103431 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
*
1103496 ACTTGTTCAACCTTTTGCTTAATTTCATCCAATTGATGGATCATTCATTTCCAGAGGAAGAGTTC
66 ACTTGTTCAACCTTTTGCTTAATTTCATCCAATTGATGGATCATTCATTACCAGA-GAAG-GTTC
1103561 ATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
129 ATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1103626 CCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTT
191 CCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTT
1103665 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
1103730 ACTTGTTCAACCTTTTGCTTAATTTCAT-CATTTGATGGATCA-ACATTACCAGAGAAGGTTCAT
66 ACTTGTTCAACCTTTTGCTTAATTTCATCCAATTGATGGATCATTCATTACCAGAGAAGGTTCAT
**
1103793 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-TT
131 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
1103857 TGTTT
196 TGTTT
1103862 GATACTATCA
Statistics
Matches: 413, Mismatches: 11, Indels: 16
0.94 0.03 0.04
Matches are distributed among these distances:
226 7 0.02
227 48 0.12
228 85 0.21
229 27 0.07
230 22 0.05
231 21 0.05
232 9 0.02
233 14 0.03
234 180 0.44
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (229 bp):
CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACCTTTTGCTTAATTTCATCCAATTGATGGATCATTCATTACCAGAGAAGGTTCAT
AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
TGTTTAAATTCATCACTTGATGGATCATTCTTTT
Found at i:1104195 original size:3 final size:3
Alignment explanation
Indices: 1104187--1104258 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
1104177 ATTAATTTAT
* * * * * *
1104187 TTA TTA TTA TTA TAA TTA TAA ATA TTA TTA TTA TAA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1104235 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1104259 AATACATTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1104252 original size:24 final size:24
Alignment explanation
Indices: 1104187--1104253 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
1104177 ATTAATTTAT
*
1104187 TTATTATTATTATAATTATAAATA
1 TTATTATTATTATTATTATAAATA
*
1104211 TTATTATTATAATTATTATAAATA
1 TTATTATTATTATTATTATAAATA
1104235 TTATTATTATTATTATTAT
1 TTATTATTATTATTATTAT
1104254 TATTAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTATTATTATTATTATAAATA
Found at i:1104278 original size:9 final size:9
Alignment explanation
Indices: 1104201--1104280 Score: 60
Period size: 9 Copynumber: 9.1 Consensus size: 9
1104191 TATTATTATA
1104201 ATTATAAAT
1 ATTATAAAT
1104210 ATTAT---T
1 ATTATAAAT
*
1104216 ATTATAATT
1 ATTATAAAT
1104225 ATTATAAAT
1 ATTATAAAT
* *
1104234 ATTATTATT
1 ATTATAAAT
* *
1104243 ATTATTATT
1 ATTATAAAT
1104252 ATTATTAAAT
1 ATTA-TAAAT
*
1104262 A-CATTAAAT
1 ATTA-TAAAT
1104271 ATTATAAAT
1 ATTATAAAT
1104280 A
1 A
1104281 ATGATAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
6 6 0.10
9 48 0.81
10 5 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTATAAAT
Found at i:1104406 original size:19 final size:19
Alignment explanation
Indices: 1104382--1104427 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1104372 CCCGTATGCC
** *
1104382 GCCGCCTCAATGGTTTCCA
1 GCCGCCTCAACAGCTTCCA
1104401 GCCGCCTCAACAGCTTCCA
1 GCCGCCTCAACAGCTTCCA
1104420 GCCGCCTC
1 GCCGCCTC
1104428 TGCTGCCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.20
Consensus pattern (19 bp):
GCCGCCTCAACAGCTTCCA
Found at i:1108894 original size:14 final size:14
Alignment explanation
Indices: 1108877--1108903 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1108867 CATGTTAGTA
1108877 TTAACATTAATTTT
1 TTAACATTAATTTT
1108891 TTAACATTAATTT
1 TTAACATTAATTT
1108904 ATGATGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAACATTAATTTT
Found at i:1122440 original size:14 final size:14
Alignment explanation
Indices: 1122421--1122454 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1122411 ACAATCCATT
1122421 AATTAAATTTAATA
1 AATTAAATTTAATA
1122435 AATTAAATTTAATA
1 AATTAAATTTAATA
1122449 AATTAA
1 AATTAA
1122455 TAATACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAAATTTAATA
Found at i:1125426 original size:15 final size:15
Alignment explanation
Indices: 1125390--1125420 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1125380 ACAGGTGGAG
1125390 AGTTTTTATTCTTTT
1 AGTTTTTATTCTTTT
1125405 AGTTTTTATTCTTTT
1 AGTTTTTATTCTTTT
1125420 A
1 A
1125421 TCTTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
AGTTTTTATTCTTTT
Found at i:1132075 original size:16 final size:16
Alignment explanation
Indices: 1132054--1132096 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1132044 AAAAACCTAA
* *
1132054 AAAATTTATTGCATTT
1 AAAATTAATTACATTT
1132070 AAAATTAATTACATTT
1 AAAATTAATTACATTT
1132086 AAAATTAATTA
1 AAAATTAATTA
1132097 AGTTTGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (16 bp):
AAAATTAATTACATTT
Found at i:1135506 original size:2 final size:2
Alignment explanation
Indices: 1135499--1135534 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1135489 ATCCTTTCAA
1135499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1135535 CACTTATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135837 original size:22 final size:21
Alignment explanation
Indices: 1135794--1135837 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
1135784 AAACACACAA
1135794 AAAGAAAGCAAAAATAAAAAT
1 AAAGAAAGCAAAAATAAAAAT
1135815 AAAGAAAG-AAAAATTGAAAAAT
1 AAAGAAAGCAAAAA-T-AAAAAT
1135837 A
1 A
1135838 GAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.11
Consensus pattern (21 bp):
AAAGAAAGCAAAAATAAAAAT
Found at i:1135840 original size:20 final size:19
Alignment explanation
Indices: 1135792--1135841 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
1135782 AAAAACACAC
1135792 AAAA-AGAAAGCAAAAATA
1 AAAATAGAAAGCAAAAATA
1135810 AAAATAAAGAAAG-AAAAATTGA
1 AAAAT--AGAAAGCAAAAA-T-A
1135832 AAAATAGAAA
1 AAAATAGAAA
1135842 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.15
20 10 0.37
21 7 0.26
22 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAATAGAAAGCAAAAATA
Found at i:1135857 original size:17 final size:18
Alignment explanation
Indices: 1135820--1135869 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1135810 AAAATAAAGA
*
1135820 AAGAAAAATTGAAAAATAG
1 AAGAAAAA-AGAAAAATAG
1135839 AA-AATAAAAGAAAAA-AG
1 AAGAA-AAAAGAAAAATAG
1135856 AAGAAAAAAGAAAA
1 AAGAAAAAAGAAAA
1135870 GAAAGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 13 0.46
18 10 0.36
19 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (18 bp):
AAGAAAAAAGAAAAATAG
Found at i:1135862 original size:27 final size:27
Alignment explanation
Indices: 1135778--1135888 Score: 91
Period size: 29 Copynumber: 3.9 Consensus size: 27
1135768 AAGAATAGAT
* *
1135778 AGAAAAAAACACACAAAAAGAAAGCAAAA
1 AGAAAAAAA-AGA-AAAAAGAAAGAAAAA
* *
1135807 ATAAAAATAAAGAAAGAAA-AATTGAAAAA
1 AGAAAAA-AAAGAAA-AAAGAA-AGAAAAA
1135836 TAGAAAATAAAAGAAAAAAG-AAGAAAAA
1 -AGAAAA-AAAAGAAAAAAGAAAGAAAAA
* *
1135864 AGAAAAGAAAGAAATAAGAAAGAAA
1 AGAAAAAAAAGAAAAAAGAAAGAAA
1135889 GCCGATAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
26 10 0.15
27 12 0.18
28 10 0.15
29 20 0.30
30 14 0.21
31 1 0.01
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.06
Consensus pattern (27 bp):
AGAAAAAAAAGAAAAAAGAAAGAAAAA
Found at i:1135869 original size:16 final size:17
Alignment explanation
Indices: 1135792--1135884 Score: 57
Period size: 16 Copynumber: 5.2 Consensus size: 17
1135782 AAAAACACAC
*
1135792 AAAAAGAAAGCAAAAATAAA
1 AAAAAGAAAG--AAAA-AAG
*
1135812 AATAAAGAAAGAAAAATTG
1 AA-AAAGAAAGAAAAA-AG
*
1135831 AAAAATAGAAA-ATAAAAG
1 -AAAA-AGAAAGAAAAAAG
1135849 AAAAA-AGAAGAAAAAAG
1 AAAAAGA-AAGAAAAAAG
*
1135866 -AAAAGAAAGAAATAAG
1 AAAAAGAAAGAAAAAAG
1135882 AAA
1 AAA
1135885 GAAAGCCGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
15 1 0.02
16 16 0.27
17 13 0.22
18 2 0.03
19 10 0.17
20 9 0.15
21 8 0.14
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:1135885 original size:15 final size:16
Alignment explanation
Indices: 1135844--1135889 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1135834 AATAGAAAAT
*
1135844 AAAAGAAAAAAGAAGAA
1 AAAAGAAAAGA-AAGAA
1135861 AAAAGAAAAGAAAGAA
1 AAAAGAAAAGAAAGAA
*
1135877 ATAAG-AAAGAAAG
1 AAAAGAAAAGAAAG
1135890 CCGATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAAAGAA
Found at i:1137537 original size:4 final size:4
Alignment explanation
Indices: 1137528--1140692 Score: 5381
Period size: 4 Copynumber: 805.8 Consensus size: 4
1137518 CATTTAAGTG
*
1137528 CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137576 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137624 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137672 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137720 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137768 CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137814 CATA CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1137861 CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA C-TA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
1137906 CATA CATA CATA CAT- -ATA CATA C--A CATA CA-G CATA GA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* **
1137948 CAT- -ATA AATA CATA CATA CATA TGTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
1137994 CATA CATG TATG TATA TATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
1138042 CATA CATA CATA CATA CATA CATA TATG CATG CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138090 CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATAA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT-A
*
1138137 TATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138184 CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138231 CATA CATA CAGA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138279 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138327 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138375 CATA CATA TGCATA GATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA --CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138425 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138473 CATA CATA CATA CATA CAGA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138521 CATA CATA CATA CATA CATA CAGA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138569 CATA CATA CATA CATA C-TA CATA CATA CATA CAT- -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138614 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138662 CATA CATA CATA CATA CATA CATA TCATA CATA CA-A CATA TA-A CATA
1 CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA
1138709 CATA CATA CATA CA-A CAT- -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138754 CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138800 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138847 CATA CAGA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138895 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1138943 CA-A CATA C-TA CATA CATA C--A CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1138987 CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CACA -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139032 CATA CATA CATA CATA C-TA CATA CATA CATA CATA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139078 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139126 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139174 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139222 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
1139270 CATA CATA CATA CATA CATA CATA CATA CCTA CATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1139318 CATA CATA CATA CCTA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1139366 CATA CATA CATA CATA CATA CATA CATA TGCATA GATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA --CATA CATA CATA CATA CATA
* *
1139416 TAAA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1139462 CATA -ATA TATA CATA CATA CATA CATA CATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1139507 CATA CATA CATA TATA CATA CATA CATA CATA CATA CA-A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1139554 CATAA CATA CATA CATA CATA CATA CATA CATA CATA CATA TATA CATA
1 CAT-A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139603 CATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139649 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139697 CATA CATA CATA CATA CATA CATA CA-A C-TA CATA CATA CAATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C-ATA CATA
1139744 CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA C-TA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1139790 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATAGA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT--A CATA
1139840 -ATA CATA CATA CATA CATA CAATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA C-ATA CATA CATA CATA CATA CATA CATA
* * *
1139888 CATA CATA CATA CATA CATA CACA CACA CACA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1139936 C--A CACA CATA CATA CAATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA C-ATA CATA CATA CATA CATA CATA CATA CATA
1139983 CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140030 CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CA-A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140075 CATA CATA CA-A CATA CATA CATA CATA CATA CATA CATA CATA C-TA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140121 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1140169 CATA CATA CATA CAT- -ATA CATA CATA CATA TATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140215 CATA CATA CAT- -ATA CATA CATA CAT- -ATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140259 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140307 CATA CATA CATA CATA CATA CATA -ATA CATA CATA CATA CAT- -ATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140352 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140400 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1140448 CATA CAAA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140496 CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140542 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140590 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140638 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1140686 CATA CAT
1 CATA CAT
1140693 TTTACAGATT
Statistics
Matches: 3018, Mismatches: 61, Indels: 164
0.93 0.02 0.05
Matches are distributed among these distances:
2 42 0.01
3 78 0.03
4 2863 0.95
5 23 0.01
6 12 0.00
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1141962 original size:139 final size:139
Alignment explanation
Indices: 1141712--1142506 Score: 721
Period size: 139 Copynumber: 5.8 Consensus size: 139
1141702 GATAAACCAC
*
1141712 TCAACATTT-TCAGTGGAGAGTTCATAATAAGAAGAACTCATCC-AA-TGAAGGAGAAGAAGTTC
1 TCAACATTTCT-AGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAGTG--GGAGAAGAAGTTC
* * * *
1141774 ATAATGAGAAGAACTTGTTCAACCTTAGTTTGATTCATCACATATGGAGTTGAATCAAAAATACC
63 ATAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAGACACACC
1141839 TCACTCGAGGGA
128 TCACTCGAGGGA
*
1141851 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAGTGGGAGAAGAAGTTTATA
1 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAGTGGGAGAAGAAGTTCATA
* * *
1141916 ATGAGAAGAACTTGTCCAACCTTAGCTTGATTCATCACATTTGGAGTTGAATCAGCCACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAGACACACCTCA
1141981 CTCGAGGGA
131 CTCGAGGGA
* * * * * *
1141990 TTAACATTTCTATTGGAGAGTTCATAATGAGAAGAGCTCATCCTAAGAGGGAGAACAAGTTCATA
1 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAGTGGGAGAAGAAGTTCATA
*
1142055 ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAGTCACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAGACACACCTCA
* *
1142120 TTCGAGAGA
131 CTCGAGGGA
* * * *** *
1142129 TCAATATTTCCT-GTGGAGAGTTTATAATGAGAAGAATTCATCCGACAAAAGGAGAAAAAGTTCA
1 TCAACATTT-CTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AGTGGGAGAAGAAGTTCA
* ** ** * * * * * ** *
1142193 TAATGAGCAGAGTTTGTTTGATCTATCGCTCGATTCA-CA-GTAT----TTCAAATCAGTGACGC
64 TAATGAGAAGAACTTGTTCAACCT-TAGCTTGATTCATCACATATGGAGTT-GAATCAGACACAC
* * *
1142252 ATCGCTTGAGGGA
127 CTCACTCGAGGGA
* * * * * * ** *
1142265 TTAACACTTT-AAATGGAGAGTTCAAAATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTCGT
1 TCAACA-TTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAGTGGGAGAAGAAGTTCAT
* * * * * * *
1142329 AATGAGAAGAGCTTGTTCGACCTATCA-CTCGATTCA-CAACA-CT----TCGAATCA-TCAATA
65 AATGAGAAGAACTTGTTCAACCT-T-AGCTTGATTCATC-ACATATGGAGTTGAATCAGAC-ACA
**
1142386 CCTCACTCGAATGA
126 CCTCACTCGAGGGA
* * * * *
1142400 TCAACATGTCCAGGGGAGAGTTCATAATAAGAAGAACTCATCCGATA-AGGGAGAAGAAGTTCAT
1 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AGTGGGAGAAGAAGTTCAT
* * *
1142464 AATAAGAAGAACTTGTTCAACCTTAGCGTGTTTCCATCACATA
65 AATGAGAAGAACTTGTTCAACCTTAGCTTGATT-CATCACATA
1142507 AGAAGTTGGA
Statistics
Matches: 542, Mismatches: 95, Indels: 41
0.80 0.14 0.06
Matches are distributed among these distances:
133 1 0.00
134 8 0.01
135 137 0.25
136 54 0.10
137 3 0.01
139 287 0.53
140 40 0.07
141 12 0.02
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (139 bp):
TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAGTGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAGACACACCTCA
CTCGAGGGA
Found at i:1142590 original size:42 final size:41
Alignment explanation
Indices: 1142496--1142612 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 41
1142486 TTAGCGTGTT
*
1142496 TCCATCACATAAGAAGTTGG---AACATCACCGATTTTTGCTTA
1 TCCATCACATAAGAAGTTGGATCAACATCA-C-A-TTTCGCTTA
*
1142537 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGC-TA
1 TCCATCACATAAGAAGTTGGATCAACATCA-CATTTCGCTTA
*
1142578 GTCCATCACATAAGAAGTTGGATCAGCATCACATT
1 -TCCATCACATAAGAAGTTGGATCAACATCACATT
1142613 GGATCAACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
41 25 0.37
42 33 0.49
43 1 0.01
44 8 0.12
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (41 bp):
TCCATCACATAAGAAGTTGGATCAACATCACATTTCGCTTA
Found at i:1142806 original size:3 final size:3
Alignment explanation
Indices: 1142800--1142876 Score: 73
Period size: 3 Copynumber: 24.3 Consensus size: 3
1142790 TTTTAATATG
* * *
1142800 TTA TTA TAA TTA TAA TTA TTTA TTA TTG TTA TTA TTA TTTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA -TTA
* *
1142848 TCA TTA ATA TTA TTA TTA TTA TTA CTTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA T
1142877 AATTTTTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 48 0.80
4 12 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1142822 original size:19 final size:19
Alignment explanation
Indices: 1142800--1142844 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1142790 TTTTAATATG
1142800 TTATTATAATTATAATTAT
1 TTATTATAATTATAATTAT
** *
1142819 TTATTATTGTTATTATTAT
1 TTATTATAATTATAATTAT
1142838 TTATTAT
1 TTATTAT
1142845 TTATCATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTATAATTATAATTAT
Found at i:1146458 original size:2 final size:2
Alignment explanation
Indices: 1146453--1146478 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1146443 AAATACAAAC
1146453 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
1146479 TATCAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1151023 original size:24 final size:24
Alignment explanation
Indices: 1150996--1151056 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
1150986 ACACTCTATA
1150996 GTGTATCGGTACATCTCTTAACGT
1 GTGTATCGGTACATCTCTTAACGT
*
1151020 GTGTATCGGTACATCTGTTAACGT
1 GTGTATCGGTACATCTCTTAACGT
*
1151044 GTGTATCGATACA
1 GTGTATCGGTACA
1151057 CTACCTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (24 bp):
GTGTATCGGTACATCTCTTAACGT
Found at i:1157601 original size:72 final size:71
Alignment explanation
Indices: 1157525--1157765 Score: 168
Period size: 76 Copynumber: 3.2 Consensus size: 71
1157515 TGAAAATACA
1157525 AATAAATAAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAA
1 AATAAA-AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAA
1157590 CTAATTT
65 CTAATTT
* * * *
1157597 AATAAAAATATAAGCATATATTTTAA-AAACA-GTTAGA-ATTG-TATGAGTTCACGTAATATTG
1 AATAAAAA-ATAA--ATA-A--TAAAGAAACATG-CA-ACATGGATATCA-TT-A-G--AT-TTG
* ** **
1157658 ATAAAAGAAAAATAA-TGAAAATACA
52 -TAAAA-TATTATAACT---AAT-TT
1157683 AATAAATAAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAA
1 AATAAA-AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAA
1157748 CTAATTT
65 CTAATTT
1157755 AATAAAAAATA
1 AATAAAAAATA
1157766 TAAGCATATA
Statistics
Matches: 125, Mismatches: 18, Indels: 53
0.64 0.09 0.27
Matches are distributed among these distances:
71 7 0.06
72 16 0.13
73 3 0.02
74 3 0.02
75 11 0.09
76 17 0.14
77 8 0.06
78 3 0.02
80 3 0.02
81 8 0.06
82 17 0.14
83 11 0.09
84 3 0.02
85 3 0.02
86 10 0.08
87 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.30
Consensus pattern (71 bp):
AATAAAAAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAAC
TAATTT
Found at i:1157642 original size:158 final size:159
Alignment explanation
Indices: 1157467--1157783 Score: 627
Period size: 158 Copynumber: 2.0 Consensus size: 159
1157457 AAATATTTAG
1157467 ACAGTTAGAATTGTATGAGTTCACGTAATATTGATAAAAGAAAAATAATGAAAATACAAATAAAT
1 ACAGTTAGAATTGTATGAGTTCACGTAATATTGATAAAAGAAAAATAATGAAAATACAAATAAAT
1157532 AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAACTAATTT
66 AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAACTAATTT
1157597 AAT-AAAAATATAAGCATATATTTTAAAA
131 AATAAAAAATATAAGCATATATTTTAAAA
1157625 ACAGTTAGAATTGTATGAGTTCACGTAATATTGATAAAAGAAAAATAATGAAAATACAAATAAAT
1 ACAGTTAGAATTGTATGAGTTCACGTAATATTGATAAAAGAAAAATAATGAAAATACAAATAAAT
1157690 AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAACTAATTT
66 AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAACTAATTT
1157755 AATAAAAAATATAAGCATATATTTTAAAA
131 AATAAAAAATATAAGCATATATTTTAAAA
1157784 TTAAAAATGA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 133 0.84
159 25 0.16
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.30
Consensus pattern (159 bp):
ACAGTTAGAATTGTATGAGTTCACGTAATATTGATAAAAGAAAAATAATGAAAATACAAATAAAT
AAATAAATAATAAAGAAACATGCAACATGGATATCATTAGATTTGTAAAATATTATAACTAATTT
AATAAAAAATATAAGCATATATTTTAAAA
Found at i:1159870 original size:12 final size:12
Alignment explanation
Indices: 1159833--1159892 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
1159823 GCTCCTCTTA
1159833 GCTTCTCTTCTC
1 GCTTCTCTTCTC
* *
1159845 GCTCCTC-T-TA
1 GCTTCTCTTCTC
1159855 GCTTCTCTTCTC
1 GCTTCTCTTCTC
*
1159867 GCTTCTC-T-TA
1 GCTTCTCTTCTC
1159877 GCTTCTCTTCTC
1 GCTTCTCTTCTC
1159889 GCTT
1 GCTT
1159893 TCCAACCTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 15 0.39
11 4 0.11
12 19 0.50
ACGTcount: A:0.03, C:0.38, G:0.10, T:0.48
Consensus pattern (12 bp):
GCTTCTCTTCTC
Found at i:1159880 original size:10 final size:10
Alignment explanation
Indices: 1159827--1159885 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
1159817 TATCTCGCTC
1159827 CTCTTAGCTT
1 CTCTTAGCTT
* *
1159837 CTCTTCTCGCTC
1 CTC-T-TAGCTT
1159849 CTCTTAGCTT
1 CTCTTAGCTT
*
1159859 CTCTTCTCGCTT
1 CTC-T-TAGCTT
1159871 CTCTTAGCTT
1 CTCTTAGCTT
1159881 CTCTT
1 CTCTT
1159886 CTCGCTTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 20 0.51
11 4 0.10
12 15 0.38
ACGTcount: A:0.05, C:0.37, G:0.08, T:0.49
Consensus pattern (10 bp):
CTCTTAGCTT
Found at i:1159892 original size:22 final size:22
Alignment explanation
Indices: 1159819--1159891 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
1159809 GACTGGCCTA
1159819 TCTCGCTCCTCTTAGCTTCTCT
1 TCTCGCTCCTCTTAGCTTCTCT
1159841 TCTCGCTCCTCTTAGCTTCTCT
1 TCTCGCTCCTCTTAGCTTCTCT
*
1159863 TCTCGCTTCTCTTAGCTTCTCT
1 TCTCGCTCCTCTTAGCTTCTCT
1159885 TCTCGCT
1 TCTCGCT
1159892 TTCCAACCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.04, C:0.40, G:0.10, T:0.47
Consensus pattern (22 bp):
TCTCGCTCCTCTTAGCTTCTCT
Found at i:1160340 original size:18 final size:18
Alignment explanation
Indices: 1160317--1160369 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1160307 GCACTGAATT
*
1160317 TGTCCCGAAT-GATCACTA
1 TGTCCCG-ATGGACCACTA
1160335 TGTCCCGATGGACCACTA
1 TGTCCCGATGGACCACTA
** *
1160353 TGTATCGAAGGACCACT
1 TGTCCCGATGGACCACT
1160370 CCTTAAGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (18 bp):
TGTCCCGATGGACCACTA
Found at i:1161508 original size:21 final size:20
Alignment explanation
Indices: 1161464--1161500 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1161454 ATCTCATTCA
*
1161464 TTATGTCAATATCATATAAC
1 TTATGTAAATATCATATAAC
1161484 TTATGTAAATAT-ATATA
1 TTATGTAAATATCATATA
1161501 TCACTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (20 bp):
TTATGTAAATATCATATAAC
Found at i:1171029 original size:21 final size:21
Alignment explanation
Indices: 1171004--1171056 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1170994 ACATAAGTTT
*
1171004 AAACATCCATCAAACAAA-TCC
1 AAACATCCAACAAACAAAGT-C
*
1171025 AAACATCCAACAATCAAAGTC
1 AAACATCCAACAAACAAAGTC
1171046 AAACAATCCAA
1 AAAC-ATCCAA
1171057 AAGCAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.55, C:0.30, G:0.02, T:0.13
Consensus pattern (21 bp):
AAACATCCAACAAACAAAGTC
Found at i:1172976 original size:23 final size:21
Alignment explanation
Indices: 1172923--1173005 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
1172913 CTAGAACCCC
* * *
1172923 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGAATCGGTTCCCCTT
*
1172944 CGGGGGGAATCGGTTCCCCTT
1 CAGGGGGAATCGGTTCCCCTT
1172965 CAAAGGGGGAATCGGTTCCCCTT
1 C--AGGGGGAATCGGTTCCCCTT
* *
1172988 CAGGGGGTATCGATTCCC
1 CAGGGGGAATCGGTTCCC
1173006 TCTGCACCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 33 0.62
23 20 0.38
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (21 bp):
CAGGGGGAATCGGTTCCCCTT
Found at i:1177635 original size:23 final size:22
Alignment explanation
Indices: 1177561--1177635 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 22
1177551 AAATTATTTA
1177561 AAATAAATCAATCCATAC-AACT
1 AAATAAATCAATCCATACTAA-T
**
1177583 ACAATAATAAATCAATCCATA-TTTT
1 ---A-AATAAATCAATCCATACTAAT
1177608 AAAATACAATCAATCCATACTAAT
1 -AAATA-AATCAATCCATACTAAT
1177632 AAAT
1 AAAT
1177636 TATTTAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 4 0.10
23 18 0.43
24 2 0.05
25 2 0.05
26 16 0.38
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:1177664 original size:22 final size:22
Alignment explanation
Indices: 1177638--1177680 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177628 TAATAAATTA
1177638 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1177660 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1177681 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1177689 original size:22 final size:22
Alignment explanation
Indices: 1177640--1177688 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1177630 ATAAATTATT
**
1177640 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1177662 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1177685 TAAA
1 TAAA
1177689 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1177694 original size:54 final size:54
Alignment explanation
Indices: 1177588--1178025 Score: 427
Period size: 54 Copynumber: 8.1 Consensus size: 54
1177578 CAACTACAAT
1177588 AATAAATCAATCCATATTTTAAAATACAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAAATTATTTAA
1177643 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*** * * *
1177697 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** * ** * * * **
1177745 AATAAATCAATCCATACTAATAAATTATTTAAAAT--AAACCAATCCA-TATTTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAA
* * ** * * * *
1177799 AATAAAGCATTCCATACTAATAAATTATTTAAAATAAATCAAT-CT-ATACAACTA--CAA
1 AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATACTAATA-AATTATTTAA
*
1177856 TAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1177911 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1177965 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1178019 AATAAAT
1 AATAAAT
1178026 TATTTTAAAA
Statistics
Matches: 327, Mismatches: 33, Indels: 47
0.80 0.08 0.12
Matches are distributed among these distances:
48 28 0.09
49 3 0.01
50 7 0.02
52 15 0.05
53 9 0.03
54 196 0.60
55 34 0.10
57 7 0.02
58 21 0.06
59 4 0.01
60 3 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1177740 original size:80 final size:80
Alignment explanation
Indices: 1177643--1177792 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
1177633 AATTATTTAA
*
1177643 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
1177708 CCATACAACTACAAT
66 CCATACAACTACAAT
*
1177723 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
1177788 CCATA
66 CCATA
1177793 TTTTAAAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
CCATACAACTACAAT
Found at i:1177769 original size:22 final size:23
Alignment explanation
Indices: 1177694--1177768 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
1177684 ATAAATTATT
1177694 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
1177716 CTACAATAATAAATCAATCTATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
1177742 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
1177765 TAAA
1 TAAA
1177769 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Done.